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Background: Interactions between plants and diverse root-associated fungi are essential drivers of forest ecosystem dynamics. The symbiosis is potentially dependent on multiple ecological factors/processes such as host/symbiont specificity, background soil microbiome, inter-root dispersal of symbionts, and fungus–fungus interactions within roots. Nonetheless, it has remained a major challenge to reveal the mechanisms by which those multiple factors/processes determine the assembly of root-associated fungal communities. Based on the framework of joint species distribution modeling, we examined 1,615 root-tips samples collected in a cool-temperate forest to reveal how root-associated fungal community structure was collectively formed through filtering by host plants, associations with background soil fungi, spatial autocorrelation, and symbiont–symbiont interactions. In addition, to detect fungi that drive the assembly of the entire root-associated fungal community, we inferred networks of direct fungus–fungus associations by a statistical modeling that could account for implicit environmental effects. Results: The fine-scale community structure of root-associated fungi were best explained by the statistical model including the four ecological factors/processes. Meanwhile, among partial models, those including background soil fungal community structure and within-root fungus–fungus interactions showed the highest performance. When fine-root distributions were examined, ectomycorrhizal fungi tended to show stronger associations with background soil community structure and spatially autocorrelated patterns than other fungal guilds. In contrast, the distributions of root-endophytic fungi were inferred to depend greatly on fungus–fungus interactions. An additional statistical analysis further suggested that some endophytic fungi, such as Phialocephala and Leptodontidium, were placed at the core positions within the web of direct associations with other root-associated fungi. Conclusion: By applying emerging statistical frameworks to intensive datasets of root-associated fungal communities, we demonstrated background soil fungal community structure and fungus–fungus associations within roots, as well as filtering by host plants and spatial autocorrelation in ecological processes, could collectively drive the assembly of root-associated fungi. We also found that basic assembly rules could differ between mycorrhizal and endophytic fungi, both of which were major components of forest ecosystems. Consequently, knowledge of how multiple ecological factors/processes differentially drive the assembly of multiple fungal guilds is indispensable for comprehensively understanding the mechanisms by which terrestrial ecosystem dynamics are organized by plant–fungal symbiosis. [ABSTRACT FROM AUTHOR]

Background: Pecan [Carya illinoinensis (Wangenh.) Koch] is a widely cultivated dried fruit and woody oil tree with high economic value. Continuous sole planting of pecan caused some land to lie idle and deterioration of soil conditions. Tree and medicinal crops intercropping represents an environmental-friendly and economically feasible solution to these issues. Thus, we aimed to explore the underlying mechanism by which intercropping improved soil condition by regulating the interactions of the soil microbiome and metabolome. In this study, pecans were intercropped with medicinal crops caper spurge and honeysuckle on a tree farm in China. A combined analysis of soil microbiomes and metabolomes was performed to discover the effects of intercropping on bulk and rhizosphere soils. Results: The results showed that intercropping improved the edaphic properties of bulk soil and promoted the growth of pecan and caper spurge. Intercropping also significantly altered the structures of both bacterial and fungal communities in bulk soil, stabilised the enrichment of nitrogen-cyclic bacteria, for instance, Bacillus, and decreased the relative abundances of plant–pathogenic fungi, for instance, Fusarium. In addition, the result of metabolomic analysis showed that intercropping promoted the synthesis of functional compounds, such as trehalose and ethanolamine, which enhanced plant disease resistance in bulk soils. Moreover, the co-occurrence networks of microbiomes and metabolomes of bulk soils revealed that Bacillus was significantly correlated with Fusarium, Alternaria, and trehalose under intercropping patterns. Furthermore, analysis of microbiomes and metabolomes in the rhizosphere soil of caper spurge and honeysuckle revealed that Penicillium and Rhizomicrobium were significantly increased by intercropping and showed more dynamic connections with other genera and metabolites compared with single planting. Conclusions: Overall, intercropping pecans with caper spurge and honeysuckle can improve soil conditions and promote plant growth through microbiological and metabolomics integrated analyses. This study provides valuable information and theoretical basis for optimizing land resource utilisation and improving soil conditions in tree fields like pecan fields via intercropping, thereby reducing production losses and ensuring economic benefits. [ABSTRACT FROM AUTHOR]

A type of symbolic association network for the development of reputation is described and tested. Associations between people in these networks are not based on individual interaction, but rather are created by "reputational entrepreneurs" based on perceived symbolic association between people. We argue the intent of this type of connection is to add to the reputational information about those connected and we test whether a network of such associations influence cultural recognition. To do this, we use dyadic connections between classical music composers created by conductors for orchestra performance and determine whether a composer's symbolic association network (SAN) aids recognition in publications. We find SANs to have a significant impact on the extent of reputational recognition, even when holding a composer's individual status achievements constant. Composers with a large symbolic association network and those who bridge unconnected composers tend to receive more recognition. We discuss the influence of symbolic association networks on perception of reputational significance. We suggest SANs may advance research in reputation and culture particularly when considering actors whose reputation is active beyond their work or lifetime, such as artists, writers, musicians, and historical figures. • A type of symbolic association network (SAN) for reputation development and recognition is proposed and tested. • SANs are symbolically created by "reputational entrepreneurs" to produce reputational understandings about those connected. • SANs between composers created by orchestra performance are modeled to test effect on composer's recognition in publications. • Classical music composers with a large SAN and those bridging unconnected composers in performance receive more recognition in publications. [ABSTRACT FROM AUTHOR]

The potential promise of the microbiome to ameliorate a wide range of societal and ecological challenges, from disease prevention and treatment to the restoration of entire ecosystems, hinges not only on microbiome engineering but also on the stability of beneficial microbiomes. Yet the properties of microbiome stability remain elusive and challenging to discern due to the complexity of interactions and often intractable diversity within these communities of bacteria, archaea, fungi, and other microeukaryotes. Networks are powerful tools for the study of complex microbiomes, with the potential to elucidate structural patterns of stable communities and generate testable hypotheses for experimental validation. However, the implementation of these analyses introduces a cascade of dichotomies and decision trees due to the lack of consensus on best practices. Here, we provide a road map for network-based microbiome studies with an emphasis on discerning properties of stability. We identify important considerations for data preparation, network construction, and interpretation of network properties. We also highlight remaining limitations and outstanding needs for this field. This review also serves to clarify the varying schools of thought on the application of network theory for microbiome studies and to identify practices that enhance the reproducibility and validity of future work. Cpsfgx247MkAJpWMo7kUUg Video Abstract [ABSTRACT FROM AUTHOR]

Abstract Background Pecan [Carya illinoinensis (Wangenh.) Koch] is a widely cultivated dried fruit and woody oil tree with high economic value. Continuous sole planting of pecan caused some land to lie idle and deterioration of soil conditions. Tree and medicinal crops intercropping represents an environmental-friendly and economically feasible solution to these issues. Thus, we aimed to explore the underlying mechanism by which intercropping improved soil condition by regulating the interactions of the soil microbiome and metabolome. In this study, pecans were intercropped with medicinal crops caper spurge and honeysuckle on a tree farm in China. A combined analysis of soil microbiomes and metabolomes was performed to discover the effects of intercropping on bulk and rhizosphere soils. Results The results showed that intercropping improved the edaphic properties of bulk soil and promoted the growth of pecan and caper spurge. Intercropping also significantly altered the structures of both bacterial and fungal communities in bulk soil, stabilised the enrichment of nitrogen-cyclic bacteria, for instance, Bacillus, and decreased the relative abundances of plant–pathogenic fungi, for instance, Fusarium. In addition, the result of metabolomic analysis showed that intercropping promoted the synthesis of functional compounds, such as trehalose and ethanolamine, which enhanced plant disease resistance in bulk soils. Moreover, the co-occurrence networks of microbiomes and metabolomes of bulk soils revealed that Bacillus was significantly correlated with Fusarium, Alternaria, and trehalose under intercropping patterns. Furthermore, analysis of microbiomes and metabolomes in the rhizosphere soil of caper spurge and honeysuckle revealed that Penicillium and Rhizomicrobium were significantly increased by intercropping and showed more dynamic connections with other genera and metabolites compared with single planting. Conclusions Overall, intercropping pecans with caper spurge and honeysuckle can improve soil conditions and promote plant growth through microbiological and metabolomics integrated analyses. This study provides valuable information and theoretical basis for optimizing land resource utilisation and improving soil conditions in tree fields like pecan fields via intercropping, thereby reducing production losses and ensuring economic benefits. Graphical Abstract

Abstract The potential promise of the microbiome to ameliorate a wide range of societal and ecological challenges, from disease prevention and treatment to the restoration of entire ecosystems, hinges not only on microbiome engineering but also on the stability of beneficial microbiomes. Yet the properties of microbiome stability remain elusive and challenging to discern due to the complexity of interactions and often intractable diversity within these communities of bacteria, archaea, fungi, and other microeukaryotes. Networks are powerful tools for the study of complex microbiomes, with the potential to elucidate structural patterns of stable communities and generate testable hypotheses for experimental validation. However, the implementation of these analyses introduces a cascade of dichotomies and decision trees due to the lack of consensus on best practices. Here, we provide a road map for network-based microbiome studies with an emphasis on discerning properties of stability. We identify important considerations for data preparation, network construction, and interpretation of network properties. We also highlight remaining limitations and outstanding needs for this field. This review also serves to clarify the varying schools of thought on the application of network theory for microbiome studies and to identify practices that enhance the reproducibility and validity of future work. Video Abstract

