Distinct large-scale biogeographic patterns of fungal communities in bulk soil and soybean rhizosphere in China

Bacterial community assembly processes mediate soil functioning under cadmium stress in the agroecosystem

Elucidating the effects of community assembly processes on soil functioning represents a crucial challenge in theoretical ecology, particularly under cadmium (Cd) stress, where our understanding remains limited. In this study, we therefore used amplicon sequencing and a quantitative-PCR-based chip to analyze the changes in bacterial community characteristics, soil functioning and their interrelationships in agroecosystems under different levels of Cd stress. The results indicated that Cd stress led to a decline in community diversity (Z-score), network complexity and stability, an increase in species turnover, and a regulation of community structure. Cd stress significantly increased the relative importance of dispersal limitation and homogeneous selection, reducing community drift and rendering the community more deterministic. Finally, Cd stress significantly reduced soil functional potential (Z-score) and soil functional stability (Z-score), impairing soil carbon, nitrogen, phosphorus, and sulfur cycling. It is noteworthy that correlation and random forest analyses revealed significant effects of specific community assembly processes, including dispersal limitation, homogeneous selection, drift (and others), on changes in soil functional potential (Z-score). The results emphasize the pivotal role of community assembly processes in dictating soil functioning under Cd stress, thereby offering novel insights into the comprehension of microbial-driven mechanisms governing soil functioning.

Exploring the function of key species in different composting stages for effective waste biotransformation

Composting is a microbial-driven process that plays a vital role in recycling waste and promoting sustainable production. To develop more effective bioaugmentation strategies, this study examined three successive stages in an aerobic composting system, focusing on microbial community adaptation to high-temperature stress (mode_2) and nutrient-poor conditions (mode_3). The results revealed a shift from an r-strategy (rapid growth) to a K-strategy (thriving under resource-limited conditions). Community succession was predominantly driven by deterministic processes (>90 %) and exhibited strong cooperative interactions. Using multiple statistical approaches, key species were identified for each condition. These species enhanced microbial network connectivity under environmental stresses, increasing network edges by 29 %-35 %. Under high-temperature stress, Bacillus and Ureibacillus maintained core functions, while Chelativorans and Aeribacillus contributed to key metabolic pathways, including amino acid metabolism. In nutrient-poor conditions, Saccharomonospora and Pseudoxanthomonas enhanced overall system functionality, and Novibacillus played a key role in carbon and nitrogen cycling, particularly nitrogen fixation. Predictive models for microbial community stability (R2 = 0.68-0.97) were developed based on these key species to enable rapid assessment of system stability. Overall, this study identifies essential microbes involved in composting across different environmental conditions and clarifies their functional roles, providing valuable insights for optimizing aerobic composting efficiency and advancing waste resource management.

Decoding endosperm endophytes in Pinus armandi: a crucial indicator for host response to climate change

BACKGROUND

Plant-associated microorganisms significantly contribute to plant survival in diverse environments. However, limited information is available regarding the involvement of endophytes in responding to climate change and their potential to enhance host plants' adaptation to future environmental shifts. Pinus armandi, endemic to China and widely distributed in climate-sensitive regions, serves as an ideal subject for investigating microbiome interactions that assist host plants in climate change response. Despite this, a comprehensive understanding of the diversity, community composition, and factors influencing endosperm endophytes in P. armandi, as well as the response of these endophytes to climate change, remains elusive.

RESULTS

In this study, transcriptome data from 55 P. armandi samples from 13 populations were analyzed to evaluate the composition and diversity of active endosperm endophytes and predict their response to future climate change. The results revealed variations in community composition, phylogenetic diversity, and interaction network between the northern and southern groups. Temperature and precipitation correlated with endosperm endophytic species richness and diversity. Under projected future climate conditions, the northern group exhibits greater genomic vulnerability and anticipates increased threats, reflecting a corresponding trend in endosperm endophytes, particularly within the Ascomycota community.

CONCLUSION

The consistent threat trend from climate change impacting both hosts and endophytes emphasizes the potential importance of host-related fungi as crucial indicators for predicting future climate impacts. Meanwhile, this study establishes an initial framework for exploring host-microbial interactions within the context of climate warming and provides valuable insights for studies related to plant protection.

Distribution patterns of fungal community diversity in the dominant tree species Dacrydium pectinatum and Vatica mangachapoi in tropical rainforests

Plant microbial communities are shaped by plant compartments, but the patterns of fungal communities in aboveground and belowground compartments, and which environmental factors can affect them, remain unknown. Here, to address this research gap, high-throughput sequencing technology was performed to investigate the diversity of fungal communities in leaves' and roots' compartments of Dacrydium pectinatum and Vatica mangachapoi from Hainan Island of China. Fungal communities in leaves and roots exhibited significant differences. Eurotiomycetes (16.57%) and Dothideomycetes (45.57%) were predominantly found in leaves, while Agaricomycetes (36.53%) dominated in roots. Compared to the roots, the leaf compartments had higher α-diversity. According to the Mantel test, soil pH mainly influenced roots, while the main driving factors for leaves were rainfall and temperature. The proportion of dispersal-limited processes in rhizoplane (76.67%) and root endosphere (73.81%) were greater than that in leaf epiphytic (62.38%) and leaf endophytic (68.1%), driven by ectomycorrhizal fungi with known dispersal limitations. In summary, the compositions of the leaf and root fungal communities of both endangered tree species differed, partly driven by environmental factors unique to each compartment. Our results provide valuable theoretical and practical insights for preserving tropical tree species.

IMPORTANCE

Understanding the assembly of microbial communities across different compartments is a prerequisite for harnessing them to enhance plant growth. Our findings reveal significant differences in fungal community structures between the root and leaf compartments. Compared to the roots, the leaf compartments exhibited higher α-diversity. While soil pH mainly influenced fungal communities in the roots, the primary drivers for the leaves were rainfall and temperature. The dispersal-limited processes of fungal communities in the roots were greater than those in the leaves, primarily influenced by mycorrhizal fungi. These findings demonstrate compartment-specific plant-microbe interactions and environmental responses, offering actionable insights for conserving tropical tree species through habitat optimization (e.g., soil pH management) and dispersal corridor preservation. This compartment-aware perspective enhances our ability to leverage microbial functions to improve the resilience of endangered trees in the face of climate change.

Response patterns and community assembly processes of gut microbiota in grass carp subjected to various protein sources and their implications for growth and metabolism

Feed nutrients are crucial in shaping the gut microbial community, especially for complex interactions. While much research focused on the impacts of dietary protein levels, exploration of protein sources remains insufficient. Accordingly, this study specifically investigated the effects of four protein sources [Clostridium autoethanolicum protein (CAP), cottonseed protein concentrate (CPC), Chlorella vulgaris meal (CVP), and Tenebrio molitor meal (TM)] replacing dietary soybean meal on microbial co-occurrence networks and key metabolic taxa. A 56-day feeding trial involved 1500 grass carp (20.00 g) fed five experimental diets, each incorporating one of the experimental protein sources. Results revealed that CPC and CVP diets improved the weight gain and specific growth rate, with the CPC group demonstrating the highest biomass gain and the CVP group exhibiting the best feed conversion ratio. Findings further indicated that SM-free diets enhanced intestinal immunity and barrier function while negatively impacting microbial diversity. Additional profiling revealed that each treatment exhibited distinct abundance profiles and unique species, with Firmicutes, Bacteroidota, and Proteobacteria as the dominant phyla and key genera such as Bacteroides, Erysipelatoclostridium, and Cetobacterium. Stochastic mechanisms drove the community assembly process, and prolonged SM-free diets led to simplified networks with increased generalists and specialists. Functional gene analysis highlighted roles in amino acid, carbohydrate, and lipid metabolism, underscoring the impact of protein sources on aquatic microbial communities and host-microbiome interactions. Overall, the study suggests the potential suitability of several protein sources as soybean meal substitutes, emphasizing the importance of further investigation into optimal inclusion levels for diverse proteins.

Diverse adaptation strategies of generalists and specialists to metal and salinity stress in the coastal sediments

Understanding the distinct roles and responses of bacterial community to environmental stressors is crucial for effective ecosystem management and conservation. Despite this, there is limited research on how environmental gradients specifically impact generalist and specialist subcommunities. This study investigates these subcommunities in the sediments of Jinzhou Bay, highlighting their distinct responses to environmental gradients. Generalists thrive in disturbed environments due to their broad ecological tolerances, while specialists show higher diversity in the stable, less contaminated upstream areas. At the genus level, Porphyrobacter and Subgroup_23 were identified as the dominant taxa of generalists, while Woeseia and Lutibacter were the dominant species of specialists. Physicochemical parameters, especially metals and salinity, significantly influence subcommunity composition. Generalists are adaptable to a wider range of factors, whereas specialists are affected by specific parameters, reflecting their narrower niches. The generalists exhibit a greater abundance of salinity tolerance genes compared to the specialists; however, this trend does not extend to metal resistance genes. Keystone taxa, primarily specialists, play crucial roles in maintaining community stability. Our results underscore the importance of considering both generalists and specialists in ecological assessments, offering insights for the management and conservation of bacterial microbial diversity in coastal ecosystems.

