Distance-decay Relationship Research Articles

Geographic and temporal distance–decay relationships across taxa

Communities that are farther away from one another in distance or time tend to be more dissimilar. These relationships are often referred to as ‘distance–decay' relationships, relating compositional dissimilarity of communities to geographic distance or exploring compositional shifts through time at a single site. The data required to explore both relationships simultaneously – and their potential interactions – require standardized sampling through time across a set of geographically unique sites. We used data on five taxonomic groups sampled between 2013 and 2021 as part of the National Ecological Observatory Network (NEON) to explore evidence for geographic and temporal distance–decay relationships. Links between these relationships were explored by estimating the temporal consistency of geographic distance–decay relationships and estimating the strength of geographic patterns in temporal distance–decay relationships. Overall, we found evidence for geographic and temporal distance–decay relationships across the five studied taxa, but detected no temporal signal in geographic distance–decay relationships and no spatial signal in temporal distance–decay relationships. Together, this highlights that community composition changes across geographic and temporal gradients, but that the drivers of these changes may depend on different drivers at different scales.

Trophic relationships between protists and bacteria and fungi drive the biogeography of rhizosphere soil microbial community and impact plant physiological and ecological functions

Rhizosphere microorganisms play a vital role in enhancing plant health, productivity, and the accumulation of secondary metabolites. Currently, there is a limited understanding of the ecological processes that control the assembly of community. To address the role of microbial interactions in assembly and for functioning of the rhizosphere soil microbiota, we collected rhizosphere soil samples from Anisodus tanguticus on the Tibetan Plateau spanning 1500 kilometers, and sequenced the bacteria, fungi, archaea, and protist communities. We observed a significant but weak distance-decay relationship in the microbial communities of rhizosphere soil. Our comprehensive analysis of spatial, abiotic, and biotic factors showed that trophic relationships between protists and bacteria and fungi predominantly influenced the alpha and beta diversity of bacterial, fungal, and protistan communities, while abiotic factors had a greater impact on archaeal communities, including soil pH, available phosphorus, total phosphorus and mean annual temperature. Importantly, microbial interactions had a more significant influence on Anisodus tanguticus physiological and ecological functions compared to individual microorganisms. Network analyses revealed that bacteria occupy a central position of the co-occurrence network and play a crucial role of connector within this community. The addition of protists increased the stability of bacterial, fungal, and archaeal networks. Overall, our findings indicate that trophic relationships play an important role in assembly and for functioning of the rhizosphere soil microbiota. Bacterial communities serve as a crucial link between different kingdoms of microorganisms in the rhizosphere community. These findings help us to fully harness the beneficial functions of rhizosphere microorganisms for plants and achieve sustainable use of biological resources.

Climate and Environmental Variables Drive Stream Biofilm Bacterial and Fungal Diversity on Tropical Mountainsides.

High mountain freshwater systems are particularly sensitive to the impacts of global warming and relevant environmental changes. Microorganisms contribute substantially to biogeochemical processes, yet their distribution patterns and driving mechanism in alpine streams remain understudied. Here, we examined the bacterial and fungal community compositions in stream biofilm along the elevational gradient of 745-1874 m on Mt. Kilimanjaro and explored their alpha and beta diversity patterns and the underlying environmental drivers. We found that the species richness and evenness monotonically increased towards higher elevations for bacteria, while were non-significant for fungi. However, both bacterial and fungal communities showed consistent elevational distance-decay relationships, i.e., the dissimilarity of assemblage composition increased with greater elevational differences. Bacterial alpha diversity patterns were mainly affected by chemical variables such as total nitrogen and phosphorus, while fungi were affectedby physical variables such as riparian shading and stream width. Notably, climatic variables such as mean annual temperature strongly affected the elevational succession of bacterial and fungal community compositions. Our study is the first exploration of microbial biodiversity and their underlying driving mechanisms for stream ecosystems in tropical alpine regions. Our findings provide insights on the response patterns of tropical aquatic microbial community composition and diversity under climate change.

