Kivenson Veronika, Paul Blair G, Valentine David L
Interdepartmental Graduate Program in Marine Science, University of California, Santa Barbara, Santa Barbara, CA, United States.
Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States.
Front Microbiol. 2021 Jul 14;12:680620. doi: 10.3389/fmicb.2021.680620. eCollection 2021.
Marine benthic environments may be shaped by anthropogenic and other localized events, leading to changes in microbial community composition evident decades after a disturbance. Marine sediments in particular harbor exceptional taxonomic diversity and can shed light on distinctive evolutionary strategies. Genetic code expansion is a strategy that increases the structural and functional diversity of proteins in cells, by repurposing stop codons to encode non-canonical amino acids: pyrrolysine (Pyl) and selenocysteine (Sec). Here, we report both a study of the microbiome at a deep sea industrial waste dumpsite and an unanticipated discovery of codon reassignment in its most abundant member, with potential ramifications for interpreting microbial interactions with ocean-dumped wastes. The genomes of abundant Deltaproteobacteria from the sediments of a deep-ocean chemical waste dump site have undergone genetic code expansion. Pyl and Sec in these organisms appear to augment trimethylamine (TMA) and one-carbon metabolism, representing an increased metabolic versatility. The inferred metabolism of these sulfate-reducing bacteria places them in competition with methylotrophic methanogens for TMA, a contention further supported by earlier isotope tracer studies and reanalysis of metatranscriptomic studies. A survey of genomic data further reveals a broad geographic distribution of a niche group of similarly specialized Deltaproteobacteria, including at sulfidic sites in the Atlantic Ocean, Gulf of Mexico, Guaymas Basin, and North Sea, as well as in terrestrial and estuarine environments. These findings reveal an important biogeochemical role for specialized Deltaproteobacteria at the interface of the carbon, nitrogen, selenium, and sulfur cycles, with their niche adaptation and ecological success potentially augmented by genetic code expansion.
海洋底栖环境可能受到人为和其他局部事件的影响，导致干扰数十年后微生物群落组成发生明显变化。特别是海洋沉积物具有异常丰富的分类多样性，能够揭示独特的进化策略。遗传密码扩展是一种通过重新利用终止密码子来编码非标准氨基酸（吡咯赖氨酸（Pyl）和硒代半胱氨酸（Sec））从而增加细胞中蛋白质结构和功能多样性的策略。在此，我们报告了一项对深海工业垃圾倾倒场微生物群落的研究，以及在其最丰富成员中意外发现的密码子重新分配现象，这可能对解释微生物与海洋倾倒废物之间的相互作用产生影响。来自深海化学废物倾倒场沉积物中丰富的δ-变形菌纲细菌的基因组经历了遗传密码扩展。这些生物体中的Pyl和Sec似乎增强了三甲胺（TMA）和一碳代谢，代表了代谢多样性的增加。这些硫酸盐还原细菌的推断代谢使它们与甲基营养型产甲烷菌在TMA方面存在竞争，早期的同位素示踪研究和对宏转录组学研究的重新分析进一步支持了这一观点。对基因组数据的调查进一步揭示了一组类似特殊化的δ-变形菌纲在广泛地理区域的分布，包括在大西洋、墨西哥湾、瓜伊马斯盆地和北海的硫化物位点，以及陆地和河口环境。这些发现揭示了特殊化的δ-变形菌纲在碳、氮、硒和硫循环界面的重要生物地球化学作用，其生态位适应和生态成功可能因遗传密码扩展而增强。
