Reanalysis and simulation suggest a phylogenetic microarray does not accurately profile microbial communities

The second generation (G2) PhyloChip is designed to detect over 8700 bacteria and archaeal and has been used over 50 publications and conference presentations. Many of those publications reveal that the PhyloChip measures of species richness greatly exceed statistical estimates of richness based on other methods. An examination of probes downloaded from Greengenes suggested that the system may have the potential to distort the observed community structure. This may be due to the sharing of probes by taxa; more than 21% of the taxa in that downloaded data have no unique probes. In-silico simulations using these data showed that a population of 64 taxa representing a typical anaerobic subterranean community returned 96 different taxa, including 15 families incorrectly called present and 19 families incorrectly called absent. A study of nasal and oropharyngeal microbial communities by Lemon et al (2010) found some 1325 taxa using the G2 PhyloChip, however, about 950 of these taxa have, in the downloaded data, no unique probes and cannot be definitively called present. Finally, data from Brodie et al (2007), when re-examined, indicate that the abundance of the majority of detected taxa, are highly correlated with one another, suggesting that many probe sets do not act independently. Based on our analyses of downloaded data, we conclude that outputs from the G2 PhyloChip should be treated with some caution, and that the presence of taxa represented solely by non-unique probes be independently verified.     

Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants

Dietary intervention with extensively hydrolyzed casein formula supplemented with Lactobacillus rhamnosus GG (EHCF+LGG) accelerates tolerance acquisition in infants with cow''s milk allergy (CMA). We examined whether this effect is attributable, at least in part, to an influence on the gut microbiota. Fecal samples from healthy controls (n=20) and from CMA infants (n=19) before and after treatment with EHCF with (n=12) and without (n=7) supplementation with LGG were compared by 16S rRNA-based operational taxonomic unit clustering and oligotyping. Differential feature selection and generalized linear model fitting revealed that the CMA infants have a diverse gut microbial community structure dominated by Lachnospiraceae (20.5±9.7%) and Ruminococcaceae (16.2±9.1%). Blautia, Roseburia and Coprococcus were significantly enriched following treatment with EHCF and LGG, but only one genus, Oscillospira, was significantly different between infants that became tolerant and those that remained allergic. However, most tolerant infants showed a significant increase in fecal butyrate levels, and those taxa that were significantly enriched in these samples, Blautia and Roseburia, exhibited specific strain-level demarcations between tolerant and allergic infants. Our data suggest that EHCF+LGG promotes tolerance in infants with CMA, in part, by influencing the strain-level bacterial community structure of the infant gut.     

High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment

There is increasing interest in harnessing the functional capacities of indigenous microbial communities to transform and remediate a wide range of environmental contaminants. Information about which community members respond to stimulation can guide the interpretation and development of remediation approaches. To comprehensively determine community membership and abundance patterns among a suite of samples associated with uranium bioremediation experiments, we employed a high-density microarray (PhyloChip). Samples were unstimulated, naturally reducing, or collected during Fe(III) (early) and sulfate reduction (late biostimulation) from an acetate re-amended/amended aquifer in Rifle, Colorado, and from laboratory experiments using field-collected materials. Deep community sampling with PhyloChip identified hundreds-to-thousands of operational taxonomic units (OTUs) present during amendment, and revealed close similarity among highly enriched taxa from drill core and groundwater well-deployed column sediment. Overall, phylogenetic data suggested that stimulated community membership was most affected by a carryover effect between annual stimulation events. Nevertheless, OTUs within the Fe(III)- and sulfate-reducing lineages, Desulfuromonadales and Desulfobacterales, were repeatedly stimulated. Less consistent, co-enriched taxa represented additional lineages associated with Fe(III) and sulfate reduction (e.g. Desulfovibrionales; Syntrophobacterales; Peptococcaceae) and autotrophic sulfur oxidation (Sulfurovum; Campylobacterales). Data implies complex membership among highly stimulated taxa and, by inference, biogeochemical responses to acetate, a nonfermentable substrate.     

