1
|
Yue J, Yang F, Xiao Y, Lin S, He Z, Wang S, Zhao J, Yuan J, Li L, Liu L. Comamonas endophytica sp. nov., a novel indole acetic acid producing endophyte isolated from bamboo in China. Int J Syst Evol Microbiol 2024; 74. [PMID: 38190243 DOI: 10.1099/ijsem.0.006217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
Two novel indole acetic acid-producing strains, 5MLIRT and D4N7, were isolated from Indosasa shibataeoides in Yongzhou, Hunan province, and Phyllostachys edulis in Hangzhou, Zhejiang province, respectively. Based on their 16S rRNA sequences, strains 5MLIRT and D4N7 were closely related to Comamonas antarcticus 16-35-5T (98.4 % sequence similarity), and the results of 92-core gene phylogenetic trees showed that strains 5MLIRT and D4N7 formed a phylogenetic lineage within the clade comprising Comamonas species. The complete genome size of strain 5MLIRT was 4.49 Mb including two plasmids, and the DNA G+C content was 66.5 mol%. The draft genome of strain D4N7 was 4.26 Mb with 66.7 mol% G+C content. The average nucleotide identity and digital DNA-DNA hybridization values among strain 5MLIRT and species in the genus Comamonas were all below the species delineation threshold. The colonies of strain 5MLIRT and D4N7 were circular with regular margins, convex, pale yellow and 1.0-2.0 mm in diameter when incubated at 30 °C for 3 days. Strains 5MLIRT and D4N7 grew optimally at 30 °C, pH 7.0 and 1.0 % NaCl. The respiratory isoprenoid quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Polyphasic analyses indicated that strains 5MLIRT and D4N7 could be distinguished from related validly named Comamonas species and represent a novel species of the genus Comamonas, for which the name Comamonas endophytica sp. nov. is proposed. The type strain is 5MLIRT (=ACCC 62069T=GDMCC 1.2958T=JCM 35331T).
Collapse
Affiliation(s)
- Jinjun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang 311400, PR China
| | - Fu Yang
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Youtie Xiao
- Hunan Jiuyishan National Nature Reserve Administration Bureau, Hunan 425603, PR China
| | - Seqiao Lin
- Hunan Jiuyishan National Nature Reserve Administration Bureau, Hunan 425603, PR China
| | - Zhengping He
- Hunan Jiuyishan National Nature Reserve Administration Bureau, Hunan 425603, PR China
| | - Siyu Wang
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jiayi Zhao
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jinling Yuan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang 311400, PR China
| | - Lubin Li
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Lei Liu
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| |
Collapse
|
2
|
Ryan MP, Sevjahova L, Gorman R, White S. The Emergence of the Genus Comamonas as Important Opportunistic Pathogens. Pathogens 2022; 11:pathogens11091032. [PMID: 36145464 PMCID: PMC9504711 DOI: 10.3390/pathogens11091032] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
Comamonas spp. are non-fermenting Gram-negative bacilli. They were first discovered in 1894, and since then, twenty-four species have been characterized. The natural habitat of these bacteria is soil, wastewater/sludge, fresh water such as ponds and rivers, and the animal intestinal microbiome. They were also isolated from industrial settings, such as activated sludge and polluted soil, and from the hospital environment and clinical samples, such as urine, pus, blood, feces, and kidney. Comamonas spp. are associated with environmental bioremediation and are considered an important environmental bacterium rather than a human pathogen. However, in the 1980s, they became a concern when several human infections associated with these species were reported. Here, the Comamonas genus was examined in terms of its members, identification techniques, and pathogenicity. Seventy-seven infection cases associated with these microorganisms that have been discussed in the literature were identified and investigated in this project. All relevant information regarding year of infection, country of origin, patient information such as age, sex, underlying medical conditions if any, type of infection caused by the Comamonas species, antibiotic susceptibility testing, treatment, and outcomes for the patient were extracted from case reports. The findings suggest that even though Comamonas spp. are thought of as being of low virulence, they have caused harmful health conditions in many healthy individuals and even death in patients with underlying conditions. Antimicrobial treatment of infections associated with these species, in general, was not very difficult; however, it can become an issue in the future because some strains are already resistant to different classes of antibiotics. Therefore, these pathogens should be considered of such importance that they should be included in the hospital screening programs.