Diversity of plant pollen sources, microbial communities, and phenolic compounds present in bee pollen and bee bread

The pollination of several crops, as well as wild plants, depends on honeybees. To get the nutrients required for growth and survival, honeybee colonies are dependent on pollen supply. Bee pollen (BP) is partially packed in honeycomb cells and processed into beebread (BB) by microbial metabolism. The composition of pollen is highly variable and is mainly dependent on ecological habitat, geographical origin, honey plants, climatic conditions, and seasonal variations. Although there are important differences between the BP and the BB, little comparative chemical and microbiological data on this topic exists in the literature, particularly for samples with the same origin. In this study, BP and BB pollen samples were collected from two apiaries located in the Campania and Molise regions of Southern Italy. Phenolic profiles were detected via HPLC, while antioxidant activity was determined by ABTS·+ and DPPH· assay. The next-generation sequencing (NGS) based on RNA analysis of 16S (rRNA) and internal transcribed spacer (ITS2) regions were used to investigate the microbial community (bacteria and fungi) and botanical origin of the BP and BB. Chemical analysis showed a higher content of flavonols in BP (rutin, myricetin, quercetin, and kaempferol), while in BB there was a higher content of phenolic acids. The NGS analysis revealed that the microbial communities and pollen sources are dependent on the geographical location of apiaries. In addition, diversity was highlighted between the microbial communities present in the BP and BB samples collected from each apiary.

Survey of gut microbial biogeography and their functional niche in the grow-finishing swine of ordinary feeding

Background

Swine represent one of the most economically significant livestock worldwide, and their intestinal microbial communities are crucial for maintaining physiological development and regulating host metabolism. While extensive research has focused on the fecal microbiota of swine, investigations into microbial communities across different intestinal segments remain limited.

Objective

This study aims to elucidate the intestinal microbiota of swine by analyzing luminal contents from different intestinal segments, including the duodenum, jejunum, ileum, cecum, and colon.

Methods

We employed 16S rRNA sequencing to explore the diversity and structure of gut microbial biogeography, microbial functional niches, and their associated pathways.

Results

Our findings reveal significantly lower microbial richness and diversity in the small intestine (duodenum, jejunum, and ileum) compared to the large intestine (cecum and colon) (p < 0.05). At the phylum level, Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant phyla, collectively accounting for over 90% of the total sequences. In the small intestine, Proteobacteria (4.76-34.2%), Actinobacteria, and Fusobacteriota were more abundant, whereas in the large intestine, Firmicutes (89.8-90.4%) was predominated. At the genus level, Fusobacterium, Corynebacterium, Rothia, Bradyrhizobium, and Brevundimonas were predominant in duodenum. Romboutsia, Clostridium_sensu_stricto_1, Terrisporobacter, and Jeotgalicoccus demonstrated greater abundances in the jejunum and ileum. Oscillospiraceae_UCG-005 in the cecum and Christensenellaceae_R-7_group in the colon were more abundant with 16.4 and 20.2% relative abundances, respectively. The specialists detected from the duodenum to the colon were all the predominant genera in each intestinal segment with relatively higher relative abundance. For instance, Romboutsia (3.06-36.1%), Clostridium_sensu_stricto_1 (5.31-18.6%), and Terrisporobacter (0.849-5.72%) were dominant genera and specialists in the small intestine, associated with enriched pathways of Amino acid metabolism and Lipid metabolism. Conversely, Oscillospiraceae_UCG-005 (16.4%, 4.06%) and Christensenellaceae_R-7_group (5.44%, 20.2%) are predominant genera and specialists within the large intestine, linked to pathways involved in Glycan biosynthesis and metabolism pathway, as well as the Biosynthesis of other secondary metabolites.

Conclusion

These highlight the importance of genus specialists compared to genus generalists. The findings provide essential data for assessing the role of the intestinal microbiome in maintaining and enhancing swine health and productivity, offering fundamental guidance for further exploration of host-microbe interaction mechanisms and regulatory pathways.

Variation and assembly mechanisms of Rhinolophus ferrumequinum skin and cave environmental fungal communities during hibernation periods

Animal skin acts as the barrier against invasion by pathogens and microbial colonizers. Environmental microbiota plays a significant role in shaping these microbial communities, which, in turn, have profound implications for host health. Previous research has focused on characterizing microorganisms on bats' skin and in their roosting environments, particularly bacterial communities. The emergence of white-nose syndrome, caused by the fungal-pathogen Pseudogymnoascus destructans, highlights the importance of understanding fungal dynamics in cave ecosystems and on bats' skin. In this study, we employed ITS amplicon sequencing to investigate the fungal community associated with the skin of Rhinolophus ferrumequinum and surfaces within hibernacula. In addition, we utilized neutral community and null models to assess the relative importance of stochastic and deterministic processes in fungal community assembly. The infection status of P. destructans did not significantly impact fungal community composition either on bat skin or cave environments. However, fungal diversity was significantly higher in cave environments compared to bat skin. Notably, potentially inhibitory genera of fungal pathogens were present in both bats and cave environments during hibernation. Furthermore, the composition and structure of fungal communities on both bat skin and cave environments varied across hibernation periods. Our findings suggest neutral processes primarily drive the assembly of fungal communities associated with hibernating R. ferrumequinum and cave environments, with dispersal limitation exerting a significant influence. This study provides insights into the fungal communities associated with hibernating R. ferrumequinum and cave environments.IMPORTANCEAnimal habitats provide sources and reservoirs for host microorganisms, making it critical to understand changes in microbial communities between habitats and hosts. While most studies have focused on bacterial microorganisms, research on fungal communities is lacking. This study investigated how community dynamics and assembly processes differ between the skin of hibernating Rhinolophus ferrumequinum and the cave environments under pathogen stress. We found significant differences in the composition and structure of the fungal communities between bat skin and roosting cave environments. Fungal genera with potential inhibitory effects on pathogens were found in all bat skin and cave environments. In addition, dispersal limitations during stochastic processes were a key factor in the formation of environmental fungal communities on bat skin and in caves. These findings offer new insights for exploring pathogen-host-environment-microbe interactions.

Dynamics of wheat rhizosphere microbiome and its impact on grain production across growth stages

Crop plant microbiomes are increasingly seen as important in plant nutrition and health, and a key to maintaining food productivity. Currently, little is known of the temporal changes that occur in the wheat rhizosphere microbiome as the plant develops, and how this varies among different sites. We used a pot-based mesocosm experiment with the same modern wheat cultivar grown in eight soils from across the North China Plain, a major wheat producing area. DNA from rhizosphere soil was taken from wheat plants, from seedling up to grain harvesting stage, and amplicon sequenced for prokaryotes and microeukaryotes, followed by community analysis. Our results showed that rhizosphere diversity of prokaryotes and microeukaryotes increased over time in most sites. While there was turnover between earlier- and later-arriving species, the predominant successional model was accumulation, with early arrivals remaining in place as others colonized the rhizosphere. Rhizosphere community network modularity and stability increased during the development and maturation of the wheat plant. The abundances of certain stage-specific keystone species were correlated with eventual grain yield - suggesting a potentially important role in wheat production. Some keystone species belonged to groups previously implicated in various functions. This study provides a basis for further experimental investigation of the wheat rhizosphere microbiome, its role in determining crop yields, and the potential for microbiome engineering to promote yields. The sequential arrival and accumulation of microbiota suggests that deliberate inoculation might accelerate this process.

Increasing pesticide diversity impairs soil microbial functions

Pesticide application is essential for stabilizing agricultural production. However, the effects of increasing pesticide diversity on soil microbial functions remain unclear, particularly under varying nitrogen (N) fertilizer management practices. In this study, we investigated the stochasticity of soil microbes and multitrophic networks through amplicon sequencing, assessed soil community functions related to carbon (C), N, phosphorus (P), and sulfur (S) cycling, and characterized the dominant bacterial life history strategies via metagenomics along a gradient of increasing pesticide diversity under two N addition levels. Our findings show that higher pesticide diversity enriches the abundance of bacterial specialists and opportunists capable of degrading or resisting pesticides, reducing the proportion of bacterial generalists in the absence of N addition. These shifts can complicate multitrophic microbial networks. Under increased pesticide diversity, selective pressure may drive bacteria to streamline their average genome size to conserve energy while enhancing C, N, P, and S metabolic capacities, thus accelerating soil nutrient loss. In comparison, N addition was found to reduce bacterial niche differentiation at higher pesticide diversity, mitigating the impacts of network complexity and functional traits associated with pesticide diversity, ultimately alleviating soil nutrient loss. Our results reveal the contrasting impacts of pesticide diversity on microbial functions under different N input scenarios and emphasize that strategic N fertilizer management can mitigate the ecological effects of pesticide use in agricultural systems.

