Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States.
Boone Pickens School of Geology, Oklahoma State University, Stillwater, OK, United States.
Syst Appl Microbiol. 2020 Mar;43(2):126057. doi: 10.1016/j.syapm.2020.126057. Epub 2020 Jan 22.
We report on the characterization of a novel genomic assembly (ARYD3) recovered from formation water (17.6% salinity) and crude oil enrichment amended by isolated soy proteins (0.2%), and incubated for 100 days under anaerobic conditions at 50°C. Phylogenetic and phylogenomic analysis demonstrated that the ARYD3 is unaffiliated with all currently described bacterial phyla and candidate phyla, as evident by the low AAI (34.7%), shared gene content (19.4%), and 78.9% 16S rRNA gene sequence similarity to Halothiobacillus neapolitanus, its closest cultured relative. Genomic characterization predicts a slow-growing, non-spore forming, and non-motile Gram-negative rod. Adaptation to high salinity is potentially mediated by the production of the compatible solutes cyclic 2,3-diphosphoglycerate (cDPG), α-glucosylglycerate, as well as the uptake of glycine betaine. Metabolically, the genome encodes primarily aminolytic capabilities for a wide range of amino acids and peptides. Interestingly, evidence of propionate degradation to succinate via methyl-malonyl CoA was identified, suggesting possible capability for syntrophic propionate degradation. Analysis of ARYD3 global distribution patterns identified its occurrence in a very small fraction of Earth Microbiome Project datasets examined (318/27,068), where it consistently represented an extremely rare fraction (maximum 0.28%, average 0.004%) of the overall community. We propose the Candidatus name Mcinerneyibacterium aminivorans gen. nov, sp. nov. for ARYD3, with the genome serving as the type material for the novel family Mcinerneyibacteriaceae fam. nov., order Mcinerneyibacteriales ord. nov., class Mcinerneyibacteria class nov., and phylum Mcinerneyibacteriota phyl. nov. The type material genome assembly is deposited in GenBank under accession number VSIX00000000.
我们报告了从地层水中（盐度为 17.6%）和经分离的大豆蛋白（0.2%）富集的原油中回收的新型基因组组装（ARYD3）的特征，该组装在 50°C 下厌氧条件下孵育 100 天。系统发育和系统基因组分析表明，ARYD3 与所有目前描述的细菌门和候选门都没有关系，这可以从低 AAI（34.7%）、共享的基因含量（19.4%）和与最接近的培养相关菌 Halothiobacillus neapolitanus 的 78.9% 16S rRNA 基因序列相似性看出。基因组特征预测其为生长缓慢、不形成孢子和非运动性革兰氏阴性棒状菌。高盐度的适应可能是通过产生相容溶质环 2,3-二磷酸甘油酸（cDPG）、α-葡糖基甘油酸以及甘氨酸甜菜碱的摄取来介导的。在代谢方面，基因组主要编码用于广泛氨基酸和肽的氨裂解能力。有趣的是，通过甲基丙二酰辅酶 A 鉴定了丙酸降解为琥珀酸的证据，这表明可能具有协同丙酸降解的能力。对 ARYD3 全球分布模式的分析表明，它仅在很小一部分地球微生物组计划（Earth Microbiome Project）数据集（318/27,068）中出现，其中它始终代表着非常罕见的一部分（最高 0.28%，平均 0.004%）的总体群落。我们建议将 ARYD3 命名为 Mcinerneyibacterium aminivorans gen. nov., sp. nov.，并以基因组作为新型科 Mcinerneyibacteriaceae fam. nov.、目 Mcinerneyibacteriales ord. nov.、类 Mcinerneyibacteria class nov.和门 Mcinerneyibacteriota phyl. nov.的模式种。该模式材料基因组组装已在 GenBank 中以 VSIX00000000 号入库。
