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Lin SY, Lin TY, Hameed A, Tsai CF, Young CC. Description of Aliirhizobium terrae sp. nov., A Plant Growth-Promoting Bacterium Isolated from a Maize-Rice Rotation Agriculture Field. Curr Microbiol 2024; 81:328. [PMID: 39186081 DOI: 10.1007/s00284-024-03845-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024]
Abstract
A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-CFT758T, isolated from a maize-rice rotation agriculture field in Taiwan. The cells are aerobic, Gram-stain-negative, rod-shaped, positive for catalase and oxidase, and grow at 20-30 °C (optimal 30 ℃), at pH 6.0-8.0 (optimal 8.0), and with 0-4% (w/v) NaCl (optimum, 2-3%). Phylogenetic analysis based on 16S rRNA gene sequencing, the strain CC-CFT758T belongs to the genus "Aliirhizobium" of the family Rhizobiaceae. The closest known relatives of this strain are "Aliirhizobium wenxiniae" 166T (with 98.7% similarity), "Aliirhizobium cellulosilyticum" SEMIA 448T (with 97.9% similarity), and "Aliirhizobium smilacinae" PTYR-5T (with 97.0% similarity). The genome size was 5.9 Mbp, with a G + C content of 60.6%. Values of digital DNA-DNA hybridization between the strain and closely related species were 29.5% for "Ali. cellulosilyticum", and 23.9% for "Ali. wenxiniae" and "Ali. smilacinae". Strain CC-CFT758T exhibited the highest orthologous average nucleotide identity (OrthoANI) values with members of the genus "Aliirhizobium", ranging from 80.4 to 81.6% (n = 3). Chemotaxonomical analysis indicated that strain CC-CFT758T contained C16:0, C16:0 3OH, C19:0 cyclo ω8c, C14:0 3OH/iso-C16:1 I, and C18:2 ω6,9c/ante C18:0 as dominant fatty acids, and the major polyamines were putrescine and spermidine. The polar lipids comprised diphosphatidylglycerol, phosphatidylcholin, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, seven unidentified aminolipids, three unidentified phospholipids, and two unidentified polar lipids. Strain CC-CFT758T exhibited distinct phylogenetic, phenotypic, and chemotaxonomic characteristics, as well as unique results in comparative analysis of 16S rRNA gene sequence, OrthoANI, AAI, dDDH, and phylogenomic placement. Therefore, this strain represents a new species of the genus "Aliirhizobium", for which the name Aliirhizobium terrae sp. nov. is proposed, with the type strain is CC-CFT758T (= BCRC 81364T = JCM 35482T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung, 40227, Taiwan
| | - Tzu-Yu Lin
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, Karnataka, India
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung, 40227, Taiwan
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung, 40227, Taiwan.
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, 145, XingDa Rd, Taichung, 40227, Taiwan.
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Lin SY, Hameed A, Tsai CF, Young CC. Description of Flavobacterium agricola sp. nov., an auxin producing bacterium isolated from paddy field. Antonie Van Leeuwenhoek 2023; 116:1345-1357. [PMID: 37837564 DOI: 10.1007/s10482-023-01891-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023]
Abstract
An auxin-producing bacterial strain, CC-SYL302T, was isolated from paddy soil in Taiwan and identified using a polyphasic taxonomic approach. The cells were observed to be aerobic, non-motile, non-spore-forming rods, and tested positive for catalase and oxidase. Produced carotenoid but flexirubin-type pigments were absent. Optimal growth of strain CC-SYL302T was observed at 25 °C, pH 7.0, and with 2% (w/v) NaCl present. Based on analysis of 16S rRNA gene sequences, it was determined that strain CC-SYL302T belongs to the genus Flavobacterium of the Flavobacteriaceae family. The closest known relatives of this strain are F. tangerinum YIM 102701-2 T (with 93.3% similarity) and F. cucumis R2A45-3 T (with 93.1% similarity). Digital DNA-DNA hybridization (dDDH) values were calculated to assess the genetic distance between strain CC-SYL302T and its closest relatives, with mean values of 21.3% for F. tangerinum and 20.4% for F. cucumis. Strain CC-SYL302T exhibited the highest orthologous average nucleotide identity (OrthoANI) values with members of the Flavobacterium genus, ranging from 67.2 to 72.1% (n = 22). The dominating cellular fatty acids (> 5%) included iso-C14:0, iso-C15:0, iso-C16:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C16:1 ω6c/C16:1 ω7c and C16:0 10-methyl/iso-C17:1 ω9c. The polar lipid profile consisted of phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid, and nine unidentified polar lipids. The genome (2.7 Mb) contained 33.6% GC content, and the major polyamines were putrescine and sym-homospermidine. Strain CC-SYL302T exhibits distinct phylogenetic, phenotypic, and chemotaxonomic characteristics, as well as unique results in comparative analysis of 16S rRNA gene sequence, OrthoANI, dDDH, and phylogenomic placement. Therefore, it is proposed that this strain represents a new species of the Flavobacterium genus, for which the name Flavobacterium agricola sp. nov. is proposed. The type strain is CC-SYL302T (= BCRC 81320 T = JCM 34764 T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xing Da Rd., Taichung City, 40227, Taiwan
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya University, Mangalore, Karnataka, India
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xing Da Rd., Taichung City, 40227, Taiwan
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xing Da Rd., Taichung City, 40227, Taiwan.
