@article {pmid38037395,
year = {2023},
author = {Nguyen, PN and Rehan, SM},
title = {Wild bee and pollen microbiomes across an urban-rural divide.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiad158},
pmid = {38037395},
issn = {1574-6941},
abstract = {Wild pollinators and their microbiota are sensitive to land use changes from anthropogenic activities that disrupt landscape and environmental features. As urbanization and agriculture affect bee habitats, human led disturbances are driving changes in bee microbiomes, potentially leading to dysbiosis detrimental to bee fitness. This study examines the bacterial, fungal, and plant compositions of the small carpenter bee, Ceratina calcarata, and its pollen provisions across an urban-rural divide. We performed metabarcoding of C. calcarata and provisions in Toronto by targeting the 16S rRNA, ITS, and rbcL regions. Despite similar plant composition and diversity across bees and their provisions, there was a greater microbial diversity in pollen provisions than in bees. By characterizing the differences in land use, climate, and pesticide residues that differentiate urban and rural landscapes, we find that urban areas support elevated levels of microbial diversity and more complex networks between microbes and plants than rural areas. However, urban areas may lead to lower relative abundances of known beneficial symbionts and increased levels of pathogens, such as Ascosphaera and Alternaria fungi. Further, rural pollen provisions indicate elevated pesticide residues that may dysregulate symbiosis. As anthropogenic activities continue to alter land use, ever changing environments threaten microbiota crucial in maintaining bee health.},
}

@article {pmid38034649,
year = {2023},
author = {Morales-Cortés, VI and Domínguez-Soberanes, J and Hernández-Lozano, LC and Licon, CC and Estevez-Rioja, A and Peralta-Contreras, M},
title = {Sensory characterization of functional guava symbiotic petit cheese product.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21747},
pmid = {38034649},
issn = {2405-8440},
abstract = {The consumption of functional dairy products continues to rise due to consumer needs. This study aimed to develop a dairy guava functional symbiotic petit cheese product that included probiotics (Bifidobacterium animalis subsp. lactis BB-12, Chr. Hansen, Denmark) and prebiotics (inulin), which had adequate organoleptic characteristics. Moreover, adequate physicochemical, microbiological, and sensory characteristics during its shelf life were expected. A pasteurized skim milk curd flavored with a guava pulp was stabilized with gelatin to formulate this product. As sweeteners, iso maltol, erythritol, and Luo Han Guo extract from monk fruit (Siraitia Grosvenorii) were added. The prebiotic used was inulin, and the probiotic (Bifidobacterium animalis subsp. lactis BB-12, Chr. Hansen, Denmark). The product was kept refrigerated (4 °C) during the shelf life of 28 days. For the organoleptic analysis (100 consumers), the evaluations performed were: (1) overall liking (OL), (2) CATA (Check all that apply) testing 19 attributes, and (3) purchase intention was evaluated. Results were analyzed with FIZZ Software Biosystèmes. During shelf life, (1) physicochemical, microbiological, and sensory tests were performed. The product was evaluated as "liked much'' (7.16 out of 9); it was described as a creamy (71 %) natural product (73 %) with a fruity odor (57 %). It could be suitable for marketing because 82 % of the consumers would buy it. The product's probiotic character (over 1 × 10[6]) was established through a microbiological count. On day one, the CFU was found to be 4.15 × 10[8], and after 28 days, 1.98 × 10[8] CFU of viable Bifidobacterium animalis subsp. lactis BB-12, leading us to establish its probiotic characteristics. The shelf life was estimated at 21 days.},
}

@article {pmid38034552,
year = {2023},
author = {Arifuzzaman, M and Mamidi, S and Sanz-Saez, A and Zakeri, H and Scaboo, A and Fritschi, FB},
title = {Identification of loci associated with water use efficiency and symbiotic nitrogen fixation in soybean.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1271849},
pmid = {38034552},
issn = {1664-462X},
abstract = {Soybean (Glycine max) production is greatly affected by persistent and/or intermittent droughts in rainfed soybean-growing regions worldwide. Symbiotic N2 fixation (SNF) in soybean can also be significantly hampered even under moderate drought stress. The objective of this study was to identify genomic regions associated with shoot carbon isotope ratio (δ[13]C) as a surrogate measure for water use efficiency (WUE), nitrogen isotope ratio (δ[15]N) to assess relative SNF, N concentration ([N]), and carbon/nitrogen ratio (C/N). Genome-wide association mapping was performed with 105 genotypes and approximately 4 million single-nucleotide polymorphism markers derived from whole-genome resequencing information. A total of 11, 21, 22, and 22 genomic loci associated with δ[13]C, δ[15]N, [N], and C/N, respectively, were identified in two environments. Nine of these 76 loci were stable across environments, as they were detected in both environments. In addition to the 62 novel loci identified, 14 loci aligned with previously reported quantitative trait loci for different C and N traits related to drought, WUE, and N2 fixation in soybean. A total of 58 Glyma gene models encoding for different genes related to the four traits were identified in the vicinity of the genomic loci.},
}

@article {pmid38031601,
year = {2023},
author = {Zartdinova, R and Nikitin, A},
title = {Calcium in the Life Cycle of Legume Root Nodules.},
journal = {Indian journal of microbiology},
volume = {63},
number = {4},
pages = {410-420},
pmid = {38031601},
issn = {0046-8991},
abstract = {The present review highlights both the fundamental questions of calcium localization, compartmentation, and its participation in symbiosome signaling cascades during nodule formation and functioning. Apparently, the main link of such signaling is the calmodulin…calcium- and calmodulin-dependent protein kinases…CYCLOPS…NIN…target genes cascade. The minimum threshold level of calcium as a signaling agent in the presence of intracellular reserves determines the possibility of oligotrophy and ultraoligotrophy in relation to this element. During the functioning of root nodules, the Ca[2+]-ATPases activity maintains homeostasis of low calcium concentrations in the cytosol of nodule parenchyma cells. Disturbation of this homeostasis can trigger the root nodule senescence. The same reasons determine the increase in the effectiveness of symbiosis with the help of seed priming with sources of calcium. Examples of calcium response polymorphism in components of nitrogen fixing simbiosis important in practical terms are shown.},
}

@article {pmid38031529,
year = {2023},
author = {Sanders, WB},
title = {The disadvantages of current proposals to redefine lichens: A comment on Hawksworth & Grube (2020): 'Lichens redefined as complex ecosystems'.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19321},
pmid = {38031529},
issn = {1469-8137},
}

@article {pmid38031487,
year = {2023},
author = {Hawksworth, DL and Grube, M},
title = {Reflections on lichens as ecosystems.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19418},
pmid = {38031487},
issn = {1469-8137},
}

@article {pmid38030972,
year = {2023},
author = {Wu, F and Zhao, M and Zhang, Y and Si, W and Cheng, B and Li, X},
title = {Systematic analysis of the Rboh gene family in seven gramineous plants and its roles in response to arbuscular mycorrhizal fungi in maize.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {603},
pmid = {38030972},
issn = {1471-2229},
support = {GXXT-2019-032//Collaborative Innovation Project for Universities in Anhui Province/ ; U21A20235//National Natural Science Foundation of China/ ; 202204c06020021//The key research and development Program of Anhui Province/ ; },
mesh = {*Mycorrhizae/physiology ; Zea mays/metabolism ; Phylogeny ; Symbiosis ; Plant Roots/genetics ; Gene Expression Regulation, Plant ; },
abstract = {BACKGROUND: Plant respiratory burst oxidase homolog (Rboh) gene family produces reactive oxygen species (ROS), and it plays key roles in plant-microbe interaction. Most Rboh gene family-related studies mainly focused on dicotyledonous plants; however, little is known about the roles of Rboh genes in gramineae.

RESULTS: A total of 106 Rboh genes were identified in seven gramineae species, including Zea mays, Sorghum bicolor, Brachypodium distachyon, Oryza sativa, Setaria italica, Hordeum vulgare, and Triticum aestivum. The Rboh protein sequences showed high similarities, suggesting that they may have conserved functions across different species. Duplication mode analysis detected whole-genome/segmental duplication (WGD)/(SD) and dispersed in the seven species. Interestingly, two local duplication (LD, including tandem and proximal duplication) modes were found in Z. mays, S. italica and H. vulgare, while four LD were detected in T. aestivum, indicating that these genes may have similar functions. Collinearity analysis indicated that Rboh genes are at a stable evolution state in all the seven species. Besides, Rboh genes from Z. mays were closely related to those from S. bicolor, consistent with the current understanding of plant evolutionary history. Phylogenetic analysis showed that the genes in the subgroups I and II may participate in plant-AM fungus symbiosis. Cis-element analysis showed that different numbers of elements are related to fungal induction in the promoter region. Expression profiles of Rboh genes in Z. mays suggested that Rboh genes had distinct spatial expression patterns. By inoculation with AM fungi, our transcriptome analysis showed that the expression of Rboh genes varies upon AM fungal inoculation. In particularly, ZmRbohF was significantly upregulated after inoculation with AM fungi. pZmRbohF::GUS expression analyses indicated that ZmRbohF was induced by arbuscular mycorrhizal fungi in maize. By comparing WT and ZmRbohF mutant, we found ZmRbohF had limited impact on the establishment of maize-AM fungi symbiosis, but play critical roles in regulating the proper development of arbuscules.

CONCLUSIONS: This study provides a comprehensive analysis of the evolution relationship of Rboh genes in seven gramineae species. Results showed that several Rboh genes regulate maize-AM fungal symbiosis process. This study provides valuable information for further studies of Rboh genes in gramineae.},
}

*Mycorrhizae/physiology
Zea mays/metabolism
Phylogeny
Symbiosis
Plant Roots/genetics
Gene Expression Regulation, Plant

@article {pmid38029803,
year = {2023},
author = {Zhang, Y and Liu, L and Huang, G and Yang, C and Tian, W and Ge, Z and Zhang, B and Wang, S and Zhang, H},
title = {Enhancing humification and microbial interactions during co-composting of pig manure and wine grape pomace: The role of biochar and Fe2O3.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130120},
doi = {10.1016/j.biortech.2023.130120},
pmid = {38029803},
issn = {1873-2976},
abstract = {Phenol-rich wine grape pomace (WGP) improves the conversion of pig manure (PM) into humic acid (HA) during composting. However, the impact of using combinations of Fe2O3 and biochar known to promote compost maturation remains uncertain. This research explored the individual and combined influence of biochar and Fe2O3 during the co-composting of PM and WGP. The findings revealed that Fe2O3 boosts microbial network symbiosis (3233 links), augments the HA yield to 3.38 by promoting polysaccharide C-O stretching, and improves the germination index to 124.82 %. Limited microbial interactions, increased by biochar, resulted in a lower HA yield (2.50). However, the combination weakened the stretching of aromatics and quinones, which contribute to the formation of HA, resulting in reduced the humification to 2.73. In addition, Bacillus and Actinomadura were identified as pivotal factors affecting HA content. This study highlights Fe2O3 and biochar's roles in phenol-rich compost humification, but combined use reduces efficacy.},
}

@article {pmid38029247,
year = {2023},
author = {Jiao, X and Li, Z},
title = {Temporal dynamics and composition of ocular surface microbiota in C57BL/6J mice: uncovering a 12h ultradian rhythm.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1244454},
pmid = {38029247},
issn = {2235-2988},
abstract = {PURPOSE: This study aimed to investigate the presence of rhythmic fluctuations in the composition, abundance, and functions of commensal core bacteria on the ocular surface of C57BL/6J mice.

METHODS: Male C57BL/6J mice, aged 12 weeks, were subjected to a 12-hour light/12-hour dark cycle. Ocular surface tissue samples were collected at four time points (ZT) over a 24-hour period at six-hour intervals. The core ocular surface microbiota's oscillation cycles and frequencies were assessed using 16S rRNA gene sequencing targeting the V3-V4 region, along with the JTK_CYCLE algorithm. Functional predictions of these bacteria were conducted using PICRUSt2.

RESULTS: Deep sequencing of the ocular surface microbiota highlighted the high abundance of commensal bacteria, with Proteobacteria, Actinobacteriota, and Firmicutes collectively constituting over 90% of the total sample abundance. Among the 22 core bacterial genera, 11 exhibited robust 12-hour rhythms, including Halomonas, Pelagibacterium, Pseudomonas, Nesterenkonia, norank_f_Hyphomonadaceae, Stenotrophomonas, Anoxybacillus, Acinetobacter, Zoogloea, Brevibacillus, and Ralstonia. Further taxonomic analysis indicated significant intra-cluster similarities and inter-cluster differences at the order, family, and genus levels during ZT0/12 and ZT6/18. Community interaction networks and functional prediction analyses revealed synchronized 12-hour rhythmic oscillations in neural, immune, metabolic, and other pathways associated with symbiotic bacteria.

CONCLUSION: This study demonstrates the presence of ultradian rhythmic oscillations in commensal bacteria on the ocular surface of normal C57BL/6J mice, with a 12-hour cycle. These findings suggest a crucial role for ultradian rhythms in maintaining ocular surface homeostasis in the host.},
}

@article {pmid38029204,
year = {2023},
author = {Venice, F and Vizzini, A and Danti, R and Della Rocca, G and Mello, A},
title = {Responses of a soil fungal community to severe windstorm damages in an old silver fir stand.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1246874},
pmid = {38029204},
issn = {1664-302X},
abstract = {Forests are increasingly threatened by climate change and the Anthropocene seems to have favored the emergence and adaptation of pathogens. Robust monitoring methods are required to prevent biodiversity and ecosystems losses, and this imposes the choice of bioindicators of habitat health. Fungal communities are increasingly recognized as fundamental components in nearly all natural and artificial environments, and their ecosystem services have a huge impact in maintaining and restoring the functionality of ecosystems. We coupled metabarcoding and soil analyses to infer the dynamics of a fungal community inhabiting the old silver fir stand in Vallombrosa (Italy), which is known to be afflicted by both Armillaria and Annosum root rot. The forest was affected in 2015, by a windstorm which caused a partial falling and uprooting of trees. The remaining stand, not affected by the windstorm, was used as a comparison to infer the consequences of the ecosystem disturbance. We demonstrated that the abundance of pathogens alone is not able to explain the soil fungal differences shown by the two areas. The fungal community as a whole was equally rich in the two areas, even if a reduction of the core ectomycorrhizal mycobiome was observed in the wind-damaged area, accompanied by the increase of wood saprotrophs and arbuscular mycorrhizas. We hypothesize a reshaping of the fungal community and a potentially ongoing re-generation of its functionalities. Our hypothesis is driven by the evidence that key symbiotic, endophytic, and saprotrophic guilds are still present and diversified in the wind-damaged area, and that dominance of single taxa or biodiversity loss was not observed from a mycological point of view. With the present study, we aim at providing evidence that fungal communities are fundamental for the monitoring and the conservation of threatened forest ecosystems.},
}

@article {pmid38029197,
year = {2023},
author = {Zhang, Q and Chang, S and Yang, Y and Xi, C and Dong, Y and Liu, L and He, Y and Liu, Y and Cai, B and Liu, T},
title = {Endophyte-inoculated rhizomes of Paris polyphylla improve polyphyllin biosynthesis and yield: a transcriptomic analysis of the underlying mechanism.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1261140},
pmid = {38029197},
issn = {1664-302X},
abstract = {INTRODUCTION: Polyphyllin from Paris polyphylla var. yunnanensis exhibits anti-inflammatory, analgesic, antibacterial, and antiviral properties. However, the current production of polyphyllin can barely meet market demand. To improve the content of polyphyllin produced by P. polyphylla, two endophyte strains, Bacillus cereus LgD2 and Fusarium oxysporum TPB, were isolated from Paris fargesii Franch. and inoculated in the roots of P. polyphylla. Both symbiotic strains significantly promoted the accumulation of saponins in P. polyphylla.

METHODS: The content of polyphyllin in rhizomes of P. polyphylla treated with TPB with LgD2 strain was determined using High Performance Liquid Chromatography and the expressed genes were analyzed by RNA-seq. Gene Ontology and Kyoto Encyclopedia of Genes annotations were performed on the differentially expressed genes, a clustering tree of UDP-glycosyltransferase (UGT) and cytochrome P450 (CYP450) gene families was constructed, and UGT and CYP450 involved in the biosynthesis of polyphyllin were predicted using weighted correlation network analysis (WGCNA).

RESULTS: RNA-seq and qRT-PCR analyses showed that endophytic inoculation did not promote polyphyllin accumulation by enhancing the upstream terpene biosynthesis pathway, but probably by up-regulating the downstream CYP450 and UGT genes associated with polyphyllin biosynthesis. Genomes enrichment analyses of differentially expressed genes indicated that inoculation with LgD2 and TPB played a positive role in promoting the defense against pathogenic bacteria, enhancing the biosynthesis of carbohydrates, attenuating the process of nitrogen metabolism, and maintaining the equilibrium of the redox reaction homeostasis, potentially indirectly enhancing the polyphyllin yield of P. polyphylla. By combining differentially expressed genes screening, WGCNA, and phylogenetic tree analyses, 17 CYP450 and 2 UGT candidate genes involved in the biosynthesis of polyphyllin I, polyphyllin II, polyphyllin VII, polyphyllin D, and polyphyllin H were identified. These results suggest that endophytes probably effectively promote the accumulation of polyphyllin by regulating key downstream genes in biosynthetic pathways.

