Actinobacterial community dynamics in long term managed grasslands

Palace Leas, a long-term experiment at Cockle Park Farm, Northumberland, UK was established in winter 1896–1897 since when the 13 plots have received regular and virtually unchanged mineral fertiliser and farm yard manure inputs. Fertilisers have had a profound impact on soil pH with the organically fertilised plots showing a significantly higher pH than those receiving mineral fertiliser where ammonium sulphate has led to soil acidification. Here, we investigate the impact of organic and mineral fertilisers on the actinobacterial community structure of these soils using terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene analysis. To differentiate fertiliser effects from seasonal variation, soils were sampled three times over one growing season between May and September 2004 and January 2005. Community profiles obtained using T-RFLP were analysed using multivariate statistics to investigate the relationship between community structure, seasonality and fertiliser management. Soil pH was shown to be the most significant edaphic factor influencing actinobacterial communities. Canonical correspondence analysis, used to investigate the relationship between the 16S rRNA gene community profiles and the environmental parameters, showed that actinobacterial communities also responded to soil water content with major changes evident over the summer months between May and September. Quantitative PCR of the actinobacterial and fungal 16S and 18S rRNA genes, respectively suggested that fungal rRNA gene copy numbers were negatively correlated (P = 0.0131) with increasing actinobacterial signals. A similar relationship (P = 0.000365) was also evident when fatty acid methyl esters indicative of actinobacterial biomass (10-methyloctadecanoic acid) were compared with the amounts of fungal octadecadienoic acid (18:2ω9,12). These results show clearly that soil pH is a major driver of change in actinobacterial communities and that genera such as Arthrobacter and Micrococcus are particularly abundant in soils receiving organic inputs whilst others such as Streptomyces, Acidimicrobium and Actinospica are more prevalent in acid soils. The importance of these findings in terms of fungal abundance and potential disease suppression are discussed.     

Dispersal limitation and the assembly of soil Actinobacteria communities in a long-term chronosequence

It is uncertain whether the same ecological forces that structure plant and animal communities also shape microbial communities, especially those residing in soil. We sought to uncover the relative importance of present-day environmental characteristics, climatic variation, and historical contingencies in shaping soil actinobacterial communities in a long-term chronosequence. Actinobacteria communities were characterized in surface soil samples from four replicate forest stands with nearly identical edaphic and ecological properties, which range from 9500 to 14,000 years following glacial retreat in Michigan. Terminal restriction fragment length polymorphism (TRFLP) profiles and clone libraries of the actinobacterial 16S rRNA gene were constructed in each site for phenetic and phylogenetic analysis to determine whether dispersal limitation occurred following glacial retreat, or if community composition was determined by environmental heterogeneity. At every level of examination, actinobacterial community composition most closely correlated with distance, a surrogate for time, than with biogeochemical, plant community, or climatic characteristics. Despite correlation with leaf litter C:N and annual temperature, the significant and consistent relationship of biological communities with time since glacial retreat provides evidence that dispersal limitation is an ecological force structuring actinobacterial communities in soil over long periods of time.     

Actinobacterial Community Structure in Soils Receiving Long-Term Organic and Inorganic Amendments

The impact of long-term organic and inorganic amendments on the actinobacterial community in soils was studied. Denaturing gradient gel electrophoresis patterns based on the V3 region of 16S rRNA suggested that there was no significant difference between the communities occurring in the different amendments. However, analysis of the clone libraries of the actinobacterial communities by the use of multiple statistical approaches showed that these communities were significantly different from each other. Results showed that long-term organic and inorganic soil amendments did not significantly alter the overall phylogenetic diversity of the actinobacterial communities but did significantly change the community structure.     

Biogeography of bacterial communities in hot springs: a focus on the actinobacteria

Actinobacteria are ubiquitous in soil, freshwater and marine ecosystems. Although various studies have focused on the microbial ecology of this phylum, data are scant on the ecology of actinobacteria endemic to hot springs. Here, we have investigated the molecular diversity of eubacteria, with specific focus on the actinobacteria in hot springs in Zambia, China, New Zealand and Kenya. Temperature and pH values at sampling sites ranged between 44.5 and 86.5?°C and 5-10, respectively. Non-metric multidimensional scaling analysis of 16S rRNA gene T-RFLP patterns showed that samples could be separated by geographical location. Multivariate analysis showed that actinobacterial community composition was best predicted by changes in pH and temperature, whereas temperature alone was the most important variable explaining differences in bacterial community structure. Using 16S rRNA gene libraries, 28 major actinobacterial OTUs were found. Both molecular techniques indicated that many of the actinobacterial phylotypes were unique and exclusive to the respective sample. Collectively, these results support the view that both actinobacterial diversity and endemism are high in hot spring ecosystems.     

