Microbial Community Assembly Processes Research Articles

Ecological influences of sulfadiazine on rhizosphere soil microbial communities in ryegrass (Lolium perenne L.)-soil potting systems: Perspectives on diversity, co-occurrence networks, and assembly processes

Microorganisms in the soil are crucial constituents of land ecosystems, significantly influencing their structure and functionality. However, the accumulation of antibiotics in agricultural practices may negatively affect these microbial communities. The objective of this study was to explore the ecological effects of the sulfonamide drug sulfadiazine (SDZ) on the rhizosphere soil microbial communities of ryegrass (Lolium perenne L.). A potting system experiment was constructed by exposing for 45 days after treatments with different initial concentrations of SDZ (0, 1, 10, and 30 mg/kg) to assess the effects of SDZ on soil microbial diversity, bacterial-fungal co-occurrence networks, and community assembly processes. The findings indicated that SDZ treatment significantly altered the community composition, especially for bacteria in the phylum Proteobacteria and Gemmatimonadota and fungi in the phylum Mortierellomycota and Aphelidiomycota. Network analysis revealed that SDZ stress caused alterations in microbial interaction patterns, especially at high treatment concentrations, and reduced network connectivity. In addition, SDZ significantly affected microbial community assembly processes, where stochastic processes were enhanced in bacterial communities, while fungal communities showed a balance of stochastic and deterministic processes. Analysis of environmental variables revealed that the presence of SDZ may disrupt the link between soil microorganisms and soil nitrogen compounds. The results provide new perspectives for understanding the ecological impacts of antibiotic residues in agroecosystems and provide a scientific basis for soil health management.

Soil total phosphorus mediate the assembly processes of rhizosphere microbial communities of ficus species in a tropical rainforest

Revealing the assembly processes of plant rhizosphere microbial communities and the underlying influencing factors is essential for understanding the biodiversity and function of forest ecosystem. However, it remains unclear how deterministic and stochastic processes shape community structure and their relative importance in phosphorus-limited tropical environments. Here, we investigated the diversity, composition, and assembly processes of rhizosphere microbial communities of Ficus species in the Xishuangbanna region of southwest China, using methods such as high-throughput sequencing, variance partitioning analysis and null model analysis. We found that the community assembly processes of bacteria and fungi were primarily dominated by deterministic processes, with the fungal group being more deterministic than the bacteria group. Soil total phosphorus (TP) was the primary determinant of the composition and assembly of the rhizosphere microbial community, explaining 12.58% and 21.35% of the compositional variation in bacterial and fungal communities, respectively, and accounting for 14% of the microbial community assembly, but has a minor impact on their alpha diversity. This study highlights the distinct environmental driving factors of community composition and community assembly. The exposed positive relationship between soil TP and microbial deterministic process has inspiration for link of microbial community functions to soil function and sustainable forest management.

Divergent Assembly Processes of Phyllosphere and Rhizosphere Microbial Communities Along Environmental Gradient.

The underlying assembly processes of surface microbial communities are crucial for host plants and ecosystem functions. However, the relative importance of stochastic and deterministic processes in shaping epiphytic microbes remains poorly understood in both the phyllosphere and rhizosphere. Here, we compared the spatial variations in epiphytic microbial communities of two dominant grasses along a 1400 km transect on the Tibetan Plateau and assessed the assembly processes between the phyllosphere and rhizosphere. We found significant variations in epiphytic microbial community compositions between plant compartments and host species. Stochastic processes (drift and homogenizing dispersal) predominantly shaped microbial communities in both the phyllosphere and rhizosphere, with a greater contribution of stochastic processes in the phyllosphere. As environmental heterogeneity intensified, we found a transition from stochasticity to determinism in affecting the microbial assembly. This transition to homogeneous or variable selection depended on plant compartments and host species. Our study is among the first to compare the contribution of stochastic versus deterministic processes to epiphytic community assembly between the phyllosphere and rhizosphere on the Tibetan Plateau. These findings advance our knowledge of epiphytic microbial assembly and disentangle how host plants exploit the microbiome for improved performance and functioning in stressful alpine ecosystems.

