iNAP: An integrated network analysis pipeline for microbiome studies

Community stability of free-living and particle-attached prokaryotes in coastal waters across four seasons: insights from 9.5 years of weekly sampling

Free-living (FL) and particle-attached (PA) prokaryotes, having distinct ecological niches, play significant roles in marine ecosystems. These communities respond rapidly to environmental changes and exhibit seasonal patterns. However, their temporal stability, crucial for maintaining microbial community structure and function, remains poorly understood. This study assessed community stability, particularly in terms of resistance to environmental perturbations, and inferred regulatory mechanisms using weekly collected samples over 9.5 years from FL and PA communities in coastal water. Short-read amplicon sequencing revealed habitat-specific microbial compositions, with Actinobacteria and Euryarchaeota dominating FL community, while Planctomycetes and Verrucomicrobia prevailed in PA community. Network analysis, constructed based on relative abundance, uncovered seasonal co-occurrence patterns and highlighted keystone taxa, such as Nitrosopumilus in FL and Synechococcus in PA community, as critical for maintaining stability within specific seasons and niches. Seasonal variations in community stability indices suggest that higher network complexity can enhance resistance; however, excessive interactions with greater complexity may also undermine it. Furthermore, it was found that FL community stability was primarily affected by abiotic factors, likely due to direct exposure to environmental changes, whereas PA community stability was more influenced by biotic factors, as their association with particles fosters localized interactions and biological processes. These findings reveal the intricate balance between network complexity and stability and the importance of niche-specific approaches in ecological research. Our results contribute to a deeper understanding of marine microbial niche partitioning and provide insights into ecosystem management and conservation strategies, particularly regarding keystone taxa.

Changes in the assembly and functional adaptation of endophytic microbial communities in Amorphophallus species with different levels of resistance to necrotrophic bacterial pathogen stress

Pcc is one of the key pathogenic factors responsible for destructive soft rot in konjac. To date, the assembly and functional adaptation of the plant endophytic microbiome under Pcc stress remain poorly understood. Here, we found that Pcc stress leads to rapid reorganization of the endogenous microbiome in multiple organs of both susceptible and resistant konjac plants. Under Pcc stress, the negative interactions within the bacterial-fungal interdomain network intensified, suggesting an increase in ecological competition between bacterial and fungal taxa. We further discovered that the relative abundance dynamics of the classes Dothideomycetes and Sordariomycetes, as core fungal taxa, changed in response to Pcc stress. By isolating culturable microorganisms, we demonstrated that 46 fungal strains strongly inhibited the growth of Pcc. This implies that endophytic fungal taxa in konjac may protect the host plant through ecological competition or by inhibiting the growth of pathogenic bacteria. Metagenomic analysis demonstrated that microbial communities associated with resistant Amorphophallus muelleri exhibited unique advantages over susceptible Amorphophallus konjac in enhancing environmental adaptability, regulating plant immune signaling, strengthening cell walls, and inducing defense responses. Our work provides important evidence that endophytic fungal taxa play a key role in the host plant's defense against necrotizing bacterial pathogens.

Dynamic microbial community assembly and molecular ecological network responses in biological activated carbon filters: effects of algal organic matter exposure and empty bed contact time

Biological activated carbon (BAC) filtration plays a crucial role in advanced drinking water treatment. Recent researches have shifted from decontamination performance evaluation to process optimization and customization of microbial communities. The responses of microbial communities to seasonal water quality variations caused by algal outbreaks or deaths, and operational conditions of filtration medium and empty bed contact time (EBCT), along with dynamics of assembly processes and molecular ecological networks remain insufficiently understood. Herein, the decontamination performance of four BAC columns packed with varied physicochemical properties of granular activated carbon (GAC), exposed to algal organic matter (AOM) and changes of EBCT was investigated. Microbial diversity, assembly mechanisms, and dynamics of molecular ecological networks were systematically evaluated. Results showed that coal-based BAC exhibited superior decontamination performance under AOM exposure, with average removals of CODMn (47.23 %), UV254 (55.82 %), and NH4+-N (65.01 %), along with higher microbial diversity and richness than that of wood-based BAC. AOM exposure increased microbial diversity, while shortened EBCT reduced it. Deterministic processes in community assembly intensified under both AOM exposure and a shortened EBCT of 10 min, the proportion were up to 82 % and 75 %, respectively. AOM exposure increased network scale and complexity, whereas the opposite trend was observed with a shortened EBCT of 10min. Structural equation modeling identified that influent water quality (path coefficient = 1.00) was the dominant driver of microbial diversity, followed by GAC properties (0.30) and EBCT (-0.35). These findings provide insights for microbial community customization and BAC process optimization to control algal-derived organic contamination.

Spatial variation and influencing factors of planktonic and sedimentary bacterial communities in Daliao River estuary, Northeast China

Planktonic and sedimentary bacteria play distinct yet vital roles in maintaining the ecological balance of riverine and estuarine ecosystems. Understanding their composition and ecological functions is essential for effective ecosystem management and conservation. In this study, water and sediment samples were collected from the Daliao River, a major tributary of the Liao River basin in Northeast China, to explore the spatial variation of planktonic and sedimentary bacterial communities and identify the factors driving their distribution. The results exhibited significant differences in physicochemical properties of water and sediments along the river, which influenced bacterial diversity and community structure. Beta diversity analysis further revealed clear distinctions between planktonic and sedimentary communities. Proteobacteria and Bacteroidetes were the dominant phyla in both habitats, with Pseudomonas, Acinetobacter, and Woeseia identified as the most prevalent genera. Ecological network analysis indicated that planktonic bacterial communities exhibited a higher proportion of negative correlations and contained more potential keystone taxa compared to sedimentary communities. Functional gene analysis showed a notable presence of genes associated with nitrogen and phosphorus cycles, with nitrogen cycling genes being particularly abundant in planktonic communities. The pH and electrical conductivity emerged as the primary drivers influencing the structure and function of planktonic and sedimentary bacterial communities. Additionally, nutrients such as NO3--N and SO42- played significant roles in shaping planktonic bacterial communities. This study advances the understanding of microbial dynamics in riverine and estuarine ecosystems, providing a scientific basis for mitigating eutrophication, optimizing ecological restoration strategies, and strengthening holistic assessments of aquatic ecosystem health.

Progressing towards eco-friendly agricultural management: Utilizing Ginkgo biloba leaf litter for potato common scab control

Soil ecological degradation intensifies soil-borne crop diseases. Employing eco-friendly and economical strategies to restore soil health is imperative for managing soil diseases. Here, we focused on potato common scab (PCS), a worldwide soil-borne disease caused by Streptomyces spp., and evaluated the suppression effects of Ginkgo leaf litter (GL) and its extract (GE), while elucidating their mechanisms. The results showed that both GL and GE significantly reduced the PCS disease index, with GL achieving over 50 % suppression in both pot and field trials. Both treatments effectively antagonized the PCS pathogen, reducing its relative abundance in bulk soil and geocaulosphere soil. The soil bacterial community was significantly correlated with the disease index, with the bacterial community in bulk soil making a particularly notable contribution to disease suppression, accounting for 52 % of the effect. Furthermore, GL and GE enhanced the stochastic processes in bacterial community assembly, and increased the complexity of bacterial co-occurrence networks. Notably, the microbial community restructured by GE significantly inhibited the expression of the pathogen's toxin gene, txtAB, decreasing its level from 104.5 copies per gram of soil to 102.1 copies, marking a decline exceeding two orders of magnitude. ASV339 (Aeromicrobium) and ASV932 (Achromobacter) were identified as key microbes, and their respective strains, Aeromicrobium OH2-5 and Achromobacter YD1-3, were isolated. The growth curve and biomass of these strains were positively influenced by GE, demonstrating Ginkgo leaves' enriching effect on beneficial microorganisms. These strains exhibited potent antagonistic activity against the PCS pathogen. Additionally, GE alleviated reactive oxygen species stress and up-regulated the defense-related gene PR1 in potato plants. This study validates the potential of Ginkgo leaf litter as a soil amendment additive for suppressing PCS and reveals its multifaceted mechanisms.

Bacteroides thetaiotaomicron: A symbiotic ally against diarrhea along with modulation of gut microbial ecological networks via tryptophan metabolism and AHR-Nrf2 signaling

INTRODUCTION

Bacteroides is a crucial mucosal symbiotic bacterium in mammals, with Bacteroides thetaiotaomicron (B. thetaiotaomicron) being particularly noteworthy as a glyco-specialist due to its significant nutritional impact. However, the potential effects of B. thetaiotaomicron on host health remain underexplored.

OBJECTIVES

This study aimed to investigate the patterns of microbial community changes and the molecular mechanisms mediated by microbial metabolites in alleviating piglet diarrhea through B. thetaiotaomicron intervention.

METHODS

Cold stress was induced in piglets to trigger stress-induced diarrhea. The control group and B group were administered a blank medium and 1 × 108 CFU of B. thetaiotaomicron, respectively, on days 1, 3, and 5. The diarrhea rate and growth performance of the piglets were recorded during the experimental period. Based on 16S rRNA gene amplicon sequencing, microbial ecological networks analysis, and metabolomics analysis, the composition and changes of the colonic microbiota and metabolites were analyzed. The antibacterial capacity and anti-inflammatory molecular mechanisms of B. thetaiotaomicron metabolites were analyzed through in vitro antibacterial assays and inflammatory cell models.