Reconstruction characteristics of gut microbiota from patients with type 1 diabetes affect the phenotypic reproducibility of glucose metabolism in mice

The human microbiota-associated (HMA) mice model, especially the germ-free (GF)-humanized mice, has been widely used to probe the causal relationships between gut microbiota and human diseases such as type 1 diabetes (T1D). However, most studies have not clarified the extent to which the reconstruction of the human donor microbiota in recipient mice correlates with corresponding phenotypic reproducibility. In this study, we transplanted fecal microbiota from five patients with T1D and four healthy people into GF mice, and microbiota from each donor were transplanted into 10 mice. Mice with similar microbiota structure to the donor exhibited better phenotypic reproducibility. The characteristics of the microbial community assembly of donors also influenced the phenotypic reproducibility in mice, and individuals with a higher proportion of stochastic processes showed more severe disorders. Microbes enriched in patients with T1D had a stronger colonization potential in mice with impaired glucose metabolism, and microbiota functional features related to T1D were better reproduced in these mice. This indicates that assembly traits and colonization efficacy of microbiota influence phenotypic reproducibility in GF-humanized mice. Our findings provide important insights for using HMA mice models to explore links between gut microbiota and human diseases.

Interactions between SDBS and Hydrilla verticillata - epiphytic biofilm in wetland receiving STPs effluents: Nutrients removal and epiphytic microbial assembly

The fate and effects of sodium dodecyl benzene sulfonate (SDBS) in sewage treatment plants effluents on nutrients and submerged macrophytes are far from clear in wetlands. This study conducted a 24-day experiment to investigate changes in nutrients and epiphytic biofilm of Hydrilla verticillata in wetlands receiving effluents with 0.5, 2 and 5 mg L-1 SDBS. The decrease of SDBS in overlying water followed pseudo-first-order kinetic equation, with over 80 % of SDBS removal achieved. 2 and 5 mg L-1 SDBS decreased nutrient removal efficiency, induced oxidative stress response and damaged cells of H. verticillata. SDBS altered bacterial and eukaryotic community diversity. 0.5 mg L-1 SDBS can promote carbon fixation and methane oxidation of microorganisms. Network analysis revealed that 0.5 mg L-1 SDBS decreased the stability of epiphytic ecosystems. Mantel tests indicated significant influences of SDBS, temperature, and total nitrogen on epiphytic microbial communities.

From nature to urbanity: exploring phyllosphere microbiome and functional gene responses to the Anthropocene

The Anthropocene exerts various pressures and influences on the stability and function of the Earth's ecosystems. However, our understanding of how the microbiome responds in form and function to these disturbances is still limited, particularly when considering the phyllosphere, which represents one of the largest microbial reservoirs in the terrestrial ecosystem. In this study, we comprehensively characterized tree phyllosphere bacteria and associated nutrient-cycling genes in natural, rural, suburban, and urban habitats in China. Results revealed that phyllosphere bacterial community diversity, richness, stability, and composition heterogeneity were greatest at the most disturbed sites. Stochastic processes primarily governed the assembly of phyllosphere bacterial communities, although the role of deterministic processes (environmental selection) in shaping these communities gradually increased as we moved from rural to urban sites. Our findings also suggest that human disturbance is associated with the reduced influence of drift as increasingly layered environmental filters deterministically constrain phyllosphere bacterial communities. The intensification of human activity was mirrored in changes in functional gene expression within the phyllosphere microbiome, resulting in enhanced gene abundance, diversity, and compositional variation in highly human-driven disturbed environments. Furthermore, we found that while the relative proportion of core microbial taxa decreased in disturbed habitats, a core set of microbial taxa shaped the distributional characteristics of both microbiomes and functional genes at all levels of disturbance. In sum, this study offers valuable insights into how anthropogenic disturbance may influence phyllosphere microbial dynamics and improves our understanding of the intricate relationship between environmental stressors, microbial communities, and plant function within the Anthropocene.

Enhanced remediation of real agricultural runoff in surface-flow constructed wetlands by coupling composite substrate-packed bio-balls, submerged plants and functional bacteria: Performance and mechanisms

Import of agricultural runoff containing nutrients considerably contributes to eutrophication of receiving water bodies. Surface-flow constructed wetlands (SFCWs) are commonly applied for agricultural runoff purification, but the performance is usually unsatisfactory. In this study, suspended bio-balls filled with zeolite and iron-carbon (Fe-C) composite substrates, submerged macrophyte (Ceratophyllum demersum) and functional denitrifying bacteria were collectively added into SFCW microcosms to enhance the remediation efficiency for real agricultural runoff with high nutrient concentrations and low content of bioavailable organic matter. The bio-ball added SFCWs achieved notably higher pollutant removal efficiencies (21.1%, 80.2% and 47.5% for chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP), respectively) than the control (COD: 6.9%, TN: 64.4%, TP: 27.9%), because of the versatile functions of filling materials for pollutant removal. C. demersum plantation (COD: 44.2%, TN: 82.8% and TP: 53.7%) and functional bacteria inoculation (COD: 51.8%, TN: 85.8% and TP: 55.1%) further enhanced the efficiency of the SFCWs for agricultural runoff remediation. Bio-ball addition and C. demersum plantation significantly increased the humification degree and reduced the molecular weight of dissolved organic matter (DOM) in the agricultural runoff. Moreover, the two intensification measures also notably reduced organic and nitrogen contents in the wetland sediment. Remarkable distinction in bacterial community distribution patterns was observed in the SFCW sediment and filling substrates in bio-balls. Keystone genera including Clostridium_sensu_stricto_1 and Bacillus in the zeolite, Sphingomonas and Exiguobacterium in the Fe-C substrates and Sediminibacterium in the sediment might be critical for agricultural runoff remediation in the SFCW microcosms. The study highlights a high potential of the intensified SFCWs by these coupling measures for agricultural runoff remediation.

Rhizospheric bacterial communities against microplastics (MPs): Novel ecological strategies based on the niche differentiation

Considerable amounts of microplastics (MPs) are stocked in plant rhizospheres, yielding adverse effects on rhizospheric microorganisms and threatening plant health. However, the adaptation of the rhizospheric microbiota for MPs remains largely unknown. Here, to evaluate the adaptive strategies of rhizospheric bacterial communities against MPs, we characterized the spatial dissimilarities in MPs properties and bacterial communities from mangrove non-rhizosphere to rhizosphere to root hair sediments. Consequently, two strategies were uncovered: (1) Bacterial communities showed significant niche differentiation induced by the increasingly enriched MPs evaluated by piecewise structural equation modeling (piecewise SEM), as increasing specialization (10.2 % to 19.4 % to 23.0 % of specialists) and decreasing generalization (10.4 % to 10.2 % to 8.7 % of generalists). (2) A self-remediation strategy of enhancing microbial plastic-degrading potentials was determined in bacterial communities, tightly coupled to the increase of specialists (linear regression analysis, R2 = 0.54, P < 0.001) and increasing MPs weathering degrees visualized by the scanning electron microscopy (SEM) from non-rhizosphere to rhizosphere to root hair regions. Our study provides a novel insight into the ecological strategies that rhizospheric microbes utilize against MPs, and broadens our knowledge of the interaction between soil microbes and global MPs pollution.

Key bacterial taxa with specific metabolisms and life history strategies sustain soil microbial network stability exposed to carbendazim and deoxynivalenol

Co-contamination of carbendazim (CBD) and deoxynivalenol (DON) is common in agricultural soils, yet their ecological impact on soil microbiome remains poorly assessed. Here, we investigated the influence of CBD and DON on the structure, function, and co-occurrence networks of soil microbiome. The combined treatment of CBD and DON significantly exacerbated the negative impacts on soil microbial diversity, functional diversity, and microbial network stability compared to individual treatments. Specifically, Lysobacter, Gemmatimonas, Nitrospira, Massilia, and Bacillus were identified as indicator species for CBD and DON. Simultaneously, the abundance of genes involved in key ecological functions, such as nitrification (amoA) and organic phosphorus mineralization (phoAD), was significantly reduced. Notably, key bacterial taxa Nitrospira and Gemmatimonas, with K-life history strategy and capabilities for nitrification and organic nitrogen mineralization, played crucial roles in promoting positive interactions in networks. Furthermore, variance partitioning analysis (VPA) and structural equation modeling (SEM) demonstrated that the abundance and niche breadth of key bacterial taxa were the primary drivers of microbial network stability. In conclusion, our study provides new insights into how soil microbiomes and networks respond to pesticides and mycotoxins, aiding in a more comprehensive assessment of exposure risks.

