Community Assembly Mechanisms Research Articles

Differential patterns and assembly processes of bacterial communities from distinct microhabitats in a subtropical estuary

Estuarine ecosystems interconnect freshwater and marine environments, and comprise multiple highly dynamic and complex microhabitats. The resident microbiota in estuary is influenced by contrasting microenvironmental heterogeneity. However, the bacterial patterns and assembly processes in different microhabitats of estuarine ecosystem are not well studied. Here, we investigated the bacterial diversity, functions and community assembly mechanisms of mangrove soil, river sediment and overlying water in a subtropical estuary. Results showed that similar profiles of bacterial communities existed in the mangrove soil and river sediment and were dominated by Proteobacteria, Bacteroidetes and Acidobacteria. In terms of different microhabitats, the lowest alpha diversity of bacterial communities was found in overlying water and were dominated by Proteobacteria, Actinobacteria and Bacteroidetes. Meanwhile, the functional potential genes associated with carbon metabolisms were also substantially different in the three microhabitats. The relative abundance of genes connected to aerobic carbon respiration was significantly higher in overlying water than in the other two microhabitats. Bacterial communities in river sediments were enriched for genes associated with aerobic methane oxidation. The strong environmental heterogeneity of the three nearby microhabitats shaped the taxonomic and functional composition of the bacterial communities in estuarine ecosystem. Moreover, the plant rhizosphere effect increased the proportion of the dispersal limitation processes in mangrove soils compared to that in river sediments, while the overlying water was fluid and had less environmental selection processes compared to that in mangrove soil and river sediment. The bacterial communities in river sediment construct a more clustered network, while the overlying water network showed the highest complexity. Our findings reveal the differences of bacterial patterns and community assembly mechanisms in distinct microhabitats of estuarine ecosystems, and provide important insights for a comprehensive understanding of the mechanisms to maintain estuarine wetland conservation under environmental changes.

Soil nematode community assembly in a primary tropical lowland rainforest

More than half of the world's tropical lowland rainforests have been lost due to conversion to agricultural land (such as rubber plantations). Thus, ecological restoration in degraded tropical lowland rainforests is crucial. The first step to restoration is restoring soil functioning (i.e., soil fertility, carbon, and nitrogen cycling) to levels similar to those in the primary tropical lowland rainforest. This requires understanding soil nematode community assembly in primary tropical lowland rainforest, which has never been explored in this habitat. In this study, we measured species compositions of plant and soil nematode communities and soil characteristics (pH, total and available nitrogen, phosphorus, and soil water content) in a primary tropical lowland rainforest, which is located on Hainan Island, China. We performed two tests (the null-model test and distance-based Moran's eigenvector maps (MEM) and redundancy analysis-based variance partitioning) to quantify the relative contribution of the deterministic (abiotic filtering and biotic interactions) and stochastic processes (random processes and dispersal limitation) to the soil nematode community. We found that a deterministic process (habitat filtering) determined nematode community assembly in our tropical lowland rainforest. Moreover, soil properties, but not plant diversity, were the key determinants of nematode community assembly. We have, for the first time, managed to identify factors that contribute to the nematode community assembly in the tropical lowland rainforest. This quantified community assembly mechanism can guide future soil functioning recovery of the tropical lowland rainforest.

Microplastic polymer properties as deterministic factors driving terrestrial plastisphere microbiome assembly and succession in the field.

