Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils

Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities.     

Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field

To better understand the distribution of soil microbial communities at multiple spatial scales, a survey was conducted to examine the spatial organization of community structure in a wheat field in eastern Virginia (USA). Nearly 200 soil samples were collected at a variety of separation distances ranging from 2.5 cm to 11 m. Whole-community DNA was extracted from each sample, and community structure was compared using amplified fragment length polymorphism (AFLP) DNA fingerprinting. Relative similarity was calculated between each pair of samples and compared using geostatistical variogram analysis to study autocorrelation as a function of separation distance. Spatial autocorrelation was found at scales ranging from 30 cm to more than 6 m, depending on the sampling extent considered. In some locations, up to four different correlation length scales were detected. The presence of nested scales of variability suggests that the environmental factors regulating the development of the communities in this soil may operate at different scales. Kriging was used to generate maps of the spatial organization of communities across the plot, and the results demonstrated that bacterial distributions can be highly structured, even within a habitat that appears relatively homogeneous at the plot and field scale. Different subsets of the microbial community were distributed differently across the plot, and this is thought to be due to the variable response of individual populations to spatial heterogeneity associated with soil properties.     

Spatial Analysis of Archaeal Community Structure in Grassland Soil

The complex structure of soil and the heterogeneity of resources available to microorganisms have implications for sampling regimens when the structure and diversity of microbial communities are analyzed. To assess the heterogeneity in community structure, archaeal communities, which typically contain sequences belonging to the nonthermophilic Crenarchaeota, were examined at two contrasting spatial scales by using PCR-denaturing gradient gel electrophoresis (DGGE) analysis followed by unweighted pair group method with arithmetic mean analysis of 16S rRNA- and ribosomal DNA-derived profiles. A macroscale analysis was carried out with soil cores taken at 2-m intervals along triplicate 8-m transects from both managed (improved) and natural (unimproved) grassland rhizosphere soils. A microscale analysis was carried out with a single soil core by assessing the effects of both sample size (10, 1, and 0.1 g) and distance between samples. The much reduced complexity of archaeal profiles compared to the complexity typical of the bacterial community facilitated visual comparison of profiles based on band presence and revealed different levels of heterogeneity between sets of samples. At the macroscale level, heterogeneity over the transect could not be related to grassland type. Substantial heterogeneity was observed across both improved and unimproved transects, except for one improved transect that exhibited substantial homogeneity, so that profiles for a single core were largely representative of the entire transect. At the smaller scale, the heterogeneity of the archaeal community structure varied with sample size within a single 8- by 8-cm core. The archaeal DGGE profiles for replicate 10-g soil samples were similar, while those for 1-g samples and 0.1-g samples showed greater heterogeneity. In addition, there was no relationship between the archaeal profiles and the distance between 1- or 0.1-g samples, although relationships between community structure and distance of separation may occur at a smaller scale. Our findings demonstrate the care required when workers attempt to obtain a representative picture of microbial community structure in the soil environment.     

Spatial analysis of archaeal community structure in grassland soil

The complex structure of soil and the heterogeneity of resources available to microorganisms have implications for sampling regimens when the structure and diversity of microbial communities are analyzed. To assess the heterogeneity in community structure, archaeal communities, which typically contain sequences belonging to the nonthermophilic Crenarchaeota, were examined at two contrasting spatial scales by using PCR-denaturing gradient gel electrophoresis (DGGE) analysis followed by unweighted pair group method with arithmetic mean analysis of 16S rRNA- and ribosomal DNA-derived profiles. A macroscale analysis was carried out with soil cores taken at 2-m intervals along triplicate 8-m transects from both managed (improved) and natural (unimproved) grassland rhizosphere soils. A microscale analysis was carried out with a single soil core by assessing the effects of both sample size (10, 1, and 0.1 g) and distance between samples. The much reduced complexity of archaeal profiles compared to the complexity typical of the bacterial community facilitated visual comparison of profiles based on band presence and revealed different levels of heterogeneity between sets of samples. At the macroscale level, heterogeneity over the transect could not be related to grassland type. Substantial heterogeneity was observed across both improved and unimproved transects, except for one improved transect that exhibited substantial homogeneity, so that profiles for a single core were largely representative of the entire transect. At the smaller scale, the heterogeneity of the archaeal community structure varied with sample size within a single 8- by 8-cm core. The archaeal DGGE profiles for replicate 10-g soil samples were similar, while those for 1-g samples and 0.1-g samples showed greater heterogeneity. In addition, there was no relationship between the archaeal profiles and the distance between 1- or 0.1-g samples, although relationships between community structure and distance of separation may occur at a smaller scale. Our findings demonstrate the care required when workers attempt to obtain a representative picture of microbial community structure in the soil environment.     