RESULTS

B. thetaiotaomicron administration alleviated diarrhea and improved the growth performance of piglets. It modulated the composition and interactions of the intestinal microbiota, with microbial metabolites primarily enriched in the tryptophan metabolism pathway-especially indole and its derivatives, which were closely associated with host phenotypes. In vitro co-culture experiments showed that B. thetaiotaomicron metabolites inhibited the growth of pathogenic bacteria. Further experiments demonstrated that these metabolites, including indole, enhanced epithelial barrier function and attenuated TNF-α-induced inflammation and apoptosis in Caco-2 cells, highlighting the involvement of the AHR-Nrf2 signaling pathway in mediating these protective effects.

CONCLUSION

In conclusion, this study offers a theoretical framework for understanding the role of the symbiotic bacterium B. thetaiotaomicron in the gut microbiota ecosystem during diarrhea and its interactions with the host's intestinal tract.

Changes in the community composition and function of the rhizosphere microbiome in tobacco plants with Fusarium root rot

Introduction

Tobacco root rot caused by Fusarium spp. is a soil-borne vascular disease that severely affects tobacco production worldwide. To date, the community composition and functional shifts of the rhizosphere microbiome in tobacco plants infected with Fusarium root rot remain poorly understood.

Methods

In this study, we analyzed the differences in the compositions and functions of the bacterial and fungal communities in the rhizosphere and root endosphere of healthy tobacco plants and tobacco with Fusarium root rot using amplicon sequencing and metagenomic sequencing.

Results and discussion

Our results showed that Fusarium root rot disrupted the stability of bacteria-fungi interkingdom networks and reduced the network complexity. Compared to healthy tobacco plants, the Chao1 index of bacterial communities in the rhizosphere soil of diseased plants increased by 4.09% (P < 0.05), while the Shannon and Chao1 indices of fungal communities decreased by 13.87 and 8.17%, respectively (P < 0.05). In the root tissues of diseased plants, the Shannon index of bacterial and fungal communities decreased by 17.71-27.05% (P < 0.05). Additionally, we observed that the rhizosphere microbial community of diseased tobacco plants shifted toward a pathological combination, with a significant increase in the relative abundance of harmful microbes such as Alternaria, Fusarium, and Filobasidium (89.46-921.29%) and a notable decrease in the relative abundance of beneficial microbes such as Lysobacter, Streptomyces, Mortierella, and Penicillium (48.48-81.56%). Metagenomic analysis further revealed that the tobacco rhizosphere microbial communities of diseased plants played a significant role in basic biological metabolism, energy production and conversion, signal transduction, and N metabolism, but their functions involved in C metabolism were significantly weakened. Our findings provide new insights into the changes in and interactions within the rhizosphere and root endosphere microbiomes of tobacco plants under the stress of Fusarium soil-borne fungal pathogens, while laying the foundation for the exploration, development, and utilization of beneficial microbial resources in healthy tobacco plants in the future.

The Same Source of Microbes has a Divergent Assembly Trajectory Along a Hot Spring Flowing Path

Hot spring microbial mats represent intricate biofilms that establish self-sustaining ecosystems, hosting diverse microbial communities which facilitate a range of biochemical processes and contribute to the structural and functional complexity of these systems. While community structuring across mat depth has received substantial attention, mechanisms shaping horizontal spatial composition and functional structure of these communities remain understudied. Here, we explored the contributions of species source, local environment and species interaction to microbial community assembly processes in six microbial mat regions following a flow direction with a temperature decreasing from 73.3°C to 52.8°C. Surprisingly, we found that despite divergent community structures and potential functions across different microbial mats, large proportions of the community members (45.50%-80.29%) in the recipient mat communities originated from the same source community at the upper limit of temperature for photosynthetic life. This finding indicated that the source species were dispersed with water and subsequently filtered and shaped by local environmental factors. Furthermore, critical species with specific functional attributes played a pivotal role in community assembly by influencing potential interactions with other microorganisms. Therefore, species dispersal via water flow, environmental variables, and local species interaction jointly governed microbial assembly, elucidating assembly processes in the horizontal dimension of hot spring microbial mats and providing insights into microbial community assembly within extreme biospheres.

Impacts of forest expansion on microbial diversity and community assembly in fragmented mountain ecosystems

Under the influence of global climate change and human activities, forest expansion has become increasingly significant in shaping ecosystems. However, its effects on soil microbial communities remain poorly understood. This study investigates the impacts of forest expansion on soil bacteria, fungi, and protists within mountaintop forest ecosystems. Soil samples were collected from three forest habitats: non-forest expansion mountaintops (NFE-Top), forest expansion mountaintops (FE-Top) and mountain bottoms (FE-Bottom). This study revealed that forest expansion promoted microbial sharing between mountaintop and bottom forests, resulting in greater community similarity between FE-Top and FE-Bottom compared to NFE-Top and FE-Bottom. Notably, forest expansion significantly reduced microbial diversity and altered community composition, particularly within bacterial communities. Microbial network analyses indicated that forest expansion mountaintops were more stable, with higher robustness, and lower vulnerability than non-forest expansion mountaintops. Stochastic assembly processes dominated the microbial communities across all forest habitats, with their relative importance increasing after forest expansion. Furthermore, forest expansion decreased the community-level habitat niche breadth of microbial communities. Distinct environmental factors were the primary indicators of microbial community dissimilarities across different habitats, with TP, pH, and moisture acting as key indicators of these differences in NFE-Top, FE-Top, and FE-Bottom, respectively. These findings highlight the important role of forest expansion in shaping microbial community dynamics and emphasize the potential of microbial communities as indicators of ecosystem changes.

Different Land Use Systems in the Brazilian Cerrado and Their Effects on Soil Bacterial Communities

The effect of agricultural practices on soil bacterial communities is not constant and depends a lot on the climatic context, changes in the soil characteristics, land use, and agricultural strategy. Thus, knowledge about how different land use systems in the Cerrado influence the diversity and taxonomic structure of microbial communities under the same soil type remains limited. In this context, the objective of this work was to analyze and compare the bacterial communities of Cerrado soil under two different land use systems (cover crop and potato cultivation) and in a neighboring native Cerrado area. For this, we used high-throughput amplicon sequencing of 16S rRNA genes (metabarcoding) to characterize the bacterial community at different taxonomic levels in a native Cerrado area, in a potato crop area, and in an area with cover crops. Our data indicated significant impacts on soil physicochemical properties and enzymatic activity, which directly reflect the dynamics of bacterial communities. The three bacterial phyla with the highest relative abundance in the three areas were Proteobacteria, Actinobacteriota, and Acidobacteriota. At the taxonomic class level, small variations were observed among areas, while at the amplicon sequence variant (ASV) level, these variations were more pronounced. The alpha diversity indices showed that the bacterial communities among the areas are rich and diverse. Bray-Curtis and Jaccard distance-based PCoA demonstrated an overlap of bacterial communities present in the cover crop area with the native Cerrado area and separation from the potato cultivation area. The in silico prediction demonstrated that the native Cerrado area presented the highest values of functional diversity of the soil bacterial community compared to the others. Thus, our results provide a holistic view of how different land use systems in the Cerrado can influence the taxonomic and functional diversity of soil bacterial communities.

Compositional shifts and co-occurrence patterns of topsoil bacteria and micro-eukaryotes across a permafrost thaw gradient in alpine meadows of the Qilian Mountains, China

Soil microorganisms play a pivotal role in the biogeochemical cycles of alpine meadow ecosystems, especially in the context of permafrost thaw. However, the mechanisms driving microbial community responses to environmental changes, such as variations in active layer thickness (ALT) of permafrost, remain poorly understood. This study utilized next-generation sequencing to explore the composition and co-occurrence patterns of soil microbial communities, focusing on bacteria and micro-eukaryotes along a permafrost thaw gradient. The results showed a decline in bacterial alpha diversity with increasing permafrost thaw, whereas micro-eukaryotic diversity exhibited an opposite trend. Although changes in microbial community composition were observed in permafrost and seasonally frozen soils, these shifts were not statistically significant. Bacterial communities exhibited a greater differentiation between frozen and seasonally frozen soils, a pattern not mirrored in eukaryotic communities. Linear discriminant analysis effect size analysis revealed a higher number of potential biomarkers in bacterial communities compared with micro-eukaryotes. Bacterial co-occurrence networks were more complex, with more nodes, edges, and positive linkages than those of micro-eukaryotes. Key factors such as soil texture, ALT, and bulk density significantly influenced bacterial community structures, particularly affecting the relative abundances of the Acidobacteria, Proteobacteria, and Actinobacteria phyla. In contrast, fungal communities (e.g., Nucletmycea, Rhizaria, Chloroplastida, and Discosea groups) were more affected by electrical conductivity, vegetation coverage, and ALT. This study highlights the distinct responses of soil bacteria and micro-eukaryotes to permafrost thaw, offering insights into microbial community stability under global climate change.IMPORTANCEThis study sheds light on how permafrost thaw affects microbial life in the soil, with broader implications for understanding climate change impacts. As permafrost degrades, it alters the types and numbers of microbes in the soil. These microbes play essential roles in environmental processes, such as nutrient cycling and greenhouse gas emissions. By observing shifts from bacteria-dominated to fungi-dominated communities as permafrost thaws, the study highlights potential changes in these processes. Importantly, this research suggests that the stability of microbial networks decreases with permafrost degradation, potentially disrupting the delicate balance of these ecosystems. The findings not only deepen our understanding of microbial responses to changing climates but also support the development of strategies to monitor and potentially mitigate the effects of climate change on fragile high-altitude ecosystems.

