Functional analysis of the archaea, bacteria, and viruses from a halite endolithic microbial community

Halite endoliths (salt rocks) in the Atacama Desert represent one of the most extreme environments on Earth. We obtained a 9.6 Gb high quality shotgun metagenome from halite nodules collected in the Salar Grande area. Our metagenome is unique because it has high sequencing depth, low diversity, and representative members from all 3 domains of life and from viruses. Taxonomic assignment of the metagenomic reads confirmed that the community was dominated by members of the Archaea, including Nanohaloarchaea, and also comprised members of the Bacteria and Eukarya. The functional annotation of the metagenome revealed that the cyanobacterium Halothece was responsible for most of the CO2 fixed in the community and that a number of archaea and bacteria carried out photoheterotrophy, via light-driven proton pumps, increasing the energy budget of the community from light. Our analysis predicted that the alga identified in the community has one of the lowest protein isoelectric point (pI) distributions of any reported eukaryote. Its pI profile was similar to that of halophiles using a “salt-in” strategy. Our genome assembly produced a nanohaloarchaeon genome of 1.2 Mbp. We have named this new microorganism Candidatus Nanopetramus SG9. Analysis of its genome sequence revealed a photoheterotrophic life style, a low median isoelectric point for all its predicted proteins, suggesting a “salt-in” strategist, and the presence of a unique CRISPR/Cas system in its genome; one of the spacers from this unique CRISPR/Cas system matched a partial viral genome from the metagenome. We developed new methods to identify viral genomic content from metagenome data, resulting in the identification of over 30 complete or near complete viral or proviral genomes in the halite metagenome. These viral genomes were diverse in genome structure, gene content, host, and genome size. Putative hosts for these viruses included Halobacteriaceae, Nanohaloarchaea, and Cyanobacteria. Despite the dependence on deliquescence of the halite community for liquid water availability, this study revealed an ecosystem spanning three phylogenetic domains, containing a large diversity of viruses, and a predominant “salt-in” strategy to balance the high osmotic pressure of the environment.

阿塔卡马沙漠（Atacama Desert）中的盐生隐岩（halite endoliths，即盐岩）生境是地球已知最极端的环境之一。本研究从格兰德盐沼（Salar Grande）区域采集的盐结核（halite nodules）中，获得了一份9.6 Gb的高质量鸟枪宏基因组（shotgun metagenome）。该宏基因组具有独特性：测序深度高、物种多样性低，且覆盖了生命三大域（three domains of life）以及病毒的代表性类群。对宏基因组测序读段（metagenomic reads）的分类学注释证实，该群落以古菌（Archaea）类群为优势类群，其中包括纳米嗜盐古菌（Nanohaloarchaea），同时还包含细菌（Bacteria）与真核生物（Eukarya）类群。宏基因组的功能注释（functional annotation）结果显示，席藻属（Halothece）负责该群落中绝大多数的二氧化碳固定（CO2 fixation）过程；多种古菌与细菌则通过光驱动质子泵（light-driven proton pumps）进行光异养代谢（photoheterotrophy），借助光能提升了群落的能量收支（energy budget）。本研究分析预测，群落中鉴定出的藻类拥有所有已报道真核生物中最低的蛋白质等电点（protein isoelectric point, pI）分布之一，其等电点特征与采用"盐入"策略（salt-in strategy）的嗜盐微生物高度相似。通过基因组组装（genome assembly），我们获得了一条1.2 Mbp的纳米嗜盐古菌基因组，并将该新型微生物命名为候选纳米嗜盐杆菌属（Candidatus Nanopetramus）SG9。对其基因组序列的分析表明，该菌具备光异养生活方式，其所有预测蛋白的平均等电点较低，表明其为采用"盐入"策略的嗜盐微生物，且基因组中存在一套独特的CRISPR/Cas系统；该系统的一段间隔序列（spacer）与本宏基因组中鉴定出的一段部分病毒基因组序列相匹配。我们开发了用于从宏基因组数据中鉴定病毒基因组组分的新方法，据此在该盐岩宏基因组中鉴定出30余条完整或近完整的病毒或前病毒（provirus）基因组。这些病毒基因组在基因组结构、基因组成、宿主范围与基因组大小上均呈现出丰富多样性，其潜在宿主包括盐杆菌科（Halobacteriaceae）、纳米嗜盐古菌以及蓝细菌类群。尽管该盐岩群落依赖盐渍物潮解获取液态水，本研究仍揭示了一个涵盖三大生命系统发育域的生态系统，其包含大量多样的病毒类群，并以"盐入"策略作为平衡环境高渗透压的核心适应手段。