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Zhou Z, Keiblinger KM, Huang Y, Bhople P, Shi X, Yang S, Yu F, Liu D. Virome and metagenomic sequencing reveal the impact of microbial inoculants on suppressions of antibiotic resistome and viruses during co-composting. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135355. [PMID: 39068883 DOI: 10.1016/j.jhazmat.2024.135355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/01/2024] [Accepted: 07/26/2024] [Indexed: 07/30/2024]
Abstract
Co-composting with exogenous microbial inoculant, presents an effective approach for the harmless utilization of livestock manure and agroforestry wastes. However, the impact of inoculant application on the variations of viral and antibiotic resistance genes (ARGs) remains poorly understood, particularly under varying manure quantity (low 10 % vs. high 20 % w/w). Thus, employing virome and metagenomic sequencing, we examined the influence of Streptomyces-Bacillus Inoculants (SBI) on viral communities, phytopathogen, ARGs, mobile genetic elements, and their interrelations. Our results indicate that SBI shifted dominant bacterial species from Phenylobacterium to thermotropic Bordetella, and the quantity of manure mediates the effect of SBI on whole bacterial community. Major ARGs and genetic elements experienced substantial changes with SBI addition. There was a higher ARGs elimination rate in the composts with low (∼76 %) than those with high manure (∼70 %) application. Virus emerged as a critical factor influencing ARG dynamics. We observed a significant variation in virus community, transitioning from Gemycircularvirus- (∼95 %) to Chlamydiamicrovirus-dominance. RDA analysis revealed that Gemycircularvirus was the most influential taxon in shaping ARGs, with its abundance decreased approximately 80 % after composting. Collectively, these findings underscore the role of microbial inoculants in modulating virus communities and ARGs during biowaste co-composting.
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Affiliation(s)
- Ziyan Zhou
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Katharina Maria Keiblinger
- Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life-Sciences, Vienna 1190, Austria
| | - Yimei Huang
- Key Laboratory of Plant Nutrition and The Agri-environment in Northwest China, Ministry of Agriculture, Key Laboratory of Low-carbon Green Agriculture in Northwestern China, Ministry of Agriculture and Rural Affairs, College of Natural Resources and Environment, Northwest A&F University, Shaanxi 712100, China
| | - Parag Bhople
- Crops, Environment, and Land Use Department, Environment Research Centre, Teagasc, Johnstown Castle, Wexford Y35TC98, Ireland
| | - Xiaofei Shi
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Shimei Yang
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fuqiang Yu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Dong Liu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Zayulina KS, Prokofeva MI, Elcheninov AG, Voytova MP, Novikov AA, Kochetkova TV, Kublanov IV. Arenimonas fontis sp. nov., a bacterium isolated from Chukotka hot spring, Arctic region, Russia. Int J Syst Evol Microbiol 2020; 70:2726-2731. [PMID: 32176605 DOI: 10.1099/ijsem.0.004099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A moderately thermophilic, neutrophilic, aerobic, Gram-negative bacterium, strain 3729kT, was isolated from a thermal spring of the Chukotka Peninsula, Arctic region, Russia. It grew chemoorganoheterotrophically, utilizing proteinaceous substrates, including highly rigid keratins as well as various polysaccharides (glucomannan, locust bean gum, gum guar and xanthan gum). The major fatty acids of strain 3729kT were iso-C15 : 0 (60.9%), iso-C17 : 0 (12.0%), C16 : 0 (9.9%) and iso-C16 : 0 (7.4%). Isoprenoid quinones were Q-8 (95%) and Q-9 (5%). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and three unidentified polar lipids. Strain 3729kT was inhibited by chloramphenicol, neomycin, novobiocin, kanamycin, tetracycline, ampicillin and polymyxin B, but resistant to rifampicin, vancomycin and streptomycin. At the same time, strain 3729kT inhibited growth of Micrococcus luteus and its genome possessed genes for antimicrobial activity against Gram-positive bacteria (a single putative bacteriocin and several secreted lysozymes and peptidoglycan lytic transglycosylases). The DNA G+C content was 69.8 mol%. 16S rRNA gene sequence-based phylogenetic analysis placed strain 3729kT into a distinct species/genus-level branch within the family Xanthomonadaceae (Proteobacteria). Phylogenetic analysis of 120 conservative protein sequences of all Xanthomonadaceae with validly published names and publicly available genomic sequences supported a species-level position of strain 3729kT within the genus Arenimonas. Pairwise ANI values between strain 3729kT and other Arenimonas species were of 75-80 %, supporting the proposal of a novel species. Accordingly, Arenimonas fontis sp. nov., with the type strain 3729kT (=VMK В-3232Т=DSM 105847T), was proposed.