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan.
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Lv YT, Chen X, Zhang X, Zhu C, Pan Y, Sun T, Wang L. Denitrification for acidic wastewater treatment: Long-term performance, microbial communities, and nitrous oxide emissions. J Biosci Bioeng 2022; 134:513-520. [PMID: 36216689 DOI: 10.1016/j.jbiosc.2022.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022]
Abstract
Acidic nitrogenous wastewater often requires alkali pretreatment before biological treatment, which results in increased system complexity and operating costs. The demonstration of denitrification under acidic conditions would provide a theoretical basis for the direct treatment of such wastewater. In this study, the denitrification performance, microbial community, and nitrous oxide (N2O) emissions under acidic conditions were investigated using a sequencing batch reactor. When the influent pH decreased from 5.5 to 4.5, the sequencing batch reactor removed 99.8 ± 0.2% of the nitrate and 92.5 ± 1.6% (n = 171) of the chemical oxygen demand, and the production efficiency of N2O increased significantly to 11.45%. This was 2.6-fold higher than that observed at pH 5.5. The long-term denitrification treatment of acidic wastewater (pH 4.5) led to the formation of granular sludge, and Thauera, Allorhizobium-Neorhizobium-Parararhizobium-Rhizobium, and Diaphorobacter became the dominant microbes with a collective abundance of 81.3%. More importantly, only 0.25% of the nitrate was denitrified as N2O, and the batch test revealed that the emissions of N2O decreased with the increase in sludge size. These results indicate that denitrifying granular sludge formed under acidic conditions and denitrifying bacteria capable of N2O reduction proliferated, which both resulted in a significant reduction in the release of N2O.
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Affiliation(s)
- Yong-Tao Lv
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China; Key Laboratory of Membrane Separation of Shaanxi Province, Research Institute of Membrane Separation Technology of Shaanxi Province, No. 13 Yanta Road, Xi'an 710055, China; Key Laboratory of Environmental Engineering of Shaanxi Province, No. 13 Yanta Road, Xi'an 710055, China.
