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Bibliography on: Microbial Ecology

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ESP: PubMed Auto Bibliography 23 Aug 2019 at 01:44 Created: 

Microbial Ecology

Wikipedia: Microbial Ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses. Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×1030 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

Created with PubMed® Query: "microbial ecology" NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-08-22

Damjanovic K, Menéndez P, Blackall LL, et al (2019)

Early Life Stages of a Common Broadcast Spawning Coral Associate with Specific Bacterial Communities Despite Lack of Internalized Bacteria.

Microbial ecology pii:10.1007/s00248-019-01428-1 [Epub ahead of print].

Coral-associated bacteria are critical for the well-being of their host and may play essential roles during ontogeny, as suggested by the vertical transmission of some bacteria in brooding corals. Bacterial acquisition patterns in broadcast spawners remain uncertain, as 16S rRNA gene metabarcoding of coral early life stages suggests the presence of bacterial communities, which have not been detected by microscopic examinations. Here, we combined 16S rRNA gene metabarcoding with fluorescence in situ hybridization (FISH) microscopy to analyze bacterial assemblages in Acropora tenuis egg-sperm bundles, embryos, and larvae following a spawning event. Metabarcoding results indicated that A. tenuis offspring ≤ 4-day-old were associated with diverse and dynamic bacterial microbiomes, dominated by Rhodobacteraceae, Alteromonadaceae, and Oceanospirillaceae. While FISH analyses confirmed the lack of internalized bacteria in A. tenuis offspring, metabarcoding showed that even the earliest life stages examined (egg-sperm bundles and two-cell stages) were associated with a diverse bacterial community, suggesting the bacteria were confined to the mucus layer. These results can be explained by vertical transmission of certain taxa (mainly Endozoicomonas) in the mucus surrounding the gametes within bundles, or by horizontal bacterial transmission through the release of bacteria by spawning adults into the water column.

RevDate: 2019-08-22

Onywera H, Williamson AL, Mbulawa ZZA, et al (2019)

Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study.

PeerJ, 7:e7488 pii:7488.

Background: Lactobacillus spp. are common bacteria in the cervical and vaginal microbiota (CVM) and are thought to represent a "healthy" cervicovaginal state. Several studies have found an independent association between ethnicity/race and cervical and vaginal microbiota (CVM) composition. Women of sub-Saharan African descent appear to be significantly more likely to have non-Lactobacillus-dominated CVM compared to women of European descent. The factors contributing to these differences remain to be fully elucidated. The CVM of Black South African women and factors influencing their CVM remain understudied. In this study, we characterized the cervical microbiota of reproductive-age South African women and assessed the associations of these microbiota with participants' metadata.

Methods: The cervical microbiota from cervical DNA of 62 reproductive-age women were profiled by Ion Torrent sequencing the V4 hypervariable region of the bacterial 16S ribosomal RNA (rRNA) gene and analyzed with the Quantitative Insights Into Microbial Ecology (QIIME), UPARSE, and metagenomeSeq tools. Associations between cervical microbiota and participants' metadata were assessed using GraphPad Prism, R packages and an in-house script.

Results: The cervical microbiota clustered into three distinct community state types (CSTs): Lactobacillus iners-dominated cervical microbiota (CST I (38.7%, 24/62)), unclassified Lactobacillus-dominated cervical microbiota (CST II (4.8%, 3/62)), and diverse cervical microbiota (CST III (56.5%, 35/62)) with an array of heterogeneous bacteria, predominantly the bacterial vaginosis (BV)-associated Gardnerella, Prevotella, Sneathia, and Shuttleworthia. CST III was associated with BV (p = 0.001). Women in CST I were more likely to be on hormonal contraception, especially progestin-based, compared to women in CST III (odds ratio: 5.2 (95% CI [1.6-17.2]); p = 0.005). Women on hormonal contraception had a significantly lower alpha (Shannon indices: 0.9 (0.2-1.9) versus 2.3 (0.6-2.3); p = 0.025) and beta (permutational multivariate analysis of variance (PERMANOVA) pseudo-F statistic =4.31, p = 0.019) diversity compared to non-users. There was no significant difference in the alpha (Shannon indices: 1.0 (0.3-2.2) versus 1.9 (0.3-2.2); p = 0.483) and beta (PERMANOVA pseudo-F statistic = 0.89, p = 0.373) diversity in women with versus without human papillomavirus infection.

Conclusions: The majority of Black women in our study had non-Lactobacillus-dominated cervical microbiota. Additional studies are needed to examine whether such microbiota represent abnormal, intermediate or variant states of health. Lastly, the association of hormonal contraception with L. iners dominance requires further in-depth research to confirm this association, determine its biological mechanism and whether it has a beneficial effect on the cervicovaginal health.

RevDate: 2019-08-22

Weiner BG, Posfai A, NS Wingreen (2019)

Spatial ecology of territorial populations.

Proceedings of the National Academy of Sciences of the United States of America pii:1911570116 [Epub ahead of print].

Many ecosystems, from vegetation to biofilms, are composed of territorial populations that compete for both nutrients and physical space. What are the implications of such spatial organization for biodiversity? To address this question, we developed and analyzed a model of territorial resource competition. In the model, all species obey trade-offs inspired by biophysical constraints on metabolism; the species occupy nonoverlapping territories, while nutrients diffuse in space. We find that the nutrient diffusion time is an important control parameter for both biodiversity and the timescale of population dynamics. Interestingly, fast nutrient diffusion allows the populations of some species to fluctuate to zero, leading to extinctions. Moreover, territorial competition spontaneously gives rise to both multistability and the Allee effect (in which a minimum population is required for survival), so that small perturbations can have major ecological effects. While the assumption of trade-offs allows for the coexistence of more species than the number of nutrients-thus violating the principle of competitive exclusion-overall biodiversity is curbed by the domination of "oligotroph" species. Importantly, in contrast to well-mixed models, spatial structure renders diversity robust to inequalities in metabolic trade-offs. Our results suggest that territorial ecosystems can display high biodiversity and rich dynamics simply due to competition for resources in a spatial community.

RevDate: 2019-08-21

Sun Y, Liu Y, Pan J, et al (2019)

Perspectives on Cultivation Strategies of Archaea.

Microbial ecology pii:10.1007/s00248-019-01422-7 [Epub ahead of print].

Archaea have been recognized as a major domain of life since the 1970s and occupy a key position in the tree of life. Recent advances in culture-independent approaches have greatly accelerated the research son Archaea. However, many hypotheses concerning the diversity, physiology, and evolution of archaea are waiting to be confirmed by culture-base experiments. Consequently, archaeal isolates are in great demand. On the other hand, traditional approaches of archaeal cultivation are rarely successful and require urgent improvement. Here, we review the current practices and applicable microbial cultivation techniques, to inform on potential strategies that could improve archaeal cultivation in the future. We first summarize the current knowledge on archaeal diversity, with an emphasis on cultivated and uncultivated lineages pertinent to future research. Possible causes for the low success rate of the current cultivation practices are then discussed to propose future improvements. Finally, innovative insights for archaeal cultivation are described, including (1) medium refinement for selective cultivation based on the genetic and transcriptional information; (2) consideration of the up-to-date archaeal culturing skills; and (3) application of multiple cultivation techniques, such as co-culture, direct interspecies electron transfer (DIET), single-cell isolation, high-throughput culturing (HTC), and simulation of the natural habitat. Improved cultivation efforts should allow successful isolation of as yet uncultured archaea, contributing to the much-needed physiological investigation of archaea.

RevDate: 2019-08-21

Nasser NA, Gregory BRB, Steele RE, et al (2019)

Behind the Organic Veil: Assessing the Impact of Chemical Deflocculation on Organic Content Reduction and Lacustrine Arcellinida (Testate Amoebae) Analysis.

Microbial ecology pii:10.1007/s00248-019-01429-0 [Epub ahead of print].

Arcellinida (testate lobose amoebae) are widely used as bio-indicators of lacustrine environmental change. Too much obscuring organic material in a gridded wet Petri dish preparation makes it difficult to observe all specimens present and slows quantification as the organic material has to be carefully worked through with a dissection probe. Chemical deflocculation using soda ash (Na2CO3·H2O), potassium hydroxide (KOH), or sodium hexametaphosphate ((NaPO3)6) has previously been shown to disaggregate and reduce organic content in lake sediments, but to date, no attempt has been made to comparatively evaluate the efficiency of these deflocculants in disaggregating organic content and their impact on Arcellinida analysis in lacustrine sediments. Here, we assess the effectiveness of soda ash, potassium hydroxide, and sodium hexametaphosphate treatments on removing organic content and the impact of those digestions on Arcellinida preservation in 126 sample aliquots subdivided from three sediment samples (YK-20, YK-25, and YK-57) collected from three lakes near Yellowknife, Northwest Territories, Canada. Following treatment, cluster analysis and Bray-Curtis dissimilarity matrix (BCDM) were utilized to determine whether treatments resulted in dissolution-driven changes in Arcellinida assemblage composition. Observed Arcellinida tests in aliquots increased drastically after treatment of organic-rich samples (47.5-452.7% in organic-rich aliquots and by 14.8% in aliquots with less organic matter). The BCDM results revealed that treatment with 5% KOH resulted in the highest reduction in observed organic content without significantly affecting Arcellinida assemblage structure, while soda ash and sodium hexametaphosphate treatments resulted in marginal organic matter reduction and caused severe damage to the arcellinidan tests.

RevDate: 2019-08-21

Taroni JN (2019)

Making Workshops Work: Insights from EDAMAME.

mSystems, 4(4): pii:4/4/e00467-19.

Microbiology, like many areas of life science research, is increasingly data-intensive. As such, bioinformatics and data science skills have become essential to leverage microbiome sequencing data for discovery. Short intensive courses have sprung up as formal computational training opportunities at individual institutions fail to meet demands. In this issue, Shade et al. (A. Shade, T. K. Dunivin, J. Choi, T. K. Teal, et al., mSystems 4:e00297-19, 2019, share their experience and approach in executing the annual, weeklong Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop from 2014 to 2018. EDAMAME introduced learners to general scientific computing concepts and domain-specific data analysis approaches. Workshop learners self-reported appreciable gains in understanding and ability. This report on the EDAMAME workshop strategy and lessons learned will help others in the life sciences to plan, execute, and assess short hands-on computing-intensive courses that support research in a particular domain.

RevDate: 2019-08-21

Shade A, Dunivin TK, Choi J, et al (2019)

Strategies for Building Computing Skills To Support Microbiome Analysis: a Five-Year Perspective from the EDAMAME Workshop.

mSystems, 4(4): pii:4/4/e00297-19.

Here, we report our educational approach and learner evaluations of the first 5 years of the Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop, held annually at Michigan State University's Kellogg Biological Station from 2014 to 2018. We hope this information will be useful for others who want to organize computing-intensive workshops and will encourage quantitative skill development among microbiologists.IMPORTANCE High-throughput sequencing and related statistical and bioinformatic analyses have become routine in microbiology in the past decade, but there are few formal training opportunities to develop these skills. A weeklong workshop can offer sufficient time for novices to become introduced to best computing practices and common workflows in sequence analysis. We report our experiences in executing such a workshop targeted to professional learners (graduate students, postdoctoral scientists, faculty, and research staff).

RevDate: 2019-08-21

Sun Z, Huang S, Zhu P, et al (2019)

A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children.

mSystems, 4(4): pii:4/4/e00293-19.

A quantitative and objective indicator for skin health via the microbiome is of great interest for personalized skin care, but differences among skin sites and across human populations can make this goal challenging. A three-city (two Chinese and one American) comparison of skin microbiota from atopic dermatitis (AD) and healthy pediatric cohorts revealed that, although city has the greatest effect size (the skin microbiome can predict the originated city with near 100% accuracy), a microbial index of skin health (MiSH) based on 25 bacterial genera can diagnose AD with 83 to ∼95% accuracy within each city and 86.4% accuracy across cities (area under the concentration-time curve [AUC], 0.90). Moreover, nonlesional skin sites across the bodies of AD-active children (which include shank, arm, popliteal fossa, elbow, antecubital fossa, knee, neck, and axilla) harbor a distinct but lesional state-like microbiome that features relative enrichment of Staphylococcus aureus over healthy individuals, confirming the extension of microbiome dysbiosis across body surface in AD patients. Intriguingly, pretreatment MiSH classifies children with identical AD clinical symptoms into two host types with distinct microbial diversity and treatment effects of corticosteroid therapy. These findings suggest that MiSH has the potential to diagnose AD, assess risk-prone state of skin, and predict treatment response in children across human populations.IMPORTANCE MiSH, which is based on the skin microbiome, can quantitatively assess pediatric skin health across cohorts from distinct countries over large geographic distances. Moreover, the index can identify a risk-prone skin state and compare treatment effect in children, suggesting applications in diagnosis and patient stratification.

RevDate: 2019-08-20

Velazquez S, Griffiths W, Dietz L, et al (2019)

From one species to another: A review on the interaction of chemistry and microbiology in relation to cleaning in the built environment.

Indoor air [Epub ahead of print].

Since the advent of soap, personal hygiene practices have revolved around removal, sterilization, and disinfection - both of visible soil and microscopic organisms - for a myriad of cultural, aesthetic, or health-related reasons. Cleaning methods and products vary widely in their recommended use, effectiveness, risk to users or building occupants, environmental sustainability, and ecological impact. Advancements in science and technology have facilitated in-depth analyses of the indoor microbiome and studies in this field suggest that the traditional "scorched-earth cleaning" mentality - that surfaces must be completely sterilized and prevent microbial establishment - may contribute to long-term human health consequences. Moreover, the materials, products, activities, and microbial communities indoors all contribute to, or remove, chemical species to the indoor environment. This review examines the effects of cleaning with respect to the interaction of chemistry, indoor microbiology, and human health. PRACTICAL IMPLICATIONS: Simple interventions, such as hand washing, can dramatically improve health and reduce infectious disease. Chemical intervention, while effective, may encourage the development of microbial resistance over time if not implemented properly. Microbial communities adapt, reassemble, and persist, and recent theory in microbial ecology suggests that curating microbial communities may be more sustainable than perpetually attempting to remove them. This article is protected by copyright. All rights reserved.

RevDate: 2019-08-20

Tang Y, Dai T, Su Z, et al (2019)

A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology.

Microbial ecology pii:10.1007/s00248-019-01421-8 [Epub ahead of print].

Current technologies could identify the abundance and functions of specific microbes, and evaluate their individual effects on microbial ecology. However, these microbes interact with each other, as well as environmental factors, in the form of complex network. Determination of their combined ecological influences remains a challenge. In this study, we developed a tripartite microbial-environment network (TMEN) analysis method that integrates microbial abundance, metabolic function, and environmental data as a tripartite network to investigate the combined ecological effects of microbes. Applying TMEN to analyzing the microbial-environment community structure in the sediments of Hangzhou Bay, one of the most seriously polluted coastal areas in China, we found that microbes were well-organized into 4 bacterial communities and 9 archaeal communities. The total organic carbon, sulfate, chemical oxygen demand, salinity, and nitrogen-related indexes were detected as crucial environmental factors in the microbial-environmental network. With close interactions with these environmental factors, Nitrospirales and Methanimicrococcu were identified as hub microbes with connection advantage. Our TMEN method could close the gap between lack of efficient statistical and computational approaches and the booming of large-scale microbial genomic and environmental data. Based on TMEN, we discovered a potential microbial ecological mechanism that crucial species with significant influence on the microbial community ecology would possess one or two of the community advantages for enhancing their ecological status and essentiality, including abundance advantage and connection advantage.

RevDate: 2019-08-17

In 't Zandt MH, Kip N, Frank J, et al (2019)

High abundance of Methanobacteriales and Syntrophobacterales may help to prevent corrosion of metal sheet piles.

Applied and environmental microbiology pii:AEM.01369-19 [Epub ahead of print].

Iron sheet piles are widely used in flood protection, dike construction and river bank reinforcement. Their corrosion leads to gradual deterioration and often makes replacement necessary. Natural deposit layers on these sheet piles can prevent degradation and significantly increase their lifespan. However, little is known about the mechanisms of natural protective layer formation. Here, we studied the microbial diversity of corrosion-protective deposit layers on iron sheet piles at the Gouderak pumping station in Zuid-Holland, the Netherlands. Deposit layers, surrounding sediment and top sediment samples were analyzed for soil physicochemical parameters, microbial diversity and metabolic potential. Methanogens appeared to be enriched 18-fold in the deposit layers. After sequencing, metagenome assembly and binning, we obtained four near-complete draft genomes of microorganisms (Methanobacteriales, two Coriobacteriales and Syntrophobacterales) that were highly enriched in the deposit layers, strongly indicating a potential role in corrosion protection. Coriobacteriales and Syntrophobacterales could be part of a microbial foodweb degrading organic matter to supply methanogenic substrates. Methane-producing Methanobacteriales could metabolize iron which may initially lead to mild corrosion but potentially stimulates the formation of a carbonate-rich protective deposit layer in the long term. In addition, Methanobacteriales and Coriobacteriales have the potential to interact with metal surfaces via direct interspecies or extracellular electron transfer. In conclusion, our study provides valuable insights into microbial populations involved in iron corrosion protection and potentially enables the development of novel strategies for in-situ screening of iron sheet piles in order to reduce risks and develop more sustainable replacement practices.Importance Iron sheet piles are widely used to reinforce dikes and river banks. Damage due to iron corrosion poses a significant safety risk and has major economical impacts. Different groups of microorganisms are known to either stimulate or inhibit the corrosion process. Recently, natural corrosion-protective deposit layers were found on sheet piles. Analyses of the microbial composition indicated a potential role for methane-producing archaea. However, the full metabolic potential of the microbial communities within these protective layers has not been determined. The significance of this work lies in the reconstruction of the microbial food web of natural corrosion-protective layers isolated from non-corroding metal sheet piles. With this work, we provide insights into the microbiological mechanisms that potentially promote corrosion protection in freshwater ecosystems. Our findings could support the development of screening protocols to assess the integrity of iron sheet piles to decide whether replacement is required.

RevDate: 2019-08-17

Bale NJ, Palatinszky M, Rijpstra WIC, et al (2019)

The membrane lipid composition of the moderately thermophilic ammonia-oxidizing archaeon Ca. Nitrosotenuis uzonensis at different growth temperatures.

Applied and environmental microbiology pii:AEM.01332-19 [Epub ahead of print].

