Microbial Community Assembly Processes Research Articles

Conversion of grassland to cropland altered soil nitrogen-related microbial communities at large scales

Land-use changes may dramatically disturb underground microbial biodiversity, especially in the fragile ecological areas. However, the impact of conversion of grassland to cropland on soil nitrogen (N)-related microbial communities is not fully understood in the farming-pastoral ecotone of northern China. Therefore, 24 paired grassland and cropland soil samples were collected in this region to investigate the community structure and assembly processes of soil N-related microorganisms via amplicon sequencing of nifH, archaeal and bacterial amoA, and nxrB genes. The results showed higher ammonia-oxidizing bacteria (AOB) alpha diversity but a lower nitrite-oxidizing bacteria (NOB) diversity in cropland soil compared to grassland soil. Non-metric multidimensional scaling ordinations revealed that diazotroph, AOB and NOB communities differed considerably between grassland and cropland soil. Soil microbial co-occurrence networks showed that conversion of grassland to cropland significantly lowered the average degree, average clustering coefficient, total nodes and links, resulting in less complex microbial networks in cropland soil. Land-use change altered AOB community assembly processes, resulting from a stochasticity-dominated process in grassland soil to a determinism-dominated process in cropland soil. In contrast, deterministic processes were dominant in diazotroph community assembly, whereas stochastic processes were dominant in constructing ammonia-oxidizing archaea and NOB communities in both grassland and cropland soil. These results provide novel evidence that the conversion of grassland to cropland altered the diversity and assembly processes of soil microbial communities involved in soil N-cycling processes, which has important implications for the potential changes in soil functions under land-use changes.

Assembly processes of abundant and rare microbial communities in orchard soil under a cover crop at different periods

Soil microorganisms play key roles in agricultural ecosystems. However, little is known about their dynamic diversity patterns and community assembly processes, especially in the rare microbial biosphere in agriculture systems. In this study, we determined the responses of diversities and assembly processes of abundant and rare bacterial and fungal subcommunities to agricultural practice (i.e. cover crop) in a semiarid orchard soil by using 16S and ITS rRNA gene sequencing. We found that the community structures of abundant and rare taxa exhibited a similar response to cover crop or growth periods. Growth periods significantly changed the bacterial and fungal subcommunities structure. Only the fungal subcommunities structure was affected by cover crop. The community assembly of abundant and rare fungi was respectively dominated by stochastic process and deterministic process and less affected by cover crop and growth period. For abundant bacteria, the assembly process was dominated by heterogeneous and undominated processes, and the importance of heterogeneous selection process was increased by cover crop at setting and maturing period. The assembly process of rare bacterial community was dominated by a homogeneous selection and the relative importance of dispersal limitation was increased at maturing period. We also found that the assembly processes of abundant taxa were significantly related to the soil DON, NH4+-N, NO3–-N and pH, while the assembly processes of rare taxa were significantly related to the soil DOC, AP and SOC. Our results provide new insights into the formation of the microbial community in orchard soil under a cover crop, especially the seasonal succession of abundant and rare bacterial and fungal subcommunities.

Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments

The microbial community composition and biogeochemical dynamics of coastal permeable (sand) sediments differs from cohesive (mud) sediments. Tide- and wave-driven hydrodynamic disturbance causes spatiotemporal variations in oxygen levels, which select for microbial generalists and disrupt redox cascades. In this work, we profiled microbial communities and biogeochemical dynamics in sediment profiles from three sites varying in their exposure to hydrodynamic disturbance. Strong variations in sediment geochemistry, biogeochemical activities, and microbial abundance, composition, and capabilities were observed between the sites. Most of these variations, except for microbial abundance and diversity, significantly correlated with the relative disturbance level of each sample. In line with previous findings, metabolically flexible habitat generalists (e.g., Flavobacteriaceae, Woeseaiceae, Rhodobacteraceae) dominated in all samples. However, we present evidence that aerobic specialists such as ammonia-oxidizing archaea (Nitrosopumilaceae) were more abundant and active in more disturbed samples, whereas bacteria capable of sulfate reduction (e.g., uncultured Desulfobacterales), dissimilatory nitrate reduction to ammonium (DNRA; e.g., Ignavibacteriaceae), and sulfide-dependent chemolithoautotrophy (e.g., Sulfurovaceae) were enriched and active in less disturbed samples. These findings are supported by insights from nine deeply sequenced metagenomes and 169 derived metagenome-assembled genomes. Altogether, these findings suggest that hydrodynamic disturbance is a critical factor controlling microbial community assembly and biogeochemical processes in coastal sediments. Moreover, they strengthen our understanding of the relationships between microbial composition and biogeochemical processes in these unique environments.