土壤微生物群落构建理论与时空演变特征

土壤微生物作为陆地生态系统的重要组成部分,直接或间接地参与几乎所有的土壤生态过程,在物质循环、能量转换以及污染物降解等过程中都发挥着重要作用。对土壤微生物时空演变规律及其形成机制的研究,不仅是微生物演变和进化的基础科学问题,也是预测微生物及其所介导的生态功能对环境条件变化响应、适应和反馈的理论依据。讨论了土壤微生物群落的定义、测度方法和指标,认为群落是联系动植物宏观生态学与微生物生态学的基础,群落构建机制是宏观和微观生态学都需要研究的核心科学问题;从生态学的群落构建理论出发,阐述了包括生态位理论/中性理论、过程理论和多样性-稳定性理论在土壤微生物时空演变研究中的应用,以及微生物群落在时间和空间上的分布特征及其尺度效应;确立了以微生物群落构建理论为基础、不同时空尺度下土壤微生物群落演变特征为主要内容的微生物演变研究的基本框架。     

Changes in Bacterial and Archaeal Community Structure and Functional Diversity along a Geochemically Variable Soil Profile

Spatial heterogeneity in physical, chemical, and biological properties of soils allows for the proliferation of diverse microbial communities. Factors influencing the structuring of microbial communities, including availability of nutrients and water, pH, and soil texture, can vary considerably with soil depth and within soil aggregates. Here we investigated changes in the microbial and functional communities within soil aggregates obtained along a soil profile spanning the surface, vadose zone, and saturated soil environments. The composition and diversity of microbial communities and specific functional groups involved in key pathways in the geochemical cycling of nitrogen, Fe, and sulfur were characterized using a coupled approach involving cultivation-independent analysis of both 16S rRNA (bacterial and archaeal) and functional genes (amoA and dsrAB) as well as cultivation-based analysis of Fe(III)-reducing organisms. Here we found that the microbial communities and putative ammonia-oxidizing and Fe(III)-reducing communities varied greatly along the soil profile, likely reflecting differences in carbon availability, water content, and pH. In particular, the Crenarchaeota 16S rRNA sequences are largely unique to each horizon, sharing a distribution and diversity similar to those of the putative (amoA-based) ammonia-oxidizing archaeal community. Anaerobic microenvironments within soil aggregates also appear to allow for both anaerobic- and aerobic-based metabolisms, further highlighting the complexity and spatial heterogeneity impacting microbial community structure and metabolic potential within soils.     

How do microbiota associated with an invasive seaweed vary across scales?

Communities are shaped by scale dependent processes. To study the diversity and variation of microbial communities across scales, the invasive and widespread seaweed Agarophyton vermiculophyllum presents a unique opportunity. We characterized pro‐ and eukaryotic communities associated with this holobiont across its known distribution range, which stretches over the northern hemisphere. Our data reveal that community composition and diversity in the holobiont vary at local but also larger geographic scales. While processes acting at the local scale (i.e., within population) are the main structuring drivers of associated microbial communities, changes in community composition also depend on processes acting at larger geographic scales. Interestingly, the largest analysed scale (i.e., native and non‐native ranges) explained variation in the prevalence of predicted functional groups, which could suggest a functional shift in microbiota occurred over the course of the invasion process. While high variability in microbiota at the local scale supports A. vermiculophyllum to be a generalist host, we also identified a number of core taxa. These geographically independent holobiont members imply that cointroduction of specific microbiota may have additionally promoted the invasion process.     

Quantifying the relative roles of selective and neutral processes in defining eukaryotic microbial communities

We have a limited understanding of the relative contributions of different processes that regulate microbial communities, which are crucial components of both natural and agricultural ecosystems. The contributions of selective and neutral processes in defining community composition are often confounded in field studies because as one moves through space, environments also change. Managed ecosystems provide an excellent opportunity to control for this and evaluate the relative strength of these processes by minimising differences between comparable niches separated at different geographic scales. We use next-generation sequencing to characterize the variance in fungal communities inhabiting adjacent fruit, soil and bark in comparable vineyards across 1000 kms in New Zealand. By compartmentalizing community variation, we reveal that niche explains at least four times more community variance than geographic location. We go beyond merely demonstrating that different communities are found in both different niches and locations by quantifying the forces that define these patterns. Overall, selection unsurprisingly predominantly shapes these microbial communities, but we show the balance of neutral processes also have a significant role in defining community assemblage in eukaryotic microbes.     

