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Bao Z, Wang C, Cao J, Zhang T, Guo Y, Sato Y, Nishizawa T, Ohta H. Tardiphaga alba sp. nov., a heavy-metal-tolerant bacterium isolated from garden soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38197779 DOI: 10.1099/ijsem.0.006238] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024] Open
Abstract
A previously undescribed, heavy-metal-tolerant, motile, Gram-negative bacterium, designated strain SK50-23T, was characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SK50-23T was closely related to Tardiphaga robiniae LMG 26467T and the non-phototrophic 'Rhodopseudomonas boonkerdii' NS23T (98.1 and 97.3 % 16S rRNA gene sequence similarity, respectively). Strain SK50-23T possessed a circular genome of 5.86 Mb, with a DNA G+C content of 61.9 mol%. Digital DNA-DNA hybridization showed 20.8-21.6 % similarity between strain SK50-23T and related species. In addition, the whole-genome average nucleotide identity values between strain SK50-23T and related species ranged from 75.1 to 83.5 %. The major cellular fatty acid identified in strain SK50-23T was C18 : 1ω7c, and the main isoprenoid quinone present was ubiquinone Q-10. Strain SK50-23T could be assigned to the genus Tardiphaga with the species name Tardiphaga alba sp. nov. based on morphological, chemotaxonomic and genome-based taxonomic characteristics, and 16S rRNA gene-based phylogenetic characteristics. The type strain of the proposed novel species is SK50-23T (=NBRC 108825T=CGMCC No. 1.12037T).
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Affiliation(s)
- Zhihua Bao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan
| | - Chaojun Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Jiahui Cao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Tingting Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Yong Guo
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
- Present address: Institute for Plant Protection, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8605, Japan
| | - Yoshinori Sato
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
- Present address: Center for Conservation Science and Restoration Techniques, National Research Institute for Cultural Properties, Tokyo, Taito-ku, Tokyo 110-8713, Japan
| | - Tomoyasu Nishizawa
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan
| | - Hiroyuki Ohta
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan
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Yao C, Zhang Q, Lin X, Zhao J, Zhang X. Seasonal Hypoxia Enhances Benthic Nitrogen Fixation and Shapes Specific Diazotrophic Community in the Eutrophic Marine Ranch. Processes (Basel) 2023; 11:138. [DOI: 10.3390/pr11010138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Recently, a growing number of studies have confirmed that biological nitrogen fixation is also an important reactive nitrogen source in coastal regions. However, how benthic nitrogen fixation and diazotrophic community in coastal regions respond to seasonal hypoxia remains largely unknown. In this study, we investigated the spatiotemporal pattern of potential nitrogen fixation rate and diazotrophic abundance and community in sediments of a eutrophic marine ranch experiencing summer hypoxia using 15N tracing and high throughput sequencing techniques. The results showed that potential nitrogen fixation rates ranged from 0.013 to 10.199 μmol kg−1 h−1, and were significantly enhanced by summer hypoxia (ANOVA, p < 0.05). However, nifH gene abundance peaked in June. The diazotrophic community was dominated by Geobacteraceae (>60%), followed by Desulfobulbaceae (13.61%). Bottom water oxygen, pH, Chl-a concentration, and sediment NH4+ significantly regulated benthic nitrogen fixation, while the variation of diazotrophic community was explained by sediment TOC, TN, and Fe content (p < 0.05). This study highlighted that hypoxia stimulated benthic nitrogen fixation, which counteracted the nitrogen removal by denitrification and anammox, and could further aggregate eutrophication of the coastal marine ranch. Moreover, the result emphasized the importance of nitrogen fixation in coastal regions for the global N budget.
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Wang T, Wang X, Tian W, Yao L, Li Y, Chen Z, Han H. Screening of Heavy Metal-Immobilizing Bacteria and Its Effect on Reducing Cd 2+ and Pb 2+ Concentrations in Water Spinach ( Ipomoea aquatic Forsk.). Int J Environ Res Public Health 2020; 17:ijerph17093122. [PMID: 32365834 PMCID: PMC7246948 DOI: 10.3390/ijerph17093122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 01/09/2023]
Abstract
Microbial immobilization is considered as a novel and environmentally friendly technology that uses microbes to reduce heavy metals accumulation in plants. To explore microbial resources which are useful in these applications, three water spinach rhizosphere soils polluted by different levels of heavy metals (heavy pollution (CQ), medium pollution (JZ), and relative clean (NF)) were collected. The community composition of heavy metal-immobilizing bacteria in rhizosphere soils and its effects on reducing the Cd2+ and Pb2+ concentrations in water spinach were evaluated. Four hundred strains were isolated from the CQ (belonging to 3 phyla and 14 genera), JZ (belonging to 4 phyla and 25 genera) and NF (belonged to 6 phyla and 34 genera) samples, respectively. In the CQ sample, 137 strains showed a strong ability to immobilize Cd2+ and Pb2+, giving Cd2+ and Pb2+ removal rates of greater than 80% in solution; Brevundimonas, Serratia, and Pseudoarthrobacter were the main genera. In total, 62 strains showed a strong ability to immobilize Cd2+ and Pb2+ in the JZ sample and Bacillus and Serratia were the main genera. A total of 22 strains showed a strong ability to immobilize Cd2+ and Pb2+ in the NF sample, and Bacillus was the main genus. Compared to the control, Enterobacter bugandensis CQ-7, Bacillus thuringensis CQ-33, and Klebsiella michiganensis CQ-169 significantly increased the dry weight (17.16-148%) of water spinach and reduced the contents of Cd2+ (59.78-72.41%) and Pb2+ (43.36-74.21%) in water spinach. Moreover, the soluble protein and Vc contents in the shoots of water spinach were also significantly increased (72.1-193%) in the presence of strains CQ-7, CQ-33 and CQ-169 compared to the control. In addition, the contents of Cd and Pb in the shoots of water spinach meet the standard for limit of Cd2+ and Pb2+ in vegetables in the presence of strains CQ-7, CQ-33 and CQ-169. Thus, the results provide strains as resources and a theoretical basis for the remediation of Cd- and Pb-contaminated farmlands for the safe production of vegetables.