Effects of Cascade Reservoirs on Spatiotemporal Dynamics of the Sedimentary Bacterial Community: Co-occurrence Patterns, Assembly Mechanisms, and Potential Functions.

Dam construction as an important anthropogenic activity significantly influences ecological processes in altered freshwater bodies. However, the effects of multiple cascade dams on microbial communities have been largely overlooked. In this study, the spatiotemporal distribution, co-occurrence relationships, assembly mechanisms, and functional profiles of sedimentary bacterial communities were systematically investigated in 12 cascade reservoirs across two typical karst basins in southwest China over four seasons. A significant spatiotemporal heterogeneity was observed in bacterial abundance and diversity. Co-occurrence patterns in the Wujiang Basin exhibited greater edge counts, graph density, average degree, robustness, and reduced modularity, suggesting more intimate and stronger ecological interactions among species than in the Pearl River Basin. Furthermore, Armatimonadota and Desulfobacterota, identified as keystone species, occupied a more prominent niche than the dominant species. A notable distance-decay relationship between geographical distance and community dissimilarities was identified in the Pearl River Basin. Importantly, in the Wujiang Basin, water temperature emerged as the primary seasonal variable steering the deterministic process of bacterial communities, whereas 58.5% of the explained community variance in the neutral community model (NCM) indicated that stochastic processes governed community assembly in the Pearl River Basin. Additionally, principal component analysis (PCA) revealed more pronounced seasonal dynamics in nitrogen functional compositions than spatial variation in the Wujiang Basin. Redundancy analysis (RDA) results indicated that in the Wujiang Basin, environmental factors and in Pearl River Basin, geographical distance, reservoir age, and hydraulic retention time (HRT), respectively, influenced the abundance of nitrogen-related genes. Notably, these findings offer novel insights: building multiple cascade reservoirs could lead to a cascading decrease in biodiversity and resilience in the river-reservoir ecosystem.

Eutrophication increases the similarity of cyanobacterial community features in lakes and reservoirs

Eutrophication of inland waters is a mostly anthropogenic phenomenon impacting aquatic biodiversity worldwide, and might change biotic community structure and ecosystem functions. However, little is known about the patterns of cyanobacterial community variations and changes both on alpha and beta diversity levels in response to eutrophication. Here, we investigated cyanobacterial communities sampled at 140 sites from 59 lakes and reservoirs along a strong eutrophication gradient in eastern China through using CPC-IGS and 16S rRNA gene amplicon sequencing. We found that taxonomic diversity increased, but phylogenetic diversity decreased significantly along the eutrophication gradient. Both niche width and niche overlap of cyanobacteria significantly decreased from low- to high-nutrient waterbodies. Cyanobacterial community distance-decay relationship became weaker from mesotrophic to hypereutrophic waterbodies, while ecological uniqueness (i.e., local contributions to beta diversity) tended to increase in high-nutrient waterbodies. Latitude and longitude were more important in shaping cyanobacterial community structure than other environmental variables. These findings suggest that eutrophication affects alpha and beta diversity of cyanobacterial communities, leading to increasingly similar community structures in lakes and reservoirs with a higher level of eutrophication. Our work highlights how cyanobacterial communities respond to anthropogenic eutrophication and calls for an urgent need to develop conservation and management strategies to control lake eutrophication and protect freshwater biodiversity.

Distinct biogeographic patterns in Glomeromycotinian and Mucoromycotinian arbuscular mycorrhizal fungi across China: A meta-analysis