A Molecular Comparison of Plumage and Soil Bacteria Across Biogeographic,Ecological, and Taxonomic Scales

We used molecular methods to determine the microbial community of soil and avian plumage across biogeographic, ecological, and taxonomic scales. A total of 17 soil and 116 feather samples were collected from five avian species across multiple habitat types within one Neotropical and one temperate locality. Hypotheses regarding patterns of microbial composition relative to acquisition and dispersal of plumage bacteria in the ecosystem were tested by comparing microbial communities within and between soil and plumage. Samples from the plumage of American Redstarts (Setophaga ruticilla) were collected across both habitat types and geographic scales for intraspecific comparisons. The microbial diversity in avian plumage was moderately diverse and was dominated by Pseudomonas species. Despite a highly significant individual bird effect on microbial composition of the plumage, we detected significant biogeographic and type of habitat effects. Pseudomonas species were more abundant on the temperate site when all avian species were included in the analysis, and Bacillus subtilis and Xanthomonas groups were more abundant on the Neotropical site for redstarts alone. However, 16S rDNA sequence libraries were not significantly different between Jamaican and Maryland redstarts. Biogeographic and habitat effects were significant and more pronounced for soil samples indicating lower dispersal of soil microbiota. We detected a significant difference between soil and plumage microbial communities suggesting that soil plays a small role in plumage bacterial acquisition. Our results suggest bacterial communities on the plumage of birds are dynamic and may change at different stages in a bird’s annual cycle.     

The influence of sampling strategies and spatial variation on the detected soil bacterial communities under three different land-use types

To determine the influence of pooling strategies on detected soil bacterial communities, we sampled 45 soil cores each from a eucalypt woodland, a sown pasture and a revegetated site in an Australian landscape. We assessed the spatial variation within each land-use plot, including the influence of sampling distance, soil chemical characteristics and, where appropriate, proximity to trees on the soil bacterial community, by generating terminal restriction fragment length polymorphism profiles of the bacterial 16S rRNA genes. The soil bacterial community under the revegetated site was more similar to the original woodland than the pasture, and this result was found regardless of the soil- or the DNA-pooling strategy used. Analyzing as few as eight cores per plot was sufficient to detect significant differences between the bacterial communities under the different plots to be distinguished. Soil pH was found to be most strongly associated with soil bacterial community composition within the plots and there was no association found with proximity to trees. This study has investigated sampling strategies for further research into the transitions of soil microbial communities with land-use change across broader temporal and spatial scales.     

Mechanisms of soil bacterial and fungal community assembly differ among and within islands

The study of islands has made substantial contributions to the development of evolutionary and ecological theory. However, we know little about microbial community assembly on islands. Using soil microbial data collected from 29 lake islands and nearby mainland, we examined the assembly mechanisms of soil bacterial and fungal communities among and within islands. We found that deterministic processes, especially homogeneous selection, tended to be more important in shaping the assembly of soil bacterial communities among islands, while stochastic processes tended to be more important within islands. Moreover, increasing island area increased the importance of homogeneous selection, but reduced the importance of variable selection, for soil bacterial community assembly within islands. By contrast, stochastic processes tended to dominate soil fungal community assembly both among and within islands, with dispersal limitation playing a more important role within than among islands. Our results highlight the scale- and taxon-dependence of insular soil microbial community assembly, suggesting that spatial scale should be explicitly considered when evaluating the influences of habitat fragmentation on soil microbial communities.     

Soil-Borne Bacterial Structure and Diversity Does Not Reflect Community Activity in Pampa Biome

The Pampa biome is considered one of the main hotspots of the world’s biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated.     

Local soil characteristics determine the microbial communities under forest understorey plants along a latitudinal gradient

The soil microbial community is essential for maintaining ecosystem functioning and is intimately linked with the plant community. Yet, little is known on how soil microbial communities in the root zone vary at continental scales within plant species. Here we assess the effects of soil chemistry, large-scale environmental conditions (i.e. temperature, precipitation and nitrogen deposition) and forest land-use history on the soil microbial communities (measured by phospholipid fatty acids) in the root zone of four plant species (Geum urbanum, Milium effusum, Poa nemoralis and Stachys sylvatica) in forests along a 1700 km latitudinal gradient in Europe.Soil microbial communities differed significantly among plant species, and soil chemistry was the main determinant of the microbial community composition within each plant species. Influential soil chemical variables for microbial communities were plant species-specific; soil acidity, however, was often an important factor. Large-scale environmental conditions, together with soil chemistry, only explained the microbial community composition in M. effusum and P. nemoralis. Forest land-use history did not affect the soil microbial community composition.Our results underpin the dominant role of soil chemistry in shaping microbial community composition variation within plant species at the continental scale, and provide insights into the composition and functionality of soil microbial communities in forest ecosystems.     