DISCUSSION: This study provides a new approach for investigating the regulatory mechanisms of endophytes that promote the production and accumulation of polyphyllin in P. polyphylla, providing a basis for further elucidating the mechanisms of plant-endophyte interactions.},
}

@article {pmid38029157,
year = {2023},
author = {Liu, M and Ding, J and Lu, M},
title = {Influence of symbiotic bacteria on the susceptibility of Plagiodera versicolora to Beauveria bassiana infection.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1290925},
pmid = {38029157},
issn = {1664-302X},
abstract = {The symbiotic bacterial microbiota of insects has been shown to play essential roles in processes related to physiology, metabolism, and innate immunity. In this study, the symbiotic microbiome of Plagiodera versicolora at different developmental stages was analyzed using 16S rRNA high-throughput sequencing. The result showed that symbiotic bacteria community in P. versicolora was primarily made up of Actinobacteriota, Proteobacteria, Firmicutes, Bacteroidota, and Dependentiae. The bacterial composition among different age individuals were highly diverse, while 65 core genera were distributed in all samples which recommend core bacterial microbiome. The 8 species core bacteria were isolated from all samples, and all of them were classified as Pseudomonas sp. Among them, five species have been proven to promote the vegetable growth of Beauveria bassiana. Moreover, the virulence of B. bassiana against nonaxenic larvae exceeded B. bassiana against axenic larvae, and the introduction of the Pseudomonas sp. to axenic larvae augmented the virulence of fungi. Taken together, our study demonstrates that the symbiotic bacteria of P. versicolora are highly dissimilar, and Pseudomonas sp. core bacteria can promote host infection by entomopathogenic fungus. This result emphasizes the potential for harnessing these findings in the development of effective pest management strategies.},
}

@article {pmid38029104,
year = {2023},
author = {Carrouel, F and Kanoute, A and Lvovschi, VE and Bourgeois, D},
title = {Periodontal pathogens of the interdental microbiota in a 3 months pregnant population with an intact periodontium.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1275180},
doi = {10.3389/fmicb.2023.1275180},
pmid = {38029104},
issn = {1664-302X},
abstract = {Steroid hormones and the oral microbiota of pregnant women both appear as cumulative risk factors for gingivitis. This cross-sectional study, using real-time PCR, investigated the composition and diversity of the microbiota in interdental spaces of 3 months pregnant women with intact periodontium according the 2018 EFP/AAP classification. Bacteria identified were belonged to the red (Porphyromonas gingivalis Treponema denticola, and Tanerella forsythia), orange (Fusobacterium nucleatum, Prevotella intermedia, Campylobacter rectus, and Parvimonas micra), and green (Eikenella corrodens and A. actinomycetencomitans) Socransky complexes. Approximatively 10[9.11] bacteria were counted per interdental space in pregnant women. Bacteria from the red complex represented 33.80% versus 62.81% for the orange group versus 3.39% for the green group of the total number spread over the 3 groups. Dietary habits and physical activity did not have a significant impact on interdental microbiota, although a decrease in the median amount of 9 periodontopathogens was observed when fruit and vegetable consumption increased. Pregnant women who brushed their teeth at least twice a day had lower counts of total bacteria and 9 periodontal pathogens than those who brushed less. In 3 months pregnant women at high risk of periodontal disease (>30% bleeding sites), the dendogram revealed 2 clusters of the 9 periodontopathogens. This provides further support for the "key pathogen" hypothesis, among which Porphyromonas gingivalis plays a key role, indicating that specific bacteria in limited quantities can influence the host immune system and convert the microbiota from symbiotic to dysbiotic to induce inflammatory disorder. As a result, this study reported that 3 months pregnant women with healthy periodontium had high levels of interdental bleeding and a dysbiotic microbiota with periodontal pathogens of the Socransky orange and red complexes. These subjects were therefore potentially at increased risk of developing periodontal disease and, consequently, an adverse pregnancy outcome. So, preventive oral prophylaxis measures, in particular individual interdental prophylaxis, should be implemented as soon as pregnancy is established.},
}

@article {pmid38028661,
year = {2023},
author = {Mazarakis, A and Bernhard-Skala, C and Braun, M and Peters, I},
title = {What is critical for human-centered AI at work? - Toward an interdisciplinary theory.},
journal = {Frontiers in artificial intelligence},
volume = {6},
number = {},
pages = {1257057},
doi = {10.3389/frai.2023.1257057},
pmid = {38028661},
issn = {2624-8212},
abstract = {Human-centered artificial intelligence (HCAI) has gained momentum in the scientific discourse but still lacks clarity. In particular, disciplinary differences regarding the scope of HCAI have become apparent and were criticized, calling for a systematic mapping of conceptualizations-especially with regard to the work context. This article compares how human factors and ergonomics (HFE), psychology, human-computer interaction (HCI), information science, and adult education view HCAI and discusses their normative, theoretical, and methodological approaches toward HCAI, as well as the implications for research and practice. It will be argued that an interdisciplinary approach is critical for developing, transferring, and implementing HCAI at work. Additionally, it will be shown that the presented disciplines are well-suited for conceptualizing HCAI and bringing it into practice since they are united in one aspect: they all place the human being in the center of their theory and research. Many critical aspects for successful HCAI, as well as minimum fields of action, were further identified, such as human capability and controllability (HFE perspective), autonomy and trust (psychology and HCI perspective), learning and teaching designs across target groups (adult education perspective), as much as information behavior and information literacy (information science perspective). As such, the article lays the ground for a theory of human-centered interdisciplinary AI, i.e., the Synergistic Human-AI Symbiosis Theory (SHAST), whose conceptual framework and founding pillars will be introduced.},
}

@article {pmid38028650,
year = {2023},
author = {Carrell, AA and Clark, M and Jawdy, S and Muchero, W and Alexandre, G and Labbé, JL and Rush, TA},
title = {Interactions with microbial consortia have variable effects in organic carbon and production of exometabolites among genotypes of Populus trichocarpa.},
journal = {Plant direct},
volume = {7},
number = {11},
pages = {e544},
doi = {10.1002/pld3.544},
pmid = {38028650},
issn = {2475-4455},
abstract = {Poplar is a short-rotation woody crop frequently studied for its significance as a sustainable bioenergy source. The successful establishment of a poplar plantation partially depends on its rhizosphere-a dynamic zone governed by complex interactions between plant roots and a plethora of commensal, mutualistic, symbiotic, or pathogenic microbes that shape plant fitness. In an exploratory endeavor, we investigated the effects of a consortium consisting of ectomycorrhizal fungi and a beneficial Pseudomonas sp. strain GM41 on plant growth (including height, stem girth, leaf, and root growth) and as well as growth rate over time, across four Populus trichocarpa genotypes. Additionally, we compared the level of total organic carbon and plant exometabolite profiles across different poplar genotypes in the presence of the microbial consortium. These data revealed no significant difference in plant growth parameters between the treatments and the control across four different poplar genotypes at 7 weeks post-inoculation. However, total organic carbon and exometabolite profiles were significantly different between the genotypes and the treatments. These findings suggest that this microbial consortium has the potential to trigger early signaling responses in poplar, influencing its metabolism in ways crucial for later developmental processes and stress tolerance.},
}

@article {pmid38028595,
year = {2023},
author = {Adedayo, AA and Babalola, OO},
title = {Genomic mechanisms of plant growth-promoting bacteria in the production of leguminous crops.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1276003},
doi = {10.3389/fgene.2023.1276003},
pmid = {38028595},
issn = {1664-8021},
abstract = {Legumes are highly nutritious in proteins and are good food for humans and animals because of their nutritional values. Plant growth-promoting bacteria (PGPR) are microbes dwelling in the rhizosphere soil of a plant contributing to the healthy status, growth promotion of crops, and preventing the invasion of diseases. Root exudates produced from the leguminous plants' roots can lure microbes to migrate to the rhizosphere region in other to carry out their potential activities which reveals the symbiotic association of the leguminous plant and the PGPR (rhizobia). To have a better cognition of the PGPR in the rhizosphere of leguminous plants, genomic analyses would be conducted employing various genomic sequences to observe the microbial community and their functions in the soil. Comparative genomic mechanism of plant growth-promoting rhizobacteria (PGPR) was discussed in this review which reveals the activities including plant growth promotion, phosphate solubilization, production of hormones, and plant growth-promoting genes required for plant development. Progress in genomics to improve the collection of genotyping data was revealed in this review. Furthermore, the review also revealed the significance of plant breeding and other analyses involving transcriptomics in bioeconomy promotion. This technological innovation improves abundant yield and nutritional requirements of the crops in unfavorable environmental conditions.},
}

@article {pmid38027833,
year = {2023},
author = {Widodo, },
title = {A new technique inversion Time-Domain electromagnetic data.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21638},
doi = {10.1016/j.heliyon.2023.e21638},
pmid = {38027833},
issn = {2405-8440},
abstract = {Time-Domain Electromagnetic (TDEM) data modeling, especially for central-loop configurations, is often achieved through 1D inversion models. This study aims to enhance the accuracy and efficiency of TDEM data inversion by employing the Born Approximation method to address calculation and convergence speed issues. We also utilize the modified Symbiotic Organism Search (mSOS), a global optimization algorithm capable of handling multi-minimum problems in non-linear objective functions, to optimize the inversion process. Our research includes the assessment of the accuracy and performance of this approach through inversion modeling on both synthetic and field data. The accuracy of the synthetic data was evaluated based on the algorithm's capability to retrieve the values of the synthetic data, as indicated by the small relative error between the synthetic model parameters and the calculated model. In the case of field data modeling, the accuracy relied on the consistency achieved when modeling the data with different numbers of layers. Additionally, we considered the time required to perform the inversion as an evaluation metric for inversion performance. For the synthetic data case, the algorithm produced relatively accurate models with misfit values of approximately 0 % and low relative error values. In the field data case, the inversion models demonstrated consistency and reduced misfit values when the data was modeled with different numbers of layers, specifically 8.72 % for the 2-layer model, 3.92 % for the 3-layer model, and 2.61 % for the 4- and 5-layer models. Both datasets required less than 19 min for 10,000 iterations. These findings highlight the innovative nature of the mSOS algorithm and its potential for practical applications in TDEM inversion studies.},
}

@article {pmid38025720,
year = {2023},
author = {Sánchez-Matiz, JJ and Díaz-Ariza, LA},
title = {Glomeromycota associations with bamboos (Bambusoideae) worldwide, a qualitative systematic review of a promising symbiosis.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16151},
doi = {10.7717/peerj.16151},
pmid = {38025720},
issn = {2167-8359},
abstract = {BACKGROUND: Around the world, bamboos are ecologically, economically, and culturally important plants, particularly in tropical regions of Asia, America, and Africa. The association of this plant group with arbuscular mycorrhizal fungi belonging to the phylum Glomeromycota is still a poorly studied field, which limits understanding of the reported ecological and physiological benefits for the plant, fungus, soil, and ecosystems under this symbiosis relationship.

METHODS: Through a qualitative systematic review following the PRISMA framework for the collection, synthesis, and reporting of evidence, this paper presents a compilation of the research conducted on the biology and ecology of the symbiotic relationship between Glomeromycota and Bambusoideae from around the world. This review is based on academic databases enriched with documents retrieved using different online databases and the Google Scholar search engine.

RESULTS: The literature search yielded over 6,000 publications, from which 18 studies were included in the present review after a process of selection and validation. The information gathered from the publications included over 25 bamboo species and nine Glomeromycota genera from eight families, distributed across five countries on two continents.

CONCLUSION: This review presents the current state of knowledge regarding the symbiosis between Glomeromycota and Bambusoideae, while reflecting on the challenges and scarcity of research on this promising association found across the world.},
}

@article {pmid38025692,
year = {2023},
author = {Li, Y and Huang, Y and Wronski, T and Huang, M},
title = {Diversity of bacteria associated with lichens in Mt. Yunmeng in Beijing, China.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16442},
doi = {10.7717/peerj.16442},
pmid = {38025692},
issn = {2167-8359},
abstract = {Lichens host highly complex and diverse microbial communities, which may perform essential functions in these symbiotic micro-ecosystems. In this research, sequencing of 16S rRNA was used to investigate the bacterial communities associated with lichens of two growth forms (foliose and crustose). Results showed that Pseudomonadota, Actinomycetota and Acidobacteriota were dominant phyla in both types of lichens, while Acetobacterales and Hyphomicrobiales were the dominant orders. Alpha diversity index showed that the richness of bacteria hosted by foliose lichens was significantly higher than that hosted by crustose ones. Principal co-ordinates analysis showed a significant difference between beta diversity of the foliose lichen-associated bacterial communities and those of crustose lichen-associated ones. Gene function prediction showed most functions, annotated by the lichen-associated bacteria, to be related to metabolism, suggesting that related bacteria may provide nutrients to their hosts. Generally, our results propose that microbial communities play important roles in fixing nitrogen, providing nutrients, and controlling harmful microorganisms, and are therefore an integral and indispensable part of lichens.},
}

@article {pmid38023845,
year = {2023},
author = {Liu, X and Feng, Z and Zhang, W and Yao, Q and Zhu, H},
title = {Exogenous myristate promotes the colonization of arbuscular mycorrhizal fungi in tomato.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1250684},
doi = {10.3389/fpls.2023.1250684},
pmid = {38023845},
issn = {1664-462X},
abstract = {Arbuscular mycorrhizal fungi (AMF) can establish symbiotic associations with the roots of most terrestrial plants, thereby improving the tolerance of the host plants to biotic and abiotic stresses. Although AMF cannot synthesize lipids de novo, they can obtain lipids from the root cells for their growth and development. A recent study reveals that AMF can directly take up myristate (C14:0 lipid) from the environment and produce a large amount of hyphae in asymbiotic status; however, the effect of environmental lipids on AM symbiosis is still unclear. In this study, we inoculated tomato (Solanum lycopersicum) with AMF in an in vitro dual culture system and a sand culture system, and then applied exogenous myristate to the substrate, in order to explore the effect of exogenous lipids on the mycorrhizal colonization of AMF. We investigated the hyphae growth, development, and colonization of AMF, and examined the gene expression involved in phosphate transport, lipid biosynthesis, and transport. Results indicate that exogenous lipids significantly stimulated the growth and branching of hyphae, and significantly increased the number of hyphopodia and mycorrhizal colonization of AMF, with arbuscular abundance and intraradical spores or vesicles being the most promoted. In contrast, exogenous myristate decreased the growth range and host tropism of the germ tubes, and largely inhibited the exchange of nutrition between symbionts. As a result, exogenous myristate did not affect the plant growth. This study suggests that lipids promote mycorrhizal colonization by enhancing the growth and development of AMF hyphae and increasing their contact opportunities with plant roots. To the best of our knowledge, this is the first report that shows that lipids promote the colonization of AMF. Our study highlights the importance of better understanding the roles of environmental lipids in the establishment and maintenance of AM symbiosis and, thus, in agricultural production.},
}

@article {pmid38023592,
year = {2023},
author = {Yun, HM and Hyun, S},
title = {Role of gut commensal bacteria in juvenile developmental growth of the host: insights from Drosophila studies.},
journal = {Animal cells and systems},
volume = {27},
number = {1},
pages = {329-339},
doi = {10.1080/19768354.2023.2282726},
pmid = {38023592},
issn = {1976-8354},
abstract = {The gut microbiome plays a crucial role in maintaining health in a variety of organisms, from insects to humans. Further, beneficial symbiotic microbes are believed to contribute to improving the quality of life of the host. Drosophila is an optimal model for studying host-commensal microbe interactions because it allows for convenient manipulation of intestinal microbial composition. Fly microbiota has a simple taxonomic composition and can be cultivated and genetically tracked. This permits functional studies and analyses of the molecular mechanisms underlying their effects on host physiological processes. In this context, we briefly introduce the principle of juvenile developmental growth in Drosophila. Then, we discuss the current understanding of the molecular mechanisms underlying the effects of gut commensal bacteria, such as Lactiplantibacillus plantarum and Acetobacter pomorum, in the fly gut microbiome on Drosophila juvenile growth, including specific actions of gut hormones and metabolites in conserved cellular signaling systems, such as the insulin/insulin-like (IIS) and the target of rapamycin (TOR) pathways. Given the similarities in tissue function/structure, as well as the high conservation of physiological systems between Drosophila and mammals, findings from the Drosophila model system will have significant implications for understanding the mechanisms underlying the interaction between the host and the gut microbiome in metazoans.},
}

@article {pmid38023456,
year = {2023},
author = {Liang, J},
title = {Harmonizing minds and machines: survey on transformative power of machine learning in music.},
journal = {Frontiers in neurorobotics},
volume = {17},
number = {},
pages = {1267561},
doi = {10.3389/fnbot.2023.1267561},
pmid = {38023456},
issn = {1662-5218},
abstract = {This survey explores the symbiotic relationship between Machine Learning (ML) and music, focusing on the transformative role of Artificial Intelligence (AI) in the musical sphere. Beginning with a historical contextualization of the intertwined trajectories of music and technology, the paper discusses the progressive use of ML in music analysis and creation. Emphasis is placed on present applications and future potential. A detailed examination of music information retrieval, automatic music transcription, music recommendation, and algorithmic composition presents state-of-the-art algorithms and their respective functionalities. The paper underscores recent advancements, including ML-assisted music production and emotion-driven music generation. The survey concludes with a prospective contemplation of future directions of ML within music, highlighting the ongoing growth, novel applications, and anticipation of deeper integration of ML across musical domains. This comprehensive study asserts the profound potential of ML to revolutionize the musical landscape and encourages further exploration and advancement in this emerging interdisciplinary field.},
}

@article {pmid38020871,
year = {2023},
author = {Li, D and Xia, W and Cui, X and Zhao, M and Huang, K and Wang, X and Shen, J and Chen, H and Zhu, L},
title = {The putatively high-altitude adaptation of macaque monkeys: Evidence from the fecal metabolome and gut microbiome.},
journal = {Evolutionary applications},
volume = {16},
number = {10},
pages = {1708-1720},
doi = {10.1111/eva.13595},
pmid = {38020871},
issn = {1752-4571},
abstract = {Animals living in high-altitude environments, such as the Tibetan Plateau, must face harsh environmental conditions (e.g., hypoxia, cold, and strong UV radiation). These animals' physiological adaptations (e.g., increased red cell production and turnover rate) might also be associated with the gut microbial response. Bilirubin is a component of red blood cell turnover or destruction and is excreted into the intestine and reduced to urobilinoids and/or urobilinogen by gut bacteria. Here, we found that the feces of macaques living in high-altitude regions look significantly browner (with a high concentration of stercobilin, a component from urobilinoids) than those living in low-altitude regions. We also found that gut microbes involved in urobilinogen reduction (e.g., beta-glucuronidase) were enriched in the high-altitude mammal population compared to the low-altitude population. Moreover, the spatial-temporal change in gut microbial function was more profound in the low-altitude macaques than in the high-altitude population, which might be attributed to profound changes in food resources in the low-altitude regions. Therefore, we conclude that a high-altitude environment's stress influences living animals and their symbiotic microbiota.},
}

@article {pmid38020682,
year = {2023},
author = {McPherson, AE and Abram, PK and Curtis, CI and Wannop, ER and Dudzic, JP and Perlman, SJ},
title = {Dynamic changes in Wolbachia infection over a single generation of Drosophila suzukii, across a wide range of resource availability.},
journal = {Ecology and evolution},
volume = {13},
number = {11},
pages = {e10722},
doi = {10.1002/ece3.10722},
pmid = {38020682},
issn = {2045-7758},
abstract = {Wolbachia bacteria are maternally inherited symbionts that commonly infect terrestrial arthropods. Many Wolbachia reach high frequencies in their hosts by manipulating their reproduction, for example by causing reproductive incompatibilities between infected male and uninfected female hosts. However, not all strains manipulate reproduction, and a key unresolved question is how these non-manipulative Wolbachia persist in their hosts, often at intermediate to high frequencies. One such strain, wSuz, infects the invasive fruit pest Drosophila suzukii, spotted-wing drosophila. Here, we tested the hypothesis that wSuz infection provides a competitive benefit when resources are limited. Over the course of one season, we established population cages with varying amounts of food in a semi-field setting and seeded them with a 50:50 mixture of flies with and without Wolbachia. We predicted that Wolbachia-infected individuals should have higher survival and faster development than their uninfected counterparts when there was little available food. We found that while food availability strongly impacted fly fitness, there was no difference in development times or survival between Wolbachia-infected and uninfected flies. Interestingly, however, Wolbachia infection frequencies changed dramatically, with infections either increasing or decreasing by as much as 30% in a single generation, suggesting the possibility of unidentified factors shaping Wolbachia infection over the course of the season.},
}

@article {pmid38019961,
year = {2023},
author = {Carobene, A and Padoan, A and Cabitza, F and Banfi, G and Plebani, M},
title = {Rising adoption of artificial intelligence in scientific publishing: evaluating the role, risks, and ethical implications in paper drafting and review process.},
journal = {Clinical chemistry and laboratory medicine},
volume = {},
number = {},
pages = {},
pmid = {38019961},
issn = {1437-4331},
abstract = {BACKGROUND: In the rapid evolving landscape of artificial intelligence (AI), scientific publishing is experiencing significant transformations. AI tools, while offering unparalleled efficiencies in paper drafting and peer review, also introduce notable ethical concerns.

CONTENT: This study delineates AI's dual role in scientific publishing: as a co-creator in the writing and review of scientific papers and as an ethical challenge. We first explore the potential of AI as an enhancer of efficiency, efficacy, and quality in creating scientific papers. A critical assessment follows, evaluating the risks vs. rewards for researchers, especially those early in their careers, emphasizing the need to maintain a balance between AI's capabilities and fostering independent reasoning and creativity. Subsequently, we delve into the ethical dilemmas of AI's involvement, particularly concerning originality, plagiarism, and preserving the genuine essence of scientific discourse. The evolving dynamics further highlight an overlooked aspect: the inadequate recognition of human reviewers in the academic community. With the increasing volume of scientific literature, tangible metrics and incentives for reviewers are proposed as essential to ensure a balanced academic environment.

SUMMARY: AI's incorporation in scientific publishing is promising yet comes with significant ethical and operational challenges. The role of human reviewers is accentuated, ensuring authenticity in an AI-influenced environment.