Particle-attached bacterial communities are more susceptible to seasonal environmental fluctuations in mesotrophic than eutrophic tropical reservoirs

Particle-attached bacterial (PAB) communities play pivotal roles in water organic matter decomposition, nutrient cycling, and the natural self-purification processes. However, we know little about their responses to seasonal environmental fluctuations, under eutrophication in reservoir ecosystems. In this study, we studied the shifts of PAB communities to seasonal environmental fluctuations in tropical China. Trophic state index (TSI) indicated that the studied reservoirs ranged from mesotrophic to eutrophic state with a gradual increase in TSI from 31 to 58. In eutrophic reservoirs, Cyanobacteria, especially Raphidiopsis raciborskii, significantly increased in its relative abundance from the wet to dry season, but Synechococcales and Microcystaceae decreased. In contrast, the relative abundance of Clostridia, Bacilli, Coriobacteriia, Enterobacteriales, and Vibrionales were more susceptible to seasonal environmental fluctuations in mesotrophic than eutrophic reservoirs. PAB co-occurrence relationships in mesotrophic reservoirs varied more greatly in response to seasonal environmental fluctuations, compared with eutrophic reservoirs, in terms of topological properties of connectedness, average degree, robustness, and vulnerability. Our results further demonstrated that the seasonal stability of PAB co-occurrence relationships was strongly correlative with TSI through mediating key bacterial taxa and community biodiversity. We proposed that eutrophication dramatically reduced the seasonal variation of PAB community compositions and co-occurring relationships in reservoir ecosystems.

Seasonal lake ice cover drives the restructuring of bacteria-archaea and bacteria-fungi interdomain ecological networks across diverse habitats

The coexistence of different microbial communities is fundamental to the sustainability of many ecosystems, yet our understanding of the relationships among microbial communities in plateau cold-region lakes affected by seasonal ice cover remains limited. This research involved investigating three lakes in the Inner Mongolia segment of the Yellow River basin during frozen and unfrozen periods in two habitats: water bodies and sediments. The research examined the composition and function of bacteria, archaea, and fungi across different times and habitats within the basin, their response to environmental variables in water and sediment, and inter-domain interactions between bacteria-archaea and bacteria-fungi were compared using interdomain ecological network (IDEN). The findings indicate significant variations in the structures of bacterial, archaeal, and fungal communities across different periods and habitats, with the pH of the water body being a crucial environmental variable affecting microbial community composition. In the frozen period, the functionality of microbial communities, especially in terms of energy metabolism, was significantly impacted, with water bodies experiencing more pronounced effects than sediments. Archaea and fungi significantly contribute to the stability of bacterial communities across various habitats, especially in ice-covered conditions, where stronger associations between bacterial communities, archaea, and fungi promote the microbial communities' adaptability to cold stress. Furthermore, our results indicate that the primary environmental variable influencing the structure of IDENs is the nutrient salt content in both water bodies and sediments. This study broadens our understanding of the responses and feedback mechanisms of inter-domain microbial interactions in lakes influenced by seasonal ice cover.

Differentiated response mechanisms of soil microbial communities to nitrogen deposition driven by tree species variations in subtropical planted forests

Introduction

The increasing rate of atmospheric nitrogen deposition has severely affected the structure and function of these ecosystems. Although nitrogen deposition is increasing globally, the responses of soil microbial communities in subtropical planted forests remain inadequately studied.

Methods

In this study, a four-year experimental simulation was conducted to assess the impacts of varying nitrogen deposition levels (CK: 0 g·N·m-2·a-1; N10: 10 g·N·m-2·a-1; N20: 20 g·N·m-2·a-1; N25: 25 g·N·m-2·a-1) on two subtropical tree species, Pinus yunnanensis Franch. and Pinus armandii Franch. High-throughput sequencing was performed using the Illumina MiSeq platform. Statistical analyses, including analysis of variance (ANOVA), linear mixed-effects models, principal coordinate analysis (PCoA), analysis of similarity (ANOSIM), redundancy analysis (RDA), random forest analysis, and structural equation modeling (SEM), were used to examine the short-term responses of soil nutrients, bacterial communities, and fungal community structures to nitrogen deposition.

Results and discussion

The results showed that species differences led to variations in soil properties between the two forests, particularly a significant increase in soil pH in P. yunnanensis Franch. forests and a significant decrease in soil pH in P. armandii Franch. forests. Nitrogen addition did not significantly affect microbial diversity in either P. yunnanensis Franch. or P. armandii Franch. soils; however, forest type differences had a significant impact on bacterial diversity. The nitrogen addition significantly affected the relative abundance of specific microbial communities in both forest types, particularly altering the fungal community structure in the P. yunnanensis Franch forests, while no significant changes were observed in the bacterial community structure in either forest type. Furthermore, nitrogen addition increased the network complexity of bacterial communities in P. yunnanensis Franch. forests while decreasing network complexity in P. armandii Franch. forests. Structural equation modeling indicated that nitrogen addition regulates soil bacterial and fungal diversity in both forest types by modifying nitrogen availability.

Purpose and significance

These findings provide insights into the potential long-term impacts of nitrogen deposition on subtropical planted forest ecosystems and offer a theoretical basis for sustainable forest management and regulatory practices.

Microplastic induces microbial nitrogen limitation further alters microbial nitrogentransformation: Insights from metagenomic analysis

Microplastic has a significant impact on soil microbial communities, which play crucial roles in soil nitrogen (N) cycles. However, there is a limited understanding of their influences on genes associated with the entire N cycling pathways. Through a 120-day soil incubation using conventional (PE and PET) and biodegradable microplastics (PLA and PBAT), coupled with 16S rRNA and metagenomic sequencing, we investigated the responses of N-cycling genes to microplastics in two contrasting soils (i.e. black soil and loess soil). We found that biodegradable microplastics strongly altered microbial N functional profiles, and enhanced the abundance of numerous key genes involved in N fixation, organic N mineralization, N reduction, and denitrification. Furthermore, biodegradable microplastics significantly decreased net N mineralization (Nm) compared to control and conventional microplastic treatments, suggesting microbial N immobilization outweighed N mineralization. Analysis of the function-taxon bipartite network showed that the Nm was well predicted for the abundances and diversity of bacteria within specific modules, with Nm decreasing, the abundances of specific taxa in a given network modules increasing. These results indicated that biodegradable microplastics act as a carbon source to select specific taxa involved in enhancing N bioavailability (e.g., N fixation and organic N mineralization) to meet microbial N demand, which in turn filtered the bacterial community (decreased diversity but increased abundances) and gradually formed specific function-taxon modules. Comparing the two soils, microbes in the less fertile alkaline loess soil were more sensitive to biodegradable microplastics than those in the nutrient-rich acid black soil. Our study indicated that increasing usage of biodegradable plastics in the future may lead to accelerated soil microbial N limitation and transformation.

Exposure to thiazole pesticides disrupts pathogens and undermines keystone status of rare taxa within bacterial ecological networks

Considering the sensitivity of rare microbial taxa to environmental disturbances and their critical roles in ecosystems, it is essential to investigate how soil microbial communities (particularly rare microbes) respond to pesticide exposure. In this study, we found that thiazole pesticides significantly reduced the severity of potato common scab and effectively disrupted the pathogen's cell membrane integrity. Notably, hierarchical partitioning analysis indicated that the rare microbial taxa in potato geocaulosphere soil constitute key clusters influencing disease incidence. Within bacterial molecular ecological networks, nodes corresponding to these rare taxa generally exhibited higher degrees compared to those of more abundant taxa. However, pesticide exposure reduced the number of keystone nodes and substantially weakened the hub status of rare bacterial taxa in these networks. These findings suggest that, although thiazole pesticides effectively eradicate pathogens, they may also pose a non-negligible potential risk to rare taxa in agricultural ecosystems.

Culture-dependent and -independent analyses reveal unique community structure and function in the external mycelial cortices of Ophiocordyceps sinensis

Ophiocordyceps sinensis, also known as DongChong XiaCao (DCXC) in China, is a complex of the parasitic fungus Hirsutella sinensis and its caterpillars host living in extreme alpine environments on the Qinghai-Tibetan Plateau. Wild resources of O. sinensis are threatened by over-harvesting due to its perceived high medicinal value. In recent years, numerous studies have pointed out that endofungal bacteria play an important role in fungal spore germination and zygote formation. In this sense, studying the endofungal bacteria of O. sinensis is of great interest regarding the conservation of this species. In this study, we investigated the community structure (abundance and rare sub-communities) and function of the soil-mycelial-sclerotia-stromata continuum endofungal bacteria in O. sinensis from the Qilian Mountain region of the Tibetan Plateau by using amplicon and macro-genome sequencing technologies. Based on the results, rare taxa exhibited more differences among the components, and enrichment and co-occurrence network analyses revealed that abundant taxa played a more important role. We further found that endofungal bacteria in external mycelial cortices have unique community structures and functions. In particular, they play an important role in material cycling, potentially providing essential nutrients during the lifecycle of O. sinensis. We successfully isolated 52 endofungal bacterial strains using high-throughput isolation techniques, some of them were undetected by high-throughput sequencing. We systematically investigated the structure and function of endofungal bacteria of the O. sinensis, providing a solid foundation for the cultivation and conservation of wild resources of this species at an industrial scale.