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Affiliation(s)
- Kseniya S Zayulina
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, 117312, prospect 60-Letya Oktyabrya 7/2, Moscow, Russia
| | - Maria I Prokofeva
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, 117312, prospect 60-Letya Oktyabrya 7/2, Moscow, Russia
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, 117312, prospect 60-Letya Oktyabrya 7/2, Moscow, Russia
| | - Margarita P Voytova
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, 117312, prospect 60-Letya Oktyabrya 7/2, Moscow, Russia
| | - Andrei A Novikov
- Gubkin University, 119991, Leninsky prospect, 65-1, Moscow, Russia
| | - Tatiana V Kochetkova
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, 117312, prospect 60-Letya Oktyabrya 7/2, Moscow, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, 117312, prospect 60-Letya Oktyabrya 7/2, Moscow, Russia
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Han DM, Chun BH, Kim HM, Khan SA, Jeon CO. Arenimonas terrae sp. nov., isolated from orchard soil. Int J Syst Evol Microbiol 2019; 70:537-542. [PMID: 31644421 DOI: 10.1099/ijsem.0.003785] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic bacterial strain, designated R29T, was isolated from orchard soil in Hwasun, South Korea. Cells were non-motile rods with catalase and oxidase activities. Growth was observed at 15-40 °C (optimum, 30 °C) and pH 7.0-9.0. Ubiquinone-8 was identified as the predominant isoprenoid quinone. Major polar lipids consisted of phosphatidylethanolamine, six phospholipids, an unidentified aminolipid and two unidentified polar lipids. Strain R29T contained iso-C15 : 0, iso-C16 : 0 and summed feature 9 (comprising iso-C17 : 1 ω9c/10-methyl-C16 : 0) as major cellular fatty acids. The G+C content of the genomic DNA calculated from the whole-genome sequence was 69.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that R29T was most closely related to Arenimonas daejeonensis T7-07T and Arenimonas malthae CC-JY-1T with sequence similarities of 98.0 and 96.9 %, respectively The average nucleotide identity and in silico DNA-DNA hybridization values between R29T and the type strains of A. daejeonensis and A. malthae were 87.0 % and 31.6 % and 83.4 % and 26.1 %, respectively. On the basis of the phenotypic, chemotaxonomic and molecular features, strain R29T represents a novel species of the genus Arenimonas, for which the name Arenimonas terrae sp. nov. is proposed. The type strain is R29T (=KACC 19896T=JCM 33216T).
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Affiliation(s)
- Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Byung Hee Chun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyung Min Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Shehzad Abid Khan
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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4
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Liu H, Ren L, Lu P, Sun L, Zhu G. Arenimonas caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2018; 68:2996-3000. [PMID: 30040064 DOI: 10.1099/ijsem.0.002937] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-spore-forming, motile and rod-shaped strain, z29T, was isolated from the active sludge of a municipal wastewater treatment plant at Wuhu, Anhui, PR China. Phylogenetic analysis of the 16S rRNA gene revealed that strain z29T is most closely related to the genus Arenimonas, showing the highest similarity to Arenimonas donghaensis HO3-R19T (97.14 %), Arenimonas aestuarii S2-21T (96.46 %), Arenimonas daejeonensis T7-07T (96.24 %) and Arenimonas taoyuanensis YN2-31AT (96.23 %). The only respiratory quinone of strain z29T was ubiquinone 8 (Q-8). The major cellular fatty acids (>10 %) were iso-C15 : 0, iso-C16 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 010-methyl). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The genomic DNA G+C content was 70.2 mol%. Genomic comparison between strain z29T and Arenimonas donghaensis HO3-R19T revealed 83.72 % average nucleotide identity. Based on the phenotypic and chemotaxonomic results together with phylogenetical analysis, strain z29T is classified as representing a novel species of the genus Arenimonas, for which the name Arenimonas caeni sp. nov. is proposed. The type strain is z29T (=JCM 32091T=CCTCC AB 2017067T).
