The genus Cobetia is classified within the family Halomonadaceae, order Oceanospirillales, and class Gammaproteobacteria within the phylum Proteobacteria. The genus is characterized by gram-negative, straight, rod-shaped cells of 1.6–4.0 by 0.8–1.2 µm that occur singly and in pairs . Some reports have also revealed that members of the genus Cobetia can produce an alkaline phosphatase with unusually high specific activity [2, 3], can synthesize hydroxyectoine under NaCl induction and are tolerant to osmotic stress , and have antibiofilm activity . In addition, cloning and expression have been performed for several of its functional genes, such as ectABC and its promotor sequence in Cobetia marina CICC10367 , the L-asparaginase gene (CobAsnase) in Cobetia amphilecti AMI6 , and alkaline phosphatase in Cobetia marina . Cobetia amphilecti has the ability to remove excess ammonia-N in seawater ponds, removing 61.7% of the total ammonia-N (50 mg/L) in 8 hr. It also boosted the growth of the Pacific white shrimp Litopenaeus vannamei (p < 0.05) at a concentration of 107 CFU/mL, with no harmful effects on the shrimp's immune system . However, no analysis was conducted at the genetic level.
The Halomonas family was described as a new genus by Vreeland in 1980. In 1996, Dobson & Franzmann proposed that members of the genera Deleya, Halomonas, and Halovibrio should be placed in the genus Halomonas within the phylum Proteobacteria. The genus Halomonas was described as a facultative anaerobe with gram-negative, straight or curved rodlike cells [10, 11]. Halomonas is distributed in Lake Pengyanco on the Tibetan Plateau , the Bohai Gulf of the Yellow Sea in China , the Pentha beach of Odisha in India , Urmia Lake in Iran and other places ; it grows in Gobi soil , salt lake sediment , the liquid in the stems of Populus euphratica , the rhizosphere sand of a coastal sand dune plant  and other environments, with slight or moderate halophily. Among Halomonas sp., Halomonas bluephagenesis is a relatively comprehensively studied species with engineering tools and methods for genetic modification available. Due to its potential for use in contamination treatment, it can be grown under open and continuous processes not only in the lab but also at an at least 1000 L fermentor scale . To date, many studies have explored its potential for the production of L-threonine , starch , 3-hydroxypropionate , functional polyhydroxyalkanoates , bioplastic PHB and ectoine . Halomonas can grow under high salt concentrations at alkaline pH and can resist contamination by other microbes, so it has good prospects for various applications.
The characteristics of high pressure and low temperature in the deep ocean are favorable for CO2 dissolution, and the ocean stores 50 times as much CO2 as the atmosphere . The ocean determines the concentration of carbon dioxide in the atmosphere over the long term. The traditional view is that marine biological productivity occurs mainly in the euphotic layer, relying on carbon dioxide fixation by light energy autotrophs . Cyanobacteria are the most well-known photoautotrophic organisms in the ocean, and their photoautotrophy has even been proposed as a major carbon pathway . The energy requirements below the euphotic layer are mainly supplied from particulate organic matter input from the euphotic layer, which is mineralized and releases energy in the middle ocean . However, research has found that the input energy of the euphotic layer is less than the energy demand of the lower layer. Moreover, the imbalance in the energy budget within the deep sea becomes increasingly obvious with increasing ocean depth [28–31].
Swan proposed that unidentified prokaryotes fix inorganic carbon at globally significant rates in the immense dark ocean, and their activities may partly reconcile the current discrepancies in the dark ocean’s carbon budget. He also demonstrated potential chemolithoautotrophy in several uncultured Proteobacterial lineages that are ubiquitous in the dark oxygenated ocean . The pelagic realm of the dark ocean was reported to represent a key site for the remineralization of organic matter and for long-term carbon storage and burial in the biosphere . The dark ocean below 200 meters comprises approximately 75% of global oceanic volume and contains more than 98% of the global dissolved inorganic carbon pool .