OUTLOOK: As the scientific community treads the path of AI integration, a balanced symbiosis between AI's efficiency and human discernment is pivotal. Emphasizing human expertise, while exploit artificial intelligence responsibly, will determine the trajectory of an ethically sound and efficient AI-augmented future in scientific publishing.},
}

@article {pmid38018541,
year = {2023},
author = {Varshney, U},
title = {Co-evolution of the translation apparatus and eukaryotes.},
journal = {Journal of biosciences},
volume = {48},
number = {},
pages = {},
pmid = {38018541},
issn = {0973-7138},
abstract = {The symbiotic evolution between the two prokaryotic domains of life (bacteria and archaea) is believed to have given rise to the third domain of life, the eukaryotes. Common to all three domains of life, is an ancient mechanism of ribosome-mediated protein synthesis (translation). Can the evolutionary history of the protein translation apparatus shed light on the evolutionary history of life forms? This commentary addresses this broad question with the spotlight on a specific component of the translation apparatus.},
}

@article {pmid38017446,
year = {2023},
author = {Wu, YH and Qin, Y and Cai, QQ and Liu, M and He, DM and Chen, X and Wang, H and Yan, ZY},
title = {Effect the accumulation of bioactive constituents of a medicinal plant (Salvia Miltiorrhiza Bge.) by arbuscular mycorrhizal fungi community.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {597},
pmid = {38017446},
issn = {1471-2229},
support = {81973416//National Natural Science Foundation of China/ ; 2021YFS0045//the Science and Technology Department of Sichuan Province/ ; },
abstract = {BACKGROUND: Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with various terrestrial plants and have attracted considerable interest as biofertilizers for improving the quality and yield of medicinal plants. Despite the widespread distribution of AMFs in Salvia miltiorrhiza Bunge's roots, research on the impact of multiple AMFs on biomass and active ingredient accumulations has not been conducted. In this study, the effects of five native AMFs (Glomus formosanum, Septoglomus constrictum, Rhizophagus manihotis, Acaulospora laevis, and Ambispora gerdemannii) and twenty-six communities on the root biomass and active ingredient concentrations of S. miltiorrhiza were assessed using the total factor design method.

RESULTS: Thirty-one treatment groups formed symbiotic relationships with S. miltiorrhiza based on the pot culture results, and the colonization rate ranged from 54.83% to 89.97%. AMF communities had higher colonization rates and total phenolic acid concentration than single AMF, and communities also appeared to have higher root fresh weight, dry weight, and total phenolic acid concentration than single inoculations. As AMF richness increased, there was a rising trend in root biomass and total tanshinone accumulations (ATTS), while total phenolic acid accumulations (ATP) showed a decreasing trend. This suggests that plant productivity was influenced by the AMF richness, with higher inoculation benefits observed when the communities contained three or four AMFs. Additionally, the affinities of AMF members were also connected to plant productivity. The inoculation effect of closely related AMFs within the same family, such as G. formosanum, S. constrictum, and R. manihotis, consistently yielded lower than that of mono-inoculation when any combinations were applied. The co-inoculation of S. miltiorrhiza with nearby or distant AMFs from two families, such as G. formosanum, R. manihotis, and Ac. laevis or Am. gerdemannii resulted in an increase of ATP and ATTS by more than 50%. AMF communities appear to be more beneficial to the yield of bioactive constituents than the single AMF, but overall community inoculation effects are related to the composition of AMFs and the relationship between members.

CONCLUSION: This study reveals that the AMF community has great potential to improve the productivity and the accumulation of bioactive constituents in S. miltiorrhiza, indicating that it is an effective way to achieve sustainable agricultural development through using the AMF community.},
}

@article {pmid38016867,
year = {2023},
author = {Quevarec, L and Brasseur, G and Aragnol, D and Robaglia, C},
title = {Tracking the early events of photosymbiosis evolution.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2023.11.005},
pmid = {38016867},
issn = {1878-4372},
abstract = {Oxygenic photosynthesis evolved in cyanobacteria around 3.2 giga-annum (Ga) ago and was acquired by eukaryotes starting around 1.8 Ga ago by endosymbiosis. Photosymbiosis results either from integration of a photosynthetic bacteria by heterotrophic eukaryotes (primary photosymbiosis) or by successive integration of photosymbiotic eukaryotes by heterotrophic eukaryotes (secondary photosymbiosis). Primary endosymbiosis is thought to have been a rare event, whereas secondary and higher-order photosymbiosis evolved multiple times independently in different taxa. Despite its recurrent evolution, the molecular and cellular mechanisms underlying photosymbiosis are unknown. In this opinion, we discuss the primary events leading to the establishment of photosymbiosis, and we present recent research suggesting that, in some cases, domestication occurred instead of symbiosis, and how oxygen and host immunity can be involved in symbiont maintenance.},
}

@article {pmid38016543,
year = {2023},
author = {Biswas, A and Chakraborty, S},
title = {Assessment of microbial population in integrated CW-MFC system and investigation of organics and fecal coliform removal pathway.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168809},
doi = {10.1016/j.scitotenv.2023.168809},
pmid = {38016543},
issn = {1879-1026},
abstract = {The current study is focused on understanding the operational mechanism of an integrated constructed wetland-microbial fuel cell (CW-MFC) reactor emphasizing fecal coliform (FC) removal. Few studies are available in the literature investigating the inherent mechanisms of pathogen inactivation in a CW-MFC system. Raw domestic wastewater was treated in three vertical reactors, one planted constructed wetland (R1), one planted CW-MFC (R2), and one unplanted CW-MFC (R3). Spatial analysis of treated effluents showed a considerable amount of organics and fecal coliform removal at the vicinity of the anode in R2. Assessment of the microbial population inside all the reactors revealed that EABs (Firmicutes, Bacteroidetes, and Actinobacteria) were more abundant in R2 compared to R1 and R3. During the activity study, biomass obtained from R2 showed a maximum substrate utilization rate of 1.27 mg COD mgVSS[-1] d[-1]. Kinetic batch studies were carried out for FC removal in all the reactors, and the maximum first order FC removal rate was obtained at the anode of R2 as 2.13 d[-1] when operated in closed circuit mode. This value was much higher than the natural die-off rate of FCs in raw wastewater which was 1.16 d[-1]. Simultaneous bioelectricity monitoring inferred that voltage generation can be correlated to faster FC inactivation, which was probably due to EABs outcompeting other exogenous microbes in a preferable anaerobic environment with the presence of an anode. Reactor R2 was found to be functioning as a symbiotic bio-electrochemical mesocosm.},
}

@article {pmid38016408,
year = {2023},
author = {Li, J and Li, Y and Xiao, H and Li, W and Ye, F and Wang, L and Li, Y and Wang, C and Wu, Y and Xuan, R and Huang, Y and Huang, J},
title = {The intestinal microflora diversity of aboriginal chickens in Jiangxi province, China.},
journal = {Poultry science},
volume = {103},
number = {2},
pages = {103198},
doi = {10.1016/j.psj.2023.103198},
pmid = {38016408},
issn = {1525-3171},
abstract = {Intestinal microbiota can coevolve with host to form symbiotic relationship and be participated in the regulation of host physiological function. At present, there is no clear explanation on the effect of intestinal microflora in Jiangxi aboriginal chickens. Here, we investigated the association between gut microbiota and host genome of Jiangxi local chickens using 16S rRNA sequencing and genome-wide association studies (GWAS). The results showed that the breeds and genders had important effects on the intestinal microbiota of chickens. A total of 28 SNPs in 14 regions of the chicken genome were related to the relative abundance of microorganisms in 5 genera: Clostridium_sensu_stricto_1, Enterococcus, Gallibacterium, Turicibacter, and Rikenellaceae_RC9_gut_group. A total of 17 candidate genes were identified composition of chicken microbiome and show an association between the host genome and the chicken intestinal microbiota, which also unveiled the diversity of intestinal microbes in Jiangxi chickens. Given the correlation between chicken genome and intestinal microbe found in the present study, a new idea for the protection of aboriginal chicken genetic resources in China could be provided.},
}

@article {pmid38016378,
year = {2023},
author = {Cao, X and Cheng, XW and Liu, YY and Dai, HW and Gan, RY},
title = {Inhibition of pathogenic microbes in oral infectious diseases by natural products: Sources, mechanisms, and challenges.},
journal = {Microbiological research},
volume = {279},
number = {},
pages = {127548},
doi = {10.1016/j.micres.2023.127548},
pmid = {38016378},
issn = {1618-0623},
abstract = {The maintenance of oral health is of utmost importance for an individual's holistic well-being and standard of living. Within the oral cavity, symbiotic microorganisms actively safeguard themselves against potential foreign diseases by upholding a multifaceted equilibrium. Nevertheless, the occurrence of an imbalance can give rise to a range of oral infectious ailments, such as dental caries, periodontitis, and oral candidiasis. Presently, clinical interventions encompass the physical elimination of pathogens and the administration of antibiotics to regulate bacterial and fungal infections. Given the limitations of various antimicrobial drugs frequently employed in dental practice, the rising incidence of oral inflammation, and the escalating bacterial resistance to antibiotics, it is imperative to explore alternative remedies that are dependable, efficacious, and affordable for the prevention and management of oral infectious ailments. There is an increasing interest in the creation of novel antimicrobial agents derived from natural sources, which possess attributes such as safety, cost-effectiveness, and minimal adverse effects. This review provides a comprehensive overview of the impact of natural products on the development and progression of oral infectious diseases. Specifically, these products exert their influences by mitigating dental biofilm formation, impeding the proliferation of oral pathogens, and hindering bacterial adhesion to tooth surfaces. The review also encompasses an examination of the various classes of natural products, their antimicrobial mechanisms, and their potential therapeutic applications and limitations in the context of oral infections. The insights garnered from this review can support the promising application of natural products as viable therapeutic options for managing oral infectious diseases.},
}

@article {pmid38016137,
year = {2023},
author = {Azarm, A and Koosha, M and Dalimi, A and Zahraie-Ramazani, A and Akhavan, AA and Saeidi, Z and Mohebali, M and Azam, K and Vatandoost, H and Oshaghi, MA},
title = {Association Between Wolbachia Infection and Susceptibility to Deltamethrin Insecticide in Phlebotomus papatasi (Diptera: Psychodidae), the Main Vector of Zoonotic Cutaneous Leishmaniasis.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1089/vbz.2023.0085},
pmid = {38016137},
issn = {1557-7759},
abstract = {Background: Phlebotomus papatasi (Diptera: Psychodidae) is the main vector of zoonotic cutaneous leishmaniasis. Wolbachia is a symbiotic alphaproteobacteria of arthropods that can be involved in susceptibility or resistance. This study aimed to investigate the relationship between Wolbachia and Deltamethrin susceptibility/resistance in Ph. papatasi. Deltamethrin filter papers (0.00002%) were used to test sand fly field collected from southern Iran. After the test, PCR amplification of the Wolbachia surface protein gene (wsp) was used to measure Wolbachia infection rate in the killed, surviving, and control groups. Result: The rates of infection by Wolbachia strain (wPap, super group A) differed between killed (susceptible) and surviving (resistant) Ph. papatasi specimens. The rate of Wolbachia infection in susceptible individuals was more than twice (2.3) (39% vs. 17%) in resistant individuals with the same genetic background. This difference was highly significant (p < 0.001), indicating a positive association between Wolbachia infection and susceptibility to Deltamethrin. In addition, the results showed that Deltamethrin can act as a PCR inhibitor during detection of Wolbachia in Ph. papatasi. Conclusion: Results of this study show that Wolbachia is associated with Deltamethrin susceptibility level in Ph. papatasi. Also, as Deltamethrin has been identified as a PCR inhibitor, great care must be taken in interpreting Wolbachia infection status in infected populations. The results of this study may provide information for a better understanding of the host-symbiont relationship, as well as application of host symbiosis in pest management.},
}

@article {pmid38014981,
year = {2023},
author = {Ball, LM and Bronstein, E and Liechti, GW and Maurelli, AT},
title = {Neisseria gonorrhoeae drives Chlamydia trachomatis into a persistence-like state during in vitro co-infection.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0017923},
doi = {10.1128/iai.00179-23},
pmid = {38014981},
issn = {1098-5522},
abstract = {Chlamydia trachomatis and Neisseria gonorrhoeae are the most prevalent bacterial sexually transmitted infections (STIs) globally. Despite frequent co-infections in patients, few studies have investigated how mono-infections may differ from co-infections. We hypothesized that a symbiotic relationship between the pathogens could account for the high rates of clinical co-infection. During in vitro co-infection, we observed an unexpected phenotype where the C. trachomatis developmental cycle was impaired by N. gonorrhoeae. C. trachomatis is an obligate intracellular pathogen with a unique biphasic developmental cycle progressing from infectious elementary bodies (EB) to replicative reticulate bodies (RB), and back. After 12 hours of co-infection, we observed fewer EBs than in a mono-infection. Chlamydial genome copy number remained equivalent between mono- and co-infections. This is a hallmark of Chlamydial persistence. Chlamydial persistence alters inclusion morphology but varies depending on the stimulus/stress. We observed larger, but fewer, Chlamydia during co-infection. Tryptophan depletion can induce Chlamydial persistence, but tryptophan supplementation did not reverse the co-infection phenotype. Only viable and actively growing N. gonorrhoeae produced the inhibition phenotype in C. trachomatis. Piliated N. gonorrhoeae had the strongest effect on C. trachomatis, but hyperpiliated or non-piliated N. gonorrhoeae still produced the phenotype. EB development was modestly impaired when N. gonorrhoeae were grown in transwells above the infected monolayer. C. trachomatis serovar L2 was not impaired during co-infection. Chlamydial impairment could be due to cytoskeletal or osmotic stress caused by an as-yet-undefined mechanism. We conclude that N. gonorrhoeae induces a persistence-like state in C. trachomatis that is serovar dependent.},
}

@article {pmid38013749,
year = {2023},
author = {Tran, TT and van Leeuwen, J and Tran, DTM and Bush, SR},
title = {Beyond compliance: public voluntary standards and their effect on state institutional capacity in Vietnam.},
journal = {Journal of environmental policy & planning},
volume = {25},
number = {5},
pages = {511-523},
pmid = {38013749},
issn = {1522-7200},
abstract = {Public certification standards have received limited scholarly attention, especially the institutional capacity of public authorities that develop and implement these standards to address complex challenges, such as the promotion of industrial ecology and industrial symbiosis for enhancing resource use efficiency. This research uses an institutional capacity assessment framework to examine the ways in which a voluntary public standard for certifying eco-industrial parks affected the Vietnamese state's capacity to coordinate and implement industrial ecology. The article draws upon the interviews and a review of official documentation to show that the benefits of public standards extend beyond compliance to the enhancement of state capacities to coordinate complex policy domains such as industrial ecology. The findings contribute to providing a basis to redesign standard-setting processes to move beyond end-user compliance and provide insights into how public actors can more effectively address 'systemic' sustainability challenges - from circular economy ambitions to the Sustainable Development Goals.},
}

@article {pmid38013635,
year = {2023},
author = {Ntui, VO and Tripathi, JN and Shah, T and Tripathi, L},
title = {Targeted knockout of early nodulin-like 3 (MusaENODL3) gene in banana reveals its function in resistance to Xanthomonas wilt disease.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.14248},
pmid = {38013635},
issn = {1467-7652},
support = {//CGIAR research program for roots, tubers, and banana/ ; USAID//The United States Agency for International Development (USAID)/ ; },
abstract = {Nodulins and nodulin-like proteins play an essential role in the symbiotic associations between legumes and Rhizobium bacteria. Their role extends beyond the leguminous species, as numerous nodulin-like proteins, including early nodulin-like proteins (ENODL), have been identified in various non-leguminous plants, implying their involvement in functions beyond nodulation, such as nutrient transport and growth modulation. Some ENODL proteins have been associated with plant defense against pathogens, as evident in banana infected with Xanthomonas campestris pv. musacearum (Xcm) causing banana Xanthomonas wilt (BXW) disease. Nonetheless, the specific role of ENODL in plant defense remains to be fully elucidated. The MusaENODL3 gene was found to be repressed in BXW-resistant banana progenitor 'Musa balbisiana' and 20-fold upregulated in BXW-susceptible cultivar 'Gonja Manjaya' upon early infection with Xcm. To further unravel the role of the ENODL gene in disease resistance, the CRISPR/Cas9 system was employed to disrupt the MusaENODL3 gene in 'Gonja Manjaya' precisely. Analysis of the enodl3 edited events confirmed the accurate manipulation of the MusaENODL3 gene. Disease resistance and gene expression analysis demonstrated that editing the MusaENODL3 gene resulted in resistance to BXW disease, with 50% of the edited plants remaining asymptomatic. The identification and manipulation of the MusaENODL3 gene highlight its potential as a critical player in plant-pathogen interactions, offering new opportunities for enhancing disease resistance in crops like banana, an important staple food crop and source of income for resource-poor farmers in the tropics. This study provides the first evidence of the direct role of the ENODL3 gene in developing disease-resistant plants.},
}

@article {pmid38013492,
year = {2023},
author = {Giovannetti, M and Binci, F and Navazio, L and Genre, A},
title = {Nonbinary fungal signals and calcium-mediated transduction in plant immunity and symbiosis.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19433},
pmid = {38013492},
issn = {1469-8137},
support = {PRID - BIRD180317//Dipartimento di Biologia, Università degli Studi di Padova/ ; PRID - BIRD214519//Dipartimento di Biologia, Università degli Studi di Padova/ ; //European Commission/ ; 2022NW97JX//Ministero dell'Università e della Ricerca/ ; //Università di Torino - Dipartimento di Scienze della Vita e Biologia dei Sistemi/ ; },
abstract = {Chitin oligomers (COs) are among the most common and active fungal elicitors of plant responses. Short-chain COs from symbiotic arbuscular mycorrhizal fungi activate accommodation responses in the host root, while long-chain COs from pathogenic fungi are acknowledged to trigger defence responses. The modulation of intracellular calcium concentration - a common second messenger in a wide variety of plant signal transduction processes - plays a central role in both signalling pathways with distinct signature features. Nevertheless, mounting evidence suggests that plant immunity and symbiosis signalling partially overlap at multiple levels. We here elaborate on recent findings on this topic, highlighting the nonbinary nature of chitin-based fungal signals, their perception and their interpretation through Ca[2+] -mediated intracellular signals. Based on this, we propose that plant perception of symbiotic and pathogenic fungi is less clear-cut than previously described and involves a more complex scenario in which partially overlapping and blurred signalling mechanisms act upstream of the unambiguous regulation of gene expression driving accommodation or defence responses.},
}

@article {pmid38011635,
year = {2023},
author = {Choueiry, F and Gold, A and Xu, R and Zhang, S and Zhu, J},
title = {Secondary-Electrospray Ionization Mass Spectrometry-Based Online Analyses of Mouse Volatilome Uncover Gut Microbiome-Dictated Metabolic Changes in the Host.},
journal = {Journal of the American Society for Mass Spectrometry},
volume = {},
number = {},
pages = {},
doi = {10.1021/jasms.3c00304},
pmid = {38011635},
issn = {1879-1123},
abstract = {The symbiotic relationship between the gut microbial population is capable of regulating numerous aspects of host physiology, including metabolism. Bacteria can modulate the metabolic processes of the host by feeding on nutritional components within the lumen and releasing bioactive components into circulation. Endogenous volatile organic compound (VOC) synthesis is dependent on the availability of precursors found in mammalian metabolism. Herein, we report that microbial-mediated metabolic influences can alter the host volatilome and the prominent volatile changes can be uncovered by a novel volatile analysis technique named secondary electrospray ionization mass spectrometry. Mice were subjected to an antibiotic cocktail to deplete the microbiome and then inoculated with either single strain bacteria or fecal matter transplantation (FMT) to replete the microbial population in the gut. VOC sampling was achieved by using an advanced secondary electrospray ionization (SESI) source that directly mounted onto a Thermo Q-Exactive high-resolution mass spectrometer (HRMS). A principal component analysis summarizing the volatile profiles of the mice revealed independent clustering of each strain of the FMT-inoculated groups, suggesting unique volatile profiles. The Mummichog algorithm uncovered phenylalanine metabolism as a significantly altered metabolic profile in the volatilome of the microbiome-repleted mice. Our results indicated that the systemic metabolic changes incurred by the host are translated to unique volatile profiles correlated to the diversity of the microbial population colonized within the host. It is thus possible to take advantage of SESI-HRMS-based platforms for noninvasive screening of VOCs to determine the contribution of various microbial colonization within human gut that may impact host health.},
}