Fine root endophytes, recently reclassified as Mucoromycotinian arbuscular mycorrhizal fungi (M-AMF), are now recognized as functionally important as Glomeromycotinian AMF (G-AMF). However, little is known about the biogeography and ecology of M-AMF and G-AMF communities, particularly on a large scale, preventing a systematic assessment of ecosystem diversity and functioning. Here, we investigated the biogeographic assemblies and ecological diversity patterns of both G-AMF and M-AMF, using published 18S rDNA amplicon datasets and associated metadata from 575 soil samples in six ecosystems across China. Contrasting with G-AMF, putative M-AMF were rare in natural/semi-natural sites, where their communities were a subset of those in agricultural sites characterized by intensive disturbances, suggesting different ecological niches that they could occupy. Spatial and environmental factors (e.g., vegetation type) significantly influenced both fungal communities, with soil total‑nitrogen and mean-annual-precipitation being the strongest predictors for G-AMF and M-AMF richness, respectively. Both groups exhibited a strong spatial distance-decay relationship, shaped more by environmental filtering than spatial effects for M-AMF, and the opposite for G-AMF, presumably because stochasticity (e.g., drift) dominantly structured G-AMF communities; while the narrower niche breadth (at community-level) of M-AMF compared to G-AMF suggested its more susceptibility to environmental differences. Furthermore, co-occurrence network links between G-AMF and M-AMF were prevalent across ecosystems, and were predicted to play a key role in stabilizing overall communities harboring both fungi. Based on the macroecological spatial scale datasets, this study provides solid evidence that the two AMF groups have distinct ecological preferences at the continental scale in China, and also highlights the potential impacts of anthropogenic activities on distributions of AMF. These results advance our knowledge of the ecological differences between the two fungal groups in terrestrial ecosystems, suggesting the need for further field-based investigation that may lead to a more sophisticated understanding of ecosystem function and sustainable management.

Ecological and functional differences of abundant and rare sub-communities in wastewater treatment plants across China

The microbial community in activated sludge is composed of a small number of abundant sub-community with high abundance and a large number of rare sub-community with limited abundance. Our knowledge regarding the ecological properties of both abundant and rare sub-communities in activated sludge is limited. This article presented an analysis of functional prediction, assembly mechanisms, and biogeographic distribution characteristics of abundant and rare sub-communities in 211 activated sludge samples from 60 wastewater treatment plants across China. Moreover, this study investigated the dominant factors influencing the community structure of these two microbial groups. The results showed that the functions associated with carbon and nitrogen cycling were primarily detected in abundant sub-community, while rare sub-community were primarily involved in sulfur cycling. Both microbial groups were mainly influenced by dispersal limitation, which, to some extent, resulted in a distance-decay relationship in their biogeographic distribution. Moreover, a higher spatial turnover rate of rare sub-communities (0.0887) suggested that spatial differences in microbial community structure among different WWTPs may mainly result from rare sub-community. Moreover, SEM showed that geographic locations affected rare sub-communities greatly, which agreed with their higher dispersal limitation and turnover rate. In contrast, influent characteristics showed stronger correlations with abundant sub-communities, suggesting that abundant sub-community may contribute more to the removal of pollutants. This study enhanced our understanding of abundant and rare microorganisms in activated sludge especially the role of rare species and provided scientific evidence for precise regulation and control of wastewater treatment plants.

Natural grass coverage enriches arbuscular mycorrhizal fungal communities in subtropical citrus orchards through the regulation of Glomus on a regional scale

Arbuscular mycorrhizal (AM) fungi are ubiquitous soil fungi in orchard ecosystem, conferring a diverse array of benefits to citrus plants. However, how natural grass coverage, a common phenomenon in citrus orchards in southern China, shifts AM fungal communities in subtropical citrus orchards is far from being understood, especially on a regional scale, which impedes the understanding of the indigenous AM fungal adaptations. In this study, natural grass coverage rate, soil chemical properties, and soil AM fungal community in 80 sampling sites spanning 179, 700 km2 area in subtropical citrus orchards were investigated. The result of 18S rRNA gene high-throughput sequencing revealed that a total of eight AM fungal genera were identified and Glomus (90.15 %) was dominant genus in the community in citrus orchards. Natural grass coverage significantly increased soil organic matter (SOM), soil available phosphorus, and AM fungal alpha diversity, especially Glomus. Variation partitioning analysis revealed that grass coverage rate explained more variation in AM fungal alpha diversity than SOM. All the contrasting AM fungal species between different grass coverage rates and all the core AM fungal species belonged to Glomus. Null model analysis revealed that determinism played a slightly larger role in the assembly process of AM fungal communities than stochasticity with a distance-decay relationship. Moreover, natural grass coverage increased the relative importance of stochasticity in the community assembly. Taken together, these results suggest that maintaining natural grass coverage (naturally growing grass) is an effective nature-based solution for enriching AM fungal communities, which is essential for the sustainability of citrus production.