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Affiliation(s)
- Hongming Liu
- 1Institute of Molecular Biology and Biotechnology, Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, No. 1 Beijing East Road, Wuhu, 241000, Anhui, PR China
| | - Lei Ren
- 2Agricultural College of Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Peng Lu
- 1Institute of Molecular Biology and Biotechnology, Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, No. 1 Beijing East Road, Wuhu, 241000, Anhui, PR China
| | - Lina Sun
- 3Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, PR China
| | - Guoping Zhu
- 1Institute of Molecular Biology and Biotechnology, Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, No. 1 Beijing East Road, Wuhu, 241000, Anhui, PR China
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5
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Kanjanasuntree R, Kim JH, Yoon JH, Sukhoom A, Kantachote D, Kim W. Arenimonas halophila sp. nov., isolated from soil. Int J Syst Evol Microbiol 2018; 68:2188-2193. [PMID: 29745867 DOI: 10.1099/ijsem.0.002801] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, aerobic, non-motile, rod-shaped bacterium, designated CAU 1453T, was isolated from soil and its taxonomic position was investigated using a polyphasic approach. Strain CAU 1453T grew optimally at 30 °C and at pH 6.5 in the presence of 1 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that CAU 1453T represented a member of the genus Arenimonas and was most closely related to Arenimonas donghaensis KACC 11381T (97.2 % similarity). CAU 1453T contained ubiquinone-8 (Q-8) as the predominant isoprenoid quinone and iso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids. The polar lipids consisted of diphosphatidylglycerol, a phosphoglycolipid, an aminophospholipid, two unidentified phospholipids and two unidentified glycolipids. CAU 1453T showed low DNA-DNA relatedness with the most closely related strain, A. donghaensis KACC 11381T (26.5 %). The DNA G+C content was 67.3 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, CAU 1453T represents a novel species of the genus Arenimonas, for which the name Arenimonas halophila sp. nov. is proposed. The type strain is CAU 1453T (=KCTC 62235T=NBRC 113093T).
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Affiliation(s)
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ampaitip Sukhoom
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Duangporn Kantachote
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
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Xu L, Sun JQ, Liu X, Liu XZ, Qiao MQ, Wu XL. Arenimonas soli sp. nov., isolated from saline-alkaline soil. Int J Syst Evol Microbiol 2017; 67:2829-2833. [PMID: 28853685 DOI: 10.1099/ijsem.0.002026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, non-motile, aerobic bacterial strain, designated Y3L17T, was isolated from the saline-alkaline soil of a farmland, Hangjin Banner, Inner Mongolia, northern China. Y3L17T could grow at 15-45 °C (optimum 35 °C), pH 6.0-10.0 (optimum pH 8.0) and with 0-4 % (w/v) NaCl (optimum 0 %). The results of phylogenetic analysis based on the 16S rRNA gene and gyrB gene sequences revealed that Y3L17T tightly clustered with strains of members of the genus Arenimonas, sharing the highest 16S rRNA gene similarities with Arenimonas aestuarii S2-21T (99.5 %) and Arenimonas donghaensis HO3-R19T (98.2 %), and lower similarities (<97 %) with all the other type strains of species of this genus. However, Y3L17T shared only 92.62 % gyrB gene similarities with A. aestuarii S2-21T. The DNA-DNA hybridization values of Y3L17T with A. aestuariiS2-21T and A. donghaensis HO3-R19T were 20.1±2.5 and 18.2±3.2 %, respectively. Y3L17T contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, five unknown phospholipids and one unknown lipid as the major polar lipids. Ubiquinone-8 (Q-8) was the predominant respiratory quinone, while iso-C15 : 0, iso-C17 : 0ω9c and iso-C11 : 0 3-OH were the major cellular fatty acids. Its genomic DNA G+C content was 65.4 mol%. On the basis of its phenotypic, phylogenetic and genotypic characteristics, Y3L17T represents a novel species within the genus Arenimonas, for which the name Arenimonas soli sp. nov. is proposed, the type strain is Y3L17T (=CGMCC 1.15905T =KCTC 52420T).
