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Wang X, Chen H, Wang J, Yuan S, Jiao D, Wang S, Liu Y, Li Y, Dai J, Li S, Qiu D. Parachitinimonas caeni gen. nov., sp. nov., a novel member of family Burkholderiaceae isolated from activated sludge collected in Shenzhen, PR China. Int J Syst Evol Microbiol 2024; 74. [PMID: 38284383 DOI: 10.1099/ijsem.0.006249] [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: 01/30/2024] Open
Abstract
A Gram-stain-negative, strictly aerobic and filamentous bacterial strain, designated as DQS-5T, was isolated from the activated sludge of a municipal sewage treatment plant in Shenzhen, PR China. Optimal growth was observed at 28 °C and pH 7.5. Catalase and oxidase activities were detected. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DQS-5T was most closely related to the genera Chitinimonas and Chitinivorax (91.0-93.4 % and 92.5 % 16S rRNA gene sequence similarity, respectively) and was close to the member of the family Burkholderiaceae. The complete genome sequence of strain DQS-5T contains 5 653 844 bp and 57.3 mol% G+C. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between the genome of strain DQS-5T and those of its close relatives were 75.9-77.2, 19.0-20.3 and 57.2-61.8 %, respectively. Chemotaxonomic analysis of strain DQS-5T indicated that the sole respiratory quinone was ubiquinone-8, the predominant cellular fatty acids were C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid and aminolipid. The phylogenetic, genotypic, phenotypic and chemotaxonomic data demonstrate that strain DQS-5T represents a novel species in a novel genus within the family Burkholderiaceae, for which the name Parachitinimonas caeni gen. nov., sp. nov., is proposed. Strain DQS-5T (=KCTC 92788T=CCTCC AB 2022320T) is the type and only strain of P. caeni.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Han Chen
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jing Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Siliang Yuan
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Dian Jiao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shanhui Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yaqi Liu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yan Li
- China University of Geosciences (CUG), Wuhan 430074, PR China
| | - Jingcheng Dai
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Shuyang Li
- Wuhan Ammunition Life-tech Co. Ltd., Wuhan 430000, PR China
| | - Dongru Qiu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
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Herpell JB, Vanwijnsberghe S, Peeters C, Schindler F, Fragner L, Bejtović M, Weckwerth W, Vandamme P. Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor. Int J Syst Evol Microbiol 2021; 71:004969. [PMID: 34542391 PMCID: PMC8549267 DOI: 10.1099/ijsem.0.004969] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022] Open
Abstract
A novel bacterium, designated strain Msb3T, was recently isolated from leaves of the yam family plant Dioscorea bulbifera (Dioscoreaceae). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Paraburkholderia with Paraburkholderia xenovorans as nearest validly named neighbour taxon (99.3 % sequence similarity towards the P. xenovorans type strain). Earlier genome sequence analysis revealed a genome of 8.35 Mb in size with a G+C content of 62.5 mol%, which was distributed over two chromosomes and three plasmids. Here, we confirm that strain Msb3T represents a novel Paraburkholderia species. In silico DNA-DNA hybridization and average nucleotide identity (OrthoANIu) analyses towards P. xenovorans LB400T yielded 58.4 % dDDH and 94.5 % orthoANIu. Phenotypic and metabolic characterization revealed growth at 15 °C on tryptic soy agar, growth in the presence of 1 % NaCl and the lack of assimilation of phenylacetic acid as distinctive features. Together, these data demonstrate that strain Msb3T represents a novel species of the genus Paraburkholderia, for which we propose the name Paraburkholderia dioscoreae sp. nov. The type strain is Msb3T (=LMG 31881T, DSM 111632T, CECT 30342T).
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Affiliation(s)
- Johannes B. Herpell
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Sarah Vanwijnsberghe
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Florian Schindler
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Lena Fragner
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Mersad Bejtović
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Wilhelm RC, Cyle KT, Martinez CE, Karasz DC, Newman JD, Buckley DH. Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana. Int J Syst Evol Microbiol 2020; 70:5093-5105. [PMID: 32809929 DOI: 10.1099/ijsem.0.004387] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Two bacterial strains, 1NT and 5NT, were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1NT (0.65×1.85 µm) and 5NT (0.6×1.85 µm) are Gram-stain-negative, aerobic, motile, non-sporulating and exist as single rods, diplobacilli or in chains of varying length. During growth in dilute media (≤0.1× tryptic soy broth; TSB), cells are primarily motile with flagella. At higher concentrations (≥0.3× TSB), cells of both strains increasingly form non-motile chains, and cells of 5NT elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1NT and 5NT occurred at 25-30 °C, pH 6.5-7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1NT and 5NT were distinct from one another and their closest related type strains: Paraburkholderia madseniana RP11T, Paraburkholderia aspalathi LMG 27731T and Paraburkholderia caffeinilytica CF1T. The genomes of 1NT and 5NT had an average nucleotide identity (91.6 and 91.3%) and in silico DNA-DNA hybridization values (45.8%±2.6 and 45.5%±2.5) and differed in functional gene content from their closest related type strains. The composition of fatty acids and patterns of substrate use, including the catabolism of phenolic acids, also differentiated strains 1NT and 5NT from each other and their closest relatives. The only ubiquinone present in strains 1NT and 5NT was Q-8. The major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed features 2 (3OH-C14 : 0 / C16 : 1 iso I), 3 (C16 : 1 ω6c/ω7c) and 8 (C18 : 1 ω7c/ω6c). A third bacterium, strain RL16-012-BIC-B, was isolated from soil associated with shallow roots and was determined to be a strain of P. madseniana (ANI, 98.8%; 16S rRNA gene similarity, 100%). Characterizations of strain RL16-012-BIC-B (DSM 110723=LMG 31706) led to proposed emendments to the species description of P. madseniana. Our polyphasic approach demonstrated that strains 1NT and 5NT represent novel species from the genus Paraburkholderia for which the names Paraburkholderia solitsugae sp. nov. (type strain 1NT=DSM 110721T=LMG 31704T) and Paraburkholderia elongata sp. nov. (type strain 5NT=DSM 110722T=LMG 31705T) are proposed.