@article {pmid38010368,
year = {2023},
author = {Yeo, XY and Chae, WR and Lee, HU and Bae, HG and Pettersson, S and Grandjean, J and Han, W and Jung, S},
title = {Nuanced contribution of gut microbiome in the early brain development of mice.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2283911},
doi = {10.1080/19490976.2023.2283911},
pmid = {38010368},
issn = {1949-0984},
abstract = {The complex symbiotic relationship between the mammalian body and gut microbiome plays a critical role in the health outcomes of offspring later in life. The gut microbiome modulates virtually all physiological functions through direct or indirect interactions to maintain physiological homeostasis. Previous studies indicate a link between maternal/early-life gut microbiome, brain development, and behavioral outcomes relating to social cognition. Here we present direct evidence of the role of the gut microbiome in brain development. Through magnetic resonance imaging (MRI), we investigated the impact of the gut microbiome on brain organization and structure using germ-free (GF) mice and conventionalized mice, with the gut microbiome reintroduced after weaning. We found broad changes in brain volume in GF mice that persist despite the reintroduction of gut microbes at weaning. These data suggest a direct link between the maternal gut or early-postnatal microbe and their impact on brain developmental programming.},
}

@article {pmid38009998,
year = {2023},
author = {Naka, H and Haygood, MG},
title = {The dual role of TonB genes in turnerbactin uptake and carbohydrate utilization in the shipworm symbiont Teredinibacter turnerae.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0074423},
doi = {10.1128/aem.00744-23},
pmid = {38009998},
issn = {1098-5336},
abstract = {This study highlights diversity in iron acquisition and regulation in bacteria. The mechanisms of iron acquisition and its regulation in Teredinibacter turnerae, as well as its connection to cellulose utilization, a hallmark phenotype of T. turnerae, expand the paradigm of bacterial iron acquisition. Two of the four TonB genes identified in T. turnerae exhibit functional redundancy and play a crucial role in siderophore-mediated iron transport. Unlike typical TonB genes in bacteria, none of the TonB genes in T. turnerae are clearly iron regulated. This unusual regulation could be explained by another important finding in this study, namely, that the two TonB genes involved in iron transport are also essential for cellulose utilization as a carbon source, leading to the expression of TonB genes even under iron-rich conditions.},
}

@article {pmid38009979,
year = {2023},
author = {Roda, C and Clúa, J and Eylenstein, A and Greco, M and Ariel, F and Zanetti, ME and Blanco, FA},
title = {The C subunit of the nuclear factor Y binds to the Cyclin P4;1 promoter to modulate nodule organogenesis and infection during symbiosis in Phaseolus vulgaris.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19419},
pmid = {38009979},
issn = {1469-8137},
support = {PICT 2019/00029;//Agencia Nacional de Promoción Científica y Tecnológica/ ; PICT2020-00053//Agencia Nacional de Promoción Científica y Tecnológica/ ; },
}

@article {pmid38009302,
year = {2023},
author = {Ferrer-Orgaz, S and Tiwari, M and Isidra-Arellano, MC and Pozas-Rodriguez, EA and Vernié, T and Rich, MK and Mbengue, M and Formey, D and Delaux, PM and Ané, JM and Valdés-López, O},
title = {Early Phosphorylated Protein 1 is required to activate the early rhizobial infection program.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19423},
pmid = {38009302},
issn = {1469-8137},
support = {OPP1172165//Bill and Melinda Gates Foundation/ ; DE-SC0018247//DOE/ ; 101001675//European Union's Horizon 2020/ ; ANR-10-LABX-41//Laboratoire d'Excellence TULIP/ ; 2010789//NSF-IOS/ ; IN201320//Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica/ ; },
}

@article {pmid38008224,
year = {2023},
author = {Ruangwicha, J and Chiersilp, B and Suyotha, W},
title = {Green biorefinery of shrimp shell waste for α-chitin and high-value co-products through successive fermentation by co-lactic acid bacteria and proteolytic fungus.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130106},
doi = {10.1016/j.biortech.2023.130106},
pmid = {38008224},
issn = {1873-2976},
abstract = {Green biorefinery process was conducted to extract α-chitin and high-value co-products from shrimp shell waste through microbial fermentation using mature coconut water (MCW) as a sole nutrient source. Symbiotic co-lactic acid fermentation (Co-LAF) by Lactobacillus plantarum and Streptococcus thermophilus produced higher levels of lactic acid (LA) and protease activity than their mono-cultures, which led to greater demineralization (DM) and deproteinization (DP) of shrimp shell powder (SSP). After optimizing Co-LAF through Response Surface Methodology and successive fermentation by an acid-active proteolytic fungus Rhizopus oligosporus, the highest DM of 94.0 ± 0.91 % and DP of 86.7 ± 0.1 % were achieved. Based on FT-IR, XRD, and SEM analysis, the bio-extracted chitin had similar structural characteristics to commercial α-chitin but with better quality. These strategies not only contribute to environmentally-friendly and cost-effective extraction of α-chitin (303 ± 18 mg/g-SSP), but also co-produce LA (57.18 ± 0.89 g/L), acid protease (4.33 ± 0.5 U/mL), bio-calcium (277 ± 12 mg-CaSO4/g-SSP), protein hydrolysate (268 ± 5 mg/g-SSP), and pigments (28.78 ± 1.56 µg/g-SSP).},
}

@article {pmid38008016,
year = {2023},
author = {Zhu, J and Miao, X and Li, X and Zhang, Y and Lou, Y and Chen, H and Liu, X},
title = {Granulomatous lobular mastitis co-existing with ductal carcinoma in situ: Report of three cases and review of the literature.},
journal = {Annals of diagnostic pathology},
volume = {68},
number = {},
pages = {152241},
doi = {10.1016/j.anndiagpath.2023.152241},
pmid = {38008016},
issn = {1532-8198},
abstract = {Granulomatous lobular mastitis (GLM) is a benign and infrequent chronic breast ailment. Although this lesion can be clinically and radiographically mistaken for early-onset breast cancer, it is a rare occurrence for the two to coexist. This report describes three such cases. In all three patients, the primary signs and symptoms were related to the formation of diffuse breast masses or abscesses. Breast ultrasound and MRI revealed glandular edema and dilated breast ducts. The biopsies of all lesions exhibited both granulomatous inflammation confined to the lobules of the breast, abundant interstitial inflammatory cell infiltrates, and apparently cancerous cells located in dilated ducts with intact basement membranes. The surgically excised specimens confirmed the diagnosis of GLM and ductal carcinoma in situ (DCIS) in all three patients who underwent breast mass resection. By clinical imaging and clinical manifestations, GLM may obscure a concurrent DCIS, as highlighted by the cases reported herein.},
}

@article {pmid38007735,
year = {2023},
author = {Guo, Y and Liang, L and Liang, W},
title = {Exploring of Diverse Plant Communities and Adaptation to Drought Conditions Based on Advanced Logistics Model with Variable Growth.},
journal = {Studies in health technology and informatics},
volume = {308},
number = {},
pages = {137-145},
doi = {10.3233/SHTI230834},
pmid = {38007735},
issn = {1879-8365},
abstract = {Bio reciprocal symbiosis is very common in nature, such as soybeans providing food for rhizobia, which uses atmospheric nitrogen to synthesize nitrogen to provide nutrients to soybeans. This paper proposes an advanced Logistic model that adjusts to changes in precipitation and an environmental capacity parameter that varies with the level of symbiosis. The aim is to precisely depict the symbiotic relationship between plants and the interplay among symbiosis, competition, and independent growth of each population in the plant community, as precipitation changes by adapting finite difference method and tertiary Hermit interpolation. The model in this paper offers a comprehensive understanding of how plant populations interact with one another, providing valuable insights into the dynamics of plant growth and development. This paper finally finds that a combination of woody and herbaceous plants had the highest growth rate and total biomass, while herbaceous-only plants required 7 times longer to reach environmental capacity. This paper also reveals that irregular weather patterns, and different levels of species biomass can have different impacts on the recovery time of plant communities after drought or damage, and different types of pollution can have various effects on the community's regeneration, while the effect of overgrazing is the smallest.},
}

@article {pmid38007500,
year = {2023},
author = {Matthews, JL and Hoch, L and Raina, JB and Pablo, M and Hughes, DJ and Camp, EF and Seymour, JR and Ralph, PJ and Suggett, DJ and Herdean, A},
title = {Symbiodiniaceae photophysiology and stress resilience is enhanced by microbial associations.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20724},
pmid = {38007500},
issn = {2045-2322},
mesh = {Animals ; *Anthozoa/physiology ; Photosynthesis ; Temperature ; Bacteria ; Photosystem II Protein Complex ; *Dinoflagellida/physiology ; Symbiosis ; },
abstract = {Symbiodiniaceae form associations with extra- and intracellular bacterial symbionts, both in culture and in symbiosis with corals. Bacterial associates can regulate Symbiodiniaceae fitness in terms of growth, calcification and photophysiology. However, the influence of these bacteria on interactive stressors, such as temperature and light, which are known to influence Symbiodiniaceae physiology, remains unclear. Here, we examined the photophysiological response of two Symbiodiniaceae species (Symbiodinium microadriaticum and Breviolum minutum) cultured under acute temperature and light stress with specific bacterial partners from their microbiome (Labrenzia (Roseibium) alexandrii, Marinobacter adhaerens or Muricauda aquimarina). Overall, bacterial presence positively impacted Symbiodiniaceae core photosynthetic health (photosystem II [PSII] quantum yield) and photoprotective capacity (non-photochemical quenching; NPQ) compared to cultures with all extracellular bacteria removed, although specific benefits were variable across Symbiodiniaceae genera and growth phase. Symbiodiniaceae co-cultured with M. aquimarina displayed an inverse NPQ response under high temperatures and light, and those with L. alexandrii demonstrated a lowered threshold for induction of NPQ, potentially through the provision of antioxidant compounds such as zeaxanthin (produced by Muricauda spp.) and dimethylsulfoniopropionate (DMSP; produced by this strain of L. alexandrii). Our co-culture approach empirically demonstrates the benefits bacteria can deliver to Symbiodiniaceae photochemical performance, providing evidence that bacterial associates can play important functional roles for Symbiodiniaceae.},
}

Animals
*Anthozoa/physiology
Photosynthesis
Temperature
Bacteria
Photosystem II Protein Complex
*Dinoflagellida/physiology
Symbiosis

@article {pmid38007126,
year = {2023},
author = {Förster, F and Reynaud, S and Sauzéat, L and Ferrier-Pagès, C and Samankassou, E and Sheldrake, TE},
title = {Increased coral biomineralization due to enhanced symbiotic activity upon volcanic ash exposure.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168694},
doi = {10.1016/j.scitotenv.2023.168694},
pmid = {38007126},
issn = {1879-1026},
abstract = {Coral reefs, which are among the most productive ecosystems on earth, are in global decline due to rapid climate change. Volcanic activity also results in extreme environmental changes at local to global scales, and may have significant impacts on coral reefs compared to other natural disturbances. During explosive eruptions, large amounts of volcanic ash are generated, significantly disrupting ecosystems close to a volcano, and depositing ash over distal areas (10s - 1000s of km depending on i.a. eruption size and wind direction). Once volcanic ash interacts with seawater, the dissolution of metals leads to a rapid change in the geochemical properties of the seawater column. Here, we report the first known effects of volcanic ash on the physiology and elemental cycling of a symbiotic scleractinian coral under laboratory conditions. Nubbins of the branching coral Stylophora pistillata were reared in aquaria under controlled conditions (insolation, temperature, and pH), while environmental parameters, effective quantum yield, and skeletal growth rate were monitored. Half the aquaria were exposed to volcanic ash every other day for 6 weeks (250 mg L[-1] week[-1]), which induced significant changes in the fluorescence-derived photochemical parameters (ΦPSII, Fv/Fm, NPQ, rETR), directly enhanced the efficiency of symbiont photosynthesis (Pg, Pn), and lead to increased biomineralization rates. Enhancement of symbiont photosynthesis is induced by the supply of essential metals (Fe and Mn), derived from volcanic ash leaching in ambient seawater or within the organism following ingestion. The beneficial role of volcanic ash as an important micronutrient source is supported by the fact that neither photophysiological stress nor signs of lipid peroxidation were detected. Subaerial volcanism affects micronutrient cycling in the coral ecosystem, but the implication for coral ecophysiology on a reef scale remains to be tested. Nevertheless, exposure to volcanic ash can improve coral health and thus influence resilience to external stressors.},
}

@article {pmid38006561,
year = {2024},
author = {Bordenstein, SR},
title = {Isolation of Phage WO Particles from Wolbachia-Infected Arthropods.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {337-348},
pmid = {38006561},
issn = {1940-6029},
mesh = {Animals ; *Arthropods ; *Wolbachia/genetics ; *Bacteriophages/genetics ; Prophages ; Myoviridae ; },
abstract = {Nearly all arthropod-associated Wolbachia contain intact and/or genomic remnants of phage WO, temperate bacteriophages that facilitate horizontal gene transfer, genomic rearrangement of the bacterial chromosome, and symbiotic interactions between Wolbachia and their arthropod hosts. Integrated prophage WO genomes produce active, lytic particles; but the lack of a cell-free culturing system for Wolbachia render them difficult to purify and study. This chapter describes polyethylene glycol (PEG) precipitation of phage particles from Wolbachia-infected arthropods, followed by confirmation of phage WO isolation and purification using electron microscopy and PCR.},
}

Animals
*Arthropods
*Wolbachia/genetics
*Bacteriophages/genetics
Prophages
Myoviridae

@article {pmid38006559,
year = {2024},
author = {Cortez, CT and Murphy, RO and Owens, IM and Beckmann, JF},
title = {Use of Drosophila Transgenics to Identify Functions for Symbiont Effectors.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {301-320},
doi = {10.1007/978-1-0716-3553-7_18},
pmid = {38006559},
issn = {1940-6029},
abstract = {Wolbachia, one of the most successful and studied insect symbionts, and Drosophila, one of the most understood model insects, can be exploited as complementary tools to unravel mechanisms of insect symbiosis. Although Wolbachia itself cannot be grown axenically as clonal isolates or genetically manipulated by standard methods, its reproductive phenotypes, including cytoplasmic incompatibility (CI), have been elucidated using well-developed molecular tools and precise transgenic manipulations available for Drosophila melanogaster. Current research only scratches the surface of how Drosophila can provide a tool for understanding Wolbachia's evolutionary success and the molecular roles of its genetic elements. Here, we briefly outline basic methodologies inherent to transgenic Drosophila systems that have already contributed significant advances in understanding CI, but may be unfamiliar to those who lack experience in Drosophila genetics. In the future, these approaches will continue providing significant insights into Wolbachia that undoubtedly will be extended to other insect symbionts and their biological capabilities.},
}

@article {pmid38006556,
year = {2024},
author = {Duplouy, A},
title = {Validating a Mitochondrial Sweep Accompanying the Rapid Spread of a Maternally Inherited Symbiont.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {239-247},
pmid = {38006556},
issn = {1940-6029},
abstract = {Maternally inherited symbiotic bacteria that interfere with the reproduction of their hosts can contribute to selective sweeps of mitochondrial haplotypes through hitch-hiking or coordinate inheritance of cytoplasmic bacteria and host mitochondria. The sweep will be manifested by genetic variations of mitochondrial genomic DNA of symbiont-infected hosts relative to their uninfected counterparts. In particular, at the population level, infected specimens will show a reduced mitochondrial DNA polymorphism compared to that in the nuclear DNA. This may challenge the use of mitochondrial DNA sequences as neutral genetic markers, as the mitochondrial patterns will reflect the evolutionary history of parasitism, rather than the sole evolutionary history of the host. Here, I describe a detailed step-by-step procedure to infer the occurrence and timing of symbiont-induced mitochondrial sweeps in host species.},
}

@article {pmid38006552,
year = {2024},
author = {Zhang, M and Xi, Z},
title = {Wolbachia Transinfection Via Embryonic Microinjection.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {175-188},
pmid = {38006552},
issn = {1940-6029},
abstract = {The process of transferring Wolbachia from one species to another to establish a stable, maternally inherited infection in the target species is known as transinfection. The success of transinfection is primarily achieved through embryonic microinjection, which is the most direct and efficient means of delivering Wolbachia into the germline of the target species and establishing stable maternal transmission. For the fundamental studies, transinfection is often used to characterize Wolbachia-host interactions, including Wolbachia host range, the role of host or bacterial factors in symbiosis, and evolution of Wolbachia-host associations. For the applied studies, use of transinfection to generate a novel infection in the target species is the first step to build the weapon for both population replacement and population suppression for controlling insect pests or their transmitted diseases. For the primary dengue vector Aedes aegypti and Anopheles vectors of malaria, which either do not naturally carry Wolbachia or are infected with strains that lack necessary features for implementation, transinfection can be established by introducing a novel strain capable of inducing both cytoplasmic incompatibility (CI) and pathogen blocking. For A. albopictus and Culex mosquito species, which naturally harbor CI-inducing Wolbachia, transinfection can be achieved by either introducing a novel strain to generate superinfection or replacing the native infection with a different Wolbachia strain in a symbiont-free line, which is derived from antibiotic treatment of the wild type. Here, we use A. aegypti as an example to describe the Wolbachia transinfection method, which can be adapted to other insect species, such as planthoppers, according to their specific developmental requirements.},
}

@article {pmid38006547,
year = {2024},
author = {Kakumanu, ML and Hickin, ML and Schal, C},
title = {Detection, Quantification, and Elimination of Wolbachia in Bed Bugs.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {97-114},
pmid = {38006547},
issn = {1940-6029},
abstract = {Wolbachia is an obligatory nutritional symbiont of the common bed bug, Cimex lectularius, providing B-vitamins to its host. The biological significance of Wolbachia to bed bugs is investigated primarily by eliminating the symbiont with antibiotics, which is followed by confirmation with molecular assays. In this chapter, we describe a protocol for eliminating Wolbachia in bed bugs using the ansamycin antibiotic rifampicin (also known as rifampin) and three molecular methods to accurately detect and quantify the Wolbachia gene copies in bed bug samples. We describe the digital droplet PCR (ddPCR), a highly sensitive technique for absolute quantification of low abundance target genes, which has proven to be a valuable technique for confirmation of the elimination of Wolbachia.},
}

@article {pmid38006542,
year = {2024},
author = {Fallon, AM},
title = {Wolbachia: Advancing into a Second Century.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {1-13},
pmid = {38006542},
issn = {1940-6029},
abstract = {Wolbachia pipientis had its scientific debut nearly a century ago and has recently emerged as a target for therapeutic treatment of filarial infections and an attractive tool for control of arthropod pests. Wolbachia was known as a biological entity before DNA was recognized as the molecule that carries the genetic information on which life depends, and before arthropods and nematodes were grouped in the Ecdysozoa. Today, some investigators consider Wolbachia the most abundant endosymbiont on earth, given the numbers of its hosts and its diverse mutualistic, commensal, and parasitic roles in their life histories. Recent advances in molecular technologies have revolutionized our understanding of Wolbachia and its associated reproductive phenotypes. New models have emerged for its investigation, and substantial progress has been made towards Wolbachia-based interventions in medicine and agriculture. Here I introduce Wolbachia, with a focus on aspects of its biology that are covered in greater detail in subsequent chapters.},
}

@article {pmid38006236,
year = {2023},
author = {Watanabe, D},
title = {Sake yeast symbiosis with lactic acid bacteria and alcoholic fermentation.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbad167},
pmid = {38006236},
issn = {1347-6947},
abstract = {The yeast Saccharomyces cerevisiae plays a pivotal role in the production of fermented foods by converting sugars in ingredients into ethanol through alcoholic fermentation. However, how accurate is our understanding of its biological significance? Although yeast is essential to produce alcoholic beverages and bioethanol, yeast does not yield ethanol for humankind. Yeast obtains energy in the form of ATP for its own vital processes through alcoholic fermentation, which generates ethanol as a byproduct. The production of ethanol may have more significance for yeast, since many other organisms do not produce ethanol, a highly toxic substance, to obtain energy. The key to address this issue has not been found using conventional microbiology, where yeasts are isolated and cultured in pure form. This review focuses on a possible novel role of yeast alcohol fermentation, which is revealed through our recent studies of microbial interactions.},
}

@article {pmid38006200,
year = {2023},
author = {Houldcroft, CJ and Underdown, S},
title = {Infectious disease in the Pleistocene: Old friends or old foes?.},
journal = {American journal of biological anthropology},
volume = {182},
number = {4},
pages = {513-531},
doi = {10.1002/ajpa.24737},
pmid = {38006200},
issn = {2692-7691},
support = {//Oxford Brookes University/ ; },
abstract = {The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.},
}