Ca. Nitrosotenuis uzonensis is the only cultured moderately thermophilic member of the thaumarchaeotal order Nitrosopumilales (NP) that contains many mesophilic marine strains. We examined its membrane lipid composition at different growth temperatures (37, 46 and 50 °C). Its lipids were all membrane-spanning glycerol dialkyl glycerol tetraethers (GDGTs), with 0 to 4 cyclopentane moieties. Crenarchaeol (cren), the characteristic thaumarchaeotal GDGT, and its isomer (cren') were present in high abundance (30-70 %). The GDGT polar headgroups were mono-, di- and trihexoses and hexose/phosphohexose. The ratio of glycolipid to phospholipid GDGTs was highest in the cultures grown at 50 °C. With increasing growth temperature, the relative contribution of cren and cren' increased, while GDGT-0 to GDGT-4 (including isomers) decreased. TEX86 (tetraether index of tetraethers consisting of 86 carbons)-derived temperatures were much lower than the actual growth temperatures, further demonstrating that TEX86 does not accurately reflect the membrane lipid adaptation of thermophilic Thaumarchaeota. As temperature increased, specific GDGTs changed relative to their isomers, possibly representing temperature adaption-induced changes in cyclopentane ring stereochemistry. Comparison of a wide range of thaumarcheotal core lipid compositions revealed the Ca. N. uzonensis cultures clustered separately from other members of the NP order and the Nitrososphaerales (NS) order. While phylogeny generally seems to have a strong influence on GDGT distribution, our analysis of Ca. Nitrosotenuis uzonensis demonstrates that its terrestrial, higher temperature niche has led to a lipid composition that clearly differentiates it from other NP members and that this difference is mostly driven by its high cren' content.Importance For Thaumarchaeota the ratio of their Glycerol Dialkyl Glycerol Tetraether (GDGT) lipids depends on growth temperature, a premise that forms the basis of the widely applied TEX86 paleotemperature proxy. A thorough understanding of which GDGTs are produced by which Thaumarchaeota and what the effect of temperature is on their GDGT composition is essential for constraining the TEX86 proxy. Ca. Nitrosotenuis uzonensis is a moderately thermophilic Thaumarchaeote enriched from a thermal spring, setting it apart in its environmental niche from the other marine mesophilic members of its order. Indeed, we found that the GDGT composition of Ca. N. uzonensis cultures was distinct from other members of its order and was more similar to other thermophilic, terrestrial Thaumarchaeota. This suggests that while phylogeny has a strong influence on GDGT distribution, the environmental niche that a Thaumarchaeote inhabits also shapes its GDGT composition.

RevDate: 2019-08-16

Jiang Y, Xu ZW, Wang RZ, et al (2019)

[Effects of long-term fertilization and water addition on soil properties and plant community characteristics in a semiarid grassland.].

Ying yong sheng tai xue bao = The journal of applied ecology, 30(7):2470-2480.

We summarized the effects of fertilization and water addition on some soil properties and plant community characteristics in a long-term field experiment established in 2005 in a degraded grassland in Duolun, Inner Mongolia, China. The results showed that nitrogen (N) addition resulted in surface soil acidification and decreased acid buffering capacity, increased the availability of carbon (C), N, phosphorus (P), sulfur (S) and DTPA-extractable iron (Fe), manganese (Mn), and copper (Cu) contents, depleted the sum of base cations calcium (Ca), magnesium (Mg), potassium (K) and sodium (Na), decreased the diversity of soil microbial community. Nitrogen addition enhanced the uptake of N, P, S, K, Mn, Cu and Zn by plants, while inhibited plant Fe uptake, but with no effect on the uptake of Ca or Mg. Nitrogen addition increased aboveground net primary productivity (ANPP) but declined plant species diversity and community stability. Phosphorus addition alone increased total P and Olsen-P contents and fungal abundance in the surface soil, and improved N, P and S uptake by leaves, but had no significant influence on other soil basic chemical properties, ANPP, and plant species diversity. Water addition could improve the resistance of plant community, but its contribution to ANPP was limited by soil N availa-bility. Water addition could buffer soil acidification and the decline of microbial and plant diversity induced by N addition. Under the treatments of N and water addition or P and water addition, the diversity and function of soil microorganisms were affected by plant community structure and function. Long-term controlled field experiments were useful for understanding ecosystem structure and functions of grasslands. However, to uncover the underlying mechanisms in grassland ecosystem ecology, single-site experiments should be incorporated with multiple-site controlled field experiments in different regions. More attentions should be paid to the linkage of above- and below-ground ecological processes.

RevDate: 2019-08-15

Deng Y, Ruan Y, Ma B, et al (2019)

Multi-omics analysis reveals niche and fitness differences in typical denitrification microbial aggregations.

Environment international, 132:105085 pii:S0160-4120(19)32115-4 [Epub ahead of print].

Suspended floc and fixed biofilm are two commonly applied strategies for heterotrophic denitrification in wastewater treatment. These two strategies use different carbon sources and reside within different ecological niches for microbial aggregation, which were hypothesized to show distinct microbial structures and metabolic fitness. We surveyed three floc reactors and three biofilm reactors for denitrification and determined if there were distinct microbial aggregations. Multiple molecular omics approaches were used to determine the microbial community composition, co-occurrence network and metabolic pathways. Proteobacteria was the dominating and most active phylum among all samples. Carbon source played an important role in shaping the microbial community composition while the distribution of functional protein was largely influenced by salinity. We found that the topological network features had different ecological patterns and that the microorganisms in the biofilm reactors had more nodes but less interactions than those in floc reactors. The large niche differences in the biofilm reactors explained the observed high microbial diversity, functional redundancy and resulting high system stability. We also observed a lower proportion of denitrifiers and higher resistance to oxygen and salinity perturbation in the biofilm reactors than the floc reactors. Our findings support our hypothesis that niche differences caused a distinct microbial structure and increased microbial ecology distribution, which has the potential to improve system efficiency and stability.

RevDate: 2019-08-15

Pérez-Jaramillo JE, de Hollander M, Ramírez CA, et al (2019)

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia.

Microbiome, 7(1):114 pii:10.1186/s40168-019-0727-1.

BACKGROUND: Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood.

RESULTS: Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil.

CONCLUSIONS: Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.

RevDate: 2019-08-14

Posada-Perlaza CE, Ramírez-Rojas A, Porras P, et al (2019)

Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes.

Scientific reports, 9(1):11764 pii:10.1038/s41598-019-48200-6.

The increase in antibiotic resistant bacteria has raised global concern regarding the future effectiveness of antibiotics. Human activities that influence microbial communities and environmental resistomes can generate additional risks to human health. In this work, we characterized aquatic microbial communities and their resistomes in samples collected at three sites along the Bogotá River and from wastewaters at three city hospitals, and investigated community profiles and antibiotic resistance genes (ARGs) as a function of anthropogenic contamination. The presence of antibiotics and other commonly used drugs increased in locations highly impacted by human activities, while the diverse microbial communities varied among sites and sampling times, separating upstream river samples from more contaminated hospital and river samples. Clinically relevant antibiotic resistant pathogens and ARGs were more abundant in contaminated water samples. Tracking of resistant determinants to upstream river waters and city sources suggested that human activities foster the spread of ARGs, some of which were co-localized with mobile genetic elements in assembled metagenomic contigs. Human contamination of this water ecosystem changed both community structure and environmental resistomes that can pose a risk to human health.

RevDate: 2019-08-14

Small CM, Currey M, Beck EA, et al (2019)

Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome.

mSystems, 4(4): pii:4/4/e00331-19.

Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same laboratory environment. Using careful experimental design and intensive sampling of individuals, we addressed technical and biological sources of variation in 16S-based estimates of microbial diversity. After employing a two-tiered bead beating approach that comprised tissue homogenization followed by microbial lysis in subsamples, we found an extremely minor effect of DNA isolation protocol relative to among-host microbial diversity differences. Abundance estimates for rare operational taxonomic units (OTUs), however, showed much lower reproducibility. Gut microbiome composition was highly variable across fish-even among cohoused siblings-relative to technical replicates, but a subtle effect of host genotype (stickleback line) was nevertheless detected for some microbial taxa.IMPORTANCE Our findings demonstrate the importance of appropriately quantifying biological and technical variance components when attempting to understand major influences on high-throughput microbiome data. Our focus was on understanding among-host (biological) variance in community metrics and its magnitude in relation to within-host (technical) variance, because meaningful comparisons among individuals are necessary in addressing major questions in host-microbe ecology and evolution, such as heritability of the microbiome. Our study design and insights should provide a useful example for others desiring to quantify microbiome variation at biological levels in the face of various technical factors in a variety of systems.

RevDate: 2019-08-13

Kröber E, Ö Eyice (2019)

Profiling of Active Microorganisms by Stable Isotope Probing-Metagenomics.

Methods in molecular biology (Clifton, N.J.), 2046:151-161.

Stable isotope probing (SIP) provides researchers a culture-independent method to retrieve nucleic acids from active microbial populations performing a specific metabolic activity in complex ecosystems. In recent years, the use of the SIP method in microbial ecology studies has been accelerated. This is partly due to the advances in sequencing and bioinformatics tools, which enable fast and reliable analysis of DNA and RNA from the SIP experiments. One of these sequencing tools, metagenomics, has contributed significantly to the body of knowledge by providing data not only on taxonomy but also on the key functional genes in specific metabolic pathways and their relative abundances. In this chapter, we provide a general background on the application of the SIP-metagenomics approach in microbial ecology and a workflow for the analysis of metagenomic datasets using the most up-to-date bioinformatics tools.

RevDate: 2019-08-13

Finley BK, Hayer M, Mau RL, et al (2019)

Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing.

Methods in molecular biology (Clifton, N.J.), 2046:137-149.

Quantitative stable isotope probing (qSIP) measures rates of taxon-specific element assimilation in intact microbial communities, utilizing substrates labeled with a heavy isotope.The laboratory protocol for qSIP is nearly identical to that for conventional stable isotope probing, with two key additions: (1) in qSIP, qPCR measurements are conducted on each density fraction recovered after isopycnic separation, and (2) in qSIP, multiple density fractions are sequenced spanning the entire range of densities over which nucleic acids were recovered. qSIP goes beyond identifying taxa assimilating a substrate, as it also allows for measuring that assimilation for each taxon within a given microbial community. Here, we describe an analysis process necessary to determine atom fraction excess of a heavy stable isotope added to an environmental sample for a given taxon's DNA.

RevDate: 2019-08-13

Mayali X, Weber PK, Nuccio E, et al (2019)

Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS.

Methods in molecular biology (Clifton, N.J.), 2046:71-87.

Chip-SIP is a stable isotope probing (SIP) method for linking microbial identity and function in mixed communities and is capable of analyzing multiple isotopes (13C, 15N, and 18O) simultaneously. This method uses a high-density microarray to separate taxon-specific 16S (or 18S) rRNA genes and a high sensitivity magnetic sector secondary ion mass spectrometer (SIMS) to determine the relative isotope incorporation of the rRNA at each probe location. Using a maskless array synthesizer (MAS), we synthesize multiple unique sequences to target hundreds of taxa at the ribosomal operational taxonomic unit (OTU) level on an array surface, and then analyze it with a NanoSIMS 50, using its high-spatial resolution imaging capability to generate isotope ratios for individual probes. The Chip-SIP method has been used in diverse systems, including surface marine and estuarine water, rhizosphere, and peat soils, to quantify taxon-specific relative incorporation of different substrates in complex microbial communities. Depending on the hypothesis and experimental design, Chip-SIP allows the user to compare the same community incorporating different substrates, different communities incorporating the same substrate(s), or quantify how a community responds to treatment effects, such as temperature or nutrient concentrations.

RevDate: 2019-08-13

Taubert M (2019)

SIP-Metaproteomics: Linking Microbial Taxonomy, Function, and Activity.

Methods in molecular biology (Clifton, N.J.), 2046:57-69.

Stable isotope probing combined with metaproteomics enables the detection and characterization of active key species in microbial populations under near-natural conditions, which greatly helps to understand the metabolic functions of complex microbial communities. This is achieved by providing growth substrates labeled with heavy isotopes such as 13C, which will be assimilated into microbial biomass. After subsequent extraction of proteins and proteolytic cleavage into peptides, the heavy isotope enrichment can be detected by high-resolution mass spectrometric analysis, and linked to the functional and taxonomic characterization of these biomarkers. Here we provide protocols for obtaining isotopically labeled proteins and for downstream SIP-metaproteomics analysis.

RevDate: 2019-08-13

Ghori NU, Moreira-Grez B, Vuong P, et al (2019)

RNA Stable Isotope Probing (RNA-SIP).

Methods in molecular biology (Clifton, N.J.), 2046:31-44.

Stable isotope probing is a combined molecular and isotopic technique used to probe the identity and function of uncultivated microorganisms within environmental samples. Employing stable isotopes of common elements such as carbon and nitrogen, RNA-SIP exploits an increase in the buoyant density of RNA caused by the active metabolism and incorporation of heavier mass isotopes into the RNA after cellular utilization of labeled substrates pulsed into the community. Labeled RNAs are subsequently separated from unlabeled RNAs by density gradient centrifugation followed by identification of the RNAs by sequencing. Therefore, RNA stable isotope probing is a culture-independent technique that provides simultaneous information about microbiome community, composition and function. This chapter presents the detailed protocol for performing an RNA-SIP experiment, including the formation, ultracentrifugation, and fractional analyses of stable isotope-labeled RNAs extracted from environmental samples.

RevDate: 2019-08-13

Bockoven AA, Bondy EC, Flores MJ, et al (2019)

What Goes Up Might Come Down: the Spectacular Spread of an Endosymbiont Is Followed by Its Decline a Decade Later.

Microbial ecology pii:10.1007/s00248-019-01417-4 [Epub ahead of print].

Facultative, intracellular bacterial symbionts of arthropods may dramatically affect host biology and reproduction. The length of these symbiont-host associations may be thousands to millions of years, and while symbiont loss is predicted, there have been very few observations of a decline of symbiont infection rates. In a population of the sweet potato whitefly species (Bemisia tabaci MEAM1) in Arizona, USA, we documented the frequency decline of a strain of Rickettsia in the Rickettsia bellii clade from near-fixation in 2011 to 36% of whiteflies infected in 2017. In previous studies, Rickettsia had been shown to increase from 1 to 97% from 2000 to 2006 and remained at high frequency for at least five years. At that time, Rickettsia infection was associated with both fitness benefits and female bias. In the current study, we established matrilines of whiteflies from the field (2016, Rickettsia infection frequency = 58%) and studied (a) Rickettsia vertical transmission, (b) fitness and sex ratios associated with Rickettsia infection, (c) symbiont titer, and (d) bacterial communities within whiteflies. The vertical transmission rate was high, approximately 98%. Rickettsia infection in the matrilines was not associated with fitness benefits or sex ratio bias and appeared to be slightly costly, as more Rickettsia-infected individuals produced non-hatching eggs. Overall, the titer of Rickettsia in the matrilines was lower in 2016 than in the whiteflies collected in 2011, but the titer distribution appeared bimodal, with high- and low-titer lines, and constancy of the average titer within lines over three generations. We found neither association between Rickettsia titer and fitness benefits or sex ratio bias nor evidence that Rickettsia was replaced by another secondary symbiont. The change in the interaction between symbiont and host in 2016 whiteflies may explain the drop in symbiont frequency we observed.

RevDate: 2019-08-10

Bolyen E, Rideout JR, Dillon MR, et al (2019)

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

RevDate: 2019-08-10

Xu X, Zhu X, Wang C, et al (2019)

microRNA-650 promotes inflammation induced apoptosis of intestinal epithelioid cells by targeting NLRP6.

Biochemical and biophysical research communications pii:S0006-291X(19)31213-6 [Epub ahead of print].

Ulcerative colitis (UC), a serious threat to public health, is one of the main forms of inflammatory bowel disease, whereas the molecular mechanisms underlying ulcerative colitis induced by inflammation still remain elusive. NPLR6 gene is previously shown to regulate intestinal homeostasis and regulate the colonic microbial ecology. Here, we report that microRNA-650 (miR-650) plays an important role in the pathogenesis of UC as an upstream regulator of NPLR6 gene. MiR-650 is proved overexpressed in the inflamed mucosa of patients with ulcerative colitis and the DSS induced colitis model mice by qRT-PCR. Over-expression of miR-650 leads to increased apoptosis of Caco-2 and IEC-6 cells, and the DSS-induced mice aggravation, while knock-down of miR-650 shows opposite effects. Through constructing luciferase reporter genes containing 3'-untranslated regions of NLRP6, we further demonstrate that miR-650 inhibits NLRP6 through binding to its 3'-untranslated regions. Overexpression of NLRP6 in Caco-2 and IEC-6 cells suppress the increase apoptosis induced by miR-650 overexpression. Overall, the findings of this study indicate the role of miR-650 in ulcerative colitis, which provides a new target for therapeutic treatment.

RevDate: 2019-08-10

Hassan Z, Sultana M, Khan SI, et al (2019)

Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation?.

Microorganisms, 7(8): pii:microorganisms7080246.

Millions of people worldwide are at risk of arsenic poisoning from their drinking water. In Bangladesh the problem extends to rural drinking water wells, where non-biological solutions are not feasible. In serial enrichment cultures of water from various Bangladesh drinking water wells, we found transfer-persistent arsenite oxidation activity under four conditions (aerobic/anaerobic; heterotrophic/autotrophic). This suggests that biological decontamination may help ameliorate the problem. The enriched microbial communities were phylogenetically at least as diverse as the unenriched communities: they contained a bonanza of 16S rRNA gene sequences. These related to Hydrogenophaga, Acinetobacter, Dechloromonas, Comamonas, and Rhizobium/Agrobacterium species. In addition, the enriched microbiomes contained genes highly similar to the arsenite oxidase (aioA) gene of chemolithoautotrophic (e.g., Paracoccus sp. SY) and heterotrophic arsenite-oxidizing strains. The enriched cultures also contained aioA phylotypes not detected in the previous survey of uncultivated samples from the same wells. Anaerobic enrichments disclosed a wider diversity of arsenite oxidizing aioA phylotypes than did aerobic enrichments. The cultivatable chemolithoautotrophic and heterotrophic arsenite oxidizers are of great interest for future in or ex-situ arsenic bioremediation technologies for the detoxification of drinking water by oxidizing arsenite to arsenate that should then precipitates with iron oxides. The microbial activities required for such a technology seem present, amplifiable, diverse and hence robust.

RevDate: 2019-08-09

Arevalo P, VanInsberghe D, Elsherbini J, et al (2019)

A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations.

Cell, 178(4):820-834.e14.

