Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'
Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'
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DOI：
10.1038/nmicrobiol.2016.198
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发表时间：
2017-02-01
影响因子：
28.3
通讯作者：
Fierer, Noah
中科院分区：
文献类型：
--
作者：
Brewer, Tess E.;Handley, Kim M.;Fierer, Noah
尽管疣微菌门内的细菌普遍存在于世界各地的土壤中，但它们在分离株收藏和基因组数据库中的代表性不足。在这里，我们描述了斯巴达细菌纲中的一个疣状微生物群，它与任何先前描述的分类群没有密切关系。我们检查了 1,000 多种土壤，发现这种分细菌系统型普遍存在，并且始终是最丰富的土壤细菌系统型之一，特别是在草原上，它通常是最丰富的。我们从土壤宏基因组中重建了该系统发育型的近乎完整的基因组，并提出了临时名称“Candidatus Udaeobacter copiosus”。加州。对于一种世界性土壤细菌来说，U. copiosus 基因组异常小，通过一项测量估计仅为 2.81 Mbp，而土壤细菌的预测有效平均基因组大小为 4.74 Mbp。代谢重建表明 Ca。 U. copiosus 是一种需氧异养生物，具有许多推定的氨基酸和维生素营养缺陷型。 Ca 的种群规模较大、基因组相对较小以及多种假定的营养缺陷型特征。 U. copiosus表明它可能正在经历精简选择以最小化细胞结构，这种现象以前被认为仅限于水生细菌。尽管许多土壤细菌需要相对较大、复杂的基因组才能在土壤中成功，但 Ca. U. copiosus 似乎使用了另一种策略，牺牲代谢多功能性以提高效率，从而在土壤环境中占据主导地位。
Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the world, they are under-represented in both isolate collections and genomic databases. Here, we describe a single verrucomicrobial group within the class Spartobacteria that is not closely related to any previously described taxa. We examined more than 1,000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name 'Candidatus Udaeobacter copiosus'. The Ca. U. copiosus genome is unusually small for a cosmopolitan soil bacterium, estimated by one measure to be only 2.81 Mbp, compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests that Ca. U. copiosus is an aerobic heterotroph with numerous putative amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggest that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil, Ca. U. copiosus appears to use an alternative strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.