Dataset Information

The microbial gene diversity along an elevation gradient of the Tibetan grassland.

ABSTRACT: Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore the potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C-cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations, whereas ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by Canonical correspondence analysis, Mantel tests and the similarity tests that soil pH, temperature, NH4(+)-N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. On the basis of these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N-cycling genes and consequently microbe-mediated soil N dynamics.

SUBMITTER: Yang Y

PROVIDER: S-EPMC3906809 | biostudies-other | 2014 Feb

REPOSITORIES: biostudies-other

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The microbial gene diversity along an elevation gradient of the Tibetan grassland.

Yang Yunfeng Y Gao Ying Y Wang Shiping S Xu Depeng D Yu Hao H Wu Linwei L Lin Qiaoyan Q Hu Yigang Y Li Xiangzhen X He Zhili Z Deng Ye Y Zhou Jizhong J

The ISME journal 20130829 2

Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore the potential microbial responses to climate changes via a strategy of space-for-time subst ...[more]

PMID: 23985745

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Project description:Soil microbial community composition and extracellular enzyme activity are two main drivers of biogeochemical cycling. Knowledge about their elevational patterns is of great importance for predicting ecosystem functioning in response to climate change. Nevertheless, there is no consensus on how soil microbial community composition and extracellular enzyme activity vary with elevation, and little is known about their elevational variations on the eastern Qinghai-Tibetan Plateau, a region sensitive to global change. We therefore investigated the soil microbial community composition using phospholipid fatty acids (PLFAs) analysis, and enzyme activities at 2,820 m (coniferous and broadleaved mixed forest), 3,160 m (dark coniferous forest), 3,420 m (alpine dwarf forest), and 4,280 m (alpine shrubland) above sea level. Our results showed that soil microbial community composition and extracellular enzyme activities changed significantly along the elevational gradient. Biomass of total microbes, bacteria, and arbuscular mycorrhizal fungi at the highest elevation were the significantly lowest among the four elevations. In contrast, extracellular enzyme activities involved in carbon (C)-, nitrogen (N)-, and phosphorus (P)- acquiring exhibited the maximum values at the highest elevation. Total nutrients and available nutrients, especially P availability jointly explained the elevational pattern of soil microbial community, while the elevational variation of extracellular enzyme activities was dependent on total nutrients. Microbial metabolism was mainly C- and P-limited with an increasing C limitation but a decreasing P limitation along the elevational gradient, which was related significantly to mean annual temperature and total P. These results indicated a vital role of soil P in driving the elevational patterns of soil microbial community and metabolism. Overall, the study highlighted the contrasting responses of soil microbial biomass and extracellular enzyme activities to elevation, possibly suggesting the differences in adaption strategy between population growth and resource acquisition responding to elevation. The results provide essential information for understanding and predicting the response of belowground community and function to climate change on the eastern Qinghai-Tibetan Plateau.

Project description:Microbial community diversity is often correlated with physical environmental stresses like acidity, salinity, and temperature. For example, species diversity usually declines with increasing temperature above 20°C. However, few studies have examined whether the genetic functional diversity of community metagenomes varies in a similar way as species diversity along stress gradients. Here, we investigated bacterial communities in thermal spring sediments ranging from 21 to 88°C, representing communities of 330 to 3,800 bacterial and archaeal species based on 16S rRNA gene amplicon analysis. Metagenomes were sequenced, and Pfam abundances were used as a proxy for metagenomic functional diversity. Significant decreases in both species diversity and Pfam diversity were observed with increasing temperatures. The relationship between Pfam diversity and species diversity followed a power function with the steepest slopes in the high-temperature, low-diversity region of the gradient. Species additions to simple thermophilic communities added many new Pfams, while species additions to complex mesophilic communities added relatively fewer new Pfams, indicating that species diversity does not approach saturation as rapidly as Pfam diversity does. Many Pfams appeared to have distinct temperature ceilings of 60 to 80°C. This study suggests that temperature stress limits both taxonomic and functional diversity of microbial communities, but in a quantitatively different manner. Lower functional diversity at higher temperatures is probably due to two factors, including (i) the absence of many enzymes not adapted to thermophilic conditions, and (ii) the fact that high-temperature communities are comprised of fewer species with smaller average genomes and, therefore, contain fewer rare functions. IMPORTANCE Only recently have microbial ecologists begun to assess quantitatively how microbial species diversity correlates with environmental factors like pH, temperature, and salinity. However, still, very few studies have examined how the number of distinct biochemical functions of microbial communities, termed functional diversity, varies with the same environmental factors. Our study examined 18 microbial communities sampled across a wide temperature gradient and found that increasing temperature reduced both species and functional diversity, but in different ways. Initially, functional diversity increased sharply with increasing species diversity but eventually plateaued, following a power function. This pattern has been previously predicted in theoretical models, but our study validates this predicted power function with field metagenomic data. This study also presents a unique overview of the distribution of metabolic functions along a temperature gradient, demonstrating that many functions have temperature "ceilings" above which they are no longer found.

Dataset Information

The microbial gene diversity along an elevation gradient of the Tibetan grassland.

Publications

The microbial gene diversity along an elevation gradient of the Tibetan grassland.

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