From surviving to thriving, the assembly processes of microbial communities in stone biodeterioration: A case study of the West Lake UNESCO World Heritage area in China

Serious concerns regarding stone biodeterioration have been raised due to the loss of aesthetic value and hidden dangers in stone cultural heritages and buildings. Stone biodeterioration involves a complex ecological interplay among organisms, however, the ecological mechanisms (deterministic or stochastic processes) that determine the microbial community on stone remain poorly understood. Here, using both amplicon and shotgun metagenomic sequencing approaches, we comprehensively investigated the biodiversity, assembly, and function of communities (including prokaryotes, fungi, microfauna, and plants) on various types of deteriorating limestone across different habitats in Feilaifeng. By generalizing classic ecological models to stone habitats, we further uncovered and quantified the mechanisms underlying microbial community assembly processes and microbial interactions within the biodeteriorated limestone. Community profiling revealed stable ecosystem functional potential despite high taxonomic variation across different biodeterioration types, suggesting non-random community assembly. Increased niche differentiation occurred in prokaryotes and fungi but not in microfauna and plant during biodeterioration. Certain microbial groups such as nitrifying archaea and bacteria showed wider niche breadth and likely contributing to the initiation, succession and expansion of stone biodeterioration. Consistently, prokaryotes were more strongly structured by selection-based deterministic processes, while micro-eukaryotes were more influenced by dispersal and drift-based stochastic processes. Importantly, microbial coexistence maintains network robustness within stone microbiotas, highlighting mutual cooperation among functional microorganisms. These results provide new insights into microbial community assembly mechanisms in stone ecosystems and may aid in the sustainable conservation of stone materials of interest.

Relative Importance of Deterministic and Stochastic Processes on Soil Microbial Community Assembly in Temperate Grasslands.

Changes in species composition across communities, i.e., β-diversity, is a central focus of ecology. Compared to macroorganisms, the β-diversity of soil microbes and its drivers are less studied. Whether the determinants of soil microbial β-diversity are consistent between soil depths and between abundant and rare microorganisms remains controversial. Here, using the 16S-rRNA of soil bacteria and archaea sampled at different soil depths (0–10 and 30–50 cm) from 32 sites along an aridity gradient of 1500 km in the temperate grasslands in northern China, we compared the effects of deterministic and stochastic processes on the taxonomic and phylogenetic β-diversity of soil microbes. Using variation partitioning and null models, we found that the taxonomic β-diversity of the overall bacterial communities was more strongly determined by deterministic processes in both soil layers (the explanatory power of environmental distance in topsoil: 25.4%; subsoil: 47.4%), while their phylogenetic counterpart was more strongly determined by stochastic processes (the explanatory power of spatial distance in topsoil: 42.1; subsoil 24.7%). However, in terms of abundance, both the taxonomic and phylogenetic β-diversity of the abundant bacteria in both soil layers was more strongly determined by deterministic processes, while those of rare bacteria were more strongly determined by stochastic processes. In comparison with bacteria, both the taxonomic and phylogenetic β-diversity of the overall abundant and rare archaea were strongly determined by deterministic processes. Among the variables representing deterministic processes, contemporary and historical climate and aboveground vegetation dominated the microbial β-diversity of the overall and abundant microbes of both domains in topsoils, but soil geochemistry dominated in subsoils. This study presents a comprehensive understanding on the β-diversity of soil microbial communities in the temperate grasslands in northern China. Our findings highlight the importance of soil depth, phylogenetic turnover, and species abundance in the assembly processes of soil microbial communities.

Host specificity of the gut microbiome.

