A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.
A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.
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DOI：
10.1186/s40168-018-0548-7
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发表时间：
2018-09-19
期刊：
影响因子：
15.5
通讯作者：
Muyzer G
中科院分区：
文献类型：
--
作者：
Vavourakis CD;Andrei AS;Mehrshad M;Ghai R;Sorokin DY;Muyzer G
高盐苏打湖以极高的可溶性碳酸盐碱度为特征。尽管钠湖盐水的pH值和含盐量都很高，但钠湖沉积物的微生物群落却很少受到微生物学家的关注。在这里，我们对苏打湖沉积物进行了宏基因组测序，首次对这些复杂的极端环境中发现的分类多样性进行了广泛的概述，并对最丰富的未培养的原核生物谱系获得了新的生理见解。我们对从4个西伯利亚碱湖表层沉积物中获得的5个宏基因组进行了测序，这些碱湖的pH值为10，含盐量在70至400 g L−1之间。16S rRNA基因序列大部分来自细菌，即使在盐饱和的湖泊中也是如此。大多数otu被分配到没有文化的家庭。我们重建了871个宏基因组组装基因组（MAGs），跨越超过45个门，并发现了候选门辐射（Candidate phyla Radiation， CPR）的第一批极端微生物成员。5个新种是最占优势的群落成员。新的优势谱系被发现在以前很好的功能基团涉及碳，硫和氮循环。此外，至少有四个细菌门编码了Wood-Ljungdahl途径的关键酶，这些细菌门以前从未与这种古老的厌氧碳固定和异化途径相关，包括放线菌。我们对高盐苏打湖沉积物宏基因组的首次测序工作取得了两个重要进展。首先，我们证明了存在并获得了CPR亲卤碱基成员和数百个其他新的原核生物谱系的第一个基因组。苏打湖CPR是一个功能多样化的群体，但本研究中最丰富的生物可能是发酵剂，可能在初级碳降解中起作用。其次，我们在更多的分类类群中发现了存在Wood-Ljungdahl途径的证据，而不是那些包含已知的同质醋酸菌、硫酸盐还原剂和产甲烷菌的类群。由于只有少数环境宏基因组学研究针对沉积物微生物群落，而且从未达到这种程度，我们希望我们的发现不仅与了解盐碱性环境有关，而且还可以用于为未来的海洋和淡水沉积物研究设定目标。本文的在线版本（10.1186/s40168-018-0548-7）包含补充材料，可供授权用户使用。
Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages. We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L−1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria. Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments. The online version of this article (10.1186/s40168-018-0548-7) contains supplementary material, which is available to authorized users.
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影响因子：
4.1
作者：
Basak, Nitai;Das, Debabrata
通讯作者：
Das, Debabrata
影响因子：
15.5
作者：
Danczak RE;Johnston MD;Kenah C;Slattery M;Wrighton KC;Wilkins MJ
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Wilkins MJ
DOI：
10.1038/ismej.2017.39
发表时间：
2017-08
期刊：
The ISME journal
影响因子：
--
作者：
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通讯作者：
Banfield JF
影响因子：
4.3
作者：
Hauss, T;Dante, S;Haines, TH
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Haines, TH
影响因子：
3.7
作者：
Ahn AC;Meier-Kolthoff JP;Overmars L;Richter M;Woyke T;Sorokin DY;Muyzer G
通讯作者：
Muyzer G