Supplementary information and georeferenced photomosaic of the Chapopote bubble site during RV METEOR cruise M114/2

Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts of MOX symbionts in hosts from a group previously assumed to have low microbial abundances. These symbionts belonged to the Marine Methylotrophic Group 2 clade. They are host-specific and likely vertically transmitted, based on their presence in sponge embryos and streamlined genomes, which lacked genes typical of related free-living MOX. Moreover, genes known to play a role in host–symbiont interactions, such as those that encode eukaryote-like proteins, were abundant and expressed. Methane assimilation by the symbionts was one of the most highly expressed metabolic pathways in the sponges. Molecular and stable carbon isotope patterns of lipids confirmed that methane-derived carbon was incorporated into the hosts. Our results revealed that two species of sponges, although distantly related, independently established highly specific, nutritional symbioses with two closely related methanotrophs. This convergence in symbiont acquisition underscores the strong selective advantage for these sponges in harboring MOX bacteria in the food-limited deep sea.

海绵承载着极其多样的微生物共生体，但其微生物所提供的益生功能却鲜为人知。本研究报道了两种采自深海沥青冷泉的海绵新物种，并证实它们与甲烷氧化（methane-oxidizing, MOX）细菌形成了营养共生关系。宏基因组学（metagenomics）与成像分析结果显示，在此前被认为微生物丰度较低的海绵类群宿主中，MOX共生菌的丰度异乎寻常地高。这些共生菌隶属于海洋甲基营养菌群2分支（Marine Methylotrophic Group 2 clade）。鉴于它们存在于海绵胚胎中且基因组高度精简——缺失自由生活同类MOX菌的典型基因，这些共生菌具有宿主特异性，且大概率通过垂直传播方式传递。此外，参与宿主-共生菌互作的基因（如编码真核样蛋白（eukaryote-like proteins）的基因）不仅丰富，且表达活跃。共生菌的甲烷同化通路是海绵体内表达量最高的代谢通路之一。脂质的分子特征与稳定碳同位素（stable carbon isotope）模式证实，甲烷衍生的碳被整合进入宿主机体。本研究结果表明，尽管两种海绵亲缘关系较远，但它们分别与两种近缘的甲烷营养体（methanotrophs）建立了高度特异性的营养共生关系。这种共生体获取方式上的趋同演化，凸显了在食物匮乏的深海环境中，海绵携带MOX细菌所具备的极强选择优势。