Dispersal of microbes from grassland fire smoke to soils.

Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of fields including agriculture, restoration, plant disease, and biodiversity.

Phosphorus resource partitioning underpins diversity patterns and assembly processes of microbial communities in plateau karst lakes

Eutrophication triggered by internal phosphorus (P) poses a substantial threat to the biodiversity of organisms in freshwater ecosystems. However, little is known about the linkages between P resource partitioning and microbial succession, especially in karst sediments. Here, we studied the diversity patterns and assembly processes of bacterial and archaeal communities in sediment cores from two historically hyper-eutrophicated karst lakes, Hongfeng Lake and Aha Lake, and investigated the relative contribution of P fractions to them. Our null and neutral models consistently indicated that bacterial and archaeal community assembly was judged to be deterministic rather than stochastic. We found a monotonically decreasing pattern for bacterial Shannon diversity toward deep sediments in Aha Lake, but U- or hump-shaped patterns for archaea in Hongfeng and Aha Lakes. Intriguingly, the community dissimilarity Bray–Curtis of bacteria and archaea consistently increased with increasing depth distance, with slopes of 0.0080 and 0.0069 in Hongfeng Lake and 0.0078 and 0.0087 in Aha Lake, respectively. Such cross-taxon congruence was well-supported by equivalent ecological processes (i.e., environmental selection). For bacteria and archaea, Shannon diversity was primarily affected by the total P (TP) fractions such as the loosely adsorbed TP or calcium-bound TP and sediment TP. Their community composition was significantly (P < 0.05) affected by calcium-bound inorganic P (Pi), loosely adsorbed Pi and reductant-soluble Pi. Although sediment properties were important, bacterial and archaeal diversity or community composition were well-explained by the Pi fractions, with high direct or indirect effects. In particular, Pi fractions exhibited stronger effects on bacterial and archaeal characteristics than organic P fractions. Taken together, our study provides novel insights into the ecological importance of P resource partitioning to microbial succession, which has crucial implications for disentangling the biogeochemical processes of P cycling in aquatic ecosystems.

Peanut–cotton intercropping to enhance soil ecosystem multifunctionality: Roles of microbial keystone taxa, assembly processes, and C-cycling profiles

Legume-based intercropping, such as the peanut–cotton system, stands out as a promising strategy for enhancing soil ecosystem multifunctionality (EMF); however, the underlying microbial mechanisms driving these enhancements remain inadequately explored. In this study, after implementing peanut–cotton intercropping for six consecutive years, a data set of 13 ecosystem functional indicators including 41 soil variables, was obtained and used to quantify the average EMF index. We investigated changes in microbial keystone taxa in co-occurrence networks, community assembly processes, carbon (C) cycling profiles, and their collective impacts on soil EMF. Soil EMF increased by an average of 140.0 % in the peanut–cotton intercropping system, compared with monoculture systems of both peanut and cotton, driven by significant increases in C-cycling (159.9 %), nutrient provisioning (91.2 %), and microbial growth efficiency functions (53.9 %). The peanut–cotton intercropping system significantly increased the average well-color developments (AWCD), abundance of C-fixation and C-degradation genes, and related pathways, resulting in a highly vigorous microbial C-cycling profile. The microbial community assembly processes shifted from a balance of stochastic and deterministic processes in monocultures to predominantly deterministic processes (> 70 %) in the intercropping system. Additionally, the peanut–cotton intercropping system fostered a more efficient and stable bacterial–fungal cross-kingdom network than the monocultures, characterized by a higher average clustering coefficient, higher robustness, and shorter average path length. This intercropping system also recruited a group of keystone taxa affiliated with Proteobacteria, Actinobacteria, and Ascomycota phyla. The enhancement of EMF in the peanut–cotton intercropping system resulted from the positive impact of key microbial community members and their assembly, C/N ratios, AWCD, and C-fixation and C-degradation genes. Our study provides insights into the complex ecological linkages between microbial communities, C-cycling profiles, and soil ecosystem functions, providing valuable insights into the microbial mechanisms underlying the benefits of intercropping systems.