@article {pmid38005785,
year = {2023},
author = {Amoako, FK and Sulieman, S and Mühling, KH},
title = {Mineral and Carbon Metabolic Adjustments in Nodules of Symbiotically Grown Faba Bean (Vicia faba L.) Varieties in Response to Organic Phosphorus Supplementation.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {22},
pages = {},
pmid = {38005785},
issn = {2223-7747},
abstract = {Phosphorus (P) is a major limiting factor for legume and symbiotic nitrogen fixation (SNF). Although overall adaptations of legumes to P supplementation have been extensively studied in connection with inorganic P, little information is currently available regarding nodulation or SNF responses to organic P (Po) in hydroponics. We investigated the mineral and carbon metabolism of Po-induced nodules of two contrasting faba bean varieties grown hydroponically under inorganic P (Pi), viz., in P-deficient (2 µM KH2PO4, -Pi), sufficient-P (200 µM KH2PO4, +Pi), and phytic acid (200 µM, Po) conditions, and were inoculated with Rhizobium leguminosarum bv. viciae 3841 and grown for 30 days. The results consistently reveal similar growth and biomass partitioning patterns between +Pi and Po, with both varying substantially from -Pi. In comparison, +Pi and Po observed equivalent accumulations of overall elemental P concentrations, with both increasing by 114 and 119%, respectively, relative to -Pi. A principal component analysis on metabolites showed a clear separation of the -Pi treatment from the others, with +Pi and Po correlating closely together, highlighting the nonsignificant differences between them. Additionally, the δ[15]N abundance of shoots, roots, and nodules was not significantly different between treatments and varieties and exhibited negative δ[15]N signatures for all tissues. Our study provides a novel perspective on mineral and carbon metabolism and their regulation of the growth, functioning, and reprogramming of nodules upon phytate supply.},
}

@article {pmid38004797,
year = {2023},
author = {Ngwenya, ZD and Dakora, FD},
title = {Symbiotic Functioning and Photosynthetic Rates Induced by Rhizobia Associated with Jack Bean (Canavalia ensiformis L.) Nodulation in Eswatini.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004797},
issn = {2076-2607},
abstract = {Improving the efficiency of the legume-rhizobia symbiosis in African soils for increased grain yield would require the use of highly effective strains capable of nodulating a wide range of legume plants. This study assessed the photosynthetic functioning, N2 fixation, relative symbiotic effectiveness (%RSE) and C assimilation of 22 jack bean (Canavalia ensiformis L.) microsymbionts in Eswatini soils as a first step to identifying superior isolates for inoculant production. The results showed variable nodule number, nodule dry matter, shoot biomass and photosynthetic rates among the strains tested under glasshouse conditions. Both symbiotic parameters and C accumulation differed among the test isolates at the shoot, root and whole-plant levels. Although 7 of the 22 jack bean isolates showed much greater relative symbiotic efficiency than the commercial Bradyrhizobium strain XS21, only one isolate (TUTCEeS2) was statistically superior to the inoculant strain, which indicates its potential for use in inoculant formulation after field testing. Furthermore, the isolates that recorded high %RSE elicited greater amounts of fixed N.},
}

@article {pmid38004772,
year = {2023},
author = {Zhang, P and Meng, S and Bao, G and Li, Y and Feng, X and Lu, H and Ma, J and Wei, X and Liu, W},
title = {Effect of Epichloë Endophyte on the Growth and Carbon Allocation of Its Host Plant Stipa purpurea under Hemiparasitic Root Stress.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004772},
issn = {2076-2607},
support = {2022-ZJ-715//the basic research program of science and technology of Qinghai Province, China/ ; 32060398 and U21A20239//The Natural Science Foundation of China/ ; },
abstract = {Epichloë endophytes not only affect the growth and resistance of their host plants but also confer nutrient benefits to parasitized hosts. In this study, we used Pedicularis kansuensis to parasitize Stipa purpurea, both with and without endophytic fungi, and to establish a parasitic system. In this study, endophytic fungal infection was found to increase the dry weight of the leaf, stem, and leaf sheath, as well as the plant height, root length, tiller number, aboveground biomass, and underground biomass of S. purpurea under root hemiparasitic stress. Meanwhile, the [13]C allocation of the leaf sheaths and roots of S. purpurea increased as the density of P. kansuensis increased, while the [13]C allocation of the leaf sheaths and roots of E+ S. purpurea was lower than that of E- S. purpurea. The [13]C allocation of the stem, leaf sheath, and root of E+ S. purpurea was higher than that of its E- counterpart. Furthermore, the content of photosynthetic [13]C and the [13]C partition rate of the stems, leaves, roots, and entire plant of S. purpurea and P. kansuensis transferred from S. purpurea increased as the density of P. kansuensis increased. These results will generate new insights into the potential role of symbiotic microorganisms in regulating the interaction between root hemiparasites and their hosts.},
}

@article {pmid38004718,
year = {2023},
author = {Kampen, H and Werner, D},
title = {Biting Midges (Diptera: Ceratopogonidae) as Vectors of Viruses.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004718},
issn = {2076-2607},
abstract = {Biting midges of the genus Culicoides occur almost globally and can regionally and seasonally reach high abundances. Most species are hematophagous, feeding on all groups of vertebrates, including humans. In addition to being nuisance pests, they are able to transmit disease agents, with some viruses causing high morbidity and/or mortality in ruminants, horses and humans. Despite their impact on animal husbandry, public health and tourism, knowledge on the biology and ecology of culicoid biting midges and their interactions with ingested pathogens or symbiotic microorganisms is limited. Research is challenging due to unknown larval habitats, the insects' tiny size, the inability to establish and breed most species in the laboratory and the laborious maintenance of colonies of the few species that can be reared in the laboratory. Consequently, the natural transmission of pathogens has experimentally been demonstrated for few species while, for others, only indirect evidence of vector potential exists. Most experimental data are available for Culicoides sonorensis and C. nubeculosus, the only species kept in western-world insectaries. This contribution gives an overview on important biting midge vectors, transmitted viruses, culicoid-borne viral diseases and their epidemiologies and summarizes the little knowledge on interactions between biting midges, their microflora and culicoid-borne arboviruses.},
}

@article {pmid38004678,
year = {2023},
author = {Mondal, S and Somani, J and Roy, S and Babu, A and Pandey, AK},
title = {Insect Microbial Symbionts: Ecology, Interactions, and Biological Significance.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/microorganisms11112665},
pmid = {38004678},
issn = {2076-2607},
support = {BT/PR45283/NER/95/1919/2022//Department of Biotechnology/ ; },
abstract = {The guts of insect pests are typical habitats for microbial colonization and the presence of bacterial species inside the gut confers several potential advantages to the insects. These gut bacteria are located symbiotically inside the digestive tracts of insects and help in food digestion, phytotoxin breakdown, and pesticide detoxification. Different shapes and chemical assets of insect gastrointestinal tracts have a significant impact on the structure and makeup of the microbial population. The number of microbial communities inside the gastrointestinal system differs owing to the varying shape and chemical composition of digestive tracts. Due to their short generation times and rapid evolutionary rates, insect gut bacteria can develop numerous metabolic pathways and can adapt to diverse ecological niches. In addition, despite hindering insecticide management programs, they still have several biotechnological uses, including industrial, clinical, and environmental uses. This review discusses the prevalent bacterial species associated with insect guts, their mode of symbiotic interaction, their role in insecticide resistance, and various other biological significance, along with knowledge gaps and future perspectives. The practical consequences of the gut microbiome and its interaction with the insect host may lead to encountering the mechanisms behind the evolution of pesticide resistance in insects.},
}

@article {pmid38004180,
year = {2023},
author = {Zhou, J and Ho, V},
title = {Role of Baseline Gut Microbiota on Response to Fiber Intervention in Individuals with Irritable Bowel Syndrome.},
journal = {Nutrients},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/nu15224786},
pmid = {38004180},
issn = {2072-6643},
support = {Investigator Initiated Funding Scheme//Nestlé Foundation/ ; },
abstract = {Irritable bowel syndrome (IBS) is one of the most prevalent functional gut disorders in the world. Partially hydrolyzed guar gum, a low-viscosity soluble fiber, has shown promise in the management of IBS-related symptoms. In this study, we aimed to determine if an individual's baseline gut microbiota impacted their response to a partially hydrolyzed guar gum intervention. Patients diagnosed with IBS undertook a 90-day intervention and follow-up. IBS symptom severity, tolerability, quality-of-life, and fecal microbiome composition were recorded during this study. Patients with normal microbiota diversity (Shannon index ≥ 3) showed significant improvements to IBS symptom scores, quality-of-life, and better tolerated the intervention compared to patients with low microbiota diversity (Shannon index < 3). Our findings suggest that an individual's baseline microbiome composition exerts a substantial influence on their response to fiber intervention. Future investigations should explore a symbiotic approach to the treatment of IBS.},
}

@article {pmid38003711,
year = {2023},
author = {Zhu, Z and Yu, T and Li, F and Zhang, Y and Liu, C and Chen, Q and Xin, D},
title = {NopC/T/L Signal Crosstalk Gene GmPHT1-4.},
journal = {International journal of molecular sciences},
volume = {24},
number = {22},
pages = {},
doi = {10.3390/ijms242216521},
pmid = {38003711},
issn = {1422-0067},
support = {National Natural Science Foundation of China//National Natural Science Foundation of China/ ; High oil and yield germplasm development and breeding utilization//High oil and yield germplasm development and breeding utilization/ ; National Key Research and Development Program of China//National Key Research and Development Program of China/ ; },
abstract = {Symbiotic nodulation between leguminous plants and rhizobia is a critical biological interaction. The type III secretion system (T3SS) employed by rhizobia manipulates the host's nodulation signaling, analogous to mechanisms used by certain bacterial pathogens for effector protein delivery into host cells. This investigation explores the interactive signaling among type III effectors HH103ΩNopC, HH103ΩNopT, and HH103ΩNopL from SinoRhizobium fredii HH103. Experimental results revealed that these effectors positively regulate nodule formation. Transcriptomic analysis pinpointed GmPHT1-4 as the key gene facilitating this effector-mediated signaling. Overexpression of GmPHT1-4 enhances nodulation, indicating a dual function in nodulation and phosphorus homeostasis. This research elucidates the intricate regulatory network governing Rhizobium-soybean (Glycine max (L.) Merr) interactions and the complex interplay between type III effectors.},
}

@article {pmid38003367,
year = {2023},
author = {Zhang, D and Wu, Q and Zhao, Y and Yan, Z and Xiao, A and Yu, H and Cao, Y},
title = {Dual RNA-Seq Analysis Pinpoints a Balanced Regulation between Symbiosis and Immunity in Medicago truncatula-Sinorhizobium meliloti Symbiotic Nodules.},
journal = {International journal of molecular sciences},
volume = {24},
number = {22},
pages = {},
doi = {10.3390/ijms242216178},
pmid = {38003367},
issn = {1422-0067},
support = {32090063//National Natural Science Foundation of China/ ; 32000191//National Natural Science Foundation of China/ ; AML2023B01//self-inovation project from the national laboratory/ ; },
abstract = {Legume-rhizobial symbiosis initiates the formation of root nodules, within which rhizobia reside and differentiate into bacteroids to convert nitrogen into ammonium, facilitating plant growth. This process raises a fundamental question: how is plant immunity modulated within nodules when exposed to a substantial number of foreign bacteria? In Medicago truncatula, a mutation in the NAD1 (Nodules with Activated Defense 1) gene exclusively results in the formation of necrotic nodules combined with activated immunity, underscoring the critical role of NAD1 in suppressing immunity within nodules. In this study, we employed a dual RNA-seq transcriptomic technology to comprehensively analyze gene expression from both hosts and symbionts in the nad1-1 mutant nodules at different developmental stages (6 dpi and 10 dpi). We identified 89 differentially expressed genes (DEGs) related to symbiotic nitrogen fixation and 89 DEGs from M. truncatula associated with immunity in the nad1-1 nodules. Concurrently, we identified 27 rhizobial DEGs in the fix and nif genes of Sinorhizobium meliloti. Furthermore, we identified 56 DEGs from S. meliloti that are related to stress responses to ROS and NO. Our analyses of nitrogen fixation-defective plant nad1-1 mutants with overactivated defenses suggest that the host employs plant immunity to regulate the substantial bacterial colonization in nodules. These findings shed light on the role of NAD1 in inhibiting the plant's immune response to maintain numerous rhizobial endosymbiosis in nodules.},
}

@article {pmid38003319,
year = {2023},
author = {Svietlova, N and Reichelt, M and Zhyr, L and Majumder, A and Scholz, SS and Grabe, V and Krapp, A and Oelmüller, R and Mithöfer, A},
title = {The Beneficial Fungus Mortierella hyalina Modulates Amino Acid Homeostasis in Arabidopsis under Nitrogen Starvation.},
journal = {International journal of molecular sciences},
volume = {24},
number = {22},
pages = {},
doi = {10.3390/ijms242216128},
pmid = {38003319},
issn = {1422-0067},
support = {A139316//Volkswagen Foundation/ ; },
abstract = {Non-mycorrhizal but beneficial fungi often mitigate (a)biotic stress-related traits in host plants. The underlying molecular mechanisms are mostly still unknown, as in the interaction between the endophytic growth-promoting soil fungus Mortierella hyalina and Arabidopsis thaliana. Here, abiotic stress in the form of nitrogen (N) deficiency was used to investigate the effects of the fungus on colonized plants. In particular, the hypothesis was investigated that fungal infection could influence N deficiency via an interaction with the high-affinity nitrate transporter NRT2.4, which is induced by N deficiency. For this purpose, Arabidopsis wild-type nrt2.4 knock-out and NRT2.4 reporter lines were grown on media with different nitrate concentrations with or without M. hyalina colonization. We used chemical analysis methods to determine the amino acids and phytohormones. Experimental evidence suggests that the fungus does not modulate NRT2.4 expression under N starvation. Instead, M. hyalina alleviates N starvation in other ways: The fungus supplies nitrogen ([15]N) to the N-starved plant. The presence of the fungus restores the plants' amino acid homeostasis, which was out of balance due to N deficiency, and causes a strong accumulation of branched-chain amino acids. We conclude that the plant does not need to invest in defense and resources for growth are maintained, which in turn benefits the fungus, suggesting that this interaction should be considered a mutualistic symbiosis.},
}

@article {pmid38003254,
year = {2023},
author = {Kaya, C and Uğurlar, F and Adamakis, IS},
title = {Epigenetic and Hormonal Modulation in Plant-Plant Growth-Promoting Microorganism Symbiosis for Drought-Resilient Agriculture.},
journal = {International journal of molecular sciences},
volume = {24},
number = {22},
pages = {},
doi = {10.3390/ijms242216064},
pmid = {38003254},
issn = {1422-0067},
abstract = {Plant growth-promoting microorganisms (PGPMs) have emerged as valuable allies for enhancing plant growth, health, and productivity across diverse environmental conditions. However, the complex molecular mechanisms governing plant-PGPM symbiosis under the climatic hazard of drought, which is critically challenging global food security, remain largely unknown. This comprehensive review explores the involved molecular interactions that underpin plant-PGPM partnerships during drought stress, thereby offering insights into hormonal regulation and epigenetic modulation. This review explores the challenges and prospects associated with optimizing and deploying PGPMs to promote sustainable agriculture in the face of drought stress. In summary, it offers strategic recommendations to propel research efforts and facilitate the practical implementation of PGPMs, thereby enhancing their efficacy in mitigating drought-detrimental effects in agricultural soils.},
}

@article {pmid38002796,
year = {2023},
author = {Wong, PY and Yip, C and Lemberg, DA and Day, AS and Leach, ST},
title = {Evolution of a Pathogenic Microbiome.},
journal = {Journal of clinical medicine},
volume = {12},
number = {22},
pages = {},
doi = {10.3390/jcm12227184},
pmid = {38002796},
issn = {2077-0383},
abstract = {The process of microbiome development arguably begins before birth. Vertical transmission of bacteria from the mother to the infant is a keystone event in microbiome development. Subsequent to birth, the developing microbiome is vulnerable to influence from a wide range of factors. Additionally, the microbiome can influence the health and development of the host infant. This intricate interaction of the gastrointestinal microbiome and the host has been described as both symbiotic and dysbiotic. Defining these terms, a symbiotic microbiome is where the microbiome and host provide mutual benefit to each other. A pathogenic microbiome, or more precisely a gastrointestinal microbiome associated with disease, is increasing described as dysbiotic. This review seeks to investigate the factors that contribute to evolving a disease-causing or 'dysbiotic' microbiome. This review covers the development of the gastrointestinal microbiome in infants, the interaction of the microbiome with the host, and its contribution to host immunity and investigates specific features of the gastrointestinal microbiome that are associated with disease.},
}

@article {pmid38002331,
year = {2023},
author = {Chen, H and Li, Y and Yin, Y and Li, J and Li, L and Wu, K and Fang, L and Zeng, S},
title = {Gibberellic Acid Inhibits Dendrobium nobile-Piriformospora Symbiosis by Regulating the Expression of Cell Wall Metabolism Genes.},
journal = {Biomolecules},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/biom13111649},
pmid = {38002331},
issn = {2218-273X},
support = {2022B1111040003//the Guangdong Research and Development Program of Key Areas/ ; E11510BH01//the China Postdoctoral Science Foundation/ ; 2022KJ121//the Guangdong Modern Agricultural Industry Technology System Program/ ; },
abstract = {Orchid seeds lack endosperms and depend on mycorrhizal fungi for germination and nutrition acquisition under natural conditions. Piriformospora indica is a mycorrhizal fungus that promotes seed germination and seedling development in epiphytic orchids, such as Dendrobium nobile. To understand the impact of P. indica on D. nobile seed germination, we examined endogenous hormone levels by using liquid chromatography-mass spectrometry. We performed transcriptomic analysis of D. nobile protocorm at two developmental stages under asymbiotic germination (AG) and symbiotic germination (SG) conditions. The result showed that the level of endogenous IAA in the SG protocorm treatments was significantly higher than that in the AG protocorm treatments. Meanwhile, GA3 was only detected in the SG protocorm stages. IAA and GA synthesis and signaling genes were upregulated in the SG protocorm stages. Exogenous GA3 application inhibited fungal colonization inside the protocorm, and a GA biosynthesis inhibitor (PAC) promoted fungal colonization. Furthermore, we found that PAC prevented fungal hyphae collapse and degeneration in the protocorm, and differentially expressed genes related to cell wall metabolism were identified between the SG and AG protocorm stages. Exogenous GA3 upregulated SRC2 and LRX4 expression, leading to decreased fungal colonization. Meanwhile, GA inhibitors upregulated EXP6, EXB16, and EXP10-2 expression, leading to increased fungal colonization. Our findings suggest that GA regulates the expression of cell wall metabolism genes in D. nobile, thereby inhibiting the establishment of mycorrhizal symbiosis.},
}

@article {pmid38001333,
year = {2023},
author = {Güngör, B and Biró, JB and Domonkos, Á and Horváth, B and Kaló, P},
title = {Targeted mutagenesis of Medicago truncatula Nodule-specific Cysteine-Rich (NCR) genes using the Agrobacterium rhizogenes-mediated CRISPR/Cas9 system.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20676},
pmid = {38001333},
issn = {2045-2322},
support = {OTKA 119652//Hungarian National Research Fund/National Research, Development and Innovation Office/ ; 129547//Hungarian National Research Fund/National Research, Development and Innovation Office/ ; 132646//Hungarian National Research Fund/National Research, Development and Innovation Office/ ; HUN17-03//Collaborative Research Programme ICGEB/ ; },
abstract = {The host-produced nodule specific cysteine-rich (NCR) peptides control the terminal differentiation of endosymbiotic rhizobia in the nodules of IRLC legumes. Although the Medicago truncatula genome encodes about 700 NCR peptides, only few of them have been proven to be crucial for nitrogen-fixing symbiosis. In this study, we applied the CRISPR/Cas9 gene editing technology to generate knockout mutants of NCR genes for which no genetic or functional data were previously available. We have developed a workflow to analyse the mutation and the symbiotic phenotype of individual nodules formed on Agrobacterium rhizogenes-mediated transgenic hairy roots. The selected NCR genes were successfully edited by the CRISPR/Cas9 system and nodules formed on knockout hairy roots showed wild type phenotype indicating that peptides NCR068, NCR089, NCR128 and NCR161 are not essential for symbiosis between M. truncatula Jemalong and Sinorhizobium medicae WSM419. We regenerated stable mutants edited for the NCR068 from hairy roots obtained by A. rhizogenes-mediated transformation. The analysis of the symbiotic phenotype of stable ncr068 mutants showed that peptide NCR068 is not required for symbiosis with S. meliloti strains 2011 and FSM-MA either. Our study reports that gene editing can help to elicit the role of certain NCRs in symbiotic nitrogen fixation.},
}

