A research team led by Prof. QIAN Peiyuan from The Hong Kong University of Science and Technology (HKUST) has made a groundbreaking discovery regarding the deep-sea black coral, Bathypathes pseudoalternata. Collaborating with the Southern Marine Science and Engineering Guangdong Laboratory in Guangzhou and the Yellow Sea Fisheries Research Institute of the Chinese Academy of Fishery Sciences, the team published their findings in the prestigious journal Cell Host & Microbe in March 2024. This study provides a comprehensive understanding of the adaptive strategies employed by this coral and its symbiotic microbiome.
The research presents the first detailed hologenomic analysis of B. pseudoalternata, revealing how this deep-sea coral thrives in extreme environments through mechanisms such as nutritional complementarity, metabolic cooperation, and immune regulation. The findings introduce a novel conceptual model that illustrates how deep-sea corals maintain a simplified, efficient, and functionally complementary symbiotic system. This model serves as a vital reference for identifying functional gene resources in deep-sea ecosystems.
To explore how B. pseudoalternata sustains its symbiotic consortium, the research team developed an integrated analytical framework. This framework encompassed host genomics, microbial community profiling, symbiont genomes, spatial localization, and transcriptional activity. Their multi-layered approach facilitated a systematic interpretation of symbiotic stability and the nutritional cooperation necessary for the coral’s survival.
The research revealed a high-quality, chromosome-level genome for B. pseudoalternata, consisting of 16 chromosomes. An analysis of gene family expansions showed significant enrichment in pathways related to nutrient uptake, endocytosis, lysosomal function, and immune responses. These findings highlight the coral’s strategies for enhancing material absorption and cellular digestion in nutrient-poor deep-sea environments. Notably, the coral genome lacks complete biosynthetic pathways for several essential amino acids and vitamins, indicating its reliance on symbiotic microbes for vital metabolic inputs.
Microbial analyses conducted on samples collected from various depths across the western Pacific Ocean demonstrated that B. pseudoalternata hosts a stable and streamlined microbiome distinct from its surrounding environment. This suggests a strong host selection process for functionally important symbionts that collectively support the coral’s survival in harsh deep-sea conditions.
Among the key symbionts identified, ammonia-oxidizing archaea exhibit carbon-fixation capabilities and ammonia oxidation pathways that contribute to detoxification and the synthesis of essential metabolites for the host. A newly identified alphaproteobacteria species provides crucial nutrients such as heme, lipoic acid, glutathione, and fatty acids. Additionally, two highly reduced species within the Oceanoplasmataceae family encode CRISPR/Cas and restriction-modification systems, creating an antiviral defense mechanism for the coral.
“Our research highlights the remarkable adaptability of deep-sea corals and underscores the importance of their symbiotic relationships with microbiomes in extreme environments,” said Prof. QIAN. The study received support from various organizations, including the National Natural Science Foundation for Young Scientist of China and the National Key R&D Program of China, among others.
The collaborative effort involved several researchers, with co-corresponding authors including Dr. SHAO Changwei from CAFS, Dr. MENG Liang and Dr. LIU Shanshan, both from BGI Research, and Prof. QIAN. Contributing equally as co-first authors were WEI Zhanfei from CAFS, LAN Yi from HKUST, and MENG Li-Hui from Qingdao Agricultural University.
This research adds significant value to the understanding of deep-sea ecosystems and the intricate relationships between corals and their microbial partners, paving the way for further studies in marine biology and ecology.
