Distance-decay Pattern Research Articles

Riverine microbial community assembly with watercourse distance–decay patterns in the north–south transitional zone of China

Deciphering the spatiotemporal patterns and ecological processes of microbiota is a key challenge in community assembly research. The microbial patterns in complex mountain rivers and the ecological processes influencing community assembly remain poorly understood. In the present study, water samples were collected from Weihe and Hanjiang Rivers, including their tributaries, in the transitional zone between North and South China in autumn 2017 and spring 2018. We analyzed watercourse and geographic distance-based patterns of riverine microbiota through sequencing of 16S rRNA genes and multivariate statistical analyses. The distance–decay patterns in water quality factors based on geographic and watercourse distances were similar across seasons. However, the distance–decay patterns in riverine microbiota based on watercourse distance were stronger than those based on geographic distance in both seasons. Deterministic processes were predominantly responsible for community assembly in different seasons, with homogeneous selection making the highest contribution: 89.40 % in autumn and 83.33 % in spring. Autumn precipitation facilitated microbial dispersal, as indicated by the dispersal limitation of 5.01 % and 10.25 % in autumn and spring, respectively. Dispersal and environmental selection synergistically drove microbial community assembly in autumn. The results could enable a broader understanding of microbial community assembly with watercourse distance–decay patterns in complex mountain rivers.

Root-centric β diversity reveals functional homogeneity while phylogenetic heterogeneity in a subtropical forest.

Root-centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e., β diversity) remains largely unknown. As β diversity can reflect the degree of community-wide biotic homogenization, such information is crucial for better inference of below-ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0-30 cm soil profiles in a subtropical forest in China. Root segments were identified into 138 species with DNA-barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw ) and mean nearest neighbor distance (Dnn ) to quantify species ecological differences, we first tested the non-random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes. Additionally, we examined the distance-decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Phylogenetic Dpw (e.g., interfamily species) turnover exhibited a distance-decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, both functional and phylogenetic Dnn (e.g., intrageneric species) exhibited an inverted distance-decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic and functional divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host-specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root-centric β diversity in mediating community structures and functions largely ignored in previous studies.

Stochasticity-driven weekly fluctuations distinguished the temporal pattern of particle-associated microorganisms from its free-living counterparts in temperate coastal seawater

Microbial community dynamics directly determine their ecosystem functioning. Despite the well-known annual recurrence pattern, little is known how different lifestyles affect the temporal variation and how community assembly mechanisms change over different temporal scales. Here, through a high-resolution observation of size fractionated samples over 60 consecutive weeks, we investigate the distinction in weekly distribution pattern and assembly mechanism between free-living (FL) and particle-associated (PA) communities in highly dynamic coastal environments. A clear pattern of annual recurrence was observed, which was more pronounced in FL compared to PA, resulting in higher temporal specificity in the former samples. Both the two size fractions displayed significant temporal distance-decay patterns, yet the PA community showed a higher magnitude of community variation between adjacent weeks, likely caused by sudden, drastic and long-lived blooms of heterotrophic bacteria. Generally, determinism (environmental selection) had a greater effect on the community assembly than stochasticity (random birth, death, and dispersal events), with significant contributions from temperature and inorganic nutrients. However, a clear shift in the temporal assembly pattern was observed, transitioning from a prevalence of stochastic processes driving short-term (within a month) fluctuations to a dominance of deterministic processes over longer time intervals. Between adjacent weeks, stochasticity was more important in the community assembly of PA than FL. This study revealed that stochastic processes can lead to rapid, dramatic and irregular PA community fluctuations, indicating weak resistance and resilience to disturbances, which considering the role of PA microbes in carbon processing would significantly affect the coastal carbon cycle. Our results provided a new insight into the microbial community assembly mechanisms in the temporal dimension.