@article {pmid38000723,
year = {2023},
author = {Mao, Q and Xie, Z and Pinzon-Nuñez, DA and Issaka, S and Liu, T and Zhang, L and Irshad, S},
title = {Leptolyngbya sp. XZMQ and Bacillus XZM co-inoculation reduced sunflower arsenic toxicity by regulating rhizosphere microbial structure and enzyme activity.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {123001},
doi = {10.1016/j.envpol.2023.123001},
pmid = {38000723},
issn = {1873-6424},
abstract = {Microorganisms are of great significance for arsenic (As) toxicity amelioration in plants as soil fertility is directly affected by microbes. In this study, we innovatively explored the effects of indigenous cyanobacteria (Leptolyngbya sp. XZMQ) and plant growth-promoting bacteria (PGPB) (Bacillus XZM) on the growth and As absorption of sunflower plants from As-contaminated soil. Results showed that single inoculation and co-inoculation stimulated the growth of sunflower plants (Helianthus annuus L.), enhanced enzyme activities, and reduced As contents. In comparison to the control group, single innoculation of microalgae and bacteria in the rhizosphere increased extracellular polymeric substances (EPS) by 21.99% and 14.36%, respectively, whereas co-inoculation increased them by 35%. Compared with the non-inoculated group, As concentration in the roots, stems and leaves of sunflower plants decreased by 38%, 70% and 41%, respectively, under co-inoculation conditions. Inoculation of Leptolyngbya sp. XZMQ significantly increased the abundance of nifH in soil, while co-inoculation of cyanobacteria and Bacillus XZM significantly increased the abundance of cbbL, indicating that the coupling of Leptolyngbya sp. XZMQ and Bacillus XZM could stimulate the activity of nitrogen-fixing and carbon-fixing microorganisms and increased soil fertility. Moreover, this co-inoculation increased the enzyme activities (catalase, sucrase, urease) in the rhizosphere soil of sunflower and reduced the toxic effect of As on plant. Among these, the activities of catalase, peroxidase, and superoxide dismutase decreased. Meanwhile, co-inoculation enables cyanobacteria and bacteria to attach and entangle in the root area of the plant and develop as symbiotic association, which reduced As toxicity. Co-inoculation increased the abundance of aioA, arrA, arsC, and arsM genes in soil, especially the abundance of microorganisms with aioA and arsM, which reduced the mobility and bioavailability of As in soil, hence, reduced the absorption of As by plants. This study provides a theoretical basis for soil microbial remediation in mining areas.},
}

@article {pmid38001306,
year = {2023},
author = {Li, Y and Wu, Y and Yang, Z and Shi, R and Zhang, L and Feng, Z and Wei, G and Chou, M},
title = {The Rpf107 gene, a homolog of LOR, is required for the symbiotic nodulation of Robinia pseudoacacia.},
journal = {Planta},
volume = {259},
number = {1},
pages = {6},
pmid = {38001306},
issn = {1432-2048},
support = {41977052//National Natural Science Foundation of China/ ; 2020ZDLNY07-09//Key Research & Development program of Shaanxi Province/ ; },
abstract = {Rpf107 is involved in the infection process of rhizobia and the maintenance of symbiotic nitrogen fixation in black locust root nodules. The LURP-one related (LOR) protein family plays a pivotal role in mediating plant defense responses against both biotic and abiotic stresses. However, our understanding of its function in the symbiotic interaction between legumes and rhizobia remains limited. Here, Rpf107, a homolog of LOR, was identified in Robinia pseudoacacia (black locust). The subcellular localization of Rpf107 was analyzed, and its function was investigated using RNA interference (RNAi) and overexpression techniques. The subcellular localization assay revealed that Rpf107 was mainly distributed in the plasma membrane and nucleus. Rpf107 silencing prevented rhizobial infection and hampered plant growth. The number of infected cells in the nitrogen fixation zone of the Rpf107-RNAi nodules was also noticeably lower than that in the control nodules. Notably, Rpf107 silencing resulted in bacteroid degradation and the premature aging of nodules. In contrast, the overexpression of Rpf107 delayed the senescence of nodules and prolonged the nitrogen-fixing ability of nodules. These results demonstrate that Rpf107 was involved in the infection of rhizobia and the maintenance of symbiotic nitrogen fixation in black locust root nodules. The findings reveal that a member of the LOR protein family plays a role in leguminous root nodule symbiosis, which is helpful to clarify the functions of plant LOR protein family and fully understand the molecular mechanisms underlying legume-rhizobium symbiosis.},
}

@article {pmid38001080,
year = {2023},
author = {Choi, W and Mangal, U and Park, JY and Kim, JY and Jun, T and Jung, JW and Choi, M and Jung, S and Lee, M and Na, JY and Ryu, DY and Kim, JM and Kwon, JS and Koh, WG and Lee, S and Hwang, PTJ and Lee, KJ and Jung, UW and Cha, JK and Choi, SH and Hong, J},
title = {Occlusive membranes for guided regeneration of inflamed tissue defects.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7687},
pmid = {38001080},
issn = {2041-1723},
support = {KRIT-CT-21-034//Ministry of National Defense, Republic of Korea | Defense Acquisition Program Administration (DAPA)/ ; NRF-2022K2A9A1A0609182711//National Research Foundation of Korea (NRF)/ ; HI22C1609//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; },
abstract = {Guided bone regeneration aided by the application of occlusive membranes is a promising therapy for diverse inflammatory periodontal diseases. Symbiosis, homeostasis between the host microbiome and cells, occurs in the oral environment under normal, but not pathologic, conditions. Here, we develop a symbiotically integrating occlusive membrane by mimicking the tooth enamel growth or multiple nucleation biomineralization processes. We perform human saliva and in vivo canine experiments to confirm that the symbiotically integrating occlusive membrane induces a symbiotic healing environment. Moreover, we show that the membrane exhibits tractability and enzymatic stability, maintaining the healing space during the entire guided bone regeneration therapy period. We apply the symbiotically integrating occlusive membrane to treat inflammatory-challenged cases in vivo, namely, the open and closed healing of canine premolars with severe periodontitis. We find that the membrane promotes symbiosis, prevents negative inflammatory responses, and improves cellular integration. Finally, we show that guided bone regeneration therapy with the symbiotically integrating occlusive membrane achieves fast healing of gingival soft tissue and alveolar bone.},
}

@article {pmid38001035,
year = {2023},
author = {Kamran, M and Melville, KT and Waters, MT},
title = {Karrikin signalling: impacts on plant development and abiotic stress tolerance.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erad476},
pmid = {38001035},
issn = {1460-2431},
abstract = {Plants rely upon a diverse range of metabolites to control growth and development, and to overcome stress that results from suboptimal conditions. Karrikins (KARs) are a class of butenolide compounds found in smoke that stimulate seed germination and regulate various developmental processes in plants. KARs are perceived via a plant α/β-hydrolase called KARRIKIN INSENSITIVE2 (KAI2), which also functions as a receptor for a postulated phytohormone, provisionally termed KAI2-ligand (KL). Considered natural analogues of KL, KARs have been extensively studied for their effects on plant growth and their crosstalk with plant hormones. The perception and response pathway for KAR-KL signalling is closely related to that of strigolactones, another class of butenolides with numerous functions in regulating plant growth. KAR-KL signalling influences seed germination, seedling photomorphogenesis, root system architecture, abiotic stress responses, and arbuscular mycorrhizal symbiosis. Here, we summarise the current knowledge of KAR-KL signalling, focussing on its role in plant development, its effects on stress tolerance, and its interaction with other signalling mechanisms.},
}

@article {pmid38000749,
year = {2023},
author = {Lewin, S and Wende, S and Wehrhan, M and Verch, G and Ganugi, P and Sommer, M and Kolb, S},
title = {Cereals rhizosphere microbiome undergoes host selection of nitrogen cycle guilds correlated to crop productivity.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168794},
doi = {10.1016/j.scitotenv.2023.168794},
pmid = {38000749},
issn = {1879-1026},
abstract = {Sustainable transformation of agricultural plant production requires the reduction of nitrogen (N) fertilizer application. Such a reduced N fertilizer application may impede crop production due to an altered symbiosis of crops and their rhizosphere microbiome, since reduced N input may affect the competition and synergisms with the plant. The assessment of such changes in the crop microbiome functionalities at spatial scales relevant for agricultural management remains challenging. We investigated in a field plot experiment how and if the N cycling guilds of the rhizosphere of globally relevant cereal crops - winter barley, wheat and rye - are influenced by reduced N fertilization. Crop productivity was assessed by remote sensing of the shoot biomass. Microbial N cycling guilds were investigated by metagenomics targeting diazotrophs, nitrifiers, denitrifiers and the dissimilatory nitrate to ammonium reducing guild (DNRA). The functional composition of microbial N cycling guilds was explained by crop productivity parameters and soil pH, and diverged substantially between the crop species. The responses of individual microbial N cycling guild abundances to shoot dry weight and rhizosphere nitrate content was modulated by the N fertilization treatments and the crop species, which was identified based on regression analyses. Thus, characteristic shifts in the microbial N cycling guild acquisition associated with the crop host species were resolved. Particularly, the rhizosphere of rye was enriched with potentially N-preserving microbial guilds - diazotrophs and the DNRA guild - when no fertilizer was applied. We speculate that the acquisition of microbial N cycling guilds was the result of plant species-specific acquisition strategies. Thus, the investigated cereal crop holobionts have likely different symbiotic strategies that make them differently resilient against reduced N fertilizer inputs. Furthermore, we demonstrated that these belowground patterns of N cycling guilds from the rhizosphere microbiome are linked to remotely sensed aboveground plant productivity.},
}

@article {pmid38000638,
year = {2023},
author = {Dai, C and Wang, F},
title = {Potential applications of microalgae-bacteria consortia in wastewater treatment and biorefinery.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130019},
doi = {10.1016/j.biortech.2023.130019},
pmid = {38000638},
issn = {1873-2976},
abstract = {The use of microalgae-bacteria consortia (MBC) for wastewater treatment has garnered attention as their interactions impart greater environmental adaptability and stability compared with that obtained by only microalgae or bacteria use, thereby improving the efficiency of pollutant removal and bio-product productivity. Additionally, the value-added bio-products produced via biorefineries can improve economic competitiveness and environmental sustainability. Therefore, this review focuses on the interaction between microalgae and bacteria that leads to nutrient exchange, gene transfer and signal transduction to comprehensively understand the interaction mechanisms underlying their strong adaptability. In addition, it includes recent research in which MBC has been efficiently used to treat various wastewater. Moreover, the review summarizes the use of MBC-produced biomass in a biorefining context to produce biofuel, biomaterial, high-value bio-products and bio-fertilizer. Overall, more effort is needed to identify the symbiotic mechanism in MBC to provide a foundation for circular bio-economy and environmentally friendly development programmes.},
}

@article {pmid38000489,
year = {2023},
author = {Jin, G and Kim, IH and Kim, Y},
title = {The Lrp transcriptional factor of an entomopathogenic bacterium, Xenorhabdus hominickii, activates non-ribosomal peptide synthetases to suppress insect immunity.},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {105101},
doi = {10.1016/j.dci.2023.105101},
pmid = {38000489},
issn = {1879-0089},
abstract = {Two bacterial genera, Xenorhabdus and Photorhabdus, are mutually symbiotic to the entomopathogenic nematodes, Steinernema and Heterorhabditis, respectively. The infective juveniles deliver the symbiotic bacteria to the hemocoel of target insects, in which the bacteria proliferate and help the development of the host nematode. The successful parasitism of the nematode-bacterial complex depends on host immunosuppression by the bacteria via their secondary metabolites. Leucine-responsive regulatory protein (Lrp) is a global bacterial transcriptional factor that plays a crucial role in parasitism. However, its regulatory targets to suppress insect immunity are not clearly understood. This study investigated the bacterial genes regulated by Lrp and the subsequent production of secondary metabolites in Xenorhabdus hominickii. Lrp expression occurred at the early infection stage of the bacteria in a target insect, Spodoptera exigua. A preliminary in silico screening indicated that 3.7% genes among 4075 predicted genes encoded in X. hominickii had the Lrp-response element on their promoters, including two non-ribosomal peptide synthetases (NRPSs). Eight NRPS (NRPS1-NRPS8) genes were predicted in the bacterial genome, in which six NRPS (NRPS3-NRPS8) expressions were positively correlated with Lrp expression in the infected larvae of S. exigua. Exchange of the Lrp promoter with an inducible promoter altered the production of the secondary metabolites and the NRPS expression levels. The immunosuppressive activities of X. hominickii were dependent on the Lrp expression level. The metabolites produced by Lrp expression included the eicosanoid-biosynthesis inhibitors and hemolytic factors. A cyclic dipeptide (=cPF) was produced by the bacteria at high Lrp expression and inhibited the phospholipase A2 activity of S. exigua in a competitive inhibitory manner. These results suggest that Lrp is a global transcriptional factor of X. hominickii and plays a crucial role in insect immunosuppression by modulating NRPS expression.},
}

@article {pmid37999398,
year = {2023},
author = {Jahajeeah, D and Ranghoo-Sanmukhiya, M and Schäfer, G},
title = {Metabolic Profiling, Antiviral Activity and the Microbiome of Some Mauritian Soft Corals.},
journal = {Marine drugs},
volume = {21},
number = {11},
pages = {},
pmid = {37999398},
issn = {1660-3397},
support = {WS/MUS22-01//International Centre for Genetic Engineering and Biotechnology/ ; },
abstract = {Soft corals, recognized as sessile marine invertebrates, rely mainly on chemical, rather than physical defense, by secreting intricate secondary metabolites with plausible pharmaceutical implication. Their ecological niche encompasses a diverse community of symbiotic microorganisms which potentially contribute to the biosynthesis of these bioactive metabolites. The emergence of new viruses and heightened viral resistance underscores the urgency to explore novel pharmacological reservoirs. Thus, marine organisms, notably soft corals and their symbionts, have drawn substantial attention. In this study, the chemical composition of four Mauritian soft corals: Sinularia polydactya, Cespitularia simplex, Lobophytum patulum, and Lobophytum crassum was investigated using LC-MS techniques. Concurrently, Illumina 16S metagenomic sequencing was used to identify the associated bacterial communities in the named soft corals. The presence of unique biologically important compounds and vast microbial communities found therein was further followed up to assess their antiviral effects against SARS-CoV-2 and HPV pseudovirus infection. Strikingly, among the studied soft corals, L. patulum displayed an expansive repertoire of unique metabolites alongside a heightened bacterial consort. Moreover, L. patulum extracts exerted some promising antiviral activity against SARS-CoV-2 and HPV pseudovirus infection, and our findings suggest that L. patulum may have the potential to serve as a therapeutic agent in the prevention of infectious diseases, thereby warranting further investigation.},
}

@article {pmid37999393,
year = {2023},
author = {Chukwudulue, UM and Barger, N and Dubovis, M and Luzzatto Knaan, T},
title = {Natural Products and Pharmacological Properties of Symbiotic Bacillota (Firmicutes) of Marine Macroalgae.},
journal = {Marine drugs},
volume = {21},
number = {11},
pages = {},
pmid = {37999393},
issn = {1660-3397},
abstract = {The shift from the terrestrial to the marine environment to discover natural products has given rise to novel bioactive compounds, some of which have been approved for human medicine. However, the ocean, which makes up nearly three-quarters of the Earth's surface, contains macro- and microorganisms whose natural products are yet to be explored. Among these underexplored marine organisms are macroalgae and their symbiotic microbes, such as Bacillota, a phylum of mostly Gram-positive bacteria previously known as Firmicutes. Macroalgae-associated Bacillota often produce chemical compounds that protect them and their hosts from competitive and harmful rivals. Here, we summarised the natural products made by macroalgae-associated Bacillota and their pharmacological properties. We discovered that these Bacillota are efficient producers of novel biologically active molecules. However, only a few macroalgae had been investigated for chemical constituents of their Bacillota: nine brown, five red and one green algae. Thus, Bacillota, especially from the marine habitat, should be investigated for potential pharmaceutical leads. Moreover, additional diverse biological assays for the isolated molecules of macroalgae Bacillota should be implemented to expand their bioactivity profiles, as only antibacterial properties were tested for most compounds.},
}

@article {pmid37999195,
year = {2023},
author = {Alonazi, M and Alshahrani, HM and Kouki, F and Almalki, NS and Mahmud, A and Majdoubi, J},
title = {Deep Convolutional Neural Network with Symbiotic Organism Search-Based Human Activity Recognition for Cognitive Health Assessment.},
journal = {Biomimetics (Basel, Switzerland)},
volume = {8},
number = {7},
pages = {},
pmid = {37999195},
issn = {2313-7673},
support = {PNURSP2023R237//Princess Nourah bint Abdulrahman University/ ; },
abstract = {Cognitive assessment plays a vital role in clinical care and research fields related to cognitive aging and cognitive health. Lately, researchers have worked towards providing resolutions to measure individual cognitive health; however, it is still difficult to use those resolutions from the real world, and therefore using deep neural networks to evaluate cognitive health is becoming a hot research topic. Deep learning and human activity recognition are two domains that have received attention for the past few years. The former is for its relevance in application fields like health monitoring or ambient assisted living, and the latter is due to their excellent performance and recent achievements in various fields of application, namely, speech and image recognition. This research develops a novel Symbiotic Organism Search with a Deep Convolutional Neural Network-based Human Activity Recognition (SOSDCNN-HAR) model for Cognitive Health Assessment. The goal of the SOSDCNN-HAR model is to recognize human activities in an end-to-end way. For the noise elimination process, the presented SOSDCNN-HAR model involves the Wiener filtering (WF) technique. In addition, the presented SOSDCNN-HAR model follows a RetinaNet-based feature extractor for automated extraction of features. Moreover, the SOS procedure is exploited as a hyperparameter optimizing tool to enhance recognition efficiency. Furthermore, a gated recurrent unit (GRU) prototype can be employed as a categorizer to allot proper class labels. The performance validation of the SOSDCNN-HAR prototype is examined using a set of benchmark datasets. A far-reaching experimental examination reported the betterment of the SOSDCNN-HAR prototype over current approaches with enhanced precision of 86.51% and 89.50% on Penn Action and NW-UCLA datasets, respectively.},
}

@article {pmid37999039,
year = {2023},
author = {El Yamlahi, Y and Bel Mokhtar, N and Maurady, A and Britel, MR and Batargias, C and Mutembei, DE and Nyingilili, HS and Malulu, DJ and Malele, II and Asimakis, E and Stathopoulou, P and Tsiamis, G},
title = {Characterization of the Bacterial Profile from Natural and Laboratory Glossina Populations.},
journal = {Insects},
volume = {14},
number = {11},
pages = {},
pmid = {37999039},
issn = {2075-4450},
support = {URT-22658//FAO/IAEA Agriculture and Biotechnology Laboratories/ ; },
abstract = {Tsetse flies (Glossina spp.; Diptera: Glossinidae) are viviparous flies that feed on blood and are found exclusively in sub-Saharan Africa. They are the only cyclic vectors of African trypanosomes, responsible for human African trypanosomiasis (HAT) and animal African trypanosomiasis (AAT). In this study, we employed high throughput sequencing of the 16S rRNA gene to unravel the diversity of symbiotic bacteria in five wild and three laboratory populations of tsetse species (Glossina pallidipes, G. morsitans, G. swynnertoni, and G. austeni). The aim was to assess the dynamics of bacterial diversity both within each laboratory and wild population in relation to the developmental stage, insect age, gender, and location. Our results indicated that the bacterial communities associated with the four studied Glossina species were significantly influenced by their region of origin, with wild samples being more diverse compared to the laboratory samples. We also observed that the larval microbiota was significantly different than the adults. Furthermore, the sex and the species did not significantly influence the formation of the bacterial profile of the laboratory colonies once these populations were kept under the same rearing conditions. In addition, Wigglesworthia, Acinetobacter, and Sodalis were the most abundant bacterial genera in all the samples, while Wolbachia was significantly abundant in G. morsitans compared to the other studied species. The operational taxonomic unit (OTU) co-occurrence network for each location (VVBD insectary, Doma, Makao, and Msubugwe) indicated a high variability between G. pallidipes and the other species in terms of the number of mutual exclusion and copresence interactions. In particular, some bacterial genera, like Wigglesworthia and Sodalis, with high relative abundance, were also characterized by a high degree of interactions.},
}

