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Viruses shape microbial communities, food web dynamics, and carbon and nutrient cycling in diverse ecosystems. However, little is known about the patterns and drivers of viral community composition, particularly in soil, precluding a predictive understanding of viral impacts on terrestrial habitats. To investigate soil viral community assembly processes, here we analyzed 43 soil viromes from a rainfall manipulation experiment in a Mediterranean grassland in California. We identified 5,315 viral populations (viral operational taxonomic units [vOTUs] with a representative sequence ≥10 kbp) and found that viral community composition exhibited a highly significant distance–decay relationship within the 200-m2 field site. This pattern was recapitulated by the intrapopulation microheterogeneity trends of prevalent vOTUs (detected in ≥90% of the viromes), which tended to exhibit negative correlations between spatial distance and the genomic similarity of their predominant allelic variants. Although significant spatial structuring was also observed in the bacterial and archaeal communities, the signal was dampened relative to the viromes, suggesting differences in local assembly drivers for viruses and prokaryotes and/or differences in the temporal scales captured by viromes and total DNA. Despite the overwhelming spatial signal, evidence for environmental filtering was revealed in a protein-sharing network analysis, wherein a group of related vOTUs predicted to infect actinobacteria was shown to be significantly enriched in low-moisture samples distributed throughout the field. Overall, our results indicate a highly diverse, dynamic, active, and spatially structured soil virosphere capable of rapid responses to changing environmental conditions.

1. Despite recent advances in understanding community ecology of ectomycorrhizal fungi, little is known about their spatial patterning and the underlying mechanisms driving these patterns across different ecosystems. 2. This meta-study aimed to elucidate the scale, rate and causes of spatial structure of ectomycorrhizal fungal communities in different ecosystems by analysing 16 and 55 sites at the local and global scales, respectively. We examined the distance decay of similarity relationship in species-and phylogenetic lineage-based communities in relation to sampling and environmental variables. 3. Tropical ectomycorrhizal fungal communities exhibited stronger distance-decay patterns compared to non-tropical communities. Distance from the equator and sampling area were the main determinants of the extent of distance decay in fungal communities. The rate of distance decay was negatively related to host density at the local scale. At the global scale, lineage-level community similarity decayed faster with latitude than with longitude. 4. Synthesis. Spatial processes play a stronger role and over a greater scale in structuring local communities of ectomycorrhizal fungi than previously anticipated, particularly in ecosystems with greater vegetation age and closer to the equator. Greater rate of distance decay occurs in ecosystems with lower host density that may stem from increasing dispersal and establishment limitation. The relatively strong latitude effect on distance decay of lineage-level community similarity suggests that climate affects large-scale spatial processes and may cause phylogenetic clustering of ectomycorrhizal fungi at the global scale.

Much of Earth's biodiversity has the capacity to engage in dormancy, a reversible state of reduced metabolic activity. By increasing resilience to unfavourable conditions, dormancy leads to the accumulation of ‘seed banks’. These reservoirs of genetic and phenotypic diversity should diminish the strength of environmental filtering and increase rates of dispersal. Although prevalent among single-celled organisms, evidence that dormancy influences patterns of microbial biogeography is lacking. We constructed geographical and environmental distance–decay relationships (DDRs) for the total (DNA) and active (RNA) portions of bacterial communities in a regional-scale 16S rRNA survey of forested ponds in Indiana, USA. As predicted, total communities harboured greater diversity and exhibited weaker DDRs than active communities. These observations were robust to random resampling and different community metrics. To evaluate the processes underlying the biogeographic patterns, we developed a platform of mechanistic models that used the geographical coordinates and environmental characteristics of our study system. Based on more than 10 6 simulations, our models approximated the empirical DDRs when there was strong environmental filtering along with the presence of long-lived seed banks. By contrast, the inclusion of dispersal generally decreased model performance. Together, our findings support recent theoretical predictions that seed banks can influence the biogeographic patterns of microbial communities. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