An integrative methodology framework for assessing regional ecological risk by land degradation using the case of the Qinghai–Tibet Plateau

Land degradation poses significant threats to the sustainability of ecosystem structures, functions, and services, leading to increasing ecological risks. However, integrative assessment of the ecological risk driven by land degradation remains a challenge. In this study, we established a methodological framework for assessing regional ecological risk by integrating degenerative land use transitions with multiple ecological indicators. Specifically, 11 degradation modes of land use transitions and 7 indicators on ecosystem structures, functions, and services are quantitatively integrated using remote sensing data from 2000 to 2020 in the Qinghai-Tibet Plateau of China. Results revealed that the comprehensive ecological risk of the plateau is higher in the southern and northern regions. Furthermore, we found that land development from forests towards cropland and degradation towards grasslands lead to higher ecological risks than grassland development and degradation. The ecological risk tends to show a significant distance decay pattern around the patches with land degradation. Our research framework provides an efficient, explicit, and transferable means of exploring spatiotemporal changes in ecological risk caused by degenerative land use transitions at the regional scale. It presents a constructive tool for facilitating regional-scale land use and ecosystem management planning and assessment.

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

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

Distance decay and directional diffusion of ecoclimate teleconnections driven by regional-scale tree die-off

Climate change is triggering regional-scale alterations in vegetation including land cover change such as forest die-off. At sufficient magnitudes, land cover change from forest die-off in one region can change not only local climate but also vegetation including agriculture elsewhere via changes in larger scale climate patterns, termed an ‘ecoclimate teleconnection’. Ecoclimate teleconnections can therefore have impacts on vegetative growth in distant regions, but the degrees to which the impact decays with distance or directionally diffuses relative to the initial perturbation are general properties that have not been evaluated. We used the Community Earth system model to study this, examining the implications of tree die-off in 14 major US forested regions. For each case we evaluated the ecological impact across North America as a function of distance and direction from the location of regional tree die-off. We found that the effects on gross primary productivity (GPP) generally decayed linearly with distance, with notable exceptions. Distance from the region of tree die-off alone explained up to ∼30% of the variance in many regions. We also found that the GPP impact was not uniform across directions and that including an additional term to account for direction to regional land cover change from tree die-off was statistically significant for nearly all regions and explained up to ∼40% of the variance in many regions, comparable in magnitude to the influence of El Nino on GPP in the Western US. Our results provide novel insights into the generality of distance decay and directional diffusion of ecoclimate teleconnections, and suggest that it may be hard to identify expected impacts of tree die-off without case-specific simulations. Such patterns of distance decay, directional diffusion, and their exceptions are relevant for cross-regional policy that links forests and other agriculture (e.g. US Department of Agriculture).

Environmental DNA unveiling the fish community structure and diversity features in the Yangtze River basin

Fish, as top predators in aquatic ecosystems, play an important role in maintaining the structure and functioning of these ecosystems, making their diversity a topic of great interest. This study focused on the Yangtze River Basin to investigate the fish community structure and diversity using environmental DNA (eDNA) technology. The results showed that a total of 71616 fish operational taxonomic units (OTUs) and 90 fish belonging to 23 families were detected, with the Cyprinidae family being the dominant group, followed by the Cobitidae, Amblycipitidae, etc. Compared to historical traditional morphological fish surveys, the quantity of fish detected using eDNA was relatively low, but the overall distribution pattern of fish communities was generally consistent. The highest fish Shannon-Wiener diversity index in the Yangtze River Basin sites reaches 2.60 with an average value of 1.25. The fish diversity index was higher in the downstream compared to the middle and upstream regions, and there were significant differences among different sampling sites. Significant environmental factors influencing α-diversity included chlorophyll-a, chemical oxygen demand, dissolved oxygen, total nitrogen, and elevation. Non-metric multidimensional scaling (NMDS) analysis revealed significant differences in fish community composition between the upstream and middle/lower reaches of the Yangtze River, while the composition of fish communities in the middle and lower reaches was more similar. Redundancy analysis (RDA) indicated that total organic carbon (TOC) was positively correlated with fish community distribution in the upstream, while water temperature and NO3–N were negatively correlated with fish distribution in the upstream. NH3–N and CODMn were negatively correlated with fish distribution in the middle and downstream regions, indicating a relatively severe water pollution in these areas. Additionally, fish communities in the Yangtze River displayed a typical distance decay pattern.