Delineating ecologically meaningful populations among microbes is important for identifying their roles in environmental and host-associated microbiomes. Here, we introduce a metric of recent gene flow, which when applied to co-existing microbes, identifies congruent genetic and ecological units separated by strong gene flow discontinuities from their next of kin. We then develop a pipeline to identify genome regions within these units that show differential adaptation and allow mapping of populations onto environmental variables or host associations. Using this reverse ecology approach, we show that the human commensal bacterium Ruminococcus gnavus breaks up into sharply delineated populations that show different associations with health and disease. Defining populations by recent gene flow in this way will facilitate the analysis of bacterial and archaeal genomes using ecological and evolutionary theory developed for plants and animals, thus allowing for testing unifying principles across all biology.

RevDate: 2019-08-09

Lv Y, Qin X, Jia H, et al (2019)

The Association between Gut Microbiota Composition and Body Mass Index in Chinese Male College Students, as Analyzed by Next-generation Sequencing.

The British journal of nutrition pii:S0007114519001909 [Epub ahead of print].

Altered gut microbial ecology contributes to the development of metabolic diseases including obesity. However, studies based on different populations have generated conflicting results due to diet, environment, methodologies, etc. The aim of our study was to explore the association between gut microbiota and Body Mass Index (BMI) in Chinese college students. 16S next-generation sequencing (NGS) was used to test the gut microbiota of 9 lean, 9 overweight/obesity, and 10 normal-weight male college students. The differences of gut microbiota distribution among three groups were compared, and the relationship between the richness, diversity, composition of gut microbiota and BMI were analyzed. The predominant phyla Bacteroidetes and Firmicutes were further confirmed by real-time PCR. Metagenomic biomarker discovery was conducted by Linear discriminant analysis (LDA) Effect Size (LEfSe). NGS revealed that gut microbiota composition was different among three groups, but there was no difference in the abundance ratio of Firmicutes/ Bacteroidetes. Several bacterial taxa were in linear relationship with BMI (positive relationship: uncultured bacterium (Bacteroides genus); negative relationship: Porphyromonadaceae, Acidaminococcaceae, Rikenellaceae, Desulfovibrionaceae, Blautia, Anaerotruncus, Parabacteroides, Alistipes). Moreover, gut microbiota diversity decreased with the increase of BMI. And LEfSe analyze indicated that Blautia, Anaerotruncus and its uncultured species were significantly enriched in the lean group (LDA score≥3), Parasuterella and its uncultured species were significantly enriched in the overweight/obese groups(LDA score≥3). In general, gut microbiota composition and microbial diversity were associated with BMI in Chinese male college students. Our results might enrich the understanding between gut microbiota and obesity.

RevDate: 2019-08-09

Ramamurthy T, Mutreja A, Weill FX, et al (2019)

Revisiting the Global Epidemiology of Cholera in Conjuction With the Genomics of Vibrio cholerae.

Frontiers in public health, 7:203.

Toxigenic Vibrio cholerae is responsible for 1.4 to 4.3 million cases with about 21,000-143,000 deaths per year. Dominance of O1 and O139 serogroups, classical and El tor biotypes, alterations in CTX phages and the pathogenicity Islands are some of the major features of V. cholerae isolates that are responsible for cholera epidemics. Whole-genome sequencing (WGS) based analyses of single-nucleotide polymorphisms (SNPs) and other infrequent genetic variants provide a robust phylogenetic framework. Recent studies on the global transmission of pandemic V. cholerae O1 strains have shown the existence of eight different phyletic lineages. In these, the classical and El Tor biotype strains were separated as two distinctly evolved lineages. The frequency of SNP accumulation and the temporal and geographical distribution supports the perception that the seventh cholera pandemic (7CP) has spread from the Bay of Bengal region in three independent but overlapping waves. The 2010 Haitian outbreak shared a common ancestor with South-Asian wave-3 strains. In West Africa and East/Southern Africa, cholera epidemics are caused by single expanded lineage, which has been introduced several times since 1970. The Latin American epidemics that occurred in 1991 and 2010 were the result of introductions of two 7CP sublineages. Sublineages representing wave-3 have caused huge outbreaks in Haiti and Yemen. The Ogawa-Inaba serotype switchover in several cholera epidemics are believed to be due to the involvement of certain selection mechanism(s) rather than due to random events. V. cholerae O139 serogroup is phylogenetically related to the 7CP El Tor, and almost all these isolates belonged to the multilocus sequence type-69. Additional phenotypic and genotypic information have been generated to understand the pathogenicity of classical and El Tor vibrios. Presence of integrative conjugative elements (ICE) with antibiotic resistance gene cassettes, clustered regularly interspaced short palindromic repeats-associated protein system and ctxAB promoter based ToxRS expression of cholera toxin (CT) separates classical and El Tor biotypes. With the availability of WGS information, several important applications including, molecular typing, antimicrobial resistance, new diagnostics, and vaccination strategies could be generated.

RevDate: 2019-08-09

Fernández-Martínez MÁ, Dos Santos Severino R, Moreno-Paz M, et al (2019)

Prokaryotic Community Structure and Metabolisms in Shallow Subsurface of Atacama Desert Playas and Alluvial Fans After Heavy Rains: Repairing and Preparing for Next Dry Period.

Frontiers in microbiology, 10:1641.

The Atacama Desert, the oldest and driest desert on Earth, displays significant rains only once per decade. To investigate how microbial communities take advantage of these sporadic wet events, we carried out a geomicrobiological study a few days after a heavy rain event in 2015. Different physicochemical and microbial community analyses were conducted on samples collected from playas and an alluvial fan from surface, 10, 20, 50, and 80 cm depth. Gravimetric moisture content peaks were measured in 10 and 20 cm depth samples (from 1.65 to 4.1% w/w maximum values) while, in general, main anions such as chloride, nitrate, and sulfate concentrations increased with depth, with maximum values of 13-1,125; 168-10,109; and 9,904-30,952 ppm, respectively. Small organic anions such as formate and acetate had maximum concentrations from 2.61 to 3.44 ppm and 6.73 to 28.75 ppm, respectively. Microbial diversity inferred from DNA analysis showed Actinobacteria and Alphaproteobacteria as the most abundant and widespread bacterial taxa among the samples, followed by Chloroflexi and Firmicutes at specific sites. Archaea were mainly dominated by Nitrososphaerales, Methanobacteria, with the detection of other groups such as Halobacteria. Metaproteomics showed a high and even distribution of proteins involved in primary metabolic processes such as energy production and biosynthetic pathways, and a limited but remarkable presence of proteins related to resistance to environmental stressors such as radiation, oxidation, or desiccation. The results indicated that extra humidity in the system allows the microbial community to repair, and prepare for the upcoming hyperarid period. Additionally, it supplies biomarkers to the medium whose preservation potential could be high under strong desiccation conditions and relevant for planetary exploration.

RevDate: 2019-08-09

Cardini U, Bartoli M, Lücker S, et al (2019)

Chemosymbiotic bivalves contribute to the nitrogen budget of seagrass ecosystems.

The ISME journal pii:10.1038/s41396-019-0486-9 [Epub ahead of print].

In many seagrass sediments, lucinid bivalves and their sulfur-oxidizing symbionts are thought to underpin key ecosystem functions, but little is known about their role in nutrient cycles, particularly nitrogen. We used natural stable isotopes, elemental analyses, and stable isotope probing to study the ecological stoichiometry of a lucinid symbiosis in spring and fall. Chemoautotrophy appeared to dominate in fall, when chemoautotrophic carbon fixation rates were up to one order of magnitude higher as compared with the spring, suggesting a flexible nutritional mutualism. In fall, an isotope pool dilution experiment revealed carbon limitation of the symbiosis and ammonium excretion rates up to tenfold higher compared with fluxes reported for nonsymbiotic marine bivalves. These results provide evidence that lucinid bivalves can contribute substantial amounts of ammonium to the ecosystem. Given the preference of seagrasses for this nitrogen source, lucinid bivalves' contribution may boost productivity of these important blue carbon ecosystems.

RevDate: 2019-08-08

Barone M, Turroni S, Rampelli S, et al (2019)

Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context.

PloS one, 14(8):e0220619 pii:PONE-D-18-35733.

The modern Paleolithic diet (MPD), featured by the consumption of vegetables, fruit, nuts, seeds, eggs, fish and lean meat, while excluding grains, dairy products, salt and refined sugar, has gained substantial public attention in recent years because of its potential multiple health benefits. However, to date little is known about the actual impact of this dietary pattern on the gut microbiome (GM) and its implications for human health. In the current scenario where Western diets, low in fiber while rich in industrialized and processed foods, are considered one of the leading causes of maladaptive GM changes along human evolution, likely contributing to the increasing incidence of chronic non-communicable diseases, we hypothesize that the MPD could modulate the Western GM towards a more "ancestral" configuration. In an attempt to shed light on this, here we profiled the GM structure of urban Italian subjects adhering to the MPD, and compared data with other urban Italians following a Mediterranean Diet (MD), as well as worldwide traditional hunter-gatherer populations from previous publications. Notwithstanding a strong geography effect on the GM structure, our results show an unexpectedly high degree of biodiversity in MPD subjects, which well approximates that of traditional populations. The GM of MPD individuals also shows some peculiarities, including a high relative abundance of bile-tolerant and fat-loving microorganisms. The consumption of plant-based foods-albeit with the exclusion of grains and pulses-along with the minimization of the intake of processed foods, both hallmarks of the MPD, could therefore contribute to partially rewild the GM but caution should be taken in adhering to this dietary pattern in the long term.

RevDate: 2019-08-08

Gray L, G Kernaghan (2019)

Fungal Succession During the Decomposition of Ectomycorrhizal Fine Roots.

Microbial ecology pii:10.1007/s00248-019-01418-3 [Epub ahead of print].

Ectomycorrhizal (ECM) fine roots account for a substantial proportion of forest production and their decomposition releases large amounts of nutrients to the soil ecosystem. However, little is known about the fungi involved in ECM decomposition, including assemblages of fungal saprotrophs, endophytes, and the ECM fungi themselves. To follow fungal succession during the degradation of senescing fine roots, understory seedlings of Abies balsamea and Picea rubens at two sites in the Acadian forest of Nova Scotia were either severed at the root collar or left as controls. Root systems were collected sequentially over two growing seasons and assessed for fine root loss and ECM mantle integrity. ECM were identified by ITS-PCR and grouped into broad morphological categories. Fungal communities colonizing the senescing fine roots were also monitored by systematically constructing clone libraries over the course of the experiment. ECM with cottony, weakly pigmented mantles (e.g., Cortinarius) degraded within the first year. Those with cottony, but intensely pigmented mantles (Piloderma), and smooth mantles with weak pigmentation (Russulaceae) degraded more slowly. Smooth, melanized ECM (Cenococcum and Tomentella) generally maintained integrity over the course of the experiment. Rates of fine root loss and changes in ECM mantle integrity were positively correlated with soil temperature. ECM DNA was detected throughout the experiment, and was not replaced by that of saprotrophic species during the two seasons sampled. However, fungal root endophytes (e.g., Helotiaceae) initially increased in abundance and then decreased as mantles degraded, suggesting a possible role in ECM decomposition.

RevDate: 2019-08-08

Ning D, Deng Y, Tiedje JM, et al (2019)

A general framework for quantitatively assessing ecological stochasticity.

Proceedings of the National Academy of Sciences of the United States of America pii:1904623116 [Epub ahead of print].

Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. Here we propose a general mathematical framework to quantify ecological stochasticity under different situations in which deterministic factors drive the communities more similar or dissimilar than null expectation. An index, normalized stochasticity ratio (NST), was developed with 50% as the boundary point between more deterministic (<50%) and more stochastic (>50%) assembly. NST was tested with simulated communities by considering abiotic filtering, competition, environmental noise, and spatial scales. All tested approaches showed limited performance at large spatial scales or under very high environmental noise. However, in all of the other simulated scenarios, NST showed high accuracy (0.90 to 1.00) and precision (0.91 to 0.99), with averages of 0.37 higher accuracy (0.1 to 0.7) and 0.33 higher precision (0.0 to 1.8) than previous approaches. NST was also applied to estimate stochasticity in the succession of a groundwater microbial community in response to organic carbon (vegetable oil) injection. Our results showed that community assembly was shifted from more deterministic (NST = 21%) to more stochastic (NST = 70%) right after organic carbon input. As the vegetable oil was consumed, the community gradually returned to be more deterministic (NST = 27%). In addition, our results demonstrated that null model algorithms and community similarity metrics had strong effects on quantifying ecological stochasticity.

RevDate: 2019-08-07

Moss JA, Henriksson NL, Pakulski JD, et al (2019)

Oceanic Microplankton Do Not Adhere to the Latitudinal Diversity Gradient.

Microbial ecology pii:10.1007/s00248-019-01413-8 [Epub ahead of print].

A latitudinal biodiversity gradient has captivated ecologists for years, and has become a widely recognized pattern in biogeography, manifest as an increase in biodiversity from the poles to the tropics. Oceanographers have attempted to discern whether these distribution patterns are shared with marine biota, and a lively debate has emerged concerning the global distribution of microbes. Limitations in sampling resolution for such large-scale assessments have often prohibited definitive conclusions. We evaluated microbial planktonic communities along a ~ 15,400-km Pacific Ocean transect with DNA from samples acquired every 2 degrees of latitude within a 3-month period between late August and early November 2003. Next-generation sequencing targeting the Bacteria, Archaea, and Eukarya yielded ~ 10.8 million high-quality sequences. Beta-analysis revealed geographic patterns of microbial communities, primarily the Bacteria and Archaea domains. None of the domains exhibited a unimodal pattern of alpha-diversity with respect to latitude. Bacteria communities increased in richness from Arctic to Antarctic waters, whereas Archaea and Eukarya communities showed no latitudinal or polar trends. Based on our analyses, environmental factors related to latitude thought to influence various macrofauna may not define microplankton diversity patterns of richness in the global ocean.

RevDate: 2019-08-07

Ziels RM, Nobu MK, DZ Sousa (2019)

Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics.

mSystems, 4(4): pii:4/4/e00159-19.

Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable-isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in 13C after growing on [13C]butyrate. Differential abundance analysis of recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in heavy [13C]DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (<95%) with any cultured representative species, indicating that it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for acetoclastic methanogenesis, indicating that it was enriched in 13C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to identify in situ interspecies metabolic cooperation within syntrophic consortia important to anaerobic waste treatment as well as global carbon cycling.IMPORTANCE Predicting the metabolic potential and ecophysiology of mixed microbial communities remains a major challenge, especially for slow-growing anaerobes that are difficult to isolate. Unraveling the in situ metabolic activities of uncultured species may enable a more descriptive framework to model substrate transformations by microbiomes, which has broad implications for advancing the fields of biotechnology, global biogeochemistry, and human health. Here, we investigated the in situ function of mixed microbiomes by combining stable-isotope probing with metagenomics to identify the genomes of active syntrophic populations converting butyrate, a C4 fatty acid, into methane within anaerobic digesters. This approach thus moves beyond the mere presence of metabolic genes to resolve "who is doing what" by obtaining confirmatory assimilation of the labeled substrate into the DNA signature. Our findings provide a framework to further link the genomic identities of uncultured microbes with their ecological function within microbiomes driving many important biotechnological and global processes.

RevDate: 2019-08-07

Su X, Jing G, McDonald D, et al (2019)

Reply to Sun et al., "Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy".

mBio, 10(4): pii:mBio.01234-19.

RevDate: 2019-08-06

Siddiqee MH, Henry R, Deletic A, et al (2019)

Salmonella from a Microtidal Estuary Are Capable of Invading Human Intestinal Cell Lines.

Microbial ecology pii:10.1007/s00248-019-01419-2 [Epub ahead of print].

Faecal contamination poses health risks for the recreational users of urban estuaries. However, our understanding of the potential pathogenicity of faecal microbes in these environments is limited. To this end, a study was conducted to understand the spatial and seasonal distribution of Salmonella in water and sediments of the Yarra River estuary, Melbourne, Australia. Among 210 samples in total, culturable Salmonella were recovered from 27%, 17%, and 19% of water, bank, and bed sediment samples, respectively. The combined detection increased from 15% in winter to 32% in summer (p < 0.05) indicating seasonal variation as potential part of public health risk assessments. Further, pathogenic potential of the Salmonella isolates was characterised via the quantification of attachment and invasion capacity using human epithelial colorectal cell line Caco-2 on a subset of isolates (n = 62). While all of these isolates could attach and invade Caco-2 cells, 52% and 13% of these showed greater attachment and invasiveness, respectively, than the corresponding mean values for S. Typhimurium ATCC14028 control. Isolates from winter were on average more invasive (seven out of eight isolates with the highest invasiveness recovered from the colder sampling period) than the isolates from summer, and Salmonella collected during summer showed lower invasion (p < 0.05) compared with the control. Similar low invasion compared with the same control was observed for isolates recovered from bank sediment (p < 0.05). While the higher prevalence in summer may imply higher risks during these peak recreational periods, it is essential that this information is used in combination with quantitative microbial risk assessments to fully understand the health risks posed by Salmonella in microtidal estuaries.

RevDate: 2019-08-06

Hale L, Feng W, Yin H, et al (2019)

Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon.

The ISME journal pii:10.1038/s41396-019-0485-x [Epub ahead of print].

The susceptibility of soil organic carbon (SOC) in tundra to microbial decomposition under warmer climate scenarios potentially threatens a massive positive feedback to climate change, but the underlying mechanisms of stable SOC decomposition remain elusive. Herein, Alaskan tundra soils from three depths (a fibric O horizon with litter and course roots, an O horizon with decomposing litter and roots, and a mineral-organic mix, laying just above the permafrost) were incubated. Resulting respiration data were assimilated into a 3-pool model to derive decomposition kinetic parameters for fast, slow, and passive SOC pools. Bacterial, archaeal, and fungal taxa and microbial functional genes were profiled throughout the 3-year incubation. Correlation analyses and a Random Forest approach revealed associations between model parameters and microbial community profiles, taxa, and traits. There were more associations between the microbial community data and the SOC decomposition parameters of slow and passive SOC pools than those of the fast SOC pool. Also, microbial community profiles were better predictors of model parameters in deeper soils, which had higher mineral contents and relatively greater quantities of old SOC than in surface soils. Overall, our analyses revealed the functional potential of microbial communities to decompose tundra SOC through a suite of specialized genes and taxa. These results portray divergent strategies by which microbial communities access SOC pools across varying depths, lending mechanistic insights into the vulnerability of what is considered stable SOC in tundra regions.

RevDate: 2019-08-06

Andrade-Martínez JS, Moreno-Gallego JL, A Reyes (2019)

Defining a Core Genome for the Herpesvirales and Exploring their Evolutionary Relationship with the Caudovirales.

Scientific reports, 9(1):11342 pii:10.1038/s41598-019-47742-z.