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Affiliation(s)
- Roland C Wilhelm
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - K Taylor Cyle
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Carmen Enid Martinez
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - David C Karasz
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | | | - Daniel H Buckley
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
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Wilhelm RC, Murphy SJL, Feriancek NM, Karasz DC, DeRito CM, Newman JD, Buckley DH. Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil. Int J Syst Evol Microbiol 2020; 70:2137-2146. [PMID: 32027304 DOI: 10.1099/ijsem.0.004029] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
RP11T was isolated from forest soil following enrichment with 4-hydroxybenzoic acid. Cells of RP11T are aerobic, non-sporulating, exhibit swimming motility, and are rods (0.8 µm by 1.4 µm) that often occur as diplobacillus or in short chains (3-4 cells). Optimal growth on minimal media containing 4-hydroxybenzoic acid (µ=0.216 hr-1) occurred at 30 °C, pH 6.5 or 7.0 and 0% salinity. Comparative chemotaxonomic, genomic and phylogenetic analyses revealed the isolate was distinct from its closest relative type strains identified as Paraburkholderia aspalathi LMG 27731T, Paraburkholderia fungorum LMG 16225T and Paraburkholderia caffeinilytica CF1T. Strain RP11T is genetically distinct from P. aspalathi, its closest relative, in terms of 16S rRNA gene sequence similarity (98.7%), genomic average nucleotide identity (94%) and in silico DNA-DNA hybridization (56.7 %±2.8). The composition of fatty acids and substrate utilization pattern differentiated strain RP11T from its closest relatives, including growth on phthalic acid. Strain RP11T encoded the greatest number of aromatic degradation genes of all eleven closely related type strains and uniquely encoded a phthalic acid dioxygenase and paralog of the 3-hydroxybenzoate 4-monooxygenase. The only ubiquinone detected in strain RP11T was Q-8, and the major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω7c/ω6c). On the basis of this polyphasic approach, it was determined that strain RP11T represents a novel species from the genus Paraburkholderia for which the name Paraburkholderia madseniana sp. nov. is proposed. The type strain is RP11T (=DSM 110123T=LMG 31517T).
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Affiliation(s)
- Roland C Wilhelm
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Sean J L Murphy
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Nicole M Feriancek
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - David C Karasz
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Christopher M DeRito
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY, 14853, USA
| | | | - Daniel H Buckley
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
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Environmental interactions are regulated by temperature in Burkholderia seminalis TC3.4.2R3. Sci Rep 2019; 9:5486. [PMID: 30940839 PMCID: PMC6445077 DOI: 10.1038/s41598-019-41778-x] [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: 06/29/2018] [Accepted: 03/12/2019] [Indexed: 11/08/2022] Open
Abstract
Burkholderia seminalis strain TC3.4.2R3 is an endophytic bacterium isolated from sugarcane roots that produces antimicrobial compounds, facilitating its ability to act as a biocontrol agent against phytopathogenic bacteria. In this study, we investigated the thermoregulation of B. seminalis TC3.4.2R3 at 28 °C (environmental stimulus) and 37 °C (host-associated stimulus) at the transcriptional and phenotypic levels. The production of biofilms and exopolysaccharides such as capsular polysaccharides and the biocontrol of phytopathogenic fungi were enhanced at 28 °C. At 37 °C, several metabolic pathways were activated, particularly those implicated in energy production, stress responses and the biosynthesis of transporters. Motility, growth and virulence in the Galleria mellonella larvae infection model were more significant at 37 °C. Our data suggest that the regulation of capsule expression could be important in virulence against G. mellonella larvae at 37 °C. In contrast, B. seminalis TC3.4.2R3 failed to cause death in infected BALB/c mice, even at an infective dose of 107 CFU.mL-1. We conclude that temperature drives the regulation of gene expression in B. seminalis during its interactions with the environment.