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β‐diversity) along ecological gradients. Here, we characterize soil microbial β‐diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β‐diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β‐diversities with respect to plant β‐diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β‐diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β‐diversities were mostly related to plant β‐diversity, while bacterial β‐diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β‐diversities with plant β‐diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β‐diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early‐evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.     

Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes

The deep sequencing of 16S rRNA genes amplified by universal primers has revolutionized our understanding of microbial communities by allowing the characterization of the diversity of the uncultured majority. However, some universal primers also amplify eukaryotic rRNA genes, leading to a decrease in the efficiency of sequencing of prokaryotic 16S rRNA genes with possible mischaracterization of the diversity in the microbial community. In this study, we compared 16S rRNA gene sequences from genome-sequenced strains and identified candidates for non-degenerate universal primers that could be used for the amplification of prokaryotic 16S rRNA genes. The 50 identified candidates were investigated to calculate their coverage for prokaryotic and eukaryotic rRNA genes, including those from uncultured taxa and eukaryotic organelles, and a novel universal primer set, 342F-806R, covering many prokaryotic, but not eukaryotic, rRNA genes was identified. This primer set was validated by the amplification of 16S rRNA genes from a soil metagenomic sample and subsequent pyrosequencing using the Roche 454 platform. The same sample was also used for pyrosequencing of the amplicons by employing a commonly used primer set, 338F-533R, and for shotgun metagenomic sequencing using the Illumina platform. Our comparison of the taxonomic compositions inferred by the three sequencing experiments indicated that the non-degenerate 342F-806R primer set can characterize the taxonomic composition of the microbial community without substantial bias, and is highly expected to be applicable to the analysis of a wide variety of microbial communities.     

Community Structure Comparison Using FAME Analysis of Desert Varnish and Soil,Mojave Desert,California

While a number of studies have shown that a close association exists between microorganisms and varnished rocks, there is little hard evidence to support the existence of either specific desert varnish communities, or any role these microbes might play in the genesis of the varnish layers. To this end, we analyzed fatty acid methyl esters (FAMEs) of samples collected from the Mojave desert of southern California to compare the microbial community structure of desert varnish with the adjacent desert soil. These analyses indicated prokaryotic and fungal communities in both desert varnish and soil samples. FAMEs specific to gram-positive bacteria were found more often, and in greater abundance in varnish samples than in adjacent soils. This may represent a higher preservation potential of gram-positive bacteria fatty acids in varnish, a source area of varnish microorganisms dominated by gram-positive bacteria, or a varnish community dominated by gram-positive microorganisms. Heterogeneity in fatty acids was documented between varnished rocks and soils from different localities, as well as between samples collected from the same locality. This heterogeneity suggests that there are significant differences in the community structure of the microbial fauna found in varnish samples compared to the adjacent soil, and that desert varnish in the Mojave desert is not characterized by a unique and ubiquitous microbial community. These results suggest that the varnish is not a homogeneous and unique environment for biota, and provide no support for the hypothesis that the varnish layers are biogenic in origin.     

Causes and consequences of pattern diversification in a spatially self-organizing microbial community

Surface-attached microbial communities constitute a vast amount of life on our planet. They contribute to all major biogeochemical cycles, provide essential services to our society and environment, and have important effects on human health and disease. They typically consist of different interacting genotypes that arrange themselves non-randomly across space (referred to hereafter as spatial self-organization). While spatial self-organization is important for the functioning, ecology, and evolution of these communities, the underlying determinants of spatial self-organization remain unclear. Here, we performed a combination of experiments, statistical modeling, and mathematical simulations with a synthetic cross-feeding microbial community consisting of two isogenic strains. We found that two different patterns of spatial self-organization emerged at the same length and time scales, thus demonstrating pattern diversification. This pattern diversification was not caused by initial environmental heterogeneity or by genetic heterogeneity within populations. Instead, it was caused by nongenetic heterogeneity within populations, and we provide evidence that the source of this nongenetic heterogeneity is local differences in the initial spatial positionings of individuals. We further demonstrate that the different patterns exhibit different community-level properties; namely, they have different expansion speeds. Together, our results demonstrate that pattern diversification can emerge in the absence of initial environmental heterogeneity or genetic heterogeneity within populations and can affect community-level properties, thus providing novel insights into the causes and consequences of microbial spatial self-organization.Subject terms: Microbial ecology, Microbial ecology, Biofilms     

Does plant community plasticity mediate microbial homeostasis?