Distinct mechanisms shape prokaryotic community assembly across different land-use intensification

Changes in land-use intensity can have a far-reaching impact on river water quality and prokaryotic community composition. While research has been conducted to investigate the assembly mechanism of prokaryotic communities, the contributions of neutral theory and niche theory to prokaryotic community assembly under different land-use intensities remain unknown. In this study, a total of 251 sampling sites were set up in the Yangtze River basin to explore the assembly mechanism under different land-use intensities. Briefly, a "source" landscape can generate pollution, whereas a "sink" landscape can prevent pollution. Firstly, our result showed that higher land-use intensity might disturb the balance between the "source" and "sink" landscape patterns, resulting in water quality deterioration. Then the prokaryotic community assembly was classified into five ecological processes, namely homogeneous selection, homogenizing dispersal, undominated processes, dispersal limitation, and variable selection. The higher land-use intensity was found to strengthen the homogeneous selection, leading to the homogenization of the community at the whole basin scale. Finally, our findings demonstrated that the Yangtze River Basin's prokaryotic community displayed a distance-decay pattern when land-use intensity was low, with a greater contribution from neutral theory to its assembly. On the other hand, with a higher land-use intensity, the degradation of the aquatic environment increased the impacts of environmental filtering on the prokaryotic community, and niche theory played a stronger role in its assembly. Our findings show how land-use intensity influence the formation of prokaryotic communities, which will be an invaluable guide for managing land use and understanding the prokaryotic community assembly mechanisms in the Yangtze River Basin.

Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America.

As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.

Spatiotemporal dynamics of high and low nucleic acid-content bacterial communities in Chinese coastal seawater: assembly process, co-occurrence relationship and the ecological functions.

Studies of high nucleic acid-content (HNA) and low nucleic acid-content (LNA) bacterial communities are updating our view of their distributions and taxonomic composition. However, there are still large gaps in our knowledge of the composition, assembly processes, co-occurrence relationships and ecological functions of HNA and LNA bacterial communities. Here, using 16S rRNA gene amplicon sequencing, we investigated the spatiotemporal dynamics, assembly processes, co-occurrence relationships and ecological functions of HNA and LNA bacterial communities in the samples collected in summer and winter in Chinese coastal seas. The communities of HNA and LNA bacteria had clear spatiotemporal patterns and LNA bacteria was phylogenetically less diverse than HNA bacteria in both seasons. The distribution of HNA and LNA bacteria were significantly affected by the environmental factors and a significant seasonal-consistent distance-decay patterns were found in HNA and LNA bacteria. Furthermore, a quantitative assessment of ecological processes revealed that dispersal limitation, homogeneous selection exerted important roles in the community assembly of HNA and LNA bacteria. More importantly, we observed seasonality in the co-occurrence relationships: closer inter-taxa connections of HNA bacterial communities in winter than in summer and the opposite is true in the LNA bacterial communities. Some ecological functions, such as: phototrophy, photoautotrophy, oxygenic photoautotrophy, were different between HNA and LNA bacteria. These results provide a better understanding of spatiotemporal patterns, processes, and the ecological functions of HNA and LNA bacterial communities in Chinese coastal seawater.

The assembly, biogeography and co-occurrence of abundant and rare microbial communities in a karst river

Karst rivers are highly susceptible to environmental disturbance due to their robust hydraulic connectivity. However, current knowledge of the mechanisms that regulate the assembly of bacterial and protistan subcommunities in river ecosystems, particularly in karst regions, is limited. By employing 16S and 18S rRNA gene amplicon sequencing, we explored how the diversities and assembly of abundant and rare bacterial and protistan subcommunities adapt to the local environmental variables in a karst river. Both bacterial and protistan rare subcommunities in karst river environments showed a similar biogeography to their abundant subcommunities. Also, a significant distance-decay pattern was observed in all components of the bacterial and protistan subcommunities along the Chishui River, with the rare subcommunities showing a more pronounced distance-decay pattern compared to the abundant subcommunities. Except protist rare subcommunity, the abundant and rare bacterial and abundant protistan subcommunities were strongly structured by the dispersal limitation processes rather than heterogeneous selection. Either bacteria or temperature, elevation and conductivity were the primary drivers for both abundant and rare subcommunities. Additionally, our results suggested that the rare subcommunities contribute significantly to the persistence and stability of microbial networks in the Chishui River, as they exhibited a higher number of keystones compared to the abundant subcommunities. Overall, our study revealed that in the karst river ecosystem, abundant bacterial subcommunities had a higher potential for environmental adaptation than rare bacterial and protistan subcommunities and identified the factors that moderate their assembly processes.