Interactions between soil bacterial communities, assembly processes and microbial functions along the elevational gradient

The distribution of microbial communities along elevational gradients has been widely reported, but whether there are linkages between soil microbial diversity, community assembly processes and microbial functions in elevational patterns, and whether the patterns are influenced by micro-topography (e.g. slope direction), remain unclear. Here, we collected soils from two slope directions (i.e. north-facing slope and east-facing slope) along the elevational gradient (∼2000 m elevational range) of a mountain ecosystem. Unexpectedly, for bacterial alpha diversity or microbial functions (i.e. multifunctionality), we found consistent elevational patterns for both slope directions, with alpha diversity showing a hump-shaped pattern and microbial functions exhibiting a linearly increasing trend. Similarly, for both slope directions, there were significant elevational distance-decay relationships in the bacterial beta diversity pattern. The elevational patterns of soil bacterial diversity were determined by the transitions of community assembly processes, while microbial functions were mainly influenced by bacterial community composition. These results suggest that soil bacterial diversity, community assembly processes and microbial functions are interactive along an elevational gradient, and that these interactions are independent of slope direction. Our study adds new insights into the elevational patterns of soil bacterial communities and their drivers and ecological consequences in mountain ecosystems.

Functional redundancy across space and time in litter‐degrading fungal communities

AbstractIntroductionMicrobial‐driven litter decomposition contributes significantly to global carbon (C) turnover. Fungi play central roles in the degradation process due to their ability to hydrolyse recalcitrant litter components. The spatiotemporal variations in taxonomic composition of litter‐degrading fungi have been well documented. However, associated variations in litter‐degradation‐related functional composition of fungal communities remain unexplored.Materials and MethodsIn this study, a 16‐week field‐based buried rice straw experiment was conducted at three experimental sites across subtropical China in combination with laboratory 13C‐straw‐based DNA stable‐isotope probing (DNA‐SIP) microcosm experiments. Amplicon sequencing combined with shotgun metagenomic sequencing were the approaches of choice.ResultsThe field experiment showed that the taxonomic composition of the straw‐degrading fungal community was highly variable while the functional composition was rather stable. The higher permutational multivariate analysis of variation F scores (20.904−48.660) and the steeper slopes (1.92 E‐04−4.15E‐04) of the distance decay relationship for taxonomic composition than for function across periods (with lower F scores = 7.047−21.601 and gradual slopes = −1.33 E‐05 to −1.03E‐04) both indicated that the spatiotemporal patterns of functional composition in litter‐degrading fungi community were more conserved. The laboratory DNA‐SIP confirmed the field observations and showed that the conserved functional composition in litter‐degrading fungi was underpinned by a high functional redundancy of Basidiomycota.ConclusionFunction and taxonomy of litter‐degrading fungi were decoupled. The functional composition of the litter‐degrading fungal community was highly conserved in space and time, the taxonomic composition less so. The main drivers behind the observed taxonomic decoupling are probably/most likely functional redundancy and metabolic niche selection resulting in conservation of function, with changing environmental conditions and dispersal limitation drove the observed high taxonomic turnover of the community over the course of the litter degradation progression. Our study provides valuable insights in the ecology of fungi and their roles in in global C sequestration for ecosystem sustainable development.