The order Herpesvirales encompasses a wide variety of important and broadly distributed human pathogens. During the last decades, similarities in the viral cycle and the structure of some of their proteins with those of the order Caudovirales, the tailed bacterial viruses, have brought speculation regarding the existence of an evolutionary relationship between these clades. To evaluate such hypothesis, we used over 600 Herpesvirales and 2000 Caudovirales complete genomes to search for the presence or absence of clusters of orthologous protein domains and constructed a dendrogram based on their compositional similarities. The results obtained strongly suggest an evolutionary relationship between the two orders. Furthermore, they allowed to propose a core genome for the Herpesvirales, composed of 4 proteins, including the ATPase subunit of the DNA-packaging terminase, the only protein with previously verified conservation. Accordingly, a phylogenetic tree constructed with sequences derived from the clusters associated to these proteins grouped the Herpesvirales strains accordingly to the established families and subfamilies. Overall, this work provides results supporting the hypothesis that the two orders are evolutionarily related and contributes to the understanding of the history of the Herpesvirales.

RevDate: 2019-08-05

Vigneron A, Lovejoy C, Cruaud P, et al (2019)

Contrasting Winter Versus Summer Microbial Communities and Metabolic Functions in a Permafrost Thaw Lake.

Frontiers in microbiology, 10:1656.

Permafrost thawing results in the formation of thermokarst lakes, which are biogeochemical hotspots in northern landscapes and strong emitters of greenhouse gasses to the atmosphere. Most studies of thermokarst lakes have been in summer, despite the predominance of winter and ice-cover over much of the year, and the microbial ecology of these waters under ice remains poorly understood. Here we first compared the summer versus winter microbiomes of a subarctic thermokarst lake using DNA- and RNA-based 16S rRNA amplicon sequencing and qPCR. We then applied comparative metagenomics and used genomic bin reconstruction to compare the two seasons for changes in potential metabolic functions in the thermokarst lake microbiome. In summer, the microbial community was dominated by Actinobacteria and Betaproteobacteria, with phototrophic and aerobic pathways consistent with the utilization of labile and photodegraded substrates. The microbial community was strikingly different in winter, with dominance of methanogens, Planctomycetes, Chloroflexi and Deltaproteobacteria, along with various taxa of the Patescibacteria/Candidate Phyla Radiation (Parcubacteria, Microgenomates, Omnitrophica, Aminicenantes). The latter group was underestimated or absent in the amplicon survey, but accounted for about a third of the metagenomic reads. The winter lineages were associated with multiple reductive metabolic processes, fermentations and pathways for the mobilization and degradation of complex organic matter, along with a strong potential for syntrophy or cross-feeding. The results imply that the summer community represents a transient stage of the annual cycle, and that carbon dioxide and methane production continue through the prolonged season of ice cover via a taxonomically distinct winter community and diverse mechanisms of permafrost carbon transformation.

RevDate: 2019-08-05

Osorio H, Mettert E, Kiley P, et al (2019)

Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans.

Frontiers in microbiology, 10:1642.

The ability to conserve energy in the presence or absence of oxygen provides a metabolic versatility that confers an advantage in natural ecosystems. The switch between alternative electron transport systems is controlled by the fumarate nitrate reduction transcription factor (FNR) that senses oxygen via an oxygen-sensitive [4Fe-4S]2+ iron-sulfur cluster. Under O2 limiting conditions, FNR plays a key role in allowing bacteria to transition from aerobic to anaerobic lifestyles. This is thought to occur via transcriptional activation of genes involved in anaerobic respiratory pathways and by repression of genes involved in aerobic energy production. The Proteobacterium Acidithiobacillus ferrooxidans is a model species for extremely acidophilic microorganisms that are capable of aerobic and anaerobic growth on elemental sulfur coupled to oxygen and ferric iron reduction, respectively. In this study, an FNR-like protein (FNRAF) was discovered in At. ferrooxidans that exhibits a primary amino acid sequence and major motifs and domains characteristic of the FNR family of proteins, including an effector binding domain with at least three of the four cysteines known to coordinate an [4Fe-4S]2+ center, a dimerization domain, and a DNA binding domain. Western blotting with antibodies against Escherichia coli FNR (FNREC) recognized FNRAF. FNRAF was able to drive expression from the FNR-responsive E. coli promoter PnarG, suggesting that it is functionally active as an FNR-like protein. Upon air exposure, FNRAF demonstrated an unusual lack of sensitivity to oxygen compared to the archetypal FNREC. Comparison of the primary amino acid sequence of FNRAF with that of other natural and mutated FNRs, including FNREC, coupled with an analysis of the predicted tertiary structure of FNRAF using the crystal structure of the related FNR from Aliivibrio fisheri as a template revealed a number of amino acid changes that could potentially stabilize FNRAF in the presence of oxygen. These include a truncated N terminus and amino acid changes both around the putative Fe-S cluster coordinating cysteines and also in the dimer interface. Increased O2 stability could allow At. ferrooxidans to survive in environments with fluctuating O2 concentrations, providing an evolutionary advantage in natural, and engineered environments where oxygen gradients shape the bacterial community.

RevDate: 2019-08-05

Gupta VVSR, Bramley RGV, Greenfield P, et al (2019)

Vineyard Soil Microbiome Composition Related to Rotundone Concentration in Australian Cool Climate 'Peppery' Shiraz Grapes.

Frontiers in microbiology, 10:1607.

Soil microbial communities have an integral association with plants and play an important role in shaping plant nutrition, health, crop productivity and product quality. The influence of bacteria and fungi on wine fermentation is well known. However, little is known about the role of soil microbes, other than microbial pathogens, on grape composition or their role in vintage or site (terroir) impacts on grape composition. In this study, we used an amplicon sequencing approach to investigate the potential relationships between soil microbes and inherent spatial variation in grape metabolite composition - specifically, the concentration of the 'impact aroma compound' rotundone in Shiraz grapes (Vitis vinifera L.) grown in a 6.1 ha vineyard in the Grampians region of Victoria, Australia. Previous work had demonstrated temporal stability in patterns of within-vineyard spatial variation in rotundone concentration, enabling identification of defined 'zones' of inherently 'low' or 'high' concentration of this grape metabolite. 16S rRNA and ITS region-amplicon sequencing analysis of microbial communities in the surface soils collected from these zones indicated marked differences between zones in the genetic diversity and composition of the soil bacterial and fungal microbiome. Soils in the High rotundone zone exhibited higher diversity of bacteria, but lower diversity of fungi, compared to the soils in the Low rotundone zone. In addition, the network analysis of the microbial community in the High rotundone zone soils appeared well structured, especially with respect to the bacterial community, compared to that in the Low rotundone zone soils. The key differences in the microbial community structure between the rotundone zones are obvious for taxa/groups of both bacteria and fungi, particularly for bacteria belonging to Acidobacteria-GP4 and GP7, Rhizobiales, Gaiellaceae, Alphaproteobacteria and the Nectriaceae and Tremellaceae families of fungi. Although mulching in some parts of the vineyard caused changes in bacterial and fungal composition and overall microbial catabolic diversity and activity, its effects did not mask the rotundone zone-based variation. This finding of a systematic rotundone zone-based variation in soil microbiomes suggests an opportunity to bring together understanding of microbial ecology, plant biochemistry, and viticultural management for improved management of grape metabolism, composition and wine flavor.

RevDate: 2019-08-04

Frankel-Bricker J, Song MJ, Benner MJ, et al (2019)

Variation in the Microbiota Associated with Daphnia magna Across Genotypes, Populations, and Temperature.

Microbial ecology pii:10.1007/s00248-019-01412-9 [Epub ahead of print].

Studies of how the microbiome varies among individuals, populations, and abiotic conditions are critical for understanding this key component of an organism's biology and ecology. In the case of Daphnia, aquatic microcrustaceans widely used in population/community ecology and environmental science studies, understanding factors that influence microbiome shifts among individuals is useful for both basic and applied research contexts. In this study, we assess differences in the microbiome among genotypes of D. magna collected from three regions along a large latitudinal gradient (Finland, Germany, and Israel). After being reared in the lab for many years, we sought to characterize any differences in genotype- or population-specific microbial communities, and to assess whether the microbiota varied among temperatures. Our study is similar to a recent comparison of the microbial communities among D. magna genotypes raised in different temperatures published by Sullam et al. (Microb Ecol 76(2):506-517, 2017), and as such represents one of the first examples of a reproducible result in microbiome research. Like the previous study, we find evidence for a strong effect of temperature on the microbiome of D. magna, although across a much smaller temperature range representing potential near-future climates. In addition, we find evidence that the microbiomes of D. magna genotypes from different regions are distinct, even years after being brought into the laboratory. Finally, our results highlight a potentially common finding in the expanding area of microbiome research-differences among treatments are not necessarily observed in the most abundant taxonomic groups. This highlights the importance of considering sampling scheme and depth of coverage when characterizing the microbiome, as different experimental designs can significantly impact taxon-specific results, even when large-scale effects are reproduced.

RevDate: 2019-08-03

Cowan DA, Hopkins DW, Jones BE, et al (2019)

Microbiomics of Namib Desert habitats.

Extremophiles : life under extreme conditions pii:10.1007/s00792-019-01122-7 [Epub ahead of print].

The Namib Desert is one of the world's only truly coastal desert ecosystem. Until the end of the 1st decade of the twenty-first century, very little was known of the microbiology of this southwestern African desert, with the few reported studies being based solely on culture-dependent approaches. However, from 2010, an intense research program was undertaken by researchers from the University of the Western Cape Institute for Microbial Biotechnology and Metagenomics, and subsequently the University of Pretoria Centre for Microbial Ecology and Genomics, and their collaborators, led to a more detailed understanding of the ecology of the indigenous microbial communities in many Namib Desert biotopes. Namib Desert soils and the associated specialized niche communities are inhabited by a wide array of prokaryotic, lower eukaryotic and virus/phage taxa. These communities are highly heterogeneous on both small and large spatial scales, with community composition impacted by a range of macro- and micro-environmental factors, from water regime to soil particle size. Community functionality is also surprisingly non-homogeneous, with some taxa retaining functionality even under hyper-arid soil conditions, and with subtle changes in gene expression and phylotype abundances even on diel timescales. Despite the growing understanding of the structure and function of Namib Desert microbiomes, there remain enormous gaps in our knowledge. We have yet to quantify many of the processes in these soil communities, from regional nutrient cycling to community growth rates. Despite the progress that has been made, we still have little knowledge of either the role of phages in microbial community dynamics or inter-species interactions. Furthermore, the intense research efforts of the past decade have highlighted the immense scope for future microbiological research in this dynamic, enigmatic and charismatic region of Africa.

RevDate: 2019-08-03

Lawley B, Otal A, Moloney-Geany K, et al (2019)

Comparison of the development of the fecal microbiota of Indonesian and New Zealand children during the first year of life reveals differences in bifidobacterial taxa and microbiota complexity at 12 months.

Applied and environmental microbiology pii:AEM.01105-19 [Epub ahead of print].

The biological succession that occurs in the gut of infants inhabiting Western countries during the first year of life is broadly predictable in terms of the increasing complexity of microbiota composition. Less information is available about microbiotas in Asian countries where environmental, nutritional and cultural influences may differentially affect the composition and development of the microbial community. We compared the fecal microbiotas of Indonesian (n = 204) and New Zealand (NZ; n = 74) infants aged 6-7 months and 12 months. Comparisons were made by analysis of 16S rRNA gene sequences, and associated derivation of community diversity metrics, relative abundances of bacterial families, detection of enterotypes, and co-occurrence correlation networks. Abundances of Bifidobacterium longum subspecies infantis and longum were made by quantitative PCR. All observations supported the view that the Indonesian and NZ infant microbiotas developed in complexity over time, but the changes were much greater in NZ infants. B. longum subsp. infantis dominated the microbiota of Indonesian children whereas subsp. longum was dominant in NZ children. Network analysis showed that the niche model (trophic adaptation results in preferential colonization) of microbiota assemblage was supported in Indonesian infants, whereas the neutral (stochastic) model was supported by the development of the microbiota of NZ infants. The results of the study show that the development of the fecal microbiota is not the same for infants in all countries and points to the necessity of obtaining a better understanding of the factors that control the colonization of the gut in early life.Importance This study addresses the microbiology of a natural ecosystem (the infant bowel) associated with children in a rural setting in Indonesia and an urban environment in New Zealand. Analysis of DNA sequences generated from the microbial community (microbiota) in the feces of the infants during the first year of life showed marked differences in the composition and complexity of the bacterial collections. The differences were most likely due to differences in the prevalence and duration of breastfeeding of infants in the two countries. These kinds of studies are essential in developing concepts of microbial ecology that relate to the influence of nutrition and environment on the development of the gut microbiota and in determining the long-term effects of microbiological events in early life on human health and well-being.

RevDate: 2019-08-02

Zhu YG, Zhao Y, Zhu D, et al (2019)

Soil biota, antimicrobial resistance and planetary health.

Environment international, 131:105059 pii:S0160-4120(19)31017-7 [Epub ahead of print].

The concept of planetary health acknowledges the links between ecosystems, biodiversity and human health and well-being. Soil, the critical component of the interconnected ecosystem, is the most biodiverse habitat on Earth, and soil microbiomes play a major role in human health and well-being through ecosystem services such as nutrient cycling, pollutant remediation and synthesis of bioactive compounds such as antimicrobials. Soil is also a natural source of antimicrobial resistance, which is often termed intrinsic resistance. However, increasing use and misuse of antimicrobials in humans and animals in recent decades has increased both the diversity and prevalence of antimicrobial resistance in soils, particularly in areas affected by human and animal wastes, such as organic manures and reclaimed wastewater, and also by air transmission. Antimicrobials and antimicrobial resistance are two sides of the sword, while antimicrobials are essential in health care; globally, antimicrobial resistance is jeopardizing the effectiveness of antimicrobial drugs, thus threatening human health. Soil is a crucial pathway through which humans are exposed to antimicrobial resistance determinants, including those harbored by human pathogens. In this review, we use the nexus of antimicrobials and antimicrobial resistance as a focus to discuss the role of soil in planetary health and illustrate the impacts of soil microbiomes on human health and well-being. This review examines the sources and dynamics of antimicrobial resistance in soils and uses the perspective of planetary health to track the movement of antimicrobial-resistance genes between environmental compartments, including soil, water, food and air.

RevDate: 2019-08-02

Jakob F, Quintero Y, Musacchio A, et al (2019)

Acetic acid bacteria encode two levansucrase types of different ecological relationship.

Environmental microbiology [Epub ahead of print].

Acetic acid bacteria (AAB) are associated with plants and insects. Determinants for the targeting and occupation of these widely different environments are unknown. However, most of these natural habitats share plant-derived sucrose, which can be metabolized by some AAB via polyfructose building levansucrases (LS) known to be involved in biofilm formation. Here, we propose two LS types (T) encoded by AAB as determinants for habitat selection, which emerged from vertical (T1) and horizontal (T2) lines of evolution and differ in their genetic organization, structural features and secretion mechanism, as well as their occurrence in proteobacteria. T1-LS are secreted by plant-pathogenic α- and γ-proteobacteria, while T2-LS genes are common in diazotrophic, plant-growth promoting α-, β- and γ-proteobacteria. This knowledge may be exploited for a better understanding of microbial ecology, plant health and biofilm formation by sucrase-secreting proteobacteria in eukaryotic hosts. This article is protected by copyright. All rights reserved.

RevDate: 2019-08-02

Brink LR, Matazel K, Piccolo BD, et al (2019)

Neonatal Diet Impacts Bioregional Microbiota Composition in Piglets Fed Human Breast Milk or Infant Formula.

The Journal of nutrition pii:5542982 [Epub ahead of print].

BACKGROUND: Early infant diet influences postnatal gut microbial development, which in turn can modulate the developing immune system.

OBJECTIVES: The aim of this study was to characterize diet-specific bioregional microbiota differences in piglets fed either human breast milk (HM) or infant formula.

METHODS: Male piglets (White Dutch Landrace Duroc) were raised on HM or cow milk formula (MF) from postnatal day (PND) 2 to PND 21 and weaned to an ad libitum diet until PND 51. Piglets were euthanized on either PND 21 or PND 51, and the gastrointestinal contents were collected for 16s RNA sequencing. Data were analyzed using the Quantitative Insight into Microbial Ecology. Diversity measurements (Chao1 and Shannon) and the Wald test were used to determine relative abundance.

RESULTS: At PND 21, the ileal luminal region of HM-fed piglets showed lower Chao1 operational taxonomic unit diversity, while Shannon diversity was lower in cecal, proximal colon (PC), and distal colon (DC) luminal regions, relative to MF-fed piglets. In addition, at PND 51, the HM-fed piglets had lower genera diversity within the jejunum, ileum, PC, and DC luminal regions, relative to MF-fed piglets. At PND 21, Turicibacter was 4- to 5-fold lower in the HM-fed piglets' ileal, cecal, PC, and DC luminal regions, relative to the MF-fed piglets. Campylobacter is 3- to 6-fold higher in HM-fed piglets duodenal, ileal, cecal, PC, and DC luminal regions, in comparison to MF-fed piglets. Furthermore, the large intestine (cecum, PC, and rectum) luminal region of HM-fed piglets showed 4- to 7-fold higher genera that belong to class Bacteroidia, in comparison to MF-fed piglets at PND 21. In addition, at PND 51 distal colon lumen of HM-fed piglets showed 1.5-fold higher genera from class Bacteroidia than the MF-fed piglets.

CONCLUSIONS: In the large intestinal regions (cecum, PC, and rectum), MF diet alters microbiota composition, relative to HM diet, with sustained effects after weaning from the neonatal diet. These microbiota changes could impact immune system and health outcomes later in life.

RevDate: 2019-08-02

Mosina NL, Schubert WD, DA Cowan (2019)

Characterization and homology modelling of a novel multi-modular and multi-functional Paenibacillus mucilaginosus glycoside hydrolase.

Extremophiles : life under extreme conditions pii:10.1007/s00792-019-01121-8 [Epub ahead of print].

Glycoside hydrolases, particularly cellulases, xylanases and mannanases, are essential for the depolymerisation of lignocellulosic substrates in various industrial bio-processes. In the present study, a novel glycoside hydrolase from Paenibacillus mucilaginosus (PmGH) was expressed in E. coli, purified and characterised. Functional analysis indicated that PmGH is a 130 kDa thermophilic multi-modular and multi-functional enzyme, comprising a GH5, a GH6 and two CBM3 domains and exhibiting cellulase, mannanase and xylanase activities. The enzyme displayed optimum hydrolytic activities at pH 6 and 60 °C and moderate thermostability. Homology modelling of the full-length protein highlighted the structural and functional novelty of native PmGH, with no close structural homologs identified. However, homology modelling of the individual GH5, GH6 and the two CBM3 domains yielded excellent models based on related structures from the Protein Data Bank. The catalytic GH5 and GH6 domains displayed a (β/α)8 and a distorted seven stranded (β/α) fold, respectively. The distinct homology at the domain level but low homology of the full-length protein suggests that this protein evolved by exogenous gene acquisition and recombination.

