Genome reduction and microbe-host interactions drive adaptation of a sulfur-oxidizing bacterium associated with a cold seep sponge

As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored “differential coverage binning” method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed “Gsub”) may represent a new deep-sea SOB group. Microscopic observations suggest that Gsub is probably an extracellular symbiont. Gsub has complete sulfide oxidation and carbon fixation pathways, suggesting a chemoautotrophic lifestyle. Comparative genomics with other sponge-associated SOB and free-living SOB revealed significant genome reduction in Gsub, characterized by the loss of genes for carbohydrate metabolism, motility, DNA repair, ...

作为最古老的后生动物（metazoan），海绵与特定的微生物共生体已建立起紧密的共生关系。然而，深海海绵中化能自养硫氧化共生体的特征与生理特性，在很大程度上仍未被探明。我们针对22-Gb的宏基因组序列，采用定制化的差异覆盖度分箱法（differential coverage binning），成功恢复得到了在冷泉海绵Suberites sp.菌群中占主导地位的硫氧化细菌（SOB）的近乎完整基因组。系统发育分析表明，这株被命名为"Gsub"的未分类γ-变形菌纲细菌，可能代表一个全新的深海硫氧化细菌类群。显微镜观测结果显示，Gsub大概率为胞外共生体。Gsub拥有完整的硫化物氧化与固碳通路，这表明其具备化能自养的生活方式。通过与其他海绵共生硫氧化细菌以及自由生活硫氧化细菌开展比较基因组学分析，我们发现Gsub存在显著的基因组缩减现象，其特征为丢失了碳水化合物代谢、运动相关以及DNA修复等相关基因……