Collapse
|
3
|
Suzuki Y, Nakano R, Nakano A, Tasaki H, Asada T, Horiuchi S, Saito K, Watanabe M, Nomura Y, Kitagawa D, Lee ST, Ui K, Koizumi A, Nishihara Y, Sekine T, Sakata R, Ogawa M, Ohnishi M, Tsuruya K, Kasahara K, Yano H. Comamonas thiooxydans Expressing a Plasmid-Encoded IMP-1 Carbapenemase Isolated From Continuous Ambulatory Peritoneal Dialysis of an Inpatient in Japan. Front Microbiol 2022; 13:808993. [PMID: 35265058 PMCID: PMC8899508 DOI: 10.3389/fmicb.2022.808993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yuki Suzuki
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Ryuichi Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Hikari Tasaki
- Department of Nephrology, Nara Medical University, Kashihara, Japan
| | - Tomoko Asada
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Saori Horiuchi
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Kai Saito
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Mako Watanabe
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Yasumistu Nomura
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Daisuke Kitagawa
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Sang-Tae Lee
- Central Clinical Laboratory, Nara Medical University, Kashihara, Japan
| | - Koji Ui
- Central Clinical Laboratory, Nara Medical University, Kashihara, Japan
| | - Akira Koizumi
- Central Clinical Laboratory, Nara Medical University, Kashihara, Japan
| | - Yuji Nishihara
- Center for Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Takahiro Sekine
- Center for Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Ryuji Sakata
- Department of Bacteriology, BML Inc., Kawagoe, Japan
| | - Miho Ogawa
- Department of Bacteriology, BML Inc., Kawagoe, Japan
| | - Masahito Ohnishi
- Central Clinical Laboratory, Nara Medical University, Kashihara, Japan
| | - Kazuhiko Tsuruya
- Department of Nephrology, Nara Medical University, Kashihara, Japan
| | - Kei Kasahara
- Center for Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Hisakazu Yano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| |
Collapse
|
4
|
Park EH, Kim YS, Cha CJ. Comamonas fluminis sp. nov., isolated from the Han River, Republic of Korea. Int J Syst Evol Microbiol 2022; 72. [PMID: 35316175 DOI: 10.1099/ijsem.0.005287] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic and motile bacterial strain, designated CJ34T, was isolated from Han River water in the Republic of Korea. Strain CJ34T grew optimally on tryptic soy agar at 30 °C and pH 7.0 in the absence of NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequence showed that strain CJ34T belonged to the genus Comamonas within the family Comamonadaceae and was most closely related to Comamonas testosteroni ATCC 11996T and Comamonas thiooxydans DSM 17888T (both 98.63 % similarity). The average nucleotide identity values between strain CJ34T and two closely related type strains C. testosteroni ATCC 11996T and C. thiooxydans DSM 17888T were 82.77 and 82.73 %, respectively. The major isoprenoid quinone of strain CJ34T was ubiquinone Q-8. The major cellular fatty acids of strain CJ34T were C16 : 0, C16 : 1 ω6c and/or C16 : 1 ω7c and C18 : 1 ω6c and/or C18 : 1 ω7c. The predominant polar lipids of strain CJ34T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. Whole genome sequencing revealed that strain CJ34T had a genome of 4.9 Mbp and the G+C content of the genomic DNA was 59.73 mol%. On the basis of the results of this polyphasic taxonomy study, strain CJ34T represents a novel species in the genus Comamonas, for which the name Comamonas fluminis sp. nov. is proposed. The type strain is CJ34T (=KACC 22237T=JCM 34454T).
