Integrated metagenomic and metaproteomic analyses reveal bacterial micro-ecological mechanisms in coral bleaching

Abstract

ABSTRACT Coral bleaching has been rapidly increasing in recent years due to abnormally elevated temperature, leading to massive damage to coral reefs worldwide. Understanding the processes and micro-ecological mechanisms of coral symbionts in response to bleaching is crucial as evidence accumulates that micro-organisms (particularly the bacteria) contribute to the health and recovery of coral, especially during heat stress. However, the exact functional mechanism of bacteria has not yet been fully elucidated. In this study, we performed metagenomic and metaproteomic analyses of healthy and bleached Acropora muricata corals to identify taxonomic and functional shifts in coral symbionts during a natural thermal bleaching event on Hainan Island. The results showed that symbiont species tended to be more abundant in bleached corals than healthy corals, and the bacterial community appeared to be crucial to coral bleaching. The relative abundance of opportunistic pathogens dramatically increased in bleached corals, accompanied by the reduction of beneficial bacteria. In addition, a direct comparison of metagenomic data sets indicated major changes in functional genes, with bleached corals exhibiting significant metabolic enrichment, while healthy corals maintained lower metabolism and energy consumption. Carbohydrate-active enzyme genes were remarkably activated, and virulence factors were highly represented in bleached corals, which was directly related to the increased abundance of pathogenic bacteria. Metaproteomic analysis also demonstrated that bleaching greatly affected photosynthesis and energy metabolism of coral symbionts. Among them, the biological processes of photosynthesis and chlorophyll biosynthesis were common in healthy corals, while pathways involved in gluconeogenesis and apoptosis were significantly enriched in bleached corals. Bacteria-mediated processes in healthy corals contribute to maintaining the basic functions of symbionts and resisting stress, whereas the proliferation of pathogenic bacteria in bleached corals leads to metabolic abnormalities of symbionts, showing enhanced energy metabolism and catalytic activity. In summary, the two omics analyzes revealed that bleaching caused enormous physiological damage to corals, and bacterial imbalance and dysfunction were the potential micro-ecological mechanisms underlying this event. IMPORTANCE Coral reefs worldwide are facing rapid decline due to coral bleaching. However, knowledge of the physiological characteristics and molecular mechanisms of coral symbionts respond to stress is scarce. Here, metagenomic and metaproteomic approaches were utilized to shed light on the changes in the composition and functions of coral symbiotic bacteria during coral bleaching. The results demonstrated that coral bleaching significantly affected the composition of symbionts, with bacterial communities dominating in bleached corals. Through differential analyses of gene and protein expression, it becomes evident that symbionts experience functional disturbances in response to heat stress. These disturbances result in abnormal energy metabolism, which could potentially compromise the health and resilience of the symbionts. Furthermore, our findings highlighted the highly diverse microbial communities of coral symbionts, with beneficial bacteria providing critical services to corals in stress responses and pathogenic bacteria driving coral bleaching. This study provides comprehensive insights into the complex response mechanisms of coral symbionts under heat stress from the micro-ecological perspective and offers fundamental data for future monitoring of coral health.