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Kim H, Bae MJ, Yu SM, Oh J, Lee CS, Yeon Jo B, Chae JC, Kim JH. Ephemeroptericola cinctiostellae gen. nov., sp. nov., isolated from gut of an aquatic insect. Int J Syst Evol Microbiol 2019; 69:1546-1550. [PMID: 30932804 DOI: 10.1099/ijsem.0.003296] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, catalase- and oxidase-positive, non-motile bacterium, designated F02T, was isolated from of gut of Cincticostellalevanidovae (Tshernova). Growth occurred at a temperature range of 4-30 °C, at pH 6-9 and in the presence of 0-0.5 % (w/v) NaCl. Phylogenetic analysis demonstrated that the 16S rRNA gene sequence of strain F02T shared the highest similarity to that of the type strain of Hydromonas duriensis A2P5T (96.82 %). The major isoprenoid quinone was Q-8. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and iso-C13 : 0 3-OH. The polyamines were cadaverine and putrescine. Combined data from phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strain F02T represents a novel genus and species, for which the name Ephemeroptericolacinctiostellae gen. nov., sp. nov. is proposed. The type strain of Ephemeroptericola cinctiostellae gen. nov., sp. nov. is F02T (=FBCC 500047T=KCTC 62567T=JCM 32722T).
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Affiliation(s)
- Hyangmi Kim
- 2Division of Biotechnology, Chonbuk National University, Iksan 54596, Republic of Korea.,1Bioresources Culture Collection Division, NNIBR, Sangju 37242, Republic of Korea
| | - Mi-Jung Bae
- 3Biodiversity Conservation & Change Research Division, NNIBR, Sangju 37242, Republic of Korea
| | - Sang Mi Yu
- 4Freshwater Bioresources Utilization Division, NNIBR, Sangju 37242, Republic of Korea
| | - Jeongsu Oh
- 5Bioresource Information Research Division, NNIBR, Sangju 37242, Republic of Korea
| | - Chang Soo Lee
- 1Bioresources Culture Collection Division, NNIBR, Sangju 37242, Republic of Korea
| | - Bok Yeon Jo
- 1Bioresources Culture Collection Division, NNIBR, Sangju 37242, Republic of Korea
| | - Jong-Chan Chae
- 2Division of Biotechnology, Chonbuk National University, Iksan 54596, Republic of Korea
| | - Jee-Hwan Kim
- 1Bioresources Culture Collection Division, NNIBR, Sangju 37242, Republic of Korea
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Lee JW, Kim YE, Park SJ. Burkholderia alba sp. nov., isolated from a soil sample on Halla mountain in Jeju island. J Microbiol 2018; 56:312-316. [PMID: 29721827 DOI: 10.1007/s12275-018-8034-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 11/29/2022]
Abstract
A rod-shaped, round and white colony-forming strain AD18T was isolated from the soil on Halla mountain in Jeju Island, Republic of Korea. Comparative analysis of 16S rRNA gene sequence revealed that this strain was closely related to Burkholderia oklahomensis C6786T (98.8%), Burkholderia thailandensis KCTC 23190T (98.5%). DNA-DNA relatedness (14.6%) indicated that the strain AD18T represents a distinct species that is separate from B. oklahomensis C6786T. The isolate grew at pH 5.0-9.0 (optimum, pH 7.0), 0-3% (w/v) NaCl (optimum, 0%), and temperature 10-40°C (optimum 35°C). The sole quinone of the strain was Q-8, and the predominant fatty acids were C16:0, C17:0 cyclo, and C19:0 cyclo ω8c. The genomic DNA G + C content of AD18T was 65.6 mol%. Based on these findings, strain AD18T is proposed to be a novel species in the genus Burkholderia, for which the name Burkholderia alba sp. nov. is proposed (= KCCM 43268T = JCM 32403T). The type strain is AD18T.
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Affiliation(s)
- Jae-Won Lee
- Department of Biology, Jeju National University, Jeju, 63243, Republic of Korea
| | - Ye-Eun Kim
- Department of Biology, Jeju National University, Jeju, 63243, Republic of Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju, 63243, Republic of Korea.
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Mehrotra A, Sreekrishnan TR. Heavy metal bioleaching and sludge stabilization in a single-stage reactor using indigenous acidophilic heterotrophs. ENVIRONMENTAL TECHNOLOGY 2017; 38:2709-2724. [PMID: 28043205 DOI: 10.1080/09593330.2016.1275821] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Simultaneous sludge digestion and metal leaching (SSDML) have been reported at mesophilic temperature. It is generally perceived that while sludge stabilization is effected by heterotrophs at neutral pH, metal bioleaching is done by acidophilic autotrophs. However, little information is available on the microbial communities involved in the process. This study carried out SSDML in a single-stage reactor using sludge indigenous microorganisms and looked at the bacterial communities responsible for the process. Volatile suspended solids were reduced by more than 40%. The concentration of zinc, copper, chromium, cadmium and nickel decreased by more than 45% in the dry sludge. Acidophilic species of Alicyclobacillus genus were the dominant heterotrophs. A few heterotrophic bacteria were detected which can oxidize iron (Alicyclobacillus ferrooxydans, Alicyclobacillus ferripilum and Ferrimicrobium acidiphilum). Acidithiobacillus ferrooxidans (autotroph) was responsible for the oxidation of both iron and sulfur which lead to a change in the pH from neutral to acidic. The presence of acidophilic heterotrophs, which can oxidize either iron or sulfur, enhanced the efficiency of SSDML process with respect to sludge stabilization and metal leaching. This study shows that it is possible to carry out the SSDML in a single-stage reactor with indigenous microorganisms.