@article {pmid37998900,
year = {2023},
author = {Marchetta, A and Papale, M and Rappazzo, AC and Rizzo, C and Camacho, A and Rochera, C and Azzaro, M and Urzì, C and Lo Giudice, A and De Leo, F},
title = {A Deep Insight into the Diversity of Microfungal Communities in Arctic and Antarctic Lakes.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {11},
pages = {},
pmid = {37998900},
issn = {2309-608X},
support = {PNRA18_00194//Italian National Antarctic Research Program project MicroPolArS 2020-2023./ ; },
abstract = {We assessed fungal diversity in water and sediment samples obtained from five Arctic lakes in Ny-Ålesund (Svalbard Islands, High Arctic) and five Antarctic lakes on Livingston and Deception Islands (South Shetland Islands), using DNA metabarcoding. A total of 1,639,074 fungal DNA reads were detected and assigned to 5980 ASVs amplicon sequence variants (ASVs), with only 102 (1.7%) that were shared between the two Polar regions. For Arctic lakes, unknown fungal taxa dominated the sequence assemblages, suggesting the dominance of possibly undescribed fungi. The phylum Chytridiomycota was the most represented in the majority of Arctic and Antarctic samples, followed by Rozellomycota, Ascomycota, Basidiomycota, and the less frequent Monoblepharomycota, Aphelidiomycota, Mortierellomycota, Mucoromycota, and Neocallimastigomycota. At the genus level, the most abundant genera included psychrotolerant and cosmopolitan cold-adapted fungi including Alternaria, Cladosporium, Cadophora, Ulvella (Ascomycota), Leucosporidium, Vishniacozyma (Basidiomycota), and Betamyces (Chytridiomycota). The assemblages displayed high diversity and richness. The assigned diversity was composed mainly of taxa recognized as saprophytic fungi, followed by pathogenic and symbiotic fungi.},
}

@article {pmid37998876,
year = {2023},
author = {Ni, Y and Cao, L and Li, W and Zhang, Q and Feng, R and Zhao, Z and Zhao, X},
title = {The Research Status and Prospects of Floccularia luteovirens: A Mycorrhizal Fungus with Edible Fruiting Bodies.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {11},
pages = {},
pmid = {37998876},
issn = {2309-608X},
support = {No.2022JDRC0034//Xu Zhao/ ; ASTIP-IUA-2023005//Xu Zhao/ ; },
abstract = {Floccularia luteovirens, a rare wild edible and medicinal fungus, is endemic to the Tibetan plateau. However, attempts to artificially domesticate this species have not been successful, resulting in extremely limited utilization of this valuable resource. This paper presents the geographical distribution of F. luteovirens, along with its ecological and biological characteristics. It explores population relations, symbiotic relationships, soil microbial community relations, fruiting body occurrence conditions, nutritional metabolism, and reproductive patterns. The cultivation techniques, as well as the edible and medicinal value of this mushroom, are also reviewed. Through an overall analysis of the physiological characteristics and current research status of F. luteovirens, the paper discusses its development prospects. The aim is to provide a reference for other researchers and promote its artificial domestication, resource development, and utilization.},
}

@article {pmid37998032,
year = {2023},
author = {Li, X and Yang, L and Jiang, S and Zhou, F and Jiang, S and Li, Y and Chen, X and Yang, Q and Duan, Y and Huang, J},
title = {Effect of Fly Maggot Protein as Dietary on Growth and Intestinal Microbial Community of Pacific White Shrimp Litopenaeus vannamei.},
journal = {Biology},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/biology12111433},
pmid = {37998032},
issn = {2079-7737},
support = {2022YFD2400104, 2022SPY02001，2022SPY00002，2022SJS02001, CARS-48, CAFS (NO.2023TD34)//National Key R & D Program of China (2022YFD2400104), Rural Revitalization Strategy Special Fund Seed Industry Revitalization Project of Guangdong Province (2022SPY02001，2022SPY00002，2022SJS02001), China Agriculture Research System of MOF and MARA(CARS-48/ ; },
abstract = {As the intensive development of aquaculture persists, the demand for fishmeal continues to grow; however, since fishery resources are limited, the price of fishmeal remains high. Therefore, there is an urgent need to develop new sources of protein. They are rich in proteins, fatty acids, amino acids, chitin, vitamins, minerals, and antibacterial substances. Maggot meal-based diet is an ideal source of high-quality animal protein and a new type of protein-based immune enhancer with good application prospects in animal husbandry and aquaculture. In the present study, we investigated the effects of three different diets containing maggot protein on the growth and intestinal microflora of Litopenaeus vannamei. The shrimp were fed either a control feed (no fly maggot protein added), FM feed (compound feed with 30% fresh fly maggot protein added), FF feed (fermented fly maggot protein), or HT feed (high-temperature pelleted fly maggot protein) for eight weeks. The results showed that fresh fly maggot protein in the feed was detrimental to shrimp growth, whereas fermented and high-temperature-pelleted fly maggot protein improved shrimp growth and survival. The effects of different fly maggot protein treatments on the intestinal microbiota of L. vannamei also varied. Fermented fly maggot protein feed and high-temperature-pelleted fly maggot protein feed increased the relative abundance of Ruegeria and Pseudomonas, which increased the abundance of beneficial bacteria and thus inhibited the growth of harmful bacteria. In contrast, fresh fly maggot proteins alter the intestinal microbiome, disrupting symbiotic relationships between bacteria, and causing invasion by Vibrio and antibiotic-resistant bacteria. These results suggest that fresh fly maggot proteins affect the composition of intestinal microorganisms, which is detrimental to the intestinal tract of L. vannamei, whereas fermented fly maggot protein feed affected the growth of L. vannamei positively by improving the composition of intestinal microorganisms.},
}

@article {pmid37997205,
year = {2023},
author = {Zheng, L and Zhao, S and Zhou, Y and Yang, G and Chen, A and Li, X and Wang, J and Tian, J and Liao, H and Wang, X},
title = {The soybean sugar transporter GmSWEET6 participates in sucrose transport towards fungi during arbuscular mycorrhizal symbiosis.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.14772},
pmid = {37997205},
issn = {1365-3040},
support = {2021YFF1000500//National Key Research and Development Program of China/ ; 31672237//National Natural Science Foundation of China/ ; },
abstract = {In arbuscular mycorrhizal (AM) symbiosis, sugars in root cortical cells could be exported as glucose or sucrose into peri-arbuscular space for use by AM fungi. However, no sugar transporter has been identified to be involved in sucrose export. An AM-inducible SWEET transporter, GmSWEET6, was functionally characterised in soybean, and its role in AM symbiosis was investigated via transgenic plants. The expression of GmSWEET6 was enhanced by inoculation with the cooperative fungal strain in both leaves and roots. Heterologous expression in a yeast mutant showed that GmSWEET6 mainly transported sucrose. Transgenic plants overexpressing GmSWEET6 increased sucrose concentration in root exudates. Overexpression or knockdown of GmSWEET6 decreased plant dry weight, P content, and sugar concentrations in non-mycorrhizal plants, which were partly recovered in mycorrhizal plants. Intriguingly, overexpression of GmSWEET6 increased root P content and decreased the percentage of degraded arbuscules, while knockdown of GmSWEET6 increased root sugar concentrations in RNAi2 plants and the percentage of degraded arbuscules in RNAi1 plants compared with wild-type plants when inoculated with AM fungi. These results in combination with subcellular localisation of GmSWEET6 to peri-arbuscular membranes strongly suggest that GmSWEET6 is required for AM symbiosis by mediating sucrose efflux towards fungi.},
}

@article {pmid37996841,
year = {2023},
author = {Alhusayni, S and Roswanjaya, YP and Rutten, L and Huisman, R and Bertram, S and Sharma, T and Schon, M and Kohlen, W and Klein, J and Geurts, R},
title = {A rare non-canonical splice site in Trema orientalis SYMRK does not affect its dual symbiotic functioning in endomycorrhiza and rhizobium nodulation.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {587},
pmid = {37996841},
issn = {1471-2229},
support = {10598//Ministry of Education, King Faisal University, Saudi Arabia/ ; 8245-ID//Ministry of Research, Technology, and Higher Education of the Republic of Indonesia/ ; OPP1172165//ENSA project funded by the Bill & Melinda Gates Foundation to the University of Cambridge/ ; OPP1172165//ENSA project funded by the Bill & Melinda Gates Foundation to the University of Cambridge/ ; OPP1172165//ENSA project funded by the Bill & Melinda Gates Foundation to the University of Cambridge/ ; VI.Veni.212.132//Dutch Science Organization (Nederlandse Organisatie voor Wetenschappelijk Onderzoek)/ ; },
abstract = {BACKGROUND: Nitrogen-fixing nodules occur in ten related taxonomic lineages interspersed with lineages of non-nodulating plant species. Nodules result from an endosymbiosis between plants and diazotrophic bacteria; rhizobia in the case of legumes and Parasponia and Frankia in the case of actinorhizal species. Nodulating plants share a conserved set of symbiosis genes, whereas related non-nodulating sister species show pseudogenization of several key nodulation-specific genes. Signalling and cellular mechanisms critical for nodulation have been co-opted from the more ancient plant-fungal arbuscular endomycorrhizal symbiosis. Studies in legumes and actinorhizal plants uncovered a key component in symbiotic signalling, the LRR-type SYMBIOSIS RECEPTOR KINASE (SYMRK). SYMRK is essential for nodulation and arbuscular endomycorrhizal symbiosis. To our surprise, however, despite its arbuscular endomycorrhizal symbiosis capacities, we observed a seemingly critical mutation in a donor splice site in the SYMRK gene of Trema orientalis, the non-nodulating sister species of Parasponia. This led us to investigate the symbiotic functioning of SYMRK in the Trema-Parasponia lineage and to address the question of to what extent a single nucleotide polymorphism in a donor splice site affects the symbiotic functioning of SYMRK.

RESULTS: We show that SYMRK is essential for nodulation and endomycorrhization in Parasponia andersonii. Subsequently, it is revealed that the 5'-intron donor splice site of SYMRK intron 12 is variable and, in most dicotyledon species, doesn't contain the canonical dinucleotide 'GT' signature but the much less common motif 'GC'. Strikingly, in T. orientalis, this motif is converted into a rare non-canonical 5'-intron donor splice site 'GA'. This SYMRK allele, however, is fully functional and spreads in the T. orientalis population of Malaysian Borneo. A further investigation into the occurrence of the non-canonical GA-AG splice sites confirmed that these are extremely rare.

CONCLUSION: SYMRK functioning is highly conserved in legumes, actinorhizal plants, and Parasponia. The gene possesses a non-common 5'-intron GC donor splice site in intron 12, which is converted into a GA in T. orientalis accessions of Malaysian Borneo. The discovery of this functional GA-AG splice site in SYMRK highlights a gap in our understanding of splice donor sites.},
}

@article {pmid37995699,
year = {2023},
author = {Zhang, J and Liu, S and Liu, CB and Zhang, M and Fu, XQ and Wang, YL and Song, T and Chao, ZF and Han, ML and Tian, Z and Chao, DY},
title = {Natural variants of molybdate transporters contribute to yield traits of soybean by affecting auxin synthesis.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.10.072},
pmid = {37995699},
issn = {1879-0445},
abstract = {Soybean (Glycine max) is a crop with high demand for molybdenum (Mo) and typically requires Mo fertilization to achieve maximum yield potential. However, the genetic basis underlying the natural variation of Mo concentration in soybean and its impact on soybean agronomic performance is still poorly understood. Here, we performed a genome-wide association study (GWAS) to identify GmMOT1.1 and GmMOT1.2 that drive the natural variation of soybean Mo concentration and confer agronomic traits by affecting auxin synthesis. The soybean population exhibits five haplotypes of the two genes, with the haplotype 5 demonstrating the highest expression of GmMOT1.1 and GmMOT1.2, as well as the highest transport activities of their proteins. Further studies showed that GmMOT1.1 and GmMOT1.2 improve soybean yield, especially when cultivated in acidic or slightly acidic soil. Surprisingly, these two genes contribute to soybean growth by enhancing the activity of indole-3-acetaldehyde (IAAld) aldehyde oxidase (AO), leading to increased indole-3-acetic acid (IAA) synthesis, rather than being involved in symbiotic nitrogen fixation or nitrogen assimilation. Furthermore, the geographical distribution of five haplotypes in China and their correlation with soil pH suggest the potential significance of GmMOT1.1 and GmMOT1.2 in soybean breeding strategies.},
}

@article {pmid37994686,
year = {2023},
author = {Li, Z and Dong, Y and Ge, M and Zhang, Q and Sun, Y and Dai, M and Zhang, X and Li, X and Wang, Z and Xu, Q},
title = {Symbiotic relationship of Comaster schlegelii (Crinoidea: Comatulidae) And Gymnolophus obscura (Ophiuroidea: Ophiotrichidae) derived from stable isotope and fatty acid analyses.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icad128},
pmid = {37994686},
issn = {1557-7023},
abstract = {Coral reef community exhibit high species diversity and a broad range of biological relationships including widespread symbiosis and complex food utilization patterns. In our study, we investigated the symbiotic relationship between the commonly crinoid host Comaster schlegelii and its ophiuroid obligatory symbiont Gymnolophus obscura. Using a combination of fatty acid biomarkers and stable isotopic compositions, we explored differences in their organic matter utilization strategies and nutritional relationships. The result of stable isotopes revealed that G. obscura had higher δ15N values than its crinoid host. Particulate organic matter and phytoplankton were identified as the primary food sources for both species, however C. schlegelii showed a higher proportional contribution from benthic microalgae. Fatty acid markers showed that C. schlegelii was more dependent on benthic microalgae such as diatoms, and less on debritic organic matter and bacteria than G. obscura. Elevated δ15N values of G. obscura and similar food source contribution rates between the host and symbiont suggest that ophiuroid feeds on materials filtered by crinoids and have similar diet to the host. Our results provide insights into the symbiotic patterns of crinoids and ophiuroids, while also supplying foundational data on how symbiotic reef species select organic matter utilization strategies to adapt to their environment.},
}

@article {pmid37992950,
year = {2023},
author = {Gómez-Gallego, T and Molina-Luzón, MJ and Conéjéro, G and Berthomieu, P and Ferrol, N},
title = {The arbuscular mycorrhizal fungus Rhizophagus irregularis uses the copper exporting ATPase RiCRD1 as a major strategy for copper detoxification.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {122990},
doi = {10.1016/j.envpol.2023.122990},
pmid = {37992950},
issn = {1873-6424},
abstract = {Arbuscular mycorrhizal (AM) fungi establish a mutualistic symbiosis with most land plants. AM fungi regulate plant copper (Cu) acquisition both in Cu deficient and polluted soils. Here, we report characterization of RiCRD1, a Rhizophagus irregularis gene putatively encoding a Cu transporting ATPase. Based on its sequence analysis, RiCRD1 was identified as a plasma membrane Cu [+] efflux protein of the P1B1-ATPase subfamily. As revealed by heterologous complementation assays in yeast, RiCRD1 encodes a functional protein capable of conferring increased tolerance against Cu. In the extraradical mycelium, RiCRD1 expression was highly up-regulated in response to high concentrations of Cu in the medium. Comparison of the expression patterns of different players of metal tolerance in R. irregularis under high Cu levels suggests that this fungus could mainly use a metal efflux based-strategy to cope with Cu toxicity. RiCRD1 was also expressed in the intraradical fungal structures and, more specifically, in the arbuscules, which suggests a role for RiCRD1 in Cu release from the fungus to the symbiotic interface. Overall, our results show that RiCRD1 encodes a protein which could have a pivotal dual role in Cu homeostasis in R. irregularis, playing a role in Cu detoxification in the extraradical mycelium and in Cu transfer to the apoplast of the symbiotic interface in the arbuscules.},
}

@article {pmid37992160,
year = {2023},
author = {Coffroth, MA and Buccella, LA and Eaton, KM and Lasker, HR and Gooding, AT and Franklin, H},
title = {What makes a winner? Symbiont and host dynamics determine Caribbean octocoral resilience to bleaching.},
journal = {Science advances},
volume = {9},
number = {47},
pages = {eadj6788},
doi = {10.1126/sciadv.adj6788},
pmid = {37992160},
issn = {2375-2548},
mesh = {Animals ; Ecosystem ; Coral Reefs ; *Anthozoa/physiology ; Caribbean Region ; *Dinoflagellida/genetics ; Symbiosis ; },
abstract = {Unlike reef-building, scleractinian corals, Caribbean soft corals (octocorals) have not suffered marked declines in abundance associated with anthropogenic ocean warming. Both octocorals and reef-building scleractinians depend on a nutritional symbiosis with single-celled algae living within their tissues. In both groups, increased ocean temperatures can induce symbiont loss (bleaching) and coral death. Multiple heat waves from 2014 to 2016 resulted in widespread damage to reef ecosystems and provided an opportunity to examine the bleaching response of three Caribbean octocoral species. Symbiont densities declined during the heat waves but recovered quickly, and colony mortality was low. The dominant symbiont genotypes within a host generally did not change, and all colonies hosted symbiont species in the genus Breviolum. Their association with thermally tolerant symbionts likely contributes to the octocoral holobiont's resistance to mortality and the resilience of their symbiont populations. The resistance and resilience of Caribbean octocorals offer clues for the future of coral reefs.},
}

Animals
Ecosystem
Coral Reefs
*Anthozoa/physiology
Caribbean Region
*Dinoflagellida/genetics
Symbiosis

@article {pmid37991578,
year = {2023},
author = {Liu, HH and Chen, L and Shao, HB and Gao, S and Hong, XY and Bing, XL},
title = {Environmental Factors and the Symbiont Cardinium Influence the Bacterial Microbiome of Spider Mites Across the Landscape.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {1},
pmid = {37991578},
issn = {1432-184X},
support = {32001905 and 32020103011//National Natural Science Foundation of China/ ; 32001905 and 32020103011//National Natural Science Foundation of China/ ; 2022YFC2601000//National Key Research and Development Program of China/ ; BK20211213//Natural Science Foundation of Jiangsu Province/ ; KJQN202110//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Humans ; Animals ; *Tetranychidae ; RNA, Ribosomal, 16S/genetics ; Bacteroidetes/genetics ; *Arthropods ; *Microbiota ; },
abstract = {Microbes play a key role in the biology, ecology, and evolution of arthropods. Despite accumulating data on microbial communities in arthropods that feed on plants using piercing-sucking mouthparts, we still lack a comprehensive understanding of the composition and assembly factors of the microbiota, particularly in field-collected spider mites. Here, we applied 16S rRNA amplicon sequencing to investigate the characters of the bacterial community in 140 samples representing 420 mite individuals, belonging to eight Tetranychus species (Acari: Tetranychidae) collected from 26 sites in China. The results showed that the bacterial composition of spider mites varied significantly among different species, locations, and plants. The environment showed a significant influence on the bacterial community of spider mites, with different relative contributions. Latitude and precipitation were found to be the main factors influencing the bacterial community composition. The dissimilarity of bacterial community and geographical distance between mite locations were significantly correlated. The assembly of spider mite bacterial communities seemed to be mainly influenced by stochastic processes. Furthermore, the symbiont Cardinium was found to be important in shaping the microbiota of many Tetranychus species. The relative abundance of Cardinium was > 50% in T. viennensis, T. urticae G, T. urticae R, and T. turkestani. Removing Cardinium reads from our analysis significantly changed Shannon diversity index and weighted beta diversity in these species. Altogether, this study provides novel insights into bacterial diversity patterns that contribute to our knowledge of the symbiotic relationships between arthropods and their bacterial communities.},
}