Abstract Background Cabbage Fusarium wilt (CFW) is a devastating disease caused by the soil-borne fungus Fusarium oxysporum f. sp. conglutinans (Foc). One of the optimal measures for managing CFW is the employment of tolerant/resistant cabbage varieties. However, the interplay between plant genotypes and the pathogen Foc in shaping the rhizosphere microbial community, and the consequent influence of these microbial assemblages on biological resistance, remains inadequately understood. Results Based on amplicon metabarcoding data, we observed distinct differences in the fungal alpha diversity index (Shannon index) and beta diversity index (unweighted Bray–Curtis dissimilarity) within the rhizosphere of the YR (resistant to Foc) and ZG (susceptible to Foc) cabbage varieties, irrespective of Foc inoculation. Notably, the Shannon diversity shifts in the resistant YR variety were more pronounced following Foc inoculation. Disease-resistant plant variety demonstrate a higher propensity for harboring beneficial microorganisms, such as Pseudomonas, and exhibit superior capabilities in evading harmful microorganisms, in contrast to their disease-susceptible counterparts. Furthermore, the network analysis was performed on rhizosphere-associated microorganisms, including both bacteria and fungi. The networks of association recovered from YR exhibited greater complexity, robustness, and density, regardless of Foc inoculation. Following Foc infection in the YR rhizosphere, there was a notable increase in the dominant bacterium NA13, which is also a hub taxon in the microbial network. Reintroducing NA13 into the soil significantly improved disease resistance in the susceptible ZG variety, by directly inhibiting Foc and triggering defense mechanisms in the roots. Conclusions The rhizosphere microbial communities of these two cabbage varieties are markedly distinct, with the introduction of the pathogen eliciting significant alterations in their microbial networks which is correlated with susceptibility or resistance to soil-borne pathogens. Furthermore, we identified a rhizobacteria species that significantly boosts disease resistance in susceptible cabbages. Our results indicated that the induction of resistance genes leading to varied responses in microbial communities to pathogens may partly explain the differing susceptibilities of the cabbage varieties tested to CFW. Video Abstract

Abstract Background Construction of co-occurrence networks in metagenomic data often employs correlation to infer pairwise relationships between microbes. However, biological systems are complex and often display qualities non-linear in nature. Therefore, the reliance on correlation alone may overlook important relationships and fail to capture the full breadth of intricacies presented in underlying interaction networks. It is of interest to incorporate metrics that are not only robust in detecting linear relationships, but non-linear ones as well. Results In this paper, we explore the use of various mutual information (MI) estimation approaches for quantifying pairwise relationships in biological data and compare their performances against two traditional measures–Pearson’s correlation coefficient, r, and Spearman’s rank correlation coefficient, ρ. Metrics are tested on both simulated data designed to mimic pairwise relationships that may be found in ecological systems and real data from a previous study on C. diff infection. The results demonstrate that, in the case of asymmetric relationships, mutual information estimators can provide better detection ability than Pearson’s or Spearman’s correlation coefficients. Specifically, we find that these estimators have elevated performances in the detection of exploitative relationships, demonstrating the potential benefit of including them in future metagenomic studies. Conclusions Mutual information (MI) can uncover complex pairwise relationships in biological data that may be missed by traditional measures of association. The inclusion of such relationships when constructing co-occurrence networks can result in a more comprehensive analysis than the use of correlation alone.

Background: Cabbage Fusarium wilt (CFW) is a devastating disease caused by the soil-borne fungus Fusarium oxysporum f. sp. conglutinans (Foc). One of the optimal measures for managing CFW is the employment of tolerant/resistant cabbage varieties. However, the interplay between plant genotypes and the pathogen Foc in shaping the rhizosphere microbial community, and the consequent influence of these microbial assemblages on biological resistance, remains inadequately understood. Results: Based on amplicon metabarcoding data, we observed distinct differences in the fungal alpha diversity index (Shannon index) and beta diversity index (unweighted Bray–Curtis dissimilarity) within the rhizosphere of the YR (resistant to Foc) and ZG (susceptible to Foc) cabbage varieties, irrespective of Foc inoculation. Notably, the Shannon diversity shifts in the resistant YR variety were more pronounced following Foc inoculation. Disease-resistant plant variety demonstrate a higher propensity for harboring beneficial microorganisms, such as Pseudomonas, and exhibit superior capabilities in evading harmful microorganisms, in contrast to their disease-susceptible counterparts. Furthermore, the network analysis was performed on rhizosphere-associated microorganisms, including both bacteria and fungi. The networks of association recovered from YR exhibited greater complexity, robustness, and density, regardless of Foc inoculation. Following Foc infection in the YR rhizosphere, there was a notable increase in the dominant bacterium NA13, which is also a hub taxon in the microbial network. Reintroducing NA13 into the soil significantly improved disease resistance in the susceptible ZG variety, by directly inhibiting Foc and triggering defense mechanisms in the roots. Conclusions: The rhizosphere microbial communities of these two cabbage varieties are markedly distinct, with the introduction of the pathogen eliciting significant alterations in their microbial networks which is correlated with susceptibility or resistance to soil-borne pathogens. Furthermore, we identified a rhizobacteria species that significantly boosts disease resistance in susceptible cabbages. Our results indicated that the induction of resistance genes leading to varied responses in microbial communities to pathogens may partly explain the differing susceptibilities of the cabbage varieties tested to CFW. -meKq2qaHpqpKck3NvZ8m1 Video Abstract [ABSTRACT FROM AUTHOR]

Background: Construction of co-occurrence networks in metagenomic data often employs correlation to infer pairwise relationships between microbes. However, biological systems are complex and often display qualities non-linear in nature. Therefore, the reliance on correlation alone may overlook important relationships and fail to capture the full breadth of intricacies presented in underlying interaction networks. It is of interest to incorporate metrics that are not only robust in detecting linear relationships, but non-linear ones as well. Results: In this paper, we explore the use of various mutual information (MI) estimation approaches for quantifying pairwise relationships in biological data and compare their performances against two traditional measures–Pearson's correlation coefficient, r, and Spearman's rank correlation coefficient, ρ. Metrics are tested on both simulated data designed to mimic pairwise relationships that may be found in ecological systems and real data from a previous study on C. diff infection. The results demonstrate that, in the case of asymmetric relationships, mutual information estimators can provide better detection ability than Pearson's or Spearman's correlation coefficients. Specifically, we find that these estimators have elevated performances in the detection of exploitative relationships, demonstrating the potential benefit of including them in future metagenomic studies. Conclusions: Mutual information (MI) can uncover complex pairwise relationships in biological data that may be missed by traditional measures of association. The inclusion of such relationships when constructing co-occurrence networks can result in a more comprehensive analysis than the use of correlation alone. [ABSTRACT FROM AUTHOR]

While afforestation mitigates climate concerns, the impact of afforestation on ecological assembly processes and multiple soil functions (multifunctionality) in afforested areas remains unclear. The Xiong'an New Area plantation forests (Pinus and Sophora forests) in North China were selected to examine the effects of plantation types across four distinct seasons on soil microbiomes. Three functional categories (nutrient stocks, organic matter decomposition, and microbial functional genes) of multifunctionality and the average (net) multifunctionality were quantified. All these categories are directly related to soil functions. The results showed that net soil multifunctionality as a broad function did not change seasonally, unlike other narrow functional categories. Bacterial communities were deterministically (variable selection and homogenous selection) structured, whereas the stochastic process of dispersal limitation was mainly responsible for the assembly and turnover of fungal and protist communities. In Pinus forests, winter initiates a sudden shift from deterministic to stochastic processes in bacterial community assembly, accompanied by decreased Shannon diversity and heightened nutrient cycling (nutrient stocks and organic matter decomposition). This indicates the potential vulnerability of deterministic assembly to seasonal fluctuations, particularly in environments rich in nutrients. The results predicted that protist community composition was uniquely structured with C-related functional activities relative to bacterial and fungal β-diversity variations, which were mostly explained by seasonal variations. Our study highlighted the importance of the protist phagocytosis process on soil microbial interactions through the predicted impact of protist α-diversity on microbial cooccurrence network parameters. This association might be driven by the high abundance of protist consumers as the main predators of bacterial and fungal lineages in our sampling plots. Our findings reveal that the complexity of microbial co-occurrence interactions was considerably higher in spring, perhaps attributing thermal variability and increased resource availability within spring that foster microbial diversity and network complexity. This study contributes to local ecosystem prospects to model the behavior of soil biota seasonally and their implied effects on soil functioning and microbial assembly processes, which will benefit global-scale afforestation programs by promoting novel, precise, and rational plantation forests for future environmental sustainability and self-sufficiency. [ABSTRACT FROM AUTHOR]