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Affiliation(s)
- Akanksha Mehrotra
- a Department of Biochemical Engineering and Biotechnology , Indian Institute of Technology Delhi , New Delhi , India
| | - T R Sreekrishnan
- a Department of Biochemical Engineering and Biotechnology , Indian Institute of Technology Delhi , New Delhi , India
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Weber CF, King GM. Volcanic Soils as Sources of Novel CO-Oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a Member of the Burkholderia cepacia Complex. Front Microbiol 2017; 8:207. [PMID: 28270796 PMCID: PMC5318905 DOI: 10.3389/fmicb.2017.00207] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/30/2017] [Indexed: 11/16/2022] Open
Abstract
Previous studies showed that members of the Burkholderiales were important in the succession of aerobic, molybdenum-dependent CO oxidizing-bacteria on volcanic soils. During these studies, four isolates were obtained from Kilauea Volcano (Hawai‘i, USA); one strain was isolated from Pico de Orizaba (Mexico) during a separate study. Based on 16S rRNA gene sequence similarities, the Pico de Orizaba isolate and the isolates from Kilauea Volcano were provisionally assigned to the genera Burkholderia and Paraburkholderia, respectively. Each of the isolates possessed a form I coxL gene that encoded the catalytic subunit of carbon monoxide dehydrogenase (CODH); none of the most closely related type strains possessed coxL or oxidized CO. Genome sequences for Paraburkholderia type strains facilitated an analysis of 16S rRNA gene sequence similarities and average nucleotide identities (ANI). ANI did not exceed 95% (the recommended cutoff for species differentiation) for any of the pairwise comparisons among 27 reference strains related to the new isolates. However, since the highest 16S rRNA gene sequence similarity among this set of reference strains was 98.93%, DNA-DNA hybridizations (DDH) were performed for two isolates whose 16S rRNA gene sequence similarities with their nearest phylogenetic neighbors were 98.96 and 99.11%. In both cases DDH values were <16%. Based on multiple variables, four of the isolates represent novel species within the Paraburkholderia: Paraburkholderia hiiakae sp. nov. (type strain I2T = DSM 28029T = LMG 27952T); Paraburkholderia paradisi sp. nov. (type strain WAT = DSM 28027T = LMG 27949T); Paraburkholderia peleae sp. nov. (type strain PP52-1T = DSM 28028T = LMG 27950T); and Paraburkholderia metrosideri sp. nov. (type strain DNBP6-1T = DSM 28030T = LMG 28140T). The remaining isolate represents the first CO-oxidizing member of the Burkholderia cepacia complex: Burkholderia alpina sp. nov. (type strain PO-04-17-38T = DSM 28031T = LMG 28138T).
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Affiliation(s)
- Carolyn F Weber
- Department of Biological Sciences, Louisiana State UniversityBaton Rouge, LA, USA; College of Health Sciences, Des Moines UniversityDes Moines, IA, USA
| | - Gary M King
- Department of Biological Sciences, Louisiana State University Baton Rouge, LA, USA
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da Silva PRA, Vidal MS, de Paula Soares C, Polese V, Simões-Araújo JL, Baldani JI. Selection and evaluation of reference genes for RT-qPCR expression studies on Burkholderia tropica strain Ppe8, a sugarcane-associated diazotrophic bacterium grown with different carbon sources or sugarcane juice. Antonie van Leeuwenhoek 2016; 109:1493-1502. [PMID: 27535840 DOI: 10.1007/s10482-016-0751-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/05/2016] [Indexed: 12/15/2022]
Abstract
Among the members of the genus Burkholderia, Burkholderia tropica has the ability to fix nitrogen and promote sugarcane plant growth as well as act as a biological control agent. There is little information about how this bacterium metabolizes carbohydrates as well as those carbon sources found in the sugarcane juice that accumulates in stems during plant growth. Reverse transcription quantitative PCR (RT-qPCR) can be used to evaluate changes in gene expression during bacterial growth on different carbon sources. Here we tested the expression of six reference genes, lpxC, gyrB, recA, rpoA, rpoB, and rpoD, when cells were grown with glucose, fructose, sucrose, mannitol, aconitic acid, and sugarcane juice as carbon sources. The lpxC, gyrB, and recA were selected as the most stable reference genes based on geNorm and NormFinder software analyses. Validation of these three reference genes during strain Ppe8 growth on the same carbon sources showed that genes involved in glycogen biosynthesis (glgA, glgB, glgC) and trehalose biosynthesis (treY and treZ) were highly expressed when Ppe8 was grown in aconitic acid relative to other carbon sources, while otsA expression (trehalose biosynthesis) was reduced with all carbon sources. In addition, the expression level of the ORF_6066 (gluconolactonase) gene was reduced on sugarcane juice. The results confirmed the stability of the three selected reference genes (lpxC, gyrB, and recA) during the RT-qPCR and also their robustness by evaluating the relative expression of genes involved in glycogen and trehalose biosynthesis when strain Ppe8 was grown on different carbon sources and sugarcane juice.
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Affiliation(s)
- Paula Renata Alves da Silva
- Curso de Pós-graduação em Fitotecnia, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
- Embrapa Agrobiologia, BR465, Km07, Seropédica, RJ, 23890-000, Brazil
| | | | - Cleiton de Paula Soares
- Curso de Pós-graduação em Fitotecnia, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
- Embrapa Agrobiologia, BR465, Km07, Seropédica, RJ, 23890-000, Brazil
| | - Valéria Polese
- Curso de Pós-graduação em Fitotecnia, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
- Embrapa Agrobiologia, BR465, Km07, Seropédica, RJ, 23890-000, Brazil
| | | | - José Ivo Baldani
- Embrapa Agrobiologia, BR465, Km07, Seropédica, RJ, 23890-000, Brazil.