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Affiliation(s)
- Tiejun Wang
- Collaborative Innovation of Water Security for the Water Source Region of Mid-line of the South-to-North Diversion Project of Henan Province, College of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, China; (T.W.); (X.W.); (L.Y.)
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China;
| | - Xiaoyu Wang
- Collaborative Innovation of Water Security for the Water Source Region of Mid-line of the South-to-North Diversion Project of Henan Province, College of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, China; (T.W.); (X.W.); (L.Y.)
| | - Wei Tian
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China;
| | - Lunguang Yao
- Collaborative Innovation of Water Security for the Water Source Region of Mid-line of the South-to-North Diversion Project of Henan Province, College of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, China; (T.W.); (X.W.); (L.Y.)
| | - Yadong Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China;
| | - Zhaojin Chen
- Collaborative Innovation of Water Security for the Water Source Region of Mid-line of the South-to-North Diversion Project of Henan Province, College of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, China; (T.W.); (X.W.); (L.Y.)
- Correspondence: (Z.C.); (H.H.); Tel.: +86-377-63525027 (Z.C. & H.H.)
| | - Hui Han
- Collaborative Innovation of Water Security for the Water Source Region of Mid-line of the South-to-North Diversion Project of Henan Province, College of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, China; (T.W.); (X.W.); (L.Y.)
- Correspondence: (Z.C.); (H.H.); Tel.: +86-377-63525027 (Z.C. & H.H.)
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Tindall BJ. The name Bradyrhizobiaceae Garrity et al. 2006 contains Nitrobacter Winogradsky 1892 (Approved Lists 1980), the nomenclatural type of the family Nitrobacteraceae Buchanan 1917 (Approved Lists 1980), is illegitimate and proposals to alter the wording of Rule 54 of the International Code of Nomenclature of Prokaryotes to clarify the fact that the family name Bradyrhizobiaceae Garrity et al. 2006 is replaced by the family name Nitrobacteraceae Buchanan 1917 (Approved Lists 1980) the only correct name. Int J Syst Evol Microbiol 2019; 69:2609-11. [DOI: 10.1099/ijsem.0.003253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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De Meyer SE, Coorevits A, Willems A. Tardiphaga robiniae gen. nov., sp. nov., a new genus in the family Bradyrhizobiaceae isolated from Robinia pseudoacacia in Flanders (Belgium). Syst Appl Microbiol 2012; 35:205-14. [PMID: 22444281 DOI: 10.1016/j.syapm.2012.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 01/24/2012] [Accepted: 02/11/2012] [Indexed: 11/20/2022]
Abstract
Gram-negative, rod-shaped bacteria were isolated from Robinia pseudoacacia root nodules. On the basis of the 16S rRNA gene phylogeny, they are closely related to Bradyrhizobium, Rhodopseudomonas and Nitrobacter species (97% sequence similarity), belonging to the class Alphaproteobacteria and family Bradyrhizobiaceae. The results of physiological and biochemical tests together with sequence analysis of housekeeping genes (atpD, dnaK, gyrB, recA and rpoB) allowed differentiation of this group from other validly published Bradyrhizobiaceae genera. NodA, nodC and nifH genes could not be amplified. On the basis of genotypic and phenotypic data, these organisms represent a novel genus and species for which the name Tardiphaga robiniae gen. nov., sp. nov. (LMG 26467(T)=CCUG 61473(T)), is proposed.
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Noisangiam R, Nuntagij A, Pongsilp N, Boonkerd N, Denduangboripant J, Ronson C, Teaumroong N. Erratum to “Heavy metal tolerant Metalliresistens boonkerdii gen. nov., sp. nov., a new genus in the family Bradyrhizobiaceae isolated from soil in Thailand” [Syst. Appl. Microbiol. 33 (2010) 374–382]. Proposal of Rhodopseudomonas boonkerdii sp. nov., a new heavy metal tolerant bacterium isolated from Thailand. Syst Appl Microbiol 2011. [DOI: 10.1016/j.syapm.2011.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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