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Affiliation(s)
- Lian Xu
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Ji-Quan Sun
- College of Engineering, Peking University, Beijing 100871, PR China.,Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Xia Liu
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Xiao-Zhen Liu
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Ming-Quan Qiao
- Sinopec Shengli Oilfield Xinchun Oil Production Plant, Dongying 257000, PR China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing 100871, PR China
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7
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Arenimonas alkanexedens sp. nov., isolated from a frozen soil sample. Antonie van Leeuwenhoek 2017; 110:1027-1034. [DOI: 10.1007/s10482-017-0876-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 04/18/2017] [Indexed: 10/19/2022]
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Han SI, Kim JO, Lee YR, Ekpeghere KI, Koh SC, Whang KS. Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment. Antonie van Leeuwenhoek 2016; 109:785-92. [PMID: 27108138 DOI: 10.1007/s10482-016-0678-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 03/09/2016] [Indexed: 11/28/2022]
Abstract
A denitrifying bacterium, designated strain E4-1(T), was isolated from a bioreactor for tannery wastewater treatment, and its taxonomic position was investigated using a polyphasic approach. Strain E4-1(T), a facultative anaerobic bacterium, was observed to grow between 0 and 12 % (w/v) NaCl, between pH 3.0 and 12.0. Cells were found to be oxidase-positive and catalase-negative. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain E4-1(T) forms a distinct lineage with respect to closely related genera in the family Xanthomonadaceae, and is closely related to Chiayiivirga, Aquimonas and Dokdonella, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93.9 %. The predominant respiratory quinone was determined to be ubiquinone-8 (Q-8) and the major cellular fatty acids were determined to be iso-C15:0, iso-C17:1 ω9c, iso-C11:0 and iso-C11:0 3OH. Based on physiological, biochemical and chemotaxonomic properties together with results of comparative 16S rRNA gene sequence analysis, strain E4-1(T) is considered to represent a novel species in a new genus, for which the name Denitratimonas tolerans gen. nov., sp. nov. is proposed. The type strain is E4-1(T) (=KACC 17565(T) = NCAIM B 025327(T)).
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Affiliation(s)
- Song-Ih Han
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea
| | - Ju-Ok Kim
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea
| | - Ye-Rim Lee
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea
| | - Kalu I Ekpeghere
- Department of Environmental Engineering, Korea Maritime University, Busan, 606-791, Republic of Korea
| | - Sung-Cheol Koh
- Department of Environmental Engineering, Korea Maritime University, Busan, 606-791, Republic of Korea.
| | - Kyung-Sook Whang
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea. .,Institute of Microbial Ecology and Resources, Mokwon University, Daejeon, 35349, Republic of Korea.
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9
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Arenimonas aestuarii sp. nov., isolated from estuary sediment. Int J Syst Evol Microbiol 2016; 66:1527-1532. [DOI: 10.1099/ijsem.0.000913] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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10
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Chen F, Wang H, Cao Y, Li X, Wang G. High quality draft genomic sequence of Arenimonas donghaensis DSM 18148(T). Stand Genomic Sci 2015; 10:59. [PMID: 26380644 PMCID: PMC4572611 DOI: 10.1186/s40793-015-0055-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 08/05/2015] [Indexed: 01/21/2023] Open
Abstract
Arenimonas donghaensis is the type species of genus Arenimonas which belongs to family Xanthomonadaceae within Gammaproteobacteria. In this study, a total of five type strains of Arenimonas were sequenced. The draft genomic information of A. donghaensis DSM 18148(T) is described and compared with other four genomes of Arenimonas. The genome size of A. donghaensis DSM 18148(T) is 2,977,056 bp distributed in 51 contigs, containing 2685 protein-coding genes and 49 RNA genes.
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Affiliation(s)
- Fang Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Hui Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Yajing Cao
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Xiangyang Li
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
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Makk J, Homonnay ZG, Kéki Z, Nemes-Barnás K, Márialigeti K, Schumann P, Tóth EM. Arenimonas subflava sp. nov., isolated from a drinking water network, and emended description of the genus Arenimonas. Int J Syst Evol Microbiol 2015; 65:1915-1921. [PMID: 25795065 DOI: 10.1099/ijs.0.000201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strain designated PYM3-14T was isolated from the drinking water network of Budapest (Hungary) and was studied by polyphasic taxonomic methods. The straight-rod-shaped cells stained Gram-negative, were aerobic and non-motile. Phylogenetic analysis of the 16S rRNA gene sequence of strain PYM3-14T revealed a clear affiliation with members of the family Xanthomonadaceae within the class Gammaproteobacteria. The 16S rRNA gene sequence of strain PYM3-14T showed the closest sequence similarities to Arenimonas daechungensis CH15-1T (96.2 %), Arenimonas oryziterrae YC6267T (95.2 %) and Lysobacter brunescens UASM DT (94.4 %). The DNA G+C content of strain PYM3-14T, measured by two different methods (52.0 mol% and 55.9 mol%, respectively), was much lower than that of any member of the genus Arenimonas. The predominant fatty acids (>8 %) were iso-C16:0, iso-C15:0, iso-C14:0, iso-C17:1ω9c and C16:1ω7c alcohol. Strain PYM3-14T contained Q-8 as the major ubiquinone and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylmonomethylethanolamine as the major polar lipids. According to phenotypic and genotypic data strain PYM3-14T represents a novel species of the genus Arenimonas, for which the name Arenimonas subflava sp. nov. is proposed. The type strain is PYM3-14T ( = NCAIM B 02508T = DSM 25526T). On the basis of new data obtained in this study, an emended description of the genus Arenimonas is also proposed.