Microbial homeostasis—constant microbial element ratios along resource gradients—is a core ecological tenet, yet not all systems display homeostasis. We suggest investigations of homeostasis mechanisms must also consider plant–microbial interactions. Specifically, we hypothesized that ecosystems with strong plant community plasticity to changing resources will have homeostatic microbial communities, with less microbial resource cost, because plants reduce variance in resource stoichiometry. Using long‐term nutrient additions in two ecosystems with differing plant response, we fail to support our hypothesis because although homeostasis appears stronger in the system with stronger plant response, microbial mechanisms were also stronger. However, our conclusions were undermined by high heterogeneity in resources, which may be common in ecosystem‐level studies, and methodological assumptions may be exacerbated by shifting plant communities. We propose our study as a starting point for further ecosystem‐scale investigations, with higher replication to address microbial and soil variability, and improved insight into microbial assimilable resources.     

Analysis of the microbial community and geochemistry of a sediment core from Great Slave Lake, Canada

Sediment cores taken from Great Slave Lake, Canada, were analysed to investigate their metabolically active microbial populations and geochemistry. The amplification of cDNA detected metabolically active bacterial (50 separate bands) and archaeal (49 separate band) communities. The bacterial communities were further resolved indicating active actinobacterial and γ-proteobacterial communities (36 and 43 individual bands respectively). Redundancy discriminate analysis and Monte Carlo permutation testing demonstrated the significant impact of geochemical parameters on microbial community structures. Geochemical analyses suggest that the upper 0.4 m represents soil weathering and erosion in the lake catchment. An increase in organic carbon in the lower core suggests either more primary productivity, indicating warmer climate conditions, associated with Holocene Climatic Optimum conditions pre 5,000 years BP or change from a reducing environment in the lower core to an oxidizing environment during more recent deposition. Drivers for bacterial, archaeal and actinobacterial community structures were sediment particle size, and its mineral composition. Depth also significantly affected γ- proteobacterial community structure. In contrast the organic carbon content did not significantly shape the microbial community structures within the sediment. This study indicates that geochemical parameters significantly contribute to microbial community structure in these sediments.     

Environmental Heterogeneity, Animal Disturbances, Microsite Characteristics, and Seedling Establishment in a Quercus havardii Community

In restoration experiments it is imperative to consider the study of mechanisms of how species are maintained and preserved in a system. This paper reports on the results of a field experiment examining the growth and survival of seedlings of Schizachyrium scoparium, a dominant perennial bunchgrass member of the Quercus havardii (sand shinnery oak) communities of semiarid western Texas, on mounds of displaced soil produced by Sylvilagus auduboni (rabbit). The central question posed is: does environmental heterogeneity created by small mammals influence seedling survival and growth? The specific questions addressed are: (1) Does seedling survival, growth, and nutrient uptake vary when grown on mounds, off-mound soils, and artificially created mounds?; (2) What is the influence of the microbial and litter components of mound soils on seedling survival?; and (3) In communities where animal disturbances create environmental heterogeneity and may impact seedling establishment, is it possible to artificially create mounds that could serve a similar function? Results show that characteristics of mound soils increase seedling survival, shoot and root biomass, root length, number of tillers, mycorrhizal infection, and nutrient uptake more in plants grown on mounds than off mounds. Both the microbial and litter components of mound soils are essential components of this effect. Artificial mounds generated from soils associated with the herbaceous community were more similar to intact rabbit mounds than artificial mounds generated from soils associated with the oaks. The results indicate that rabbits produce rich patches (both nutrient and microbial) favorable to the growth of seedlings of the dominant bunchgrass, and point to the potential importance of rabbit disturbances in shaping the dynamics of this plant community. Thus, rabbit-generated disturbances produce environmental heterogeneity in the sand shinnery oak community, similar to that produced by harvester ants in this community as shown by an earlier study. Small animal activity that results in soil displacement, and influences soil characteristics, may indirectly contribute to the persistence of certain plant species within a community. Thus, disturbances may well operate in semiarid communities to produce nutrient and microbe rich microsites which may function to maintain diversity.