Introduction: Currently, straw biodegradation and soil improvement in rice)mushroom rotation systems have attracted much attention. However, there is still a lack of studies on the effects of rice-mushroom rotation on yield, soil properties and microbial succession. Methods: In this study, no treatment (CK), green manure return (GM) and rice straw return (RS) were used as controls to fully evaluate the effect of Stropharia rugosoannulata cultivation substrate return (SRS) on soil properties and microorganisms. Results: The results indicated that rice yield, soil nutrient (organic matter, organic carbon, total nitrogen, available nitrogen and available potassium) and soil enzyme (urease, saccharase, lignin peroxidase and laccase) activities had positive responses to the rice-mushroom rotation. At the interannual level, microbial diversity varied significantly among treatments, with the rice-mushroom rotation significantly increasing the relative alpha diversity index of soil bacteria and enriching beneficial microbial communities such as Rhizobium, Bacillus and Trichoderma for rice growth. Soil nutrients and enzymatic activities were significantly correlated with microbial communities during rice-mushroom rotation. The fungal-bacterial co-occurrence networks were modular, and Latescibacterota, Chloroflexi, Gemmatimonadota and Patescibacteria were closely related to the accumulation of nutrients in the soil. The structural equation model (SEM) showed that fungal diversity responded more to changes in soil nutrients than did bacterial diversity. Discussion: Overall, the rice-mushroom rotation model improved soil nutrients and rice yields, enriched beneficial microorganisms and maintained microbial diversity. This study provides new insights into the use of S. rugosoannulata cultivation substrates in the sustainable development of agroecosystems. [ABSTRACT FROM AUTHOR]

Aims: Endophytes could assist the host plant in the acquisition of nutrients and tolerance of stresses during their long symbiotic life cycle with the host plant. Blueberry (Vaccinium spp.) is adapted to acidic soils and can inhabit harsh soil conditions. However, the dynamic variation of its endosphere microbial community under long-term cultivation remains unclear. Methods: We collected blueberry root samples of four age groups (4a, 8a, 17a, and 33a). The diversity and composition of bacterial and fungal communities in the root endosphere were analyzed, and their co-occurrence networks were constructed to explore interkingdom interactions and keystone taxa. Results: As the major phylum of the endosphere, the relative abundance of Actinobacteria decreased with the age of the blueberry, whereas Proteobacteria increased. The fungal communities were dominated by Sordariomycetes, Eurotiomycetes, and Agaricomycetes, and these were not regularly altered with the increased blueberry age. The co-occurrence network revealed that positive interactions were observed in the bacterial and fungal communities and were consistently dominant within both intrakingdom and interkingdom networks. Among the interkingdom network, keystone taxa were identified for bacteria mainly belonging to Proteobacteria and Actinobacteria of bacteria, as well as for fungi of Ascomycota, which have potentially beneficial effects on host plants. Conclusions: Our study reveals although the diversity and composition varied with blueberry age in the root endosphere, their positive interactions of intrakingdom or interkingdom consistently dominate the network, and it may be such positive beneficial interactions that maintain the health of host plant during long-term symbiosis. [ABSTRACT FROM AUTHOR]

Environmental heterogeneity partly drives microbial succession in arthropods, while the microbial assembly mechanisms during environmental changes remain largely unknown. Here, we explored the temporal dynamics and assembly mechanisms within both bacterial and fungal communities in Liriomyza huidobrensis (Blanchard) during the transition from field to laboratory conditions. We observed a decrease in bacterial diversity and complexity of bacterial-fungal co-occurrence networks in leaf miners transitioning from wild to captive environments. Both neutral and null models revealed that stochastic processes, particularly drift (contributing over 70%), play a crucial role in governing bacterial and fungal community assembly. The relative contribution of ecological processes such as dispersal, drift, and selection varied among leaf miners transitioning from wild to captive states. Furthermore, we propose a hypothetical scenario for the assembly and succession of microbial communities in the leaf miner during the short- and long-term transition from the wild to captivity. Our findings suggest that environmental heterogeneity determines the ecological processes governing bacterial and fungal community assembly in leaf miners, offering new insights into microbiome and mycobiome assembly mechanisms in invasive pests amidst environmental change. [ABSTRACT FROM AUTHOR]

In aquatic ecosystems with low nutrient levels, organic aggregates (OAs) act as nutrient hotspots, hosting a diverse range of microbial species compared to those in the water column. Lake eutrophication, marked by intensified and prolonged cyanobacterial blooms, significantly impacts material and energy cycling processes, potentially altering the ecological traits of both free-living (FL) and particle-attached (PA) bacteria. However, the extent to which observed patterns of FL and PA bacterial diversity, community assembly, and stability extend to hypereutrophic lakes remains understudied. To address this gap, we investigated bacterial diversity, composition, assembly processes, and stability within hypereutrophic Lake Xingyun. Our results revealed that FL bacterial communities exhibited higher α-diversity than PA counterparts, coupled with discernible taxonomic compositions. Both bacterial communities showed distinct seasonality, influenced by cyanobacterial bloom intensity. Environmental factors accounted for 71.1% and 54.2% of the variation among FL and PA bacteria, respectively. The assembly of the PA bacterial community was predominantly stochastic, while FL assembly was more deterministic. The FL network demonstrated greater stability, complexity, and negative interactions, indicative of competitive relationships, while the PA network showed a prevalence of positive correlations, suggesting mutualistic interactions. Importantly, these findings differ from observations in oligotrophic, mesotrophic, and eutrophic lakes. Overall, this research provides valuable insights into the interplay among bacterial fractions, enhancing our understanding of nutrient status and cyanobacterial blooms in shaping bacterial communities. [ABSTRACT FROM AUTHOR]

Background and aims: The diversity and stability of belowground microbiota communities influence plant health. However, changes over time in the microbiome composition associated with healthy and diseased trees remains poorly understood. The goal of this study is to understand the changes in belowground microbial community associated with Verticillium wilt of smoke trees to provide a basis for the combination of biological agents and chemical measures to combat Verticillium wilt of smoke trees. Methods: In this study, we used an amplicon-based approach to reveal distinct differences in the diversity, structure and composition of the belowground microbial communities of healthy and diseased smoke trees from June to October. Results: The structure, composition and interactions of the belowground microbial communities are different between healthy and diseased smoke trees from June to October. The co-occurrence networks of the belowground microbial community changed with the severity of the disease over time. Additionally, the structural community of healthy and diseased trees showed a shift in keystone OTUs. Conclusions: This study improves our understanding of the belowground microbial community composition associated with smoke trees in healthy and diseased conditions, offering the potential to both manipulate the plant microbiome to promote plant health and to provide an integrated management strategy of smoke tree. [ABSTRACT FROM AUTHOR]

Reducing nitrogen fertilizer application highlights its role in optimizing soil bacterial communities to achieve sustainable agriculture. However, the specific mechanisms of bacterial community change under these conditions are not yet clear. In this study, we employed long-term field experiments and high-throughput sequencing to analyze how varying levels of nitrogen application influence the soil bacterial community structure and co-occurrence networks. The results show that reducing the nitrogen inputs significantly enhances the diversity and evenness of the soil bacterial communities, possibly due to the diminished dominance of nitrogen-sensitive taxa, which in turn liberates the ecological niches for less competitive species. Furthermore, changes in the complexity and stability of the bacterial co-occurrence networks suggest increased community resilience and a shift toward more mutualistic interactions. These findings underline the potential of reduced nitrogen application to alleviate competitive pressures among bacterial species, thereby promoting a more diverse and stable microbial ecosystem, highlighting the role of competitive release in fostering microbial diversity. This research contributes to our understanding of how nitrogen management can influence soil health and offers insights into sustainable agricultural practices. [ABSTRACT FROM AUTHOR]

Biotic stresses, such as plant viruses, e.g., cotton leaf curl virus (CLCuV), can alter root-associated and leaf-associated microbial diversities in plants. There are complex ecological dynamics at play, with each microbe contributing to a multitude of biotic and abiotic interactions, thus deciding the stability of the plant's ecosystem in response to the disease. Deciphering these networks of interactions is a challenging task. The inferential research in microbiome is also at a nascent stage, often constrained by the underlying analytical assumptions and the limitations with respect to the depth of sequencing. There is also no real consensus on network-wide statistics to identify the influential microbial players in a network. Guided by the latest developments in network science, including recently published metrics such as Integrated View of Influence (IVI) and some other centrality measures, this study provides an exposé of the most influential nodes in the rhizospheric and phyllospheric microbial networks of the cotton leaf curl disease (CLCuD) susceptible, partially tolerant, and resistant cotton varieties. It is evident from our results that the CLCuDresistant Gossypium arboreum possesses an equal share of keystone species, which helps it to withstand ecological pressures. In the resistant variety, the phyllosphere harbors the most influential nodes, whereas in the susceptible variety, they are present in the rhizosphere. Based on hubness score, spreading score, and IVI, the top 10 occurring keystone species in the FDH-228 (resistant) variety include Actinokineospora, Cohnella, Thermobacillus, Clostridium, Desulfofarcimen, and MDD-D21. Elusimicrobia, Clostridium-sensu-stricto_12, Candidatus woesebacteria, and Dyella were identified as the most influential nodes in the PFV-1 (partially tolerant) variety. In the PFV-2 (susceptible) variety, the keystone species were identified as Georginia, Nesterenkonia, Elusimicrobia MVP-88, Acetivibrio, Tepedisphaerales, Chelatococcus, Nitrosospira, and RCP2- 54. This concept deciphers the diseased and healthy plant's response to viral disease, which may be microbially mediated. [ABSTRACT FROM AUTHOR]

This study seeks to deliver a comprehensive bibliometric analysis of blockchain research undertaken from 2013 to 2023. It seeks to map the field’s evolution, highlight emerging trends, and identify key contributors and thematic areas. Understanding these aspects is crucial for guiding future research and policymaking in the rapidly growing domain of blockchain technology. The study utilises a systematic bibliometric analysis approach and the Scopus database was used for collecting data. The analysis includes keyword trends, citation patterns, author productivity, and network analysis. The results reveal significant expansion and diversification in blockchain research, with 13,369 publications and 52,009 contributing authors. Key metrics include a total citation count of 266,483 and an average of 19.93 citations per paper, underscoring the field’s scholarly impact. The study identifies core research themes such as smart contracts, security, IoT integration, and emerging topics like AI and sustainability. The findings highlight the interdisciplinary nature of blockchain research and its global distribution, with notable contributions from China and the United States. The study’s reliance on selected databases and predefined keywords may exclude relevant grey literature and industry reports. Future research should integrate these sources for a more complete view. This study provides a panoramic view of blockchain research, offering valuable insights into its development, current state, and future directions. Identifying key trends, influential contributors, and emerging themes contributes to the academic discourse and supports strategic planning for researchers, practitioners, and policymakers engaged in blockchain technology.