Mean annual precipitation modulates the assembly of high-affinity methanotroph communities and methane oxidation activity across grasslands

Grasslands have an important global role in biological methane (CH4) oxidation and therefore it is crucial to understand the key factors determining the assembly of high-affinity methanotroph populations and explore mechanisms that regulate CH4 oxidation activity in these ecosystems. This study explored the linkage between high-affinity methanotroph community assembly processes and CH4 oxidation potential across three grassland types in Inner Mongolia with or without livestock grazing. We found the largest proportion of deterministic selection in temperate desert grasslands, but it was increasingly structured by stochastic dispersal in temperate meadow and temperate typical grasslands. The distance decay relationship (DDR) and variation partitioning analysis (VPA) showed the strongest relationship and highest proportion of environmental factors in desert grasslands, followed by meadow and typical grasslands. Mean annual precipitation (MAP), environmental factors (moisture content, soil organic matter), and microbial traits (abundance, diversity and normalized stochasticity ratio) were significantly related with CH4 oxidation activity. Multiple statistical analyses consistently indicated the key role of MAP in shaping high-affinity methanotroph community diversity, composition, co-occurrence networks, assembly processes and CH4 oxidation activity. We found an association of increasing stochastic assembly and high-affinity methanotroph diversity with decreasing CH4 oxidation potential. This study revealed the mechanisms governing high-affinity methanotroph community assembly processes and integrates high-affinity methanotroph community assembly with CH4 oxidation activity in grassland soils.

Global diversity and biogeography of DNA viral communities in activated sludge systems

BackgroundActivated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses that regulate microbial metabolism and nutrient cycling, significantly influencing the stability of AS systems. However, our knowledge about the diversity of viral taxonomic groups and functional traits in global AS systems is still limited. To address this gap, we investigated the global diversity and biogeography of DNA viral communities in AS systems using 85,114 viral operational taxonomic units (vOTUs) recovered from 144 AS samples collected across 54 WWTPs from 13 different countries.ResultsAS viral communities and their functional traits exhibited distance-decay relationship (DDR) at the global scale and latitudinal diversity gradient (LDG) from equator to mid-latitude. Furthermore, it was observed that AS viral community and functional gene structures were largely driven by the geographic factors and wastewater types, of which the geographic factors were more important. Carrying and disseminating auxiliary metabolic genes (AMGs) associated with the degradation of polysaccharides, sulfate reduction, denitrification, and organic phosphoester hydrolysis, as well as the lysis of crucial functional microbes that govern biogeochemical cycles were two major ways by which viruses could regulate AS functions. It was worth noting that our study revealed a high abundance of antibiotic resistance genes (ARGs) in viral genomes, suggesting that viruses were key reservoirs of ARGs in AS systems.ConclusionsOur results demonstrated the highly diverse taxonomic groups and functional traits of viruses in AS systems. Viral lysis of host microbes and virus-mediated HGT can regulate the biogeochemical and nutrient cycles, thus affecting the performance of AS systems. These findings provide important insights into the viral diversity, function, and ecology in AS systems on a global scale.-K8pwvbs3fYC6bGWQ-q_MyVideo