Distinct stochastic processes drive bacterial community assembly and co-occurrence patterns with common antibiotic resistance genes in two highly urbanised coastal ecosystems of the Pearl River Estuary

To comprehensively elucidate the ecology of the bacterial community and antibiotic resistance genes (ARGs) in urbanised coastal ecosystems, this study investigated the variations of bacterial community and five common types of ARGs, the impacting factors and assembly of bacterial community, as well as their co-occurrence relationships in two ecosystems of the Pearl River Estuary (PRE). The bacterial community composition and structure of the nearshore ecosystem (NSE) and the eight mouths of the PRE (EPR) markedly differed, with 38 phyla shared between these two ecosystems. The abundances of 10 ARGs and bacterial community diversity were significantly higher in the EPR than NSE. Moreover, 67.82% and 27.82% of the variation in the bacterial community was explained by spatial (44.42%/8.63%) and environmental (23.40%/19.19%) variables in the NSE and EPR, respectively. Significant distance-decay patterns were observed, and distinct stochastic processes (undominated processes or dispersal limitation) dominated bacterial community assembly in the NSE and EPR. Furthermore, co-occurrence patterns showed significant positive correlations between 48/182 ASVs belonging to 6/15 bacterial phyla and 8/11 ARGs in the NSE/EPR, with six common dominant hosts. These results clarify the drivers and mechanism shaping the bacterial community, providing further proof for potential ARG bacterial hosts in urbanised estuarine ecosystems.

Microfauna community assembly and cascading relationship with microflora in cropland ecosystems along a latitudinal gradient

Cropland ecosystems are environmentally more homogeneous than natural ecosystems due to anthropogenic management. However, it is unclear whether there is similar convergence in soil fauna diversity and community assembly in croplands with different latitudes. Therefore, the study on the latitudinal pattern and community assembly processes of soil microfauna across a transect spanning 3200 km of croplands was conducted. The results indicated that the β diversity of plant parasites, fungivores, and bacterivores showed a decreasing trend and that of omnivores-predators at higher levels followed a unimodal distribution along a latitudinal gradient. The dissimilarity of soil microfauna communities increased with geographical distance, which exhibited a strong distance decay pattern. The β diversity partitioning analysis suggested that species replacement had the greatest influence for all trophic groups, except for omnivores-predators that were driven by a combination of richness differences and species replacement. The stochastic processes shaping the microfauna assembly prevailed over deterministic processes. Ecological drift and homogenizing dispersal of the stochastic processes accounted for 50.4% and 37% of total variations respectively, and heterogeneous selection of the deterministic processes for 10%. Both soil and climatic factors had a direct impact on soil microflora and plant parasites, and indirect impact on bacterivores, fungivores, and omnivores-predators through mediating microflora communities. The partial least squares path modeling and co-occurrence analysis all showed that the soil microfauna assembly was inextricably linked to soil microflora and their network complexity exhibited a significant increasing trend along the latitudinal gradient. Further studies are needed to optimize the molecular database of soil microfauna and construct models for predicting their community distribution patterns.

