1
|
Huang Y, Abdugheni R, Ma J, Wang R, Gao L, Liu Y, Li W, Cai M, Li L. Halomonas flagellata sp. nov., a halophilic bacterium isolated from saline soil in Xinjiang. Arch Microbiol 2023; 205:340. [PMID: 37750964 DOI: 10.1007/s00203-023-03670-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/27/2023]
Abstract
A Gram-stain-negative, strictly aerobic, motile, slightly curved rod-shaped bacterium with multiple flagella, designated strain EGI 63088T, was isolated from a bulk soil of Kalidium foliatum, collected from Wujiaqu in Xinjiang Uighur Autonomous Region, PR China. The optimal growth temperature, salinity, and pH for strain EGI 63088T growth were 30 °C, 3% (w/v) NaCl and 8, respectively. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain EGI 63088T showed the highest sequence similarities to Halomonas heilongjiangensis 9-2T (97.94%), H. lysinitropha 3(2)T (97.51%), and H. daqiaonensis CGMCC 1.9150T (97.08%). The average nucleotide identity and digital DNA-DNA hybridization values between the strain EGI 63088T and H. heilongjiangensis 9-2T were 89.03 and 41.10%, respectively. The DNA G + C content of the genome for strain EGI 63088T was 66.3 mol%. The most prevalent antibiotic resistance and virulence-related genes in Halomonas genomes were Streptomyces cinnamoneu EF-Tu mutant, pilT, and cheY, respectively. The predominant fatty acids of strain EGI 63088T were summed feature 8 (C18: 1 ω6c and/or C18: 1 ω7c), summed feature 3 (C16: 1 ω6c and/or C16: 1 ω7c), and C16: 0; its major respiratory quinone was ubiquinone-9 (Q-9), and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. According to the above results, strain EGI 63088T is considered a novel species of the genus Halomonas, for which the name Halomonas flagellata sp. nov. is proposed. The type strain is EGI 63088T (= KCTC 92047T = CGMCC 1.19133T).
Collapse
Affiliation(s)
- Yin Huang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Jinbiao Ma
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Rui Wang
- School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, People's Republic of China
| | - Lei Gao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yonghong Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Wenjun Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Man Cai
- China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| |
Collapse
|
2
|
Liu W, Cong B, Lin J, Zhao L, Liu S. Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment. BMC Genomics 2022; 23:713. [PMID: 36261793 PMCID: PMC9580203 DOI: 10.1186/s12864-022-08942-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/13/2022] [Indexed: 11/10/2022] Open
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.
Collapse
Affiliation(s)
- Wenqi Liu
- School of Advanced Manufacturing, Fuzhou University, Fuzhou, 350108, China
| | - Bailin Cong
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
| | - Jing Lin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Linlin Zhao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Shenghao Liu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| |
Collapse
|
3
|
Kumawat C, Kumar A, Parshad J, Sharma SS, Patra A, Dogra P, Yadav GK, Dadhich SK, Verma R, Kumawat GL. Microbial Diversity and Adaptation under Salt-Affected Soils: A Review. Sustainability 2022; 14:9280. [DOI: 10.3390/su14159280] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The salinization of soil is responsible for the reduction in the growth and development of plants. As the global population increases day by day, there is a decrease in the cultivation of farmland due to the salinization of soil, which threatens food security. Salt-affected soils occur all over the world, especially in arid and semi-arid regions. The total area of global salt-affected soil is 1 billion ha, and in India, an area of nearly 6.74 million ha−1 is salt-stressed, out of which 2.95 million ha−1 are saline soil (including coastal) and 3.78 million ha−1 are alkali soil. The rectification and management of salt-stressed soils require specific approaches for sustainable crop production. Remediating salt-affected soil by chemical, physical and biological methods with available resources is recommended for agricultural purposes. Bioremediation is an eco-friendly approach compared to chemical and physical methods. The role of microorganisms has been documented by many workers for the bioremediation of such problematic soils. Halophilic Bacteria, Arbuscular mycorrhizal fungi, Cyanobacteria, plant growth-promoting rhizobacteria and microbial inoculation have been found to be effective for plant growth promotion under salt-stress conditions. The microbial mediated approaches can be adopted for the mitigation of salt-affected soil and help increase crop productivity. A microbial product consisting of beneficial halophiles maintains and enhances the soil health and the yield of the crop in salt-affected soil. This review will focus on the remediation of salt-affected soil by using microorganisms and their mechanisms in the soil and interaction with the plants.