RevDate: 2019-08-02

Bonner MTL, Allen DE, Brackin R, et al (2019)

Tropical Rainforest Restoration Plantations Are Slow to Restore the Soil Biological and Organic Carbon Characteristics of Old Growth Rainforest.

Microbial ecology pii:10.1007/s00248-019-01414-7 [Epub ahead of print].

Widespread and continuing losses of tropical old-growth forests imperil global biodiversity and alter global carbon (C) cycling. Soil organic carbon (SOC) typically declines with land use change from old-growth forest, but the underlying mechanisms are poorly understood. Ecological restoration plantations offer an established means of restoring aboveground biomass, structure and diversity of forests, but their capacity to recover the soil microbial community and SOC is unknown due to limited empirical data and consensus on the mechanisms of SOC formation. Here, we examine soil microbial community response and SOC in tropical rainforest restoration plantings, comparing them with the original old-growth forest and the previous land use (pasture). Two decades post-reforestation, we found a statistically significant but small increase in SOC in the fast-turnover particulate C fraction. Although the δ13C signature of the more stable humic organic C (HOC) fraction indicated a significant compositional turnover in reforested soils, from C4 pasture-derived C to C3 forest-derived C, this did not translate to HOC gains compared with the pasture baseline. Matched old-growth rainforest soils had significantly higher concentrations of HOC than pasture and reforested soils, and soil microbial enzyme efficiency and the ratio of gram-positive to gram-negative bacteria followed the same pattern. Restoration plantings had unique soil microbial composition and function, distinct from baseline pasture but not converging on target old growth rainforest within the examined timeframe. Our results suggest that tropical reforestation efforts could benefit from management interventions beyond re-establishing tree cover to realize the ambition of early recovery of soil microbial communities and stable SOC.

RevDate: 2019-08-02

Cania B, Vestergaard G, Kublik S, et al (2019)

Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides.

Microbial ecology pii:10.1007/s00248-019-01415-6 [Epub ahead of print].

Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and lipopolysaccharides that act as "glue" for soil particles. However, little is known about the dynamics of "soil glue" producers during the initial development of biocrusts. We hypothesized that different types of initial biocrusts harbor distinct producers of adhesive polysaccharides. To investigate this, we performed a microcosm experiment, cultivating biocrusts on two soil substrates. High-throughput shotgun sequencing was used to obtain metagenomic information on microbiomes of bulk soils from the beginning of the experiment, and biocrusts sampled after 4 and 10 months of incubation. We discovered that the relative abundance of genes involved in the biosynthesis of exopolysaccharides and lipopolysaccharides increased in biocrusts compared with bulk soils. At the same time, communities of potential "soil glue" producers that were highly similar in bulk soils underwent differentiation once biocrusts started to develop. In the bulk soils, the investigated genes were harbored mainly by Betaproteobacteria, whereas in the biocrusts, the major potential producers of adhesive polysaccharides were, aside from Alphaproteobacteria, either Cyanobacteria or Chloroflexi and Acidobacteria. Overall, our results indicate that the potential to form exopolysaccharides and lipopolysaccharides is an important bacterial trait for initial biocrusts and is maintained despite the shifts in bacterial community composition during biocrust development.

RevDate: 2019-08-02

Ayala-Usma DA, Lozano-Gutiérrez RE, C González Arango (2019)

Wood anatomy of two species of the genus Chrysochlamys (Clusiaceae: Clusioideae: Clusieae) from the northern Andes of Colombia.

Heliyon, 5(7):e02078 pii:e02078.

Chrysochlamys is a genus of neotropical angiosperms distributed in wet and riparian forests from Bolivia to Mexico in altitudes from near sea-level to close to 3000 m. The wood anatomy of two species of the genus was investigated. Branches of mature stems were collected in a secondary wet forest in Colombian Northern Andes. Slides were obtained and visualized using light microscopy. Gelatinous fiber bands were found and described in C. colombiana and C. dependens. There was a higher amount of septate fibers in the latter. Average ray height and pigment deposit content in ray cells was greater in C. colombiana relative to C. dependens, but rays were commonly wider in the second one. The diversity of vessel-ray pit shapes in C. dependens is greater than in C. colombiana. In both cases rays are considered to be paedomorphic type I. Scanty to absent axial and apotracheal parenchyma was found for both species. We discuss the similarities and differences of the two species in order to establish diagnostic wood features. Also we include brief notes in comparative anatomy with other members of the Clusieaceae family, emphasizing in the incongruences found with previous reports for the genus. This is the first descriptive work in wood anatomy of C. colombiana and C. dependens.

RevDate: 2019-08-02

Hausmann B, Vandieken V, Pjevac P, et al (2019)

Draft Genome Sequence of Desulfosporosinus fructosivorans Strain 63.6FT, Isolated from Marine Sediment in the Baltic Sea.

Microbiology resource announcements, 8(31): pii:8/31/e00427-19.

Desulfosporosinus fructosivorans strain 63.6FT is a strictly anaerobic, spore-forming, sulfate-reducing bacterium isolated from marine sediment in the Baltic Sea. Here, we report the draft genome sequence of D. fructosivorans 63.6FT.

RevDate: 2019-08-02

Schmidt JE, Vannette RL, Igwe A, et al (2019)

Effects of Agricultural Management on Rhizosphere Microbial Structure and Function in Processing Tomato Plants.

Applied and environmental microbiology, 85(16): pii:AEM.01064-19.

Agricultural management practices affect bulk soil microbial communities and the functions they carry out, but it remains unclear how these effects extend to the rhizosphere in different agroecosystem contexts. Given close linkages between rhizosphere processes and plant nutrition and productivity, understanding how management practices impact this critical zone is of great importance to optimize plant-soil interactions for agricultural sustainability. A comparison of six paired conventional-organic processing tomato farms was conducted to investigate relationships between management, soil physicochemical parameters, and rhizosphere microbial community composition and functions. Organically managed fields were higher in soil total N and NO3-N, total and labile C, plant Ca, S, and Cu, and other essential nutrients, while soil pH was higher in conventionally managed fields. Differential abundance, indicator species, and random forest analyses of rhizosphere communities revealed compositional differences between organic and conventional systems and identified management-specific microbial taxa. Phylogeny-based trait prediction showed that these differences translated into more abundant pathogenesis-related gene functions in conventional systems. Structural equation modeling revealed a greater effect of soil biological communities than physicochemical parameters on plant outcomes. These results highlight the importance of rhizosphere-specific studies, as plant selection likely interacts with management in regulating microbial communities and functions that impact agricultural productivity.IMPORTANCE Agriculture relies, in part, on close linkages between plants and the microorganisms that live in association with plant roots. These rhizosphere bacteria and fungi are distinct from microbial communities found in the rest of the soil and are even more important to plant nutrient uptake and health. Evidence from field studies shows that agricultural management practices such as fertilization and tillage shape microbial communities in bulk soil, but little is known about how these practices affect the rhizosphere. We investigated how agricultural management affects plant-soil-microbe interactions by comparing soil physical and chemical properties, plant nutrients, and rhizosphere microbial communities from paired fields under organic and conventional management. Our results show that human management effects extend even to microorganisms living in close association with plant roots and highlight the importance of these bacteria and fungi to crop nutrition and productivity.

RevDate: 2019-08-01

Wuyts S, Allonsius CN, Wittouck S, et al (2019)

Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group.

Microbial genomics [Epub ahead of print].

The genus Lactobacillus is known to be extremely diverse and consists of different phylogenetic groups that show a diversity that is roughly equal to the expected diversity of a typical bacterial genus. One of the most prominent phylogenetic groups within this genus is the Lactobacillus plantarum group, which contains the understudied Lactobacillus mudanjiangensis species. Before this study, only one L. mudanjiangensis strain, DSM 28402T, had been described, but without whole-genome analysis. In this study, three strains classified as L. mudanjiangensis were isolated from three different carrot juice fermentations and their whole-genome sequence was determined, together with the genome sequence of the type strain. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. This analysis showed that L. mudanjiangensis harboured the second largest genome size and gene count of the whole L. plantarum group. In addition, all members of this species showed the presence of a gene coding for a cellulose-degrading enzyme. Finally, three of the four L. mudanjiangensis strains studied showed the presence of pili on scanning electron microscopy (SEM) images, which were linked to conjugative gene regions, coded on a plasmid in at least two of the strains studied.

RevDate: 2019-08-01

Sapriel G, R Brosch (2019)

Shared pathogenomic patterns characterize a new phylotype, revealing transition towards host-adaptation long before speciation of Mycobacterium tuberculosis.

Genome biology and evolution pii:5542391 [Epub ahead of print].

Tuberculosis remains one of the deadliest infectious diseases of humanity. To better understand the evolutionary history of host-adaptation of tubercle bacilli (MTB), we sought for mycobacterial species that were more closely related to MTB than the previously used comparator species Mycobacterium marinum and Mycobacterium kansasii. Our phylogenomic approach revealed some recently sequenced opportunistic mycobacterial pathogens i.e. Mycobacterium decipiens, Mycobacterium lacus, Mycobacterium riyadhense, and Mycobacterium shinjukuense - that constitute a common clade with MTB, hereafter called MTB-associated phylotype (MTBAP), from which MTB have emerged. Multivariate and clustering analyses of genomic functional content revealed that the MTBAP lineage forms a clearly distinct cluster of species that share common genomic characteristics, such as loss of core genes, shift in dN/dS ratios, and massive expansion of toxin-antitoxin systems. Consistently, analysis of predicted horizontal gene transfer regions suggests that putative functions acquired by MTBAP members were markedly associated with changes in microbial ecology, e.g. adaption to intracellular stress resistance. Our study thus considerably deepens our view on MTB evolutionary history, unveiling a decisive shift that promoted conversion to host-adaptation among ancestral founders of the MTBAP lineage long before M. tuberculosis has adapted to the human host.

RevDate: 2019-08-01

Kiersztyn B, Chróst R, Kaliński T, et al (2019)

Structural and functional microbial diversity along a eutrophication gradient of interconnected lakes undergoing anthropopressure.

Scientific reports, 9(1):11144 pii:10.1038/s41598-019-47577-8.

We present the results of an analysis of the 16S rRNA-based taxonomical structure of bacteria together with an analysis of carbon source utilization ability using EcoPlate (Biolog, USA) metabolic fingerprinting assessment against the backdrop of physicochemical parameters in fifteen interconnected lakes. The lakes exhibit a wide spectrum of trophic gradients and undergo different intensities of anthropopressure. Sequences of V3-V4 16S rRNA genes binned by taxonomic assignment to family indicated that bacterial communities in the highly eutrophicated lakes were distinctly different from the bacterial communities in the meso-eutrophic lakes (ANOSIM r = 0.99, p = 0.0002) and were characterized by higher richness and more diverse taxonomical structure. Representatives of the Actinobacteria, Proteobacteria, Cyanobacteria, Planctomycetes, Verrucomicrobia, Bacteroides phyla predominated. In most cases their relative abundance was significantly correlated with lake trophic state. We found no similar clear relationship of community-level physiological profiling with lake trophic state. However, we found some significant links between the taxonomic and metabolic structure of the microbes in the studied lakes (Mantel's correlation r = 0.22, p = 0.006). The carbon source utilization ability of the studied microorganisms was affected not only by the taxonomic groups present in the lakes but also by various characteristics like a high PO43- concentration inhibiting the utilization of phosphorylated carbon.

RevDate: 2019-08-01

Otte JM, Blackwell N, Ruser R, et al (2019)

N2O formation by nitrite-induced (chemo)denitrification in coastal marine sediment.

Scientific reports, 9(1):10691 pii:10.1038/s41598-019-47172-x.

Nitrous oxide (N2O) is a potent greenhouse gas that also contributes to stratospheric ozone depletion. Besides microbial denitrification, abiotic nitrite reduction by Fe(II) (chemodenitrification) has the potential to be an important source of N2O. Here, using microcosms, we quantified N2O formation in coastal marine sediments under typical summer temperatures. Comparison between gamma-radiated and microbially-active microcosm experiments revealed that at least 15-25% of total N2O formation was caused by chemodenitrification, whereas 75-85% of total N2O was potentially produced by microbial N-transformation processes. An increase in (chemo)denitrification-based N2O formation and associated Fe(II) oxidation caused an upregulation of N2O reductase (typical nosZ) genes and a distinct community shift to potential Fe(III)-reducers (Arcobacter), Fe(II)-oxidizers (Sulfurimonas), and nitrate/nitrite-reducing microorganisms (Marinobacter). Our study suggests that chemodenitrification contributes substantially to N2O formation from marine sediments and significantly influences the N- and Fe-cycling microbial community.

RevDate: 2019-08-01

McBain AJ, O'Neill CA, Amezquita A, et al (2019)

Consumer Safety Considerations of Skin and Oral Microbiome Perturbation.

Clinical microbiology reviews, 32(4): pii:32/4/e00051-19.

SUMMARYMicrobiomes associated with human skin and the oral cavity are uniquely exposed to personal care regimes. Changes in the composition and activities of the microbial communities in these environments can be utilized to promote consumer health benefits, for example, by reducing the numbers, composition, or activities of microbes implicated in conditions such as acne, axillary odor, dandruff, and oral diseases. It is, however, important to ensure that innovative approaches for microbiome manipulation do not unsafely disrupt the microbiome or compromise health, and where major changes in the composition or activities of the microbiome may occur, these require evaluation to ensure that critical biological functions are unaffected. This article is based on a 2-day workshop held at SEAC Unilever, Sharnbrook, United Kingdom, involving 31 specialists in microbial risk assessment, skin and oral microbiome research, microbial ecology, bioinformatics, mathematical modeling, and immunology. The first day focused on understanding the potential implications of skin and oral microbiome perturbation, while approaches to characterize those perturbations were discussed during the second day. This article discusses the factors that the panel recommends be considered for personal care products that target the microbiomes of the skin and the oral cavity.

RevDate: 2019-07-31

Yao Y, Carretero-Paulet L, Y Van de Peer (2019)

Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy.

PloS one, 14(7):e0220257 pii:PONE-D-19-06654.

The potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary 'dead end', there is growing evidence that the long-term establishment of polyploidy might be linked to environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete non-polyploids at times of environmental upheaval remain indefinable. Here, we improved our recently developed bio-inspired framework, combining an artificial genome with an agent-based system, to form a population of so-called Digital Organisms (DOs), to examine the impact of WGD on evolution under different environmental scenarios mimicking extinction events of varying strength and frequency. We found that, under stable environments, DOs with non-duplicated genomes formed the majority, if not all, of the population, whereas the numbers of DOs with duplicated genomes increased under dramatically challenging environments. After tracking the evolutionary trajectories of individual genomes in terms of sequence and encoded gene regulatory networks (GRNs), we propose that duplicated GRNs might provide polyploids with better chances to acquire the drastic changes necessary to adapt to challenging conditions, thus endowing DOs with increased adaptive potential under extinction events. In contrast, under stable environments, random mutations might easily render the GRN less well adapted to such environments, a phenomenon that is exacerbated in duplicated, more complex GRNs. We believe that our results provide some additional insights into how genome duplication and polyploidy might help organisms to compete for novel niches and survive ecological turmoil, and confirm the usefulness of our computational simulation in studying the role of WGD in evolution and adaptation, helping to overcome some of the traditional limitations of evolution experiments with model organisms.

RevDate: 2019-07-31

Boll M, Geiger R, Junghare M, et al (2019)

Microbial degradation of phthalates: biochemistry and environmental implications.

Environmental microbiology reports [Epub ahead of print].

The environmentally relevant xenobiotic esters of phthalic acid (PA), isophthalic acid (IPA) and terephthalic acid (TPA) are produced on a million ton scale annually and are predominantly used as plastic polymers or plasticizers. Degradation by microorganisms is considered as the most effective means of their elimination from the environment and proceeds via hydrolysis to the corresponding phthalic acid isomers and alcohols under oxic and anoxic conditions. Further degradation of PA, IPA and TPA differs fundamentally between anaerobic and aerobic microorganisms. The latter introduce hydroxyl functionalities by dioxygenases to facilitate subsequent decarboxylation by either aromatizing dehydrogenases or cofactor-free decarboxylases. In contrast, anaerobic bacteria activate the phthalic acids isomers to the respective thioesters using CoA ligases or CoA transferases followed by decarboxylation to the central intermediate benzoyl-CoA. Decarboxylases acting on the three phthalic acid CoA thioesters belong to the UbiD enzyme family that harbor a prenylated FMN cofactor to achieve the mechanistically challenging decarboxylation. Capture of the extremely instable PA-CoA intermediate is accomplished by a massive overproduction of PCD and a balanced production of PA-CoA forming/decarboxylating enzymes. The strategy of anaerobic phthalate degradation probably represents a snapshot of an ongoing evolution of a xenobiotic degradation pathway via a short-lived reaction intermediate. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-31

Richardson M, Gottel N, Gilbert JA, et al (2019)

Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures.

mBio, 10(4): pii:mBio.01054-19.

The microbiota of the built environment is an amalgamation of both human and environmental sources. While human sources have been examined within single-family households or in public environments, it is unclear what effect a large number of cohabitating people have on the microbial communities of their shared environment. We sampled the public and private spaces of a college dormitory, disentangling individual microbial signatures and their impact on the microbiota of common spaces. We compared multiple methods for marker gene sequence clustering and found that minimum entropy decomposition (MED) was best able to distinguish between the microbial signatures of different individuals and was able to uncover more discriminative taxa across all taxonomic groups. Further, weighted UniFrac- and random forest-based graph analyses uncovered two distinct spheres of hand- or shoe-associated samples. Using graph-based clustering, we identified spheres of interaction and found that connection between these clusters was enriched for hands, implicating them as a primary means of transmission. In contrast, shoe-associated samples were found to be freely interacting, with individual shoes more connected to each other than to the floors they interact with. Individual interactions were highly dynamic, with groups of samples originating from individuals clustering freely with samples from other individuals, while all floor and shoe samples consistently clustered together.IMPORTANCE Humans leave behind a microbial trail, regardless of intention. This may allow for the identification of individuals based on the "microbial signatures" they shed in built environments. In a shared living environment, these trails intersect, and through interaction with common surfaces may become homogenized, potentially confounding our ability to link individuals to their associated microbiota. We sought to understand the factors that influence the mixing of individual signatures and how best to process sequencing data to best tease apart these signatures.