Environmental microplastic (MP) is ubiquitous in aquatic and terrestrial ecosystems providing artificial habitats for microbes. Mechanisms of MP colonization, MP polymer impacts, and effects on soil microbiomes are largely unknown in terrestrial systems. Therefore, we experimentally tested the hypothesis that MP polymer type is an important deterministic factor affecting MP community assembly by incubating common MP polymer types in situ in landfill soil for 14 months. 16S rRNA gene amplicon sequencing indicated that MP polymers have specific impacts on plastisphere microbiomes, which are subsets of the soil microbiome. Chloroflexota, Gammaproteobacteria, certain Nitrososphaerota, and Nanoarchaeota explained differences among MP polymers and time points. Plastisphere microbial community composition derived from different MP diverged over time and was enriched in potential pathogens. PICRUSt predictions of pathway abundances and quantitative PCR of functional marker genes indicated that MP polymers exerted an ambivalent effect on genetic potentials of biogeochemical cycles. Overall, the data indicate that (i) polymer type as deterministic factor rather than stochastic factors drives plastisphere community assembly, (ii) MP impacts greenhouse gas metabolism, xenobiotic degradation and pathogen distribution, and (iii) MP serves as an ideal model system for studying fundamental questions in microbial ecology such as community assembly mechanisms in terrestrial environments.

Sediment sulfate content determines assembly processes and network stability of bacteria communities of coastal land-based shrimp aquaculture ponds

Sediment bacteria communities in shrimp pond are intricately linked to ecosystem function and the provision of services, such as nutrient cycling and excess nutrient metabolism in sediment. However, little is known about the main factor (assembly processes) governing abundant and rare bacterial diversity in land-based shrimp ponds. This study quantified the composition, spatial distribution, and assembly mechanisms of bacterial communities sampled from the sediment of 78 land-based shrimp ponds distributed along approximately 1700 km of the southeastern coastal zone of China. This was done using 16S rRNA gene amplicon sequencing. The bacterial community similarities decreased with spatial distance. Variation of bacterial community was mostly attributed to deterministic (environmental filtering) processes. Sediment sulfate concentrations regulated the balance between stochastic and deterministic bacterial community assembly processes, as indicated by the negative relationship between the stochasticity ratio, and network analysis highlighted increasingly sparse interconnections and less frequent co-occurrences among bacterial communities under greater sulfate concentrations. Our results demonstrate the negative impacts of sulfates associated with coastal aquaculture on sediment bacterial community dynamics, community assembly, and ecosystem function.

Soil pqqC-harboring bacterial community response to increasing aridity in semi-arid grassland ecosystems: Diversity, co-occurrence network, and assembly process.

Aridity is increasing in several regions because of global climate change, which strongly affects the soil microbial community. The soil pqqC-harboring bacterial community plays a vital role in soil P cycling and P availability. However, the effect of shifts in aridity on the pqqC community is largely unknown. Here, based on high-throughput sequencing technology, we investigated the response patterns of the diversity, co-occurrence networks, and assembly mechanisms of the soil pqqC communities along a natural aridity gradient in adjacent pairs of natural and disturbed grasslands in Inner Mongolia, China. The results showed that the α-diversity of the pqqC community first increased and then decreased with increasing aridity in the natural grassland, while it linearly increased as aridity increased in the disturbed grassland. The pqqC community dissimilarity significantly increased with increased aridity, exhibiting a steeper change rate in the disturbed grassland than in the natural grassland. Increased aridity altered the pqqC community composition, leading to increases in the relative abundance of Actinobacteria but decreases in Proteobacteria. The composition and structure of the pqqC community showed significant differences between natural and disturbed grasslands. In addition, the network analysis revealed that aridity improved the interactions among pqqC taxa and promoted the interspecific competition of pqqC microorganisms. The pqqC community assembly was primarily governed by stochastic processes, and the relative contribution of stochastic processes increased with increasing aridity. Furthermore, disturbances could affect pqqC-harboring bacterial interactions and assembly processes. Overall, our findings fill an important knowledge gap in our understanding of the influence of aridity on the diversity and assembly mechanism of the soil pqqC community in grassland ecosystems, and this work is thus conducive to predicting the pqqC community and its ecological services in response to future climate change.

Contrasting diversity patterns and community assembly mechanisms of bacterioplankton among different aquatic habitats in Lake Taihu, a large eutrophic shallow lake in China

Eutrophication leads to the degradation of lake habitat types from macrophyte-dominated habitats (MDH) to algae-dominated habitats (ADH), which is a common environmental problem faced by many lakes. However, the variations in diversities and community assembly processes of bacterioplankton in the process of lake eutrophication have not been thoroughly elucidated. Here, we contrasted bacterial diversity patterns and processes of community assembly among ADH, MDH, and other habitats (OH) of Lake Taihu, a large shallow eutrophic lake in China with strong wind-induced disturbances. We found that the bacterial diversity patterns and potential functions between ADH and MDH were significantly different. Moreover, the contributions of purely environmental variables to the bacterial diversity patterns of all habitat types were much higher than those of spatial variables. However, the relative importance of stochasticity in the bacterial community assembly of each habitat type was much higher than that of determinism. Intriguingly, ‘undominated’ stochastic processes shape the diversity patterns of bacterioplankton in ADH, MDH, and OH of Lake Taihu. These findings demonstrate that the degradation of lake habitats caused by eutrophication can profoundly change the diversity and potential function patterns of the bacterioplankton community in lake ecosystems. Although the distinct diversity patterns of the bacterioplankton among the different aquatic habitats in Lake Taihu can be affected by deterministic processes (local environmental variables), they were dominated by stochastic processes (drift). Our study confirms that strong, disordered, wind-induced disturbances in shallow lakes could lead to strong hydrologic mixing, thus increasing the randomness of bacterial community assembly in each habitat.

Species-Abundance Distribution Patterns of Plant Communities in the Gurbantünggüt Desert, China

It is important to study the species-abundance distribution pattern in a community to reveal the mechanism of community assembly. Six abundance models (log-normal distribution model, Zipf model, Zipf–Mandelbrot model, broken stick model, niche preemption model, and Volkov model) were used to fit the species-abundance distribution pattern of six scales (10 m × 10 m, 20 m × 20 m, 40 m ×40 m, 60 m × 60 m, 80 m × 80 m, 100 m × 100 m) in fixed, semifixed, and mobile sand dunes in the Gurbantünggüt Desert, respectively. The best-fitting model was determined using the K-S test, the Chi-square test, and the Akaike information criterion. The results showed that the values of soil salinity, nutrients, water content, Shannon–Wiener diversity index (H′), Pielou evenness index (E), and Simpson index (D) were ranked in all three habitats as fixed dunes > semifixed dunes > mobile dunes. The rank curves span a narrow range on the horizontal axis at scales of 10 m × 10 m and 20 m × 20 m, and species richness is minimal. As the scale increases, the span range of the curve gradually increases, and species richness becomes higher at scales of 40 m × 40 m, 60 m × 60 m, 80 m × 80 m, and 100 m × 100 m. At the 10 m × 10 m and 20 m × 20 m scales, the broken stick model fits best in the three dune habitats. At the 40 m × 40 m and 60 m × 60 m scales, the niche preemption model fits best in the three dune habitats. At the 80 m × 80 m and 100 m × 100 m scales, the Volkov neutral model fits best in the fixed and semifixed dune habitats, and the niche preemption model fits best in the mobile dune habitats. In fixed, semifixed, and mobile dunes, both niche and neutral processes played important roles in community construction, reflecting the manifestation of the community niche-neutral continuum.

Seasonal variation significantly influenced the stochasticity of community assembly of amphibian symbiotic bacteria.

Seasonal variation has been shown to influence symbiotic bacterial community composition and structure in amphibians. It is still unknown how the symbiotic bacterial community assembly changes during different seasons, especially for amphibians who are particularly sensitive to environmental change. We found significant differences in the composition and diversity (alpha and beta diversity) of amphibian skin and gut bacteria. Co-occurrences network analysis showed that seasonal variation reduced the microbial network complexity of amphibians from summer to autumn. The normalized stochastic ratio (NST) and phylogenetic bin-based null model analysis (iCAMP) models showed that the same result that stochastic processes was the major factor regulating the symbiotic bacterial community assembly mechanisms of amphibians. From summer to autumn, the symbiotic bacterial community assembly mechanisms declined in the contribution of stochastic processes, while increasing in the contribution of deterministic processes. Dispersal limitation was the dominant microbial assembly mechanism, followed by homogeneous selection, and then heterogeneous selection in the symbiotic bacterial community communities of amphibians between summer and autumn. Furthermore, higher niche width of the symbiotic bacterial community of amphibians was found in summer than autumn. Overall, these results demonstrated that seasonal variation influenced amphibian symbiotic bacterial community between summer and autumn.

Soil microbial community assembly and stability are associated with potato (Solanum tuberosum L.) fitness under continuous cropping regime.

Continuous cropping obstacles caused by the over-cultivation of a single crop trigger soil degradation, yield reduction and the occurrence of plant disease. However, the relationships among stability, complexity and the assembly process of soil microbial community with continuous cropping obstacles remains unclear. In this study, molecular ecological networks analysis (MENs) and inter-domain ecological networks analysis (IDENs), and a new index named cohesion tools were used to calculate the stability and complexity of soil microbial communities from eight potato cultivars grown under a continuous cropping regime by using the high-throughput sequencing data. The results showed that the stability (i.e., robustness index) of the bacterial and fungal communities for cultivar ZS5 was significantly higher, and that the complexity (i.e., cohesion values) was also significantly higher in the bacterial, fungal and inter-domain communities (i.e., bacterial-fungal community) of cultivar ZS5 than other cultivars. Network analysis also revealed that Actinobacteria and Ascomycota were the dominant phyla within intra-domain networks of continuous cropping potato soil communities, while the phyla Proteobacteria and Ascomycota dominated the correlation of the bacterial-fungal network. Infer community assembly mechanism by phylogenetic-bin-based null model analysis (iCAMP) tools were used to calculate the soil bacterial and fungal communities’ assembly processes of the eight potato cultivars under continuous cropping regime, and the results showed that the bacterial community was mainly dominated by deterministic processes (64.19% - 81.31%) while the fungal community was mainly dominated by stochastic processes (78.28% - 98.99%), indicating that the continuous-cropping regime mainly influenced the potato soil bacterial community assembly process. Moreover, cultivar ZS5 possessed a relatively lower homogeneous selection, and a higher TP, TN, AP and yield than other cultivars. Our results indicated that the soil microbial network stability and complexity, and community assemble might be associated with yield and soil properties, which would be helpful in the study for resistance to potato continuous cropping obstacles.

Plant traits and community composition drive the assembly processes of abundant and rare fungi across deserts.

The difference in community assembly mechanisms between rare and abundant fungi in deserts remains unknown. Hence, we compared the distribution patterns of abundant and rare fungi, and assessed the factors driving their assembly mechanisms across major vegetation types (shrubby desert, semi-shrubby and dwarf semi-shrubby desert, dwarf semi-arboreous desert, and shrubby steppe desert) of Chinese deserts. We assessed abundant and rare fungal subcommunities base on the sequencing data of fungal ITS data. Abundant fungal assembly was more affected by neutral processes than the rare. Null model and VPA analysis indicated that heterogeneous selection dominated rare sub-communities, whereas abundant fungal assembly was mainly determined by heterogeneous selection, dispersal limitation and other, unknown processes together. As a result, abundant sub-communities exhibited a higher species turnover rate than the rare. Hierarchical partitioning analysis indicated that soil conditions and plant attributes drove the assembly processes of abundant and rare fungi, respectively. Meanwhile, the relative strength of different assembly processes differed significantly among four vegetation types. In addition, we found that plant functional traits and composition played more critical roles in shaping the assembly processes of rare fungi than those of abundant fungi. Taken together, our findings collectively suggest that rare and abundant fungi exhibit differential ecological patterns that are driven by distinct assembly processes in deserts. We emphasize that the assembly processes of abundant and rare fungi are dependent on different abiotic and biotic factors in desert ecosystems.

Untangling microbial diversity and assembly patterns in rare earth element mine drainage in South China

Ion-adsorption rare earth element (REE) deposits are the main reservoirs of REEs worldwide, and are widely exploited in South China. Microbial diversity is essential for maintaining the performance and function of mining ecosystems. Investigating the ecological patterns underlying the REE mine microbiome is essential to understand ecosystem responses to environmental changes and to improve the bioremediation of mining areas. We applied 16S rRNA and ITS gene sequence analyses to investigate the composition characteristics of prokaryotic (bacteria, archaea) and fungal communities in a river impacted by REE acid mine drainage (REE-AMD). The river formed a unique micro-ecosystem, including the main prokaryotic taxa of Proteobacteria, Acidobacteria, Crenarchaeota, and Euryarchaeota, as well as the main fungal taxa of Ascomycota, Basidiomycota, and Chytridiomycota. Analysis of microbial diversity showed that, unlike prokaryotic communities that responded drastically to pollution disturbances, fungal communities were less affected by REE-AMD, but fluctuated significantly in different seasons. Ecological network analysis revealed that fungal communities have lower connectivity and centrality, and higher modularity than prokaryotic networks, indicating that fungal communities have more stable network structures. The introduction of REE-AMD mainly reduced the complexity of the community network and the number of keystone species, while the proportion of negative prokaryotic–fungal associations in the network increased. Ecological process analysis revealed that, compared to the importance of environmental selection for prokaryotes, stochastic processes might have contributed primarily to fungal communities in REE mining areas. These findings confirm that the different assembly mechanisms of prokaryotic and fungal communities are key to the differences in their responses to environmental perturbations. The findings also provide the first insights into microbiota assembly patterns in REE-AMD and important ecological knowledge for the formation and development of microbial communities in REE mining areas.

Co-occurrence patterns and community assembly mechanisms of benthic foraminiferal communities in South Chinese bays

Benthic foraminifera are among the most important components of marine benthic communities and can provide valuable information about the structure and activity of those communities. The distribution and diversity of benthic foraminifera have been well documented, but their co-occurrence patterns and community assembly processes have rarely been elucidated. To fill this gap, we used network analysis and null/neutral model approaches to benthic foraminiferal communities in five bays in South China to evaluate the influences of environmental factors and interspecies interactions on species co-occurrence and the relative importance of deterministic and stochastic processes in shaping community structure, respectively. The spatial heterogeneity of foraminiferal communities across bays was characterized by nonmetric multidimensional scaling analysis. Variation partitioning analysis showed that heavy metals (Cr, Co, Cu, As, Sb, and Hg) were the most important factor influencing community structure, while less importance was attributed to organic matter and grain sizes, which was likely due to the low TOC contents and small variations in TOC and grain size across sites. Network analysis showed that closely related species tended to co-occur with each other, which may be mediated by environmental filtering. The network was divided into three distinct clusters: one cluster consisted of miliolid, and two were dominated by rotaliids, each of which represented a special niche according to the habitat preference of the dominant taxa. The structure of the network was highly informative, as illustrated by the fact that the observed structure was denser than that of randomly constructed networks with the same size or the same degree sequence. The frequency of occurrence of most species (70%) met neutral model expectations, indicating that neutral processes were important for the assembly of benthic foraminiferal communities. However, PER-SIMPER analysis revealed that niche-assembly processes were more important than dispersal-assembly processes in shaping species abundance. Overall, this study provides the first insight into the mechanisms maintaining the community structure and diversity of benthic foraminifera.

Long-term cultivation drives dynamic changes in the rhizosphere microbial community of blueberry.

Rhizosphere microbial communities profoundly affect plant health, productivity, and responses to environmental stress. Thus, it is of great significance to comprehensively understand the response of root-associated microbes to planting years and the complex interactions between plants and rhizosphere microbes under long-term cultivation. Therefore, four rabbiteye blueberries (Vaccinium ashei Reade) plantations established in 1988, 2004, 2013, and 2017 were selected to obtain the dynamic changes and assembly mechanisms of rhizosphere microbial communities with the increase in planting age. Rhizosphere bacterial and fungal community composition and diversity were determined using a high-throughput sequencing method. The results showed that the diversity and structure of bacterial and fungal communities in the rhizosphere of blueberries differed significantly among planting ages. A total of 926 operational taxonomic units (OTUs) in the bacterial community and 219 OTUs in the fungal community were identified as the core rhizosphere microbiome of blueberry. Linear discriminant analysis effect size (LEfSe) analysis revealed 36 and 56 distinct bacterial and fungal biomarkers, respectively. Topological features of co-occurrence network analysis showed greater complexity and more intense interactions in bacterial communities than in fungal communities. Soil pH is the main driver for shaping bacterial community structure, while available potassium is the main driver for shaping fungal community structure. In addition, the VPA results showed that edaphic factors and blueberry planting age contributed more to fungal community variations than bacterial community. Notably, ericoid mycorrhizal fungi were observed in cultivated blueberry varieties, with a marked increase in relative abundance with planting age, which may positively contribute to nutrient uptake and coping with environmental stress. Taken together, our study provides a basis for manipulating rhizosphere microbial communities to improve the sustainability of agricultural production during long-term cultivation.

Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load.

Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.

Insights into community assembly mechanisms, biogeography, and metabolic potential of particle-associated and free-living prokaryotes in tropical oligotrophic surface oceans

Heterotrophic prokaryotes constitute the largest living biomass in the ocean and can be divided into particle-associated (PA) and free-living (FL) fractions. PA and FL prokaryotic communities play critical roles in the biogeochemical cycles of particulate and dissolved organic matter; however, their community assembly processes, biogeographical distribution patterns, and functional properties in oligotrophic surface water remain to be further elucidated. Based on 16S rRNA gene sequencing and shotgun metagenomics, we investigated the assembly mechanisms, biogeography, and functional potential of PA and FL prokaryotes in the surface waters of the West Pacific and Indian Oceans. FL prokaryotic communities were predominantly structured by deterministic processes, whereas their PA counterparts appeared to be shaped by the combined action of deterministic and stochastic processes. PA and FL prokaryotes in the tropical oligotrophic surface ocean exhibit markedly different community structures and functional potentials. Bacterial PA specialists such as Lentimonas, Alteromonas, and Pirellula as well as archaeal PA specialists Marine Group II and Marine Group III were significantly more abundant in PA assemblages, whereas lineages such as Prochlorococcus, SAR11 clade, and Candidatus Actinomarina were significantly more abundant in FL communities. The metabolic potential of the PA community was more abundant in pathways such as polyamine biosynthesis, carbohydrate metabolism, and glycosaminoglycan degradation. In contrast, the FL community was more enriched in functions related to amino acid metabolism, lipid biosynthesis, and aromatic degradation.

Apex Predators Enhance Environmental Adaptation but Reduce Community Stability of Bacterioplankton in Crustacean Aquaculture Ponds.

Aquaculture environments harbor complex bacterial communities that are critical for the growth and health of culture species. Apex predators are frequently added to aquaculture ponds to improve ecosystem stability. However, limited research has explored the effects of apex predators on the composition and function of bacterioplankton communities, as well as the underlying mechanisms of community assembly. Using 16S ribosomal RNA (rRNA) high-throughput sequencing, we investigated bacterioplankton communities of crustacean aquaculture ponds with and without apex predators (mandarin fish, Siniperca chuatsi) throughout the culture process. In addition to investigating differences in bacterioplankton communities, we also explored variations in environmental adaptation, functional redundancy, and community stability. Significant differences were observed in bacterioplankton composition among different cultural stages; there was an increase in Bacteriobota and fermentation-related bacteria, but a decrease in Firmicutes and pathogens in the middle stages of aquaculture. Apex predators increased the abundance of organic matter degradation bacteria and decreased pathogens. Bacterioplankton communities under apex predator disturbances had a wider environmental breadth, indicating broader environmental adaptation. Moreover, functional prediction and network analyses revealed that communities under apex predator disturbances were less functionally redundant and unstable. Based on the null model, stochastic processes drove community assembly during aquaculture, whereas apex predators elevated the contribution of deterministic processes. Greater changes in nitrate in culture ponds caused by apex predator disturbances were decisive in controlling the balance between stochasticity and determinism in community assembly. Our study provided insight into the mechanisms underlying bacterioplankton community assembly in aquaculture systems in response to apex predator disturbances.

The divergent vertical pattern and assembly of soil bacterial and fungal communities in response to short-term warming in an alpine peatland.

Soil microbial communities are crucial in ecosystem-level decomposition and nutrient cycling processes and are sensitive to climate change in peatlands. However, the response of the vertical distribution of microbial communities to warming remains unclear in the alpine peatland. In this study, we examined the effects of warming on the vertical pattern and assembly of soil bacterial and fungal communities across three soil layers (0–10, 10–20, and 20–30 cm) in the Zoige alpine peatland under a warming treatment. Our results showed that short-term warming had no significant effects on the alpha diversity of either the bacterial or the fungal community. Although the bacterial community in the lower layers became more similar as soil temperature increased, the difference in the vertical structure of the bacterial community among different treatments was not significant. In contrast, the vertical structure of the fungal community was significantly affected by warming. The main ecological process driving the vertical assembly of the bacterial community was the niche-based process in all treatments, while soil carbon and nutrients were the main driving factors. The vertical structure of the fungal community was driven by a dispersal-based process in control plots, while the niche and dispersal processes jointly regulated the fungal communities in the warming plots. Plant biomass was significantly related to the vertical structure of the fungal community under the warming treatments. The variation in pH was significantly correlated with the assembly of the bacterial community, while soil water content, microbial biomass carbon/microbial biomass phosphorous (MBC/MBP), and microbial biomass nitrogen/ microbial biomass phosphorous (MBN/MBP) were significantly correlated with the assembly of the fungal community. These results indicate that the vertical structure and assembly of the soil bacterial and fungal communities responded differently to warming and could provide a potential mechanism of microbial community assembly in the alpine peatland in response to warming.

Assembly mechanism and co-occurrence patterns of DNRA microbial communities and imprint of nitrate reduction in the Songhua River sediments of China's largest old industrial base

Dissimilatory nitrate reduction to ammonium (DNRA) reduces nitrate to ammonium nitrogen instead of nitrogen gas, which is an important internal linking process of nitrogen cycle. No literature has reported the assembly mechanism of DNRA microbial communities. Here, the deep assembly mechanisms and co-occurrence patterns of DNRA microbial communities and imprint of nitrate reduction in Songhua River Basin (an inland river located in northeastern China) were studied. The DNRA potential rates were detected at six sampling sites, ranging from 0.25 ± 0.23 to 4.22 ± 0.61 μmol N/L/h, accounting for 33.07% to 98.08% of the total nitrate reduction. Spearman analysis indicated that the nrfA gene abundance was significantly positively correlated with the concentration of total nitrogen (TN) in sediments (p < 0.05), suggesting that nutrient inputs may enhance the metabolic potential of DNRA bacteria. Co-occurrence network and Spearman correlation analyses showed that the DNRA rates were significantly correlated with the abundance of keystone species, but not with the dominant genera (p < 0.05). Variance partitioning analysis (VPA) revealed that sediment physicochemical properties and spatial factors explained only 21.07% and 14.51% of the DNRA community variation. Null model and neutral community model both revealed stochastic processes play a major role in shaping DNRA microbial community structure. The drift was the most important process, explaining 36.36% of the community variation, followed by homogeneous selection and homogenizing dispersal, which accounted for 27.27% and 22.73%, respectively. Additionally, Geobacteraceae played an important role in DNRA and the entire bacterial community in Songhua River. This study explored the underestimated DNRA process and the deep community assembly mechanisms, which will contribute to understanding nitrate conversion and the impact of nitrogen pollution on microbial communities of river sediments in cold regions.

