Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment

BACKGROUND: Bacteria are an essential component of the earth`s biota and affect circulation of matters through their metabolic activity. They also play an important role in the carbon and nitrogen cycle in the deep-sea environment. In this paper, two strains from deep-sea sediments were investigated in order to understand nitrogen cycling involved in the deep-sea environment. RESULTS: In this paper, the basic genomic information of two strains was obtained by whole genome sequencing. The Cobetia amphilecti N-80 and Halomonas profundus 13 genome sizes are 4,160,095 bp with a GC content of 62.5% and 5,251,450 bp with a GC content of 54.84%. Through a comparison of functional analyses, we predicted the possible C and N metabolic pathways of the two strains and determined that Halomonas profundus 13 could use more carbon sources than Cobetia amphilecti N-80. The main genes associated with N metabolism in Halomonas profundus 13 are narG, narY, narI, nirS, norB, norC, nosZ, and nirD. On the contrast, nirD, using NH(4)(+) for energy, plays a main role in Cobetia amphilecti N-80. Both of them have the same genes for fixing inorganic carbon: icd, ppc, fdhA, accC, accB, accD, and accA. CONCLUSION: In this study, the whole genomes of two strains were sequenced to clarify the basic characteristics of their genomes, laying the foundation for further studying nitrogen-metabolizing bacteria. Halomonas profundus 13 can utilize more carbon sources than Cobetia amphilecti N-80, as indicated by API as well as COG and KEGG prediction results. Finally, through the analysis of the nitrification and denitrification abilities as well as the inorganic carbon fixation ability of the two strains, the related genes were identified, and the possible metabolic pathways were predicted. Together, these results provide molecular markers and theoretical support for the mechanisms of inorganic carbon fixation by deep-sea microorganisms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08942-6.