Heavy metal (HM) contamination affects the composition and structure of soil microbial communities, but there are few studies on the assembly process and co-occurrence network of soil microbial community succession driven by Cd in volcanic ecosystem. To address this gap in knowledge, we collected and analyzed soil samples from the Nvshan Volcanic area to understand the microbial characteristics in primary succession soil (PS) and secondary succession soil (SS). We found that the soil was contaminated with different levels of Cd (PS > SS), resulting in obvious heterogeneity of microorganisms. The absolute abundance of bacteria (16S rRNA gene copies) varied significantly between the two successions (P < 0.0001). The co-occurrence networks analysis showed that the number of nodes in bacterial communities was lower in PS compared to SS (1002 vs. 1004), indicating that heavy metal contamination would reduce the number of soil microbial communities. Compared with PS, bacterial communities exhibited stronger competitiveness in SS (positive: negative, P/N: 25.69 vs. 64.22), whereas fungal communities were closer symbiotic relationships (positive/negative, P/N: 15.85 vs. 14.29). The neutral community model (NCM) analysis revealed that stochastic processes predominantly governed the microbial assembly process (bacterial R2: 0.657, fungal R2: 0.686). The Mantel test analysis revealed that Cd was negatively associated with cbbLR, amoA, and phoD. The results of the Sankey diagram showed that fungi were more resistant than bacteria (27 vs. 13). This study contributes to understanding the process of soil microbial succession under Cd stress and identifying microbial strains with potential for Cd remediation.

Karst rocky desertification refers to the process of land degradation caused by various factors such as climate change and human activities including deforestation and agriculture on a fragile karst substrate. Nutrient limitation is common in karst areas. Moss crust grows widely in karst areas. The microorganisms associated with bryophytes are vital to maintaining ecological functions, including climate regulation and nutrient circulation. The synergistic effect of moss crusts and microorganisms may hold great potential for restoring degraded karst ecosystems. However, our understanding of the responses of microbial communities, especially abundant and rare taxa, to nutrient limitations and acquisition in the presence of moss crusts is limited. Different moss habitats exhibit varying patterns of nutrient availability, which also affect microbial diversity and composition. Therefore, in this study, we investigated three habitats of mosses: autochthonal bryophytes under forest, lithophytic bryophytes under forest and on cliff rock. We measured soil physicochemical properties and enzymatic activities. We conducted high-throughput sequencing and analysis of soil microorganisms. Our finding revealed that autochthonal moss crusts under forest had higher nutrient availability and a higher proportion of copiotrophic microbial communities compared to lithophytic moss crusts under forest or on cliff rock. However, enzyme activities were lower in autochthonal moss crusts under forest. Additionally, rare taxa exhibited distinct structures in all three habitats. Analysis of co-occurrence network showed that rare taxa had a relatively high proportion in the main modules. Furthermore, we found that both abundant and rare taxa were primarily assembled by stochastic processes. Soil properties significantly affected the community assembly of the rare taxa, indirectly affecting microbial diversity and complexity and finally nutrient acquisition. These findings highlight the importance of rare taxa under moss crusts for nutrient acquisition. Addressing this knowledge gap is essential for guiding ongoing ecological restoration projects in karst rocky desertification regions. [ABSTRACT FROM AUTHOR]

Introduction: An increasing number of studies have demonstrated the pivotal role of microbiota changes in the onset, progression, diagnosis, treatment, and prognosis of lung adenocarcinoma (LUAD). However, a comprehensive analysis of intratumoral microbiome variation across distinct LUAD stages has not been performed. The aim of this study was to identify the microbial markers that significantly vary during tumor stage of LUAD. Methods: Here, we used the cancer genome atlas (TCGA) database to comprehensively compare and analyze the differences in microbial composition between 267 patients with early and 224 patients with advanced LUAD. In order to determine the best biomarkers, we used the random forest (RF) model and found that the microbial markers have a certain ability in predicting the stage of LUAD. Results: We found that there were certain differences in the microbiome of patients with LUAD at different stages, especially in the tumor tissues of patients with advanced LUAD, whose co-abundance network was significantly more complex. We also found that five bacterial biomarkers (Pseudoalteromonas, Luteibacter, Caldicellulosiruptor, Loktanella, and Serratia) were correlated with LUAD stage, among which Pseudoalteromonas, Luteibacter, Caldicellulosiruptor, and Serratia were significantly overexpressed in patients with advanced LUAD. In particular, after integrating the biomarkers of mRNA, we achieved an area under the curve (AUC) of 0.70. Discussion: Our study revealed the microbial profile of patients with LUAD and the intrinsic pathogenic mechanism between the microbiome and the disease, and established a multi-omics model to determine LUAD tumor stage. [ABSTRACT FROM AUTHOR]

Simple Summary: Procambarus clarkii, an important freshwater species in China, is predominantly cultivated in an integrated rice–crayfish co-culture system. However, potential regional differences in the quality of P. clarkii have been scarcely reported. Therefore, the aim of this study was to assess the regional differences of P. clarkii through analyzing gut microbiota composition in specimens from ten major producing areas in China. Microbial sequencing analysis demonstrated that P. clarkii across various regions exhibit distinct microbial diversity and composition. These data would contribute to the assessment of the quality of P. clarkii aquaculture. The aim of this study was to assess the regional differences of Procambarus clarkii through analyzing gut microbiota in specimens from different areas in China. The P. clarkii were collected from ten integrated rice–crayfish farming systems locating across ten major producing areas as follows: Feixi (FX), Suqian (SQ), Yangzhou (YZ), Xuyi (XY), Qianjiang (QJ), Jianli (JL), Honghu (HH), Yueyang (YY), Changsha (CS), and Nanxian (NX). The composition of gut microbiota was assessed by analyzing 16S rRNA sequences. The PCoA results indicated significant differences in microbial community composition among the ten areas (R = 0.999, p = 0.001). The intestinal microbial diversity in P. clarkii cultured in rice fields from YY and CS exceeded that of other regions, with NX displaying the least diversity. At the phylum level, Proteobacteria were most abundant in HH, while Firmicutes showed increased relative abundances in FX and SQ, contrasted by lower relative abundances of Bacteroidetes in these areas. At the genus level, Ralstonia, Amedibacillus, Bacteroides, Anaerorhabdus, and Dysgonomonas were the dominant bacteria. The bacterial co-occurrence networks analysis revealed that the community structures in locations FX, SQ, XY, HH, and NX were comparatively simplistic, whereas those in the YZ, QJ, JL, YY, and CS regions displayed as more complex. In summary, the diversity and relative abundance of intestinal bacteria exhibits regional variability. These findings can offer theoretical data for evaluating the quality of P. clarkii aquaculture. [ABSTRACT FROM AUTHOR]

Plants are associated with a large diversity of microbes, and these complex plantassociated microbial communities are critical for plant health. Welsh onion (Allium fistulosum L.) is one of the key and oldest vegetable crops cultivated in Taiwan. The leaf of the Welsh onion is one of the famous spices in Taiwanese cuisine, thus, it is crucial to control foliar diseases. In recent years, Welsh onion cultivation in Taiwan has been severely threatened by the occurrence of leaf blight disease, greatly affecting their yield and quality. However, the overall picture of microbiota associated with the Welsh onion plant is still not clear as most of the recent etiological investigations were heavily based on the isolation of microorganisms from diseased plants. Therefore, studying the diversity of fungal communities associated with the leaf blight symptoms of Welsh onion may provide information regarding key taxa possibly involved in the disease. Therefore, this investigation was mainly designed to understand the major fungal communities associated with leaf blight to identify key taxa potentially involved in the disease and further evaluate any shifts in both phyllosphere and rhizosphere mycobiome assembly due to foliar pathogen infection by amplicon sequencing targeting the Internal Transcribed Spacer (ITS) 1 region of the rRNA. The alpha and beta-diversity analyses were used to compare the fungal communities and significant fungal groups were recognized based on linear discriminant analyses. Based on the results of relative abundance data and co-occurrence networks in symptomatic plants we revealed that the leaf blight of Welsh onion in Sanxing, is a disease complex mainly involving Stemphylium and Colletotrichum taxa. In addition, genera such as Aspergillus, Athelia and Colletotrichum were abundantly found associated with the symptomatic rhizosphere. Alphadiversity in some fields indicated a significant increase in species richness in the symptomatic phyllosphere compared to the asymptomatic phyllosphere. These results will broaden our knowledge of pathogens of Welsh onion associated with leaf blight symptoms and will assist in developing effective disease management strategies to control the progress of the disease. [ABSTRACT FROM AUTHOR]