1. Increasingly, ecologists conceptualize local communities as connected to a regional species pool rather than as isolated entities. By this paradigm, community structure is determined through the relative strengths of dispersal-driven regional effects and local environmental factors. However, despite explicit incorporation of dispersal, metacommunity models and frameworks often fail to capture the realities of natural systems by not accounting for the configuration of space within which organisms disperse. This shortcoming may be of particular consequence in riverine networks which consist of linearly -arranged, hierarchical, branching habitat elements. Our goal was to understand how constraints of network connectivity in riverine systems change the relative importance of local vs. regional factors in structuring communities. 2. We hypothesized that communities in more isolated headwaters of riverine networks would be structured by local forces, while mainstem sections would be structured by both local and regional processes. We examined these hypotheses using a spatially explicit regional analysis of riverine macroinvertebrate communities, focusing on change in community similarity with distance between local communities [i.e., distance-decay relationships; (DDRs)], and the change in environmental similarity with distance. Strong DDRs frequently indicate dispersal-driven dynamics. 3. There was no evidence of a DDR in headwater communities, supporting our hypothesis that dispersal is a weak structuring force. Furthermore, a positive relationship between community similarity and environmental similarity supported dynamics driven by local environmental factors (i.e., species sorting). In mainstem habitats, significant DDRs and community x environment similarity relationships suggested both dispersal-driven and environmental constraints on local community structure (i.e., mass effects). 4. We used species traits to compare communities characterized by low vs. high dispersal taxa. In headwaters, neither strength nor mode (in-network vs. out of network) of dispersal changed our results. However, outcomes in mainstems changed substantially with both dispersal mode and strength, further supporting the hypothesis that regional forces drive community dynamics in mainstems. 5. Our findings demonstrate that the balance of local and regional effects changes depending on location within riverine network with local (environmental) factors dictating community structure in headwaters, and regional (dispersal driven) forces dominating in mainstems.

Aim (i) To assess the dependence between the form of the decrease in biological similarity with distance (distance‐decay) and species range size and (ii) to introduce the use of a sigmoidal model, the Gompertz function, as a flexible alternative able to fit distance‐decay models under a wide variety of species range sizes. Location Applicable worldwide. Methods We computed distance‐decay curves from simulated communities to assess how the species range sizes shape the functional form of distance‐decay patterns (i.e. negative exponential, power‐law or sigmoidal [Gompertz] relationships). Simulations were performed using different sample sizes and species detection probabilities. We also used distribution data of South American mammals to explore the relationship between species range size and the distance‐decay form in an empirical dataset. Results Our simulations showed that the power‐law is the best supported model when range sizes tend to be small. An increase in range sizes leads to a negative exponential relationship, taking the shape of a sigmoidal (Gompertz) relationship with the largest range size values. Similar results have been found in the distance‐decay pattern of South American mammals. Remarkably, the Gompertz function fits the data reasonably well in all scenarios. Main conclusions The functional form of distance‐decay patterns depends on a key biogeographical attribute: species range size. This dependence makes it an interesting tool to detect biodiversity threats associated with species range expansion, such as the biotic homogenization of faunas. The Gompertz function is the mathematical model that best accommodates different frequency distributions of species range size and, thus, allows cross‐taxa comparison of this biogeographical and ecological pattern.

It has been widely accepted that there is a distance‐decay pattern in the soil microbiome. However, few studies have attempted to interpret the microbial distance‐decay pattern from the perspective of quantifying underlying processes. In this study, we examined the processes governing bacterial community assembly at multiple spatial scales in maize fields of Northeast China using Illumina MiSeq sequencing. Results showed that the processes governing spatial turnover in bacterial community composition shifted regularly with spatial scale, with homogenizing dispersal dominating at small spatial scales and variable selection dominating at larger scales, which in turn explained the distance‐decay pattern that closer located sites tended to have higher community similarity. Together, homogenizing dispersal and dispersal limitation resulting from geographic factors governed about 33% of spatial turnover in bacterial community composition. Deterministic selection processes had the strongest influence, at 57%, with biotic factors and abiotic environmental filtering (mainly imposed by soil pH) respectively contributing about 37% and 63% of variation. Our results provided a novel and comprehensive way to explain the distance‐decay pattern of soil microbiome via quantifying the assembly processes at multiple spatial scales, as well as the method to quantify the influence of abiotic, biotic, and geographic factors in shaping microbial community structure, thus enabling understanding of widely acknowledged microbial biogeographic patterns and microbial ecology. The processes governing spatial turnover in bacterial community composition changed regularly across space, with homogenizing dispersal dominating at small spatial scales and variable selection dominating at larger scales, which in turn explained the distance‐decay pattern that closer located sites tended to have higher community similarity.