Developing general principles of host-microorganism interactions necessitates a robust understanding of the eco-evolutionary processes that structure microbiota. Phylosymbiosis, or patterns of microbiome composition that can be predicted by host phylogeny, is a unique framework for interrogating these processes. Identifying the contexts in which phylosymbiosis does and does not occur facilitates an evaluation of the relative importance of different ecological processes in shaping the microbial community. In this Review, we summarize the prevalence of phylosymbiosis across the animal kingdom on the basis of the current literature and explore the microbial community assembly processes and related host traits that contribute to phylosymbiosis. We find that phylosymbiosis is less prevalent in taxonomically richer microbiomes and hypothesize that this pattern is a result of increased stochasticity in the assembly of complex microbial communities. We also note that despite hosting rich microbiomes, mammals commonly exhibit phylosymbiosis. We hypothesize that this pattern is a result of a unique combination of mammalian traits, including viviparous birth, lactation and the co-evolution of haemochorial placentas and the eutherian immune system, which compound to ensure deterministic microbial community assembly. Examining both the individual and the combined importance of these traits in driving phylosymbiosis provides a new framework for research in this area moving forward.

Archaeal and bacterial communities assembly and co-occurrence networks in subtropical mangrove sediments under Spartina alterniflora invasion

BackgroundMangrove ecosystems are vulnerable due to the exotic Spartina alterniflora (S. alterniflora) invasion in China. However, little is known about mangrove sediment microbial community assembly processes and interactions under S. alterniflora invasion. Here, we investigated the assembly processes and co-occurrence networks of the archaeal and bacterial communities under S. alterniflora invasion along the coastlines of Fujian province, southeast China.ResultsAssembly of overall archaeal and bacterial communities was driven predominantly by stochastic processes, and the relative role of stochasticity was stronger for bacteria than archaea. Co-occurrence network analyses showed that the network structure of bacteria was more complex than that of the archaea. The keystone taxa often had low relative abundances (conditionally rare taxa), suggesting low abundance taxa may significantly contribute to network stability. Moreover, S. alterniflora invasion increased bacterial and archaeal drift process (part of stochastic processes), and improved archaeal network complexity and stability, but decreased the network complexity and stability of bacteria. This could be attributed to S. alterniflora invasion influenced microbial communities diversity and dispersal ability, as well as soil environmental conditions.ConclusionsThis study fills a gap in the community assembly and co-occurrence patterns of both archaea and bacteria in mangrove ecosystem under S. alterniflora invasion. Thereby provides new insights of the plant invasion on mangrove microbial biogeographic distribution and co-occurrence network patterns.

Deciphering sample size effect on microbial biogeographic patterns and community assembly processes at centimeter scale

Revealing the effects of spatial heterogeneity on microorganisms is crucial for the further understanding of microbial diversity, turnover and ecological processes. However, microbial community assembly and the factors that shape it are still unknown at a centimeter scale. To address this gap, we conducted variation partitioning and null model analyses on the microbial community composition of a soil cube, divided into up to 64 sub-cubes, to investigate microbial biogeographic patterns and microbial assembly processes of 3 cm-scale sampling schemes. The results suggested that microbial community was more dispersed and distance decay relationships were more significant in sampling schemes of smaller sample size compared with those of larger sample size. We further investigated the relative importance of ecological processes and demonstrated that bacterial community assembly processes changed from variable selection to homogenous selection as the sample size increased. The importance of spatial distance and micro-environmental variables in shaping and maintaining microbial diversity was emphasized by the dynamics of spatial heterogeneity and environmental filtering. As microorganisms are spatially distributed in soil, this sampling scale dependent diversity and assembly suggests that microbial ecology questions need to be considered in more dimensions than they usually are.

Stochastic processes drive bacterial and fungal community assembly in sustainable intensive agricultural soils of Shanghai, China.