The objective of this study was to explore excellent silage production through co-ensiling whole-plant cassava and corn stalk, and different ratios of whole-plant cassava (0%, 10%, 20%, 30%, 40%, and 50%, fresh-matter basis) co-ensiled with corn stalk were analyzed based on the silage bacterial community, function profile, and microbial ecological network features. The results demonstrated that co-ensiling 30% whole-plant cassava with 70% corn stalk could be considered an efficient mode of production. The mixed silage showed great quality, as reflected by the reduced pH value and concentrations of acetic acid, butyric acid, and ammonia nitrogen and the enhanced lactic acid concentration, V-score, and nutritional value compared with corn stalk ensiled alone. Meanwhile, co-ensiling restricted the undesirable bacterial Acetobacter fabarum of corn stalk and Pseudomonas aeruginosa of whole-plant cassava and raised the abundance of lactic acid bacteria (LAB) such as Levilactobacillus brevis, Lactiplantibacillus plantarum, Lactobacillus harbinensis, etc. Besides that, the predicted functions of the bacterial community showed large differences in mixed silage compared with whole-plant cassava or corn stalk ensiled alone. Moreover, the analysis of co-occurrence networks showed that mixed silage affected microbial network features, module numbers, and bacterial relative abundances and weakened the complexity and stability of the networks compared with whole-plant cassava single silage. Furthermore, silage microbial community composition had a huge impact on the network properties, and undesirable Pseudomonas aeruginosa played a crucial role in the complexity and stability. Overall, this study revealed the characteristics of whole-plant cassava with corn stalk mixed-silage microbial communities and co-occurrence network modules, complexity, and stability and partly clarified the microbial mechanism of co-ensiling for producing high-quality silage. The findings of this study have important implications for deeply understanding the ensiling process and precisely regulating silage fermentation quality. [ABSTRACT FROM AUTHOR]

The way strong environmental gradients shape multispecific assemblages has allowed us to examine a suite of ecological and evolutionary hypotheses about structure, regulation and community responses to fluctuating environments. But whether the highly diverse co-occurring microorganisms are shaped in similar ways as macroscopic organisms across the same gradients has yet to be addressed in most ecosystems. Here, we characterize intertidal biofilm bacteria communities, comparing zonation at both the "species" and community levels, as well as network attributes, with co-occurring macroalgae and invertebrates in the same rocky shore system. The results revealed that the desiccation gradient has a more significant impact on smaller communities, while both desiccation and submersion gradients (surge) affect the larger, macroscopic communities. At the community level, we also confirmed the existence of distinct communities within each intertidal zone for microorganisms, similar to what has been previously described for macroorganisms. But our results indicated that dominant microbial organisms along the same environmental gradient exhibited less differentiation across tidal levels than their macroscopic counterparts. However, despite the substantial differences in richness, size and attributes of co-occurrence networks, both macro- and micro-communities respond to stress gradients, leading to the formation of similar zonation patterns in the intertidal rocky shore. [ABSTRACT FROM AUTHOR]

Biotic stresses, such as plant viruses, e.g., cotton leaf curl virus (CLCuV), can alter root-associated and leaf-associated microbial diversities in plants. There are complex ecological dynamics at play, with each microbe contributing to a multitude of biotic and abiotic interactions, thus deciding the stability of the plant’s ecosystem in response to the disease. Deciphering these networks of interactions is a challenging task. The inferential research in microbiome is also at a nascent stage, often constrained by the underlying analytical assumptions and the limitations with respect to the depth of sequencing. There is also no real consensus on network-wide statistics to identify the influential microbial players in a network. Guided by the latest developments in network science, including recently published metrics such as Integrated View of Influence (IVI) and some other centrality measures, this study provides an exposé of the most influential nodes in the rhizospheric and phyllospheric microbial networks of the cotton leaf curl disease (CLCuD) susceptible, partially tolerant, and resistant cotton varieties. It is evident from our results that the CLCuD-resistant Gossypium arboreum possesses an equal share of keystone species, which helps it to withstand ecological pressures. In the resistant variety, the phyllosphere harbors the most influential nodes, whereas in the susceptible variety, they are present in the rhizosphere. Based on hubness score, spreading score, and IVI, the top 10 occurring keystone species in the FDH-228 (resistant) variety include Actinokineospora, Cohnella, Thermobacillus, Clostridium, Desulfofarcimen, and MDD-D21. Elusimicrobia, Clostridium-sensu-stricto_12, Candidatus woesebacteria, and Dyella were identified as the most influential nodes in the PFV-1 (partially tolerant) variety. In the PFV-2 (susceptible) variety, the keystone species were identified as Georginia, Nesterenkonia, Elusimicrobia MVP-88, Acetivibrio, Tepedisphaerales, Chelatococcus, Nitrosospira, and RCP2-54. This concept deciphers the diseased and healthy plant’s response to viral disease, which may be microbially mediated.

Aim: The purpose of this article is to give an analysis of developing trends and research hotspots within the KLE Academy of Higher Education and Research (KAHER) Group using bibliometric methodologies. Materials and Methods: Using co-authorship, co-citation, and co-occurrence analysis, publications from the Scopus database for the years 1973–2022 are examined and analyzed on a variety of factors. R-Programming (Biblioshiny) and VOSViewer, an application for scientific visualization, are used to do the analysis. Results: There were 1721 publications in Scopus throughout the study period, with 83.9% of those being journal articles and the remaining 6% being letters and case studies. Research generally shows a constant rise with growing multi-authorship. The most sought-after magazine for publishing by the writers at KAHER is “Reproductive Health,” and they prefer to collaborate on research pieces. In addition, health-care science services and medical informatics have steadily developed into new areas of scientific interest. Originality: This study offers a thorough and comprehensive analysis of the KAHERs' formative environment. This study can serve as a solid starting point for future research and can be used to analyze how health science research has changed overtime. Conclusion: The study reveals KAHER's robust publishing productivity and impact, with a diverse output among authors and a consistent growth in the number of publications. The dominance of collaborative research, high citation rates, and the prevalence of medical research suggest the importance of international collaborations and the implementation of an institutional online repository system for enhanced research efficacy and accessibility.

Aim: The purpose of this article is to give an analysis of developing trends and research hotspots within the KLE Academy of Higher Education and Research (KAHER) Group using bibliometric methodologies. Materials and Methods: Using co-authorship, co-citation, and co-occurrence analysis, publications from the Scopus database for the years 1973–2022 are examined and analyzed on a variety of factors. R-Programming (Biblioshiny) and VOSViewer, an application for scientific visualization, are used to do the analysis. Results: There were 1721 publications in Scopus throughout the study period, with 83.9% of those being journal articles and the remaining 6% being letters and case studies. Research generally shows a constant rise with growing multi-authorship. The most sought-after magazine for publishing by the writers at KAHER is "Reproductive Health," and they prefer to collaborate on research pieces. In addition, health-care science services and medical informatics have steadily developed into new areas of scientific interest. Originality: This study offers a thorough and comprehensive analysis of the KAHERs' formative environment. This study can serve as a solid starting point for future research and can be used to analyze how health science research has changed overtime. Conclusion: The study reveals KAHER's robust publishing productivity and impact, with a diverse output among authors and a consistent growth in the number of publications. The dominance of collaborative research, high citation rates, and the prevalence of medical research suggest the importance of international collaborations and the implementation of an institutional online repository system for enhanced research efficacy and accessibility. [ABSTRACT FROM AUTHOR]

Agricultural activities are fundamental to societies, including the planting, growing, harvesting and processing of agricultural crops. However, there are a large number of occupational risks that can arise during the course of agricultural activities. These risks could result in serious injury or even death. This requires introducing and providing the relevant bodies and workers with knowledge, perception and awareness of the risk. The present study assessed the available reports on occupational health and safety using a bibliometric analysis and dimension reduction approach. Briefly, the reports were extracted from SCOPUS database. We identified 943 relevant and available peer-reviewed publications from the Scopus database. These were published between 1956 and 2022. The retrieved documents were analysed with the R-studio based software Bibliometrix. For the analysis, co-occurrences of networks, thematic maps and trending topics were analyzed. The results of the present study show that the time span of the documents ranges from 1956 to 2022 and these documents, including journals, books, book chapters and conference papers, were disseminated in 313 different sources. The estimated annual growth rate of these documents is 6.35%. Even the first paper dates back to the 1950s, the average age of the documents are 10.7. Considering the spatial distribution of the documents, USA topped at the list and was followed by Australia, Brazil, Italy, Canada, UK, and China. It is interesting to note that 'confined spaces' were found to be the trending topic according to the trend topic analysis of the keywords. Also, after the basic keywords (occupational health and safety and agriculture) of the study, ergonomics was the core keyword of the relevant analysis. Critically, the level of cooperation between countries was very low, with a rate of 0.025-0.207 for co-operation between countries (MCPs). For Turkey, the MCP was found to be 0.000. According to the thematic map, the motor theme is composed of two major clusters. One relates to food safety, risk analysis, knowledge and awareness and hygiene. To the best of our knowledge, this is the first study of its kind to identify the key issues in occupational health and safety in the agricultural industry. Therefore, the study has potential to contribute to the field. [ABSTRACT FROM AUTHOR]

