Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat
Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat
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DOI：
10.1002/lno.11401
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发表时间：
2019-12-30
影响因子：
4.5
通讯作者：
Rodriguez-Valera, Francisco
中科院分区：
文献类型：
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作者：
Cabello-Yeves, Pedro J.;Zemskaya, Tamara, I;Rodriguez-Valera, Francisco
贝加尔湖是世界上最深的湖。它的深度提供了地球上唯一的深海(1000米深)淡水栖息地，其含氧、超低营养的特征使其成为深海的淡水对应物。在这里，我们分析了1250米和1350米深的样本的超基因组，建立了231个超基因组组装基因组(MAG)。我们检测到高比例的塔乌马考古塔(约占16S rRNA读数的20%)和候选辐射门(CPR)的成员(3-4.5%)。在MAG中，我们获得了氨氧化古菌(AOA，Nitrosopumilaceae)和细菌(AOB，NitroSomonadaceae)，以及亚硝酸盐氧化菌(NitroSpirae)，表明硝化作用非常活跃。淡水SAR202的一个新分支Chloroflei和甲烷养殖菌(Methyloglobulus)也非常丰富，后者也反映了甲烷氧化的可能作用。流线型和世界性细菌的新物种，如Ca。Fonsibacter或ACI放线菌在表层更为丰富，但也存在于深水中。相反，CPRs、粘球藻属、Chloroflei属、DPANN(潜蝇纲、Parvarchaeota、Aenigmarchaeota、Nano考古门和Nanohaloarocota)古生菌或伽马保护性细菌仅在深海样品中发现。我们注意到贝加尔湖深水缺氧区与相似深度的海水之间存在着许多重要的分类和代谢差异：贝加尔湖深水水域中只发现贝加尔湖深海水样中的贝加尔氏杆菌、CPR和DPANN亚门，而海洋样品中普遍存在三角洲蛋白细菌、伽马蛋白细菌和甲蛋白细菌。在贝加尔湖深处，与海洋或其自身表面相比，发现了更多介导氨氧化和甲烷氧化、芳香化合物降解或烷烃/甲烷磺酸盐单加氧酶的基因。总体而言，在配置微生物群落时，深度似乎没有盐度那么重要。
Lake Baikal is the deepest lake in the world. Its depth provides the only bathypelagic (> 1000 m deep) freshwater habitat on Earth and its oxic, ultra-oligotrophic features make it a freshwater counterpart of the deep ocean. Here we have analyzed metagenomes from 1250 and 1350 m deep samples and built 231 metagenome-assembled genomes (MAGs). We detected high fractions of Thaumarchaeota (ca. 20% of 16S rRNA reads) and members of the candidate phyla radiation (CPR) (3-4.5%). Among the MAGs, we obtained ammonia-oxidizing archaea (AOA, Nitrosopumilaceae) and bacteria (AOB, Nitrosomonadaceae), and nitrite-oxidizers (Nitrospirae) indicating very active nitrification. A new clade of freshwater SAR202 Chloroflexi and methanotrophs (Methyloglobulus) were also remarkably abundant, the latter reflecting a possible role of methane oxidation as well. Novel species of streamlined and cosmopolitan bacteria such as Ca. Fonsibacter or acI Actinobacteria were more abundant at the surface but also present in deep waters. Conversely, CPRs, Myxococcales, Chloroflexi, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) archaea, or Gammaproteobacteria were found only in bathypelagic samples. We noted various important taxonomic and metabolic differences between deep aphotic region of Lake Baikal and marine waters of similar depth: Betaproteobacteriales, CPR, and DPANN superphylum were only found in bathypelagic Baikal, while Deltaproteobacteria, Gammaproteobacteria, or Alphaproteobacteria prevailed in oceanic samples. The genes mediating ammonia and methane oxidation, aromatic compound degradation, or alkane/methanesulfonate monooxygenases were detected in higher numbers in deep Baikal compared to their oceanic counterparts or its own surface. Overall, depth seems to be less relevant than salinity in configuring the microbial community.