Sustainable intensive cropping systems have been implemented for three decades in suburban agricultural districts of Shanghai, China. These human-managed soils have been developed from paleosol or alluvial soils across different regions. However, little is known about the geographical distribution patterns of microbes and microbial community assembly in the sustainable intensive soils after decades of anthropogenic disturbances. Here, we investigated the impact of local geochemical properties and geographic distance on stochastic/deterministic microbial community assembly processes using high-throughput sequencing and phylogenetic null modeling analysis. Our results showed that soil pH was the most important environmental factor determining bacterial and fungal community structure. Importantly, only soil organic matter was positively correlated with fungal α-diversity, suggesting the efficient use of carbon substrates in sustainable agricultural systems, compensating for the lack of chemical fertilization and reduced tillage in these systems. Both bacterial and fungal communities had robust distance-decay patterns, but the rate of turnover of bacterial taxa was faster than that of fungi. Variation in bacterial and fungal communities was mostly attributed to the simultaneous effects of environmental variables and spatial factors. We also mapped the spatial distributions of the dominant bacterial and fungal taxa across the sustainable agricultural fields, making it possible to forecast the responses of agricultural ecosystems to anthropogenic disturbance. Based on the patterns of the β-nearest taxon index, this study demonstrated that stochastic processes shaped substantial bacterial and fungal community variation in sustainable intensive agricultural soils of the Shanghai suburbs. This variation may be attributed to the increasing microbial dispersal caused by hydrological connectivity in the agricultural fields or the release from environmental stress and weakened environmental filtering across the suitable pH range preferable for most soil microbes. These results unveil assembly mechanisms of soil microbial community after several decades of sustainable intensive management, and contribute to understand the role of microbes in ecosystems in establishing a functional equilibrium which may enable sustainability to be preserved.

Changes in assembly processes of soil microbial communities during secondary succession in two subtropical forests

Soil microbes re-establish plant diversity and ecosystem functions after disturbance events. Deterministic and stochastic processes are expected to contribute to microbial community assembly during long-term ecosystem recovery. We characterized soil prokaryotic and fungal communities, to determine their assembly patterns, along two chronosequences with early to later successional subtropical forests. Prokaryotic and fungal community composition was more variable in early successional forests but converged in the later successional forests. The community composition was governed by deterministic processes in the early stages, while the relative influence of stochasticity increased in the later stages. Environmental factors that predicted the shift in deterministic and stochastic balance varied within and across successional stages. In particular, the compositional dissimilarity of plant communities strongly predicted the relative influences of the two processes during succession. These findings suggest that the relative influences of deterministic and stochastic processes in shaping microbial community assembly shift during secondary succession. Consequently, plant communities are important predictors of assembly processes in soil microbial communities during long-term ecosystem recovery.

Fungal alpha diversity influences stochasticity of bacterial and fungal community assemblies in soil aggregates in an apple orchard

Understanding the drivers of variations in the microbial community in response to different soil aggregates and agricultural practices is important in ecology. Bacteria and fungi always co-exist in different soil aggregates and the variations in their communities are driven by agricultural practices, but the factors that control the assembly of soil bacterial and fungal communities are not fully understood. In this study, we examined bacterial and fungal community assemblies in soil macroaggregates (>0.25 mm), microaggregates (0.053–0.25 mm), and smaller microaggregates (silt+clay, <0.053 mm) in an apple orchard treated with a cover crop and fertilizer. The microbial community assembly processes were analyzed based on the normalized stochasticity ratio (NST) index. The NST index was developed with 50% set as the boundary point between more deterministic (<50%) and more stochastic (>50%) assemblies. The bacterial community diversity, composition, and stochasticity of assemblies were affected more by agricultural practices and aggregates than the fungal community. Bacterial community assemblies were more stochastic in silt+clay than macroaggregates, and more stochastic (NST > 50%) than fungal communities in soil aggregates. The bacterial NST was also negatively correlated with the fungal diversity, and the fungal NST was positively correlated with the fungal diversity. Co-occurrence networks suggested that bacteria and fungi interacted less strongly in the network obtained for silt+clay compared with that for macroaggregates. The results indicated that fungi affected the bacterial community assemblies in soil aggregates, and the stochasticity of the bacterial community assemblies increased as the interactions between bacteria and fungi decreased in the soil aggregates. This study enhances our mechanistic understanding of bacterial and fungal community assembly processes and the co-existence patterns of bacteria and fungi in soil aggregates.

Gut microbiome is more stable in males than in females during the development of colorectal cancer.