Unravelling the processes involved in biodegradation of chlorinated organic pollutant: From microbial community to isolated organohalide degraders

Hundreds of studies have demonstrated the bioremediation of chlorinated organic pollutants (COPs) in flooded environments. However, the role of specific functional strains in degrading COPs under complex media such as wetlands is still unclear. Here, we focused on the microbial characteristics of COP-polluted sediments, identified the bacteria responsible for degradation and conducted a genomic analysis of these bacteria. Four strains were obtained and identified as Petrimonas sulfuriphila PET, Robertmurraya sp. CYTO, Hungatella sp. CloS1 and Enterococcus avium PseS3, respectively. They were capable of degrading a typical COP, γ-hexachlorocyclohexane (γ-HCH). The residual γ-HCH concentrations were 58.8 % (PET), 45.6 % (CYTO), 60.2 % (CloS1), and 69.3 % (PseS3) of its initial value, respectively. Strain PET, CYTO and CloS1 could degrade γ-HCH to its dehalogenation product chlorobenzene. Each strain harbors genes annotated to the pathway of halogenated organic matter degradation (e.g. 2-haloacid dehalogenase) and cobalamin biosynthesis, which are involved in the degradation of COPs. Comparative genomic analysis of the four strains and other classical organohalide-respiring bacteria (e.g. Dehalococcoides mccartyi and Sulfurospirillum multivorans DSM 12446) showed that they share orthologous clusters related to the cobalamin biosynthetic process (GO:0009236). VB12 was also detected in the culture systems of the four strains, further highlighting the importance of cobalamin in COPs degradation. In the genome of the four strains, some genes were annotated to the halogenated organic matter degradation and cobalamin biosynthesis pathway within horizontal gene transfer (HGT) regions. This further indicated that microorganisms carrying these genes can adapt faster to pollution stress through HGT. Together, these findings revealed the co-evolution mechanism of functional strains and may provide novel insights into improved bioremediation strategies for COP-polluted complex media based on generalist organochlorine-degrading bacteria.

Differential responses of soil bacteria, fungi and protists to root exudates and temperature

The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.

Rhizosphere microbial community construction during the latitudinal spread of the invader Chromolaena odorata

The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communities in the latitudinal spread of alien plants remain unclear. In this study, the rhizosphere and bulk soil of Chromolaena odorata were collected from five latitudes in Pu' er city, Yunnan Province, followed by amplicon sequencing of the soil archaeal, bacterial, and fungal communities. Alpha and beta diversity results revealed that the richness indices and the structures of the archaeal, bacterial, and fungal communities significantly differed along the latitudinal gradient. Additionally, significant differences were observed in the bacterial Shannon index, as well as in the structures of the bacterial and fungal communities between the rhizosphere and bulk soils. Due to the small spatial scale, trends of latitudinal variation in the archaeal, bacterial, and fungal communities were not pronounced. Total potassium, total phosphorus, available nitrogen, available potassium and total nitrogen were the important driving factors affecting the soil microbial community structure. Compared with those in bulk soil, co-occurrence networks in rhizosphere microbial networks presented lower complexity but greater modularity and positive connections. Among the main functional fungi, arbuscular mycorrhizae and soil saprotrophs were more abundant in the bulk soil. The significant differences in the soil microbes between rhizosphere and bulk soils further underscore the impact of C. odorata invasion on soil environments. The significant differences in the soil microbiota along latitudinal gradients, along with specific driving factors, demonstrate distinct nutrient preferences among archaea, bacteria, and fungi and indicate complex microbial responses to soil nutrient elements following the invasion of C. odorata.

Superiority of native soil core microbiomes in supporting plant growth

Native core microbiomes represent a unique opportunity to support food provision and plant-based industries. Yet, these microbiomes are often neglected when developing synthetic communities (SynComs) to support plant health and growth. Here, we study the contribution of native core, native non-core and non-native microorganisms to support plant production. We construct four alternative SynComs based on the excellent growth promoting ability of individual stain and paired non-antagonistic action. One of microbiome based SynCom (SC2) shows a high niche breadth and low average variation degree in-vitro interaction. The promoting-growth effect of SC2 can be transferred to non-sterile environment, attributing to the colonization of native core microorganisms and the improvement of rhizosphere promoting-growth function including nitrogen fixation, IAA production, and dissolved phosphorus. Further, microbial fertilizer based on SC2 and composite carrier (rapeseed cake fertilizer + rice husk carbon) increase the net biomass of plant by 129%. Our results highlight the fundamental importance of native core microorganisms to boost plant production.

Burkholderia ambifaria H8 as an effective biocontrol strain against maize stalk rot via producing volatile dimethyl disulfide

BACKGROUND

Maize stalk rot (MSR) caused by Fusarium graminearum is the primary factor contributing to the reduction in maize yield and quality. However, this soil-borne disease presents a significant challenge for sustainable control through field management and chemical agents. The screening of novel biocontrol agents can aid in developing innovative and successful strategies for MSR control.

RESULTS

A total of 407 strains of bacteria were isolated from the rhizosphere soil of a resistant maize inbred line. One strain exhibited significant antagonistic activity in plate and pot experiments, and was identified as Burkholderia ambifaria H8. The strain could significantly inhibit the mycelial growth and spore germination of F. graminearum, induce resistance to stalk rot, and promote plant growth. The volatile compounds produced by strain H8 and its secondary metabolites in the sterile fermentation broth exhibited antagonistic activity. The primary volatile compound produced by strain H8 was identified as dimethyl disulfide (DMDS) using gas chromatography tandem mass spectrometry. Through in vitro antagonistic activity assays and microscopic observation, it was confirmed that DMDS was capable of inhibiting mycelial growth and disrupting the mycelial structure of F. graminearum, suggesting it may be the major active compound for strain H8. The transcriptome data of F. graminearum further indicated that strain H8 and its volatile compounds could alter pathogenic fungi metabolism, influence the related metabolic pathways, and potentially induce cell apoptosis within F. graminearum.

CONCLUSION

Our results showed that B. ambifaria H8 was capable of producing the volatile substance dimethyl disulfide, which influenced the synthesis and permeability of cell membranes in pathogens. Thus, B. ambifaria H8 was found to be a promising biological control agent against MSR. © 2024 Society of Chemical Industry.

Distinct strategies of the habitat generalists and specialists in the Arctic sediments: Assembly processes, co-occurrence patterns, and environmental implications

Microorganisms could be classified as habitat generalists and specialists according to their niche breadth, uncovering their survival strategy is a crucial topic in ecology. Here, differences in environmental adaptation, community assemblies, co-occurrence patterns, and ecological functions between generalists and specialists were explored in the Arctic marine sediments. Compared to specialists, generalists showed lower alpha diversity but stronger environmental adaption, and dispersal limitation contributed more to the community assembly of specialists (74 %) than generalists (46 %). Furthermore, the neutral theory model demonstrated that generalists (m = 0.20) had a higher immigration rate than specialists (m = 0.02), but specialists exhibited more complex co-occurrence patterns than generalists. Our results also found that generalists may play more important roles in C, N, S metabolism but are weaker in carbon fixation and xenobiotic biodegradation and metabolism. This study would broaden our understanding of bacterial generalists' and specialists' survival strategies, and further reveal their ecological functions in marine sediments.

New insights of bacterial and eukaryotic phenotypes on the plastics collected from the typical natural habitat of the endangered crocodile lizard

Although accumulating evidence indicates that endangered animals suffer from plastic pollution, this has been largely overlooked. Here, we explored the bacteria and eukaryotes living in the plastics gathered from the natural habitat of the highly endangered crocodile lizard. The results demonstrated that the bacterial and eukaryotic communities on plastics formed a unique ecosystem that exhibited lower diversity than those in the surrounding water and soil. However, microbes displayed a more complex and stable network on plastic than that in water or soil, implying unique mechanisms of stabilization. These mechanisms enhanced their resilience and contributed to the provision of stable ecological services. Eukaryotes formed a simpler and smaller network than bacteria, indicating different survival strategies. The bacteria residing on the plastics played a significant role in carbon transformation and sequestration, which likely impacted carbon cycling in the habitat. Furthermore, microbial exchange between plastics and the crocodile lizard was observed, suggesting that plastisphere serves as a mobile gene bank for the exchange of information, including potentially harmful substances. Overall, microbes on plastic appear to significantly impact the crocodile lizard and its natural habitat via various pathways. These results provided novel insights into risks evaluation of plastic pollution and valuable guidance for government efforts in plastic pollutant control in nature reserves.