Humans
Animals
*Tetranychidae
RNA, Ribosomal, 16S/genetics
Bacteroidetes/genetics
*Arthropods
*Microbiota

@article {pmid37991548,
year = {2023},
author = {Si, W and Li, M and Wang, K and Li, J and Xu, M and Zhou, X and Bai, J and Qu, Z and Song, G and Wu, X and Guo, Y and Hu, H and Fu, D and Yang, Z and Wu, M and Yan, D and Song, X and Tian, Z},
title = {Staphylococcus warneri strain XSB102 exacerbates psoriasis and promotes keratinocyte proliferation in imiquimod-induced psoriasis-like dermatitis mice.},
journal = {Archives of microbiology},
volume = {206},
number = {1},
pages = {3},
pmid = {37991548},
issn = {1432-072X},
support = {No. 212102310184 and 202102310270//the Science and Technology Research Project of Henan Province/ ; No. 212102310184 and 202102310270//the Science and Technology Research Project of Henan Province/ ; No. 212102310184 and 202102310270//the Science and Technology Research Project of Henan Province/ ; No. 212102310184 and 202102310270//the Science and Technology Research Project of Henan Province/ ; No. 212102310184 and 202102310270//the Science and Technology Research Project of Henan Province/ ; No. LHGJ20190469//the Joint Construction Project of Health Commission of Henan Province/ ; No. LHGJ20190469//the Joint Construction Project of Health Commission of Henan Province/ ; No. LHGJ20190469//the Joint Construction Project of Health Commission of Henan Province/ ; No. LHGJ20190469//the Joint Construction Project of Health Commission of Henan Province/ ; No. 32000006//the National Natural Science Foundation of China (NSFC)/ ; No. 32000006//the National Natural Science Foundation of China (NSFC)/ ; No. 32000006//the National Natural Science Foundation of China (NSFC)/ ; No. 32000006//the National Natural Science Foundation of China (NSFC)/ ; },
abstract = {Psoriasis is one of the common chronic inflammatory skin diseases worldwide. The skin microbiota plays a role in psoriasis through regulating skin homeostasis. However, the studies on the interactions between symbiotic microbial strains and psoriasis are limited. In this study, Staphylococcus strain XSB102 was isolated from the skin of human, which was identified as Staphylococcus warneri using VITEK2 Compact. To reveal the roles of Staphylococcus warneri on psoriasis, XSB102 were applied on the back of imiquimod-induced psoriasis-like dermatitis mice. The results indicated that it exacerbated the psoriasis and significantly increased the thickening of the epidermis. Furthermore, in vitro experiments confirmed that inactivated strain XSB102 could promote the proliferation of human epidermal keratinocytes (HaCaT) cell. However, real-time quantitative PCR and immunofluorescence results suggested that the expression of inflammatory factors such as IL-17a, IL-6, and so on were not significantly increased, while extracellular matrix related factors such as Col6a3 and TGIF2 were significantly increased after XSB102 administration. This study indicates that Staphylococcus warneri XSB102 can exacerbate psoriasis and promote keratinocyte proliferation independently of inflammatory factors, which paves the way for further exploration of the relationship between skin microbiota and psoriasis.},
}

@article {pmid37991154,
year = {2023},
author = {Jaeger, ACH and Hartmann, M and Conz, RF and Six, J and Solly, EF},
title = {Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.13211},
pmid = {37991154},
issn = {1758-2229},
support = {PZ00P2_180030//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.},
}

@article {pmid37988895,
year = {2023},
author = {Ramin, E and Faria, L and Gargalo, CL and Ramin, P and Flores-Alsina, X and Andersen, MM and Gernaey, KV},
title = {Water innovation in industrial symbiosis - A global review.},
journal = {Journal of environmental management},
volume = {349},
number = {},
pages = {119578},
doi = {10.1016/j.jenvman.2023.119578},
pmid = {37988895},
issn = {1095-8630},
abstract = {Motivated by the limited attention given to water management in industrial symbiosis research, this study presents the first global review of water innovation practices in the implemented industrial symbiosis cases reported in literature. We analyze the prevalence of global water innovation practices extending beyond the commonly used broad practices of water treatment and reuse to propose six categories, including utility sharing for alternative water supply, utility sharing for wastewater treatment, water recovery, energy recovery from water, material recovery from water, and material exchange to enhance water/wastewater treatment. Our findings highlight regional variations in adoption, with Asian and Europe showcasing diverse practices. Additionally, they indicate that most symbiosis cases center on the extensive role of public utilities and shared water facilities in pursuing water innovation, while 'pure' interfirm water-related symbiosis is limited. Finally, this review highlights extensive knowledge gaps and research needs in advancing sustainable water management and innovation in industrial symbiosis. Overall, our study contributes to the development of a comprehensive framework for water innovation practices in industrial symbiosis and emphasizes the need for future research in this area.},
}

@article {pmid37986040,
year = {2023},
author = {Jemo, M and Nkenmegne, S and Buernor, AB and Raklami, A and Ambang, Z and Souleyamanou, A and Ouhdouch, Y and Hafidi, M},
title = {Mycorrhizas and Trichoderma fungi increase the accumulation of secondary metabolites in grain legume leaves and suppress foliar diseases in field-grown conditions of the humid forest of Cameroon.},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {582},
pmid = {37986040},
issn = {1471-2229},
support = {01 to UM6P//OCP Group/ ; },
abstract = {BACKGROUND: Arbuscular mycorrhizal and Trichoderma fungi alter the synthesis of secondary metabolites of plants and confer tolerance from pathogens attacks. However, there is less supportive evidence from on-field studies confirming the above-mentioned hypothesis, particularly for the humid forest zone of Cameroon where pathogens are important sources of yield losses for legumes such as soybean and common bean.

MATERIALS AND METHODS: We evaluated the impacts of mycorrhiza isolates of Rhizophagus intraradices (Ri) and Trichoderma asperellum (Ta) fungi and their co-inoculations (Ta x Ri) in the synthetizing of leaves secondary metabolites, foliar disease symptoms, growth, N and P uptake, and yields of three genotypes of soybean (TGx 1485-1D, TGx 1990-93 F, and TGx 1990-97 F) and common beans (NUA-99, DOR-701, and PNN) under field conditions of Cameroon.

RESULTS: We found that common bean plants showed a lower foliar infection rate but a higher increase in root colonization intensity, shoot dry weight, and N and P uptakes than soybeans when inoculated with Ri and Ta treatment. However, the grain yield of soybean soybean was higher (2000 kg ha [1]) than the common bean plants for the Ri × Ta treatment. The soybean genotype TGx 1990-93F had increased root colonization intensity and the lowest foliar infection rate, making it stronger and tolerant to pathogen attacks when co-inoculated with Ri × Ta fungi (F). Bean plants inoculated with Ri and the co-inoculated with Ri × Ta demonstrated lower symptoms of foliar attack, and increased root colonization, particularly the PNN variety. The total amino acid and proline accumulations were higher for soybean than common bean plants due to fungi inoculations, and soybean genotypes accumulated more excellent contents of amino acid and proline in the control (10.1 mg g[- 1] fwt) that significantly increased under the Ri × Ta inoculation (13.4 mg g[- 1] fwt).

CONCLUSIONS: Common bean plants inoculated with Ta and Ri fungi accumulated higher phenolic compounds in their leaves that aided them in overcoming the pathogen attacks than soybean plants.},
}

@article {pmid37985876,
year = {2023},
author = {Lötstedt, B and Stražar, M and Xavier, R and Regev, A and Vickovic, S},
title = {Spatial host-microbiome sequencing reveals niches in the mouse gut.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {37985876},
issn = {1546-1696},
support = {HG011014-01//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; },
abstract = {Mucosal and barrier tissues, such as the gut, lung or skin, are composed of a complex network of cells and microbes forming a tight niche that prevents pathogen colonization and supports host-microbiome symbiosis. Characterizing these networks at high molecular and cellular resolution is crucial for understanding homeostasis and disease. Here we present spatial host-microbiome sequencing (SHM-seq), an all-sequencing-based approach that captures tissue histology, polyadenylated RNAs and bacterial 16S sequences directly from a tissue by modifying spatially barcoded glass surfaces to enable simultaneous capture of host transcripts and hypervariable regions of the 16S bacterial ribosomal RNA. We applied our approach to the mouse gut as a model system, used a deep learning approach for data mapping and detected spatial niches defined by cellular composition and microbial geography. We show that subpopulations of gut cells express specific gene programs in different microenvironments characteristic of regional commensal bacteria and impact host-bacteria interactions. SHM-seq should enhance the study of native host-microbe interactions in health and disease.},
}

@article {pmid37985403,
year = {2023},
author = {Ledford, WC and Silvestri, A and Fiorilli, V and Roth, R and Rubio-Somoza, I and Lanfranco, L},
title = {A journey into the world of small RNAs in the arbuscular mycorrhizal symbiosis.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19394},
pmid = {37985403},
issn = {1469-8137},
support = {RTI2018-097262-B-I00//ERDF A way of making Europe/ ; CN_00000033//Next Generation EU/ ; //Royal Society/ ; },
abstract = {Arbuscular mycorrhizal (AM) symbiosis is a mutualistic interaction between fungi and most land plants that is underpinned by a bidirectional exchange of nutrients. AM development is a tightly regulated process that encompasses molecular communication for reciprocal recognition, fungal accommodation in root tissues and activation of symbiotic function. As such, a complex network of transcriptional regulation and molecular signaling underlies the cellular and metabolic reprogramming of host cells upon AM fungal colonization. In addition to transcription factors, small RNAs (sRNAs) are emerging as important regulators embedded in the gene network that orchestrates AM development. In addition to controlling cell-autonomous processes, plant sRNAs also function as mobile signals capable of moving to different organs and even to different plants or organisms that interact with plants. AM fungi also produce sRNAs; however, their function in the AM symbiosis remains largely unknown. Here, we discuss the contribution of host sRNAs in the development of AM symbiosis by considering their role in the transcriptional reprogramming of AM fungal colonized cells. We also describe the characteristics of AM fungal-derived sRNAs and emerging evidence for the bidirectional transfer of functional sRNAs between the two partners to mutually modulate gene expression and control the symbiosis.},
}

@article {pmid37984824,
year = {2023},
author = {Voller, F and Ardanuy, A and Taylor, AFS and Johnson, D},
title = {Maintenance of host specialisation gradients in ectomycorrhizal symbionts.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19395},
pmid = {37984824},
issn = {1469-8137},
support = {NE/M015653/1//Natural Environment Research Council/ ; },
abstract = {Many fungi that form ectomycorrhizas exhibit a degree of host specialisation, and individual trees are frequently colonised by communities of mycorrhizal fungi comprising species that fall on a gradient of specialisation along genetic, functional and taxonomic axes of variation. By contrast, arbuscular mycorrhizal fungi exhibit little specialisation. Here, we propose that host tree root morphology is a key factor that gives host plants fine-scale control over colonisation and therefore opportunities for driving specialisation and speciation of ectomycorrhizal fungi. A gradient in host specialisation is likely driven by four proximate mechanistic 'filters' comprising partner availability, signalling recognition, competition for colonisation, and symbiotic function (trade, rewards and sanctions), and the spatially restricted colonisation seen in heterorhizic roots enables these mechanisms, especially symbiotic function, to be more effective in driving the evolution of specialisation. We encourage manipulation experiments that integrate molecular genetics and isotope tracers to test these mechanisms, alongside mathematical simulations of eco-evolutionary dynamics in mycorrhizal symbioses.},
}

@article {pmid37984669,
year = {2023},
author = {Yu, M and Wang, L and Feng, P and Wang, Z and Zhu, S},
title = {Treatment of mixed wastewater by vertical rotating microalgae-bacteria symbiotic biofilm reactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130057},
doi = {10.1016/j.biortech.2023.130057},
pmid = {37984669},
issn = {1873-2976},
abstract = {A novel vertical rotating microalgae-bacteria symbiotic biofilm reactor was built to treat the mixed wastewater containing municipal and soybean soaking wastewater. The reactor was operated in both sequential batch and semi-continuous modes. Under the sequential batch operation mode, the maximum removal rates for Chemical Oxygen Demand (COD), Total Nitrogen (TN), Total Phosphorus (TP), and Ammonia Nitrogen (NH4[+]-N) of the mixed wastewater were 95.6 %, 96.1 %, 97.6 %, and 100 %, respectively. During the semi-continuous operation, the water discharge indices decreased gradually and eventually stabilized. At stabilization, the removal rates of COD, TN, and NH4[+]-N achieved 98 %, 95 %, and 99.9 %, respectively. The maximum biomass productivity of the biofilm was 2.69 g·m[-2]·d[-1]. Additionally, the carbohydrate, protein and lipid comprised approximately 22 %, 51 % and 10 % of the dry weight of Chlorella. This study demonstrates the great potential of the microalgae-bacteria symbiotic biofilm system to treat food and domestic wastewater while harvesting microalgal biomass.},
}

@article {pmid37984021,
year = {2023},
author = {Xie, W and Hao, Z and Zhou, J and Fu, W and Guo, L and Zhang, X and Chen, B},
title = {Integrated transcriptomics and metabolomics reveal specific phenolic and flavonoid accumulation in licorice (Glycyrrhiza uralensis Fisch.) induced by arbuscular mycorrhiza symbiosis under drought stress.},
journal = {Plant physiology and biochemistry : PPB},
volume = {205},
number = {},
pages = {108173},
doi = {10.1016/j.plaphy.2023.108173},
pmid = {37984021},
issn = {1873-2690},
abstract = {Arbuscular mycorrhizal (AM) symbiosis can strengthen plant defense against abiotic stress, such as drought, through multiple mechanisms; however, the specialized chemical defenses induced by AM symbiosis are largely unknown. In a pot experiment, licorice (Glycyrrhiza uralensis Fisch.) inoculated with and without arbuscular mycorrhizal fungus Rhizophagus irregularis Schenck & Smith were grown under well-watered or water deficit conditions. Transcriptomic and metabolomic analyses were combined to investigate licorice root specialized metabolism induced by AM symbiosis under drought stress. Results showed that mycorrhizal plants had few dead leaves, less biomass reduction, and less differentially expressed genes and metabolite features in response to drought compared with nonmycorrhizal plants. Transcriptomic and metabolomic data revealed that mycorrhizal roots generally accumulated lignin regardless of the water regime; however, the expression of genes involved in lignin biosynthesis was significantly downregulated by drought stress in mycorrhizal plants. By contrast, AM inoculation significantly decreased specialized metabolites accumulation, including phenolics and flavonoids under well-watered conditions, whereas these decreases turned to be nonsignificant under drought stress. Moreover, these specific phenolics and flavonoids showed significant drought-induced accumulation pattern in mycorrhizal roots. These results highlight that accumulation of specific root phenolics and flavonoids may support the drought tolerance of mycorrhizal plants.},
}

@article {pmid37983125,
year = {2023},
author = {Yang, S and Bai, M and Kwok, LY and Zhong, Z and Sun, Z},
title = {The intricate symbiotic relationship between lactic acid bacterial starters in the milk fermentation ecosystem.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/10408398.2023.2280706},
pmid = {37983125},
issn = {1549-7852},
abstract = {Fermentation is one of the most effective methods of food preservation. Since ancient times, food has been fermented using lactic acid bacteria (LAB). Fermented milk is a very intricate fermentation ecosystem, and the microbial metabolism of fermented milk largely determines its metabolic properties. The two most frequently used dairy starter strains are Streptococcus thermophilus (S. thermophilus) and Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus). To enhance both the culture growth rate and the flavor and quality of the fermented milk, it has long been customary to combine S. thermophilus and L. bulgaricus in milk fermentation due to their mutually beneficial and symbiotic relationship. On the one hand, the symbiotic relationship is reflected by the nutrient co-dependence of the two microbes at the metabolic level. On the other hand, more complex interaction mechanisms, such as quorum sensing between cells, are involved. This review summarizes the application of LAB in fermented dairy products and discusses the symbiotic mechanisms and interactions of milk LAB starter strains from the perspective of nutrient supply and intra- and interspecific quorum sensing. This review provides updated information and knowledge on microbial interactions in a fermented milk ecosystem.},
}

@article {pmid37981364,
year = {2023},
author = {Li, S and Wang, S and Wang, L and Liu, X and Wang, X and Cai, R and Yuan, Y and Yue, T and Wang, Z},
title = {Unraveling symbiotic microbial communities, metabolomics and volatilomics profiles of kombucha from diverse regions in China.},
journal = {Food research international (Ottawa, Ont.)},
volume = {174},
number = {Pt 2},
pages = {113652},
doi = {10.1016/j.foodres.2023.113652},
pmid = {37981364},
issn = {1873-7145},
mesh = {Metabolomics ; *Microbiota ; Lactones ; China ; *Saccharomycetales ; *Acetobacteraceae ; },
abstract = {Kombucha is a natural fermented beverage (mixed system). This study aimed to unravel the signatures of kombucha in China to achieve tailor-made microbial consortium. Here, biochemical parameters, microbiome, metabolite production and volatile profile were comprehensively compared and characterized across four regions (AH, HN, SD, SX), both commonalities and distinctions were highlighted. The findings revealed that yeast species yeast Starmerella, Zygosaccharomyces, Dekkera, Pichia and bacterium Komagataeibacter, Gluconobacter were the most common microbes. Additionally, the composition, distribution and stability of microbial composition in liquid phase were superior to those in biofilm. The species diversity, differences, marker and association were analyzed across four areas. Metabolite profiles revealed a total of 163 bioactive compounds (23 flavonoids, 13 phenols), and 68 differential metabolites were screened and identified. Moreover, the metabolic pathways of phenylpropanoids biosynthesis were closely linked with the highest number of metabolites, followed by flavonoid biosynthesis. Sixty-five volatile compounds (23 esters) were identified. Finally, the correlation analysis among the microbial composition and volatile and functional metabolites showed that Komagataeibacter, Gluconolactone, Zygosacchaaromycess, Starmerella and Dekkera seemed closely related to bioactive compounds, especially Komagataeibacter displayed positive correlations with 1-hexadecanol, 5-keto-D-gluconate, L-malic acid, 6-aminohexanoate, Starmerella contributed greatly to gluconolactone, thymidine, anabasine, 2-isopropylmalic acid. Additionally, Candida was related to β-damascenone and α-terpineol, and Arachnomyces and Butyricicoccus showed the consistency of associations with specific esters and alcohols. These findings provided crucial information for creating a stable synthetic microbial community structure, shedding light on fostering stable kombucha and related functional beverages.},
}

Metabolomics
*Microbiota
Lactones
China
*Saccharomycetales
*Acetobacteraceae

@article {pmid37979259,
year = {2023},
author = {Wang, J and Ma, Q and Cai, P and Sun, X and Sun, Q and Li, M and Wang, Y and Zhong, L and Xie, F},
title = {On the investigation of composite cooling/heating set gel systems based on rice starch and curdlan.},
journal = {Food chemistry},
volume = {438},
number = {},
pages = {137960},
doi = {10.1016/j.foodchem.2023.137960},
pmid = {37979259},
issn = {1873-7072},
abstract = {In pursuit of advancing the understanding of composite gel systems, this study delves into the intricate realm of rheology, structural elucidation, and mechanical attributes. Specifically, it scrutinizes the symbiotic interplay between rice starch, a cooling-set gel, and curdlan, a thermo-irreversible heating-set gel. A higher curdlan content enhances the inter-chain hydrogen bonding between rice starch and curdlan, resulting in a denser gel structure and thus increased moduli, solid-like behavior, and mechanical properties, and reduced frequency-dependence, especially at high temperatures (>65 °C). For example, with 50 % curdlan incorporation, G' (90 °C) improved by 252 %. Notably, thermal treatment can compromise the structural integrity of the rice starch gel, reducing strength and softening texture. However, this textural degradation can be effectively mitigated with, for example, 30 % curdlan incorporation, resulting in a 55-fold hardness increase at 85 °C. The knowledge gained from this work offers valuable guidance for tailoring starch-based gel products to specific properties.},
}