Collapse
Affiliation(s)
- Eun-Hee Park
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| |
Collapse
|
5
|
Park KH, Yu Z, Dong K, Lee SS. Comamonas suwonensis sp. nov., isolated from stream water in the Republic of Korea. Int J Syst Evol Microbiol 2021; 71. [PMID: 33847556 DOI: 10.1099/ijsem.0.004681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, EJ-4T, isolated from stream water collected at Seo-ho in Suwon, Republic of Korea, was characterized based on a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EJ-4T belonged to the genus Comamonas. The isolate is Gram-stain-negative, non-motile, aerobic, rod-shaped and forms pale yellow colonies on trypticase soy agar. The optimal growth of this strain was observed aerobically at 30 °C, pH 7 and 0.5 % NaCl. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 39.7 %) and C16 : 0 (32.0 %). The G+C content of strain EJ-4T was 58.4mol %. The average nucleotide identity and digital DNA-DNA hybridization values between strain EJ-4T and Comamoas testosteroni were 91.8 and 31.2 %, respectively. The major polar lipids detected in the isolate were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant isoprenoid quinone was ubiquinone-8. Based on the results of polyphasic taxonomic analysis of strain EJ-4T, we describe a novel species of the genus Comamonas, for which the name Comamonas suwonensis sp. nov. has been proposed, with EJ-4T (=KCTC 82074T=JCM 34179T=KEMB 1602-279T) as the type strain.
Collapse
Affiliation(s)
- Kyu-Hyun Park
- Department of Life Science, Graduate School, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
| | - Zhi Yu
- Department of Life Science, Graduate School, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
| | - Ke Dong
- Department of Life Science, Graduate School, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
| | - Sang-Seob Lee
- Department of Life Science, Graduate School, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
| |
Collapse
|
6
|
Guo X, Wang Q, Xu H, He X, Guo L, Liu S, Wen P, Gou J. Emergence of IMP-8-Producing Comamonas thiooxydans Causing Urinary Tract Infection in China. Front Microbiol 2021; 12:585716. [PMID: 33790873 PMCID: PMC8005532 DOI: 10.3389/fmicb.2021.585716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/19/2021] [Indexed: 11/13/2022] Open
Abstract
The emergence of carbapenem resistance (CR) caused by hydrolytic enzymes called carbapenemases has become a major concern worldwide. So far, CR genes have been widely detected in various bacteria. However, there is no report of CR gene harboring Comamonas thiooxydans. We first isolated a strain of an IMP-8-producing C. thiooxydans from a patient with urinary tract infection in China. Species identity was determined using MALDI-TOF MS analysis and carbapenemase-encoding genes were detected using PCR. The complete genomic sequence of C. thiooxydans was identified using Illumina Novaseq and Oxford Nanopore PromethION. Antimicrobial susceptibility analysis indicated that the C. thiooxydans strain ZDHYF418 was susceptible to imipenem, intermediate to meropenem, and was resistant to aztreonam, fluoroquinolones, and aminoglycosides. The blaIMP–8 gene was chromosomally located, and was part of a Tn402-like class 1 integron characterized by the following structure: DDE-type integrase/transposase/recombinase-tniB-tniQ-recombinase family protein-aac(6′)-Ib-cr-blaIMP–8-intI1. Phylogenetic analysis demonstrated that the closest relative of ZDHYF418 is C. thiooxydans QYY (accession number: CP053920.1). We detected 330 SNP differences between ZDHYF418 and C. thiooxydans QYY. Strain QYY was isolated from activated sludge in Jilin province, China in 2015. In summary, we isolated a strain of C. thiooxydans that is able to produce IMP-8 and a novel blaOXA. This is the first time that a CR gene has been identified in C. thiooxydans. The occurrence of the strain needs to be closely monitored.