Signaling molecule alleviates inhibitory impacts of surfactant on methane production during sludge and food waste co-digestion: Insights of electron bifurcation and quorum sensing

Anaerobic co-digestion of food waste (FW) and waste-activated sludge (WAS) is increasingly recognized as a viable solution for managing organic wastes. However, emerging contaminants (ECs), such as surfactant like sodium dodecylbenzene sulfonate (SDBS), can severely inhibit methane production. This study explores the potential of C6-HSL, a quorum sensing (QS) signaling molecule, to mitigate inhibitory effects of SDBS during FW and WAS co-digestion. Results demonstrated that SDBS reduced methane yields from 122.2 mL/g VSS in the control to 18.5 mL/g VSS, but supplementation with C6-HSL alleviated this inhibition, increasing yields to 115.4 mL/g VSS. C6-HSL not only restored suppressed methanogen populations but also promoted bacteria-archaea mutualisms, enhancing system resilience and stability. Additionally, C6-HSL enhanced key electron bifurcation pathways critical for overcoming thermodynamic barriers in methane metabolism, increasing the relative abundance of functional genes involved in four methane metabolism modules. Moreover, C6-HSL enhanced QS system (e.g., SecY and trpE), prompting microorganisms to activate adaptive mechanisms, such as DNA replication (e.g., rfcL and rfcS), efflux pumps (e.g., mdlA and mdlB), and bacterial chemotaxis (e.g., cheB and cheD), to counter SDBS toxicity. Correspondingly, TCA cycle (e.g., fumA and fumB) was also upregulated to ensure sufficient energy and electrons for methane production and microbial adaptation.

Interactions between fungi and bacteria hosts carrying MGEs is dominant for ARGs fate during manure mesophilic composting

The mycelial networks of fungi promote the interaction between the originally isolated bacteria, thereby potentially enhancing the exchange of nutrients and the horizontal transfer of genetic materials. However, the driving effect of fungi on antibiotic resistance genes (ARGs) during mesophilic facultative composting is still unclear. This study aims to elucidate the changes in ARGs and underlying mechanisms during the mesophilic composting of manure. Results indicated that reduction rates of ARGs in sheep and pig manure over a 90-day composting period were 34.68% and 60.10%, respectively. The sul1, sul2 and tetX were identified as recalcitrant ARGs in both composting treatments, with the additional unique recalcitrant gene addA observed in sheep manure. Fungal communities appeared to have a more significant influence on the cooperation between bacteria and fungi. Massive fungi interacted intensively with bacterial hosts carrying both ARGs and mobile genetic elements (MGEs). In sheep and pig manure, there were 53 and 38 potential bacterial hosts (genus level) carrying both ARGs and MGEs, associated close interactions with fungi. Structural equation modeling revealed that compost properties influence ARGs by affecting the abundance of core fungi and the hosts carrying MGEs, and that core fungi could also impact ARGs by influencing the bacterial hosts carrying MGEs. Core fungi have the potential to facilitate the horizontal transfer of ARGs by enhancing bacterial network interactions.

Comparative Analysis of Gut Microbiota in Patients with Irritable Bowel Syndrome and Healthy Controls

Background/Objectives: Growing evidence highlights the pivotal role of gut dysbiosis in the pathophysiology of irritable bowel syndrome (IBS). Despite this, the identification of an "IBS microbiota signature" remains elusive, primarily due to the influence of genetic, dietary, and environmental factors. To address these confounding variables, it is critical to perform comparative analyses using a control group derived from the same community as the IBS patients. This study aimed to evaluate and contrast the gut microbiota composition of IBS patients with healthy controls. Methods: We compared the gut microbiota from stool samples of 25 IBS patients diagnosed according to the Rome IV criteria, and 110 healthy subjects without acute or chronic diseases and not on continuous medication. The high-throughput sequencing of the V3-V4 regions of the 16S rRNA gene was conducted for microbiota analysis. Results: The IBS gut microbiota was richer but exhibited lower alpha diversity compared to the control group, suggesting simplification and imbalance. A beta diversity analysis revealed overall compositional differences between the two groups. A heat tree analysis highlighted key IBS-associated changes, including a decrease in Firmicutes, mainly due to Clostridia, and an increase in Bacteroidota, driven by an expansion of Bacteroidales families. Differential expression analyses identified important genera within these taxa like Bacteroides, Faecalibacterium, and Blautia, which could serve as microbiota-based biomarkers for IBS. Conclusions: Our results reveal both statistically and clinically significant differences in gut microbiota composition and diversity between IBS patients and healthy controls from the same community. These findings provide a deeper understanding of how alterations in the gut microbiota may contribute to IBS symptoms, offering new insights into the diagnosis and potential treatments.

Distribution patterns and community assembly processes of bacterial communities across different sediment habitats of subsidence lakes

Subsidence lakes, formed due to extensive underground coal mining activities, present both ecological challenges and opportunities for alternative land use practices, such as photovoltaic power generation and aquaculture. However, the ecological consequences of these anthropogenic activities on bacterial communities within subsidence lakes remain largely unexplored. To address this knowledge gap, we conducted a comprehensive investigation of bacterial communities in two typical subsidence lake districts located in Huainan, Anhui Province, China. A total of 44 sediment samples were collected across four distinct habitats: photovoltaic zones (PV), aquaculture zones (AC), photovoltaic-aquaculture zones (PV_AC), and unimpacted zones (Natural). Bacterial communities were investigated using 16S rRNA gene sequencing and various statistical methods. Our results revealed that the α-diversity and network complexity of bacterial communities in PV, PV_AC, and AC habitats are significantly higher than habitats of Natural (P < 0.01). Specifically, the α-diversity is the highest in PV habitats, while the network complexity is the highest in AC habitats. The network stability is the highest in PV and PV_AC habitats, while it is the lowest in AC. There were also significant differences in community structure among different habitats, Nitrospirota in PV (31.9%) was higher than that in the other three habitats, the percentage of Firmicute in Natural (21.96%) and PV_AC (13.70%) was higher than other two habitats, Actinobacteriota has the highest proportion in AC (20.93%). Furthermore, stochastic processes dominate community assembly in PV, PV_AC, and AC habitats, it has the highest proportion in PV, particularly on dispersal limitation (DL). However, deterministic processes prevail in Natural habitats, particularly on heterogeneous selection (HeS). Collectively, these findings highlight the significant differences in sediment bacterial communities across various habitats in subsidence lakes. Our study provides valuable insights into understanding the ecological implications of different habitats in subsidence lake ecosystems.

Disentangling the role of biotic and abiotic factors in shaping microbial biogeographic patterns in the large spatial scale ocean

Across large oceanic spatial scales, the mechanisms governing microbial community composition remain poorly understood, particularly regarding the influence of biotic factors. In this study, samples were collected over a 3772.55-km transect in the Western Pacific surface waters, with 16S and 18S ribosomal RNA gene sequencing employed to elucidate the assembly processes and drivers of microbial communities. Both eukaryotic (EM) and prokaryotic microbial (PM) communities exhibited a significant distance-decay relationship throughout the survey, although their assembly mechanisms differed. Biotic factors played a pivotal role in shaping the biogeographical patterns of both EM and PM communities, indicating that cross-domain microbial interactions significantly affect each other's distribution. Furthermore, the stability of the co-occurrence network was more strongly influenced by cross-domain microbial relationships than by keystone taxa. These findings advance our understanding of the mechanisms and biogeographical patterns sustaining microbial diversity across large oceanic spatial scales.

Anthropogenic pressure induced discontinuities of microbial communities along the river

Microorganisms play a fundamental role in driving biogeochemical functions within rivers. Theoretically, the directional flowing nature of river contributes to the continuous downstream change pattern of microbial communities. This continuity is anticipated to be influenced by human activities as anthropogenic materials lead to the mixing of environmental substances and their resident microorganisms with local communities. Here, we conducted a field investigation along the Beiyun River, which successively flows through pristine forest areas, artificial urban and agricultural areas with a length of 184 km, to explore the influence of anthropogenic events on microbial similarity, diversity, composition, co-occurrence, and assembly mechanisms in sediments along the river. Piecewise linear regression tests showed that discontinuities of microbial similarity occurred following the transitions from low to high anthropogenic pressure. LEfSe analysis illustrated that microorganisms associated with wastewater treatment plants and gut were differentially abundant in urban and agricultural streams. By quantifying contributions of ecological assembly processes, we found that the dominant role shifted from variable selection (60.78% in forest group) to homogenous selection (79.52% in urban group and 57.14% in agriculture group) as the differences in NH4+-N, NO3--N and NO2--N content decreased. Moreover, the complexity and stability of microbial networks were reduced from upstream forest streams to downstream urban and agricultural streams, indicating more fragmented networks. Our study provides enhanced knowledge about the factors controlling the microbial community assembly in rivers under increasing human pressure through the integration of physical, environmental, and ecological mechanisms, which can serve as a basis for predicting and responding to changes in ecosystem function under the intensified human pressure.

Unravelling the prognostic and operative role of intratumoural microbiota in non-small cell lung cancer: Insights from 16S rRNA and RNA sequencing

BACKGROUND

Complex interrelationships between the microbiota and cancer have been identified by several studies. However, despite delineating microbial composition in non-small cell lung cancer (NSCLC), key pathogenic microbiota and their underlying mechanisms remain unclear.