| | - Xiaolin Chen
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China; Key Laboratory of Membrane Separation of Shaanxi Province, Research Institute of Membrane Separation Technology of Shaanxi Province, No. 13 Yanta Road, Xi'an 710055, China; Key Laboratory of Environmental Engineering of Shaanxi Province, No. 13 Yanta Road, Xi'an 710055, China
| | - Xuyang Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China; Key Laboratory of Membrane Separation of Shaanxi Province, Research Institute of Membrane Separation Technology of Shaanxi Province, No. 13 Yanta Road, Xi'an 710055, China; Key Laboratory of Environmental Engineering of Shaanxi Province, No. 13 Yanta Road, Xi'an 710055, China
| | - Chuanshou Zhu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China; Key Laboratory of Membrane Separation of Shaanxi Province, Research Institute of Membrane Separation Technology of Shaanxi Province, No. 13 Yanta Road, Xi'an 710055, China; Key Laboratory of Environmental Engineering of Shaanxi Province, No. 13 Yanta Road, Xi'an 710055, China
| | - Yongbao Pan
- Shaanxi Modern Architecture Design & Research Institute Co. Ltd., No. 168 Xingtai 7th street, Xi'an 710021, China
| | - Ting Sun
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China; Key Laboratory of Membrane Separation of Shaanxi Province, Research Institute of Membrane Separation Technology of Shaanxi Province, No. 13 Yanta Road, Xi'an 710055, China; Key Laboratory of Environmental Engineering of Shaanxi Province, No. 13 Yanta Road, Xi'an 710055, China
| | - Lei Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China; Key Laboratory of Membrane Separation of Shaanxi Province, Research Institute of Membrane Separation Technology of Shaanxi Province, No. 13 Yanta Road, Xi'an 710055, China; Key Laboratory of Environmental Engineering of Shaanxi Province, No. 13 Yanta Road, Xi'an 710055, China
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Lin SY, Hameed A, Tsai CF, Young CC. Zeimonas arvi gen. nov., sp. nov., of the family Burkholderiaceae, harboring biphenyl- and phenolic acid-metabolizing genes, isolated from a long-term ecological research field. Antonie van Leeuwenhoek 2021; 114:2101-2111. [PMID: 34599477 DOI: 10.1007/s10482-021-01664-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 09/19/2021] [Indexed: 11/25/2022]
Abstract
A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT501T, harboring xenobiotic- and allelochemical-metabolizing genes, isolated from a long-term ecological research field in Taiwan. Cells of strain CC-CFT501T were catalase- and oxidase-positive, non-motile and short rods. Optimal growth occurred at 30 °C, pH 8 and 1% NaCl. Strain CC-CFT501T was found to share high 16S rRNA gene sequence similarity with the members of genera Quisquiliibacterium (94.3%, n = 1), Pandoraea (93.4-94.0%, n = 23) and Paraburkholderia (93.3-94.0%, n = 9), affiliated to the family Burkholderiaceae. Strain CC-CFT501T shared 76.4% orthologous average nucleotide identity (OrthoANI) and 20.9% digital DNA-DNA hybridization (dDDH) values with Quisquiliibacterium transsilvanicum DSM 29781T. Draft genome sequence (3.83 Mb) of strain CC-CFT501T revealed several genes encoding the proteins involved in biphenyl and phenolic acid metabolism. Fatty acid profile contained C16:0, C18:0, C10:0 3-OH, C16:1 ω7c/C16:1 ω6c and C18:1 ω7c/C18:1 ω6c in predominant amounts. The polar lipid profile consisted of phosphatidylethanolamine, thirteen unidentified amino lipids, two unidentified phospholipids and two unidentified glycolipids. The major polyamine was spermidine and ubiquinone Q-8 was the sole respiratory quinone. The DNA G + C content was 70.0 mol%. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT501T is considered to represent a novel genus and species of the family Burkholderiaceae, for which the name Zeimonas arvi gen. nov., sp. nov. is proposed. The type strain of the type species is CC-CFT501T (= BCRC 81218T = JCM 33506T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung, 40227, Taiwan
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung, 40227, Taiwan
| | - Chia-Fang Tsai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung, 40227, Taiwan
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd, Taichung, 40227, Taiwan.
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan.
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de Lajudie P, Mousavi SA, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 6 July 2020. Int J Syst Evol Microbiol 2021; 71:004784. [PMID: 33956594 PMCID: PMC8289204 DOI: 10.1099/ijsem.0.004784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/20/2021] [Indexed: 02/04/2023] Open
Affiliation(s)
- Philippe de Lajudie
- IRD, University of Montpellier, CIRAD, INRAE, SupAgro, LSTM, Montpellier, France
| | - Seyed Abdollah Mousavi
- Ecosystems and Environment Research Programme, University of Helsinki, Finland
- Department of Biology, University of Turku, Finland
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de Lajudie P, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 17 July 2019. Int J Syst Evol Microbiol 2020; 70:3563-3571. [DOI: 10.1099/ijsem.0.004157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Minutes of the closed meeting of the ICSP Subcommittee on the Taxonomy of Rhizobia and Agrobacteria held by videoconference on 17 July 2019, and list of recent species.
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