Abiotic and biotic factors structure species assembly in ecosystems both horizontally and vertically. However, the way community composition changes along comparable horizontal and vertical distances in complex three‐dimensional habitats, and the factors driving these patterns, remains poorly understood. By sampling ant assemblages at comparable vertical and horizontal spatial scales in a tropical rainforest, we tested hypotheses that predicted differences in vertical and horizontal turnover explained by different drivers in vertical and horizontal space. These drivers included environmental filtering, such as microclimate (temperature, humidity, and photosynthetic photon flux density) and microhabitat connectivity (leaf area), which are structured differently across vertical and horizontal space. We found that both ant abundance and richness decreased significantly with increasing vertical height. Although the dissimilarity between ant assemblages increased with vertical distance, indicating a clear distance‐decay pattern, the dissimilarity was higher horizontally where it appeared independent of distance. The pronounced horizontal and vertical structuring of ant assemblages across short distances is likely explained by a combination of microclimate and microhabitat connectivity. Our results demonstrate the importance of considering three‐dimensional spatial variation in local assemblages and reveal how highly diverse communities can be supported by complex habitats. By sampling ant assemblages at the comparable vertical and horizontal spatial scales in a tropical rain forest, we detected increasing difference in assemblage composition across vertical forest strata, but no effects of horizontal distance on assemblage turnover across trees. Our research highlights the importance of considering assemblage turnover in both horizontal and vertical dimensions and demonstrates how these distance‐decay patterns are influenced by microclimate and habitat connectivity within a structurally complex habitat.

The mechanisms that drive microbial turnover in time and space have received considerable attention but remain unclear, especially for situations with anthropogenic perturbation. To understand the impact of long-term oil contamination on microbial spatial turnover, 100 soil samples were taken from five oil exploration fields located in different geographic regions across China. The microbial functional diversity was analyzed with a high-throughput functional gene array, GeoChip. Our results indicated that soil microbial α-diversity (richness and Shannon diversity index) decreased significantly with contamination. All contaminated and uncontaminated samples exhibited significant spatial autocorrelation between microbial community similarity and spatial distance, as described by a distance-decay relationship (DDR). However, long-term oil exposure flattened the slopes of the DDRs of all of the functional genes and each functional group involved in C/N/P/S cycling, particularly of those involved in contaminant degradation. The relative importance of deterministic and stochastic processes in microbial assembly was determined. The decrease in microbial spatial turnover with long-term oil contamination was coupled with an increase in the proportion of deterministic processes that structured microbial assembly based on null model analysis. The results indicated long-term oil contamination significantly affects soil microbial community spatial structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.

Aim: The extent to which bacterial communities exhibit biogeographic patterns in their distribution remains unclear. We examined the relative influence of factors including geographic distance, latitude, elevation and catchment land use on the distribution and taxon richness of stream bacterial communities across New Zealand. Location: Bacterial communities were collected from biofilm growing on submerged rocks in 244 streams. Sample sites spanned a north-south gradient of over 970 km, an elevational gradient of c. 750 m and were collected from a variety of catchment types across New Zealand. Methods: We used automated ribosomal intergenic spacer analysis, a DNA fingerprinting technique, to characterize the structure and taxon richness of each bacterial community. Key attributes relating to sample location, upstream catchment land use and a suite of additional environmental parameters were collected for every site using GIS procedures. Univariate correlations between measures of bacterial community structure and latitude, elevation and distance were examined. Variance partitioning was then used to assess the relative importance of purely spatial factors versus catchment land use and environmental attributes for determining bacterial community structure and taxon richness. Results: Bacterial taxon richness was related to the geographic location of the sample site, being significantly greater at latitudes closer to the equator and reduced at higher elevations. We observed distance decay patterns in bacterial community similarity related to geographic distance and latitudinal distance, but not to elevational distance. Overall, however, bacterial community similarity and taxon richness was more closely related to variability in catchment land use than to climatic variability or geographic location. Main conclusion: Our data suggest that stream biofilm communities across New Zealand are more influenced by catchment land use attributes than by dispersal limitation.

Background Rare microbial communities represent an important component of biodiversity in soil ecosystems, co‐existing with abundant species to drive ecosystem multifunctionality and maintain its stable operation. However, knowledge remains limited regarding the geographical distribution patterns and potential driving factors of microorganisms, especially rare species, in soil ecosystems. Result Using the CycloneSEQ WT sequencing platform, we systematically investigated soil bacterial communities across 160 sampling sites in southern Jiangxi Province. Abundant and rare taxa exhibited significant compositional differences. Abundant taxa displayed stronger distance‐decay relationships and were primarily driven by climatic factors. In contrast, rare taxa demonstrated higher sensitivity to spatial factors, while the influence of soil pH was substantially stronger on rare taxa than on abundant taxa. While stochastic processes predominantly governed community assembly for both taxa, rare taxa showed greater susceptibility to homogeneous selection, whereas abundant taxa were more strongly influenced by variable selection and dispersal limitation. Network analysis indicated that abundant taxa formed tighter connections internally, while rare taxa established more extensive but looser interactions with other nodes in the network. Conclusions This study reveals different biogeographic patterns between abundant and rare bacterial taxa. Abundant taxa exhibited strong distance‐decay driven by environmental heterogeneity and dispersal limitation, whereas rare taxa showed weak distance‐decay governed by homogeneous selection, providing theoretical support for maintaining microbial diversity in agricultural soils.