Cold seeps are highly productive chemosynthetic ecosystems in the deep-sea environment. Although microbial communities affected by methane seepage have been extensively studied in sediments and seawater, there is a lack of investigation of prokaryotic communities at the surface sediments and bottom seawater. We revealed the effect of methane seepage on co-occurrence networks and ecological niches of prokaryotic communities at the surface sediments and bottom seawater in the Haima cold seep. The results showed that methane seepage could cause the migration of Mn and Ba from the surface sediments to the overlying seawater, altering the elemental distribution at seepage sites (IS) compared with non-seepage sites (NS). Principal component analysis (PCA) showed that methane seepage led to closer distances of bacterial communities between surface sediments and bottom seawater. Co-occurrence networks indicated that methane seepage led to more complex interconnections at the surface sediments and bottom seawater. In summary, methane seepage caused bacterial communities in the surface sediments and bottom seawater to become more abundant and structurally complex. This study provides a comprehensive comparison of microbial profiles at the surface sediments and bottom seawater of cold seeps in the South China Sea (SCS), illustrating the impact of seepage on bacterial community dynamics. [ABSTRACT FROM AUTHOR]

Reducing nitrogen fertilizer application highlights its role in optimizing soil bacterial communities to achieve sustainable agriculture. However, the specific mechanisms of bacterial community change under these conditions are not yet clear. In this study, we employed long-term field experiments and high-throughput sequencing to analyze how varying levels of nitrogen application influence the soil bacterial community structure and co-occurrence networks. The results show that reducing the nitrogen inputs significantly enhances the diversity and evenness of the soil bacterial communities, possibly due to the diminished dominance of nitrogen-sensitive taxa, which in turn liberates the ecological niches for less competitive species. Furthermore, changes in the complexity and stability of the bacterial co-occurrence networks suggest increased community resilience and a shift toward more mutualistic interactions. These findings underline the potential of reduced nitrogen application to alleviate competitive pressures among bacterial species, thereby promoting a more diverse and stable microbial ecosystem, highlighting the role of competitive release in fostering microbial diversity. This research contributes to our understanding of how nitrogen management can influence soil health and offers insights into sustainable agricultural practices.

Plants are associated with a large diversity of microbes, and these complex plant-associated microbial communities are critical for plant health. Welsh onion (Allium fistulosum L.) is one of the key and oldest vegetable crops cultivated in Taiwan. The leaf of the Welsh onion is one of the famous spices in Taiwanese cuisine, thus, it is crucial to control foliar diseases. In recent years, Welsh onion cultivation in Taiwan has been severely threatened by the occurrence of leaf blight disease, greatly affecting their yield and quality. However, the overall picture of microbiota associated with the Welsh onion plant is still not clear as most of the recent etiological investigations were heavily based on the isolation of microorganisms from diseased plants. Therefore, studying the diversity of fungal communities associated with the leaf blight symptoms of Welsh onion may provide information regarding key taxa possibly involved in the disease. Therefore, this investigation was mainly designed to understand the major fungal communities associated with leaf blight to identify key taxa potentially involved in the disease and further evaluate any shifts in both phyllosphere and rhizosphere mycobiome assembly due to foliar pathogen infection by amplicon sequencing targeting the Internal Transcribed Spacer (ITS) 1 region of the rRNA. The alpha and beta-diversity analyses were used to compare the fungal communities and significant fungal groups were recognized based on linear discriminant analyses. Based on the results of relative abundance data and co-occurrence networks in symptomatic plants we revealed that the leaf blight of Welsh onion in Sanxing, is a disease complex mainly involving Stemphylium and Colletotrichum taxa. In addition, genera such as Aspergillus, Athelia and Colletotrichum were abundantly found associated with the symptomatic rhizosphere. Alpha-diversity in some fields indicated a significant increase in species richness in the symptomatic phyllosphere compared to the asymptomatic phyllosphere. These results will broaden our knowledge of pathogens of Welsh onion associated with leaf blight symptoms and will assist in developing effective disease management strategies to control the progress of the disease.

ABSTRACTTerrestrial plants can influence the growth and health of adjacent plants through interspecific interaction. Here, the mechanisms of interspecific plant interaction on microbial function and nutrient utilization in the plant-soil interface (non-rhizosphere soil, rhizosphere soil, and root) were studied by soybean- and potato-poplar intercropping. First, metagenomics showed that soybean- and potato-poplar intercropping influenced the composition and co-occurrence networks of microbial communities in different ecological niches, with higher stability of the microbial community in soybean intercropping. Second, the gene abundance related to carbon metabolism, nitrogen cycling, phosphorus cycling, and sulfur cycling was increased at the poplar-soil interface in soybean intercropping. Moreover, soybean intercropping increased soil nutrient content and enzymatic activity. It showed higher metabolic potential in nutrient metabolism and transportation. Third, functional microorganisms that influenced nutrient cycling and transportation in different intercropping have been identified, namely Acidobacteria, Sphingomonas, Gemmatimonadaceae, Alphaproteobacteria, and Bradyrhizobium. Therefore, intercropping can construct microbial communities to alter metabolic functions and improve nutrient cycling and absorption. Interspecific plant interactions to influence the microbiome were revealed, opening up a new way for the precise regulation of plant microbiome.IMPORTANCEPoplar has the characteristics of wide distribution, strong adaptability, and fast growth, which is an ideal tree species for timber forest. In this study, metagenomics and elemental analysis were used to comprehensively reveal the effects of interspecific plant interactions on microbial communities and functions in different ecological niches. It can provide a theoretical basis for the development and application of the precise management model in poplar.

ABSTRACTCitizens lack knowledge about the impact of gut microbiota on health and how lifestyle and dietary choices can influence it, leading to Non-Communicable Diseases (NCDs) and affecting overall well-being. Participatory action research (PAR) is a promising approach to enhance communication and encourage individuals to adopt healthier behaviors and improve their health. In this study, we explored the feasibility of integrating the photovoice method with citizen science approaches to assess the impact of social and environmental factors on gut microbiota health. In this context, citizen science approaches entailed the involvement of participants in the collection of samples for subsequent analysis, specifically gut microbiome assessment via 16S rRNA gene sequencing. We recruited 70 volunteers and organized six photovoice groups based on age and educational background. Participants selected 64 photographs that represented the influence of daily habits on gut microbiota health and created four photovoice themes. Analysis of the gut microbiome using 16S rRNA gene sequencing identified 474 taxa, and in-depth microbial analysis revealed three clusters of people based on gut microbiome diversity and body mass index (BMI). Our findings indicate that participants enhanced their knowledge of gut microbiome health through PAR activities, and we found a correlation between lower microbial diversity, higher BMI, and better achievement of learning outcomes. Using PAR as a methodology is an effective way to increase citizens’ awareness and engagement in self-care, maintain healthy gut microbiota, and prevent NCD development. These interventions are particularly beneficial for individuals at higher risk of developing NCDs.

Root hypoxia stress and soil nutrient turnover have been related to reduced crop productivity. Aerated drip irrigation (ADI) can effectively enhance crop productivity and yield. However, the response of the soil bacterial community to different irrigation water dissolved oxygen (DO) concentrations remains elusive due to the extreme sensitivity of microorganisms to environmental variations. We investigated the effects of aerated irrigation with different concentrations of DO on soil properties and agronomic performance of cucumber, as well as the contribution of the bacterial community. We performed experiments on cucumber cultivation in Shouguang, China, including different irrigation methods (ADI: O2–10 and O3–20 mg L−1, non-aerated groundwater: O1–5 mg L−1) and nitrogen (N) application rates: 240 and 360 kg N ha−1. ADI (particularly O2) significantly improved soil properties, root growth, cucumber yields, and irrigation water use efficiency (IWUE), and appropriate DO concentrations reduced N fertilizer application and increased crop yields. Furthermore, these changes were associated with bacterial community diversity, aerobic bacteria abundance, and consolidated bacterial population stability within the network module. Environmental factors such as soil respiration rate (Rs), DO, and NO3−-N have significant effects on bacterial communities. The FAPROTAX results demonstrated enhanced nitrification (Nitrospira) and aerobic nitrite oxidation by soil bacteria under ADI, promoting the accumulation of effective soil N and improved soil fertility and crop yield. Appropriate DO concentration is conducive to the involvement of soil bacterial communities in regulating soil properties and cucumber growth performance, which are vital for the sustainable development of facility agriculture. [ABSTRACT FROM AUTHOR]