Stratification and seasonal stability of diverse bacterial communities in a Pinus merkusii (pine) forest soil in central Java,Indonesia

In Java, Indonesia, many nutrient-poor soils are intensively reforested with Pinus merkusii (pine). Information on nutrient cycles and microorganisms involved in these cycles will benefit the management of these important forests. Here, seasonal effects on the stratification of bacterial community structure in the soil profile of a tropical pine forest are described, and differences in bacterial communities are related to chemical and physical soil parameters. Culture-independent community profiles of litter, fragmented litter and mineral soil layers were made by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA-specific polymerase chain reaction (PCR) fragments. The community profiles of the different soil layers clustered separately, correlating with significant differences in organic matter content between the three layers. The bacterial communities appeared to be stable during the wet season of 1998. The drought in 1997, caused by the El Ni?o climatic effect, did not influence the bacterial communities in fragmentation and mineral soil, although moisture content and other soil parameters were markedly lower than in the wet season. However, communities in litter were influenced by drought. In the litter layer, the moisture content was significantly lower than in the fragmentation and mineral layers during the dry season. A clone library was made from a litter sample taken during the wet season. Partial sequencing of 74 clones and linking the DGGE banding positions of these clones to bands in the DGGE profile of the sample from which the clone library was derived showed considerable bacterial diversity. Alpha-proteobacteria (40.5% of the clones, of which 57% belonged to the Rhizobium-Agrobacterium group) and high-G+C content, Gram-positive bacteria (36.5%) dominated the clone library.     

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota

Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.     

Fungal guilds are evenly distributed along a vertical spruce forest soil profile while individual fungi show pronounced niche partitioning

Saprotrophic and ectomycorrhizal (EcM) forest fungi decompose organic matter and mobilize nutrients for host plants, respectively. Competition between the two guilds may cause the so-called Gadgil effect, i.e., decreased litter decomposition rates resulting in increased carbon storage in soil. The Gadgil effect was supposed to even affect global climate, highlighting the necessity to understand fungal distribution and interactions in soil. Searching for evidence of competition between saprotrophic and mycorrhizal fungi, we analyzed the distribution of fungi along a well-stratified vertical spruce forest soil profile in two seasons, i.e., autumn and the following spring. The different soil strata (i.e., two mineral horizons and two organic layers) underneath the litter layer were colonized by distinct fungal communities, which included roughly consistent proportions of all fungal guilds and phyla at each time. However, the community composition changed quantitatively between the sampling dates. Along the vertical soil profile, it differed mostly between the organic layers and the mineral soil, which is supposed to be due to differences in the predominant energy sources (i.e., aboveground litter and rhizodeposition, respectively). Network analyses revealed co-occurrences (i.e., positive correlations of individual abundances) to outweigh mutual exclusions (i.e., negative correlations) between individual fungi in each soil stratum and season. This also applied for interactions between saprotrophic and EcM fungi. Network analyses therefore provided no indications for a possible Gadgil effect. However, considering individual nutrient use efficiencies might refine insights from network analyses in future studies and facilitate linking community dynamics to ecosystem processes.     

Molecular Phylogeny and Diversity of the Salt-Tolerant Alkaliphilic Actinobacteria Inhabiting Coastal Gujarat,India

Actinobacteria is a dominant phylum in saline soil and play important roles in the process of organic matter decomposition and biogeochemical cycling. In this study, we investigated the diversity and phylogeny of the haloalkaliphilic actinobacteria that inhabited the saline soil of Coastal Gujarat (India) using conventional and molecular approaches. The actinobacteria were diversified on the basis of their growth patterns, morphology, spore color and sugar utilization. The cultivated actinobacteria were genetically diverse, with the ability to grow at high salt concentrations. The salt resistance feature was widely distributed among the isolates and not confined to any particular phylogenetic cluster. The PCR -DGGE approach was used to assess molecular diversity and to mitigate the limitation of the 16S rRNA sequence approach. Reproducible band profiles confirmed that the PCR-DGGE provided an excellent tool for the 16S rDNA heterogeneity analysis. The migration behavior of the 16S rRNA genes on the DGGE gel suggested lack of correlation between the band numbers and α-diversity. The findings highlighted the trends associated with the microbial community and signify the role of the DGGE in distinguishing a group of species that exhibit 16S rRNA based phylogenetic relatedness with distinct phenotypic characters. Based on the 16S rRNA genes, the actinobacteria were identified as belong to Nocardiopsis, Brachybacterium, Streptomyces and Prauseria. Nocardiopsis was the most predominant actinobacterial genera. The study indicated that a combination of the conventional and molecular approaches could be highly significant in analyzing the diversity of the actinobacteria from the saline habitat.     

