Heterotrophic bacteria play an important role in driving carbon cycle in the ocean. Bacterial production (BP) and respiration (BR), as well as bacterial community composition (BCC), were determined seasonally in the productive Luhuitou fringing reef and the surrounding oligotrophic ocean in the northern South China Sea, in order to address effect of substrate availability on thermal response of bacterial metabolic activity. Our results show that thermal response of heterotrophic bacteria is greater in the highly productive coral reef than the surrounding oligotrophic ocean. High substrate availability facilitates the growth of bacteria with high nucleic acid content (HNA bacteria), leading to enhanced BP in the coral reef. Temperature shapes BCC in the coral reef, triggering the growth of opportunistic bacteria. Bacterial respiration is more sensitive to temperature change than bacterial production. Warming not only favors the growth of HNA bacteria and shift BCC in the coral reef, but also enhances dissolved oxygen consumption owing to high BR, consequently threatening the survival of corals. Our findings improve our understanding of how substrate availability mediates thermal response of heterotrophic bacteria.

Bacteria,warming,microbial community structure