Chaudhari Narendrakumar M, Overholt Will A, Figueroa-Gonzalez Perla Abigail, Taubert Martin, Bornemann Till L V, Probst Alexander J, Hölzer Martin, Marz Manja, Küsel Kirsten
Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany.
German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
Environ Microbiome. 2021 Dec 14;16(1):24. doi: 10.1186/s40793-021-00395-w.
The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response to environmental drivers or host organisms. Their mechanisms employed to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges.
Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 and 0.1 µm filters after sequential filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1 µm fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2 µm fractions. On average, Patescibacteria enriched in the smaller 0.1 µm filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher proportion of rod-shape determining proteins, and of genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. Among the MAGs enriched in 0.2 µm fractions,, only 8% Patescibacteria showed highly significant one-to-one correlation, mostly with Omnitrophota. Motility and transport related genes in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota).
Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we speculate that the majority of Patescibacteria is able to attach multiple hosts just long enough to loot or exchange supplies.
高度多样的“候选帕氏菌属”（Cand. Patescibacteria）预计具有最少的生物合成和代谢途径，这阻碍了我们对其种群如何响应环境驱动因素或宿主生物而分化的理解。它们应对氧化应激所采用的机制在很大程度上尚不清楚。在这里，我们利用基因组解析宏基因组学来研究帕氏菌属在有氧和无氧地下水中的适应性基因组库，并推断其假定的宿主范围。
在六口地下水井中，“候选帕氏菌属”是在依次过滤后保留在0.2微米和0.1微米滤膜上的DNA所测序的32个宏基因组中最占优势的（高达79%）超门。在重建的1275个宏基因组组装基因组（MAG）中，291个高质量MAG被归类为“候选帕氏菌属”。“候选帕西菌属”（Cand. Paceibacteria）和“候选微基因组菌属”（Cand. Microgenomates）仅在0.1微米级分中富集，而候选分类群ABY1和“候选细杆菌属”（Cand. Gracilibacteria）在0.2微米级分中富集。平均而言，在较小的0.1微米滤膜级分中富集的帕氏菌属基因组小22%，复制指标低13.4%，杆状决定蛋白比例更高，且基因组特征表明存在IV型菌毛介导的细胞间附着。近地表水井中帕氏菌属的复制速率高于以较长水停留时间为特征的无氧下游水井。除了在有氧地下水中富集的帕氏菌属MAG中超氧化物歧化酶基因的普遍存在（83%）外，未观察到主要的代谢或系统发育差异。有氧地下水中最丰富的帕氏菌属MAG编码一种硝酸盐转运蛋白、亚硝酸还原酶和F型ATP酶，表明存在一种替代的能量守恒机制。帕氏菌属始终彼此共存，或与纳古菌门、拟杆菌门、硝化螺旋菌门和全营养菌门的成员共存。在0.2微米级分中富集的MAG中，只有8%的帕氏菌属显示出高度显著的一对一相关性，主要与全营养菌门相关。某些帕氏菌属中与运动和运输相关的基因与其他门（全营养菌门、变形菌门和纳古菌门）的基因高度相似。
除了应对氧化应激的基因外，我们几乎没有发现帕氏菌属适应有氧或无氧地下水生态位的基因组证据。鉴于我们仅能检测到少数MAG有特定的宿主偏好，我们推测大多数帕氏菌属能够附着在多个宿主上，时间刚好足够进行掠夺或交换物资。