Actinobacterial community and diversity in rhizosphere soils of Aquilaria crassna Pierre ex Lec assessed by RT-PCR and PCR-DGGE

The actinobacterial community in rhizospheres of eaglewood (Aquilaria crassna Pierre ex Lec) was analyzed using culture-independent methods of RT-PCR and PCR DGGE of 16S rRNA gene. We conducted the experiments to investigate the difference in diversity and community structure of actinobacteria with respect to sampling sites and seasons and to determine effect of plant species on selection of rhizosphere community from different sampling sites. Total genomic DNA and RNA were extracted from rhizosphere soils collected from two plantations in Phetchabun province and one plantation in each Nakhonnayok province, Rayong province and Chiang Mai province of Thailand during dry and rainy seasons. The UPGMA dendrogram generated from DGGE fingerprints showed that the actinobacterial community was separated corresponding to sampling sites, suggesting sampling sites effect. The shift in community and diversity between two seasons was detected in all sampling sites. RNA-based analyses showed that several actinobacterial groups appeared to be ubiquitous but different in metabolic activity in different environments. Species diversity (S) and simple indexes (I) indicate the increase in species diversity of actinobacteria from all sampling sites in rainy season. Cloning and sequencing of 16S rRNA gene fragments obtained from DGGE bands revealed that 14 of 40 dominant species of actinobacteria in the rhizospheres of this plant belonged to uncultured actinobacteria. Besides the uncultured actinobacteria, Nocardioides sp., Streptomyces sp., Mycobacterium sp., Rhodococcus sp. and Actinoplanes sp. were indentified and frequently found more than other genera.     

Microbial communities show parallels at sites with distinct litter and soil characteristics

Plant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated by erm resistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.     

Environmental factors influencing the distribution of rRNA from Verrucomicrobia in soil

The Verrucomicrobia constitute a newly discovered division of the Bacteria identified as a numerically abundant component of soil microbial communities in numerous sites around the world. The relative abundance of rRNA from Verrucomicrobia was investigated in the soil to examine the influence of specific environmental factors on the distribution of Verrucomicrobia and to better understand the distribution of this group in terrestrial ecosystems. The abundance of the verrucomicrobial rRNA was determined by using a novel oligonucleotide probe that is specific for verrucomicrobial 16S rRNA. The abundance of verrucomicrobial 16S rRNA in soil microbial communities was determined in relation to plant community composition and soil management history over a period of 2 years. Additional samples were analyzed to determine if verrucomicrobial rRNA relative abundance changes in relation to either soil depth or soil moisture content. The Verrucomicrobia composed 1.9+/-0.2% of the microbial community rRNA present in the 85 soil samples examined. The distribution of verrucomicrobial rRNA in the soil reveals that Verrucomicrobia are significantly affected by environmental characteristics that change in relation to time, soil history, and soil depth, and reveals that a statistically significant amount of the variation in verrucomicrobial rRNA abundance can be explained by changes in soil moisture content.     

新疆于田盐池放线菌群落结构

应用免培养技术和基于16S rRNA基因序列的系统发育分析对新疆于田盐池土壤放线菌群落结构进行研究。结果表明, 41个克隆序列属于26个OTUs, 分别分布于放线菌门放线菌亚纲(Actinobacteridae)的7个亚目和酸微菌亚纲(Acidimicrobidae), 其中链孢囊菌亚目(Streptosporangi- neae)中放线菌组成丰富, 占到了全部挑选克隆的42.3%, 是于田盐池放线菌群落中的优势菌, 而链霉菌不是高盐环境放线菌的优势菌群。在这些克隆序列中有71.8% 的克隆序列同已知序列的相似性低于97%, 属于放线菌的新类群, 这些可能的新类群中有15.3%的克隆序列与已知菌株的相似性小于85%, 这些克隆序列的分类地位都在科一级的分类单元上, 有的可能分类地位更高。这些研究结果说明于田盐池中存在有较为丰富的放线菌系统发育多样性, 并且潜藏着新类型的放线菌资源。另外, 由于微生态效应的存在, 不同高盐环境之间放线菌群落也存在明显差异。     