RevDate: 2019-07-31

Chevrette MG, Bratburd JR, Currie CR, et al (2019)

Experimental Microbiomes: Models Not to Scale.

mSystems, 4(4): pii:4/4/e00175-19.

Low-cost, high-throughput nucleic acid sequencing ushered the field of microbial ecology into a new era in which the microbial composition of nearly every conceivable environment on the planet is under examination. However, static "screenshots" derived from sequence-only approaches belie the underlying complexity of the microbe-microbe and microbe-host interactions occurring within these systems. Reductionist experimental models are essential to identify the microbes involved in interactions and to characterize the molecular mechanisms that manifest as complex host and environmental phenomena. Herein, we focus on three models (Bacillus-Streptomyces, Aliivibrio fischeri-Hawaiian bobtail squid, and gnotobiotic mice) at various levels of taxonomic complexity and experimental control used to gain molecular insight into microbe-mediated interactions. We argue that when studying microbial communities, it is crucial to consider the scope of questions that experimental systems are suited to address, especially for researchers beginning new projects. Therefore, we highlight practical applications, limitations, and tradeoffs inherent to each model.

RevDate: 2019-07-30

Cerdó T, Diéguez E, C Campoy (2019)

Early nutrition and gut microbiome: interrelationship between bacterial metabolism, immune system, brain structure and neurodevelopment.

American journal of physiology. Endocrinology and metabolism [Epub ahead of print].

Disturbances of diet during pregnancy and early postnatal life may impact colonization of gut microbiota during early life, which could influence infant health, leading to potential long-lasting consequences later in life. This is a non-systematic review that explores the recent scientific literature to provide a general perspective of this broad topic. Several studies have shown that gut microbiota composition is related to changes in metabolism, energy balance and immune system disturbances, through interaction between microbiota metabolites and host receptors by the gut-brain axis. Moreover, recent clinical studies suggest that an intestinal dysbiosis in gut microbiota may result in cognitive disorders and behavioral problems. Furthermore, recent research in the field of brain imaging focused on the study of the relationship between gut microbial ecology and large-scale brain networks, which will help to decipher the influence of the microbiome on brain function and potentially will serve to identify multiple mediators of the gut-brain axis. Thus, knowledge about optimal nutrition by modulating gut microbiota-brain axis activity, will allow a better understanding of the molecular mechanisms involved in the crosstalk between gut microbiota and the developing brain during critical windows. In addition, this knowledge will open new avenues for developing novel microbiota-modulating based diet interventions during pregnancy and early life to prevent metabolic disorders, as well as neurodevelopmental deficits and brain functional disorders.

RevDate: 2019-07-30

Cellini A, Donati I, Fiorentini L, et al (2019)

N-Acyl Homoserine Lactones and Lux Solos Regulate Social Behaviour and Virulence of Pseudomonas syringae pv. actinidiae.

Microbial ecology pii:10.1007/s00248-019-01416-5 [Epub ahead of print].

The phyllosphere is a complex environment where microbes communicate through signalling molecules in a system, generally known as quorum sensing (QS). One of the most common QS systems in Gram-negative proteobacteria is based on the production of N-acyl homoserine lactones (AHLs) by a LuxI synthase and their perception by a LuxR sensor. Pseudomonas syringae pv. actinidiae (Psa), the aetiological agent of the bacterial canker of kiwifruit, colonises plant phyllosphere before penetrating via wounds and natural openings. Since Psa genome encodes three LuxR solos without a cognate LuxI, this bacterium may perceive diffusible signals, but it cannot produce AHLs, displaying a non-canonical QS system. The elucidation of the mechanisms underlying the perception of environmental cues in the phyllosphere by this pathogen and their influence on the onset of pathogenesis are of crucial importance for a long-lasting and sustainable management of the bacterial canker of kiwifruit. Here, we report the ability of Psa to sense its own population density and the presence of surrounding bacteria. Moreover, we show that Psa can perceive AHLs, indicating that AHL-producing neighbouring bacteria may regulate Psa virulence in the host. Our results suggest that the ecological environment is important in determining Psa fitness and pathogenic potential. This opens new perspectives in the use of more advanced biochemical and microbiological tools for the control of bacterial canker of kiwifruit.

RevDate: 2019-07-29

Cagnetta C, Saerens B, Meerburg FA, et al (2019)

High-rate activated sludge systems combined with dissolved air flotation enable effective organics removal and recovery.

Bioresource technology, 291:121833 pii:S0960-8524(19)31063-6 [Epub ahead of print].

High-rate activated sludge (HRAS) systems typically generate diluted sludge which requires further thickening prior to anaerobic digestion (AD), besides the need to add considerable coagulant and flocculant for the solids separation. As an alternative to conventional gravitational settling, a dissolved air flotation (DAF) unit was coupled to a HRAS system or a high-rate contact stabilization (HiCS) system. The HRAS-DAF system allowed up to 78% removal of the influent solids, and the HiCS-DAF 67%. Both were within the range of values typically obtained for HRAS-settler systems, albeit at a lower chemical requirement. The separated sludge had a high concentration of up to 47 g COD L-1, suppressing the need of further thickening before AD. Methanation tests showed a biogas yield of up to 68% on a COD basis. The use of a DAF separation system can thus enable direct organics removal at high sludge concentration and with low chemical needs.

RevDate: 2019-07-29

Shao D, Vogtmann E, Liu A, et al (2019)

Microbial characterization of esophageal squamous cell carcinoma and gastric cardia adenocarcinoma from a high-risk region of China.

Cancer [Epub ahead of print].

BACKGROUND: Little is known about the microbiota and upper gastrointestinal tumors. Esophageal squamous cell carcinoma (ESCC) and gastric cardia adenocarcinoma (GCA) occur in adjacent organs, co-occur geographically, and share many risk factors despite being of different tissue types.

METHODS: This study characterized the microbial communities of paired tumor and nontumor samples from 67 patients with ESCC and 36 patients with GCA in Henan, China. DNA was extracted with the MoBio PowerSoil kit. The V4 region of the 16S ribosomal RNA gene was sequenced with MiniSeq and was processed with Quantitative Insights Into Microbial Ecology 1. The linear discriminant analysis effect size method was used to identify differentially abundant microbes, the Wilcoxon rank-sum test was used to test α diversity differences, and permutational multivariate analysis of variance was used to test for differences in β diversity.

RESULTS: The microbial environments of ESCC and GCA tissues were all composed primarily of Firmicutes, Bacteroidetes, and Proteobacteria. ESCC tumor tissues contained more Fusobacterium (3.2% vs 1.3%) and less Streptococcus (12.0% vs 30.2%) than nontumor tissues. GCA nontumor tissues had a greater abundance of Helicobacter (60.5% vs 11.8%), which may have been linked to the lower α diversity (58.0 vs 102.5; P = .0012) in comparison with tumor tissues. A comparison of ESCC and GCA nontumor tissues showed that the microbial composition (P = .0040) and the α diversity (87.0 vs 58.0; P = .00052) were significantly different. No significant differences were detected for α diversity within ESCC and GCA tumor tissues.

CONCLUSIONS: This study showed differences in the microbial compositions of paired ESCC and GCA tumor and nontumor tissues and differences by organ site. Large-scale, prospective cohort studies are needed to confirm these findings.

RevDate: 2019-07-29

Del Frari G, Gobbi A, Aggerbeck MR, et al (2019)

Characterization of the Wood Mycobiome of Vitis vinifera in a Vineyard Affected by Esca. Spatial Distribution of Fungal Communities and Their Putative Relation With Leaf Symptoms.

Frontiers in plant science, 10:910.

Esca is a disease complex belonging to the grapevine trunk diseases cluster. It comprises five syndromes, three main fungal pathogenic agents and several symptoms, both internal (i.e., affecting woody tissue) and external (e.g., affecting leaves and bunches). The etiology and epidemiology of this disease complex remain, in part, unclear. Some of the points that are still under discussion concern the sudden rise in disease incidence, the simultaneous presence of multiple wood pathogens in affected grapevines, the causal agents and the discontinuity in time of leaf symptoms manifestation. The standard approach to the study of esca has been mostly through culture-dependent studies, yet, leaving many questions unanswered. In this study, we used Illumina® next-generation amplicon sequencing to investigate the mycobiome of grapevines wood in a vineyard with history of esca. We characterized the wood mycobiome composition, investigated the spatial dynamics of the fungal communities in different areas of the stem and in canes, and assessed the putative link between mycobiome and leaf symptoms. An unprecedented diversity of fungi is presented (289 taxa), including five genera reported for the first time in association with grapevines wood (Debaryomyces, Trematosphaeria, Biatriospora, Lopadostoma, and Malassezia) and numerous hitherto unreported species. Esca-associated fungi Phaeomoniella chlamydospora and Fomitiporia sp. dominate the fungal community, and numerous other fungi associated with wood syndromes are also encountered (e.g., Eutypa spp., Inonotus hispidus). The spatial analysis revealed differences in diversity, evenness and taxa abundances, the unique presence of certain fungi in specific areas of the plants, and tissue specificity. Lastly, the mycobiome composition of the woody tissue in proximity to leaves manifesting 'tiger stripes' symptoms of esca, as well as in leaf-symptomatic canes, was highly similar to that of plants not exhibiting any leaf symptomatology. This observation supports the current understanding that leaf symptoms are not directly linked with the fungal communities in the wood. This work builds to the understanding of the microbial ecology of the grapevines wood, offering insights and a critical view on the current knowledge of the etiology of esca.

RevDate: 2019-07-29

Chen C, He R, Cheng Z, et al (2019)

The Seasonal Dynamics and the Influence of Human Activities on Campus Outdoor Microbial Communities.

Frontiers in microbiology, 10:1579.

Large-scale campus resembles a small "semi-open community," harboring disturbances from the exchanges of people and vehicles, wherein stressors such as temperature and population density differ among the ground surfaces of functional partitions. Therefore, it represents a special ecological niche for the study on microbial ecology in the process of urbanization. In this study, we investigated outdoor microbial communities in four campuses in Wuhan, China. We obtained 284 samples from 55 sampling sites over six seasons, as well as their matching climatic and environmental records. The structure of campus outdoor microbial communities which influenced by multiple climatic factors featured seasonality. The dispersal influence of human activities on microbial communities also contributed to this seasonal pattern non-negligibly. However, despite the microbial composition alteration in response to multiple stressors, the overall predicted function of campus outdoor microbial communities remained stable across campuses. The spatial-temporal dynamic patterns on campus outdoor microbial communities and its predicted functions have bridged the gap between microbial and macro-level ecosystems, and provided hints toward a better understanding of the effects of climatic factors and human activities on campus micro-environments.

RevDate: 2019-07-26

Mihăşan M, Babii C, Aslebagh R, et al (2019)

Exploration of Nicotine Metabolism in Paenarthrobacter nicotinovorans pAO1 by Microbial Proteomics.

Advances in experimental medicine and biology, 1140:515-529.

Proteomics, or the large-scale study of proteins, is a post-genomics field that, together with transcriptomics and metabolomics, has moved the study of bacteria to a new era based on system-wide understanding of bacterial metabolic and regulatory networks. The study of bacterial proteins or microbial proteomics has found a wide array of applications in many fields of microbiology, from food, clinical, and industrial microbiology to microbial ecology and physiology. The current chapter makes a brief technical introduction into the available approaches for the large-scale study of bacterial proteins using mass-spectrometry. Furthermore, the advantages and disadvantages of using bacteria for proteomics studies are indicated as well as several example studies where MS-based bacterial proteomics had a fundamental role in deciphering the scientific question. Finally, the proteomics study of nicotine catabolism in Paenarthrobacter nicotinovorans pAO1 using nanoLC-MS/MS is given as an in-depth example for possible applications of microbial proteomics.The nicotine degradation pathway functioning in Paenarthrobacter nicotinovorans is encoded by the catabolic megaplasmid pAO1 that contains about 40 nicotine-related genes making out the nic-gens cluster. Despite the promising biotechnological potential for the production of green-chemicals, only half of the nic-genes have been experimentally linked to nicotine. In an attempt to systematically identify all the proteins involved in nicotine degradation, a gel-based proteomics approach was used to identify a total of 801 proteins when Paenarthrobacter nicotinovorans was grown on three carbon sources: citrate, nicotine and nicotine and citrate. The differences in protein abundance showed that the bacterium is able to switch between deamination and demethylation in the lower nicotine pathway based on the available C source. Several pAO1 putative genes including a hypothetical polyketide cyclase have been shown to have a nicotine-dependent expression and we hypothesize that the polyketide cyclase would hydrolyze the N1-C6 bond from the pyridine ring with the formation of alpha-keto-glutaramate. Two chromosomal proteins, a malate dehydrogenase, and a D-3-phosphoglycerate dehydrogenase were shown to be strongly upregulated when nicotine was the sole carbon source and could be related to the production of the alpha-keto-glutaramate by the polyketide cyclase.

RevDate: 2019-07-26

Jha PN, Gomaa AB, Yanni YG, et al (2019)

Alterations in the Endophyte-Enriched Root-Associated Microbiome of Rice Receiving Growth-Promoting Treatments of Urea Fertilizer and Rhizobium Biofertilizer.

Microbial ecology pii:10.1007/s00248-019-01406-7 [Epub ahead of print].

We examined the bacterial endophyte-enriched root-associated microbiome within rice (Oryza sativa) 55 days after growth in soil with and without urea fertilizer and/or biofertilization with a growth-promotive bacterial strain (Rhizobium leguminosarum bv. trifolii E11). After treatment to deplete rhizosphere/rhizoplane communities, washed roots were macerated and their endophyte-enriched communities were analyzed by 16S ribosomal DNA 454 amplicon pyrosequencing. This analysis clustered 99,990 valid sequence reads into 1105 operational taxonomic units (OTUs) with 97% sequence identity, 133 of which represented a consolidated core assemblage representing 12.04% of the fully detected OTU richness. Taxonomic affiliations indicated Proteobacteria as the most abundant phylum (especially α- and γ-Proteobacteria classes), followed by Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, and several other phyla. Dominant genera included Rheinheimera, unclassified Rhodospirillaceae, Pseudomonas, Asticcacaulis, Sphingomonas, and Rhizobium. Several OTUs had close taxonomic affiliation to genera of diazotrophic rhizobacteria, including Rhizobium, unclassified Rhizobiales, Azospirillum, Azoarcus, unclassified Rhizobiaceae, Bradyrhizobium, Azonexus, Mesorhizobium, Devosia, Azovibrio, Azospira, Azomonas, and Azotobacter. The endophyte-enriched microbiome was restructured within roots receiving growth-promoting treatments. Compared to the untreated control, endophyte-enriched communities receiving urea and/or biofertilizer treatments were significantly reduced in OTU richness and relative read abundances. Several unique OTUs were enriched in each of the treatment communities. These alterations in structure of root-associated communities suggest dynamic interactions in the host plant microbiome, some of which may influence the well-documented positive synergistic impact of rhizobial biofertilizer inoculation plus low doses of urea-N fertilizer on growth promotion of rice, considered as one of the world's most important food crops.

RevDate: 2019-07-25

Long XE, H Yao (2019)

Phosphorus Input Alters the Assembly of Rice (Oryza sativa L.) Root-Associated Communities.

Microbial ecology pii:10.1007/s00248-019-01407-6 [Epub ahead of print].

Rice root-associated microbial community play an important role in plant nutrient acquisition, biomass production, and stress tolerance. Herein, root-associated community assembly was investigated under different phosphate input levels in phosphorus (P)-deficient paddy soil. Rice was grown in a long-term P-depleted paddy soil with 0 (P0), 50 (PL), or 200 (PH) mg P2O5 kg-1 application. DNA from root endophytes was isolated after 46 days, and PCR amplicons from archaea, bacteria, and fungi were sequenced by an Illumina Miseq PE300 platform, respectively. P application had no significant effect on rice root endophytic archaea, which were dominated by ammonia-oxidizing Candidatus Nitrososphaera. By contrast, rice root endophytic community structure of the bacteria and fungi was affected by soil P. Low P input increased endophytic bacterial diversity, whereas high P input increased rhizosphere fungi diversity. Bacillus and Pleosporales, associated with phosphate solubilization and P uptake, dominated in P0 and PH treatments, and Pseudomonas were more abundant in the PL treatment than in the P0 and PH treatments. Co-occurrence network analysis revealed a close interaction between endophytic bacteria and fungi. Soil P application affected both the rice root endosphere and soil rhizosphere microbial community and interaction between rice root endophytic bacteria, and fungi, especially species related to P cycling.

RevDate: 2019-07-25

Bolyen E, Rideout JR, Dillon MR, et al (2019)

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

RevDate: 2019-07-24

Lee JC, KS Whang (2019)

Aquibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from saltern soil.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

A Gram-stain-positive, moderately halophilic bacterium, designated strain BH258T, was isolated from solar saltern sediment sampled at Shinan in the Republic of Korea. Cells of strain BH258T were found to be strictly aerobic, motile, endospore-forming rods which could grow at 15-45 °C (optimum, 35 °C), at pH 5.5-9.0 (pH 7.0) and at salinities of 0.5-20 % (w/v) NaCl (7-10%). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH258T belongs to the genus Aquibacillus, showing highest sequence similarity to Aquibacillus koreensis BH30097T (96.1 %), Aquibacillus albus YIM 93624T (95.9 %), Aquibacillus halophilus B6BT (95.6 %) and Aquibacillus salifodinae WSY08-1T (95.1 %). The predominant isoprenoid quinone was identified as menaquinone-7, and the cell-wall peptidoglycan was found to contain meso-diaminopimelic acid as the diagnostic diamino acid. The major fatty acids were identified as anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C15 : 0. The major polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol and three unidentified phospholipids. The DNA G+C content of this novel isolate was determined to be 37.35 mol%. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic analyses in this study, strain BH258T is considered to represent a novel species of the genus Aquibacillus, for which the name Aquibacillus sediminis sp. nov. is proposed. The type strain is BH258T (=KACC 18680T=NBRC 111875T).

RevDate: 2019-07-24

Vincent Q, Chartin C, Krüger I, et al (2019)

CARBIOSOL: Biological indicators of soil quality and organic carbon in grasslands and croplands in Wallonia, Belgium.

Ecology [Epub ahead of print].