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11
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Kim S, Gong G, Min Woo H, Kim Y, Um Y. Burkholderia jirisanensis sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:1260-1267. [DOI: 10.1099/ijsem.0.000867] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Seil Kim
- Center for Bioanalysis, Korea Research Institute of Standards and Science, 267, Gajeong-ro, Yuseong-gu, Daejeon 305-340, Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Han Min Woo
- Clean Energy Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Yunje Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 136-791, Republic of Korea
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12
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Burkholderia metalliresistens sp. nov., a multiple metal-resistant and phosphate-solubilising species isolated from heavy metal-polluted soil in Southeast China. Antonie van Leeuwenhoek 2015; 107:1591-8. [PMID: 25896306 DOI: 10.1007/s10482-015-0453-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/06/2015] [Indexed: 12/13/2022]
Abstract
A metal-resistant and phosphate-solubilising bacterium, designated as strain D414(T), was isolated from heavy metal (Pb, Cd, Cu and Zn)-polluted paddy soils at the surrounding area of Dabao Mountain Mine in Southeast China. The minimum inhibitory concentrations of heavy metals for strain D414(T) were 2000 mg L(-1) (Cd), 800 mg L(-1) (Pb), 150 mg L(-1) (Cu) and 2500 mg L(-1) (Zn). The strain possessed plant growth-promoting properties, such as 1-aminocyclopropane-1-carboxylate assimilation, indole production and phosphate solubilisation. Analysis of 16S rRNA gene sequence indicated that the isolate is a member of the genus Burkholderia where strain D414(T) formed a distinct phyletic line with validly described Burkholderia species. Strain D414(T) is closely related to Burkholderia tropica DSM 15359(T), B. bannensis NBRC E25(T) and B. unamae DSM 17197(T), with 98.5, 98.3 and 98.3 % sequence similarities, respectively. Furthermore, less than 34 % DNA-DNA relatedness was detected between strain D414(T) and the type strains of the phylogenetically closest species of Burkholderia. The dominant fatty acids of strain D414(T) were C14:0, C16:0, C17:0 cyclo and C18:1 ω7c. The DNA G+C content was 62.3 ± 0.5 mol%. On the basis of genotypic, phenotypic and phylogenetic data, strain D414(T) represents a novel species, for which the name Burkholderia metalliresistens sp. nov. is proposed, with D414(T) (=CICC 10561(T) = DSM 26823(T)) as the type strain.
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13
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Sawana A, Adeolu M, Gupta RS. Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species. Front Genet 2014; 5:429. [PMID: 25566316 PMCID: PMC4271702 DOI: 10.3389/fgene.2014.00429] [Citation(s) in RCA: 296] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/21/2014] [Indexed: 01/22/2023] Open
Abstract
The genus Burkholderia contains large number of diverse species which include many clinically important organisms, phytopathogens, as well as environmental species. However, currently, there is a paucity of biochemical or molecular characteristics which can reliably distinguish different groups of Burkholderia species. We report here the results of detailed phylogenetic and comparative genomic analyses of 45 sequenced species of the genus Burkholderia. In phylogenetic trees based upon concatenated sequences for 21 conserved proteins as well as 16S rRNA gene sequence based trees, members of the genus Burkholderia grouped into two major clades. Within these main clades a number of smaller clades including those corresponding to the clinically important Burkholderia cepacia complex (BCC) and the Burkholderia pseudomallei groups were also clearly distinguished. Our comparative analysis of protein sequences from Burkholderia spp. has identified 42 highly specific molecular markers in the form of conserved sequence indels (CSIs) that are uniquely found in a number of well-defined groups of Burkholderia spp. Six of these CSIs are specific for a group of Burkholderia spp. (referred to as Clade I in this work) which contains all clinically relevant members of the genus (viz. the BCC and the B. pseudomallei group) as well as the phytopathogenic Burkholderia spp. The second main clade (Clade II), which is composed of environmental Burkholderia species, is also distinguished by 2 identified CSIs that are specific for this group. Additionally, our work has also identified multiple CSIs that serve to clearly demarcate a number of smaller groups of Burkholderia spp. including 3 CSIs that are specific for the B. cepacia complex, 4 CSIs that are uniquely found in the B. pseudomallei group, 5 CSIs that are specific for the phytopathogenic Burkholderia spp. and 22 other CSI that distinguish two groups within Clade II. The described molecular markers provide highly specific means for the demarcation of different groups of Burkholderia spp. and they also offer novel and useful targets for the development of diagnostic assays for the clinically important members of the BCC or the pseudomallei groups. Based upon the results of phylogenetic analyses, the identified CSIs and the pathogenicity profile of Burkholderia species, we are proposing a division of the genus Burkholderia into two genera. In this new proposal, the emended genus Burkholderia will correspond to the Clade I and it will contain only the clinically relevant and phytopathogenic Burkholderia species. All other Burkholderia spp., which are primarily environmental, will be transferred to a new genus Paraburkholderia gen. nov.