Environmental distances are more important than geographic distances for predicting earthworm gut bacterial community composition

Distance-decay of similarity is one of the most widely studied patterns in biogeography. Both geographic distance and environmental distance can cause distance-decay of similarity in ecological communities. Here, we studied distance-decay relationships of bacteria in the gut of an earthworm species, Eisenia nordenskioldi, which is widely distributed in Eurasian boreal region. Using high-throughput sequencing, we investigated bacterial community composition in different gut sections, together with the surrounding soil. We specifically quantified the effects of geographic distance and environmental distance on distance-decay pattern of both soil and earthworm gut bacteria. Environmental distance significantly affected soil bacteria, and bacteria in the foregut and midgut of earthworms, with those in the foregut changing most, whereas geographic distance only significantly affected bacteria in the foregut of earthworms. Both, environmental and geographic distance explained bacterial community composition in the gut of earthworms and in surrounding soil, with environmental distance being more important than geographic distance. The results indicate that bacteria in the foregut of earthworms are most sensitive to environmental changes than those in the other sections. Overall, the results suggest that homogenization processes during gut passage of earthworms contribute to similarity of soil microbial communities in space due to the production of casts of similar bacterial community composition.

Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities.

Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.

Sedimentary Vibrio Blooms in the Xisha Islands May Associate with the 2020 Coral Bleaching Event.

Coral reefs are among the most biodiverse ecosystems, providing habitats for various organisms. Studies on coral bleaching have been increasing recently, but little is known about the distribution and community assembly of coral pathogenic bacteria (e.g., several Vibrio species). We elucidated the distribution pattern and interaction relationships of total bacteria and Vibrio spp. in sediments from the Xisha Islands, which are characterized by their high coverage and diversity of coral resources. Vibrio spp. showed significantly higher relative abundance values in the Xisha Islands (1.00 × 108 copies/g) than in other areas (approximately 1 × 104 to 9.04 × 105 copies/g), indicating that the coral bleaching event of 2020 may have promoted the bloom of vibrios. A spatial shift in community composition was observed between the northern (Photobacterium rosenbergii and Vibrio ponticus) and southern (Vibrio ishigakensis and Vibrio natriegens) sites, accompanied by a clear distance-decay pattern. The spatial distance and coral species (e.g., Acroporidae and Fungiidae) had much greater correlations with the Vibrio community than did environmental factors. However, complex mechanisms may exist in the community assembly of Vibrio spp. due to the large proportion of unexplained variation. Stochastic processes may play an important role, as shown by the neutral model. Vibrio harveyi had the highest relative abundance (77.56%) and niche breadth, compared to other species, and it was negatively correlated with Acroporidae, likely reflecting its strong competitive ability and adverse effects on specific corals. Our study provides insights into the bloom and underlying assembly mechanisms of sedimentary vibrios in the Xisha Islands, thereby contributing to identify the potential indicator of coral bleaching and provide inspiration for the environmental management of coral reef areas. IMPORTANCE Coral reefs exert important roles in maintaining the sustainability of marine ecosystems but decline worldwide due to various drivers, especially pathogenic microorganisms. Here, we investigated the distribution pattern and interactions of total bacteria and Vibrio spp. in the sediments from Xisha Islands during the coral bleaching event of 2020. Our results showed that the abundances of Vibrio (1.00 × 108 copies/g) were high across the whole sites, indicating the bloom of sedimentary Vibrio spp. Coral pathogenic Vibrio species were abundant in the sediments, likely reflecting adverse effects on several kinds of corals. The compositions of the Vibrio spp. were separated by geographical location, which was mainly attributable to the spatial distance and coral species. Overall, this work contributes by providing evidence for the outbreak of coral pathogenic vibrios. The pathogenic mechanism of the dominant species (especially V. harveyi) should be comprehensively considered by laboratory infection experiments in the future.

Phylogenetic distance-decay patterns are not explained by local community assembly processes in freshwater lake microbial communities.

While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance-decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance-decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance-decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.

Biogeographical patterns of rhizosphere microbial communities in Robinia pseudoacacia forests along a north–south transect in the Loess Plateau

