The chosen few—variations in common and rare soil bacteria across biomes

Soil bacterial communities are dominated by a few abundant species, while their richness is associated with rare species with largely unknown ecological roles and biogeography. Analyses of previously published soil bacterial community data using a novel classification of common and rare bacteria indicate that only 0.4% of bacterial species can be considered common and are prevalent across biomes. The remaining bacterial species designated as rare are endemic with low relative abundances. Observations coupled with mechanistic models highlight the central role of soil wetness in shaping bacterial rarity. An individual-based model reveals systematic shifts in community composition induced by low carbon inputs in drier soils that deprive common species of exhibiting physiological advantages relative to other species. We find that only a “chosen few” common species shape bacterial communities across biomes; however, their contributions are curtailed in resource-limited environments where a larger number of rare species constitutes the soil microbiome.Subject terms: Biodiversity, Microbial ecology, Microbial ecology, Soil microbiology     

Frequent and occasional species and the shape of relative-abundance distributions

Recently, three different models have been proposed to explain the distribution of abundances in natural communities: the self‐similarity model; the zero‐sum ecological drift model; and the occasional–frequent species model of Magurran and Henderson. Here we study patterns of relative abundance in a large community of forest Hymenoptera and show that it is indeed possible to divide the community into a group of frequent species and a group of occasional species. In accordance with the third model, frequent species followed a lognormal distribution. Relative abundances of the occasional species could be described by the self‐similarity model, but did not follow a log‐series as proposed by the occasional–frequent model. The zero‐sum ecological drift model makes no explicit predictions about frequent and occasional species but the abundance distributions of the hymenopteran species did not show the excess of rare species predicted by this model. Separate fits of this model to the frequent and to the occasional species were worse than the respective fits of the lognormal and the self‐similarity model.     

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is now possible to follow the relative abundance of microbes in a community over time. These microbial communities exhibit rich ecological dynamics and an important goal of microbial ecology is to infer the ecological interactions between species directly from sequence data. Any algorithm for inferring ecological interactions must overcome three major obstacles: 1) a correlation between the abundances of two species does not imply that those species are interacting, 2) the sum constraint on the relative abundances obtained from metagenomic studies makes it difficult to infer the parameters in timeseries models, and 3) errors due to experimental uncertainty, or mis-assignment of sequencing reads into operational taxonomic units, bias inferences of species interactions due to a statistical problem called “errors-in-variables”. Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS), that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. We tested LIMITS on synthetic data and showed that it could reliably infer the topology of the inter-species ecological interactions. We then used LIMITS to characterize the species interactions in the gut microbiomes of two individuals and found that the interaction networks varied significantly between individuals. Furthermore, we found that the interaction networks of the two individuals are dominated by distinct “keystone species”, Bacteroides fragilis and Bacteroided stercosis, that have a disproportionate influence on the structure of the gut microbiome even though they are only found in moderate abundance. Based on our results, we hypothesize that the abundances of certain keystone species may be responsible for individuality in the human gut microbiome.     

营养盐加富和鱼类添加对浮游植物群落演替和多样性的影响

浮游植物是水体生态系统敞水区最重要的初级生产者,其组成与多样性反映了群落的结构类型和存在状态。通过围隔实验,模拟水库春季发生的营养盐加富和鱼类放养的干扰,分析在这两种干扰下的浮游植物群落演替过程中优势种和稀有种的变化,并通过以丰度与生物量为变量的香农和辛普森多样性指数的计算,分析浮游植物群落演替过程中的多样性变化特征。结果表明,营养盐加富干扰下的浮游植物群落的优势种变化和演替更为明显,营养盐加富与鱼类添加对浮游植物群落多样性变化的影响符合中度干扰理论。在优势种优势度变化较大的浮游植物群落演替过程中,多样性指数与浮游植物生物量有较高的负相关性。在浮游植物群落演替过程中,香农和辛普森多样性指数的变化趋势基本一致,采用丰度与生物量为变量的两种多样性指数的计算结果对实验系统中浮游植物群落多样性的分析结果没有明显的影响。     

Direct evidence that density-dependent regulation underpins the temporal stability of abundant species in a diverse animal community

