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Jiang Z, Liu S, Zhang D, Sha Z. The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean. MICROBIAL ECOLOGY 2023; 86:2781-2789. [PMID: 37552473 PMCID: PMC10640468 DOI: 10.1007/s00248-023-02284-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.
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Affiliation(s)
- Zhichen Jiang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laoshan Laboratory, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sizhen Liu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dechao Zhang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laoshan Laboratory, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhongli Sha
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laoshan Laboratory, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Complete genome sequence of the denitrifying Pseudomonas sp. strain DNDY-54 isolated from deep-sea sediment of ninety east ridge. Mar Genomics 2022; 66:100995. [DOI: 10.1016/j.margen.2022.100995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/09/2022] [Indexed: 11/19/2022]
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Nimonkar YS, Godambe T, Kulkarni A, Patel T, Paul D, Paul D, Rale V, Prakash O. Oligotrophy vs. copiotrophy in an alkaline and saline habitat of Lonar Lake. Front Microbiol 2022; 13:939984. [PMID: 35992701 PMCID: PMC9386271 DOI: 10.3389/fmicb.2022.939984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
We reported our comparative observations on oligotrophs vs. copiotrophs from a hyper-alkaline and hypersaline habitat, Lonar Lake, situated in the Buldhana district of Maharashtra, India. Cell numbers of oligotrophic and copiotrophic microbes from the sediment were enumerated by the three-tube most probable number (MPN) method using an array of nutrient-rich and oligotrophic (≈10–20 mg carbon L−1) media offering simulated natural conditions of pH and salinity. A total of 50 strains from 15 different genera and 30 different species were isolated from the highest positive dilutions of MPN to identify the taxa of oligotrophs and copiotrophic microorganisms dominating in Lonar Lake. We did not get any true oligotrophs due to their adaptation to higher carbon levels during the isolation procedure. On the contrary, several true copiotrophs, which could not adapt and survive on a low-carbon medium, were isolated. It is also observed that changes in medium composition and nutrient level altered the selection of organisms from the same sample. Our data indicate that copiotrophic microorganisms dominate the eutrophic Lonar Lake, which is also supported by the past metagenomics studies from the same site. We also reported that quick depletion of carbon from oligotrophic medium worked as a limiting factor, inducing cell death after 2–3 generations and preventing the development of visible colonies on plates and sufficient optical density in liquid medium. Therefore, a long-term supply of low levels of carbon, followed by isolation on enriched media, can serve as a good strategy in isolation of novel taxa of microorganism, with industrial or environmental importance.
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Affiliation(s)
- Yogesh S. Nimonkar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Tejashree Godambe
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Apurva Kulkarni
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Tarachand Patel
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Dhreej Paul
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Debarati Paul
- Amity Institute of Biotechnology, Amity University Uttar Pradesh (AUUP), Noida, India
| | - Vinay Rale
- Symbiosis School of Biological Sciences (SSBS) Symbiosis International (Deemed University) & Symbiosis Centre for Research & Innovation (SCRI), Symbiosis International (Deemed University), Pune, India
| | - Om Prakash
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
- *Correspondence: Om Prakash ;
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