Collapse
Affiliation(s)
- Xiaobing Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qian Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohong He
- Department of Clinical Laboratory, Women and Infants Hospital of Zhengzhou, Zhengzhou, China
| | - Lihua Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shuxiu Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Peipei Wen
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianjun Gou
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
7
|
Medina-Pascual MJ, Monzón S, Villalón P, Cuesta I, González-Romo F, Valdezate S. Saezia sanguinis gen. nov., sp. nov., a Betaproteobacteria member of order Burkholderiales, isolated from human blood. Int J Syst Evol Microbiol 2020; 70:2016-2025. [PMID: 32003711 DOI: 10.1099/ijsem.0.004010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of an unknown bacterial strain designated CNM695-12, isolated from the blood of an immunocompromised subject, was investigated via phenotypic, chemotaxonomic, genotypic and genomic analyses. Bacterial cells were determined to be Gram-stain-negative bacilli, aerobic, non-motile and non-spore-forming. The strain showed catalase activity but no oxidase activity. Optimal growth occurred at 37 °C, pH 7 and with 0-1 % NaCl. C16 : 0, summed feature 8 (comprising C18 : 1ω7c /C18:1 ω6c), and C18 : 1ω9c were the most abundant fatty acids, and ubiquinone 8 was the major respiratory quinone. The polar lipids present included phosphatidylglycerol, phosphatidylethanolamine and other aminophospholipids. The 16S rRNA gene sequence showed approximately 93.5 % similarity to those of different species with validly published names within the order Burkholderiales (e.g. Leptothrix mobilis Feox-1T, Aquabacterium commune B8T , Aquabacterium citratiphilum B4T and Schlegelella thermodepolymerans K14T). Phylogenetic analyses based on 16S rRNA gene sequences and concatenated alignments including the sequences for 107 essential proteins, revealed the strain to form a novel lineage close to members of the family Comamonadaceae. The highest average nucleotide identity and average amino acid identity values were obtained with Schlegelella thermodepolymerans K14T (69.6 and 55.7 % respectively). The genome, with a size of 3.35 Mb, had a DNA G+C content of 52.4 mol% and encoded 3056 predicted genes, 3 rRNA, 1 transfer-messengerRNA and 51 tRNA. Strain CNM695-12 thus represents a novel species belonging to a novel genus within the order Burkholderiales, for which the name Saezia sanguinis gen. nov., sp. nov. is proposed. The type strain is CNM695-12T (=DSM 104959T=CECT 9208T).
Collapse
Affiliation(s)
- María J Medina-Pascual
- Laboratorio de Referencia e Investigación en Taxonomía. Centro Nacional de Microbiología. Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Sara Monzón
- Unidad de Bioinformática (BU-ISCIII). Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Pilar Villalón
- Laboratorio de Referencia e Investigación en Taxonomía. Centro Nacional de Microbiología. Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Isabel Cuesta
- Unidad de Bioinformática (BU-ISCIII). Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | - Sylvia Valdezate
- Laboratorio de Referencia e Investigación en Taxonomía. Centro Nacional de Microbiología. Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| |
Collapse
|
8
|
Chemotaxis Towards Aromatic Compounds: Insights from Comamonas testosteroni. Int J Mol Sci 2019; 20:ijms20112701. [PMID: 31159416 PMCID: PMC6600141 DOI: 10.3390/ijms20112701] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 02/07/2023] Open
Abstract
Chemotaxis is an important physiological adaptation that allows many motile bacteria to orientate themselves for better niche adaptation. Chemotaxis is best understood in Escherichia coli. Other representative bacteria, such as Rhodobacter sphaeroides, Pseudomonas species, Helicobacter pylori, and Bacillus subtilis, also have been deeply studied and systemically summarized. These bacteria belong to α-, γ-, ε-Proteobacteria, or Firmicutes. However, β-Proteobacteria, of which many members have been identified as holding chemotactic pathways, lack a summary of chemotaxis. Comamonas testosteroni, belonging to β-Proteobacteria, grows with and chemotactically responds to a range of aromatic compounds. This paper summarizes the latest research on chemotaxis towards aromatic compounds, mainly from investigations of C. testosteroni and other Comamonas species.