Fertilization regime changes rhizosphere microbial community assembly and interaction in Phoebe bournei plantations

Fertilizer input is one of the effective forest management practices, which improves soil nutrients and microbial community compositions and promotes forest productivity. However, few studies have explored the response of rhizosphere soil microbial communities to various fertilization regimes across seasonal dynamics. Here, we collected the rhizosphere soil samples from Phoebe bournei plantations to investigate the response of community assemblages and microbial interactions of the soil microbiome to the short-term application of four typical fertilizer practices (including chemical fertilizer (CF), organic fertilizer (OF), compound microbial fertilizer (CMF), and no fertilizer control (CK)). The amendments of organic fertilizer and compound microbial fertilizer altered the composition of rhizosphere soil bacterial and fungal communities, respectively. The fertilization regime significantly affected bacterial diversity rather than fungal diversity, and rhizosphere fungi responded more sensitively than bacteria to season. Fertilization-induced fungal networks were more complex than bacterial networks. Stochastic processes governed both rhizosphere soil bacterial and fungal communities, and drift and dispersal limitation dominated soil fungal and bacterial communities, respectively. Collectively, these findings demonstrate contrasting responses to community assemblages and interactions of rhizosphere bacteria and fungi to fertilizer practices. The application of organic fertilization strengthens microbial interactions and changes the succession of key taxa in the rhizosphere habitat. KEY POINTS: • Fertilization altered the key taxa and microbial interaction • Organic fertilizer facilitated the turnover of rhizosphere microbial communities • Stochasticity governed soil fungal and bacterial community assembly.

Methanogen-methanotroph community has a more consistent and integrated structure in rice rhizosphere than in bulk soil and rhizoplane

Methanogenic and methanotrophic microbes together determine the net methane flux from rice fields. Despite much research on them as separate communities, there has been little study of combined community patterns, and how these vary between the rhizoplane (root surface), rhizosphere (soil surrounding the root) and bulk soil around rice plants, especially at larger spatial scale. We collected samples from 32 geographically scattered rice fields in east central China, amplicon targeting the mcrA gene for methanogenesis and pmoA gene for methanotrophy by using high-throughput sequencing. Distinct communities of both methanogens and methanotrophs occurred in each of the three compartments, and predominantly positive links were found between methanogens and methanotrophs in all compartments indicating cross-feeding or consortia relationships. Methanogens were acting as the network hub in the bulk soil, and methanotrophs in rhizoplane. Network complexity and stability was greater in the rhizosphere than rhizoplane and bulk soil, with no network hubs detected, suggesting the strongest effect of homeostatic influence by plant occurred in the rhizosphere. The proportion of determinism (homogeneous selection) and distance-decay relation (DDR) in rhizoplane was consistently lower than that in the rhizosphere for both communities, indicating weaker phylogenetic clustering in rice root surface. Our results have provided a better understanding of CH4 oxidation and emission in rice paddy fields and future agriculture management could take into consideration of the subtle variation among different soil compartments and interactions within methanogenic and methanotrophic communities.

Metabolites of blueberry roots at different developmental stages strongly shape microbial community structure and intra-kingdom interactions at the root-soil interface

The rhizosphere microorganisms of blueberry plants have long coexisted with their hosts under distinctively acidic soil conditions, exerting a profound influence on host performance through mutualistic symbiotic interactions. Meanwhile, plants can regulate rhizosphere microorganisms by exerting host effects to meet the functional requirements of plant growth and development. However, it remains unknown how the developmental stages of blueberry plants affect the structure, function, and interactions of the rhizosphere microbial communities. Here, we examined bacterial communities and root metabolites at three developmental stages (flower and leaf bud development stage, fruit growth and development stage, and fruit maturation stage) of blueberry plants. The results revealed that the Shannon and Chao 1 indices as well as community composition varied significantly across all three developmental stages. The relative abundance of Actinobacteria significantly increased by 10 % (p < 0.05) from stage 1 to stage 2, whereas that of Proteobacteria decreased significantly. The co-occurrence network analysis revealed a relatively complex network with 1179 edges and 365 nodes in the stage 2. Niche breadth was highest at stage 2, while niche overlap tended to increase as the plant developed. Furthermore, the untargeted metabolome analysis revealed that the number of differential metabolites of vitamins, nucleic acids, steroids, and lipids increased between stage 1 to stage2 and stage 2 to stage 3, while those for differential metabolites of carbohydrates and peptides decreased. Significant changes in expression levels of levan, L-glutamic acid, indoleacrylic acid, oleoside 11-methyl ester, threo-syringoylglycerol, gingerglycolipid B, and bovinic acid were highly correlated with the bacterial community structure. Collectively, our study reveals that significant alterations in dominant bacterial taxa are strongly correlated with the dynamics of root metabolites. These findings lay the groundwork for developing prebiotic products to enhance the beneficial effects of root microorganisms and boosting blueberry productivity via a sustainable approach.

Spatial variations impact the soil fungal communities of Larix gmelinii forests in Northeast China

Soil fungi play a critical role in the biogeochemical cycles of forest ecosystems. Larix gmelinii is a strong and important timber tree species, which forms close associations with a wide range of soil fungi. However, the temporal-spatial disparity effects on the assembly of soil fungal communities in L. gmelinii forests are poorly understood. To address these questions, a total of 120 samples, including 60 bulk soil and 60 root samples, were collected from Aershan and Genhe in July (summer) and October (autumn)2021. We obtained 7,788 operational taxonomic units (OTUs) after merging, filtering, and rarefying using high-throughput sequencing. The dominant phyla are Basidiomycota, Ascomycota, Mortierellomycota, and Mucoromycota. There were 13 dominant families, among which the families with average relative abundance more than 5% included Thelephoraceae, Mortierellaceae, Archaeorhizomycoaceae, and Inocybaceae. In the functional guilds, symbiotrophic fungi had a relative advantage in the identified functions, and the relative abundances of pathotrophic and saprotrophic fungi varied significantly between sites. There were 12 families differentially expressed across compartments, 10 families differentially expressed between seasons, and 69 families were differentially expressed between sites. The variation in alpha diversity in the bulk soil was greater than that in the rhizosphere soil. Among the three parts (compartment, season, and site), the site had a crucial effect on the beta diversity of the fungal community. Deterministic processes dominated fungal community assembly in Genhe, whereas stochastic processes dominated in Aershan. Soil physicochemical properties and climatic factors significantly affected fungal community structure, among which soil total nitrogen and pH had the greatest effect. This study highlights that spatial variations play a vital role in the structure and assembly of soil fungal communities in L. gmelinii forests, which is of great significance for us in maintaining the health of the forests.

Comparison of the Effects of LDPE and PBAT Film Residues on Soil Microbial Ecology

The plastic film is extensively applied with limited recycling, leading to the long-run residue accumulation in soil, which offers a distinctive habitat for microorganisms, and creates a plastisphere. In this study, traditional low-density polyethylene (LDPE) plastic film and biodegradable polybutylene adipate terephthalate (PBAT) plastic film materials were selected to test their effects on soil microbial ecology. Based on high-throughput sequencing, compared to the soil environment, the alpha-diversity of bacterial communities in plastisphere was lower, and the abundance of Actinobacteria increased. Plastic film residues, as bacterial habitats, exhibited greater heterogeneity and harbor unique bacterial communities. The communities were distinguished between plastisphere and soil environment by means of a random-forest (RF) machine-learning model. Prominent distinctions emerged among bacterial functions between soil environment and plastisphere, especially regarding organics degradation. The neutral model and null model indicated that the constitution of bacterial communities was dominated by random processes except in LDPE plastisphere. The bacterial co-occurrence network of the plastisphere exhibited higher complexity and modularity. This study contributes to our comprehending of characteristics of plastisphere bacterial communities in soil environment and the associated ecological risks of plastic film residues accumulation.

Effect of Altitude Gradients on the Spatial Distribution Mechanism of Soil Bacteria in Temperate Deciduous Broad-Leaved Forests

Soil bacteria are an important part of the forest ecosystem, and they play a crucial role in driving energy flow and material circulation. Currently, many uncertainties remain about how the composition and distribution patterns of bacterial communities change along altitude gradients, especially in forest ecosystems with strong altitude gradients in climate, vegetation, and soil properties. Based on dynamic site monitoring of the Baiyun Mountain Forest National Park (33°38'-33°42' N, 111°47'-111°51' E), this study used Illumina technology to sequence 120 soil samples at the site and explored the spatial distribution mechanisms and ecological processes of soil bacteria under different altitude gradients. Our results showed that the composition of soil bacterial communities varied significantly between different altitude gradients, affecting soil bacterial community building by influencing the balance between deterministic and stochastic processes; in addition, bacterial communities exhibited broader ecological niche widths and a greater degree of stochasticity under low-altitude conditions, implying that, at lower altitudes, community assembly is predominantly influenced by stochastic processes. Light was the dominant environmental factor that influenced variation in the entire bacterial community as well as other taxa across different altitude gradients. Moreover, changes in the altitude gradient could cause significant differences in the diversity and community composition of bacterial taxa. Our study revealed significant differences in bacterial community composition in the soil under different altitude gradients. The bacterial communities at low elevation gradients were mainly controlled by stochasticity processes, and bacterial community assembly was strongly influenced by deterministic processes at middle altitudes. Furthermore, light was an important environmental factor that affects differences. This study revealed that the change of altitude gradient had an important effect on the development of the soil bacterial community and provided a theoretical basis for the sustainable development and management of soil bacteria.