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Affiliation(s)
| | | | - Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, Health Sciences Center, McMaster UniversityHamilton, ON, Canada
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14
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Kim M, Kim WS, Tripathi BM, Adams J. Distinct bacterial communities dominate tropical and temperate zone leaf litter. MICROBIAL ECOLOGY 2014; 67:837-848. [PMID: 24549745 DOI: 10.1007/s00248-014-0380-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 01/30/2014] [Indexed: 06/03/2023]
Abstract
Little is known of the bacterial community of tropical rainforest leaf litter and how it might differ from temperate forest leaf litter and from the soils underneath. We sampled leaf litter in a similarly advanced stage of decay, and for comparison, we also sampled the surface layer of soil, at three tropical forest sites in Malaysia and four temperate forest sites in South Korea. Illumina sequencing targeting partial bacterial 16S ribosomal ribonucleic acid (rRNA) gene revealed that the bacterial community composition of both temperate and tropical litter is quite distinct from the soils underneath. Litter in both temperate and tropical forest was dominated by Proteobacteria and Actinobacteria, while soil is dominated by Acidobacteria and, to a lesser extent, Proteobacteria. However, bacterial communities of temperate and tropical litter clustered separately from one another on an ordination. The soil bacterial community structures were also distinctive to each climatic zone, suggesting that there must be a climate-specific biogeographical pattern in bacterial community composition. The differences were also found in the level of diversity. The temperate litter has a higher operational taxonomic unit (OTU) diversity than the tropical litter, paralleling the trend in soil diversity. Overall, it is striking that the difference in community composition between the leaf litter and the soil a few centimeters underneath is about the same as that between leaf litter in tropical and temperate climates, thousands of kilometers apart. However, one substantial difference was that the leaf litter of two tropical forest sites, Meranti and Forest Research Institute Malaysia (FRIM), was overwhelmingly dominated by the single genus Burkholderia, at 37 and 23 % of reads, respectively. The 454 sequencing result showed that most Burkholderia species in tropical leaf litter belong to nonpathogenic "plant beneficial" lineages. The differences from the temperate zone in the bacterial community of tropical forest litter may be partly a product of its differing chemistry, although the unvarying climate might also play a role, as might interactions with other organisms such as fungi. The single genus Burkholderia may be seen as potentially playing a major role in decomposition and nutrient cycling in tropical forests, but apparently not in temperate forests.
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Affiliation(s)
- Mincheol Kim
- School of Biological Sciences, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul, 151-747, Republic of Korea
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15
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Kang SR, Srinivasan S, Lee SS. Burkholderia eburnea sp. nov., isolated from peat soil. Int J Syst Evol Microbiol 2014; 64:1108-1115. [DOI: 10.1099/ijs.0.051078-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel aerobic bacterium, designated strain RR11T, was isolated from peat soil and was characterized by using a polyphasic taxonomic approach and identified in order to determine its taxonomic position. Strain RR11T is a Gram-negative, non-sporulating, motile, short-rod-shaped bacterium. 16S rRNA gene sequence analysis identified this strain as a member of the genus
Burkholderia
of the class
Betaproteobacteria
. The highest degrees of gene sequence similarity were found with
Burkholderia tropica
Ppe8T (98.0 %),
B. bannensis
E25T (97.3 %),
B. ferrariae
FeGI01T (97.1 %),
B. unamae
MTI-641T (97.1 %) and
B. heleia
SA41T (97.1 %). Strain RR11T had the following chemotaxonomic characteristics: the major ubiquinone was Q-8, the DNA G+C content was 60.8 mol%, the major fatty acids were C16 : 0, C19 : 0 cyclo ω8c and C17 : 0 cyclo and the polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown aminophospholipid. Based on its morphological, physiological and chemotaxonomic characteristics, together with 16S rRNA gene sequence comparison results, strain RR11T represents a novel species, for which the name Burkholderia eburnea sp. nov. is proposed. The type strain is strain RR11T ( = KEMC 7302-065T = JCM 18070T).
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Affiliation(s)
- Sang Rim Kang
- Department of Bioengineering, Graduate School of Kyonggi University, 94-6 Iui-dong, Yeongtong-gu, Suwon 433-760, Republic of Korea
| | - Sathiyaraj Srinivasan
- Basic Science Research Institute, Kyonggi University, 94-6 Iui-dong, Yeongtong-gu, Suwon 443-760, Republic of Korea
- Department of Bioengineering, Graduate School of Kyonggi University, 94-6 Iui-dong, Yeongtong-gu, Suwon 433-760, Republic of Korea
| | - Sang Seob Lee
- Department of Bioengineering, Graduate School of Kyonggi University, 94-6 Iui-dong, Yeongtong-gu, Suwon 433-760, Republic of Korea
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16
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De Meyer SE, Cnockaert M, Ardley JK, Van Wyk BE, Vandamme PA, Howieson JG. Burkholderia dilworthii sp. nov., isolated from Lebeckia ambigua root nodules. Int J Syst Evol Microbiol 2013; 64:1090-1095. [PMID: 24368690 DOI: 10.1099/ijs.0.058602-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains of Gram-stain-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules and authenticated on this host. Based on the 16S rRNA gene sequence phylogeny, they were shown to belong to the genus Burkholderia, with the representative strain WSM3556(T) being most closely related to Burkholderia caledonica LMG 23644(T) (98.70 % 16S rRNA gene sequence similarity) and Burkholderia rhynchosiae WSM3937(T) (98.50 %). Additionally, these strains formed a distinct group in phylogenetic trees of the housekeeping genes gyrB and recA. Chemotaxonomic data, including fatty acid profiles and analysis of respiratory quinones, supported the assignment of our strains to the genus Burkholderia. Results of DNA-DNA hybridizations, MALDI-TOF MS analysis and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from their nearest neighbour species. Therefore, these strains represent a novel species, for which the name Burkholderia dilworthii sp. nov. is proposed, with the type strain WSM3556(T) ( = LMG 27173(T) = HAMBI 3353(T)).