Gut microbial alterations have great potential to predict the development of colorectal cancer (CRC); however, how gut microbes respond to the development of CRC in males and females at the community level is unknown. We aim to investigate the differences of gut microbiota between the male and female. We reanalysed the dataset in a published project from a sex perspective at the community level by characterizing the gut microbiome in patients (including males and females) from three clinical groups representative of the stages of CRC development: healthy, adenoma, and carcinoma. The results indicated that the microbial α-diversity showed no significant difference in the male gut but had decreased significantly in the female gut with the development of CRC. In males, a significant difference in the microbial β-diversity was only observed between the healthy and carcinoma subgroups. However, significant community deviations were detected with the development of CRC in females. The microbial community assembly processes changed from deterministic to stochastic in males, whereas they became increasingly deterministic in females with the development of CRC. Moreover microbial co-occurrence associations tended to be more complicated in males; rare species were enriched in the co-occurrence network of the male gut, whereas key species loss was observed in the co-occurrence network of the female gut. The microbial communities in the male gut were more stable than those in the female gut, and microbial community assembly in the gut was sex dependent with the development of CRC. Our study suggests that sexual dimorphism needs to be considered to better predict the risk of CRC based on microbial shifts. To the best of our knowledge, this is the first report showing how gut microbes respond to the development of CRC in males and females at the community scale.

Deterministic selection dominates microbial community assembly in termite mounds

Termite mounds are an important habitat for an enormous diversity of microorganisms. However, the microbial community assembly processes in termite mounds remain unresolved, which impeded our ability to predict the biological functions of these mound-associated microbiota under the global changes. Here we conducted a large-scale investigation in northern Australia to explore biogeographical patterns of microbial community in termite mounds and identify the role of deterministic and stochastic processes in microbial community assembly. Microbial communities in termite mounds exhibited a significant distance-decay pattern, and fungi had a stronger distance-decay relationship than bacteria. The neutral community model and normalized stochasticity ratio index (NST) revealed that the deterministic selection, rather than stochastic forces, predominated the microbial community assembly in termite mounds. Deterministic processes exhibited a significantly weaker impact on bacteria (NST = 45.23%) than on fungi (NST = 33.72%), likely due to the wider habitat niche breadth and higher potential migration rate of bacteria. Random forest model further demonstrated that mean annual temperature was the most important predictor of both bacterial and fungal profiles in termite mounds. These findings improved our understanding of spatial patterns and processes of microbiome in termite mounds, which is critical to decipher the role of termite mounds associated microbes in regulating ecosystem multifunctionality.

The Transition From Stochastic to Deterministic Bacterial Community Assembly During Permafrost Thaw Succession.

The Northern high latitudes are warming twice as fast as the global average, and permafrost has become vulnerable to thaw. Changes to the environment during thaw leads to shifts in microbial communities and their associated functions, such as greenhouse gas emissions. Understanding the ecological processes that structure the identity and abundance (i.e., assembly) of pre- and post-thaw communities may improve predictions of the functional outcomes of permafrost thaw. We characterized microbial community assembly during permafrost thaw using in situ observations and a laboratory incubation of soils from the Storflaket Mire in Abisko, Sweden, where permafrost thaw has occurred over the past decade. In situ observations indicated that bacterial community assembly was driven by randomness (i.e., stochastic processes) immediately after thaw with drift and dispersal limitation being the dominant processes. As post-thaw succession progressed, environmentally driven (i.e., deterministic) processes became increasingly important in structuring microbial communities where homogenizing selection was the only process structuring upper active layer soils. Furthermore, laboratory-induced thaw reflected assembly dynamics immediately after thaw indicated by an increase in drift, but did not capture the long-term effects of permafrost thaw on microbial community dynamics. Our results did not reflect a link between assembly dynamics and carbon emissions, likely because respiration is the product of many processes in microbial communities. Identification of dominant microbial community assembly processes has the potential to improve our understanding of the ecological impact of permafrost thaw and the permafrost–climate feedback.