Deterministic assembly of grassland soil microbial communities driven by climate warming amplifies soil carbon loss

Perturbations in soil microbial communities caused by climate warming are expected to have a strong impact on biodiversity and future climate-carbon (C) feedback, especially in vulnerable habitats that are highly sensitive to environmental change. Here, we investigate the impact of four-year experimental warming on soil microbes and C cycling in the Loess Hilly Region of China. The results showed that warming led to soil C loss, mainly from labile C, and this C loss is associated with microbial response. Warming significantly decreased soil bacterial diversity and altered its community structure, especially increasing the abundance of heat-tolerant microorganisms, but had no effect on fungi. Warming also significantly increased the relative importance of homogeneous selection and decreased "drift" of bacterial and fungal communities. Moreover, warming decreased bacterial network stability but increased fungal network stability. Notably, the magnitude of soil C loss was significantly and positively correlated with differences in bacterial community characteristics under ambient and warming conditions, including diversity, composition, network stability, and community assembly. This result suggests that microbial responses to warming may amplify soil C loss. Combined, these results provide insights into soil microbial responses and C feedback in vulnerable ecosystems under climate warming scenarios.

Assembly and succession of the phyllosphere microbiome and nutrient-cycling genes during plant community development in a glacier foreland

The phyllosphere, particularly the leaf surface of plants, harbors a diverse range of microbiomes that play a vital role in the functioning of terrestrial ecosystems. However, our understanding of microbial successions and their impact on functional genes during plant community development is limited. In this study, considering core and satellite microbial taxa, we characterized the phyllosphere microbiome and functional genes in various microhabitats (i.e., leaf litter, moss and plant leaves) across the succession of a plant community in a low-altitude glacier foreland. Our findings indicate that phyllosphere microbiomes and associated ecosystem stability increase during the succession of the plant community. The abundance of core taxa increased with plant community succession and was primarily governed by deterministic processes. In contrast, satellite taxa abundance decreased during plant community succession and was mainly governed by stochastic processes. The abundance of microbial functional genes (such as C, N, and P hydrolysis and fixation) in plant leaves generally increased during the plant community succession. However, in leaf litter and moss leaves, only a subset of functional genes (e.g., C fixation and degradation, and P mineralization) showed a tendency to increase with plant community succession. Ultimately, the community of both core and satellite taxa collaboratively influenced the characteristics of phyllosphere nutrient-cycling genes, leading to the diverse profiles and fluctuating abundance of various functional genes during plant community succession. These findings offer valuable insights into the phyllosphere microbiome and plant-microbe interactions during plant community development, advancing our understanding of the succession and functional significance of the phyllosphere microbial community.

Seasonality regulates the distinct assembly patterns of microeukaryotic plankton communities in the Three Gorges Reservoir, China

The hydrographic and environmental factors along the Three Gorges Reservoir (TGR) have been significantly altered since the Three Gorges Dam (TGD) began working in 2006. Here, we collected 54 water samples, and then measured the environmental factors, followed by sequencing of the 18S rRNA gene and subsequent analysis of community assembly mechanisms. The findings indicated that the majority of environmental variables (such as AN, TP, Chl-a, CODMn, and Cu) exhibited both temporal and spatial variations due to the influences of the TGD. The distribution of different environmental factors and microeukaryotic plankton communities is influenced by the changing seasons. The community structure in TGR showed variations across three seasons, possibly due to variations in their environmental preferences, inherent dissimilarities, and seasonal succession. Furthermore, different communities exhibited a comparable distance-decay trend, suggesting that distinct taxa are likely to exhibit a similar spatial distribution. In addition, the community formation in TGR was influenced by both deterministic and stochastic factors, with the balance between them being mainly controlled by the season. Specifically, deterministic processes could explain 33.9-51.1% of community variations, while stochastic processes could contribute 23.5-32.2%. The findings of this research demonstrated that the varying ecological processes' significance relied on environmental gradients, geographical scale, and ecological conditions. This could offer a fresh outlook on comprehending the composition, assembly mechanisms, and distribution patterns of microeukaryotic plankton in reservoir ecosystems.

Diversity of fungal communities on Cabernet and Aglianico grapes from vineyards located in Southern Italy

Grape-associated microbial community is influenced by a combination of viticultural, climatic, pedological and anthropological factors, collectively known as terroir. Therefore, grapes of the same cultivar grown in different areas can be appreciated for their distinctive biogeographic characteristics. In our previous study, we showed that the phenotypic response of Aglianico and Cabernet grapevines from Molise and Sicily regions is significantly influenced by the prevailing pedoclimatic conditions, particularly soil physical properties. However, the scale at which microbial communities differ could be important in clarifying the concept of terroir, including whether it is linked to the grape variety present in a particular vineyard. To explore this further, in the research presented here, a comparative study on the fungal communities inhabiting the berry surfaces of Cabernet and Aglianico cultivars was conducted on different vineyards located in Southern Italy (Molise, Sicily and Campania regions, the first two of which had been involved in our previous study) by using high-throughput sequencing (HTS) and multivariate data analysis. The descriptive approach through relative abundance analysis showed the most abundant phyla (Ascomycota, Basidiomycota, and Chytridiomycota), families (Cladosporiaceae, Saccotheciaceae, Pleosporaceae, Saccharomycodaceae, Sporidiobolaceae, Didymellaceae, Filobasidiaceae, Bulleribasidiaceae, and Saccharomycetaceae) and genera (Cladosporium, Aureobasidium, Alternaria, Stemphylium and Filobasidium) detected on grape berries. The multivariate data analysis performed by using different packages (phyloseq, Vegan, mixOmics, microbiomeMarker and ggplot2) highlighted that the variable "vineyard location" significantly affect the fungal community, while the variable "grape variety" has no significant effect. Thus, some taxa are found to be part of specific vineyard ecosystems rather than specific grape varieties, giving additional information on the microbial contribution to wine quality, thanks to the presence of fermentative yeasts or, conversely, to the involvement in negative or detrimental roles, due to the presence of grape-deriving fungi implied in the spoilage of wine or in grapevine pathogenesis. In this connection, the main functions of core taxa fungi, whose role in the vineyard environment is still poorly understood, are also described.

Selenium and Bacillus proteolyticus SES increased Cu-Cd-Cr uptake by ryegrass: highlighting the significance of key taxa and soil enzyme activity

Many studies have focused their attention on strategies to improve soil phytoremediation efficiency. In this study, a pot experiment was carried out to investigate whether Se and Bacillus proteolyticus SES promote Cu-Cd-Cr uptake by ryegrass. To explore the effect mechanism of Se and Bacillus proteolyticus SES, rhizosphere soil physiochemical properties and rhizosphere soil bacterial properties were determined further. The findings showed that Se and Bacillus proteolyticus SES reduced 23.04% Cu, 36.85% Cd, and 9.85% Cr from the rhizosphere soil of ryegrass. Further analysis revealed that soil pH, organic matter, soil enzyme activities, and soil microbial properties were changed with Se and Bacillus proteolyticus SES application. Notably, rhizosphere key taxa (Bacteroidetes, Actinobacteria, Firmicutes, Patescibacteria, Verrucomicrobia, Chloroflexi, etc.) were significantly enriched in rhizosphere soil of ryegrass, and those taxa abundance were positively correlated with soil heavy metal contents (P < 0.01). Our study also demonstrated that in terms of explaining variations of soil Cu-Cd-Cr content under Se and Bacillus proteolyticus SES treatment, soil enzyme activities (catalase and acid phosphatase) and soil microbe properties showed 42.5% and 12.2% contributions value, respectively. Overall, our study provided solid evidence again that Se and Bacillus proteolyticus SES facilitated phytoextraction of soil Cu-Cd-Cr, and elucidated the effect of soil key microorganism and chemical factor.

