Data_Sheet_1_An Ecological Basis for Dual Genetic Code Expansion in Marine Deltaproteobacteria.docx

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.

海洋沉积物环境可能受到人为及其他局部事件的塑造，导致在干扰发生后数十年内微生物群落组成发生改变。特别是海洋沉积物拥有卓越的物种多样性，能够揭示独特的进化策略。遗传密码扩展是一种通过将终止密码子重新编码为非经典氨基酸（吡咯赖氨酸（Pyl）和硒半胱氨酸（Sec））来增加细胞中蛋白质结构和功能多样性的策略。在本研究中，我们报告了对深海工业废弃物倾倒场的微生物组的研究，以及在该地区最丰富的微生物成员中意外发现的密码子重新分配现象，这一发现可能对解读微生物与海洋倾倒废物之间的相互作用具有重要意义。富含Deltaproteobacteria的基因组，源自深海化学废弃物倾倒场的沉积物，已经经历了遗传密码扩展。这些生物体内的Pyl和Sec似乎增强了三甲胺（TMA）和一碳代谢，体现了增强的代谢多样性。对这些硫酸盐还原菌的代谢推断表明，它们与甲基营养型产甲烷菌在TMA上存在竞争关系，这一观点得到了早期同位素示踪研究和元转录组学研究再分析的支持。对基因组数据的调查进一步揭示了类似专业化的Deltaproteobacteria种群在广阔地理范围内的分布，包括大西洋的硫化物地点、墨西哥湾、瓜伊马斯盆地和北海，以及陆地和河口环境。这些发现揭示了专业化的Deltaproteobacteria在碳、氮、硒和硫循环界面上的重要生物地球化学作用，其生态位适应和生态成功可能得益于遗传密码扩展。