The influence of initial colonization by hydropsychid caddisfly larvae on the development of stream invertebrate assemblages

Many aspects of the colonization history of a disturbed site can influence the development of a biological community. Initial colonization is known to play a significant role in community development because of the facilitative or inhibitory effects that `pioneer' species can have on subsequently arriving taxa. We performed an experiment to assess how initial colonization by two species of benthic invertebrates (Trichoptera: Hydropsychidae) might influence the development of stream faunal assemblages. Substrate baskets initially colonized by either Hydropsyche depravata or Ceratopsyche bronta were placed alongside control baskets in a recently flooded stream. After baskets had colonized for 30 days, we found that species composition in treatment baskets was identical to that in control baskets, indicating that the caddisfly taxa had no selective effects on colonization of other macroinvertebrate species. We did, however, find that C. bronta facilitated the recruitment of all species in the colonist pool leading to greater overall abundance and biomass of macroinvertebrates in the final assemblages. In contrast, H. depravata had no effect on the abundance or biomass of colonizing invertebrates. The differential effects of these two taxa on abundance and biomass may have been related to differences in microhabitat complexity created by the construction of their retreats and catchnets. The results of this study support the growing recognition that colonization history does influence the structure of lotic communities, but they also suggest that even closely related taxa can play different roles as initial colonists in community development.     

Probiotic bacterium prevents cytokine-induced apoptosis in intestinal epithelial cells

Probiotic bacteria are microorganisms that benefit the host by preventing or ameliorating disease. However, little information is known regarding the scientific rationale for using probiotics as alternative medicine. The purpose of this paper is to investigate the mechanisms of probiotic beneficial effects on intestinal cell homeostasis. We now report that one such probiotic, Lactobacillus rhamnosus GG (LGG), prevents cytokine-induced apoptosis in two different intestinal epithelial cell models. Culture of LGG with either mouse or human colon cells activates the anti-apoptotic Akt/protein kinase B. This model probiotic also inhibits activation of the pro-apoptotic p38/mitogen-activated protein kinase by tumor necrosis factor, interleukin-1alpha, or gamma-interferon. Furthermore, products recovered from LGG culture broth supernatant show concentration-dependent activation of Akt and inhibition of cytokine-induced apoptosis. These observations suggest a novel mechanism of communication between probiotic microorganisms and epithelia that increases survival of intestinal cells normally found in an environment of pro-apoptotic cytokines.     

Neonatal small bowel epithelia: enhancing anti-bacterial defense with lactoferrin and Lactobacillus GG

BACKGROUND AND AIMS: Extremely preterm human infants have increased susceptibility to small bowel infection. We hypothesized that early colonization of the immature small intestine with Lactobacillus GG (LGG), and use of a recombinant lactoferrin (rhLF) to promote growth of LGG, would enhance gut defenses against enteroinvasive Escherichia coli. METHODS: Newborn rat pups were treated with nothing, intra-gastric LGG, or rhLF + LGG on days 3 and 4 of life. Gut colonization by LGG was quantified in lavaged jejunal and ileal fluid and gut wall homogenates on day 5 of life. Separate studies used similarly treated litters of newborn rats that were infected late on day 4 of life with E. coli [10(12) CFU/kg]. Sixteen hours later, the numbers of E. coli were measured in small bowel fluid and gut wall homogenates. RESULTS: Control pups initially had lactic acid bacteria colonize the bowel, but these bacteria were not LGG. Pups treated with LGG or rhLF + LGG had significantly higher numbers of LGG in the ileum versus jejunum. Contrary to our hypothesis, rhLF did not augment LGG colonization. After E. coli-related gut infection, planktonic [lavage fluid] and epithelia-adherent growth [gut wall homogenates] of E. coli in the small bowel were most effectively reduced by pre-treatment with rhLF and LGG (P < .05). CONCLUSION: Prophylactic therapy with recombinant human lactoferrin and the probiotic, Lactobacillus GG, act to enhance defenses against invasive E. coli in the nascent small intestine. We suggest that rhLF and LGG are therapeutic agents that may reduce necrotizing enterocolitis and gut-related sepsis in preterm human infants.     

