Wei Tao-Shu, Gao Zhao-Ming, Gong Lin, Li Qing-Mei, Zhou Ying-Li, Chen Hua-Guan, He Li-Sheng, Wang Yong
Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
University of Chinese Academy of Sciences, Beijing, China.
Front Microbiol. 2023 Feb 8;14:1078171. doi: 10.3389/fmicb.2023.1078171. eCollection 2023.
Sponges are widely distributed in the global ocean and harbor diverse symbiotic microbes with mutualistic relationships. However, sponge symbionts in the deep sea remain poorly studied at the genome level. Here, we report a new glass sponge species of the genus and provide a genome-centric view of its microbiome. We obtained 14 high-quality prokaryotic metagenome-assembled genomes (MAGs) affiliated with the phyla Nitrososphaerota, Pseudomonadota, Nitrospirota, Bdellovibrionota, SAR324, Bacteroidota, and Patescibacteria. In total, 13 of these MAGs probably represent new species, suggesting the high novelty of the deep-sea glass sponge microbiome. An ammonia-oxidizing Nitrososphaerota MAG B01, which accounted for up to 70% of the metagenome reads, dominated the sponge microbiomes. The B01 genome had a highly complex CRISPR array, which likely represents an advantageous evolution toward a symbiotic lifestyle and forceful ability to defend against phages. A sulfur-oxidizing Gammaproteobacteria species was the second most dominant symbiont, and a nitrite-oxidizing Nitrospirota species could also be detected, but with lower relative abundance. species represented by two MAGs, B11 and B12, were first reported as potential predatory symbionts in deep-sea glass sponges and have undergone dramatic genome reduction. Comprehensive functional analysis indicated that most of the sponge symbionts encoded CRISPR-Cas systems and eukaryotic-like proteins for symbiotic interactions with the host. Metabolic reconstruction further illustrated their essential roles in carbon, nitrogen, and sulfur cycles. In addition, diverse putative phages were identified from the sponge metagenomes. Our study expands the knowledge of microbial diversity, evolutionary adaption, and metabolic complementarity in deep-sea glass sponges.
海绵广泛分布于全球海洋中，拥有各种具有互利共生关系的共生微生物。然而，深海海绵共生体在基因组水平上仍研究不足。在此，我们报告了一个新的属的玻璃海绵物种，并提供了其微生物组的以基因组为中心的观点。我们获得了14个高质量的原核生物宏基因组组装基因组（MAG），它们隶属于亚硝化球菌门、假单胞菌门、硝化螺旋菌门、蛭弧菌门、SAR324、拟杆菌门和Patescibacteria。这些MAG中总共13个可能代表新物种，这表明深海玻璃海绵微生物组具有很高的新颖性。一个氨氧化亚硝化球菌门MAG B01，占宏基因组读数的70%，在海绵微生物组中占主导地位。B01基因组有一个高度复杂的CRISPR阵列，这可能代表了向共生生活方式的有利进化以及抵御噬菌体的强大能力。一种硫氧化γ-变形菌是第二大优势共生体，还能检测到一种亚硝酸盐氧化硝化螺旋菌，但相对丰度较低。由两个MAG（B11和B12）代表的物种首次被报道为深海玻璃海绵中的潜在捕食性共生体，并且经历了显著的基因组缩减。综合功能分析表明，大多数海绵共生体编码CRISPR-Cas系统和用于与宿主进行共生相互作用的类真核生物蛋白。代谢重建进一步说明了它们在碳、氮和硫循环中的重要作用。此外，从海绵宏基因组中鉴定出了多种推定的噬菌体。我们的研究扩展了对深海玻璃海绵中微生物多样性、进化适应性和代谢互补性的认识。
