The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA.
The ISME Journal (Impact Factor: 8.95). 07/2011; 6(2):259-72. DOI: 10.1038/ismej.2011.99
Source: PubMed

ABSTRACT One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO(2). Although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO(2) conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO(2). PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO(2), and such significant effects of eCO(2) on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO(2). Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO(2). Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure.

  • [Show abstract] [Hide abstract]
    ABSTRACT: A vast number of microorganisms colonize the leaf surface of terrestrial plants, known as the phyllosphere, and these microorganisms are thought to be of critical importance in plant growth and health. However, the taxonomic identities and ecological functions of the microorganisms inhabiting the rice phyllosphere remain poorly understood. Using a massive, parallel pyrosequencing technique, we identified the phyllosphere bacterial taxa of four different rice varieties and investigated the microbial response to elevated CO2 (eCO2) in a rice field of a free-air CO2 enrichment (FACE) facility located in Jiangsu Province, China. The results showed that the dominant phylotype, the Enterobacteriaceae family of Gammaproteobacteria, accounted for 70.6%–93.8% of the total bacterial communities in the rice phyllosphere. The dominant phylotype was stimulated by eCO2, with its relative abundance increasing from 70.6%–75.2% at ambient CO2 (aCO2) to 86.5%–93.8% at eCO2 in the phyllosphere of rice varieties IIYou084 (TY-084), YangLiangYou6 (YLY-6), and ZhenXian96 (ZX-96). The rare phylotypes, including the bacterial taxa of Sphingobacteriaceae, Xanthomonadaceae, Oxalobacteraceae, Clostridiaceae, and Pseudomonadaceae, were suppressed and their relative abundance decreased from 13.4%–23.0% at aCO2 to 1.47%–6.11% at eCO2. Furthermore, the bacterial diversity indices decreased at eCO2 in the phyllosphere of the rice varieties TY-084, YLY-6, and ZX-96. In contrast, an opposite response pattern was observed for the rice variety of YangDao8 (YD-8). In the phyllosphere of this variety, the relative abundance of the dominant phylotype, Enterobacteriaceae, decreased from 94.1% at aCO2 to 81.4% at eCO2, while that of the rare phylotypes increased from 3.37% to 6.59%. In addition, eCO2 appeared to stimulate bacterial diversity in the rice variety YD-8. Our results suggest that the phyllosphere microbial response to eCO2 might be relative abundance-dependent in paddy fields.
    Pedosphere 08/2014; 24(4):544–552. · 1.38 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex and the links between specific environmental factors, microbial community structures and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg and Mn contents were variable in N, P, K and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem. This article is protected by copyright. All rights reserved.
    FEMS Microbiology Ecology 07/2014; · 3.88 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Land degradation deteriorates biological productivity and affects environmental, social, and economic sustainability, particularly so in the semi-arid region of Northeast Brazil. Although some studies exist reporting gross measures of soil microbial parameters and processes, limited information is available on how land degradation and restoration strategies influence the diversity and composition of soil microbial communities. In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. We found that land degradation decreased the diversity of soil bacteria as indicated by both reduced operational taxonomic unit (OTU) richness and Shannon index. Soils under native vegetation and restoration had significantly higher bacterial richness and diversity than degraded soils. Redundancy analysis revealed that low soil bacterial diversity correlated with a high respiratory quotient, indicating stressed microbial communities. By contrast, soil bacterial communities in restored land positively correlated with high soil P levels. Importantly, however, we found significant differences in the soil bacterial community composition under native vegetation and in restored land, which may indicate differences in their functioning despite equal levels of bacterial diversity.
    Antonie van Leeuwenhoek 08/2014; · 2.07 Impact Factor

Full-text (2 Sources)

Available from
May 29, 2014