Structure of the human gastric bacterial community in relation to Helicobacter pylori status

The human stomach is naturally colonized by Helicobacter pylori, which, when present, dominates the gastric bacterial community. In this study, we aimed to characterize the structure of the bacterial community in the stomach of patients of differing H. pylori status. We used a high-density 16S rRNA gene microarray (PhyloChip, Affymetrix, Inc.) to hybridize 16S rRNA gene amplicons from gastric biopsy DNA of 10 rural Amerindian patients from Amazonas, Venezuela, and of two immigrants to the United States (from South Asia and Africa, respectively). H. pylori status was determined by PCR amplification of H. pylori glmM from gastric biopsy samples. Of the 12 patients, 8 (6 of the 10 Amerindians and the 2 non-Amerindians) were H. pylori glmM positive. Regardless of H. pylori status, the PhyloChip detected Helicobacteriaceae DNA in all patients, although with lower relative abundance in patients who were glmM negative. The G2-chip taxonomy analysis of PhyloChip data indicated the presence of 44 bacterial phyla (of which 16 are unclassified by the Taxonomic Outline of the Bacteria and Archaea taxonomy) in a highly uneven community dominated by only four phyla: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Positive H. pylori status was associated with increased relative abundance of non-Helicobacter bacteria from the Proteobacteria, Spirochetes and Acidobacteria, and with decreased abundance of Actinobacteria, Bacteroidetes and Firmicutes. The PhyloChip detected richness of low abundance phyla, and showed marked differences in the structure of the gastric bacterial community according to H. pylori status.     

Changes of Soil Bacterial Diversity as a Consequence of Agricultural Land Use in a Semi-Arid Ecosystem

Natural scrublands in semi-arid deserts are increasingly being converted into fields. This results in losses of characteristic flora and fauna, and may also affect microbial diversity. In the present study, the long-term effect (50 years) of such a transition on soil bacterial communities was explored at two sites typical of semi-arid deserts. Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods based on 16S rRNA gene fragments amplified from total community DNA. Denaturing gradient gel electrophoresis (DGGE) analyses revealed significant effects of the transition on community composition of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria at both sites. PhyloChip hybridization analysis uncovered that the transition negatively affected taxa such as Acidobacteria, Chloroflexi, Acidimicrobiales, Rubrobacterales, Deltaproteobacteria and Clostridia, while Alpha-, Beta- and Gammaproteobacteria, Bacteroidetes and Actinobacteria increased in abundance. Redundancy analysis suggested that the community composition of phyla responding to agricultural use (except for Spirochaetes) correlated with soil parameters that were significantly different between the agricultural and scrubland soil. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. The variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses, suggesting reduced beta diversity due to agricultural practices. The long-term use for agriculture resulted in profound changes in the bacterial community and physicochemical characteristics of former scrublands, which may irreversibly affect the natural soil ecosystem.     

Distribution of forest dwelling carabids (Coleoptera): spatial scale and the concept of communities

Associations between spatial distribution of ground-beetles (Carabidae) and environmental variables were studied over three hierarchical scales in deciduous forest in central Alberta, Canada We also examined the relationship between species abundance and distribution on several scales ranging from the local scale of our study to that of the North American temperate deciduous forest Understorey plant cover, tree cover, and occurrence of other carabids were associated with distribution of particular species at the smallest ecological scales within populations However, great differences in population sues of carabid species among five distinct sites several kilometres apart were not correlated with variation in the same environmental variables In central Alberta, abundance and extent of distribution were correlated positively among the 30 carabid species collected, and distributions of the ten species classified as 'core' species were generally aggregated at all spatial scales On the continental scale, there was a significant positive correlation between abundance and distribution for the 114 species of the entire data set, and the six species meeting the criteria of 'core' taxa on this scale, were also 'core' elements in central Alberta Further analysis of covariance of core elements of species assemblages across different taxa provides a sound empirical approach for understanding community organization     

Structure of the Phytoplankton Community and Its Relationship to Water Quality in Donghu Lake, Wuhan, China

The phytoplankton community structure, in terms of species composition, total standing crop,and abundance of the dominant algal species, at four stations in Donghu Lake, Wuhan, China, was investigated monthly from January 1994 to December 1996. A total of 260 taxa was observed, of which Chlorophyta (106 taxa) contributed the highest portion of the total number of taxa, followed by Bacillariophyta (82 taxa)and Cyanophyta (32 taxa). The total standing crop measured by means of chlorophyll a content, cell density,and cell biovolume, as well as the abundance of the dominant species, declined in the order of Station I to Station Ⅳ. Seasonal changes of the standing crop varied greatly among the four stations. Although the cell density at the four stations showed a single peak within a year, the peak density varied from July to November, dependent on the sampling year and the station. For chlorophyll a content and cell biovolume,multiple peaks were observed at Stations Ⅰ and Ⅱ, but a single peak was found at Stations Ⅲ and Ⅳ. The phytoplankton community structure indicated that the trophic status was the highest at Station Ⅰ (most eutrophic), followed by Station Ⅱ; Stations Ⅲ and Ⅳ were the least trophic areas. The long-term changes in phytoplankton community structure further suggested that changes in phytoplankton community structure were correlated with water quality, and eutrophication of Donghu Lake had been aggravated since the 1950s.     