Dispersal and Distribution of Thermophilic Endospores in Deep-Sea Ecosystems

The distance-decay relationship is a central concept in biogeography and spatial biodiversity, describing how two distinct entities decrease in similarity as the distance between them increases. The decay of community similarity with geographical distance is driven by multiple factors, such as gene drift, environmental selection, and the accumulation of mutations over time. While the distance-decay relationship has been recognized for several decades, there are certain circumstances where the biogeographical patterns of certain species and communities cannot be predicted by this relationship. The example addressed in this project is the case of thermophilic endospore-forming bacteria found in permanently cold deep ocean sediments. Thermophilic endospores (thermospores) are routinely found on the deep ocean floor, a permanently cold environment that does not support their metabolic activity (Hubert et al. 2009). Thermospores are metabolically dormant states developed by some thermophilic bacteria having optimal growth temperatures between 40°C and 70°C. There is evidence that these heat-loving bacteria originate from the deep subsurface and are transported upward to the deep ocean via geological features of the oceanic crust including geofluid fluxes in high-temperature axial systems and natural hydrocarbon seeps (Gittins et al. 2022). Due to the ability of endospores to stay viable for thousands of years and resist a wide range of physicochemical stressors, they can disperse over long distances while remaining unaffected by changing factors such as selection, drift, or mutation (Gittins et al. 2022; Fig. 1). Consequently, these thermospores have the potential to challenge the distance-decay relationship and exhibit unique biogeographical patterns. This work quantifies endospores in sediment cores at and around hydrocarbon seeps using cores from deep-sea Scotian Slope sediments. Given the challenge of quantifying specific groups of endospores (e.g., thermophiles but not mesophiles), high-temperature germination assays that allow tracking of an exponential increase in signal as spores in marine sediment samples germinate and grow can be used. Distinct exponential increases can be attributed to different populations of germinated thermospores in the post-germination growth phase and are being monitored through measurements of sulfate reduction rates (using radiolabelled 35SO4), strain-specific quantitative PCR (qPCR), and fluorescence in-situ hybridization (FISH) (Rezende et al. 2017). These measurements revealed growth dynamics enabling an estimation of the initial cell numbers using exponential functions. These approaches are being applied to samples obtained via push coring using a remotely operated vehicle at different distances from deep sea hydrocarbon seeps, to test for the presence of abundance gradients of different thermospores. Current results already show a difference in thermospore abundance between sites at different distances from the seep. Quantitative tracking of the dispersal of thermospores by oceanic currents in the deep sea provides an excellent opportunity to investigate their distribution and potential to colonize more remote habitats, improving the understanding of microbial biodiversity and biogeography on our planet. By investigating thermospores and their interactions with the geophysical features of the deep sea and deep subsurface, this study aims to challenge the canonical idea that speciation occurs with distance and presents new perspectives on the theme of microbial biogeography. The evidence supporting the subsurface origin of thermophilic endospores, along with the proposed model for their dispersal and distribution, will contribute toward improving an integrated understanding of ecology and geology and their intersection in the microbial realm.

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.

The spatial patterns of community composition, their environmental drivers and their spatial scale dependence vary markedly between fungal ecological guilds

AbstractAimHow community composition varies in space and what governs the variation has been extensively investigated in macroorganisms. However, we have only limited knowledge of microorganisms, especially fungi, despite their ecological and economic significance. Based on previous research, we define and test a series of hypotheses regarding the composition of fungal communities, their most influential drivers and their spatial scale dependence.LocationCzech Republic.Time periodPresent.Taxa studiedFungi.MethodsWe analysed the distance decay relationships, community composition and its drivers (physical distance, litter and soil chemistry, tree composition and climate) in fungi using multivariate analyses. We compared the results across three fungal ecological guilds (ectomycorrhizal fungi, saprotrophs and yeasts), two forest microhabitats (litter and bulk soil) and six spatial scales (from 5 m to 80 km) that comprehensively cover the Czech Republic.ResultsWe found that, similar to macroorganisms, the ectomycorrhizal fungi and saprotrophs showed marked distance–decay relationships, and their community composition was driven mainly by vegetation and dispersal at local scales but, at regional scales, by environmental effects. In contrast, the third fungal guild, the unicellular yeasts, showed little distance decay, suggesting extraordinary spatial homogeneity, as often seen in microorganisms, such as bacteria.Main conclusionsOur results underscore the remarkable variation in the community ecology of fungi, which seems to range well‐known patterns both from the macro‐ and the microworld. Knowledge of these patterns advances our understanding of the ecology of fungi, rather understudied organisms of significant ecological and economic importance, which our findings identify as a potentially suitable model for bridging the gaps between the biogeography of micro‐ and macroorganisms.

Macroalgal microbiome biogeography is shaped by environmental drivers rather than geographical distance.

