Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.
Appl Environ Microbiol. 2023 May 31;89(5):e0002523. doi: 10.1128/aem.00025-23. Epub 2023 Apr 26.
The Candidate Phyla Radiation (CPR), also referred to as superphylum , is a very large group of bacteria with no pure culture representatives discovered by 16S rRNA sequencing or genome-resolved metagenomic analyses of environmental samples. Within the CPR, candidate phylum , previously referred to as OD1, is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within the clade " Nealsonbacteria." Because of its persistence over many years, we hypothesized that " Nealsonbacteria" DGGOD1a must play an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, and phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10-fold) increase in the absolute abundance of " Nealsonbacteria" DGGOD1a only when the consortium was amended with crude cell lysate. These results implicate " Nealsonbacteria" in biomass recycling. Fluorescence hybridization and cryogenic transmission electron microscope images revealed that " Nealsonbacteria" DGGOD1a cells were attached to larger archaeal cells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of other " Nealsonbacteria" found in anoxic environments. An anaerobic microbial enrichment culture was used to study members of candidate phyla that are difficult to grow in the lab. We were able to visualize tiny " Nealsonbacteria" cells attached to a large cell, revealing a novel episymbiosis.
候选门辐射（CPR），也称为超门，是一组非常大的细菌，通过 16S rRNA 测序或环境样本的基因组解析宏基因组分析，尚未发现其纯培养代表。在 CPR 中，候选门，以前称为 OD1，在缺氧沉积物和地下水中普遍存在。以前，我们已经确定了一个特定的成员 （称为 DGGOD1a） 是一个产甲烷苯降解联合体的重要成员。系统发育分析将 DGGOD1a 置于“Nealsonbacteria”分支内。由于多年来的持续存在，我们假设“Nealsonbacteria”DGGOD1a 必须在联合体中维持厌氧苯代谢中发挥重要作用。为了尝试确定其生长底物，我们用各种定义的化合物（丙酮酸、乙酸盐、氢气、DNA 和磷脂）以及粗培养裂解物及其三个亚组分对培养物进行了修饰。我们观察到“Nealsonbacteria”DGGOD1a 的绝对丰度增加了 10 倍，仅当联合体用粗细胞裂解物修饰时。这些结果表明“Nealsonbacteria”参与生物量回收。荧光杂交和冷冻透射电子显微镜图像显示，“Nealsonbacteria”DGGOD1a 细胞附着在较大的古菌细胞上。这种明显的共生生活方式得到了手动编辑的完整基因组的代谢预测的支持。这是细菌-古菌共生的第一个例子之一，可能是缺氧环境中发现的其他“Nealsonbacteria”的一个特征。使用厌氧微生物富集培养物来研究难以在实验室中生长的候选门成员。我们能够观察到微小的“Nealsonbacteria”细胞附着在一个大的 细胞上，揭示了一种新的共生关系。