Collapse
|
9
|
A Nodulation-Proficient Nonrhizobial Inhabitant of Pueraria phaseoloides. ScientificWorldJournal 2019; 2019:9782684. [PMID: 31057340 PMCID: PMC6463565 DOI: 10.1155/2019/9782684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 11/17/2022] Open
Abstract
Pueraria phaseoloides is a legume cover crop, found chiefly in the wet zone of Sri Lanka. Nitrogen fixation is performed by nodular inhabitants of this cover crop, comparable to the nodule-dwelling bacteria of most other legume plants. We isolated a bacterium (Sub1) from Pueraria phaseoloides, of coccobacillus cell shape, that showed nodulation, when assessed by hydroponics, showing nodules as early as 3 weeks after reinfection. When a nifH fragment from the genome of this bacterium was amplified using a pair of nifH primers, it yielded an amplicon of 360 bp that, when sequenced, helped us identify the bacterium, as belonging to a species of Pseudacidovorax intermedius, at 99% sequence identity. When we constructed a phylogenetic tree with neighboring sequences, we encountered nifH sequences of Pseudacidovorax, forming a monophyletic cluster, which too contained a single Azospirillum species. The genus Pseudacidovorax is a bacterium that, so far, has not been associated with legume nodules. Sub1 secreted a pair of enzymes to the extracellular medium to degrade cellulose and milk proteins. The Sub1 bacterium showed biofilm formation and secreted into the extracellular medium, indole acetic acid. Sub1 also showed a "bulls eye" swarming pattern for the chemoattractant proline, while showing no significant chemotaxis movement, for naringenin, quercetin, and glutamate. Sub1 too possesses the basic genetic foundation (nifH and nifD) to produce a molybdenum-dependent nitrogenase enzyme. We finally show that this rare nonrhizobial bacterium is able to impact, positively, nodulation and shoot length of Pueraria plants, demonstrating that this beta-proteobacterium can abet the biological vigor of this legume cover crop.
Collapse
|
10
|
Hatayama K, Saito K. Calcite formation induced by Ensifer adhaerens, Microbacterium testaceum, Paeniglutamicibacter kerguelensis, Pseudomonas protegens and Rheinheimera texasensis. Antonie van Leeuwenhoek 2018; 112:711-721. [PMID: 30465324 DOI: 10.1007/s10482-018-1204-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 11/17/2018] [Indexed: 02/01/2023]
Abstract
A wide range of bacterial species are able to induce calcium carbonate precipitation. Using our own laboratory-preserved strains, we have newly discovered that Ensifer sp. MY11e, Microbacterium sp. TMd9a1, Paeniglutamicibacter sp. MSa1a, Pseudomonas sp. GTc3, and Rheinheimera sp. ATWe6 can induce the formation of calcite crystals on an agar medium. Type strains of their closely related species (Ensifer adhaerens, Microbacterium testaceum, Paeniglutamicibacter kerguelensis, Pseudomonas protegens, and Rheinheimera texasensis) could also induce calcite formation. Although the initial pH value of the agar medium was 6.1, the pH of the agar media containing calcite, induced by cultivation of the 10 bacterial strains, increased to 8.0-8.4. The ammonification (oxidative deamination) of amino acids may been responsible for this increase in pH. The crystals formed both on and around the bacterial colonies. Furthermore, when these strains (excepting two Microbacterium strains) were cultivated on a cellulose acetate membrane filter (0.20 μm pore size) resting on the surface of the agar medium (i.e., in the membrane filter culture method), the crystals formed on the agar medium separate from the bacterial cells. These results indicate that the bacterial cells did not necessarily become nucleation sites for these crystals. We also investigated whether the studied strains could be applied to the biocementation of sand, and found that only two Ensifer strains were able to form large sand lumps.