Change in a lake benthic community over a century: evidence for alternative community states

Aquatic communities are one of the most studied systems where alternative states or regime shifts have been detected. We used data spanning a century of time to test whether the zoobenthic community of Lake Mendota, Wisconsin, USA, was relatively stable through time, variable, or whether there was any evidence of alternative community states. We used multivariate statistical analyses to test for community structure similarity and whether detected differences corresponded to major changes in the local environment. Surprisingly, the benthic community in Lake Mendota was not statistically different from the mid 1960s to the present. Similarly, the benthic community was not significantly different from 1914 to the 1950s. However, between the 1950s and mid 1960s there was a dramatic change in the zoobenthic community, including the loss of key taxa and a decrease in the diversity of several major taxa. This dramatic change cannot be attributed to any single environmental factor, and is correlated with multiple factors acting simultaneously, including increased urban development, human population density, intensive agriculture, and the introduction of a major invasive species, Eurasian watermilfoil. The long-term similarity in the benthic community before and after the shift suggests two alternative states that switched with the confluence of multiple stressors.     

PCR Amplification-Independent Methods for Detection of Microbial Communities by the High-Density Microarray PhyloChip

Environmental microbial community analysis typically involves amplification by PCR, despite well-documented biases. We have developed two methods of PCR-independent microbial community analysis using the high-density microarray PhyloChip: direct hybridization of 16S rRNA (dirRNA) or rRNA converted to double-stranded cDNA (dscDNA). We compared dirRNA and dscDNA communities to PCR-amplified DNA communities using a mock community of eight taxa, as well as experiments derived from three environmental sample types: chromium-contaminated aquifer groundwater, tropical forest soil, and secondary sewage in seawater. Community profiles by both direct hybridization methods showed differences that were expected based on accompanying data but that were missing in PCR-amplified communities. Taxon richness decreased in RNA compared to that in DNA communities, suggesting a subset of 20% in soil and 60% in groundwater that is active; secondary sewage showed no difference between active and inactive populations. Direct hybridization of dscDNA and RNA is thus a viable alternative to PCR-amplified microbial community analysis, providing identification of the active populations within microbial communities that attenuate pollutants, drive global biogeochemical cycles, or proliferate disease states.     

Structure of the Phytoplankton Community and Its Relationship to Water Quality in Donghu Lake, Wuhan, China

The phytoplankton community structure, in terms of species composition, total standing crop,and abundance of the dominant algal species, at four stations in Donghu Lake, Wuhan, China, was investigated monthly from January 1994 to December 1996. A total of 260 taxa was observed, of which Chlorophyta (106 taxa) contributed the highest portion of the total number of taxa, followed by Bacillariophyta (82 taxa) and Cyanophyta (32 taxa). The total standing crop measured by means of chlorophyll a content, cell density,and cell biovolume, as well as the abundance of the dominant species, declined in the order of Station I to Station IV. Seasonal changes of the standing crop varied greatly among the four stations. Although the cell density at the four stations showed a single peak within a year, the peak density varied from July to November, dependent on the sampling year and the station. For chlorophyll a content and cell biovolume,multiple peaks were observed at Stations I and II, but a single peak was found at Stations III and IV. The phytoplankton community structure indicated that the trophic status was the highest at Station I (most eutrophic), followed by Station II; Stations III and IV were the least trophic areas. The long-term changes in phytoplankton community structure further suggested that changes in phytoplankton community structure were correlated with water quality, and eutrophication of Donghu Lake had been aggravated since the 1950s.     