METHODS

We performed 16S rRNA V3-V4 amplicon and transcriptome sequencing on cancerous and adjacent normal tissue samples from 30 patients with NSCLC, from which clinical characteristics and prognosis outcomes were collected. We used 16S rRNA sequencing to dissect microbial composition and perform prognosis correlations, and in conjunction with transcriptome sequencing, we determined potential mechanisms underpinning significant microbiota actions.

RESULTS

In comparing different sample types, we identified more pronounced beta diversity disparity between NSCLC, lung squamous cell carcinoma (LUSC) and corresponding paired normal tissues. Concurrently, LUSC and lung adenocarcinoma exhibited distinct microbial composition traits at genus levels. Subsequently, four phyla, five classes, nine orders, 17 families and 36 genera were filtered out and were related to prognosis outcomes. Intriguingly, a protective microbial cluster was identified encompassing nine genera associated with delayed disease recurrence, with functional analyses suggested that these microbiota predominantly exerted metabolism-related functions. Additionally, a harmful microbial cluster (HMC) was identified, including three genera. In this HMC and subsequent prognosis model analyses, harmful intratumoural microbiota were potentially implicated in infection, inflammation and immune regulation. Crucially, we identified a microbial genus, Peptococcus, which was as an independent, detrimental NSCLC prognostic factor and potentially impacted prognosis outcomes via tumour necrosis factor (TNF) signalling.

CONCLUSIONS

We identified a substantial connection between intratumoural microbiota and NSCLC prognosis outcomes. Protective microbiota primarily exerted metabolic functions, whereas harmful microbiota were mainly implicated in infection, inflammation and immune modulation. Furthermore, Peptococcus may be significant in adverse NSCLC prognoses and serve as a potential biomarker for patient management and cancer screening.

KEY POINTS

Four phyla, five classes, nine orders, 17 families and 36 genera have been found associated with NSCLC prognosis. We identified a protective microbial cluster associated with delayed recurrence and a harmful microbial cluster related to shorter survival and earlier recurrence. We identified Peptococcus as an independent, detrimental prognostic factor for NSCLC, potentially impacting prognosis via TNF signalling.

Effects of volcanic environment on Setaria viridis rhizospheric soil microbial keystone taxa and ecosystem multifunctionality

Keystone taxa are significant within ecosystem multifunctionality, as certain species fulfil essential functions such as recycling soil nutrients, promoting plant growth, influencing biogeochemical processes, and contributing to human health maintenance. However, there are still gaps regarding the relationship between microbial communities in volcanic rhizospheric soil and ecosystem multifunctionality. As a result, in this research, we employed Illumina MiSeq high-throughput sequencing to analyse the microbial community composition of rhizospheric soil from volcanic S. viridis. Compared with non-volcanic areas, volcanic soils have higher fungal alpha diversity and the absolute abundance of bacteria (16S gene copies) showed significant variation between the two successions (P < 0.0001). The network analysis further demonstrated that the microbial diversity in non-volcanic regions surpassed that of the volcanic area. The volcanic fungi network has more nodes and edges, is more complex than non-volcanic areas (Nodes: 425 vs. 770; Edges: 21844 vs. 74532), and more rhizosphere growth-promoting bacteria are enriched. Regression analysis and correlation networks showed that fungal communities were more closely associated with ecosystem multifunctionality than bacteria. This study lays the groundwork for examining the microbial keystone taxa in the rhizosphere of volcanic plants and offers valuable insights into the multifaceted functions of plant rhizospheric soil ecosystems.

Seasonal dynamics of environmental heterogeneity augment microbial interactions by regulating community structure in different trophic lakes

Understanding how environmental heterogeneity drives microbial communities in lakes is essential for developing effective strategies to manage and restore aquatic ecosystems. However, the mechanisms by which environmental heterogeneity influences microbial community structure, network patterns, and interactions remain largely unexplored. To bridge this gap, we collected 84 water samples from four typical lakes in China (Fuxian, Tianmu, Taihu, and Xingyun) representing a range of trophic levels, across wet and dry seasons. We assessed environmental heterogeneity using 14 water quality parameters, analyzed community structure with Jaccard and Bray-Curtis dissimilarity indices, and developed a comprehensive index to elucidate microbial network complexity. Our study reveals three key findings: (1) Environmental heterogeneity was significantly greater in dry season compared to wet season across all lakes (P < 0.05). (2) Increased environmental heterogeneity led to higher bacterioplankton community dissimilarity, with greater β-diversity observed in dry season (P < 0.05). (3) Shifts in community structure due to increased environmental heterogeneity further enhanced microbial interactions, as evidenced by more complex and interconnected co-occurrence networks in the dry season. In summary, our study demonstrates that environmental heterogeneity significantly impacts bacterioplankton community structure and subsequently enhances microbial interactions. These findings underscore the importance of considering environmental heterogeneity in lake ecosystem management, as it plays a crucial role in regulating microbial community dynamics and interactions.

Root microbiome of Panax ginseng in comparison with three other medicinal plants in the families of Araliaceae and Apiaceae

The intricate interplay between endophytic microorganisms and plants in the upkeep of biodiversity, the stability of communities, and the operation of ecosystems needs to be more adequately extensive. Although root-associated microbial communities of plants have been revealed for the last decade, the understanding of bacterial and fungal communities associated with the roots of medicinal plants remains elusive. To highlight the importance of Panax ginseng Meyer (PG) in our research, we investigated the root endophytic bacterial and fungal communities of Panax ginseng Meyer (PG), alongside Aralia cordata (AC), Angelica gigas (AG), and Peucedanum japonicum (PJ), utilizing amplicon-based community profiling and advanced bioinformatic methodologies. The study aimed to investigate the root-endophytic microbiota of ginseng and three other medicinal plants and identify similarities in microbiome composition across different plant species and families. Results revealed that root-endophytic bacterial and fungal communities were influenced by plant species and phylogenetic differences at the family level. Differential abundance tests and random forest models showed microbial features within the same plant family. PG had a distinctive microbial profile with significant B1653_o_Enterobacterales and F8_o_Helotiales. PG had a core microbiome, B10_Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and a more evenly distributed microbial network compared to AG, PJ, and AC. Our research reveals the intricate endophytic microbial communities within the roots of medicinal plants, pinpointing specific taxa that may be pivotal to their medicinal qualities and overall plant health. These insights carry notable implications for future studies, particularly those focused on the endophytes of PG and their secondary metabolites, as they deepen our understanding of plant-microbe interactions and their role in enhancing the plants' therapeutic potential.

Environmental DNA metabarcoding reveals the influence of environmental heterogeneity on microeukaryotic plankton in the offshore waters of East China Sea

Microeukaryotic plankton are essential to marine food webs and biogeochemical cycles, with coastal seas playing a critical role in aquatic ecosystems. Understanding the diversity of microeukaryotic plankton, deciphering their community structure and succession patterns, and identifying the key factors influencing these dynamics remain central challenges in coastal ecology. In this study, we examine patterns of biodiversity, community structure, and co-occurrence using environmental DNA (eDNA)-based methods. Our results show a linear correlation between α-diversity and distance from the shore, with nutrient-related factors, especially inorganic nitrogen, being the primary determinants of the spatial distribution of plankton communities. Alternation of coastal habitat have shifted the succession patterns of coastal eukaryotic plankton communities from stochastic to deterministic processes. Additionally, our observations indicate that the topology and structure of eukaryotic plankton symbiotic patterns and networks are significantly influenced by environmental heterogeneity such as nutrients, which increase the vulnerability and decrease the stability of offshore ecological networks. Overall, our study demonstrates that the distribution of microeukaryotic plankton communities is influenced by factors related to environmental heterogeneity.

Depth-dependent effects of forest diversification on soil functionality and microbial community characteristics in subtropical forests

Soil microbes are critical to the maintenance of forest ecosystem function and stability. Forest diversification, such as monocultures versus mixed forests stands, can strongly influence microbial community patterns and processes, as well as their role in soil ecosystem multifunctionality, such as in subtropical forest ecosystems. However, less is known about these patterns and processes vary with soil depth. Here, we investigated the results of an eight-year forest diversification field experiment comparing the soil ecosystem multifunctionality, bacterial and fungal community assembly, and network patterns in mixed versus monoculture plantations along vertical profiles (0-80 cm depth) in a subtropical region. We found that the introduction of broadleaf trees in coniferous monocultures led to enhanced synergies between multiple functions, thus improving soil multifunctionality. The effects of mixed plantations on the functional potential in top soils were greater than in deep soils, especially for carbon degradation genes (apu, xylA, cex, and glx). Microbial community assembly in the top layer, particularly in mixed plantations, was dominated by stochastic processes, whereas deterministic were more important in the deep layer. Soil microbial network complexity and stability were higher in the top layer of mixed plantations, but in the deep layer was monoculture. Interestingly, the changes in microbial communities and multifunctionality in the top layer were mainly related to variation in nutrients, whereas those in the deep were more influenced by soil moisture. Overall, we reveal positive effects of mixed forest stands on soil microbial characteristics and functionality compared to that of monocultures. Our findings highlighted the importance of enhancing functional diversity through the promotion of tree species diversity, and managers can better develop forest management strategies to promote soil health under global change scenarios.

A novel computational approach for the mining of signature pathways using species co-occurrence networks in gut microbiomes

BACKGROUND

Advances in metagenome sequencing data continue to enable new methods for analyzing biological systems. When handling microbial profile data, metagenome sequencing has proven to be far more comprehensive than traditional methods such as 16s rRNA data, which rely on partial sequences. Microbial community profiling can be used to obtain key biological insights that pave the way for more accurate understanding of complex systems that are critical for advancing biomedical research and healthcare. However, such attempts have mostly used partial or incomplete data to accurately capture those associations.

