Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics.
Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics.
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宏基因组学和宏转录组学揭示酸性矿山排水中优势和稀有原核生物的生态作用
DOI：
10.1038/ismej.2014.212
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发表时间：
2015-06
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--
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中科院分区：
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高通量测序正在扩大我们对环境中微生物多样性的了解。尽管如此，理解稀有和未培养微生物在自然群落中的代谢潜力和生态作用仍然是一个重大挑战。为此，我们应用了分而治之的策略，将一个海量的元基因组数据集(>；100 GBP)在序列组装中基于K-mer频率划分为子集，以低多样性的酸性矿山废水微生物群落为基础，并通过与另一个元翻译组装整合，成功地获得了11个基因组草稿，其中大多数代表尚未培养的和/或稀有的类群(相对丰度为1%)。我们报道了一个自然发生的铁尘暴种群的第一个基因组(相对丰度为90%)及其代谢潜力和基因表达谱，为这些鲜为人知但潜在重要的微生物在AMD环境中的生态作用提供了初步的分子洞察。对活性类群的基因转录分析揭示了在原位执行的主要代谢功能，包括与共生相互作用相关的碳和氮相关代谢，铁和硫氧化，这是节能和AMD产生的关键，以及对环境胁迫(重金属、低pH和氧化胁迫)的适应和响应机制。值得注意的是，固氮和硫氧化是由稀有的分类群执行的，这表明它们在AMD群落的整体功能和组装中发挥着关键作用。我们的研究证明了“分而治之”策略在高通量测序数据组装中的潜力，用于基因组重建和天然微生物组合中优势种和稀有物种的功能划分分析。
High-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a ‘divide and conquer’ strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurringFerrovumpopulation (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executedin situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Our study demonstrates the potential of the ‘divide and conquer’ strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.
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影响因子：
2.9
作者：
Hallberg, Kevin B.;Gonzalez-Toril, Elena;Johnson, D. Barrie
通讯作者：
Johnson, D. Barrie
影响因子：
4.4
作者：
Goltsman, Daniela S. Aliaga;Denef, Vincent J.;Banfield, Jillian F.
通讯作者：
Banfield, Jillian F.
影响因子：
4.4
作者：
Hallberg, KB;Coupland, K;Johnson, DB
通讯作者：
Johnson, DB
影响因子：
5.2
作者：
Gregersen LH;Bryant DA;Frigaard NU
通讯作者：
Frigaard NU
影响因子：
3.6
作者：
Hensen, Daniela;Sperling, Detlef;Dahl, Christiane
通讯作者：
Dahl, Christiane