The ocean contains one of the largest microbiomes on Earth, harboring nearly 75% and 50% of global prokaryotic biomass and production, respectively [32, 34]. Therefore, the role of dark ocean microorganisms in carbon sequestration cannot be ignored. Jiao Nianzhi found a new mechanism of marine carbon storage, named the microbial carbon pump (MCP), which is a microbioecological process that converts bioavailable dissolved organic carbon (DOC) into recalcitrant dissolved organic carbon (RDOC) . In this paper, we propose that the basic concept of MCP verifies the fact that more than 95% of organic carbon in the ocean is DOC, and nearly 95% of DOC is RDOC, which is difficult for microorganisms to degrade and can be preserved in the deep sea for thousands of years, constituting the long-term carbon storage of the ocean. However, the output of particulate organic carbon (POC) deposited from the transparent ocean layer to the deep sea is very limited, and the amount of organic carbon reaching the seabed is only approximately 0.1% of marine primary productivity. Most POC is degraded into CO2 by respiration during deposition [36–38]. Therefore, the role of dark ocean microorganisms in carbon sequestration cannot be ignored. At present, the known marine microorganisms that play an important role in fixing inorganic carbon are Thaumarchaeota , Nitrosopumilus maritimus , Nitrospira-like bacteria , and Nitrospira marina . The fixation of inorganic carbon by these microorganisms is mostly coupled with ammonia oxidation, nitrification and other reactions.
Nitrogen (N) is an abundant element on Earth and is an important building block for organic molecules such as nucleic acids, amino acids, and pigments; it is also the prime nutrient required for organismal growth and is abundant in the ocean [43, 44]. According to the plankton average C/N/P ratio (106:16:1) , the nitrogen flux released by downwardly deposited particulate organic matter should be very large . Nitrogen can be ammoniated by microorganisms to produce ammonium. Nonetheless, once ammonium is formed, in the presence of molecular oxygen, it is oxidized by nitrifying bacteria to form nitrite and nitrate . Nitrifying bacteria harvest the chemical energy stored in NH4+ and fix CO2 to synthesize the organics they need. In the absence of oxygen, NO3− can be used by many microbes as a respiratory electron acceptor, and at the same time, nitrate reduction is coupled to the anaerobic oxidation of organic carbon . An article reported that ammonia oxidation to nitrite and its subsequent oxidation provided energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling of reduced inorganic nitrogen pools and the production of new organic carbon in the dark ocean . Current research shows that deep-sea microbial nitrification serves as an important energy source in deep-sea ecosystems by fixing inorganic carbon through chemical energy autotrophy, which even directly affects the food network structure of the deep-sea ecosystem and carbon storage [29, 49]. Therefore, microorganisms can utilize ammonium nitrogen and nitrite oxidation to provide electrons and energy for nitrifying bacteria to fix inorganic carbon, which provides theoretical support for understanding marine carbon storage and enriches the theoretical basis of the nutritional structure in deep-sea ecosystems.
Dissolved organic carbon produced by microorganisms through carbon sequestration can also be further converted into inert dissolved organic carbon by microbial carbon pumps and stored in the deep sea, which can realize the long-term storage of carbon dioxide and influence the carbon flux in the deep sea. In this study, we screened two strains that could grow on both nitrifying and denitrifying medium. We sequenced their whole genomes separately to obtain their basic genomic information for subsequent analysis and to provide a molecular basis for future studies of the two strains. Upon comparing the annotation information and genomic information of the two strains, it is clear that the functional physiological activity of Halomonas profundus 13 is significantly higher than that of Cobetia amphilecti N-80. We found 7 genes related to prokaryotic fixation of inorganic carbon and 5 genes related to nitrification–denitrification in Cobetia amphilecti N-80, whereas there were 8 genes related to prokaryotic fixation of inorganic carbon and 14 genes related to nitrification–denitrification in Halomonas profundus 13. Then, we predicted the relevant metabolic pathways to provide molecular markers and theoretical support for studying biological carbon sequestration in ecosystems.