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Affiliation(s)
- Judit Makk
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Zalán G Homonnay
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Zsuzsa Kéki
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Katalin Nemes-Barnás
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Peter Schumann
- DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Erika M Tóth
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
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Zhang SY, Xiao W, Xia YS, Wang YX, Cui XL, Zhang NM. Arenimonas taoyuanensis sp. nov., a novel bacterium isolated from rice-field soil in China. Antonie van Leeuwenhoek 2015; 107:1181-7. [DOI: 10.1007/s10482-015-0409-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/19/2015] [Indexed: 12/01/2022]
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13
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Hsu YH, Lai WA, Lin SY, Hameed A, Shahina M, Shen FT, Zhu ZL, Young LS, Young CC. Chiayiivirga flava gen. nov., sp. nov., a novel bacterium of the family
Xanthomonadaceae
isolated from an agricultural soil, and emended description of the genus
Dokdonella. Int J Syst Evol Microbiol 2013; 63:3293-3300. [DOI: 10.1099/ijs.0.048579-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-reaction-negative, yellow-pigmented, aerobic, non-motile and rod-shaped bacterium designated strain CC-YHH031T was isolated from an agricultural soil collected at Chiayi County, Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CC-YHH031T formed a discrete monophyletic lineage in the family
Xanthomonadaceae
, sharing high pairwise sequence similarity of 93.5–95.2 and 94.8 % with species of the genus
Dokdonella
(94.9 % similarity to the type strain of the type species) and
Aquimonas voraii
GPTSA 20T, respectively. The genomic DNA G+C content of strain CC-YHH031T was 68.6±0.7 mol% and the predominant respiratory quinone was ubiquinone Q-8. Spermidine was the principal polyamine, with minor amounts of putrescine. Major fatty acids (>5 % of total fatty acids) were iso-C16 : 0, iso-C15 : 0, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3), iso-C17 : 1ω9c, iso-C14 : 0, iso-C11 : 0 and iso-C11 : 0 3-OH. The polar lipid profile of strain CC-YHH031T included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified aminophospholipids (APL1–2) and four unidentified phospholipids (PL1–4). Strain CC-YHH031T was distinguished particularly from the type species of the genus
Dokdonella
(
Dokdonella koreensis
) by the presence of major amounts of iso-C14 : 0 and summed feature 3 and minor amounts of iso-C17 : 0 and by the complete absence of anteiso-C17 : 0, the presence of PL1–3 and APL1–2, the absence of APL3 and the presence of putrescine in the former. On the basis of distinguishing genotypic and phenotypic evidence, strain CC-YHH031T is proposed to represent a novel genus and species within the family
Xanthomonadaceae
, for which the name Chiayiivirga flava gen. nov., sp. nov. is proposed. The type strain of Chiayiivirga flava is CC-YHH031T ( = BCRC 80273T = DSM 24163T).
