Microbially-mediated halogenation and dehalogenation cycling of organohalides in the ocean

As the Earth's largest reservoir of dissolved organic carbon, sulfur, and halogen species, the ocean is a hotspot for biogeochemical element cycling, potentially influencing global food webs and climate. Nonetheless, in contrast to the extensively studied organic carbon and sulfur cycles, investigation on the biogeochemical cycling of organohalides in the ocean is still in its infancy. Metagenome sequencing has offered new opportunities to advance our understanding of microbially mediated organohalide cycling. However, there are problems in applying publicly available orthology databases to identify organohalide-cycling genes such as inefficient database searching, inaccurate functional annotation and low coverage of organohalide-cycling genes/pathways. Therefore, it is essential to develop a comprehensive and accurate database for characterizing organohalide-cycling genes. To solve those problems, we constructed a manually curated organohalide-cycling gene database (HaloCycDB) for metagenomic analysis of microbially mediated organohalide-cycling process in the environment. Here, protein sequences from HaloCycDB were recruited from multiple public databases including UniProt, NCBI nr, KEGG, COG, eggNOG, arCOG. HaloCycDB covers 7 dehalogenation processes (oxidative dehalogenase, hydrolytic dehalogenase, reductive dehalogenase, glutathione S-transferase, methyltransferase, dehydrochlorinase, and halohydrin dehalogenase) and 4 halogenation processes (flavin-dependent halogenase, vanadium-dependent halogenase, nonheme iron-dependent halogenase, and S-adenosyl-L-methionine-dependent halogenase), containing sequences of 221 functionally-characterized genes and 187,289 representative homologous genes. HaloCycDB and the associated Python scripts will greatly promote the study of microbially mediated organohalide cycling.