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Affiliation(s)
- Sofie E De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Julie K Ardley
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Ben-Erik Van Wyk
- Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, 2006 Johannesburg, South Africa
| | - Peter A Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - John G Howieson
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia 6150, Australia
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17
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Burkholderia sprentiae sp. nov., isolated from Lebeckia ambigua root nodules. Int J Syst Evol Microbiol 2013; 63:3950-3957. [DOI: 10.1099/ijs.0.048777-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven Gram-stain-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules and authenticated on this host. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus
Burkholderia
, with the representative strain WSM5005T being most closely related to
Burkholderia tuberum
(98.08 % sequence similarity). Additionally, these strains formed a distinct group in phylogenetic trees based on the housekeeping genes gyrB and recA. Chemotaxonomic data including fatty acid profiles and analysis of respiratory quinones supported the assignment of the strains to the genus
Burkholderia
. Results of DNA–DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from the closest species of the genus
Burkholderia
with a validly published name. Therefore, these strains represent a novel species for which the name Burkholderia sprentiae sp. nov. (type strain WSM5005T = LMG 27175T = HAMBI 3357T) is proposed.
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18
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De Meyer SE, Cnockaert M, Ardley JK, Trengove RD, Garau G, Howieson JG, Vandamme P. Burkholderia rhynchosiae sp. nov., isolated from Rhynchosia ferulifolia root nodules. Int J Syst Evol Microbiol 2013; 63:3944-3949. [DOI: 10.1099/ijs.0.048751-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of Gram-stain-negative, rod-shaped bacteria were isolated from root nodules of the South African legume Rhynchosia ferulifolia and authenticated on this host. Based on phylogenetic analysis of the 16S rRNA gene, strains WSM3930 and WSM3937T belonged to the genus
Burkholderia
, with the highest degree of sequence similarity to
Burkholderia terricola
(98.84 %). Additionally, the housekeeping genes gyrB and recA were analysed since 16S rRNA gene sequences are highly similar between closely related species of the genus
Burkholderia
. The results obtained for both housekeeping genes, gyrB and recA, showed the highest degree of sequence similarity of the novel strains towards
Burkholderia caledonica
LMG 19076T (94.2 % and 94.5 %, respectively). Chemotaxonomic data, including fatty acid profiles and respiratory quinone data supported the assignment of strains WSM3930 and WSM3937T to the genus
Burkholderia
. DNA–DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains WSM3930 and WSM3937T from the most closely related species of the genus
Burkholderia
with validly published names. We conclude, therefore, that these strains represent a novel species for which the name Burkholderia rhynchosiae sp. nov. is proposed, with strain WSM3937T ( = LMG 27174T = HAMBI 3354T) as the type strain.
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Affiliation(s)
- Sofie E. De Meyer
- Centre for Rhizobium Studies, Murdoch University, Western Australia 6150, Australia
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Julie K. Ardley
- Centre for Rhizobium Studies, Murdoch University, Western Australia 6150, Australia
| | - Robert D. Trengove
- Separation Science and Metabolomics Laboratory, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Giovanni Garau
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agro-Alimentari (DiSAABA), University of Sassari, Italy
| | - John G. Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia 6150, Australia
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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19
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Stopnisek N, Bodenhausen N, Frey B, Fierer N, Eberl L, Weisskopf L. Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations. Environ Microbiol 2013; 16:1503-12. [PMID: 23945027 DOI: 10.1111/1462-2920.12211] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/04/2013] [Accepted: 07/10/2013] [Indexed: 11/30/2022]
Abstract
Bacteria belonging to the genus Burkholderia are highly versatile with respect to their ecological niches and lifestyles, ranging from nodulating tropical plants to causing melioidosis and fatal infections in cystic fibrosis patients. Despite the clinical importance and agronomical relevance of Burkholderia species, information about the factors influencing their occurrence, abundance and diversity in the environment is scarce. Recent findings have demonstrated that pH is the main predictor of soil bacterial diversity and community structure, with the highest diversity observed in neutral pH soils. As many Burkholderia species have been isolated from low pH environments, we hypothesized that acid tolerance may be a general feature of this genus, and pH a good predictor of their occurrence in soils. Using a combination of environmental surveys at trans-continental and local scales, as well as in vitro assays, we show that, unlike most bacteria, Burkholderia species have a competitive advantage in acidic soils, but are outcompeted in alkaline soils. Physiological assays and diversity analysis based on 16S rRNA clone libraries demonstrate that pH tolerance is a general phenotypic trait of the genus Burkholderia. Our results provide a basis for building a predictive understanding of the biogeographical patterns exhibited by Burkholderia sp.
