A research team led by Prof. QIAN Peiyuan, Chair Professor of the Department of Ocean Science at The Hong Kong University of Science and Technology (HKUST), in collaboration with the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), and the Yellow Sea Fisheries Research Institute of the Chinese Academy of Fishery Sciences (CAFS), has achieved a significant breakthrough in understanding the adaptive strategies of the deep-sea black coral Bathypathes pseudoalternata (B. pseudoalternata) and its symbiotic microbiome. The study has been published in the top international journal Cell Host & Microbe.
This study provides the first comprehensive hologenomic analysis of B. pseudoalternata, offering profound insights into how this deep-sea coral survives in extreme habitats through nutritional complementarity, metabolic cooperation, oxidative stress defense, antiviral protection, and immune homeostasis. The findings introduce a novel conceptual model in which deep-sea corals maintain a simplified, efficient, and functionally complementary symbiotic system, serving as a valuable reference for identifying deep-sea functional gene resources.
To address the central question of how deep-sea corals sustain a highly simplified yet efficient symbiotic consortium, the team developed an integrated analytical framework encompassing host genomics, microbial community profiling, symbiont genomes, spatial localization, and transcriptional activity. This multi-layered approach enabled a systematic interpretation of symbiotic stability, nutritional cooperation, and immune regulation in B. pseudoalternata. The researchers successfully assembled a high-quality, chromosome-level genome comprising 16 chromosomes. Gene family expansion analyses revealed enrichment in pathways associated with nutrient uptake, endocytosis and lysosomal function, and immune responses, highlighting the coral's strategy to enhance material absorption and cellular digestion under nutrient-depleted deep-sea environments. The coral genome lacks complete biosynthetic pathways for several amino acids and vitamins, indicating its genetic dependence on symbiotic microbes for essential metabolic inputs.
Microbial analyses of samples collected from various depths and regions across the western Pacific Ocean demonstrated that B. pseudoalternata hosts a stable and highly streamlined microbiome distinct from the surrounding environment, suggesting strong host selection for functionally important symbionts. The core symbionts collectively support the coral's survival in extreme deep-sea environments. Ammonia-oxidizing archaea possess carbon-fixation capacity and ammonia oxidation pathways that contribute to detoxification and the synthesis of amino acids and vitamins for the host. A newly identified alphaproteobacteria provides heme, lipoic acid, glutathione, and fatty acids that can supply nutrients to the host. Additionally, two highly reduced Oceanoplasmataceae species encode CRISPR/Cas and restriction-modification systems, forming an antiviral defense barrier for the coral. Together, these symbionts provide nutritional supplementation, detoxification functions, biosynthesis of essential metabolites, oxidative stress protection, and virus defense.
"Our research highlights the remarkable adaptability of deep-sea corals and underscores the importance of their symbiotic relationships with microbiome in extreme environments", Prof. Qian concluded.
This research was supported by the National Natural Science Foundation for Young Scientist of China, the National Key R&D Program of China, the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), the HKSAR Government, the HKUST Otto Poon Center for Climate Resilience and Sustainability, the Natural Science Foundation for Young Scientists of Shandong, China, the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao), the Major Scientific and Technological Projects of Hainan Province, the AoShan Talents Cultivation Program Supported by Laoshan National Laboratory for Marine Science and Technology, and the Central Public-interest Scientific Institution Basal Research Fund from CAFS.
The paper is co-corresponded by Dr. SHAO Changwei S (CAFS), Prof. QIAN Peiyuan (HKUST), Dr. MENG Liang (BGI Research), and Dr. LIU Shanshan (BGI Research). WEI Zhanfei (CAFS), LAN Yi (HKUST), and MENG Li-Hui (Qingdao Agricultural University) contributed equally as co-first authors.