As one of the low-carbon and high-efficient energy sources, nuclear power is developing vigorously to alleviate the crisis of global climate warming and realize carbon neutrality goals. Meanwhile, the ecological effect of thermal drainage in the nuclear power plant is significantly remarkable, which environmental assessment system has not yet referred to microorganisms. The rapid response of microbial diversity and community structure to environmental changes is crucial for ecosystem stability. This study investigated the bacterial diversity, community construction, and the co-occurrence patterns by 16S rRNA gene amplicon sequencing among gradient warming regions in Tianwan Nuclear Power Plant. The alpha diversity of the high warming region was the lowest in summer, which was dominated by Proteobacteria, whereas the highest bacterial diversity presented in high warming regions in winter, which harbored higher proportions of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. The spatial distribution of bacterial communities showed clear separation especially in summer. Strong correlations were between community compositions and environmental factors, such as salinity, DO, TN, and temperature in summer. Furthermore, remarkable seasonality in bacterial co-occurrence patterns was discovered: the robustness of the bacterial co-occurrence network was promoted in winter, while the complexity and robustness were decreased in summer due to the warming of thermal drainage. These findings reveal the potential factors underpinning the influence of thermal drainage on bacterial community structure, which make it possible to predict the ecological effect of the nuclear power plants by exploring how the microbial assembly is likely to respond to the temperature and other environmental changes. [ABSTRACT FROM AUTHOR]

Denitrifying bacteria in epiphytic biofilms play a crucial role in nitrogen cycle in aquatic habitats. However, little is known about the connection between algae and denitrifying bacteria and their assembly processes in epiphytic biofilms. Epiphytic biofilms were collected from submerged macrophytes (Patamogeton lucens and Najas marina L.) in the Caohai Lake, Guizhou, SW China, from July to November 2020 to: (1) investigate the impact of abiotic and biotic variables on denitrifying bacterial communities; (2) investigate the temporal variation of the algae-denitrifying bacteria co-occurrence networks; and (3) determine the contribution of deterministic and stochastic processes to the formation of denitrifying bacterial communities. Abiotic and biotic factors influenced the variation in the denitrifying bacterial community, as shown in the Mantel test. The co-occurrence network analysis unveiled intricate interactions among algae to denitrifying bacteria. Denitrifying bacterial community co-occurrence network complexity (larger average degrees representing stronger network complexity) increased continuously from July to September and decreased in October before increasing in November. The co-occurrence network complexity of the algae and nirS-encoding denitrifying bacteria tended to increase from July to November. The co-occurrence network complexity of the algal and denitrifying bacterial communities was modified by ammonia nitrogen (NH4+-N) and total phosphorus (TP), pH, and water temperature (WT), according to the ordinary least-squares (OLS) model. The modified stochasticity ratio (MST) results reveal that deterministic selection dominated the assembly of denitrifying bacterial communities. The influence of environmental variables to denitrifying bacterial communities, as well as characteristics of algal-bacterial co-occurrence networks and the assembly process of denitrifying bacterial communities, were discovered in epiphytic biofilms in this study. The findings could aid in the appropriate understanding and use of epiphytic biofilms denitrification function, as well as the enhancement of water quality. [ABSTRACT FROM AUTHOR]

Introduction: Soil ecosystems are threatened by crude oil contamination, requiring effective microbial remediation. However, our understanding of the key microbial taxa within the community, their interactions impacting crude oil degradation, and the stability of microbial functionality in oil degradation remain limited. Methods: To better understand these key points, we enriched a crude oil-degrading bacterial consortium generation 1 (G1) from contaminated soil and conducted three successive transfer passages (G2, G3, and G4). Integrated Cooccurrence Networks method was used to analyze microbial species correlation with crude oil components across G1-G4. Results and discussion: In this study, G1 achieved a total petroleum hydrocarbon (TPH) degradation rate of 32.29% within 10 days. Through three successive transfer passages, G2-G4 consortia were established, resulting in a gradual decrease in TPH degradation to 23.14% at the same time. Specifically, saturated hydrocarbon degradation rates ranged from 18.32% to 14.17% among G1-G4, and only G1 exhibited significant aromatic hydrocarbon degradation (15.59%). Functional annotation based on PICRUSt2 and FAPROTAX showed that functional potential of hydrocarbons degradation diminished across generations. These results demonstrated the functional instability of the bacterial consortium in crude oil degradation. The relative abundance of the Dietzia genus showed the highest positive correlation with the degradation efficiency of TPH and saturated hydrocarbons (19.48, 18.38, p < 0.05, respectively), Bacillus genus demonstrated the highest positive correlation (21.94, p < 0.05) with the efficiency of aromatic hydrocarbon degradation. The key scores of Dietzia genus decreased in successive generations. A significant positive correlation (16.56, p < 0.05) was observed between the Bacillus and Mycetocola genera exclusively in the G1 generation. The decline in crude oil degradation function during transfers was closely related to changes in the relative abundance of key genera such as Dietzia and Bacillus as well as their interactions with other genera including Mycetocola genus. Our study identified key bacterial genera involved in crude oil remediation microbiome construction, providing a theoretical basis for the next step in the construction of the oil pollution remediation microbiome. [ABSTRACT FROM AUTHOR]

Introduction: Organic agriculture is highly regarded by people for its commitment to health, ecology, care, and fairness. The soil microbial community responds quickly to environmental changes and is a good indicator for evaluating soil microecology. Therefore, from the perspective of soil microbial communities, elucidating the impact of organic management on soil microecology in tea plantations has great significance for improving local tea plantation systems. Methods: The study collected bulk soil from organic management (OM) and conventional management (CM) tea plantations in Pu’er City, a major tea-producing area in China, and analyzed their species diversity, structural composition, and co-occurrence networks using metagenomics technology. Results: Compared with CM, the diversity index (Shannon) and evenness index (Heip) of soil fungi increased by 7.38% and 84.2% in OM tea plantations, respectively. The relative abundance of microorganisms related to the nitrogen cycle increased. Specifically, there was a significant increase in Rhodobiales, a 2-fold increase in Nitrospirae, and approximately 1.95 and 2.03 times increases in unclassified genera within Betaproteobacteria and Deltaproteobacteria, respectively. The relative abundance of plant residue degradation species, Gemmatimonadetes, Ascomycota, and Basidiomycota, increased by 2.8, 1, and 1.4 times, respectively. The OM was conducive to the establishment of collaborative relationships among bacterial species and increased the diversity and complexity of species relationships in fungal communities. The network stability of soil ecosystems was promoted. The organic tea plantations’ keystone taxa contained mycorrhizal fungi (Pezoloma_ericae, Rhizophagus_irregularis, Rhizophagus_clarus), as well as species involved in soil nitrogen metabolism (Acidobacteria_bacterium, Acidobacteriia_bacterium_AA117, Sphingomonas_sp._URHD0007, Enhydrobacter_aerosaccus), pathogen (Erysiphe_pulchra), and parasites (Paramycosporidium saccamoeba). The partial least squares method (PLS-SEM) indicated that OM affected N-NH+4negatively, increasing the abundance of fungi, and thereby positively affecting the Shannon index. Conclusion: In brief, reasonable organic management can improve the diversity of soil microorganisms, increase the relative abundance of beneficial bacteria in tea plantation soil, and promote the stability of the soil microbial ecological network. [ABSTRACT FROM AUTHOR]

Genes duplicate, mutate, recombine, fuse or fission to produce new genes, or when genes are formed from de novo, novel functions arise during evolution. Researchers have tried to quantify the causes of these molecular diversification processes to know how these genes increase molecular complexity over a period of time, for instance protein domain organization. In contrast to global sequence similarity, protein domain architectures can capture key structural and functional characteristics, making them better proxies for describing functional equivalence. In Prokaryotes and eukaryotes it has proven that, domain designs are retained over significant evolutionary distances. Protein domain architectures are now being utilized to categorize and distinguish evolutionarily related proteins and find homologs among species that are evolutionarily distant from one another. Additionally, structural information stored in domain structures has accelerated homology identification and sequence search methods. Tools for functional protein annotation have been developed to discover, protein domain content, domain order, domain recurrence, and domain position as all these contribute to the prediction of protein functional accuracy. In this review, an attempt is made to summarise facts and speculations regarding the use of protein domain architecture and modularity to identify possible therapeutic targets among cellular activities based on the understanding their linked biological processes. [ABSTRACT FROM AUTHOR]

Abstract Background Soil microorganisms are in constant interaction with plants, and these interactions shape the composition of soil bacterial communities by modifying their environment. However, little is known about the relationship between microorganisms and native plants present in extreme environments that are not affected by human intervention. Using high-throughput sequencing in combination with random forest and co-occurrence network analyses, we compared soil bacterial communities inhabiting the rhizosphere surrounding soil (RSS) and the corresponding bulk soil (BS) of 21 native plant species organized into three vegetation belts along the altitudinal gradient (2400–4500 m a.s.l.) of the Talabre–Lejía transect (TLT) in the slopes of the Andes in the Atacama Desert. We assessed how each plant community influenced the taxa, potential functions, and ecological interactions of the soil bacterial communities in this extreme natural ecosystem. We tested the ability of the stress gradient hypothesis, which predicts that positive species interactions become increasingly important as stressful conditions increase, to explain the interactions among members of TLT soil microbial communities. Results Our comparison of RSS and BS compartments along the TLT provided evidence of plant-specific microbial community composition in the RSS and showed that bacterial communities modify their ecological interactions, in particular, their positive:negative connection ratios in the presence of plant roots at each vegetation belt. We also identified the taxa driving the transition of the BS to the RSS, which appear to be indicators of key host-microbial relationships in the rhizosphere of plants in response to different abiotic conditions. Finally, the potential functions of the bacterial communities also diverge between the BS and the RSS compartments, particularly in the extreme and harshest belts of the TLT. Conclusions In this study, we identified taxa of bacterial communities that establish species-specific relationships with native plants and showed that over a gradient of changing abiotic conditions, these relationships may also be plant community specific. These findings also reveal that the interactions among members of the soil microbial communities do not support the stress gradient hypothesis. However, through the RSS compartment, each plant community appears to moderate the abiotic stress gradient and increase the efficiency of the soil microbial community, suggesting that positive interactions may be context dependent.