The protection of agricultural soil quality is critical to environmental sustainability and requires relevant indicators. Total soil organic carbon (SOC) is of importance for soil quality but its slow dynamic and inherent variability do not allow early detection of changes. The project CARBIOSOL provides a dataset from agricultural soils in Wallonia (Southern Belgium), of total SOC, SOC fractions and biological indicators, selected for their relevance as indicators of soil quality. Two land-uses (sampled in 2013), 5 agricultural region (2015), seasonal variability in croplands (2016) and four management types (2017) were studied. Soil organic carbon content (total, stable fine fraction <20 µm, labile coarse fraction >20 µm), cold and hot water extractable carbon and nitrogen contents, total nitrogen, pHKCl , pHH2O , potential respiration, microbial biomass carbon and nitrogen, net nitrogen mineralisation, metabolic potential of soil bacteria, earthworm density and biomass, and two eco-physiological quotients (metabolic and microbial quotient) were measured for a total of 415 samples. The present dataset provides an important contribution for establishing a reference system of soil quality in Wallonia and eventually for large-scale studies through its integration into a global database. Moreover, the present dataset could be used to support the interpretation of measurements of fractions of SOC and biological indicators by soil analyses laboratories, which will be useful for farmers and decision makers to evaluate the effect of different management practices. Information contained in this publication or product may be reproduced, in part or in whole, and by any means for personal or public non-commercial uses, without charge or further permission, unless otherwise specified. Users are required to exercise due diligence in ensuring the accuracy of the material reproduced, indicate the complete title of the material produced and refer to this publication (including author names), indicate that the reproduction is a copy/uses official work financed by the SPW-DGO3. Commercial reproduction and distribution is prohibited, except with written permission from SPW-DGO3 and publication authors. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-24

Alviz-Gazitua P, Fuentes-Alburquenque S, Rojas LA, et al (2019)

The Response of Cupriavidus metallidurans CH34 to Cadmium Involves Inhibition of the Initiation of Biofilm Formation, Decrease in Intracellular c-di-GMP Levels, and a Novel Metal Regulated Phosphodiesterase.

Frontiers in microbiology, 10:1499.

Cadmium is a highly toxic heavy metal for biological systems. Cupriavidus metallidurans CH34 is a model strain to study heavy metal resistance and bioremediation as it is able to deal with high heavy metal concentrations. Biofilm formation by bacteria is mediated by the second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). The aim of this study was to characterize the response of C. metallidurans CH34 planktonic and biofilm cells to cadmium including their c-di-GMP regulatory pathway. Inhibition of the initiation of biofilm formation and EPS production by C. metallidurans CH34 correlates with increased concentration of cadmium. Planktonic and biofilm cells showed similar tolerance to cadmium. During exposure to cadmium an acute decrease of c-di-GMP levels in planktonic and biofilm cells was observed. Transcription analysis by RT-qPCR showed that cadmium exposure to planktonic and biofilm cells induced the expression of the urf2 gene and the mercuric reductase encoding merA gene, which belong to the Tn501/Tn21 mer operon. After exposure to cadmium, the cadA gene involved in cadmium resistance was equally upregulated in both lifestyles. Bioinformatic analysis and complementation assays indicated that the protein encoded by the urf2 gene is a functional phosphodiesterase (PDE) involved in the c-di-GMP metabolism. We propose to rename the urf2 gene as mrp gene for metal regulated PDE. An increase of the second messenger c-di-GMP content by the heterologous expression of the constitutively active diguanylate cyclase PleD correlated with an increase in biofilm formation and cadmium susceptibility. These results indicate that the response to cadmium in C. metallidurans CH34 inhibits the initiation of biofilm lifestyle and involves a decrease in c-di-GMP levels and a novel metal regulated PDE.

RevDate: 2019-07-24

Rath KM, Maheshwari A, J Rousk (2019)

Linking Microbial Community Structure to Trait Distributions and Functions Using Salinity as an Environmental Filter.

mBio, 10(4): pii:mBio.01607-19.

The structure and function of microbial communities vary along environmental gradients; however, interlinking the two has been challenging. In this study, salinity was used as an environmental filter to study how it could shape trait distributions, community structures, and the resulting functions of soil microbes. The environmental filter was applied by salinizing nonsaline soil (0 to 22 mg NaCl g-1). Our targeted community trait distribution (salt tolerance) was determined with dose-response relationships between bacterial growth and salinity. The bacterial community structure responses were resolved with Illumina 16S rRNA gene amplicon sequencing, and the microbial functions determined were respiration and bacterial and fungal growth. Salt exposure quickly resulted in filtered trait distributions, and stronger filters resulted in larger shifts. The filtered trait distributions correlated well with community composition differences, suggesting that trait distribution shifts were driven at least partly by species turnover. While salt exposure decreased respiration, microbial growth responses appeared to be characterized by competitive interactions. Fungal growth was highest when bacterial growth was inhibited by the highest salinity, and it was lowest when the bacterial growth rate peaked at intermediate salt levels. These findings corroborated a higher potential for fungal salt tolerance than bacterial salt tolerance for communities derived from a nonsaline soil. In conclusion, by using salt as an environmental filter, we could interlink the targeted trait distribution with both the community structure and resulting functions of soil microbes.IMPORTANCE Understanding the role of ecological communities in maintaining multiple ecosystem processes is a central challenge in ecology. Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial processes to community composition and structure. Here, we apply a conceptual framework to determine how microbial communities influence ecosystem processes, by applying a "top-down" trait-based approach. By determining the dependence of microbial processes on environmental factors (e.g., the tolerance to salinity), we can define the aggregate response trait distribution of the community, which then can be linked to the community structure and the resulting function performed by the microbial community.

RevDate: 2019-07-23

Shen Y, Stedtfeld RD, Guo X, et al (2019)

Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce.

Environment international, 131:105031 pii:S0160-4120(19)31270-X [Epub ahead of print].

New classes of emerging contaminants such as pharmaceuticals, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs) have received increasing attention due to rapid increases of their abundance in agroecosystems. As food consumption is a direct exposure pathway of pharmaceuticals, ARB, and ARGs to humans, it is important to understand changes of bacterial communities and ARG profiles in food crops produced with contaminated soils and waters. This study examined the level and type of ARGs and bacterial community composition in soil, and lettuce shoots and roots under soil-surface or overhead irrigation with pharmaceuticals-contaminated water, using high throughput qPCR and 16S rRNA amplicon sequencing techniques, respectively. In total 52 ARG subtypes were detected in the soil, lettuce shoot and root samples, with mobile genetic elements (MGEs), and macrolide-lincosamide-streptogramin B (MLSB) and multidrug resistance (MDR) genes as dominant types. The overall abundance and diversity of ARGs and bacteria associated with lettuce shoots under soil-surface irrigation were lower than those under overhead irrigation, indicating soil-surface irrigation may have lower risks of producing food crops with high abundance of ARGs. ARG profiles and bacterial communities were sensitive to pharmaceutical exposure, but no consistent patterns of changes were observed. MGE intl1 was consistently more abundant with pharmaceutical exposure than in the absence of pharmaceuticals. Pharmaceutical exposure enriched Proteobacteria (specifically Methylophilaceae) and decreased bacterial alpha diversity. Finally, there were significant interplays among bacteria community, antibiotic concentrations, and ARG abundance possibly involving hotspots including Sphingomonadaceae, Pirellulaceae, and Chitinophagaceae, MGEs (intl1 and tnpA_1) and MDR genes (mexF and oprJ).

RevDate: 2019-07-23

Yuan H, Mei R, Liao J, et al (2019)

Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems.

Frontiers in microbiology, 10:1536.

Microbial community assembly in engineered biological systems is often simultaneously influenced by stochastic and deterministic processes, and the nexus of these two mechanisms remains to be further investigated. Here, three lab-scale activated sludge reactors were seeded with identical inoculum and operated in parallel under eight different sludge retention time (SRT) by sequentially reducing the SRT from 15 days to 1 day. Using 16S rRNA gene amplicon sequencing data, the microbial populations at the start-up (15-day SRT) and SRT-driven (≤10-day SRT) phases were observed to be noticeably different. Clustering results demonstrated ecological succession at the start-up phase with no consistent successional steps among the three reactors, suggesting that stochastic processes played an important role in the community assembly during primary succession. At the SRT-driven phase, the three reactors shared 31 core operational taxonomic units (OTUs). Putative primary acetate utilizers and secondary metabolizers were proposed based on K-means clustering, network and synchrony analysis. The shared core populations accounted for 65% of the total abundance, indicating that the microbial communities at the SRT-driven phase were shaped predominantly by deterministic processes. Sloan's Neutral model and a null model analysis were performed to disentangle and quantify the relative influence of stochastic and deterministic processes on community assembly. The increased estimated migration rate in the neutral community model and the higher percentage of stochasticity in the null model implied that stochastic community assembly was intensified by strong deterministic factors. This was confirmed by the significantly different α- and β-diversity indices at SRTs shorter than 2 days and the observation that over half of the core OTUs were unshared or unsynchronized. Overall, this study provided quantitative insights into the nexus of stochastic and deterministic processes on microbial community assembly in a biological process.

RevDate: 2019-07-22

Lippens C, J De Vrieze (2019)

Exploiting the unwanted: Sulphate reduction enables phosphate recovery from energy-rich sludge during anaerobic digestion.

Water research, 163:114859 pii:S0043-1354(19)30625-6 [Epub ahead of print].

Anaerobic digestion is shifting from a single-purpose technology for renewable energy recovery from organic waste streams to a process for integrated resource recovery. The valorisation of high-rate energy- and phosphorus-rich sludge creates the opportunity for their combined recovery. This phosphate is present in a precipitated form in the sludge, and its release into the liquid phase is an important issue before recovery can be achieved. The objective of this research was to exploit the "unwanted" sulphate reduction process for the release of phosphate into the liquid phase during anaerobic digestion, thus, making it available for recovery. Two different treatments were considered, i.e., a control digester and a digester to which sulphate was added, each operated in triplicate for a period of 119 days. The control digester showed stable methane production at 628 ± 103 mL CH4 L-1 d-1, with a feedstock COD (chemical oxygen demand) conversion efficiency of 89.5 ± 14.6%. In contrast, the digester with sulphate addition showed a 29.9 ± 15.3% decrease in methane production, reaching an "inhibited steady state", but phosphate release into the liquid phase increased to 58.7 ± 12.9% of total P, a factor 4.5 higher than the control digester. This inhibited steady state coincided with a clear shift from a Methanosaetaceae to a Methanosarcinaceae dominated methanogenic community. Overall, the sulphate reduction process allows phosphate release during the anaerobic digestion process, yet, at the cost of a reduced methane production rate.

RevDate: 2019-07-22

Onnis-Hayden A, Majed N, Li Y, et al (2019)

Impact of Solid Residence Time (SRT) on Functionally Relevant Microbial Populations and Performance in Full-scale Enhanced Biological Phosphorus Removal (EBPR) Systems.

Water environment research : a research publication of the Water Environment Federation [Epub ahead of print].

Investigations of the impact of solid residence time (SRT) on microbial ecology and performance of Enhanced Biological Phosphorus process (EBPR) in full-scale systems has been scarce due to the challenges in isolating and examining the SRT from other complex plant-specific factors. This study performed a comprehensive evaluation of the influence of SRT on polyphosphate accumulating organisms (PAOs) and Glycogen Accumulating Organisms (GAOs) dynamics and on P removal performance at Clark County Water Reclamation District Facility in Las Vegas, US. Five parallel treatment trains with separated clarifiers were operated with five different SRTs ranging from 6 to 40 days. Microbial community analysis using multiple molecular and Raman techniques suggested that the relative abundances and diversity of PAOs and GAOs in EBPR systems is highly affected by the SRT. The resultant EBPR system stability and performance can be potentially controlled and optimized by manipulating the system SRT, and shorter SRT (<10 days) seems to be preferred. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-22

Colangelo-Lillis J, Pelikan C, Herbold CW, et al (2019)

Diversity decoupled from sulfur isotope fractionation in a sulfate-reducing microbial community.

Geobiology [Epub ahead of print].

The extent of fractionation of sulfur isotopes by sulfate-reducing microbes is dictated by genomic and environmental factors. A greater understanding of species-specific fractionations may better inform interpretation of sulfur isotopes preserved in the rock record. To examine whether gene diversity influences net isotopic fractionation in situ, we assessed environmental chemistry, sulfate reduction rates, diversity of putative sulfur-metabolizing organisms by 16S rRNA and dissimilatory sulfite reductase (dsrB) gene amplicon sequencing, and net fractionation of sulfur isotopes along a sediment transect of a hypersaline Arctic spring. In situ sulfate reduction rates yielded minimum cell-specific sulfate reduction rates < 0.3 × 10-15 moles cell-1 day-1 . Neither 16S rRNA nor dsrB diversity indices correlated with relatively constant (38‰-45‰) net isotope fractionation (ε34 Ssulfide-sulfate). Measured ε34 S values could be reproduced in a mechanistic fractionation model if 1%-2% of the microbial community (10%-60% of Deltaproteobacteria) were engaged in sulfate respiration, indicating heterogeneous respiratory activity within sulfate-reducing populations. This model indicated enzymatic kinetic diversity of Apr was more likely to correlate with sulfur fractionation than DsrB. We propose that, above a threshold Shannon diversity value of 0.8 for dsrB, the influence of the specific composition of the microbial community responsible for generating an isotope signal is overprinted by the control exerted by environmental variables on microbial physiology.

RevDate: 2019-07-20

Kumar KV, Pal A, Bai P, et al (2019)

Co-aggregation of bacterial flora isolated from the human skin surface.

Microbial pathogenesis pii:S0882-4010(18)32099-0 [Epub ahead of print].

Human hands play a prominent role in the intra and interpersonal transmission of microbes that constantly connect one's microbiome to other individuals and the environment. Along with beneficial bacteria, an individual may harbor pathogenic organisms which may get transferred to others. Thus, understanding the transmission mechanism and interaction among microbiota is crucial in preventing infection. In the present study, the ability of skin microbes, isolated from different individuals, to physically interact (coaggregate) intergenically was assessed. The bacterial flora from the hands (palm area) of similar age group students was isolated. The predominant isolates were selected and identified using 16s rRNA gene sequencing. Further, these isolates were subjected to visual coaggregation assay. A total of 27 bacteria were isolated from the human skin (palm area-fingers) of 10 individuals. These isolates belong to seven bacterial genera and 10 different species. Among 123 combinational visual coaggregation positive reactions; 53.66% showed a reaction score of +1, while 32.52%, 11.38% and 2.44% showed a score of +2, +3, and +4 respectively. Among 27 isolates, Staphylococcus haemolyticus had highest coaggregation partner of 17 followed by Acinetobacter spp. and Pseudomonas spp. with 15 partners each. The present study is the first report demonstrating the coaggregation potential of microbiota harboring the skin surface of the human hand. The study indicates that few microbes have high potential to influence coaggregation among distinct genera isolated from the skin. However, further studies are needed to understand the ability of these bacteria to coaggregate, their influence in interpersonal transmission and shaping of microbial ecology of the host skin.

RevDate: 2019-07-20

Ling S, L Hui (2019)

Evaluation of the complexity of indoor air in hospital wards based on PM2.5, real-time PCR, adenosine triphosphate bioluminescence assay, microbial culture and mass spectrometry.

BMC infectious diseases, 19(1):646 pii:10.1186/s12879-019-4249-z.

BACKGROUND: The aim of this study was to establish a set of assessment methods suitable for evaluating the complex indoor environment of hospital wards and to ascertain the composition of bacteria and microbial ecology of hospital wards.

METHODS: Colony-forming units (CFUs), PM2.5 detection, real-time PCR, and adenosine triphosphate (ATP) bioluminescence assay were employed to evaluate the complexity of indoor air in 18 wards of nine departments in a hospital and two student dormitories in a university. Subsequently, the microbial samples were quantified and identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).

RESULTS: Although the studied indices were relatively independent, the PM2.5 content was correlated with bacterial CFUs determined by passive sedimentation method, bacterial and fungal counts measured by real-time PCR, and ATP bioluminescence assay. The composition of microorganisms in the air of hospital wards differed from that in the air of student dormitories. The dominant genera in hospital wards were Staphylococcus (39.4%), Micrococcus (21.9%), Corynebacterium (11.7%), Kocuria (4.4%), Bacillus (2.9%), Streptococcus (1.6%), Moraxella (1.6%), and Enterococcus (1.3%), and the microbial ecology differed between Respiration Dept. III and other hospital departments. Additionally, 11.1 and 27.3% of bacteria in hospital wards and student dormitories were not identified, respectively.

CONCLUSIONS: Assessment of environmental quality of hospital wards should be based on comprehensive analysis with multiple indicators. There may be imbalances in the microbial diversity in the hospital wards, therefore, monitoring of the environmental quality of hospitals is important in the prevention of nosocomial infections.

RevDate: 2019-07-19

Zamorano-López N, Borrás L, Giménez JB, et al (2019)

Acclimatised rumen culture for raw microalgae conversion into biogas: Linking microbial community structure and operational parameters in anaerobic membrane bioreactors (AnMBR).

Bioresource technology, 290:121787 pii:S0960-8524(19)31017-X [Epub ahead of print].

Ruminal fluid was inoculated in an Anaerobic Membrane Reactor (AnMBR) to produce biogas from raw Scenedesmus. This work explores the microbial ecology of the system during stable operation at different solids retention times (SRT). The 16S rRNA amplicon analysis revealed that the acclimatised community was mainly composed of Anaerolineaceae, Spirochaetaceae, Lentimicrobiaceae and Cloacimonetes fermentative and hydrolytic members. During the highest biodegradability achieved in the AnMBR (62%) the dominant microorganisms were Fervidobacterium and Methanosaeta. Different microbial community clusters were observed at different SRT conditions. Interestingly, syntrophic bacteria Gelria and Smithella were enhanced after increasing 2-fold the organic loading rate, suggesting their importance in continuous systems producing biogas from raw microalgae.

RevDate: 2019-07-19

Xie M, An F, Wu J, et al (2019)

Meta-omics Reveal Microbial Assortments and Key Enzymes in bean sauce mash, a Traditional Fermented Soybean Product.

Journal of the science of food and agriculture [Epub ahead of print].

BACKGROUND: Dajiang is fermented based on the metabolism of microbial communities in bean sauce mash, a traditional fermented soybean product in China. The current study firstly investigated the metaproteome of bean sauce mash, followed by analyzed biological functions and microbial community to reveal information on strains as well as the expressed proteins to better understand the roles of the microbiota in bean sauce mash.

RESULTS: The metaproteomic results demonstrated that a total of 1415 microbial protein clusters were expressed mainly by members of Penicillium and Rhizopus and were classified into 100 cellular components, 238 biological processes and 220 molecular function categories by GO Annotation. Additionally, enzymes associated with glycolysis metabolic pathways were identified, which can provide the required energy for microbial fermentation. Furthermore, the Illumina MiSeq sequencing technology results showed the microorganism communities of bean sauce mash exhibit a higher diversity, microbiological analysis demonstrated that fungi of Penicillium, Mucor, Fusarium, Aspergillus, Rhizopus, and bacteria of Lactobacillus, Enterococcus, Fructobacillus, Staphylococcus, Carnobacterium, were the predominant genera in 22 samples.