To understand how ecosystems are structured and stabilized, and to identify when communities are at risk of damage or collapse, we need to know how the abundances of the taxa in the entire assemblage vary over ecologically meaningful timescales. Here, we present an analysis of species temporal variability within a single large vertebrate community. Using an exceptionally complete 33-year monthly time series following the dynamics of 81 species of fishes, we show that the most abundant species are least variable in terms of temporal biomass, because they are under density-dependent (negative feedback) regulation. At the other extreme, a relatively large number of low abundance transient species exhibit the greatest population variability. The high stability of the consistently common high abundance species—a result of density-dependence—is reflected in the observation that they consistently represent over 98% of total fish biomass. This leads to steady ecosystem nutrient and energy flux irrespective of the changes in species number and abundance among the large number of low abundance transient species. While the density-dependence of the core species ensures stability under the existing environmental regime, the pool of transient species may support long-term stability by replacing core species should environmental conditions change.     

Species abundance models and patterns in dragonfly communities: effects of fish predators

We investigated if dragonfly larvae community composition and species abundance curves are sensitive to variation in predation intensity, and whether the fit to a particular niche partitioning model could be used to make inferences about mechanisms structuring communities. The approach taken was to compare communities in lakes either having or lacking fish predation. Dragonfly species classified as active, strongly dominated the dragonfly communities in fishless lakes, and low active species dominated fishless lakes. As activity level is known to correlate with susceptibility to fish predation this indicates that these communities are structured by fish predation. Fitting relative abundance data to five niche partitioning models showed that the same model fitted data from both types of habitats (fish/no fish). This means that the observed differences in relative abundances were substitutive, i.e. the relative abundance of a rank stayed constant, even though the identity of the species having this rank changed. The best fit to data from both types of lakes was found for the random assortment model, which is usually interpreted as an indication that the community is not structured by within-guild interactions. This interpretation for fishless lakes did not seem to agree with other community measures (i.e. lowered diversity and evenness and no relationship between species richness and dragonfly biomass), which indicate that the community is structured by within-guild interactions. Moreover, a detail in the fitting procedure, the number of species included in the analysis, affected which model that fitted data best. Thus, we question if fitting niche partitioning models to data can provide mechanistic understanding of how resources are partitioned in natural communities.     

Dynamics of core and occasional species in the marine plankton: tintinnid ciliates in the north-west Mediterranean Sea

Aim To assess short‐term variability in the community composition and community structure of tintinnid ciliates, herbivores of the microzooplankton. Location North‐west Mediterranean Sea. Methods We sampled on 18 dates over a 4‐week period in 2004 at an open‐water site. Species were classified as ‘core species’, found on every date, or ‘occasional species’, absent on one or more dates. Species abundance distributions of the entire community, and separately the core and occasional species, were compared with geometric, log‐series and log‐normal distributions. Core and occasional species were compared in terms of the shell or lorica oral diameter (LOD), analogous to gape size. Results We found 11 core and 49 occasional species. Diversity metrics were stable compared with shifts in abundances. Core species accounted for the majority of individuals in all samples. On each date, 9–22 occasional species, representing 10–15% of the population, were found. Species richness of the occasionals was positively related to population size. The identities of the occasional species found were unrelated to the time between sampling. The species abundance distribution of the occasional population was best fit by a log‐series distribution, while that of the core species was best fit by a log‐normal distribution. The species abundance distribution of the entire community was best fit by a log‐series distribution. Most of the occasional species had LODs distinct from that of a core species and occupied size classes left empty by the core population. However, the most abundant and frequent of the occasional species had a LOD similar to that of a core species. Main conclusions Among tintinnids, which are planktonic protists, occasional species have a species abundance distribution pattern distinct from that of core species. Occasional species appeared to be composed of two groups, one of relatively abundant species and similar to core species, and a second group of ephemeral species with morphologies distinct from core species. The existence of two categories of occasional or rare species may be common: (1) those similar to, and thus perhaps able to replace, dominant species in the absence of a change in the environment; and (2) those distinct from dominant species and requiring different conditions to prosper.     