Analysis of ammonia-oxidizing bacteria populations in acid forest soil during conditions of moisture limitation

Ammonia-oxidizer numbers decreased under conditions of moisture limitation in litter, fermentation and humus layers of forest soil in the field, but the extent of regrowth after rehydration varied between layers. Nitrosospira 16S rRNA genes were amplified from all layers, regardless of moisture content or soil pH which varied between 4.1 and 5.2. Nitrosomonas spp. were detected less often, but appeared to exhibit more rapid recovery than the Nitrosospira spp. when drought conditions were relieved by rainfall.     

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land‐cover change affects belowground carbon storage and nutrient availability. We measured intra‐ and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well‐replicated, long‐term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter‐ and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land‐use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities.     

Increases in soil respiration following labile carbon additions linked to rapid shifts in soil microbial community composition

Organic matter decomposition and soil CO₂ efflux are both mediated by soil microorganisms, but the potential effects of temporal variations in microbial community composition are not considered in most analytical models of these two important processes. However, inconsistent relationships between rates of heterotrophic soil respiration and abiotic factors, including temperature and moisture, suggest that microbial community composition may be an important regulator of soil organic matter (SOM) decomposition and CO₂ efflux. We performed a short-term (12-h) laboratory incubation experiment using tropical rain forest soil amended with either water (as a control) or dissolved organic matter (DOM) leached from native plant litter, and analyzed the effects of the treatments on soil respiration and microbial community composition. The latter was determined by constructing clone libraries of small-subunit ribosomal RNA genes (SSU rRNA) extracted from the soil at the end of the incubation experiment. In contrast to the subtle effects of adding water alone, additions of DOM caused a rapid and large increase in soil CO₂ flux. DOM-stimulated CO₂ fluxes also coincided with profound shifts in the abundance of certain members of the soil microbial community. Our results suggest that natural DOM inputs may drive high rates of soil respiration by stimulating an opportunistic subset of the soil bacterial community, particularly members of the Gammaproteobacteria and Firmicutes groups. Our experiment indicates that variations in microbial community composition may influence SOM decomposition and soil respiration rates, and emphasizes the need for in situ studies of how natural variations in microbial community composition regulate soil biogeochemical processes.     

Temporal and spatial variability in soil food web structure

Heterogeneity is a prominent feature of most ecosystems. As a result of environmental heterogeneity the distribution of many soil organisms shows a temporal as well as horizontal and vertical spatial patterning. In spite of this, food webs are usually portrayed as static networks with highly aggregated trophic groups over broader scales of time and space. The variability in food web structure and its consequences have seldom been examined. Using data from a Scots pine forest soil in the Netherlands, we explored (1) the temporal and spatial variability of a detrital food web and its components, (2) the effect of taxonomic resolution on the perception of variability over time and across space, and (3) the importance of organic matter quality as an explanatory factor for variability in food web composition. Compositional variability, expressed using the Bray‐Curtis similarity index, was measured over 2.5 years using a stratified litterbag design with three organic horizons per litterbag set. Variability in community composition and organic matter degradation increased over time in the litter horizon only. Seasonal variation in community composition was larger than variation between samples from the same season in different years. Horizontal spatial variability in community composition and organic matter degradation was relatively low, with no increase in variability with increasing distance between samples. Vertically, communities and organic matter degradation was more different between the non‐adjacent litter and humus horizons than between adjacent layers. These findings imply that soil food webs, at least in temperate forest plantations, are more variable than is currently appreciated in experiments and model studies, and that organic matter turnover might be an important factor explaining variability in community composition. Species composition was more variable than functional group composition, which implies that aggregated food webs will seem less sensitive to local temporal and spatial changes than they in fact are.     

