Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India

Pandiyan, Kurinji; Kushwaha, Prity; Bagul, Samadhan Yuvraj; Chakdar, Hillol; Madhaiyan, Munusamy; Krishnamurthi, Srinivasan; Kumar, P. Anil; Karthikeyan, N.; Singh, Arjun; Kumar, Murugan; Singh, Udai B.; Saxena, Anil Kumar

doi:10.1099/ijsem.0.004611

Cited by 11 publications

(7 citation statements)

References 36 publications

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“…de/genus/halomonas) [4] at the time of writing. Most species in this genus have been isolated from diverse saline environments, such as saline lake [5][6][7][8][9][10][11], solar saltern [12][13][14] and various marine environments [15][16][17][18][19][20]. The Mariana Trench is located in the western Pacific Ocean, about 2550 km long and 70 km wide with a greatest depth of more than 11 km, representing the deepest part of the world's oceans.…”

Section: Introductionmentioning

confidence: 99%

Halomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench

Wang

Wan

Zhang

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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Two novel Gram-stain-negative, facultative anaerobic, non-flagellated, rod-shaped bacterial strains, designated MT13T and MT32, were isolated from sediment samples collected from the Mariana Trench at a depth of 8300 m. The two strains grew at −2–30 °C (optimum, 25 °C), at pH 5.5–10.0 (optimum, pH 7.5–8.0) and with 0–15 % (w/v) NaCl (optimum, 3–6 %). They did not reduce nitrate to nitrite nor hydrolyse Tweens 40 and 80, aesculin, casein, starch and DNA. The genomic G+C contents of draft genomes of strain MT13T and MT32 were 52.2 and 54.1 m ol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains MT13T and MT32 were affiliated with the genus Halomonas , with the highest similarity to the type strain of Halomonas olivaria . The values of average nucleotide identity and in silico DNA–DNA hybridization between strain MT13T and MT32, and between strain MT13T and five closely related type strains of Halomonas species indicated that strains MT13T and MT32 belonged to the same species, but represented a novel species in the genus of Halomonas . The major cellular fatty acids of strains MT13T and MT32 were C16 : 0, summed feature 3(C16 : 1 ω7c/ω6c) and summed feature 8 (C18 : 1 ω7c/ω6c). Major polar lipids of strains MT13T and MT32 included phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Ubiquinone-9 was the predominant respiratory quinone. Based on data from the present polyphasic study, strains MT13T and MT32 represent a novel species of the genus Halomonas , for which the name Halomonas profundi sp. nov. is proposed. The type strain is MT13T (=MCCC 1K06389T=KCTC 82923T).

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Section: Introductionmentioning

confidence: 99%

Halomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench

Wang

Wan

Zhang

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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“…The related genes that we found in Halomonas profundus 13 are narG, narY, narI, nirS, norB, norC, and nosZ, as well as some regulatory proteins related to nitrogen metabolism, narT, narX, narL, nirQ, and nirD. Species within this genus can generally grow at concentrations of 1-12% NaCl, and the most salt-tolerant of these species is Halomonas icarae D1-1 T [15], which can grow in 24% NaCl. The optimum NaCl concentration is generally 3-8%, with the highest optimum of 10% for Halomonas pellis L5 T [14-18, 54, 55].…”

Section: Comparison Of the Two Strainsmentioning

confidence: 80%

“…The genus Halomonas was described as a facultative anaerobe with gram-negative, straight or curved rodlike cells [11,12]. Halomonas is distributed in Lake Pengyanco on the Tibetan Plateau [13], the Bohai Gulf of the Yellow Sea in China [14], the Pentha beach of Odisha in India [15], Urmia Lake in Iran and other places [16]; it grows in Gobi soil [17], salt lake sediment [18], the liquid in the stems of Populus euphratica [19], the rhizosphere sand of a coastal sand dune plant [20] 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.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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.

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“…The related genes that we found in Halomonas profundus 13 are narG, narY, narI, nirS, norB, norC, and nosZ, as well as some regulatory proteins related to nitrogen metabolism, narT, narX, narL, nirQ, and nirD. Species within this genus can generally grow at concentrations of 1-12% NaCl, and the most salt-tolerant of these species is Halomonas icarae D1-1 T [14], which can grow in 24% NaCl. The optimum NaCl concentration is generally 3-8%, with the highest optimum of 10% for Halomonas pellis L5 T [13-17, 60, 61].…”

Section: Comparison Of the Two Strainsmentioning

confidence: 80%

“…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 [12], the Bohai Gulf of the Yellow Sea in China [13], the Pentha beach of Odisha in India [14], Urmia Lake in Iran and other places [15]; it grows in Gobi soil [16], salt lake sediment [17], the liquid in the stems of Populus euphratica [18], the rhizosphere sand of a coastal sand dune plant [19] 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 modi cation available.…”

mentioning

confidence: 99%

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

Liu

Cong²,

Zhao³

et al. 2022

Preprint

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Background: As global warming brings challenges, carbon neutralization, controlling CO2 emissions and the carbon peak are receiving increasing attention. The pelagic realm of the dark ocean represents a key site for the remineralization of organic matter, long-term carbon storage and carbon burial in the biosphere. In this paper, we explored the mechanisms of inorganic carbon fixation by deep-sea microorganisms at the genetic level.Results: In this paper, the basic genomic information of two strains was obtained by whole genome sequencing. The Cobetia amphilecti N-80 genome size is 4,160,095 bp, with a GC content of 62.5%. The Halomonas profundus 13 genome size is 5,251,450 bp, with a GC content of 54.84%. Through a comparison of the genomes and functional analyses, we predicted the C and N metabolic pathways of the two strains and determined that Halomonas profundus 13 can 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. However, nirD, using NH4+ for energy, plays a main role in Cobetia amphilecti N-80. Cobetia amphilecti N-80 and Halomonas profundus 13 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.

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Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India

Cited by 11 publications

References 36 publications

Halomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench

Halomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench

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

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

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