Core and occasional species: A new way forward

1. Various methods have been used to divide communities into core species and occasional or satellite species. Some methods are somewhat arbitrary, and there is evidence that many communities are more multimodal than bimodal. They also tend to rely on having multiple years of data.
2. A completely novel method is presented that not only has no requirement for long‐term datasets but can divide communities into multiple groups. It is based on probability a species is present, calculated using Simpson''s index and the sequential removal of species from the data.
3. The sequential Simpson''s index method was applied to species data from a grassland insect community. It was also applied to eleven other datasets that had been divided into core and occasional species in previously published studies.
4. The new method was found not only to be consistent with previous core–occasional assessments but also able to identify multimodality in species abundance distributions.
5. Although ideally used with a measure of persistence (frequency of occurrence) to rank species, community structure is consistently described even with only species abundance data.
6. The method can be applied to short or long‐term datasets and can help identify multimodality and provide valuable insight into how communities change in time or space.

     

Effects of different fish species and biomass on plankton interactions in a shallow lake

Thirty-six enclosures, surface area 4 m², were placed in Little Mere, a shallow fertile lake in Cheshire, U.K. The effects of different fish species (common carp, common bream, tench and roach) of zooplanktivorous size, and their biomass (0, 200 and 700 kg ha^–1) on water chemistry, zooplankton and phytoplankton communities were investigated. Fish biomass had a strong effect on mean zooplankton size and abundance. When fish biomass rose, larger zooplankters were replaced by more numerous smaller zooplankters. Consequently phytoplankton abundance rose in the presence of higher densities of zooplanktivorous fish, as zooplankton grazing was reduced. Fish species were also significant in determining zooplankton community size structure. In enclosures with bream there were significantly greater densities of small zooplankters than in enclosures stocked with either carp, tench and, in part, roach. When carp or roach were present, the phytoplankton had a greater abundance of Cyanophyta than when bream or tench were present. Whilst top-down effects of fish predation controlled the size partitioning of the zooplankton community, this, in turn apparently controlled the bottom-up regeneration of nutrients for the phytoplankton community. At the zooplankton–phytoplankton interface, both top-down and bottom-up processes were entwined in a reciprocal feedback mechanism with the extent and direction of that relationship altered by changes in fish species. This has consequences for the way that top-down and bottom-up processes are generalised.     

Contemporary Land Change Alters Fish Communities in a San Francisco Bay Watershed,California, U.S.A.

Urbanization is one of the leading threats to freshwater biodiversity, and urban regions continue to expand globally. Here we examined the relationship between recent urbanization and shifts in stream fish communities. We sampled fishes at 32 sites in the Alameda Creek Watershed, near San Francisco, California, in 1993–1994 and again in 2009, and we quantified univariate and multivariate changes in fish communities between the sampling periods. Sampling sites were classified into those downstream of a rapidly urbanizing area (“urbanized sites”), and those found in less impacted areas (“low-impacted sites”). We calculated the change from non-urban to urban land cover between 1993 and 2009 at two scales for each site (the total watershed and a 3km buffer zone immediately upstream of each site). Neither the mean relative abundance of native fish nor nonnative species richness changed significantly between the survey periods. However, we observed significant changes in fish community composition (as measured by Bray-Curtis dissimilarity) and a decrease in native species richness between the sampling periods at urbanized sites, but not at low-impacted sites. Moreover, the relative abundance of one native cyprinid (Lavinia symmetricus) decreased at the urbanized sites but not at low-impacted sites. Increased urbanization was associated with changes in the fish community, and this relationship was strongest at the smaller (3km buffer) scale. Our results suggest that ongoing land change alters fish communities and that contemporary resurveys are an important tool for examining how freshwater taxa are responding to recent environmental change.     

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

The abundance of different SSU rRNA (“16S”) gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly – from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data.     