Environmental filtering affects soil fungal community composition more than dispersal limitation at regional scales

The relative importance of dispersal limitation versus environmental filtering for community assembly has received much attention for macroorganisms. These processes have only recently been examined in microbial communities. Instead, microbial dispersal has mostly been measured as community composition change over space (i.e., distance decay). Here we directly examined fungal composition in airborne wind currents and soil fungal communities across a 40 000 km² regional landscape to determine if dispersal limitation or abiotic factors were structuring soil fungal communities. Over this landscape, neither airborne nor soil fungal communities exhibited compositional differences due to geographic distance. Airborne fungal communities shifted temporally while soil fungal communities were correlated with abiotic parameters. These patterns suggest that environmental filtering may have the largest influence on fungal regional community assembly in soils, especially for aerially dispersed fungal taxa. Furthermore, we found evidence that dispersal of fungal spores differs between fungal taxa and can be both a stochastic and deterministic process. The spatial range of soil fungal taxa was correlated with their average regional abundance across all sites, which may imply stochastic dispersal mechanisms. Nevertheless, spore volume was also negatively correlated with spatial range for some species. Smaller volume spores may be adapted to long-range dispersal, or establishment, suggesting that deterministic fungal traits may also influence fungal distributions. Fungal life-history traits may influence their distributions as well. Hypogeous fungal taxa exhibited high local abundance, but small spatial ranges, while epigeous fungal taxa had lower local abundance, but larger spatial ranges. This study is the first, to our knowledge, to directly sample air dispersal and soil fungal communities simultaneously across a regional landscape. We provide some of the first evidence that soil fungal communities are mostly assembled through environmental filtering and experience little dispersal limitation.     

PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa

The phylogenetic composition of bacterial communities in the rhizosphere of three potato cultivars grown at two distant field sites was analysed. Ribosomal gene fragments amplified from total community DNA were hybridized to PhyloChips. A total of 2432 operational taxonomic units (OTUs) were detected by the PhyloChips, of which 65% were found in the rhizosphere of all cultivars at both field sites. From all detected OTUs, 9% revealed a cultivar-dependent abundance at the one or the other field site and 4% at both sites. Differential abundance on the three cultivars was mainly observed for OTUs belonging to the Pseudomonadales, Actinomycetales and Enterobacteriales. More than 40% of OTUs belonging to Bradyrhizobiales, Sphingomonadales, Burkholderiales, Rhodocyclales, Xanthomonadales and Actinomycetales differed significantly in their abundance between the sites. A sequence analysis of six 16S rRNA gene clone libraries corresponded well with the taxonomic community structure evidenced by the PhyloChip hybridization. Most ribotypes matched OTUs detected by the PhyloChip. Those OTUs that responded to the potato cultivar at both field sites might be of interest in view of cultivar-specific effects on bacterial biocontrol strains and pathogens.     

Initial butyrate producers during infant gut microbiota development are endospore formers

The acquisition of the infant gut microbiota is key to establishing a host-microbiota symbiosis. Microbially produced metabolites tightly interact with the immune system, and the fermentation-derived short-chain fatty acid butyrate is considered an important mediator linked to chronic diseases later in life. The intestinal butyrate-forming bacterial population is taxonomically and functionally diverse and includes endospore formers with high transmission potential. Succession, and contribution of butyrate-producing taxa during infant gut microbiota development have been little investigated. We determined the abundance of major butyrate-forming groups and fermentation metabolites in faeces, isolated, cultivated and characterized the heat-resistant cell population, which included endospores, and compared butyrate formation efficiency of representative taxa in batch cultures. The endospore community contributed about 0.001% to total cells, and was mainly composed of the pioneer butyrate-producing Clostridium sensu stricto. We observed an increase in abundance of Faecalibacterium prausnitzii, butyrate-producing Lachnospiraceae and faecal butyrate levels with age that is likely explained by higher butyrate production capacity of contributing taxa compared with Clostridium sensu stricto. Our data suggest that a successional arrangement and an overall increase in abundance of butyrate forming populations occur during the first year of life, which is associated with an increase of intestinal butyrate formation capacity.     