Stability and Assembly Mechanisms of Butterfly Communities across Environmental Gradients of a Subtropical Mountain

Mountain ecosystems harbor evolutionarily unique and exceptionally rich biodiversity, particularly in insects. In this study, we characterized the diversity, community stability, and assembly mechanisms of butterflies on a subtropical mountain in the Chebaling National Nature Reserve, Guangdong Province, China, using grid-based monitoring across the entire region for two years. The results showed that species richness, abundance, and Faith's phylogenetic diversity decreased with increasing elevation; taxonomic diversity played a considerable role in mediating the effects of environmental changes on stability. Moreover, our results showed that stochastic processes are dominant in governing the assembly of butterfly communities across all elevational gradients, with habitats at an elevation of 416-580 m subjected to the strongest stochastic processes, whereas heterogeneous selection processes displayed stronger effects on the assembly of butterfly communities at 744-908 m, 580-744 m, and 908-1072 m, with abiotic factors inferred as the main driving forces. In addition, significant differences were detected between the barcode tree and the placement tree for the calculated β-NTI values at 416-580 m. Overall, this study provides new insights into the effects of environmental change on the stability and assembly of butterflies in Chebaling, which will be beneficial for biodiversity conservation and policy development.

Ecological evolution of algae in connected reservoirs under the influence of water transfer: Algal density, community structure, and assembly processes

Reservoir connectivity provides a solution for regional water shortages. Understanding the water quality of reservoirs and the response of algal communities to water transfer could provide the basis for a long-term evolutionary model of reservoirs. In this study, a water-algal community model was established to study the effects of water transfer on water quality and algal communities in reservoirs. The results showed that water transfer significantly decreased total nitrogen and nitrate concentrations. However, the water transfer resulted in an increase in the CODMn concentration and conductivity in the receiving reservoir. Additionally, the algal density and chlorophyll-a (chl-a) concentration showed an increase with water transfer. Bacillariophyta, Cyanophyta, and Chlorophyta were the dominant algal phyllum in all three reservoirs. Water transfer induced the evolution of the algal community by driving changes in the chemical parameters of the receiving reservoir and led to more complex relationships within the algal community. The effects of stochastic processes on algal communities were also enhanced in the receiving reservoirs. These results provide specific information for water quality safety management and eutrophication prevention in connected reservoirs.

Ecological succession of abundant and rare subcommunities during aerobic composting in the presence of residual amoxicillin

Aerobic composting increases the content of soluble nutrients and facilitates the safe treatment of livestock manure. Although different taxa play crucial roles in maintaining ecological functionality, the succession patterns of community composition and assembly of rare and abundant subcommunities during aerobic composting under antibiotic stress and their contributions to ecosystem functionality remain unclear. Therefore, this study used 16 S rRNA gene sequencing technology to reveal the response mechanisms of diverse microbial communities and the assembly processes of abundant and rare taxa to amoxicillin during aerobic composting. The results indicated that rare taxa exhibited distinct advantages in terms of diversity, community composition, and ecological niche width compared with abundant taxa, highlighting their significance in maintaining ecological community dynamics. In addition, deterministic (heterogeneous selection) and stochastic processes (dispersal limitation) play roles in the community succession and functional dynamics of abundant and rare subcommunities. The findings of this study may contribute to a better understanding of the relative importance of deterministic and stochastic assembly processes in composting systems, and the ecological functions of diverse microbial communities, ultimately leading to improved ecological environment.

Residual effects of chlorinated organic pollutants on microbial community and natural redox processes in coastal wetlands

Chlorinated organic pollutants (COPs) are common in flooded environments. To examine the residual status and effects of COPs on flooded environments, a survey of 7 coastal wetlands in Zhejiang, East China was conducted. Total COP concentrations detected from 95.69 to 412.76 ng g-1 dw. Gamma-HCH and o,p'-DDT posed the greatest risk with exceedance rates of 100% according to sediment quality guidelines. Samples with higher COP pollution had higher microbial diversity, more complex microbial networks, more deterministic community assembly processes and lower microbiome stability, indicating an improved soil function for balance cycle of substances, especially for COP degradation. Further analysis using quantitative real-time PCR suggested COP-dechlorination interacted with natural redox processes, especially sulfate reduction and methanogenesis. The positive correlation between CH4 and pentachlorobenzene indicated a potential increase in greenhouse gas emissions caused by COP pollution. Correlation between dsr gene and COPs demonstrated the ability of sulfate-reducing bacteria to degrade COPs. Particularly, facultative OHRB such as sulfate-reducing bacteria hold significant importance in the process of COP-dechlorination. This finding provides a reference for COP pollution remediation. Collectively, our study offers new insight into the residual effect of COPs in coastal wetlands and contributes to an improved understanding of bioremediation strategies for COP pollution.

Spatial variations of fungal community assembly and soil enzyme activity in rhizosphere of zonal Stipa species in inner Mongolia grassland

Rhizosphere soil fungal and enzyme activities affect the nutrient cycling of terrestrial ecosystems, and rhizosphere fungi are also important participants in the ecological process of vegetation succession, responding to changes in plant communities. Stipa is an excellent forage grass with important ecological and economic value, and has the spatial distribution pattern of floristic geographical substitution. In order to systematically investigate the synergistic response strategies of fungal communities and enzyme activities in the rhizosphere under the vegetation succession. Here we explored the turnover and assembly mechanisms of Stipa rhizosphere fungal communities and the spatial variation of metabolic activity under the succession of seven Stipa communities in northern China grassland under large scale gradients. The results indicated that the composition, abundance and diversity of fungal communities and microbial enzyme activities in rhizosphere soil differed among different Stipa species and were strikingly varied along the Stipa community changes over the geographic gradient. As the geographical distribution of Stipa community changed from east to west in grassland transect, Mortierellomycetes tended to be gradually replaced by Dothideomycetes. The null models showed that the rhizosphere fungal communities were governed primarily by the dispersal limitation of stochastic assembly processes, which showed decreased relative importance from S. grandis to S. gobica. Moreover, the MAT and MAP were the most important factors influencing the changes in the fungal community (richness, β-diversity and composition) and fungal community assembly, while SC and NP also mediated fungal community assembly processes. These findings deepen our understanding of the responses of the microbial functions and fungal community assembly processes in the rhizosphere to vegetation succession.

Changing soil available substrate primarily caused by fertilization management contributed more to soil respiration temperature sensitivity than microbial community thermal adaptation

Substrate depletion and microbial community thermal adaptation are major mechanisms that regulate the temperature sensitivity (Q10) of soil microbial respiration. Traditionally, the Q10 of soil microbial respiration is measured using laboratory incubation, which has limits in the continuous input of available substrates and the time scale for microbial community thermal adaptation. How the available substrate and the soil microbial community regulate the Q10 of soil microbial respiration under natural warming conditions remains unclear. To fill this gap in knowledge, a long-term field experiment was conducted consisting of two years of soil respiration observations combined with a soil available substrate and microbial community thermal adaptation analysis under seasonal warming conditions. The Q10 of soil respiration was calculated using the square root method, and it was more affected by the available substrate than by microbial community thermal adaptation. Fertilization management has a stronger effect on soil available substrate than temperature. As the temperature increased, NH4-N proved itself to be important for the bacterial community in the process of Q10 regulation, while dissolved organic carbon and nitrogen were key factors for the fungal community. Based on the niche breadth of microbial community composition, the changing Q10 of the soil respiration was not only closely associated with the specialist community, but also the generalist and neutralist communities. Furthermore, bacterial community thermal adaptation primarily occurred through shifts in the abundances of specialists and neutralists, while changes in species richness and species replacement occurred for the fungal generalists and neutralists. This work indicates that changing available nitrogen and DOC primarily caused by fertilization management contributed more in regulating the Q10 of soil microbial respiration than microbial community thermal adaptation, and there are different mechanisms for bacterial and fungal community thermal adaptation under warming.

Microbial community structure and co-occurrence network stability in seawater and microplastic biofilms under prometryn pollution in marine ecosystems

Prometryn has been extensively detected in marine environment because of its widespread usage in agriculture and aquaculture and has been concerns since its serious effects on aquatic organisms. However, its impact on the microbial community in the marine ecosystem including seawater and biofilm is still unclear. Therefore, a short-term indoor microcosm experiment of prometryn exposure was conducted. This study found that prometryn had a more significant impact on the structure and stability of the microbial community in seawater compared to microplastic biofilms. Additionally, we observed that the assembly of the microbial community in biofilms was more affected by stochastic processes than in seawater under the exposure of prometryn. Our study provided evidence for the increasing impact of the microbial communities under the stress of prometryn and microplastics.