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Affiliation(s)
- Nejc Stopnisek
- Institute of Plant Biology, University of Zurich, Zürich, CH-8008, Switzerland; Swiss Federal Research Station for Agronomy and Nature, Agroscope Reckenholz-Tänikon, Zürich, CH-8046, Switzerland
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20
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Tian Y, Kong BH, Liu SL, Li CL, Yu R, Liu L, Li YH. Burkholderia grimmiae sp. nov., isolated from a xerophilous moss (Grimmia montana). Int J Syst Evol Microbiol 2013; 63:2108-2113. [DOI: 10.1099/ijs.0.045492-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, rod-shaped, non-spore-forming bacterium, designated strain R27T, was isolated from the moss Grimmia montana, collected from Beijing Songshan National Nature Reserve, China, and characterized by using a polyphasic taxonomic approach. The predominant fatty acids of strain R27T were C18 : 1ω7c (33.6 %), C16 : 0 (16.3 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 15.8 %) and C17 : 0 cyclo (8.7 %) and its major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three uncharacterized aminolipids and an unknown phospholipid. Strain R27T contained Q-8 as the dominant isoprenoid quinone and the G+C content of its genomic DNA was 64.6 mol%. On the basis of 16S rRNA gene sequence comparison, strain R27T showed 99.1 % similarity to the closest related type strain,
Burkholderia zhejiangensis
OP-1T, and 97.6 % similarity to
Burkholderia glathei
ATCC 29195T. However, the DNA–DNA relatedness between strain R27T and
B. zhejiangensis
CCTCC AB 2010354T and
B. glathei
ATCC 29195T was 10.2 and 14.9 %, respectively. Based on 16S rRNA and rpoB gene sequence similarities and phenotypic and chemotaxonomic data, strain R27T is considered to represent a novel species of the genus
Burkholderia
, for which the name Burkholderia grimmiae sp. nov. is proposed. The type strain is R27T ( = CGMCC 1.11013T = DSM 25160T).
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Affiliation(s)
- Yang Tian
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Bi He Kong
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Su Lin Liu
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Chun Li Li
- New Technique Centre, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Rong Yu
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Lei Liu
- College of Life Science, Capital Normal University, Beijing 100048, PR China
| | - Yan Hong Li
- College of Life Science, Capital Normal University, Beijing 100048, PR China
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21
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Phylogenetic analysis of burkholderia species by multilocus sequence analysis. Curr Microbiol 2013; 67:51-60. [PMID: 23404651 DOI: 10.1007/s00284-013-0330-9] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 01/21/2013] [Indexed: 01/16/2023]
Abstract
Burkholderia comprises more than 60 species of environmental, clinical, and agro-biotechnological relevance. Previous phylogenetic analyses of 16S rRNA, recA, gyrB, rpoB, and acdS gene sequences as well as genome sequence comparisons of different Burkholderia species have revealed two major species clusters. In this study, we undertook a multilocus sequence analysis of 77 type and reference strains of Burkholderia using atpD, gltB, lepA, and recA genes in combination with the 16S rRNA gene sequence and employed maximum likelihood and neighbor-joining criteria to test this further. The phylogenetic analysis revealed, with high supporting values, distinct lineages within the genus Burkholderia. The two large groups were named A and B, whereas the B. rhizoxinica/B. endofungorum, and B. andropogonis groups consisted of two and one species, respectively. The group A encompasses several plant-associated and saprophytic bacterial species. The group B comprises the B. cepacia complex (opportunistic human pathogens), the B. pseudomallei subgroup, which includes both human and animal pathogens, and an assemblage of plant pathogenic species. The distinct lineages present in Burkholderia suggest that each group might represent a different genus. However, it will be necessary to analyze the full set of Burkholderia species and explore whether enough phenotypic features exist among the different clusters to propose that these groups should be considered separate genera.
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22
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Suárez-Moreno ZR, Caballero-Mellado J, Coutinho BG, Mendonça-Previato L, James EK, Venturi V. Common features of environmental and potentially beneficial plant-associated Burkholderia. MICROBIAL ECOLOGY 2012; 63:249-266. [PMID: 21850446 DOI: 10.1007/s00248-011-9929-1] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 08/01/2011] [Indexed: 05/31/2023]
Abstract
The genus Burkholderia comprises more than 60 species isolated from a wide range of niches. Although they have been shown to be diverse and ubiquitously distributed, most studies have thus far focused on the pathogenic species due to their clinical importance. However, the increasing number of recently described Burkholderia species associated with plants or with the environment has highlighted the division of the genus into two main clusters, as suggested by phylogenetical analyses. The first cluster includes human, animal, and plant pathogens, such as Burkholderia glumae, Burkholderia pseudomallei, and Burkholderia mallei, as well as the 17 defined species of the Burkholderia cepacia complex, while the other, more recently established cluster comprises more than 30 non-pathogenic species, which in most cases have been found to be associated with plants, and thus might be considered to be potentially beneficial. Several species from the latter group share characteristics that are of use when associating with plants, such as a quorum sensing system, the presence of nitrogen fixation and/or nodulation genes, and the ability to degrade aromatic compounds. This review examines the commonalities in this growing subgroup of Burkholderia species and discusses their prospective biotechnological applications.
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Affiliation(s)
- Zulma Rocío Suárez-Moreno
- Bacteriology Group, International Centre for Genetic Engineering & Biotechnology, Padriciano 99, 34149 Trieste, Italy
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