Factors Controlling Soil Microbial Biomass and Bacterial Diversity and Community Composition in a Cold Desert Ecosystem: Role of Geographic Scale

Understanding controls over the distribution of soil bacteria is a fundamental step toward describing soil ecosystems, understanding their functional capabilities, and predicting their responses to environmental change. This study investigated the controls on the biomass, species richness, and community structure and composition of soil bacterial communities in the McMurdo Dry Valleys, Antarctica, at local and regional scales. The goals of the study were to describe the relationships between abiotic characteristics and soil bacteria in this unique, microbially dominated environment, and to test the scale dependence of these relationships in a low complexity ecosystem. Samples were collected from dry mineral soils associated with snow patches, which are a significant source of water in this desert environment, at six sites located in the major basins of the Taylor and Wright Valleys. Samples were analyzed for a suite of characteristics including soil moisture, pH, electrical conductivity, soil organic matter, major nutrients and ions, microbial biomass, 16 S rRNA gene richness, and bacterial community structure and composition. Snow patches created local biogeochemical gradients while inter-basin comparisons encompassed landscape scale gradients enabling comparisons of microbial controls at two distinct spatial scales. At the organic carbon rich, mesic, low elevation sites Acidobacteria and Actinobacteria were prevalent, while Firmicutes and Proteobacteria were dominant at the high elevation, low moisture and biomass sites. Microbial parameters were significantly related with soil water content and edaphic characteristics including soil pH, organic matter, and sulfate. However, the magnitude and even the direction of these relationships varied across basins and the application of mixed effects models revealed evidence of significant contextual effects at local and regional scales. The results highlight the importance of the geographic scale of sampling when determining the controls on soil microbial community characteristics.     

Different temperature sensitivity and kinetics of soil enzymes indicate seasonal shifts in C,N and P nutrient stoichiometry in acid forest soil

Acid forest soils in the Bohemian Forest in Central Europe are biogeochemically imbalanced in organic C, N and P processing. We hypothesized that these imbalances can be due to different temperature sensitivities of soil enzyme activities and their affinities to substrate in litter and organic soil horizons. We measured potential activities of five main soil enzymes (β-glucosidase, cellobiohydrolase, Leu-aminopeptidase, Ala-aminopeptidase, and phosphatase) responsible for organic carbon, nitrogen and phosphorus acquisition. We also modeled potential in situ enzyme activities and nutrient release based on continuous in situ temperature measurements. We determined basic kinetic parameters (K_m, V_max), enzyme efficiencies (k_cat) and temperature sensitivities (E_a and Q₁₀) according to Michaelis–Menten kinetic and modified Arrhenius models. Our results showed significant differences in substrate affinities between the litter and organic soil horizons. Higher aminopeptidase affinity (lower K_m) in the litter soil horizon can lead to leaching of peptidic compounds to lower soil horizons. β-Glucosidase and phosphatase showed high temperature response following the Arrhenius model. However, both aminopeptidases showed no or even decreased activity with increasing temperature. The aminopeptidase temperature insensitivity means that peptidic compounds are degraded at the same or even lower rate in warmer and colder periods of the year in acid forest soils. This imbalance results in different release of available nutrients from plant litter and soil organic matter which may affect bacterial and fungal community composition and nutrient leaching from these ecosystems.     

Litter quality versus soil microbial community controls over decomposition: a quantitative analysis

The possible effects of soil microbial community structure on organic matter decomposition rates have been widely acknowledged, but are poorly understood. Understanding these relationships is complicated by the fact that microbial community structure and function are likely to both affect and be affected by organic matter quality and chemistry, thus it is difficult to draw mechanistic conclusions from field studies. We conducted a reciprocal soil inoculum × litter transplant laboratory incubation experiment using samples collected from a set of sites that have similar climate and plant species composition but vary significantly in bacterial community structure and litter quality. The results showed that litter quality explained the majority of variation in decomposition rates under controlled laboratory conditions: over the course of the 162-day incubation, litter quality explained nearly two-thirds (64 %) of variation in decomposition rates, and a smaller proportion (25 %) was explained by variation in the inoculum type. In addition, the relative importance of inoculum type on soil respiration increased over the course of the experiment, and was significantly higher in microcosms with lower litter quality relative to those with higher quality litter. We also used molecular phylogenetics to examine the relationships between bacterial community composition and soil respiration in samples through time. Pyrosequencing revealed that bacterial community composition explained 32 % of the variation in respiration rates. However, equal portions (i.e., 16 %) of the variation in bacterial community composition were explained by inoculum type and litter quality, reflecting the importance of both the meta-community and the environment in bacterial assembly. Taken together, these results indicate that the effects of changing microbial community composition on decomposition are likely to be smaller than the potential effects of climate change and/or litter quality changes in response to increasing atmospheric CO₂ concentrations or atmospheric nutrient deposition.