Rhizosphere microbiota play an essential role in plant productivity; however, their biogeographical patterns in restored forest ecosystems across large spatial scales remain poorly understood. We used the Ion S5TM XL sequencing platform to explore the distributions of microbial communities in the rhizosphere and bulk soil of Robinia pseudoacacia at 11 mature forest sites along a north–south precipitation gradient in the Loess Plateau, China. Microbial alpha-diversity mostly peaked in the south zone at lower latitudes, and significant distance-decay patterns were observed in both bacterial and fungal communities. Fungal communities exhibited more distinct spatial patterns in the rhizosphere than bacterial communities. The relative influence of geographic factors on bacterial/fungal community turnover in the rhizosphere (12.4/16.7%) and bulk soil (16.1/17.1%) was greater than that of local environmental factors. Microbial community assembly was mainly governed by deterministic processes (98% of nearest taxon index > 2), despite their relative importance decreasing from bulk soil to the rhizosphere in the case of bacteria. Co-occurrence patterns of sensitive taxa were more complex in the bacterial network than in the fungal network owing to a marked regional effect. Interactions of bacterial taxa differentially enriched between soil compartments were much closer than fungal interactions, indicating a stronger rhizosphere effect on bacteria. The results provide novel insights into the assembly of rhizosphere microbial communities in large-scale forest ecosystems under vegetation restoration.

The structure of microbial communities in redoximorphic microsites of Gleysol

AbstractMicrobial communities were studied in redoximorphic microsites of highly heterogeneous Gleysol at a mm scale using 16S and 18S amplicon sequencing to demonstrate if the composition of soil microbes reflects the differences in ferric and ferrous micro‐sites. In both explored gley horizons with redoximorphic features (Bg2 and Cg), ferric mottles were significantly enriched with total P and Fe and depleted of O, Si, Al, K and Ca compared with the adjacent ferrous groundmass (SEM–EDS). Ferric mottles were determined as Fe oxide coatings and hypocoatings. In Bg2, both prokaryotic and micro‐eukaryotic communities differed significantly between mottles and groundmass in composition of operational taxonomic units (OTUs) and in proportions of phyla, reflecting heterogeneities in the soil properties there. Mottles in Bg2 were characterized by increased proportion of Proteobacteria, decreased proportion of Acidobacteriota among prokaryotes and by dominance of a single proteobacterial OTU from Anaplasmataceae compared to all other samples. The composition of micro‐eukaryotes showed an opposite trend, as micro‐eukaryotes of Bg2 groundmass were unique among the other horizons, while micro‐eukaryotes of Bg2 mottles had similar composition to neighbouring horizons. Microbial communities of adjacent samples were not more similar to each other than communities of randomly selected ones in Bg2 horizon. That suggests that at mm scale, the sample distance does not represent the driving factor of microbial community composition and that the adjacent samples differ rather due to physicochemical factors. The spatial organization of microbial communities revealed in Bg2 has not reappeared in similarly organized Cg horizon, probably due to other overriding factors. The differences revealed between Bg2 and Cg horizons, including granulometric composition, content of crystalline Fe, exchangeable Al, and organic carbon, as well as exposition to groundwater, were discussed as possible reasons of the distinct organization in Cg. The similarity of pro−/eukaryotic communities of adjacent and non‐adjacent couples suggests no distance decay pattern at a mm scale. The agreement between patchiness in soil properties and microbial communities was revealed for the first time and confirms the importance of microscale patterns in soil.

Assembly processes of eukaryotic plankton communities in the world's largest drinking water diversion project

The largest engineered water diversion project–the Middle Route of the South to North Water Diversion Project (MRP), is of strategic importance in solving the problem of the northern water shortage in China. Eukaryotic plankton are important to the water quality stability in the MRP, but little has been reported about their dynamics and assembly processes, especially for abundant and rare communities. In this study, amplicon sequencing was used to investigate the eukaryotic plankton communities. The results revealed both abundant and rare communities exhibited similar distance–decay patterns, but abundant communities were particularly subject to environmental heterogeneity and played an important role in determining seasonal differences in eukaryotic plankton communities and alpha diversity. In the MRP, with its strong hydrodynamic exchange, abundant and rare communities were mainly affected by stochastic processes, especially homogenizing dispersal. In addition, abundant communities were subject to moderate variable selection (25 %) and rare communities were affected by a higher proportion of dispersal limitation (27 % vs. 10 %). The variation in water temperature and water velocity led to a shift from a stochastic to a deterministic process dominating the assembly of abundant communities. This study extends insights into the dynamics and assembly processes of abundant and rare eukaryotic plankton communities in the large, engineered drinking water diversion project, which is also useful for the management and regulation of the MRP.