Mulching drive changes in soil microbial community assembly processes and networks across aggregate fractions

Soil microbial community assembly processes and networks in croplands have been widely explored; however, their dynamics and how they regulate winter wheat yield across distinct soil aggregate fractions under the combined effects of mulching and soil horizons have not been comprehensively understood. Therefore, based on a 9-y field experiment, the responses of soil bacterial and fungal community assembly processes and interkingdom association networks to mulching were specifically investigated at the soil aggregation level. Soil properties and microbial biomass were separated into distinct mulching in the topsoil (0–10 cm), and soil water content was considered the most critical factor. The soil bacterial community was affected mainly by mulching and soil horizon compared with the fungal community in microaggregates (<0.25 mm). Notably, the bacterial community displayed more robust stochastic processes than the fungal one, and microbial interkingdom association networks were more complex and stable in micro-than macroaggregates. Soil potential carbon mineralization, pH, and total nitrogen were the dominant properties regulating winter wheat grain yield in combination with microbial community composition, assembly processes, and networks in each soil aggregate class. Wheat yield decreased under straw mulching and was mainly regulated by bacterial community composition and assembly processes. Thus, this study enhanced our understanding of the regulations for wheat yield, which could facilitate soil microbial community management at the aggregation level for sustainable crop production in mulching conservation agroecosystems.

Groundwater flow regime shapes nitrogen functional traits by affecting microbial community assembly processes in the subsurface

The complex nitrogen (N) cycle in groundwater systems is affected by both biological and environmental factors. The interactions between hydrogeological conditions and the microbial community assembly processes that impact N-cycling processes remain poorly understood. We explored the assembly patterns of N-cycling microbial communities along the groundwater flow path. The environmental heterogeneity in different hydrological phases increased along the flow path (mean Ed: 0.16–0.49), accompanied by different microbial community assembly patterns. The assembly patterns that engaged in dissimilatory nitrate reduction to ammonium (DNRA) and denitrification changed across the water-sediment phases. Nitrifying microorganisms in the discharge area were mainly influenced by heterogeneous selection (41–69 %), and were closely correlated with dissolved oxygen (DO) concentrations. Homogeneity along flow-through increased stochastic assemblies, such as downstream drift of anammox bacterial (AnAOB) communities. Thus, the N removal pathway changed from “nitrification-denitrification” in the recharge area to “partial nitrification-anammox” in the discharge area. The increasing environmental heterogeneity brought more deterministic assembly patterns of N-cycling communities, linked to higher community turnover along the groundwater flow path. This study indicated that groundwater flow regime determined microbial community assembly patterns, providing valuable insight into the response of N transitions to environmental variations in groundwater systems.

Strengthened plant-microorganism interaction after topsoil removal cause more deterministic microbial assembly processes and increased soil nitrogen mineralization

Topsoil removal, among other restoration measures, has been recognized as one of the most successful methods to restore biodiversity and ecosystem functioning in European grasslands. However, knowledge about how removal as well as other restoration methods influence interactions between plant and microbial communities is very limited. The aims of the current study were to understand the impact of topsoil removal on plant-microorganism interactions and on soil nitrogen (N) mineralization, as one example of ecosystem functioning. We examined how three different grassland restoration methods, namely ‘Harvest only’, ‘Topsoil removal’ and ‘Topsoil removal + Propagules (plant seed addition)’, affected i) the interactions between plants and soil microorganisms, ii) soil microbial community assembly processes, and iii) soil N mineralization. We compared the outcome of these three restoration methods to initial degraded and target semi-natural grasslands in the Canton of Zurich, Switzerland. We were able to show that ‘Topsoil removal’ and ‘Topsoil removal + Propagules’, but not ‘Harvest only’, reduced the soil total N pool and available N concentration, but increased soil N mineralization and strengthened the plant-microorganism interactions. Microbial community assembly processes shifted towards more deterministic after both topsoil removal treatments. These shifts could be attributed to an increase in dispersal limitation and selection due to stronger interactions between plants and soil microorganisms. The negative relationship between soil N mineralization and microbial community stochasticity indicated that microbial assembly processes, to some extent, can be incorporated into model predictions of soil functions. Overall, the results suggest that topsoil removal may change the microbial assembly processes and thus the functioning of grassland ecosystems by enhancing the interaction between plants and soil microorganisms.

Stable microbial community diversity across large-scale Antarctic water masses

The distinctive environmental attributes of the Southern Ocean underscore the indispensability of microorganisms in this region. We analyzed 208 samples obtained from four separate layers (Surface, Deep Chlorophyll Maximum, Middle, and Bottom) in the neighboring seas of the Antarctic Peninsula and the Cosmonaut Sea to explore variations in microbial composition, interactions and community assembly processes. The results demonstrated noteworthy distinctions in alpha and beta diversity across diverse communities, with the increase in water depth, a gradual rise in community diversity was observed. In particular, the co-occurrence network analysis exposed pronounced microbial interactions within the same water mass, which are notably stronger than those observed between different water masses. Co-occurrence network complexity was higher in the surface water mass than in the bottom water mass. Yet, the surface water mass exhibited greater network stability. Moreover, in the phylogenetic-based β-nearest taxon distance analyses, deterministic processes were identified as the primary factors influencing community assembly in Antarctic microorganisms. This study contributes to exploring diversity and assembly processes under the complex hydrological conditions of Antarctica.

New insights into assembly processes and driving factors of urban soil microbial community under environmental stress in Beijing

Rapid urbanization leads to drastic environmental changes, directly or indirectly affecting the structure and function of soil microbial communities. However, the ecological response of soil microbes to environmental stresses has not yet been fully explored. In this study, we used high-throughput sequencing to analyze the assembly mechanism and driving factors of soil microbial community under environmental stresses. The results indicated that environmental stresses significantly affected soil properties and the levels of beryllium, cobalt, antimony, and vanadium contamination in soil generally increased from the suburban areas toward the city core. The composition and distribution of soil microbial communities demonstrated clear differences under different levels of environmental stress, but there was no significant difference in microbial diversity. Random forest and partial least squares structural equation modeling results suggested that multiple factors influenced microbial diversity, but antimony was the key driver. The influence of environmental stress led to deterministic processes dominating microbial community assembly processes, which promoted the regional homogenization of soil microbes. Therefore, this study provides new insights into urban soil microbial management under environmental stresses.

Leaf Health Status Regulates Endophytic Microbial Community Structure, Network Complexity, and Assembly Processes in the Leaves of the Rare and Endangered Plant Species Abies fanjingshanensis.

The rare and endangered plant species Abies fanjingshanensis, which has a limited habitat, a limited distribution area, and a small population, is under severe threat, particularly due to poor leaf health. The plant endophytic microbiome is an integral part of the host, and increasing evidence indicates that the interplay between plants and endophytic microbes is a key determinant for sustaining plant fitness. However, little attention has been given to the differences in the endophytic microbial community structure, network complexity, and assembly processes in leaves with different leaf health statuses. Here, we investigated the endophytic bacterial and fungal communities in healthy leaves (HLs) and non-healthy leaves (NLs) of A. fanjingshanensis using 16S rRNA gene and internal transcribed spacer sequencing and evaluated how leaf health status affects the co-occurrence patterns and assembly processes of leaf endophytic microbial communities based on the co-occurrence networks, the niche breadth index, a neutral community model, and C-score metrics. HLs had significantly greater endophytic bacterial and fungal abundance and diversity than NLs, and there were significant differences in the endophytic microbial communities between HLs and NLs. Leaf-health-sensitive endophytic microbes were taxonomically diverse and were mainly grouped into four ecological clusters according to leaf health status. Poor leaf health reduced the complexity of the endophytic bacterial and fungal community networks, as reflected by a decrease in network nodes and edges and an increase in degrees of betweenness and assortativity. The stochastic processes of endophytic bacterial and fungal community assembly were weakened, and the deterministic processes became more important with declining leaf health. These results have important implications for understanding the ecological patterns and interactions of endophytic microbial communities in response to changing leaf health status and provide opportunities for further studies on exploiting plant endophytic microbes to conserve this endangered Abies species.

Green Roof Substrate Microbes Compose a Core Community of Stress-Tolerant Taxa.

Extensive green roofs provide for many ecosystem services in urban environments. The efficacy of these services is influenced by the vegetation structure. Despite their key role in plant performance and productivity, but also their contribution to nitrogen fixation or carbon sequestration, green roof microbial communities have received little attention so far. No study included a spatiotemporal aspect to investigate the core microbiota residing in the substrates of extensive green roofs, although these key taxa are hypothesized to be amongst the most ecologically important taxa. Here, we identified the core microbiota residing in extensive green roof substrates and investigated whether microbial community composition is affected by the vegetation that is planted on extensive green roofs. Eleven green roofs from three different cities in Flanders (Belgium), planted either with a mixture of grasses, wildflowers and succulents (Sedum spp.; Sedum-herbs-grasses roofs) or solely species of Sedum (Sedum-moss roofs), were seasonally sampled to investigate prokaryotic and fungal communities via metabarcoding. Identifying the key microbial taxa revealed that most taxa are dominant phylotypes in soils worldwide. Many bacterial core taxa are capable of nitrogen fixation, and most fungal key taxa are stress-tolerant saprotrophs, endophytes, or both. Considering that soil microbes adapted to the local edaphic conditions have been found to improve plant fitness, further investigation of the core microbiome is warranted to determine the extent to which these stress-tolerant microbes are beneficial for the vegetational layer. Although Sedum-herbs-grasses roofs contained more plant species than Sedum-moss roofs, we observed no discriminant microbial communities between both roof types, likely due to sharing the same substrate textures and the vegetational layers that became more similar throughout time. Future studies are recommended to comprehensively characterize the vegetational layer and composition to examine the primary drivers of microbial community assembly processes.

Rainfall seasonality shapes microbial assembly and niche characteristics in Yunnan Plateau lakes, China

Microorganisms are crucial components of freshwater ecosystems. Understanding the microbial community assembly processes and niche characteristics in freshwater ecosystems, which are poorly understood, is crucial for evaluating microbial ecological roles. The Yunnan Plateau lakes in China represent a freshwater ecosystem that is experiencing eutrophication due to anthropogenic activities. Here, variation in the assembly and niche characteristics of both prokaryotic and microeukaryotic communities was explored in Yunnan Plateau lakes across two seasons (dry season and rainy season) to determine the impacts of rainfall and environmental conditions on the microbial community and niche. The results showed that the environmental heterogeneity of the lakes decreased in the rainy season compared to the dry season. The microbial (bacterial and microeukaryotic) α-diversity significantly decreased during the rainy season. Deterministic processes were found to dominate microbial community assembly in both seasons. β-Diversity decomposition analysis revealed that microbial community compositional dissimilarities were dominated by species replacement processes. The co-occurrence networks indicated reduced species complexity for microbes and a destabilized network for prokaryotes prior to rainfall, while the opposite was found for microeukaryotes following rainfall. Microbial niche breadth decreased significantly in the rainy season. In addition, lower prokaryotic niche overlap, but greater microeukaryotic niche overlap, was observed after rainfall. Rainfall and environmental conditions significantly affected the microbial community assembly and niche characteristics. It can be concluded that rainfall and external pollutant input during the seasonal transition alter the lake environment, thereby regulating the microbial community and niche in these lakes. Our findings offer new insight into microbiota assembly and niche patterns in plateau lakes, further deepening the understanding of freshwater ecosystem functioning.