CONCLUSION: The profiles and insights in the current study are important to the research for bean sauce mash and related product in terms of food microbial ecology. Moreover, the strains and information obtained from this study will help the development of sufu starter cultures with unique sensory and stable quality. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-19

Hausmann B, Pjevac P, Huemer M, et al (2019)

Draft Genome Sequence of Desulfosporosinus sp. Strain Sb-LF, Isolated from an Acidic Peatland in Germany.

Microbiology resource announcements, 8(29): pii:8/29/e00428-19.

Desulfosporosinus sp. strain Sb-LF was isolated from an acidic peatland in Bavaria, Germany. Here, we report the draft genome sequence of the sulfate-reducing and lactate-utilizing strain Sb-LF.

RevDate: 2019-07-19

Han P, Yu Y, Zhou L, et al (2019)

Specific Micropollutant Biotransformation Pattern by the Comammox Bacterium Nitrospira inopinata.

Environmental science & technology [Epub ahead of print].

The recently discovered complete ammonia-oxidizing (comammox) bacteria occur in various environments, including wastewater treatment plants. To better understand their role in micropollutant biotransformation in comparison with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), we investigated the biotransformation capability of Nitrospira inopinata (the only comammox isolate) for 17 micropollutants. Asulam, fenhexamid, mianserin, and ranitidine were biotransformed by N. inopinata, Nitrososphaera gargensis (AOA), and Nitrosomonas nitrosa Nm90 (AOB). More distinctively, carbendazim, a benzimidazole fungicide, was exclusively biotransformed by N. inopinata. The biotransformation of carbendazim only occurred when N. inopinata was supplied with ammonia but not nitrite as the energy source. The exclusive biotransformation of carbendazim by N. inopinata was likely enabled by an enhanced substrate promiscuity of its unique AMO and its much higher substrate (for ammonia) affinity compared with the other two ammonia oxidizers. One major plausible transformation product (TP) of carbendazim is a hydroxylated form at the aromatic ring, which is consistent with the function of AMO. These findings provide fundamental knowledge on the micropollutant degradation potential of a comammox bacterium to better understand the fate of micropollutants in nitrifying environments.

RevDate: 2019-07-18

Mailloux BJ, Kim C, Kichuk T, et al (2019)

Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer.

Scientific reports, 9(1):10370 pii:10.1038/s41598-019-46663-1.

Determining the carbon sources for active microbial populations in the subsurface is a challenging but highly informative component of subsurface microbial ecology. This work developed a method to provide ecological insights into groundwater microbial communities by characterizing community RNA through its radiocarbon and ribosomal RNA (rRNA) signatures. RNA was chosen as the biomolecule of interest because rRNA constitutes the majority of RNA in prokaryotes, represents recently active organisms, and yields detailed taxonomic information. The method was applied to a groundwater filter collected from a shallow alluvial aquifer in Colorado. RNA was extracted, radiometrically dated, and the 16S rRNA was analyzed by RNA-Seq. The RNA had a radiocarbon signature (Δ14C) of -193.4 ± 5.6‰. Comparison of the RNA radiocarbon signature to those of potential carbon pools in the aquifer indicated that at least 51% of the RNA was derived from autotrophy, in close agreement with the RNA-Seq data, which documented the prevalence of autotrophic taxa, such as Thiobacillus and Gallionellaceae. Overall, this hybrid method for RNA analysis provided cultivation-independent information on the in-situ carbon sources of active subsurface microbes and reinforced the importance of autotrophy and the preferential utilization of dissolved over sedimentary organic matter in alluvial aquifers.

RevDate: 2019-07-17

Ranchou-Peyruse M, Auguet JC, Mazière C, et al (2019)

Geological gas-storage shapes deep life.

Environmental microbiology [Epub ahead of print].

Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad-hoc studies of the microbial ecology of some of them have suggested that sulfate-reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high-throughput sequencing and show the importance of sulfate-reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate-reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate-reducers. This aquifer was used to store town gas (containing at least 50% H2) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate-reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas-impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-17

Stres B, L Kronegger (2019)

Shift in the paradigm towards next-generation microbiology.

FEMS microbiology letters pii:5533319 [Epub ahead of print].

In this work, the position of contemporary microbiology is considered from the perspective of scientific success, and a list of historical points and lessons learned from the fields of medical microbiology, microbial ecology and systems biology are presented. In addition, patterns in the development of top-down research topics that emerged over time as well as overlapping ideas and personnel, which are the first signs of trans-domain research activities in the fields of metagenomics, metaproteomics, metatranscriptomics and metabolomics, are explored through analysis of the publication networks of 28.654 papers using the computer programme Pajek. The current state of affairs is defined, and the need for meta-analyses to leverage publication biases in the field of microbiology is put forward as a very important emerging field of microbiology, especially since microbiology is progressively dealing with multiscale systems. Consequently, the need for cross-fertilisation with other fields/disciplines instead of 'more microbiology' is needed to advance the field of microbiology as such. The reader is directed to consider how novel technologies, the introduction of big data approaches and artificial intelligence have transformed microbiology into a multi-scale field and initiated a shift away from its history of mostly manual work and towards a largely technology-, data- and statistics-driven discipline that is often coupled with automation and modelling.

RevDate: 2019-07-17

Paterson JS, Smith RJ, McKerral JC, et al (2019)

A hydrocarbon contaminated aquifer reveals a Piggyback-the-Persistent viral strategy.

FEMS microbiology ecology pii:5533318 [Epub ahead of print].

Subsurface environments hold the largest reservoir of microbes in the biosphere. They play essential roles in transforming nutrients, degrading contaminants and recycling organic matter. Here, we propose a previously unrecognized fundamental microbial process that influences aquifer bioremediation dynamics and that applies to all microbial communities. In contrast to previous models, our proposed Piggyback-the-Persistent (PtP) mechanism occurs when viruses become more dominated by those exhibiting temperate rather than lytic lifestyles driven by persistent chemicals (in our case chlorinated-hydrocarbon pollutants) that provide long term carbon sources and that refocus the aquifer carbon cycle, thus altering the microbial community. In this ultra-oligotrophic system, the virus:microbial ratio (VMR) ranges from below the detection limit of 0.0001 to 0.6, well below the common aquatic range of 3-10. Shortest-average-path network analysis revealed VMR and trichlorethene (TCE) as nodes through which ecosystem information and biomass most efficiently pass. Novel network rearrangement revealed a hierarchy of Kill-the-Winner (KtW), Piggyback-the-Winner (PtW) and PtP nodes. We propose that KtW, PtW and PtP occur simultaneously as competing strategies, with their relative importance depending on conditions at a particular time and location with unusual nutrient sources, such as TCE, appearing to contribute to a shift in this balance between viral mechanisms.

RevDate: 2019-07-17

Moye ZD, Woolston J, Abbeele PVD, et al (2019)

A Bacteriophage Cocktail Eliminates Salmonella Typhimurium from the Human Colonic Microbiome while Preserving Cytokine Signaling and Preventing Attachment to and Invasion of Human Cells by Salmonella In Vitro.

Journal of food protection [Epub ahead of print].

Nontyphoidal Salmonella strains continue to be a major cause of foodborne illness globally. One intriguing approach to reducing the risk of salmonellosis is the direct ingestion of phages targeting Salmonella to enhance natural gut resilience and provide protection during foodborne disease outbreaks. We evaluated the ability of a prophylactically administered bacteriophage cocktail, the foodborne outbreak pill (FOP) targeting Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella, to resolve a Salmonella infection in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME), a simulated gut platform populated by the human intestinal microbiome of healthy donors. The FOP preparation eliminated Salmonella enterica serovar Typhimurium from the colon compartment of the SHIME platform but health-associated metabolites, such as short-chain fatty acids and lactate, remained stable or increased in a donor-dependent manner. In studies of human intestinal cells, pretreatment of Salmonella Typhimurium with the FOP cocktail preserved lipopolysaccharide-stimulated signaling in a Caco-2-THP-1 Transwell system and prevented destruction of the Caco-2 monolayer by Salmonella. Adhesion and invasion of intestinal epithelial cells by Salmonella-a critical factor in Salmonella pathogenesis-was blunted when the bacteria were incubated with the FOP preparation before addition to the monolayer. The FOP phage cocktail was effective for (i) eliminating Salmonella from a simulated human gut without disturbing the indigenous microbiota and (ii) reducing the risk of invasion by Salmonella into the intestinal epithelia. These results suggest that the FOP preparation may be of value for reducing the risk of salmonellosis in humans, e.g., during foodborne disease outbreaks.

RevDate: 2019-07-17

Shih JL, Selph KE, Wall CB, et al (2019)

Trophic Ecology of the Tropical Pacific Sponge Mycale grandis Inferred from Amino Acid Compound-Specific Isotopic Analyses.

Microbial ecology pii:10.1007/s00248-019-01410-x [Epub ahead of print].

Many sponges host abundant and active microbial communities that may play a role in the uptake of dissolved organic matter (DOM) by the sponge holobiont, although the mechanism of DOM uptake and metabolism is uncertain. Bulk and compound-specific isotopic analysis of whole sponge, isolated sponge cells, and isolated symbiotic microbial cells of the shallow water tropical Pacific sponge Mycale grandis were used to elucidate the trophic relationships between the host sponge and its associated microbial community. δ15N and δ13C values of amino acids in M. grandis isolated sponge cells are not different from those of its bacterial symbionts. Consequently, there is no difference in trophic position of the sponge and its symbiotic microbes indicating that M. grandis sponge cell isolates do not display amino acid isotopic characteristics typical of metazoan feeding. Furthermore, both the isolated microbial and sponge cell fractions were characterized by a similarly high ΣV value-a measure of bacterial-re-synthesis of organic matter calculated from the sum of variance among individual δ15N values of trophic amino acids. These high ΣV values observed in the sponge suggest that M. grandis is not reliant on translocated photosynthate from photosymbionts or feeding on water column picoplankton, but obtains nutrition through the uptake of amino acids of bacterial origin. Our results suggest that direct assimilation of bacterially synthesized amino acids from its symbionts, either in a manner similar to translocation observed in the coral holobiont or through phagotrophic feeding, is an important if not primary pathway of amino acid acquisition for M. grandis.

RevDate: 2019-07-16

Pantoja-Feliciano IG, Soares JW, Doherty LA, et al (2019)

Acute stressor alters inter-species microbial competition for resistant starch-supplemented medium.

Gut microbes, 10(4):439-446.

Gut microbiome community dynamics are maintained by complex microbe-microbe and microbe-host interactions, which can be disturbed by stress. In vivo studies on the dynamics and manipulation of those interactions are costly and slow, but can be accelerated using in vitro fermentation. Herein, in vitro fermentation was used to determine how an acute stressor, a sudden change in diet, impacts inter-bacterial species competition for resistant starch-supplemented medium (RSM). Fermentation vessels were seeded with fecal samples collected from 10 individuals consuming a habitual diet or U.S. military rations for 21 days. Lactobacillus spp. growth in response to RSM was attenuated following ration consumption, whereas growth of Ruminococcus bromii was enhanced. These differences were not evident in the pre-fermentation samples. Findings demonstrate how incorporating in vitro fermentation into clinical studies can increase understanding of stress-induced changes in nutrient-microbiome dynamics, and suggest that sudden changes in diet may impact inter-species competition for substrates.

RevDate: 2019-07-15

Migliara G, Di Paolo C, Barbato D, et al (2019)

Multimodal surveillance of healthcare associated infections in an intensive care unit of a large teaching hospital.

Annali di igiene : medicina preventiva e di comunita, 31(5):399-413.

BACKGROUND: Healthcare-associated infections (HAIs), or nosocomial infections, represent a significant burden in terms of mortality, morbidity, length of stay and costs for patients hospitalized in intensive care units (ICUs). Surveillance systems are recommended by national and international institutions to gather data on HAIs in order to develop and evaluate interventions that reduce the risk of HAIs.

STUDY DESIGN: ere we describe the methodology and the results of the surveillance system implemented in the ICU of the Policlinico Umberto I, a large teaching hospital in Rome, from April 2016 to October 2018.

METHODS: The multimodal infection surveillance system integrates four different approaches: i) active surveillance of inpatients; ii) environmental microbiological surveillance; iii) surveillance of isolated microorganisms; and iv) behavioral surveillance of healthcare personnel. Data were collected on catheter-related bloodstream infections, ventilation-associated pneumonia, catheter-associated urinary tract infections and primary bloodstream infections that developed in patients after 48 h in the ICU. For environmental surveillance 14 points were selected for sampling (i.e. bed edges, medication carts, PC keyboards, sink faucets). The system of active surveillance of HAIs also included surveillance of microorganisms, consisting of the molecular genotyping of bacterial isolates by pulsed-field gel electrophoresis (PFGE). From 1 November 2016, monitoring of compliance with guidelines for hand hygiene (HH) and proper glove or gown use by healthcare personnel was included in the surveillance system. After the first six months (baseline phase), a multimodal intervention to improve adherence to guidelines by healthcare personnel was conducted with the ICU staff.

RESULTS: Overall, 773 patients were included in the active surveillance. The overall incidence rate of device-related HAIs was 14.1 (95% CI: 12.2-16.3) per 1000 patient-days. The monthly device-related HAI incident rate showed a decreasing trend over time, with peaks of incidence becoming progressively lower. The most common bacterial isolates were Klebsiella pneumoniae (20.7%), Acinetobacter baumannii (17.2%), Pseudomonas aeruginosa (13.4%) and Staphylococcus aureus (5.4%). Acinetobacter baumannii and Klebsiella pneumoniae showed the highest proportion of isolates with a multidrug-resistant profile. A total of 819 environmental samples were collected, from which 305 bacterial isolates were retrieved. The most frequent bacterial isolates were Acinetobacter baumannii (27.2%), Staphylococcus aureus (12.1%), Enterococcus faecalis (11.1%), Klebsiella pneumoniae (5.2%) and Pseudomonas aeruginosa (4.7%). All Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae environmental isolates were at least multidrug-resistant. Genotyping showed a limited number of major PFGE patterns for both clinical and environmental isolates of Klebsiella pneumoniae and Acinetobacter baumannii. Behavioral compliance rates significantly improved from baseline to post-intervention phase.

CONCLUSIONS: By integrating information gathered from active surveillance, environmental microbiological surveillance, surveillance of bacterial isolates and behavioral surveillance of healthcare personnel, the multimodal infection surveillance system returned a precise and detailed view of the infectious risk and microbial ecology of the ICU.

RevDate: 2019-07-15

Garcia-Mazcorro JF, Ishaq SL, Rodriguez-Herrera MV, et al (2019)

Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits.

Animal : an international journal of animal bioscience pii:S1751731119001599 [Epub ahead of print].

All livestock animal species harbour complex microbial communities throughout their digestive tract that support vital biochemical processes, thus sustaining health and productivity. In part as a consequence of the strong and ancient alliance between the host and its associated microbes, the gut microbiota is also closely related to productivity traits such as feed efficiency. This phenomenon can help researchers and producers develop new and more effective microbiome-based interventions using probiotics, also known as direct-fed microbials (DFMs), in Animal Science. Here, we focus on one type of such beneficial microorganisms, the yeast Saccharomyces. Saccharomyces is one of the most widely used microorganisms as a DFM in livestock operations. Numerous studies have investigated the effects of dietary supplementation with different species, strains and doses of Saccharomyces (mostly Saccharomyces cerevisiae) on gut microbial ecology, health, nutrition and productivity traits of several livestock species. However, the possible existence of Saccharomyces which are indigenous to the animals' digestive tract has received little attention and has never been the subject of a review. We for the first time provide a comprehensive review, with the objective of shedding light into the possible existence of indigenous Saccharomyces of the digestive tract of livestock. Saccharomyces cerevisiae is a nomadic yeast able to survive in a broad range of environments including soil, grass and silages. Therefore, it is very likely that cattle and other animals have been in direct contact with this and other types of Saccharomyces throughout their entire existence. However, to date, the majority of animal scientists seem to agree that the presence of Saccharomyces in any section of the gut only reflects dietary contamination; in other words, these are foreign organisms that are only transiently present in the gut. Importantly, this belief (i.e. that Saccharomyces come solely from the diet) is often not well grounded and does not necessarily hold for all the many other groups of microbes in the gut. In addition to summarizing the current body of literature involving Saccharomyces in the digestive tract, we discuss whether the beneficial effects associated with the consumption of Saccharomyces may be related to its foreign origin, though this concept may not necessarily satisfy the theories that have been proposed to explain probiotic efficacy in vivo. This novel review may prove useful for biomedical scientists and others wishing to improve health and productivity using Saccharomyces and other beneficial microorganisms.

RevDate: 2019-07-15

Houldcroft CJ, Rifkin RF, SJ Underdown (2019)

Human biology and ancient DNA: exploring disease, domestication and movement.

Annals of human biology, 46(2):95-98.

RevDate: 2019-07-13

White JA, Styer A, Rosenwald LC, et al (2019)

Endosymbiotic Bacteria Are Prevalent and Diverse in Agricultural Spiders.

Microbial ecology pii:10.1007/s00248-019-01411-w [Epub ahead of print].

Maternally inherited bacterial endosymbionts are common in arthropods, but their distribution and prevalence are poorly characterized in many host taxa. Initial surveys have suggested that vertically transmitted symbionts may be particularly common in spiders (Araneae). Here, we used diagnostic PCR and high-throughput sequencing to evaluate symbiont infection in 267 individual spiders representing 14 species (3 families) of agricultural spiders. We found 27 operational taxonomic units (OTUs) that are likely endosymbiotic, including multiple strains of Wolbachia, Rickettsia, and Cardinium, which are all vertically transmitted and frequently associated with reproductive manipulation of arthropod hosts. Additional strains included Rickettsiella, Spiroplasma, Rhabdochlamydia, and a novel Rickettsiales, all of which could range from pathogenic to mutualistic in their effects upon their hosts. Seventy percent of spider species had individuals that tested positive for one or more endosymbiotic OTUs, and specimens frequently contained multiple symbiotic strain types. The most symbiont-rich species, Idionella rugosa, had eight endosymbiotic OTUs, with as many as five present in the same specimen. Individual specimens within infected spider species had a variety of symbiotypes, differing from one another in the presence or absence of symbiotic strains. Our sample included both starved and unstarved specimens, and dominant bacterial OTUs were consistent per host species, regardless of feeding status. We conclude that spiders contain a remarkably diverse symbiotic microbiota. Spiders would be an informative group for investigating endosymbiont population dynamics in time and space, and unstarved specimens collected for other purposes (e.g., food web studies) could be used, with caution, for such investigations.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
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Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )