Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris

Zhaolong Nie; Kaihao Tang; Weiquan Wang; Pengxia Wang; Yunxue Guo; Yan Wang; Shuh-Ji Kao; Jianping Yin; Xiaoxue Wang

doi:10.3389/fmicb.2023.1138751

Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris

Front Microbiol. 2023 Apr 20:14:1138751. doi: 10.3389/fmicb.2023.1138751. eCollection 2023.

Authors

Zhaolong Nie^{1

2}, Kaihao Tang^{1

2

3}, Weiquan Wang², Pengxia Wang^{2

3

4}, Yunxue Guo^{2

3

4}, Yan Wang¹, Shuh-Ji Kao¹, Jianping Yin², Xiaoxue Wang^{2

3

4}

Affiliations

¹ State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China.
² Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
³ Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
⁴ University of Chinese Academy of Sciences, Beijing, China.

Abstract

Green sulfur bacteria (GSB) are a distinct group of anoxygenic phototrophic bacteria that are found in many ecological niches. Prosthecochloris, a marine representative genus of GSB, was found to be dominant in some coral skeletons. However, how coral-associated Prosthecochloris (CAP) adapts to diurnal changing microenvironments in coral skeletons is still poorly understood. In this study, three Prosthecochloris genomes were obtained through enrichment culture from the skeleton of the stony coral Galaxea fascicularis. These divergent three genomes belonged to Prosthecochloris marina and two genomes were circular. Comparative genomic analysis showed that between the CAP and non-CAP clades, CAP genomes possess specialized metabolic capacities (CO oxidation, CO₂ hydration and sulfur oxidation), gas vesicles (vertical migration in coral skeletons), and cbb ₃-type cytochrome c oxidases (oxygen tolerance and gene regulation) to adapt to the microenvironments of coral skeletons. Within the CAP clade, variable polysaccharide synthesis gene clusters and phage defense systems may endow bacteria with differential cell surface structures and phage susceptibility, driving strain-level evolution. Furthermore, mobile genetic elements (MGEs) or evidence of horizontal gene transfer (HGT) were found in most of the genomic loci containing the above genes, suggesting that MGEs play an important role in the evolutionary diversification between CAP and non-CAP strains and within CAP clade strains. Our results provide insight into the adaptive strategy and population evolution of endolithic Prosthecochloris strains in coral skeletons.

Keywords: Prosthecochloris; adaptive strategy; coral skeleton; endolithic bacteria; mobile genetic elements.