Plant and soil microbial community assembly processes across urban vacant lots

AbstractQuestionsNumerous studies on community assembly processes have been conducted in natural ecosystems. However, we know little about community assembly processes in human‐dominated urban ecosystems. Here, we asked: (1) how are the composition and functional diversity of native and exotic plant species shaped by local environment and landscape factors across urban vacant lots; and (2) how is microbial (bacterial and fungal) community composition influenced by the local environment, landscape factors, and plant species composition across urban vacant lots?LocationWe investigated 69 urban vacant lots in Yokohama, Japan.MethodsBy using a variation partitioning approach, we examined the relative importance of local environmental and landscape factors (including land use and spatial structure) in explaining variation in plant species composition and functional diversity of native or exotic species. We also explored the relative importance of local environmental and landscape factors, and plant species composition in explaining variation in microbial community composition.ResultsThe spatial structure of vacant lots determined the species composition and functional diversity of plant communities, suggesting that plant community assembly is determined by dispersal limitation. However, the functional diversity of the exotic species varied randomly, which reduced the relative importance of the spatial structure of vacant lots. Plant species composition as well as the spatial structure of vacant lots were the important drivers of the composition of soil microbial communities, despite a higher proportion of unexplained variation in their composition. Finally, we found an essential contribution of earthmoving methods in explaining the variations in both plant and microbial community composition.ConclusionPlant and microbial community composition would be largely determined by dispersal limitation across urban vacant lots. Understanding urban community assembly is critical for predicting plant and microbial communities that play an essential role in regulating urban ecosystem functioning and services.

Effects of biochar and compost on microbial community assembly and metabolic processes in glyphosate, imidacloprid and pyraclostrobin polluted soil under freeze[sbnd]thaw cycles

Biochar and organic compost are widely used in agricultural soil remediation as soil immobilization agents. However, the effects of biochar and compost on microbial community assembly processes in polluted soil under freezingthawing need to be further clarified. Therefore, a freezethaw cycle experiment was conducted with glyphosate (herbicide), imidacloprid (insecticide) and pyraclostrobin (fungicide) polluted to understand the effect of biochar and compost on microbial community assembly and metabolic behavior. We found that biochar and compost could significantly promote the degradation of glyphosate, imidacloprid and pyraclostrobin in freezethaw soil decrease the half-life of the three pesticides. The addition of immobilization agents improved soil bacterial and fungal communities and promoted the transformation from homogeneous dispersal to homogeneous selection. For soil metabolism, the combined addition of biochar and compost alleviated the pollution of glyphosate, imidacloprid and imidacloprid to soil through up-regulation of metabolites (DEMs) in amino acid metabolism pathway and down-regulation of DEMs in fatty acid metabolism pathway. The structural equation modeling (SEM) results showed that soil pH and DOC were the main driving factors affecting microbial community assembly and metabolites. In summary, the combined addition of biochar and compost reduced the adverse effects of pesticides residues.

Bridging ecological assembly process and community stability upon bacterial invasions.

Understanding the link between microbial community stability and assembly processes is crucial in microbial ecology. Here, we investigated whether the impact of biotic disturbances would depend on the processes controlling community assembly. For that, we performed an experiment using soil microcosms in which microbial communities assembled through different processes were invaded by Escherichia coli. We show that the ecological assembly process of the resident community plays a significant role in invader-resident competition, invader survival, and compositional stability of the resident community. Specifically, the resident communities primarily assembled through stochastic processes were more susceptible to invader survival. Besides, E. coli invasion acts as a biotic selection pressure, leading to competition between the invader and resident taxa, suppressing the stochasticity in the resident community. Taken together, this study provides empirical evidence for the interpretation of microbial community assemblage on their (potential) ecosystem functions and services, such as the prevention of pathogen establishment and the pathogenic states of soil microbiomes.