Collapse
Affiliation(s)
- Kouta Hatayama
- Sagami Chemical Research Institute, 2743-1 Hayakawa, Ayase, Kanagawa, 252-1193, Japan.
| | - Katsumi Saito
- Department of Applied Chemistry, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa, 259-1292, Japan
| |
Collapse
|
11
|
Hatayama K, Ushida A, Kuno T. Flavobacterium aquicola sp. nov., isolated from river water. Int J Syst Evol Microbiol 2016; 66:2789-2796. [DOI: 10.1099/ijsem.0.001057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kouta Hatayama
- Sagami Chemical Research Institute, Ayase, Kanagawa 252-1193, Japan
| | - Ayako Ushida
- Department of Life Science, College of Agriculture, Tamagawa University, Machida, Tokyo 194-8610, Japan
| | - Teruaki Kuno
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| |
Collapse
|
12
|
Kang W, Soo Kim P, Hyun DW, Lee JY, Sik Kim H, Joon Oh S, Shin NR, Bae JW. Comamonas piscis sp. nov., isolated from the intestine of a Korean rockfish, Sebastes schlegelii. Int J Syst Evol Microbiol 2016; 66:780-785. [DOI: 10.1099/ijsem.0.000790] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Woorim Kang
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - Sei Joon Oh
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 02447, Korea
| |
Collapse
|
13
|
Xie F, Ma H, Quan S, Liu D, Chen G. Comamonas phosphati sp. nov., isolated from a phosphate mine. Int J Syst Evol Microbiol 2016; 66:456-461. [DOI: 10.1099/ijsem.0.000742] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Fuhong Xie
- Henan Engineering Research Center of Industrial Enzymes, Biology Institute of Henan Academy of Sciences, Zhengzhou 450008, PR China
| | - Huan Ma
- Henan Engineering Research Center of Industrial Enzymes, Biology Institute of Henan Academy of Sciences, Zhengzhou 450008, PR China
| | - Shujing Quan
- Henan Engineering Research Center of Industrial Enzymes, Biology Institute of Henan Academy of Sciences, Zhengzhou 450008, PR China
| | - Dehai Liu
- Henan Engineering Research Center of Industrial Enzymes, Biology Institute of Henan Academy of Sciences, Zhengzhou 450008, PR China
| | - Guocan Chen
- Henan Engineering Research Center of Industrial Enzymes, Biology Institute of Henan Academy of Sciences, Zhengzhou 450008, PR China
- Henan Key Laboratory of Microbial Engineering, Biology Institute of Henan Academy of Sciences, Zhengzhou 450008, PR China
| |
Collapse
|
14
|
Hatayama K, Kuno T. Spirosoma fluviale sp. nov., isolated from river water. Int J Syst Evol Microbiol 2015; 65:3447-3450. [DOI: 10.1099/ijsem.0.000433] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated MSd3T, was isolated from a freshwater sample collected from the Hosoda River in Japan. The cells of strain MSd3T were Gram-stain-negative, non-spore-forming, aerobic, non-motile, curved rods forming rings, coils and undulating filaments. The 16S rRNA gene sequence of strain MSd3T showed closest similarity to that of Spirosoma linguale DSM 74T (97.6 % similarity) and similarity to other members of the genus Spirosoma ranged from 90.3 to 95.9 %. Strain MSd3T contained menaquinone 7 as the sole respiratory quinone. The major cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C16 : 1ω5c. The polar lipids were phosphatidylethanolamine, three unidentified aminophospholipids and three unidentified polar lipids. The DNA G+C content was 53.3 mol%. The DNA–DNA relatedness between strain MSd3T and S. linguale DSM 74T was 19 % or 25 % (reciprocal value). From the chemotaxonomic and physiological data and the levels of DNA–DNA relatedness, strain MSd3T should be classified as the representative of a novel species of the genus Spirosoma, for which the name Spirosoma fluviale sp. nov. (type strain MSd3T = JCM 30659T = DSM 29961T) is proposed.
Collapse
Affiliation(s)
- Kouta Hatayama
- Sagami Chemical Research Institute, Ayase, Kanagawa 252-1193, Japan
| | - Teruaki Kuno
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| |
Collapse
|