Does niche overlap control relative abundance in French lacustrine fish communities? A new method incorporating functional traits

1. The mechanisms that structure biological communities hold the key to understanding ecosystem functioning and the maintenance of biodiversity. Patterns of species abundances have been proposed as a means of differentiation between niche-based and neutral processes, but abundance information alone cannot provide unequivocal discrimination. 2. We combined species niche information and species' relative abundances to test the effects of two opposing structuring mechanisms (environmental filtering and niche complementarity) on species' relative abundances in French lacustrine fish communities. The test involved a novel method comparing the abundance-weighted niche overlap within communities against that expected when relative abundances were randomized among species within the community. 3. Observed overlap was consistently significantly lower than expected at random for two (swimming ability and trophic status) of four primary niche axes across lakes of differing physical environments. Thus, for these niche axes, pairs of abundant species tended to have relatively low niche overlap, while rare species tended to have relatively high niche overlap with abundant species. 4. This suggests that niche complementarity may have acted to enhance ecosystem function and that it is important for species coexistence in these fish communities. The method used may be easily applied to any sort of biological community and thus may have considerable potential for determining the generality of niche complementarity effects on community structure.     

Differences in root architecture influence attraction of fishes to mangroves: A field experiment mimicking roots of different length, orientation, and complexity

Benthic structure plays an important role as shelter and feeding habitat for demersal fauna. While many studies have investigated the relationship between structural complexity of aquatic vegetation and the number of species or abundance of motile organisms, little is known of the attractiveness of submerged mangrove roots. We tested the importance of various root attributes in attracting fish species in a field experiment using different artificial mangrove units (AMUs) with PVC pipes mimicking roots to exclude interaction with other environmental and biotic factors. We manipulated length, vertical orientation, and three-dimensional structural complexity of root mimics in the AMUs to explore their effects on the fish community variables: fish abundance, number of species and community composition. Pipe length and three-dimensional structure did not have an effect on fish community variables. Vertical pipe orientation had a significant effect and AMUs with standing pipes showed higher total fish abundances and number of species than AMUs with hanging pipes. Also community composition differed greatly between AMUs with standing versus hanging pipes. At species level, demersal fish species mainly occupied AMUs with standing pipes and occurred only at very low abundances when hanging pipes dominated in the AMUs; in contrast, the semi-pelagic swimmer Sphyraena barracuda showed a trend of higher abundance in AMUs with mainly hanging pipes. When analyzed across all AMUs, fish abundances of demersal as well as semi-pelagic species decreased significantly with increasing interspatial pipe distance among AMUs, suggesting that distance to refuge may be the underlying mechanism for the observed patterns. The above findings are important in the context of the worldwide degradation of mangroves, because human alteration to mangrove vegetation affects its structure and thus composition and size of fish communities.     

The impact of planktivorous flsh on the structure of a plankton community

SUMMARY. 1. The abundance of pianktivorous juvenile yellow perch, Perca flavescens , was manipulated in three 750 m³ enclosures in a eutrophic lake.
2. There was a significant negative relationship between fish and zoopiankton biomasses. At high fish densities the zooplankton community was dominated by small filter-feeding cladocera. primarily bosmi- nids. At low fish densities the zooplankton community was dominated by large filter-feeding cladocera, primarily daphnids.
3. There was no significant relationship between zooplankton and phytoplankton biomasses when considered over the whole experiment but there was a trend towards lower phytoplankton biomass in the enclosure dominated by daphnids during mid-summer.
4. We conclude that although planktivorous fish have a strong negative impact on zooplankton community biomass and size structure, the relationship at the next lower trophic level, zooplankton and phytoplankton, is much weaker. Therefore, the biomanipulation of planktivorous fish populations as a management technique to control phytoplankton abundance is largely ineffective.     