METHODS

This study introduces a novel computational approach for the identification of co-occurring microbial communities using the abundance and functional roles of species-level microbiome data. The proposed approach is then used to identify signature pathways associated with inflammatory bowel disease (IBD). Furthermore, we developed a computational pipeline to identify microbial species co-occurrences from metagenome data at various granularity levels.

RESULTS

When comparing the IBD group to a control group, we show that certain co-occurring communities of species are enriched for potential pathways. We also show that the identified co-occurring microbial species operate as a community to facilitate pathway enrichment.

CONCLUSIONS

The obtained findings suggest that the proposed network model, along with the computational pipeline, provide a valuable analytical tool to analyze complex biological systems and extract pathway signatures that can be used to diagnose certain health conditions.

Non-antibiotic disinfectant synchronously interferes methane production and antibiotic resistance genes propagation during sludge anaerobic digestion: Activation of microbial adaptation and reconfiguration of bacteria-archaea synergies

Waste activated sludge (WAS) presents both resource recovery potential and pollution risks, making its efficient treatment challenging. Anaerobic digestion is broadly recognized as a green and sustainable approach to WAS treatment, whose efficiency is easily impacted by the exogeneous pollutants in WAS. However, the impact of polyhexamethylene guanidine (PHMG), as a widely-used non-antibiotic disinfectant, on WAS digestion under semi-continuous flow conditions remains unclear. In this study, CH4 production decreased from 16.1 mL/g volatile suspended solids (VSS) in the control to 13.2 mL/g VSS and 0.3 mL/g VSS under low and high PHMG exposure, respectively, while PHMG increased the number of antibiotic resistance gene (ARG) copies per bacterium by 4.6-12.7 %. Molecular docking analysis revealed that PHMG could spontaneously bind to and disintegrate WAS (binding energy:2.35 and -9.62 kcal/mol), increasing the likelihood of microbial exposure to PHMG. This led to an increase in bacterial abundance and a reduction in archaeal populations, resulting in bacterial dominance in ecological niches. The network topology index in PHMG-treated reactors was consistently lower than in the control, with a higher proportion of negatively correlated links, indicating a more antagonistic relationship between bacteria and archaea. Consequently, PHMG significantly interfered with key genes involved in CH4 biosynthesis (e.g., mch and mtd). Interestingly, methanogenic activity and archaeal chemotaxis (e.g., rfk and cheA) partially recovered under low PHMG exposure due to archaeal adaptation through quorum sensing and two-component systems. However, this adaptation process also contributed to the propagation of ARGs through horizontal gene transfer, facilitated by the enhancement of mobile genetic elements and ARGs hosts. These findings confirm the ecological risks of PHMG and highlight the need for effective WAS disposal strategies.

Enrichment of marine microbes to remove nitrogen of urea wastewater under salinity stress

Salinity (NaCl) and urea concentration significantly affect the diversity, structural and physiological function of microbial communities in the biological treatment of wastewater. However, the responses of microbial in high salt and urea wastewater remain elusive. Here, we investigated microbial community function and assembly of four regions using gradient domestication experiment combined with 16S rRNA gene sequencing and statistical methods. The results showed that with the increase of salinity and urea concentration, the consortium Xiamen could still remove most urea, while the other three consortia could not. The alpha diversity of microbial community initially decreased and then increased, showing a recovery trend. After domestication, the consortium Xiamen exhibited high physiological activity and complex network structure, and the community assembly process changed from stochastic to deterministic during the domestication. Furthermore, the keystones with low abundance were associated with urea removal and important for maintain the complexity of the networks, while Arenibacter and Oceanimonas were found to be keystones in maintaining efficient urea removal in harsh environments. To sum up, environmental effects dominated by salinity and urea concentration stress drove the community assembly and species coexistence that underpinned the microbial differentiation pattern at a geographic scale. These results provided new sights for elucidate how microbial response to salinity and urea during wastewater treatment.

Multi-omics analysis reveals the genetic and environmental factors in shaping the gut resistome of a keystone rodent species

Understanding the emergence and spread of antibiotic resistance genes (ARGs) in wildlife is critical for the health of humans and animals from a "One Health" perspective. The gut microbiota serve as a reservoir for ARGs; however, it remains poorly understood how environmental and host genetic factors influence ARGs by affecting the gut microbiota. To elucidate this, we analyzed whole-genome resequencing data from 79 individuals of Brandt's vole in two geographic locations with different antibiotics usage, together with metabolomic data and shotgun sequencing data. A high diversity of ARGs (851 subtypes) was observed in vole's gut, with a large variation in ARG composition between individuals from Xilingol and Hulunbuir in China. The diversity and composition of ARGs were strongly correlated with variations in gut microbiota community structure. Genome-wide association studies revealed that 803 loci were significantly associated (P<5.05×10-9) with 31 bacterial species, and bipartite networks identified 906 bacterial species-ARGs associations. Structural equation modeling analysis showed that host genetic factors, air temperature, and presence of pollutants (Bisphenol A) significantly affected gut microbiota community structure, which eventually regulated the diversity of ARGs. The present study advances our understanding of the complex host-environment interactions that underlie the spread of ARGs in the natural environments.

Effects of filling substrates on remediation performance and sulfur transformation of sulfate reducing packed-bed bioreactors treating acid mine drainage

The filling substrate is one of key factors influencing effectiveness of sulfate reducing packed-bed bioreactor (SRPB) treating acid mine drainage (AMD). The effects of four substrates (i.e. quartz sand, steel residue, biochar, and peanut shell) on remediation performance and sulfur transformation of SRPB treating AMD was studied. The results showed that steel residue and biochar improved sulfate reduction efficiency (61% and 49%) compared to quartz sand (32%), whereas peanut shell inhibited sulfate reduction efficiency (19%), attributed to its decomposition process leading to a severe accumulation of acetic acid. More amounts of sulfides generated in steel residue bioreactor were converted into acid volatile sulfide and elemental sulfur, resulting in a significant decrease in dissolved sulfide in the effluent. Metals (Fe, Al, Zn, Cd and Cr) except for Mn were effectively immobilized in the bioreactors, particularly for Al and Cd. Sulfate reducing bacteria and sulfide oxidizing bacteria lived symbiotically in all bioreactors which exhibited similar heterogeneity in microbial distribution and function, i.e. bacterial sulfate reduction mainly occurring in bottom-middle layers and photoautotrophic sulfide oxidation in upper layer close to outlet. The microbial response mechanism to various substrate environments was revealed through co-occurrence networks analysis. This study suggests that attention should be paid to the inhibitory effect of acetic acid accumulation on sulfate reduction when using sole lignocellulosic waste (peanut shell), and steel residue and biochar could be utilized as filling substances to promote sulfate reduction.

Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species

Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.

Microbial inoculants using spent mushroom substrates as carriers improve soil multifunctionality and plant growth by changing soil microbial community structure

Peat is typically used as a carrier for microbial inoculants; however, due to its non-renewable nature alternatives need to be identified as reliable and renewable carriers for mineral-solubilizing inoculants. In pot experiments, solid microbial inoculants were comprised of peat (P), biochar (BC), and spent mushroom substrates (SMS) using Medicago sativa L. as experimental materials, and the purpose of this study is to assess the effect of solid microbial inoculants on soil multifunctionality and plant growth. The results revealed that the SMS microbial inoculant had the greatest positive impact on plant biomass and significantly stimulated soil multifunctionality which is typically managed or assessed based on various soil functions or processes that are crucial for sustaining productivity, in contrast to the peat microbial inoculant, particularly at a supply level of 100 g/pot. There was no significant correlation between soil multifunctionality and bacterial/fungal microbial diversity. However, according to the co-occurrence network of bacteria and fungi, soil multifunctionality was intimately correlated with the biodiversity of the main ecological clusters (modules) of bacteria and fungi, rather than to the entire soil microbial community structure. The keystone species of module hubs and connectors play critical roles in maintaining the stability of ecological clusters of microbial co-occurrence networks and linkages between ecological clusters. Soil pH is a major predictor of changes in plant biomass, and leads to changes therein by affecting the major ecological clusters of bacterial and fungal co-occurrence networks. These results suggested that SMS may serve as a good alternative to peat as a carrier of mineral-solubilizing microorganisms to maintain soil multifunctionality and promote plant growth.

Disentangling the assembly patterns and drivers of microbial communities during thermal stratification and mixed periods in a deep-water reservoir

Effect of periodic thermal stratification in deep-water reservoirs on aquatic ecosystems has been a research hotspot. Nevertheless, there is limited information on the response patterns of microbial communities to environmental changes under such specialized conditions. To fill this gap, samples were collected from a typical deep-water reservoir during the thermal stratification period (SP) and mixed period (MP). Three crucial questions were answered: 1) How microbial communities develop with stratified to mixed succession, 2) how the relative importance of stochastic and deterministic processes to microbial community assembly, shifted in two periods, and 3) how environmental variables drive microbial co-occurrence networks and functional group alteration. We used Illumina Miseq high-throughput sequencing to investigate the dynamics of the microbial community over two periods, constructed molecular ecological networks (MENs), and unraveled assembly processes based on null and neutral models. The results indicated that a total of 33.9 % and 27.7 % of bacterial taxa, and 23.1 % and 19.4 % of fungal taxa were enriched in the stratified and mixed periods, respectively. Nitrate, water temperature, and total phosphorus drove the variation of microbial community structure. During the thermal stratification period, stochastic processes (dispersal limitation) and deterministic processes (variable selection) dominated the assembly of bacterial and fungal communities, followed by a shift to stochastic processes dominated by dispersal limitation in two communities. The MENs results revealed that thermal stratification-induced environmental stresses increased the complexity of microbial networks but decreased its robustness, resulting in more vulnerable ecological networks. Therefore, this work provides critical ecological insights for the longevity and sustainability of water quality management in an artificially regulated engineered system.