Dams shift microbial community assembly and imprint nitrogen transformation along the Yangtze River

Dams are important for flood control, water storage, irrigation, electric generation, navigation, and have been regarded as the largest anthropogenic disturbance in aquatic ecosystems. However, how dams impact nitrogen transformation on a large watershed scale remained less studied. To explicitly address the impact of dams on nitrogen transformation, we used 16S rRNA gene sequencing to investigate the microbial dynamics and ecological processes under different dam conditions along the Yangtze River, as microbial communities are playing a key role in aquatic nitrogen transformation. Compared with landforms, dams exerted a more significant impact on the distribution patterns of microbial communities along the Yangtze River. The results showed that, by controlling suspended sand concentration, dams filtered keystone species, reshaped distribution of metacommunities, and mediated ecological assembly processes of microbial communities. Moreover, direct causal relationships between dams and nitrogen transformation were chained via microbial communities. To summarize, by combining knowledge in hydrology, microbial ecology, and biogeochemistry, this research exhibited the impact of different dams on the nitrogen transformation along a large river, and the key roles of suspended sand and microbial communities were emphasized. We anticipate a more precise modelling and prediction of nitrogen transformation in large watersheds, which may provide new perspectives for controlling the nitrogen in aquatic environments.

Quantitative estimation of stochastic and deterministic processes for soil prokaryotic community assembly in the Yellow River floodplain

AbstractThe floodplain ecosystem plays an important role in the mediation or regulation of regional ecological functions, and is the heart of ecosystem functions based on soil microbial communities. In the present study, we investigate the patterns and assembly processes of soil microbial communities along nine profile depths (up to 280 cm in depth) of three stages of floodplain community succession (channel bar, newly deposited river beach and tender floodplain) and farmland in the floodplain of the lower Yellow River. Generally, the bacterial community in agricultural soil had the highest diversity, whereas the archaeal community in the tender floodplain had the highest diversity. Compared to bacteria, the co‐occurrence network of archaea was more complex and stable and had high connectivity. Our data suggest that the resistance of bacteria and archaea to environmental changes in deep soil was higher when compared to that in surface soil. Furthermore, stochastic and deterministic processes acted concurrently to regulate the assembly of the soil microbial community in the floodplain ecosystems. However, the relative contributions of the stochastic process and deterministic process are different between the bacterial community and the archaeal community. The lowest contribution of the stochastic process in the bacterial community was in the subsoil, whereas in the archaeal community, it was the opposite. For ecological selection, bacterial communities in different soil profiles, in the succession stages and in the farmland, were mainly selected through homogeneous selection, whereas archaeal communities were selected through heterogeneous selection. Compared with the three floodplain succession stages, the microbial communities of agricultural lands were more assembled by deterministic processes.Highlights Stochastic and deterministic processes act concurrently to regulate the assembly of soil microbial community in the floodplain ecosystems. The assembly of the bacterial community was mainly affected by the homogeneous selection. The archaeal community was mainly affected by the heterogeneous selection. The microbial communities of agricultural lands were more assembled by deterministic processes.

The biogeochemical variability of Arctic thermokarst ponds is reflected by stochastic and niche-driven microbial community assembly processes.

SummaryShallow thermokarst ponds are a conspicuous landscape element of the Arctic Siberian tundra with high biogeochemical variability. Little is known about how microbes from the regional species pool assemble into local pond communities and how the resulting patterns affect functional properties such as dissolved organic carbon (DOC) remineralization and greenhouse gas (GHG) turnover. We analysed the pelagic microbiomes of 20 ponds in north‐eastern Siberia in the context of their physico‐chemical properties. Ponds were categorized as polygonal or trough according to their geomorphological origin. The diversity of bacteria and eukaryotic microbes was assessed by ribosomal gene tag sequencing. Null model analysis revealed an important role of stochastic assembly processes within ponds of identical origin, in particular for genotypes only occurring in few systems. Nevertheless, the two pond types clearly represented distinct niches for both the bacterial and eukaryotic microbial communities. Carbon dioxide concentration, indicative of heterotrophic microbial processes, varied greatly, especially in the trough ponds. Methane concentrations were lower in polygonal ponds and were correlated with the estimated abundance of methanotrophs. Thus, the overall functional variability of Arctic ponds reflects the stochastic assembly of their microbial communities. Distinct functional subcommunities can, nevertheless, be related to GHG concentrations.

Homogeneous environmental selection dominates microbial community assembly in the oligotrophic South Pacific Gyre.