Soil bacterial communities of a calcium-supplemented and a reference watershed at the Hubbard Brook Experimental Forest (HBEF), New Hampshire, USA

Soil Ca depletion because of acidic deposition-related soil chemistry changes has led to the decline of forest productivity and carbon sequestration in the northeastern USA. In 1999, acidic watershed (WS) 1 at the Hubbard Brook Experimental Forest (HBEF), NH, USA was amended with Ca silicate to restore soil Ca pools. In 2006, soil samples were collected from the Ca-amended (WS1) and reference watershed (WS3) for comparison of bacterial community composition between the two watersheds. The sites were about 125?m apart and were known to have similar stream chemistry and tree populations before Ca amendment. Ca-amended soil had higher Ca and P, and lower Al and acidity as compared with the reference soils. Analysis of bacterial populations by PhyloChip revealed that the bacterial community structure in the Ca-amended and the reference soils was significantly different and that the differences were more pronounced in the mineral soils. Overall, the relative abundance of 300 taxa was significantly affected. Numbers of detectable taxa in families such as Acidobacteriaceae, Comamonadaceae, and Pseudomonadaceae were lower in the Ca-amended soils, while Flavobacteriaceae and Geobacteraceae were higher. The other functionally important groups, e.g. ammonia-oxidizing Nitrosomonadaceae, had lower numbers of taxa in the Ca-amended organic soil but higher in the mineral soil.     

Integrated Microbial Survey Analysis of Prokaryotic Communities for the PhyloChip Microarray

PhyloTrac is an integrated desktop application for analysis of PhyloChip microarray data. PhyloTrac combined with PhyloChip provides turnkey and comprehensive identification and analysis of bacterial and archaeal communities in complex environmental samples. PhyloTrac is free for noncommercial organizations and is available for all major operating systems at http://www.phylotrac.org/.The PhyloChip is a low-cost Affymetrix GeneChip microarray, developed at Lawrence Berkeley National Laboratory (LBNL), designed to detect and quantify abundance of bacterial and archaeal taxa using signature probes targeting all known 16S rRNA gene sequences. The second generation of the PhyloChip microarray targets nearly 9,000 operational taxonomic units (OTUs), with an average of 24 probes, each 25 bp long, and the upcoming third-generation PhyloChip application will target an even larger number of OTUs. Multiple, complex environments have been successfully analyzed using the PhyloChip microarray, including, among others, air (2), soil (1), the human lung (6), and the gut (9). PhyloChip microarrays are manufactured by Affymetrix, but to date, analysis has been available only from within LBNL, limiting the accessibility of the technology. PhyloTrac addresses this limitation by providing a standardized analysis package for the PhyloChip microarray, including microarray normalization, OTU quantification, multiple interactive visualizations, and integrated analytics.     

Community Structure Dynamics of the Hermatypic Corals on Luhuitou Fringing Reef,Hainan,China.I.Species Composition and Abundance

1IntroductionStudyoncoralcommunitysuccession,especiallytherecoveryofdisturbedcoralcommu-nities,hasreceivedagreatdealoftheoreticalandempiricalattentioninthelasttwodecades(e.g.Connell1978;Grigg1983;Fitzhardinge1985;Hughes1985,1989;HughesandJackson1985;Sammarco1985;Wallace1985a,b;Colgan1987;Doneetal.1988,1991;Phongsuwan1991,etc).However,moststudiesofhermatypiccoralsuccessionhavebeenconcentratedononlyaportionofacommunityandcoveredamuchshortertimeperiodcom-paredwiththetimetakenforacoralcommunit…     

Direct and indirect effects of masting on rodent populations and tree seed survival

Many plant species are thought to benefit from mast seeding as a result of increased seed survival through predator satiation. However, in communities with many different masting species, lack of synchrony in seed production among species may decrease seed survival by maintaining seed predator populations through the intermast cycle. Similarly, masting by different plant species may have different effects on the seed predator community. We conducted a three-year study in a northeastern USA temperate deciduous forest to determine if production of large seed crops by several tree species was synchronous, and if they had similar effects on all small mammal species. We found that red oak mast crops resulted in increased densities of Peromyscus leucopus and P. maniculatus , but had no effect on Clethrionomys gapperi abundance. Conversely, C. gapperi populations, but not Peromyscus populations, appeared to increase in response to a large red maple seed crop. Differences in small mammal abundance resulted in changes in species-specific seed survival: in the year of abundant C. gapperi , experimentally placed red oak acorns had significantly higher survival than in the year of high Peromyscus abundance. Red oak acorn removal was positively correlated with Peromyscus abundance, while red maple seed removal was significantly higher with increased C. gapperi abundance. Thus, species-specific seed production had differential effects on subsequent small mammal abundance, which in turn affected seed survival. We suggest that at the level of the community, even short-term lack of synchrony in production of large seed crops can cause variation in postdispersal seed survival, through differential effects on the community of small mammal seed predators.