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

Abstract

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 NH4+ 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.

Unveiling potential virulence determinants in Vibrio isolates from Anadara tuberculosa through whole genome analyses

“…Among our isolates, we identified species that have been reported as pathogens in both humans and aquatic organisms, such as V. alginolyticus and V. parahaemolyticus. V. parahaemolyticus , a prominent cause of seafood-associated bacterial gastroenteritis worldwide ( 56 ), has also been documented as a pathogen in shrimp ( 57 – 59 ) and has been associated with significant mortality in mollusks ( 60 , 61 ). V. alginolyticus has been reported to cause superficial wound infections ( 62 ) and is linked to mass mortality events in mollusks ( 61 , 63 , 64 ).…”

In-Depth Genome Characterization and Pan-Genome Analysis of Strain KMM 296, a Producer of Highly Active Alkaline Phosphatase; Proposal for the Reclassification of Cobetia litoralis and Cobetia pacifica as the Later Heterotypic Synonyms of Cobetia amphilecti and Cobetia marina, and Emended Description of the Species Cobetia amphilecti and Cobetia marina

“…The temperature range for growth was assessed on marine agar (MA). Tolerance to NaCl was assessed in medium containing 5 g Bacto Peptone (Difco), 2 g Bacto Yeast Extract (Difco), 1 g glucose, 0.02 g KH 2 PO 4 , and 0.05 g MgSO 4 •7H 2 O per liter of distilled water with 0, 0.5, 1.0, 1.5, 2.0, 2.5, 3,4,5,6,8,10,12,15,17,19, and 20% (w/v) of NaCl. Susceptibility to antibiotics was examined via the routine disc diffusion plate method.…”

“…The genus accommodates Gram-stain-negative, aerobic, heterotrophic, halophilic, and rod-shaped bacteria, which can move by means of a single polar flagellum and/or two to seven lateral flagella [1][2][3]. Many strains of the genus Cobetia have been reported as a source of molecules and activities of biotechnological interest, and the genomic analysis of these strains has revealed their potential for the biosynthesis of biosurfactants, aromatic hydrocarbon degradation, inorganic carbon fixation, the synthesis and production of polyhydroxy-alkanoates, surface colonization, and alginate degradation [4][5][6][7][8]. Earlier, in the course of a survey of Halomonaslike bacteria inhabiting different areas of the Northwest Pacific, the strain KMM 296 was isolated from the coelomic fluid of the mussel Crenomytilus grayanus, collected from the Sea of Japan, and initially identified as a representative of the species C. marina (formerly Deleya marina) [9,10].…”