The aim of this study was to assess the regional differences of Procambarus clarkii through analyzing gut microbiota in specimens from different areas in China. The P. clarkii were collected from ten integrated rice–crayfish farming systems locating across ten major producing areas as follows: Feixi (FX), Suqian (SQ), Yangzhou (YZ), Xuyi (XY), Qianjiang (QJ), Jianli (JL), Honghu (HH), Yueyang (YY), Changsha (CS), and Nanxian (NX). The composition of gut microbiota was assessed by analyzing 16S rRNA sequences. The PCoA results indicated significant differences in microbial community composition among the ten areas (R = 0.999, p = 0.001). The intestinal microbial diversity in P. clarkii cultured in rice fields from YY and CS exceeded that of other regions, with NX displaying the least diversity. At the phylum level, Proteobacteria were most abundant in HH, while Firmicutes showed increased relative abundances in FX and SQ, contrasted by lower relative abundances of Bacteroidetes in these areas. At the genus level, Ralstonia, Amedibacillus, Bacteroides, Anaerorhabdus, and Dysgonomonas were the dominant bacteria. The bacterial co-occurrence networks analysis revealed that the community structures in locations FX, SQ, XY, HH, and NX were comparatively simplistic, whereas those in the YZ, QJ, JL, YY, and CS regions displayed as more complex. In summary, the diversity and relative abundance of intestinal bacteria exhibits regional variability. These findings can offer theoretical data for evaluating the quality of P. clarkii aquaculture.

Glossing was an important element of medieval Western manuscript culture. Yet, glosses are notoriously difficult to analyze because of their philological triviality, fluid nature, heterogeneity of origin, complex transmission histories, and anonymity. Traditional scholarly approaches such as close reading and genealogical method often do not produce satisfactory results, especially in the cases of gloss corpora that are highly organic, i.e., display the traits listed above to a significant degree. This article outlines a method for analyzing organic corpora of glosses based on their treatment as networks. The theoretical model for the proposed method is the co-occurrence network, a network model in which relationships between entities (nodes) are established based on sharing certain properties or constituent elements (edges). In the case of corpora of glosses, glossed manuscripts are assumed as nodes and glosses that particular manuscripts share in common constitute edges between them. Since gloss parallelism can arise through different processes, including randomness, the article describes two strategies that reduce such noise so that the transmission of glosses can be effectively examined. The method is demonstrated on a representative corpus – the early medieval glosses to the first book of the Etymologiae of Isidore of Seville.

ABSTRACT Crop microbiomes are widely recognized to play a role in crop stress resistance, but the ecological processes that shape crop microbiomes under water stress are unclear. Therefore, we investigated the bacterial communities of two oat (Avena sativa) and two wheat (Triticum aestivum) genotypes under different water stress conditions. Our results show that the microbial assemblage was determined by the crop compartment niche. Host selection pressure on the bacterial community increased progressively from soil to epiphyte to endophyte pathways, leading to a decrease in bacterial community diversity and network complexity. Source tracing shows that soil is the primary source of crop microbial communities and that bulk soil is the main potential source of crop microbiota. It filters gradually through the different compartment niches of the crop. We found that the phyla Actinobacteria, Proteobacteria, Gemmatimonadota, and Myxococcota were significantly enriched in bacterial communities associated with crop-resistance enzyme activity. Crop genotype influenced the composition of the rhizosphere soil microbial community, and the composition of the phylloplane microbial community was affected by water stress. IMPORTANCE In this paper, we investigated the assembly of the plant microbiome in response to water stress. We found that the determinant of microbiome assembly under water stress was the host type and that microbial communities were progressively filtered and enriched as they moved from soil to epiphyte to endophyte communities, with the main potential source being bulk soil. We also screened for bacterial communities that were significantly associated with crop enzyme activity. Our research provides insights into the manipulation of microbes in response to crop resistance to water stress.

The world is currently confronted with a complex task involving the sustainable balance of food production and long-term consumption. One way to face this challenge is through agroforestry systems (ASF). At the national level, there is relevant information on the subject; however, few studies have attempted to analyze trends in agroforestry scientific development over time. In this sense, it was proposed that the number of ASF publications related to food security and natural resource conservation increase on an annual basis. The objective of the present study was to perform a quantitative analysis of agroforestry research published between 1990 and 2022 from Web of Science in Mexico with a bibliometric approach. There were 204 publications related to agroforestry systems, recording an increase of 86 % in the last decade. Among the scientific journals analyzed, Agroforestry Systems and Journal of Ethnobiology and Ethnomedicine registered the highest number of publications and citations. The most frequent terms mentioned in publications over 32 years were the relationship between the effects of ASF on crops, traditional management, local knowledge, and the conservation of natural resources. The Universidad Nacional Autónoma de México (UNAM) is the institution with the highest number of research works on the subject, mainly by scientists Alejandro Casas Fernandez and Isabel Moreno Calles, both individually and collaboratively. In conclusion, the number of publications on ASF increased during the time period studied, primarily in the area of food security. [ABSTRACT FROM AUTHOR]

Despite the increased use of cover crops (CCs) in grain and vegetable agroecosystems, CC effects on soil nutrient availability, fruit yield, and the soil microbiome in fruit orchard agroecosystems have been less explored. To address these issues, we planted two CC-mixtures (legumes and non-legumes and non-legumes only) in the inter-row middles of two commercial Florida citrus orchards (COA and COB) for three years. Traditional weedy row middles under grower standard management were used as a control (GSC). In COA, planting either CC mixture for three years significantly increased soil organic matter content and ammonium compared to the GSC and were related to increased bacteria, archaea, and nitrogen-cycling gene abundances. Planting CCs significantly increased alpha diversity, altered bacterial and fungal community composition, and increased the relative abundance of potentially beneficial bacterial taxa in COA. The use of CCs also increased bacterial and fungal network complexity and increased specific predicted bacterial functions and fungal guilds in COA after three years compared to the GSC. However, limited CC impacts on soil properties and microbial communities were observed in COB, likely due to lower CC establishment compared to COA. During the three years, CCs had no significant impact on fruit yield in both citrus orchards compared to the GSC. Overall, our results illustrate that although CCs promote changes in soil nutrient cycling and the soil microbiome in Florida citrus orchards, these changes can be site-specific and differ between fruit orchards under the same management and soil type. [ABSTRACT FROM AUTHOR]

Biodiesel Co‐Product (BCP) amendment has been shown to decrease both nitrate leaching and nitrous oxide (N2O) emissions in acidic soil; however, the effects of BCP on the soil microbiome have not been investigated thoroughly. In this study, we investigated the response of prokaryotic and fungal communities in aspects of structure, diversity, and co‐occurrence network to the BCP amendment following complete mixing application (0–18‐cm depth) of 1.5 mg BCP‐C g−1 and surface application (0–6‐cm depth) of 4.5 mg BCP‐C g−1 via high‐throughput 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing. The amendment altered microbial communities significantly by increasing the relative abundances of Proteobacteria (Burkholderia) and Ascomycota (Trichoderma) in prokaryotic and fungal communities, respectively. Only a higher rate application (4.5 mg BCP‐C g−1) decreased prokaryotic alpha diversity, whereas all rates of amendment decreased fungal diversity. The co‐occurrence network of prokaryotes had more nodes and links and a higher average degree and clustering coefficient than the fungal network with BCP addition. The majority of keystone species in prokaryotic and fungal networks were from Proteobacteria and Ascomycota taxa. Of note, the BCP amendment significantly increased the OTU numbers of potential biocontrol agents, including Trichoderma (T.) spirale, T. koningiopsis, and T. virens, etc., while decreased OTU numbers related to plant pathogens species, particularly in the complete mixing application. Our work highlights the potential for BCP amendments to promote the assembly of a healthy soil microbiome by enhancing the abundance of potential biocontrol microbes while reducing plant pathogens species, which may contribute to soil health. [ABSTRACT FROM AUTHOR]

Ergonomics for environmental sustainability has been rapidly gaining attention in the scientific community. So far, a large part of the literature has focussed on specific dimensions of ergonomics for environmental sustainability, such as green designs, green buildings, environmental education, and sustainability frameworks. However, there is a necessity for an integrated study that presents the summary of published literature supported by detailed bibliometric characteristics. To address this gap, this study examined 418 articles on ergonomics for environmental sustainability and analysed them through bibliometric and network analysis. Major findings reveal the publication trends in ergonomics for environmental sustainability starting from 2011 to the present, the most productive and influential authors, and the most influential articles. This study also identifies the co-citation structure, bibliographical couplings and keyword co-occurrences among these articles. Findings from this study also provide a summary of the current research and present a robust roadmap for future directions in ergonomics for environmental sustainability. Practitioner summary: This paper presents a bibliometric and network analysis of the academic literature in the domain of ergonomics for environmental sustainability. The study provides comprehensive insights into the relevant literature and identifies global research foci and future scopes. This study can guide practitioners in identifying the specific aspects of ergonomics for environmental sustainability to reduce global environmental impacts. [ABSTRACT FROM AUTHOR]