Broad environmental adaptation of abundant microbial taxa in Robinia pseudoacacia forests during long-term vegetation restoration

Vegetation restoration has significant impacts on ecosystems, and a comprehensive understanding of microbial environmental adaptability could facilitate coping with ecological challenges such as environmental change and biodiversity loss. Here, abundant and rare soil bacterial and fungal communities were characterized along a 15-45-year chronosequence of forest vegetation restoration in the Loess Plateau region. Phylogenetic-bin-based null model analysis (iCAMP), niche breadth index, and co-occurrence network analysis were used to assess microbial community assembly and environmental adaptation of a Robinia pseudoacacia plantation under long-term vegetation restoration. The drift process governed community assembly of abundant and rare soil fungi and bacteria. With increasing soil total phosphorus content, the relative importance of drift increased, while dispersal limitation and heterogeneous selection exhibited opposite trends for abundant and rare fungi. Rare soil fungal composition dissimilarities were dominated by species replacement processes. Abundant microbial taxa had higher ecological niche width and contribution to ecosystem multifunctionality than rare taxa. Node property values (e.g., degree and betweenness) of abundant microbial taxa were substantially higher than those of rare microbial taxa, indicating abundant species occupied a central position in the network. This study provides insights into the diversity and stability of microbial communities during vegetation restoration in Loess Plateau. The findings highlight that abundant soil fungi and bacteria have broad environmental adaptation and major implications for soil multifunctionality under long-term vegetation restoration.

Insight into the role of niche concept in deciphering the ecological drivers of MPs-associated bacterial communities in mangrove forest

Myriad inherent and variable environmental features are controlling the assembly and succession of bacterial communities colonizing on mangrove microplastics (MPs). However, the mechanisms governing mangrove MPs-associated bacterial responses to environmental changes still remain unknown. Here, we assessed the dissimilarities of MPs-associated bacterial composition, diversity and functionality as well as quantified the niche variations of each taxon on plastispheres along river-mangrove-ocean and mangrove landward-to-seaward gradients in the Beibu Gulf, China, respectively. The bacterial richness and diversity as well as the niche breadth on mangrove sedimentary MPs dramatically decreased from landward to seaward regions. Characterizing the niche variations linked the difference of ecological drivers of MPs-associated bacterial populations and functions between river-mangrove-ocean (microplastic properties) and mangrove landward-to-seaward plastispheres (sediment physicochemical properties) to the trade-offs between selective stress exerted by inherent plastic substrates and microbial competitive stress imposed by environmental conditions. Notably, Rhodococcus erythropolis was predicted to be the generalist species and closely associated to biogeochemical cycles of mangrove plastispheres. Our work provides a reliable pathway for tackling the hidden mechanisms of environmental factors driving MPs-associated microbe from perspectives of niches and highlights the spatial dynamic variations of mangrove MPs-associated bacteria.

Dominant role of rare bacterial taxa rather than abundant taxa in driving the tailing primary succession

Primary ecological succession is imperative for tailing vegetation, driven notably by microbes that enhance tailing nutrient status. Yet, the roles of abundant and rare taxa in tailing primary succession remain underexplored. This study investigates these subcommunities across three succession stages (i.e., original tailing, biological crusts, grasslands). Throughout primary succession, alpha diversity and functional gene abundances of the rare taxa (RT) group consistently rise from bare tailings to grasslands. Conversely, the abundant taxa (AT) group displays an opposing trend. Intriguingly, employing co-occurrence networks, keystone taxa, mantel tests, similarity percentage analysis, and structural equation model, the study uncovers that RT wields a more pivotal role than AT in driving tailing primary succession. Community assembly analysis reveals stochastic control of AT and deterministic control of RT. Additionally, primary succession reinforces stochastic processes in AT, while RT's deterministic process remains unaffected. By unveiling these dynamics, the research enriches our understanding of primary ecological succession in tailings. Recognition of unique diversity patterns and community assembly mechanisms for rare and abundant subcommunities advances tailing ecosystem comprehension and informs ecological restoration strategies. This study thus contributes valuable insights to the complex interplay of microbial taxa during tailing primary succession.

Differences in Bacterial Co-Occurrence Networks and Ecological Niches at the Surface Sediments and Bottom Seawater in the Haima Cold Seep

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

Deterministic factors modulating assembly of groundwater microbial community in a nitrogen-contaminated and hydraulically-connected river-lake-floodplain ecosystem

The river-lake-floodplain system (RLFS) undergoes intensive surface-groundwater mass and energy exchanges. Some freshwater lakes are groundwater flow-through systems, serving as sinks for nitrogen (N) entering the lake. Despite the threat of cross-nitrogen contamination, the assembly of the microbial communities in the RLFS was poorly understood. Herein, the distribution, co-occurrence, and assembly pattern of microbial community were investigated in a nitrogen-contaminated and hydraulically-connected RLFS. The results showed that nitrate was widely distributed with greater accumulation on the south than on the north side, and ammonia was accumulated in the groundwater discharge area (estuary and lakeshore). The heterotrophic nitrifying bacteria and aerobic denitrifying bacteria were distributed across the entire area. In estuary and lakeshore with low levels of oxidation-reduction potential (ORP) and high levels of total organic carbon (TOC) and ammonia, dissimilatory nitrate reduction to ammonium (DNRA) bacteria were enriched. The bacterial community had close cooperative relationships, and keystone taxa harbored nitrate reduction potentials. Combined with multivariable statistics and self-organizing map (SOM) results, ammonia, TOC, and ORP acted as drivers in the spatial evolution of the bacterial community, coincidence with the predominant deterministic processes and unique niche breadth for microbial assembly. This study provides novel insight into the traits and assembly of bacterial communities and potential nitrogen cycling capacities in RLFS groundwater.

Distinct spatiotemporal succession of bacterial generalists and specialists in the lacustrine plastisphere

The assembly processes of generalists and specialists and their driving mechanisms during spatiotemporal succession is a central issue in microbial ecology but a poorly researched subject in the plastisphere. We investigated the composition variation, spatiotemporal succession, and assembly processes of bacterial generalists and specialists in the plastisphere, including non-biodegradable (NBMPs) and biodegradable microplastics (BMPs). Although the composition of generalists and specialists on NBMPs differed from that of BMPs, colonization time mainly mediated the composition variation. The relative abundance of generalists and the relative contribution of species replacement were initially increased and then decreased with colonization time, while the specialists initially decreased and then increased. Besides, the richness differences also affected the composition variation of generalists and specialists in the plastisphere, and the generalists were more susceptible to richness differences than corresponding specialists. Furthermore, the assembly of generalists in the plastisphere was dominated by deterministic processes, while stochastic processes dominated the assembly of specialists. The network stability test showed that the community stability of generalists on NBMPs and BMPs was lower than corresponding specialists. Our results suggested that different ecological assembly processes shaped the spatiotemporal succession of bacterial generalists and specialists in the plastisphere, but were less influenced by polymer types.

Cd contamination determined assembly processes and network stability of AM fungal communities in an urban green space ecosystem

The effects of cadmium (Cd) contamination on the assembly mechanism and co-occurrence patterns of arbuscular mycorrhizal (AM) fungal communities remain unclear, especially in urban green spaces. This study sequenced AM fungal communities in greenbelt soils in Zhengzhou (China). The effects of Cd contamination on the AM fungal diversity, community assembly processes, and co-occurrence patterns were explored. We found that (1) an increase in Cd contamination changed the community composition, which resulted in a significant improvement in the diversity of specialists of AM fungi and a significant decrease in the diversity of generalists. (2) Deterministic processes dominated the community assembly of specialists and stochastic processes dominated the community assembly of generalists. (3) Specialists played a more important role than generalists in maintaining the stability of AM fungal networks under Cd contamination. Overall, Cd contamination affected the ecological processes of AM fungi in urban green space ecosystems. However, the effects on the assembly processes and network stability of different AM fungi taxa (specialists and generalists) differed significantly. The present study provides deeper insight into the effect of Cd contamination on the ecological processes of AMF and is helpful in further exploring the ecological risk of Cd contamination in urban green spaces.

Patterns of bacterial distance decay and community assembly in different land-use types as influenced by tillage management and soil layers

Land use and cover change are major factors driving global change and greatly impact terrestrial organisms, especially soil microbial diversity. Little is known, however, about bacterial diversity, distribution patterns and assembly processes across different land use types. In this study, therefore, we conducted a large-scale field survey of 48 sampling sites, encompassing different land use types in Xuancheng city, China, with different degrees of soil disturbance and different soil horizons. The distance-decay relationships (DDRs), assembly processes and the spatial patterns of soil bacterial communities were investigated based on high-throughput sequencing data. We found that the DDRs might be weakened by anthropogenic disturbances, which were not observed in tilled soils, while a decreasing trend was observed along the soil horizon in untilled soils. The relative importance of environmental factors and geographic distance varied with soil tillage. Specifically, bacterial communities in tilled soils were driven by non-spatially autocorrelated environmental factors, while untilled soils were more susceptible to geographic distance. In addition, the heterogeneity of soil properties, as well as the differences in soil bacterial niche width and niche overlap, determined the assembly processes of the bacterial community, resulting in opposite trends along the soil layers in tilled and untilled soils. These findings expand the current understanding of the biogeography of soil bacterial communities across different land use types.