Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities.
Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities.
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DOI：
10.1128/msystems.01205-20
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发表时间：
2021-08-31
期刊：
影响因子：
6.4
通讯作者：
Banfield JF
中科院分区：
文献类型：
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作者：
Nicolas AM;Jaffe AL;Nuccio EE;Taga ME;Firestone MK;Banfield JF
候选Phyla Radiation(CPR)细菌和纳米古菌存在于大多数生态系统中，但在土壤中很少被检测到。我们从草原土壤中浓缩了小于0.2 μm的颗粒，从而能够有针对性地对这些生物进行元基因组分析，这些生物在土壤等主要含氧环境中几乎完全没有被探索过。我们发现了多种CPR细菌和一些古生菌序列，但没有从其他细胞生物中找到序列。采样的序列包括土壤中很少报道的Doudnabacteria(SM2F11)和Pacearchaeota，以及糖化细菌、帕氏细菌和微基因组。与散装土壤中的CPR和古菌相比，水华石门、Parvarchaeota、Aenigmarchaeota、Nano考古群和Nanohalo考古群(DPANN)的CPR和古生菌的丰度是100-1000倍，我们估计每克土壤中这些生物体约含有1-100个细胞。像迄今为止大多数CPR和DPANN测序一样，我们预测这些微生物过着共生的厌氧生活方式。然而，这里采集的糖化细菌、乳杆菌和豆腐细菌基因组中也含有泛喹酚氧化酶操纵子，这些操纵子可能是从其他细菌获得的，可能是在适应好氧土壤环境的过程中获得的。我们得出结论，CPR细菌和DPANN古菌是稀有土壤生物圈的一部分，并拥有独特的代谢平台，这些平台可能进化成在相对有毒的条件下共生。在这方面的重要性，我们调查了土壤中被忽视的微生物，候选Phyla Radiation(CPR)细菌和闪纹藻，Parvarchaeota，Aenigmarchaeota，Nano考古群，和NanoHalo考古群(DPANN)古生菌，通过从土壤中分离小颗粒的大小，一种通常用于恢复病毒元基因组的方法。这些小细胞的浓度(<；0.2 μm)使我们能够识别这些生物是稀有土壤生物圈的一部分，并对非大小分级的后基因组中不存在的基因组进行采样。我们发现，这些预测的共生体中的一些，已经在厌氧系统中进行了大量的研究，通过横向转移获得了好氧能力，这可能使其能够适应含氧土壤环境。我们估计，每克土壤中大约有1到100个这些谱系的细胞，这突显出该方法为了解稀有的土壤生物圈及其相关的遗传潜力提供了一个窗口。
Candidate Phyla Radiation (CPR) bacteria and nanoarchaea populate most ecosystems but are rarely detected in soil. We concentrated particles of less than 0.2 μm in size from grassland soil, enabling targeted metagenomic analysis of these organisms, which are almost totally unexplored in largely oxic environments such as soil. We recovered a diversity of CPR bacterial and some archaeal sequences but no sequences from other cellular organisms. The sampled sequences include Doudnabacteria (SM2F11) and Pacearchaeota, organisms rarely reported in soil, as well as Saccharibacteria, Parcubacteria, and Microgenomates. CPR and archaea of the phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) were enriched 100- to 1,000-fold compared to that in bulk soil, in which we estimate each of these organisms comprises approximately 1 to 100 cells per gram of soil. Like most CPR and DPANN sequenced to date, we predict these microorganisms live symbiotic anaerobic lifestyles. However, Saccharibacteria, Parcubacteria, and Doudnabacteria genomes sampled here also harbor ubiquinol oxidase operons that may have been acquired from other bacteria, likely during adaptation to aerobic soil environments. We conclude that CPR bacteria and DPANN archaea are part of the rare soil biosphere and harbor unique metabolic platforms that potentially evolved to live symbiotically under relatively oxic conditions. IMPORTANCE Here, we investigated overlooked microbes in soil, Candidate Phyla Radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2 μm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes. We found that some of these predicted symbionts, which have been largely studied in anaerobic systems, have acquired aerobic capacity via lateral transfer that may enable adaptation to oxic soil environments. We estimate that there are approximately 1 to 100 cells of each of these lineages per gram of soil, highlighting that the approach provides a window into the rare soil biosphere and its associated genetic potential.