He Z, Piceno Y, Deng Y, Xu M, Lu Z, DeSantis T et al. The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. ISME J 6: 259-272

Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA.
The ISME Journal (Impact Factor: 9.3). 07/2011; 6(2):259-72. DOI: 10.1038/ismej.2011.99
Source: PubMed


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.

    • "causing a shift in richness, composition and structure of soil microbial communities (Compant et al., 2010; Hayden et al., 2012; He et al., 2012). Table 1 summarizes the effect of eCO 2 on plant associated microorganisms. "
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    ABSTRACT: Alterations in plant rhizodeposition under elevated CO2 (eCO2) are likely to influence below-ground plant–microbe interactions and soil C dynamics. There are studies on influence of elevated CO2 on soil microorganisms and below-ground microbial processes. However there is general lack of information on how altered plant–microbe interactions under eCO2 will influence belowground C-sequestration. In the present review we focus on the greenhouse gas CO2 with relevance to its effect on plant associated beneficial and pathogenic microorganisms in terrestrial ecosystems. Role of these microorganisms in belowground nutrient cycling and soil aggregation is discussed with reference to soil C-sequestration. This review demonstrates that eCO2 influence the richness, composition and structure of soil microbial community and the influence is more on active microbial communities and in the vicinity of roots. High C:N ratio under eCO2 favors fungi with wider C:N ratio and nutrient acquisition ability and biological nitrogen fixers. The ecosystems with fungal-dominated soil communities may have higher C retention than bacterial dominated soil communities. However, soil C-sequestration through plant growth, is strongly controlled by availability of nitrogen and nutrients required for biological nitrogen fixation. Nitrogenous and other chemical fertilizers show positive effect on C-sequestration but carry a carbon cost. Promotion of biological nitrogen fixers, and nutrient solubilizers and mobilizers may help in maintaining soil nutrient balance for higher C-sequestration. However more data need to be generated on the response of various plant beneficial as well as pathogenic microbial communities to eCO2. We suggest that plant associated communities and related processes to be researched in long term studies for alteration under eCO2 so as to assess their C-sequestration potential and identify management strategies for enhanced sequestration.
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    • "Enhanced use of phosphorylated compounds is sign of a rapidly growing community that consumes preferably more labile compounds by the action of phosphatases. Organic matter input under elevated CO2 soil atmosphere may favour carbon polymer-degrading and fastgrowing microorganisms, as observed by He et al. (2012) in surface ecosystems. Lower consumption of phenolic compounds also show that more difficult to degrade substrates are not favoured at the beginning of the experiment. "
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    ABSTRACT: Carbon dioxide is an increasing greenhouse gas; its capture and sequestration seems a promising alternative to mitigate global warming, providing all physical, chemical and biological aspects of subsurface gas sequestration are understood. Possible leaks may change soil balance, impacting ecosystems and, consequently, human and animal health. Few data are available on the effects of augmented CO2 concentrations in soil and studies are required to define the role of biological systems and response mechanisms, and to identify CO2 bioindicators for post-injection monitoring. This study was conducted with soil from the Atlantic forest zone, in two scales: unstructured soil batch experiments, in aerobic and CO2 atmosphere, and column microcosms with unstructured and structured soil under CO2 percolation. Microbial metabolic profiles, protein synthesis and degradation activity, soils moisture, available carbon and pH were assessed. In all assays, microbial activity tended to drop with prolonged exposure to CO2. In batch and structured soils, augmented activity, biomass, species richness, besides altered metabolic profiles, all seemed linked to increased CO2. In unstructured column soil a slower pace of response was explained by low initial activity. No significant change in soil moisture was detected and stable pH indicated absence of carbonate precipitation. In conclusion, augmented CO2 changes microbiota composition, enhancing the activity of favoured anaerobic species, which could change ecosystem functions.
    Full-text · Article · Jan 2015 · International Journal of Greenhouse Gas Control
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    • "It is therefore important to understand the effects of land degradation on soil microbial community composition. Molecular profiling approaches have been widely used to describe microbial diversity in different habitat conditions (Mishra et al. 2013), such as in different soils (Zhang and Xu 2008; He et al. 2012) and extreme environments (Bahl et al. 2011; Chan et al. 2013). Terminal restriction fragment length polymorphism (T-RFLP) has been reported as a rapid, reproducible, and robust molecular technique than most other PCRbased methods for the study of microbial community structure and dynamics (Thies 2007). "
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    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.
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