The micro-ecological feature of colonies is a potential strategy for Phaeocystis globosa bloom formation

Phaeocystis globosa is among the dominant microalgae associated with harmful algal blooms. P. globosa has a polymorphic life cycle and its ecological success has been attributed to algal colony formation, however, few studies have assessed differences in microbial communities and their functional profiles between intra- and extra-colonies during P. globosa blooms. To address this, environmental and metagenomics tools were used to conduct a time-series analysis of the bacterial composition and metabolic characteristics of intra- and extra-colonies during a natural P. globosa bloom. The results show that bacterial composition, biodiversity, and network interactions differed significantly between intra- and extra-colonies. Dominant extra-colonial bacteria were Bacteroidia and Saccharimonadis, while dominant intra-colonial bacteria included Alphaproteobacteria and Gammaproteobacteria. Despite the lower richness and diversity observed in the intra-colonial bacterial community, relative to extra-colonies, the complexity and interconnectedness of the intra-colonial networks were higher. Regarding bacterial function, more functional genes were enriched in substance metabolism (polysaccharides, iron element and dimethylsulfoniopropionate) and signal communication (quorum sensing, indoleacetic acid-IAA) pathways in intra- than in extra-colonies. Conceptual model construction showed that microbial cooperative synthesis of ammonium, vitamin B12, IAA, and siderophores were strongly related to the P. globosa bloom, particularly in the intra-colonial environment. Overall, our data highlight the differences in bacterial structure and functions within and outside the colony during P. globosa blooms. These findings represent fundamental information indicating that phenotypic heterogeneity is a selective strategy that improves microbial population competitiveness and environmental adaptation, benefiting P. globosa bloom formation and persistence.

iNAP 2.0: Harnessing metabolic complementarity in microbial network analysis

With the widespread adoption of metagenomic sequencing, new perspectives have emerged for studying microbial ecological networks, yielding metabolic evidence of interspecies interactions that traditional co-occurrence networks cannot infer. This protocol introduces the integrated Network Analysis Pipeline 2.0 (iNAP 2.0), which features an innovative metabolic complementarity network for microbial studies from metagenomics sequencing data. iNAP 2.0 sets up a four-module process for metabolic interaction analysis, namely: (I) Prepare genome-scale metabolic models; (II) Infer pairwise interactions of genome-scale metabolic models; (III) Construct metabolic interaction networks; and (IV) Analyze metabolic interaction networks. Starting from metagenome-assembled or complete genomes, iNAP 2.0 offers a variety of methods to quantify the potential and trends of metabolic complementarity between models, including the PhyloMint pipeline based on phylogenetic distance-adjusted metabolic complementarity, the SMETANA (species metabolic interaction analysis) approach based on cross-feeding substrate exchange prediction, and metabolic distance calculation based on parsimonious flux balance analysis (pFBA). Notably, iNAP 2.0 integrates the random matrix theory (RMT) approach to find the suitable threshold for metabolic interaction network construction. Finally, the metabolic interaction networks can proceed to analysis using topological feature analysis such as hub node determination. In addition, a key feature of iNAP 2.0 is the identification of potentially transferable metabolites between species, presented as intermediate nodes that connect microbial nodes in the metabolic complementarity network. To illustrate these new features, we use a set of metagenome-assembled genomes as an example to comprehensively document the usage of the tools. iNAP 2.0 is available at https://inap.denglab.org.cn for all users to register and use for free.

ImageGP 2 for enhanced data visualization and reproducible analysis in biomedical research

ImageGP is an extensively utilized, open-access platform for online data visualization and analysis. Over the past 7 years, it has catered to more than 700,000 usages globally, garnering substantial user feedback. The updated version, ImageGP 2 (available at https://www.bic.ac.cn/BIC), introduces a redesigned interface leveraging cutting-edge web technologies to enhance functionality and user interaction. Key enhancements include the following: (i) Addition of modules for data format transformation, facilitating operations such as matrix merging, subsetting, and transformation between long and wide formats. (ii) Streamlined workflows with features like preparameter selection data validation and grouping of parameters with similar attributes. (iii) Expanded repertoire of visualization functions and analysis tools, including Weighted Gene Co-Expression Network Analysis, differential gene expression analysis, and FASTA sequence processing. (iv) Personalized user space for uploading large data sets, tracking analysis history, and sharing reproducible analysis data, scripts, and results. (v) Enhanced user support through a simplified error debugging feature accessible with a single click. (vi) Introduction of an R package, ImageGP, enabling local data visualization and analysis. These updates position ImageGP 2 as a versatile tool serving both wet-lab and dry-lab researchers with expanded capabilities.

Differential microbiome features in lake-river systems of Taihu basin in response to water flow disturbance

Introduction

In riverine ecosystems, dynamic interplay between hydrological conditions, such as flow rate, water level, and rainfall, significantly shape the structure and function of bacterial and microeukaryotic communities, with consequences for biogeochemical cycles and ecological stability. Lake Taihu, one of China's largest freshwater lakes, frequently experiences cyanobacterial blooms primarily driven by nutrient over-enrichment and hydrological changes, posing severe threats to water quality, aquatic life, and surrounding human populations. This study explored how varying water flow disturbances influence microbial diversity and community assembly within the interconnected river-lake systems of the East and South of Lake Taihu (ET&ST). The Taipu River in the ET region accounts for nearly one-third of Lake Taihu's outflow, while the ST region includes the Changdougang and Xiaomeigang rivers, which act as inflow rivers. These two rivers not only channel water into Lake Taihu but can also cause the backflow of lake water into the rivers, creating distinct river-lake systems subjected to different intensities of water flow disturbances.

Methods

Utilizing high-throughput sequencing, we selected 22 sampling sites in the ET and ST interconnected river-lake systems and conducted seasonally assessments of bacterial and microeukaryotic community dynamics. We then compared differences in microbial diversity, community assembly, and co-occurrence networks between the two regions under varying hydrological regimes.

Results and discussion

This study demonstrated that water flow intensity and temperature disturbances significantly influenced diversity, community structure, community assembly, ecological niches, and coexistence networks of bacterial and eukaryotic microbes. In the ET region, where water flow disturbances were stronger, microbial richness significantly increased, and phylogenetic relationships were closer, yet variations in community structure were greater than in the ST region, which experienced milder water flow disturbances. Additionally, migration and dispersal rates of microbes in the ET region, along with the impact of dispersal limitations, were significantly higher than in the ST region. High flow disturbances notably reduced microbial niche width and overlap, decreasing the complexity and stability of microbial coexistence networks. Moreover, path analysis indicated that microeukaryotic communities exhibited a stronger response to water flow disturbances than bacterial communities. Our findings underscore the critical need to consider the effects of hydrological disturbance on microbial diversity, community assembly, and coexistence networks when developing strategies to manage and protect river-lake ecosystems, particularly in efforts to control cyanobacterial blooms in Lake Taihu.

Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks

Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and metabolic complementarity networks. We apply this approach to a temperature gradient hot spring, unraveling the interplay between thermal stress and metabolic cooperation. Our analysis reveals an increase in the frequency of metabolic interactions with rising temperatures. Amino acids, coenzyme A derivatives, and carbohydrates emerge as key exchange metabolites, forming the foundation for syntrophic dependencies, in which commensalistic interactions take a greater proportion than mutualistic ones. These metabolic exchanges are most prevalent between phylogenetically distant species, especially archaea-bacteria collaborations, as a crucial adaptation to harsh environments. Furthermore, we identify a significant positive correlation between basal metabolite exchange and genome size disparity, potentially signifying a means for streamlined genomes to leverage cooperation with metabolically richer partners. This phenomenon is also confirmed by another composting system which has a similar wide range of temperature fluctuations. Our workflow provides a feasible way to decipher the metabolic complementarity mechanisms underlying microbial interactions, and our findings suggested environmental stress regulates the cooperative strategies of thermophiles, while these dependencies have been potentially hardwired into their genomes during co-evolutions.

Comparative analysis of microbial community under acclimation of linear alkylbenzene sulfonate (LAS) surfactants and degradation mechanisms of functional strains

Linear alkylbenzene sulfonate (LAS) is one of the most widely used anionic surfactants and a common toxic pollutant in wastewater. This study employed high throughput sequencing to explore the microbial community structure within activated sludge exposed to a high concentration of LAS. Genera such as Pseudomonas, Aeromonas, Thauera and Klebsiella exhibited a significant positive correlation with LAS concentrations. Furthermore, Comamonas and Klebsiella were significantly enriched under the stress of LAS. Moreover, bacterial strains with LAS-degrading capability were isolated and characterized to elucidate the degradation pathways. The Klebsiella pneumoniae isolate L1 could effectively transform more than 60 % of 25 mg/L of LAS within 72 h. Chemical analyses revealed that L1 utilized the LAS sulfonyl group as a sulfur source to support its growth. Genomic and transcriptomic analyses suggested that strain L1 may uptake LAS through the sulfate ABC transport system and remove sulfonate with sulfate and sulfite reductases.