Population and community responses of phytoplankton to fluctuating light

Light is a major resource in aquatic ecosystems and has a complex pattern of spatio-temporal variability, yet the effects of dynamic light regimes on communities of phytoplankton are largely unexplored. I examined whether and how fluctuating light supply affects the structure and dynamics of phytoplankton communities. The effect of light fluctuations was tested at two average irradiances: low, 25 μmol quanta m⁻² s⁻¹ and high, 100 μmol quanta m⁻² s⁻¹ in 2- and 18-species communities of freshwater phytoplankton. Species diversity, and abundances of individual species and higher taxa, depended significantly on both the absolute level and the degree of variability in light supply, while total density, total biomass, and species richness responded only to light level. In the two-species assemblage, fluctuations increased diversity at both low and high average irradiances and in the multispecies community fluctuations increased diversity at high irradiance but decreased diversity at low average irradiance. Species richness was higher under low average irradiance and was not affected by the presence or absence of fluctuations. Diatom abundance was increased by fluctuations, especially at low average irradiance, where they became the dominant group, while cyanobacteria and green algae dominated low constant light and all high light treatments. Within each taxonomic group, however, there was no uniform pattern in species responses to light fluctuations: both the magnitude and direction of response were species-specific. The temporal regime of light supply had a significant effect on the growth rates of individual species grown in monocultures. Species responses to the regime of light supply in monocultures qualitatively agreed with their abundances in the community experiments. The results indicate that the temporal regime of light supply may influence structure of phytoplankton communities by differentially affecting growth rates and mediating species competition. Received: 24 September 1997 / Accepted: 8 July 1998     

AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities

High throughput sequencing (HTSeq) of small ribosomal subunit amplicons has the potential for a comprehensive characterization of microbial community compositions, down to rare species. However, the error-prone nature of the multi-step experimental process requires that the resulting raw sequences are subjected to quality control procedures. These procedures often involve an abundance cutoff for rare sequences or clustering of sequences, both of which limit genetic resolution. Here we propose a simple experimental protocol that retains the high genetic resolution granted by HTSeq methods while effectively removing many low abundance sequences that are likely due to PCR and sequencing errors. According to this protocol, we split samples and submit both halves to independent PCR and sequencing runs. The resulting sequence data is graphically and quantitatively characterized by the discordance between the two experimental branches, allowing for a quick identification of problematic samples. Further, we discard sequences that are not found in both branches (“AmpliconDuo filter”). We show that the majority of sequences removed in this way, mostly low abundance but also some higher abundance sequences, show features expected from random modifications of true sequences as introduced by PCR and sequencing errors. On the other hand, the filter retains many low abundance sequences observed in both branches and thus provides a more reliable census of the rare biosphere. We find that the AmpliconDuo filter increases biological resolution as it increases apparent community similarity between biologically similar communities, while it does not affect apparent community similarities between biologically dissimilar communities. The filter does not distort overall apparent community compositions. Finally, we quantitatively explain the effect of the AmpliconDuo filter by a simple mathematical model.     

初秋南沙群岛海域网采浮游植物群落特征及其与环境因子的关系

根据2011年8-9月南沙群岛海域的生物和环境调查资料,对网采浮游植物的群落特征及其与环境因子的关系进行分析.结果表明: 在鉴定的3门34属113种网采浮游植物中,甲藻门和硅藻门种类各占57.5%和40.7%,其中硅藻门的角藻属种类最多,占30.1%.网采浮游植物平均丰度为2.12×10⁴ cell·m^-3,丰度高值区出现在北部礼乐滩多涡区域和南部万安气旋涡附近海域.蓝藻门束毛藻属是网采浮游植物的主要功能群,占海域平均丰度的77.0%.主要优势种为铁氏束毛藻、红海束毛藻和夜光梨甲藻.优势种(类)存在较明显的空间差异,蓝藻门在S₃、S₅、S₆和S₁₀~S₁₄站占优势;甲藻门在中部S₄、S₇~S₉站占优势,硅藻门在南部S₁和S₂站占优势.网采浮游植物多样性和均匀度指数分别为3.10和0.62.影响浮游植物群落特征的重要环境因子有盐度、水温、铵氮、亚硝酸盐、磷酸盐和硅酸盐,以及南沙中尺度气旋涡和南沙西部沿岸流.典范对应分析排序图较好地显示了浮游植物和环境因子之间的关系.     