Quantification of microbial community assembly processes during degradation on diverse plastispheres based on physicochemical characters and phylogenetic bin-based null model analysis

To understand the differences in degradation processes depending on the chemical properties of polymers, it is necessary to both quantify the microbiome composition and evaluate the process of microbial turnover (i.e., community assembly processes) in a variety of polymer materials. In this study, using a phylogenetic bin-based null model analysis (i.e., iCAMP), we evaluated community assembly processes from original estuary water to 37 types of polymers, which provide overwhelmingly diverse niches for microbes, in 14-day incubation experiments. First, we evaluated the polymer properties related to degradation rates. Polymers with higher adipic acid (AdA) monomer exhibited higher motility, hydrophilicity, and degradation rates, whereas those with higher aromatic monomer exhibited the opposite trends. Second, microbiome composition analysis was performed, and the microbiomes were significantly changed by the AdA or aromatic content. This was consistent with the polymer properties, suggesting that polymer motility and hydrophilicity attributable to the first-order structure modify the accessibility of the enzyme to the reaction site and hence the degradation rate, resulting in differences in microbiome community composition. Finally, we determined community assembly processes from estuary water to plastics using a phylogenetic bin-based null model analysis. The importance of heterogeneous selection was higher in mobile, hydrophilic, and fast-degrading polymers, while that of homogeneous selection was lower. This suggests that the environmental difference between before and after incubation becomes significant under rapid degradation, which select microbes adapted to biofilm environments. In addition, the more stochastic turnover prevailed, the more variation in the communities (i.e., β-diversity) increased. This suggests that turnover processes not dictated by the environment lead to instability in community compositions.

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition.

Bacteria naturally co-exist in multispecies consortia, and the ability to engineer such systems can be useful in biotechnology. Despite this, few studies have been performed to understand how bacteria form a stable community and interact with each other under nutrient-rich conditions. In this study, we investigated the effects of initial inoculum ratios on bacterial community structure using a complex medium and found that the initial inoculum ratio has no significant impact on resultant community structure or on interaction patterns between community members. The microbial population profiles were simulated using computational tools in order to understand intermicrobial relationships and to identify potential metabolic exchanges that occur during stabilization of the bacterial community. Studying microbial community assembly processes is essential for understanding fundamental ecological principles in microbial ecosystems and can be critical in predicting microbial community structure and function.

Taxonomic and functional β-diversity patterns reveal stochastic assembly rules in microbial communities of seagrass beds.

Microorganisms are important members of seagrass bed ecosystems and play a crucial role in maintaining the health of seagrasses and the ecological functions of the ecosystem. In this study, we systematically quantified the assembly processes of microbial communities in fragmented seagrass beds and examined their correlation with environmental factors. Concurrently, we explored the relative contributions of species replacement and richness differences to the taxonomic and functional β-diversity of microbial communities, investigated the potential interrelation between these components, and assessed the explanatory power of environmental factors. The results suggest that stochastic processes dominate community assembly. Taxonomic β-diversity differences are governed by species replacement, while for functional β-diversity, the contribution of richness differences slightly outweighs that of replacement processes. A weak but significant correlation (p < 0.05) exists between the two components of β-diversity in taxonomy and functionality, with almost no observed significant correlation with environmental factors. This implies significant differences in taxonomy, but functional convergence and redundancy within microbial communities. Environmental factors are insufficient to explain the β-diversity differences. In conclusion, the assembly of microbial communities in fragmented seagrass beds is governed by stochastic processes. The patterns of taxonomic and functional β-diversity provide new insights and evidence for a better understanding of these stochastic assembly rules. This has important implications for the conservation and management of fragmented seagrass beds.