High-elevation-induced decrease in soil pH weakens ecosystem multifunctionality by influencing soil microbiomes

Plant environmental stress response has become a global research hotspot, yet there is a lack of clear understanding regarding the mechanisms that maintain microbial diversity and their ecosystem services under environmental stress. In our research, we examined the effects of moderate elevation on the rhizosphere soil characteristics, microbial community composition, and ecosystem multifunctionality (EMF) within agricultural systems. Our findings revealed a notable negative correlation between EMF and elevation, indicating a decline in multifunctionality at higher elevations. Additionally, our analysis across bacterial and protistan communities showed a general decrease in microbial richness with increasing elevation. Using random forest models, pH was identified as the key environmental stressor influencing microbial communities. Furthermore, we found that microbial community diversity is negatively correlated with stability by mediating complexity. Interestingly, while pH was found to affect the complexity within bacterial networks, it did not significantly impact the ecosystem stability along the elevation gradients. Using a Binary-State Speciation and Extinction (BiSSE) model to explore the evolutionary dynamics, we found that Generalists had higher speciation rates and lower extinction rates compared to specialists, resulting in a skewed distribution towards higher net diversification for generalists under increasing environmental stress. Moreover, structural equation modeling (SEM) analysis highlighted a negative correlation between environmental stress and community diversity, but showed a positive correlation between environmental stress and degree of cooperation & competition. These interactions under environmental stress indirectly increased community stability and decreased multifunctionality. Our comprehensive study offers valuable insights into the intricate relationship among environmental factors, microbial communities, and ecosystem functions, especially in the context of varying elevation gradients. These findings contribute significantly to our understanding of how environmental stressors affect microbial diversity and ecosystem services, providing a foundation for future ecological research and management strategies in similar contexts.

Extreme trophic tales: deciphering bacterial diversity and potential functions in oligotrophic and hypereutrophic lakes

BACKGROUND

Oligotrophy and hypereutrophy represent the two extremes of lake trophic states, and understanding the distribution of bacterial communities across these contrasting conditions is crucial for advancing aquatic microbial research. Despite the significance of these extreme trophic states, bacterial community characteristics and co-occurrence patterns in such environments have been scarcely interpreted. To bridge this knowledge gap, we collected 60 water samples from Lake Fuxian (oligotrophic) and Lake Xingyun (hypereutrophic) during different hydrological periods.

RESULTS

Employing 16S rRNA gene sequencing, our findings revealed distinct community structures and metabolic potentials in bacterial communities of hypereutrophic and oligotrophic lake ecosystems. The hypereutrophic ecosystem exhibited higher bacterial α- and β-diversity compared to the oligotrophic ecosystem. Actinobacteria dominated the oligotrophic Lake Fuxian, while Cyanobacteria, Proteobacteria, and Bacteroidetes were more prevalent in the hypereutrophic Lake Xingyun. Functions associated with methanol oxidation, methylotrophy, fermentation, aromatic compound degradation, nitrogen/nitrate respiration, and nitrogen/nitrate denitrification were enriched in the oligotrophic lake, underscoring the vital role of bacteria in carbon and nitrogen cycling. In contrast, functions related to ureolysis, human pathogens, animal parasites or symbionts, and phototrophy were enriched in the hypereutrophic lake, highlighting human activity-related disturbances and potential pathogenic risks. Co-occurrence network analysis unveiled a more complex and stable bacterial network in the hypereutrophic lake compared to the oligotrophic lake.

CONCLUSION

Our study provides insights into the intricate relationships between trophic states and bacterial community structure, emphasizing significant differences in diversity, community composition, and network characteristics between extreme states of oligotrophy and hypereutrophy. Additionally, it explores the nuanced responses of bacterial communities to environmental conditions in these two contrasting trophic states.

Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation

BACKGROUND

Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.

RESULTS

During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions.

CONCLUSIONS

All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.

Assembly process and co-occurrence network of microbial community in response to free ammonia gradient distribution

Microorganisms are crucial components of the aquatic ecosystem due to their immense diversity and abundance. They are vital in sustaining ecological services, especially in maintaining essential biogeochemical cycles. Recent years have seen a substantial increase in surplus nitrogenous pollutants in aquatic ecosystems due to the heightened occurrence of anthropogenic activities. Elevated levels of free ammonia (FA, NH3), stemming from the discharge of excess nitrogenous pollutants, have caused notable fluctuations in aquatic ecosystems, leading to water eutrophication and various ecological challenges. The impact of these oscillations on microbial communities in aquatic ecosystems has not been extensively studied. This study employed 16S rRNA gene amplicon sequencing to systematically investigate the dynamics, co-occurrence networks, and assembly processes of microbial communities and their subcommunities (abundant, moderate, and rare) in the Luanhe River Diversion Project in China. Our findings indicate that NH3 concentration significantly influences the dynamics of microbial communities, with a notable decrease in community Richness and Phylogenetic Distance alongside increased community dissimilarity under higher NH3 conditions. The analysis revealed that certain microbial groups, particularly Actinobacteriaota, were notably more prevalent in environments with elevated NH3 levels, suggesting their potential resilience or adaptive responses to NH3 stress. Additionally, through co-occurrence network analysis, we observed dynamic changes in network topology and increased connectedness under NH3 stress. Key nodes, identified as connectors and module hubs, played crucial roles in maintaining network structure, particularly Cyanobacteria and Actinobacteriaota. Furthermore, stochastic processes, particularly drift and dispersal limitation, predominantly shaped the microbial communities. Within the three subcommunities, the impact of drift became more pronounced as the effect of dispersal limitation diminished. Overall, elucidating the dynamics of microbial communities in aquatic ecosystems exposed to NH3 can enhance our comprehension of the ecological mechanisms of microbial communities and provide new insights into the conservation of microbial community diversity and ecological functions.

IMPORTANCE

The research presented in this paper explores how varying concentrations of free ammonia impact microbial communities in aquatic ecosystems. By employing advanced gene sequencing techniques, the study reveals significant changes in microbial diversity and network structures in response to increased ammonia levels. Key findings indicate that high ammonia concentrations lead to a decrease in microbial richness and diversity while increasing community dissimilarity. Notably, certain microbial groups, like Actinobacteria, show resilience to ammonia stress. This research enhances our understanding of how pollution affects microbial ecosystems and underscores the importance of maintaining balanced ammonia levels to preserve microbial diversity and ecosystem health.

Sterile Diet Causes Gut Microbiome Collapse of Cancer Patients Post Hematopoietic Cell Transplantation, But Normal Diet Recovers Them

Though sterile diet, post-transplantation surgery is a clinical strategy for patient care to prevent the infiltration of gut pathogens, less is known about its effects on the gut microbiome. Here, the gut microbiome dynamics of leukemia patients following a 120-day "sterile-normal" diet strategy posthematopoietic cell transplantation are examined. In contrast to the traditional idea, a sterile diet leads to the lowest gut microbiota diversity (p < 0.05) and short-chain fatty acids, promoted the proliferation of potential pathogens such as Streptococcus (up by 16.93%) and Lactobacillus (up by 40.30%), and 43.32% reduction in nodes and an 85.33% reduction in edges within the microbial interaction's network. Interestingly, a normal diet allows the gut microbiome recovery and significantly promotes the abundance of beneficial bacteria. These results indicate that a sterile diet leads to a collapse of the patient's gut microbiome and promoted the proliferation of potential pathogens. This assay is a starting point for a more sophisticated assessment of the effects of a sterile diet. The work also suggests a basic principle for the re-establishment of microbial equilibrium that supplementation of microbial taxa may be the key to the restoration of the degraded ecosystem.

Temporal variation in production performance, biochemical and oxidative stress markers, and gut microbiota in Pekin ducks during the late growth stage

In the late growth stage of commercial Pekin ducks, a significant increase in feed intake and a decline in body weight gain have been observed, leading to impaired feed conversion efficiency. To address this issue, we investigated alterations in production performance, blood biochemical indices, ileum tissue architecture, and microbial community structure in Pekin ducks. The primary objective was to provide robust data supporting the improvement of meat duck production efficiency during the late growth stage (28-42-days-old). Forty 28-day-old Pekin ducks were randomly assigned to 8 replicates, with five ducks per replicate. The rearing period lasted 14 days, with feed and water provided ad libitum. Our findings indicated a significant increase in Pekin duck body and heart weights with advancing age (P < 0.05). Moreover, serum antioxidant enzyme and high-density lipoprotein concentrations significantly increased, whereas triglyceride levels decreased (P < 0.05). Notably, the height of the ileal villi was significantly reduced (P < 0.05). The microbial community structure of the ileum exhibited significant changes as ducks aged, accompanied by a substantial increase in microbial flora diversity, particularly with the formation of more tightly connected microbial network modules. Time-dependent enrichment was observed in microbial gene functions related to energy metabolism pathways. At the genus level, Sphingomonas and Subdoligranulum have emerged as crucial players in microbial differential functional pathways and network formation. These bacteria likely serve as the key driving factors in the dynamic microbial changes that occur in Pekin ducks over time. Overall, our findings suggest a potential decline in the absorption function of the small intestine and fat deposition performance of Pekin ducks during later growth stages, which may be attributed to the maturation and proliferation of the gut microbial community.