Acidity status and phytoplankton species richness,standing crop,and community composition in Adirondack,New York,U.S.A. lakes

The mid-summer phytoplankton communities of more than 100 Adirondack lakes ranging in pH from 4.0 to 7.2 were characterized in relation to 25 physical-chemical parameters. Phytoplankton species richness declined significantly with increasing acidity. Acidic lakes (pH < 5.0) averaged fewer than 20 species while more circumneutral waters (pH > 6.5) averaged more than 33 species. Phytoplankton abundance was not significantly correlated with any of the measured physical-chemical parameters, but standing crop parameters, i.e., chlorophyll a and phytoplankton biovolume, did correlate significantly with several parameters. Midsummer standing crop correlated best with total phosphorus concentration but acidity status affected the standing crop-phosphorus relationship. Circumneutral waters of low phosphorus content, i.e. < 10 µg·1^–1 TP, averaged 3.62 µg·1^–1 chlorophyll a whereas acidic lakes of the same phosphorus content averaged only 1.96 µg·1^–1 chlorophyll a. The midsummer chlorophyll content of lakes of high phosphorus content, i.e. > 10 µg·1^–1 TP, was not significantly affected by acidity status.Adirondack phytoplankton community composition changes with increasing acidity. The numbers of species in midsummer collections within all major taxonomic groups of algae are reduced with increasing acidity. The midsummer phytoplankton communities of acidic Adirondack lakes can generally be characterized into four broad types; 1) the depauperate clear water acid lake assemblage dominated by dinoflagellates, 2) the more diverse oligotrophic acid lake community dominated by cryptomonads, green algae, and chrysophytes, 3) the productive acid lake assemblage dominated by green algae, and 4) the chrysophyte dominated community. The major phytoplankton community types of acid lakes are associated with different levels of nutrients, aluminum concentrations, and humic influences.     

Effect of young-of-the-year walleye (Percidae: Stizostedion vitreum) on plankton dynamics and water quality in ponds

To understand the impact of young-of-the-year (YOY) fish on food web dynamics and water quality, we stocked larval walleye (9 mm TL) (Stizostedion vitreum) in six experimental ponds using two fish densities (10 and 50 fish m^–3) with three replicates. At high fish density, the average abundances of cladocerans and copepods and the Secchi depth were lower whereas abundances of rotifers and algae, gross primary productivity (GPP), pH and total phosphorus concentration were higher than at low fish density. Fish impact on bacterial abundance, dissolved oxygen, nitrogen and phosphorus concentrations, however, was not significant. The within treatment measurements of all variables except GPP were significantly different over time. Our results indicate that YOY walleye predation at high density can affect plankton community by reducing large zooplankton biomass and water clarity, and increasing phytoplankton abundance. The impact of YOY piscivorous fish on plankton should be considered when biomanipulation is applied for improvement of water quality.     

Conversion of sagebrush shrublands to exotic annual grasslands negatively impacts small mammal communities

Aim The exotic annual cheatgrass (Bromus tectorum) is fast replacing sagebrush (Artemisia tridentata) communities throughout the Great Basin Desert and nearby regions in the Western United States, impacting native plant communities and altering fire regimes, which contributes to the long‐term persistence of this weedy species. The effect of this conversion on native faunal communities remains largely unexamined. We assess the impact of conversion from native perennial to exotic annual plant communities on desert rodent communities. Location Wyoming big sagebrush shrublands and nearby sites previously converted to cheatgrass‐dominated annual grasslands in the Great Basin Desert, Utah, USA. Methods At two sites in Tooele County, Utah, USA, we investigated with Sherman live trapping whether intact sagebrush vegetation and nearby converted Bromus tectorum‐dominated vegetation differed in rodent abundance, diversity and community composition. Results Rodent abundance and species richness were considerably greater in sagebrush plots than in cheatgrass‐dominated plots. Nine species were captured in sagebrush plots; five of these were also trapped in cheatgrass plots, all at lower abundances than in the sagebrush. In contrast, cheatgrass‐dominated plots had no species that were not found in sagebrush. In addition, the site that had been converted to cheatgrass longer had lower abundances of rodents than the site more recently converted to cheatgrass‐dominated plots. Despite large differences in abundances and species richness, Simpson’s D diversity and Shannon‐Wiener diversity and Brillouin evenness indices did not differ between sagebrush and cheatgrass‐dominated plots. Main conclusions This survey of rodent communities in native sagebrush and in converted cheatgrass‐dominated vegetation suggests that the abundances and community composition of rodents may be shifting, potentially at the larger spatial scale of the entire Great Basin, where cheatgrass continues to invade and dominate more landscape at a rapid rate.