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Affiliation(s)
- Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan, ROC
| | - Wei-An Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan, ROC
| | - Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan, ROC
| | - Mariyam Shahina
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan, ROC
| | - Fo-Ting Shen
- Agricultural Biotechnology Center, National Chung Hsing University, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan, ROC
| | - Zhi-Long Zhu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan, ROC
| | - Li-Sen Young
- Department of Biotechnology, National Formosa University, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan, ROC
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14
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Arenimonas
daechungensis sp. nov., isolated from the sediment of a eutrophic reservoir. Int J Syst Evol Microbiol 2013; 63:484-489. [DOI: 10.1099/ijs.0.035410-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile, non-spore-forming and rod-shaped bacterial strain, CH15-1T, was isolated from a sediment sample taken from Daechung Reservoir, South Korea, during the late-blooming period of cyanobacteria. Strain CH15-1T grew optimally at pH 7.0 and 30 °C. A phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain CH15-1T belongs to the genus
Arenimonas
with the similarity range from 92.6–97.4 % and is closely related to
Arenimonas oryziterrae
YC6267T (97.4 %),
Arenimonas composti
TR7-09T (95.4 %),
Arenimonas
metalli CF5-1T (94.7 %),
Arenimonas malthae
CC-JY-1T (94.6 %) and
Arenimonas donghaensis
HO3-R19T (92.6 %). However, the DNA–DNA hybridization between strain CH15-1T and the closest strain,
Arenimonas oryziterrae
YC6267T, was 8.9–12.9 %. The DNA G+C content was 63.9 mol% compared to
A. oryziterrae
YC626T, 65.8 mol%. Strain CH15-1T included Q-8 as the major ubiquinone and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylmonomethylethanolamine as the major polar lipids. The major fatty acids (>5 %) were iso-C15 : 0, iso-C16 : 0, iso-C14 : 0, iso-C11 : 0 3-OH, iso-C17 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl). On the basis of phylogenetic, phenotypic and genetic data, strain CH15-1T was classified in the genus
Arenimonas
as a member of a novel species, for which the name
Arenimonas
daechungensis sp. nov. is proposed. The type strain is CH15-1T ( = KCTC 23553T = DSM 24763T).
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15
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Chen F, Shi Z, Wang G. Arenimonas metalli sp. nov., isolated from an iron mine. Int J Syst Evol Microbiol 2012; 62:1744-1749. [DOI: 10.1099/ijs.0.034132-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, aerobic, rod-shaped bacterium (CF5-1T) was isolated from Hongshan Iron Mine, Daye City, Hubei province, China. The major cellular fatty acids (>10 %) were iso-C16 : 0, iso-C15 : 0, C16 : 1ω7c alcohol and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major respiratory quinone was Q-8. The genomic DNA G+C content was 70.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CF5-1T was most closely related to
Arenimonas malthae
(95.3 % gene sequence similarity),
Arenimonas oryziterrae
(94.7 %),
Arenimonas donghaensis
(94.6 %) and
Arenimonas composti
(94.5 %). A taxonomic study using a polyphasic approach showed that strain CF5-1T represents a novel species of the genus
Arenimonas
, for which the name Arenimonas metalli sp. nov. is proposed. The type strain is CF5-1T ( = CGMCC 1.10787T = KCTC 23460T = CCTCC AB 2010449T).
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Affiliation(s)
- Fang Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Zunji Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
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16
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Abstract
A Gram-negative, aerobic, motile and rod-shaped bacterium, designated strain T7-07T, was isolated from compost in Daejeon, Korea. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain T7-07T had 99.0 % gene sequence similarity with
Arenimonas malthae
KACC 14618T and 94.7–95.9 % with other recognized species of the genus
Arenimonas
. Cells formed creamy white to yellowish colonies on R2A agar and contained Q-8 as the predominant ubiquinone, C15 : 0 iso, C16 : 0 iso, C17 : 1 iso ω9c and C11 : 0 iso 3-OH as the major fatty acids, and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine and an unknown aminolipid as the major polar lipids. The DNA G+C content of strain T7-07T was 68.3 mol%. DNA–DNA reassociation experiments between T7-07T and
Arenimonas malthae
KACC 14618T resulted in a mean relatedness value of 22.2 %. Combined genotypic and phenotypic data supported the conclusion that the strain T7-07T represents a novel species, for which the name Arenimonas daejeonensis sp. nov. is proposed. The type strain is T7-07T ( = KCTC 12667T = DSM 18060T).
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17
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Arenimonas aquaticum sp. nov., a member of the gammaproteobacterium, isolated from a freshwater reservoir. J Microbiol 2012; 50:354-8. [DOI: 10.1007/s12275-012-1301-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 12/27/2011] [Indexed: 11/26/2022]
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18
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Aslam Z, Park JH, Kim SW, Jeon CO, Chung YR. Arenimonas oryziterrae sp. nov., isolated from a field of rice (Oryza sativa L.) managed under a no-tillage regime, and reclassification of Aspromonas composti as Arenimonas composti comb. nov. Int J Syst Evol Microbiol 2009; 59:2967-72. [DOI: 10.1099/ijs.0.006031-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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19
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Weon HY, Yoo SH, Kim YJ, Lee CM, Kim BY, Jeon YA, Hong SB, Anandham R, Kwon SW. Rudaea cellulosilytica gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:2308-12. [DOI: 10.1099/ijs.0.005165-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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