Oligotrophic subtropical gyres are the largest continuous biomes on Earth and play a key role in global biogeochemical cycles. Microbial communities govern primary production and carbon cycling in the oligotrophic South Pacific Gyre, yet the ecological processes which underpin microbial biogeography in the region remain understudied. We investigated microbial biogeography and community assembly processes at three depths over a ~2,000-km the transect was longitudinal, so ran from 32°S, 170°W to 32°S, 152°W). Thus the latitude (32°S) was constant. Microbial communities in the surface waters (15 and 50m) were remarkably similar across the transect, whilst communities at the deep chlorophyll maximum were distinct from the surface waters and displayed greater compositional heterogeneity. An ecological null model approach indicated that homogeneous selection was the dominant community assembly process in both the surface waters (100%) and at the deep chlorophyll maximum (91.81%), although variable selection (2.34%) and stochastic processes (5.85%) had a minor influence at the deep chlorophyll maximum. Homogeneous selection (76.69%77.90%), dispersal limitation (15.00%-20.05%) and variable selection (3.01%-7.11%) influenced community assembly between the surface waters and the deep chlorophyll maximum. Seawater density and temperature, which were correlated, were the most important environmental modulators of the balance between stochastic and deterministic assembly processes. Our findings demonstrate remarkable similarity in microbial community composition across longitudinal scales in the oligotrophic South Pacific Gyre, underpinned by strong environmental selection which overwhelms the influence of ecological drift. These data significantly advance our understanding of microbial community dynamics in the oligotrophic subtropical gyres which dominate the Earth's surface.

History of petroleum disturbance triggering the depth-resolved assembly process of microbial communities in the vadose zone

Biogeochemical gradient forms in vadose zone, yet little is known about the assembly processes of microbial communities in this zone under petroleum disturbance. This study collected vadose zone soils at three sites with 0, 5, and 30 years of petroleum contamination to unravel the vertical microbial community successions and their assembly mechanisms. The results showed that petroleum hydrocarbons exhibited higher concentrations at the long-term contaminated site, showing negative impacts on some soil properties, retarding in the surface soils and decreasing along soil depth. Cultivable fraction of heterotrophic bacteria and microbial α-diversity decreased along depth in vadose zones with short-term/no contamination history, but exhibited an opposite trend with long-term contamination history. Petroleum contamination intensified the vertical heterogeneity of microbial communities based on the contamination time. Microbial co-occurrence network revealed the lowest species co-occurrence pattern at the long-term contaminated site. The distance-decay patterns and null model analysis together suggested distinct assembly mechanisms at three sites, where dispersal limitation (42–45%) was higher and variable and homogenizing selections were lower (37–38%) in vadose zones under petroleum disturbance than those in the uncontaminated vadose zone. Our findings help to better understand the subsurface biogeochemical cycles and bioremediation of petroleum-contaminated vadose zones.

Contrasting bacterial communities and their assembly processes in karst soils under different land use

Structure and assembly processes of soil bacterial communities under different land use at karst areas remained poorly understood to date. To address this issue, soil samples from arable land and pristine forest over a karst cave, located in the acid rain impacted area, Hubei province, were collected and subjected to high-throughput sequencing and multivariate statistical analysis. Bacterial communities and functions remarkably distinguished between soils under different land use. Both edaphic properties (the content of SO42−, C/N, pH, TN) and weathering processes, such as Si concentration, Mg/Al and Ca/Al, significantly impacted on soil bacterial community structures. Variable selections were predominant ecological processes, and pH and SO42− concentration were of significance in community assembly. Random molecular ecological network analysis revealed a more stable and complex microbial network in the forest ecosystem, which can quickly response to environmental change. Forest soil bacteria were mainly phototrophs, involving in C and N cycles, whereas those in arable soils were mainly chemoheterotrophs, capable of degrading organic fertilizers due to anthropogenic activities as confirmed by the analysis of keystone taxa, indicators and functional prediction. These results reveal that land use constructed soil bacterial communities in different aspects such as the structure, potential functions, microbial interactions and correlations with environmental variables. To our knowledge, this is the first report on bacterial community assembly in karst soils under different land use which enhances our understanding about how land use impact on microbial interaction and community assembly processes.