Contrasting patterns of host and microbiome biogeography can provide insight into the drivers of microbial community assembly. Distance-decay relationships are a classic biogeographical pattern shaped by interactions between selective and non-selective processes. Joint biogeography of microbiomes and their hosts is of increasing interest owing to the potential for microbiome-facilitated adaptation. In this study, we examine the coupled biogeography of the model macroalga Durvillaea and its microbiome using a combination of genotyping by sequencing (host) and 16S rRNA amplicon sequencing (microbiome). Alongside these approaches, we use environmental data to characterize the relationship between the microbiome, the host, and the environment. We show that although the host and microbiome exhibit shared biogeographical structure, these arise from different processes, with host biogeography showing classic signs of geographical distance decay, but with the microbiome showing environmental distance decay. Examination of microbial subcommunities, defined by abundance, revealed that the abundance of microbes is linked to environmental selection. As microbes become less common, the dominant ecological processes shift away from selective processes and towards neutral processes. Contrary to expectations, we found that ecological drift does not promote structuring of the microbiome. Our results suggest that although host macroalgae exhibit a relatively 'typical' biogeographical pattern of declining similarity with increasing geographical distance, the microbiome is more variable and is shaped primarily by environmental conditions. Our findings suggest that the Baas Becking hypothesis of 'everything is everywhere, the environment selects' might be a useful hypothesis to understand the biogeography of macroalgal microbiomes. As environmental conditions change in response to anthropogenic influences, the processes structuring the microbiome of macroalgae might shift, whereas those governing the host biogeography are less likely to change. As a result, increasingly decoupled host-microbe biogeography might be observed in response to such human influences.

Anthropogenic original DOM is a critical factor affecting LNA bacterial community assembly

We investigated the geographical and environmental distance–decay relationships for both of the two bacteria in the Haihe River, Tianjin, China. HNA bacteria exhibited a stronger geographical variation-dependent pattern while LNA bacteria exhibited a stronger environmental variation-dependent pattern. Variance partition analysis (VPA), Mantel test, and partial mantel test validated the discrepant impacts of geographical distance and environmental factors on their two communities. The heterogeneous selection dominated community assembly of LNA bacteria demonstrates their greater sensitivity to environmental conditions. As the deterministic environmental factor, anthropogenic original dissolved organic matter (DOM) functions exclusively on LNA bacteria, and it is the critical factor leading to the discrepant biogeographical patterns of LNA and HNA bacteria. LNA bacteria interact with HNA bacteria and mediate the DOM driving total bacteria assembly. The LNA keystone taxa, Pseudomonas, Rheinheimera, Candidatus Aquiluna, and hgcl clade are capable to compete with HNA bacteria for anthropogenic original DOM, and are potential indicators of anthropogenic pollution. Our research reveals the non-negligible effect of the LNA bacteria in regulating the ecological response of total bacteria.

Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau.

Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.

Assembly Processes and Biogeographical Characteristics of Soil Bacterial Sub-communities of Different Habitats in Urban Green Spaces.

The process of urbanization is one of the most important human-driven activities that reshape the natural distribution of soil microorganisms. However, it is still unclear about the effects of urbanization on the different taxonomic soil bacterial community dynamics. In this study, we collected soil samples from highly urbanized the regions of Yangtze River Delta, Beijing-Tianjin-Hebei in China, to explore the bio-geographic patterns, assembly processes, and symbiotic patterns of abundant, moderate, and rare bacterial communities. We found that the number of moderate and rare taxa species were lower than that of abundant taxa, but their α-diversity index was higher than abundant taxa. Proteobacteria, Acidobacteria, Actinobacteria, Bacterioidetes, and Chloroflexi were the dominant phylum across all three sub-communities. And the β-diversity value of rare taxa was significantly higher than those of moderate and abundant taxa. Abundant, moderate, and rare sub-communities showed a weak distance-decay relationship, and the moderate taxa had the highest turnover rate of microbial geography in the context of urbanization. Diffusion limitation was the dominant process of soil bacterial community assembly. The co-occurrence networks of abundant, moderate, and rare taxa were dominated by positive correlations. The network of moderate taxa had the highest modularity, followed by abundant taxa. The main functions of the abundant, moderate, and rare taxa were related to Chemoheterotrophy and N transformations. Redundancy analysis showed that the dispersal limitation, climate, and soil properties were the main factors dominating bio-geographic differences in soil bacterial community diversity. We conclude that human-dominated urbanization processes have generated more uncertain survival pressures on soil bacteria, which resulted in a stronger linkage but weak bio-geographic variation for soil bacteria. In the future urban planning process, we suggest that such maintenance of native vegetation and soil types should be considered to maintain the long-term stability of local microbial ecosystem functions.

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.