Disturbance legacy of a 100-year flood event: large wood accelerates plant diversity resilience on gravel-bed rivers.

Understanding biodiversity resilience after a major disturbance is a key issue in basic and applied science. Plant diversity in gravel-bed rivers is affected by flood events, which are one of the most effective disturbance agents in the flow regime, affecting species distribution, and ecosystem dynamics. Although disturbance plays a critical role in community assembly mechanisms, how plant diversity recovers after a severe disturbance, such as a 100-year flood event remains unknown. The present study examined how the disturbance legacy of large wood in gravel-bed river ecosystems contributes to the resilience of plant diversity. The present study demonstrated that the resilience of plant species in disturbance legacy sites, namely deposited large wood sites, was higher than that in open habitat sites. Indicator species analysis revealed that perennial plants were the most important indicator species of disturbance legacy sites. These results suggest that perennial species richness contributes to the resilience of high plant diversity across the disturbance legacy sites in this region. After major flood events, land managers often remove large wood and debris jams to avoid secondary disasters, such as embankment collapse. However, we suggest that large wood should be retained on the gravel beds to aid the recovery of biodiversity and ecosystems. Furthermore, understanding the relationships between disturbance legacies and ecosystem resilience can contribute to the formulation of strategies for sustainable ecosystem management and biodiversity conservation in the future.

"Realistic strategies" and neutral processes drive the community assembly based on leaf functional traits in a subtropical evergreen broad-leaved forest.

Neutral‐theory‐based stochastic and niche‐theory‐based determinative processes are commonly used to explain the mechanisms of natural community assembly. However, considerable uncertainty remains regarding the relative importance of different ecological processes in shaping forest communities. Functional traits and phylogeny provide important information about plant environmental adaptation strategies and evolutionary history and promise a better mechanistic and predictive understanding of community assembly. Based on nine leaf functional traits and phylogenetic data of 18 dominant species in a Lithocarpus glaber–Cyclobalanopsis glauca evergreen broad‐leaved forest, we analyzed the variation in traits, explored the influence of phylogeny and environment on leaf traits, and distinguished the relative effects of spatial and environmental variables on functional traits and phylogenetic compositions. The results showed the following: (i) Leaf traits had moderate intraspecific variation, and significant interspecific variation existed especially among life forms. (ii) Significant phylogenetic signals were detected only in leaf thickness and leaf area. The correlations among traits both supported “the leaf economics spectrum” at the species and community levels, and the relationships significantly increased or only a little change after removing the phylogenetic influence, which showed a lack of consistency between the leaf functional trait patterns and phylogenetic patterns. We infer the coexistent species tended to adopt “realism” to adapt to their habitats. (iii) Soil total potassium and phosphorus content, altitude, aspect, and convexity were the most critical environmental factors affecting functional traits and phylogenetic composition. Total environmental and spatial variables explained 63.38% of the variation in functional trait composition and 47.96% of the variation in phylogenetic structures. Meanwhile, the contribution of pure spatial factors was significantly higher than that of the pure environment. Stochastic processes played dominant roles in driving community functional trait assembly, but determinative processes such as environmental filtering had a stronger effect on shaping community phylogenetic structure at a fine scale.