Collapse
|
4
|
Moopantakath J, Imchen M, Kumavath R, Martínez-Espinosa RM. Ubiquitousness of Haloferax and Carotenoid Producing Genes in Arabian Sea Coastal Biosystems of India. Mar Drugs 2021; 19:442. [PMID: 34436281 DOI: 10.3390/md19080442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 12/14/2022] Open
Abstract
This study presents a comparative analysis of halophiles from the global open sea and coastal biosystems through shotgun metagenomes (n = 209) retrieved from public repositories. The open sea was significantly enriched with Prochlorococcus and Candidatus pelagibacter. Meanwhile, coastal biosystems were dominated by Marinobacter and Alcanivorax. Halophilic archaea Haloarcula and Haloquandratum, predominant in the coastal biosystem, were significantly (p < 0.05) enriched in coastal biosystems compared to the open sea. Analysis of whole genomes (n = 23,540), retrieved from EzBioCloud, detected crtI in 64.66% of genomes, while cruF was observed in 1.69% Bacteria and 40.75% Archaea. We further confirmed the viability and carotenoid pigment production by pure culture isolation (n = 1351) of extreme halophiles from sediments (n = 410 × 3) sampling at the Arabian coastline of India. All red-pigmented isolates were represented exclusively by Haloferax, resistant to saturated NaCl (6 M), and had >60% G + C content. Multidrug resistance to tetracycline, gentamicin, ampicillin, and chloramphenicol were also observed. Our study showed that coastal biosystems could be more suited for bioprospection of halophiles rather than the open sea.
Collapse
|
5
|
Wenting R, Montazersaheb S, Khan SA, Kim HM, Tarhriz V, Hejazi MA, Hejazi MS, Jeon CO. Halomonas azerica sp. nov., Isolated from Urmia Lake in Iran. Curr Microbiol 2021; 78:3299-3306. [PMID: 34132870 DOI: 10.1007/s00284-021-02482-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/26/2021] [Indexed: 11/26/2022]
Abstract
A novel moderately halophilic, Gram-staining negative and facultative aerobic bacterium, designated as TBZ9T, was isolated from water of Urmia Lake in Azerbaijan region of Iran. The cells were found to be rod-shaped and motile, growing in the form of creamy, convex and shiny colonies. The strain could grow in the presence of NaCl at concentrations 1-17% (w/v) (optimum, 3%), temperatures 10-40 °C (optimum, 30 °C) and pH 6.0-11.0 (optimum, pH 7.0) on marine agar. Strain TBZ9T 16S rRNA gene sequence was related to the genus Halomonas showing highest similarities to Halomonas arcis AJ282T (98.4%), Halomonas songnenensis NEAU-ST10-39T (98.0%) and Halomonas lutescens Q1UT (97.8%). In the phylogenetic trees, strain TBZ9T formed a distinct branch closely related to a subclade inside the Halomonas genus. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain TBZ9T and H. arcis AJ282T (20.0%, 74.0%) and H. songnenensis NEAU-ST10-39T (19.8%, 75.2%) indicated that TBZ9T represents a distinct species. Evaluation of fatty acid contents determined C10:0, C16:0, C12:0 3-OH, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) as major cellular fatty acids. The major quinone of strain TBZ9T was Q-9. Polar lipid patterns consisted of phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unidentified phospholipids (PL) and four unidentified polar lipids (L). The average DNA G + C content of strain TBZ9T is 55.4 mol%. Results from phenotypic, chemotaxonomic and molecular analysis suggest that the strain TBZ9T represents a novel species within the genus Halomonas for which the name Halomonas azerica sp. nov. is proposed. The type strain is TBZ9T (= KACC 21783T = LMG 25775T).
Collapse
Affiliation(s)
- Ruan Wenting
- Department of Life Science, Chung Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Soheila Montazersaheb
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shehzad Abid Khan
- Department of Life Science, Chung Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Hyung Min Kim
- Department of Life Science, Chung Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Amin Hejazi
- Branch for the Northwest and West Region, Agriculture Biotechnology Research Institute of Iran (ABRII), Tabriz, Iran
| | - Mohammad Saeid Hejazi
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
- Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Che Ok Jeon
- Department of Life Science, Chung Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea.
| |
Collapse
|