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Vandamme P, Peeters C, De Smet B, Price EP, Sarovich DS, Henry DA, Hird TJ, Zlosnik JEA, Mayo M, Warner J, Baker A, Currie BJ, Carlier A. Comparative Genomics of Burkholderia singularis sp. nov., a Low G+C Content, Free-Living Bacterium That Defies Taxonomic Dissection of the Genus Burkholderia. Front Microbiol 2017; 8:1679. [PMID: 28932212 PMCID: PMC5592201 DOI: 10.3389/fmicb.2017.01679] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/21/2017] [Indexed: 12/03/2022] Open
Abstract
Four Burkholderia pseudomallei-like isolates of human clinical origin were examined by a polyphasic taxonomic approach that included comparative whole genome analyses. The results demonstrated that these isolates represent a rare and unusual, novel Burkholderia species for which we propose the name B. singularis. The type strain is LMG 28154T (=CCUG 65685T). Its genome sequence has an average mol% G+C content of 64.34%, which is considerably lower than that of other Burkholderia species. The reduced G+C content of strain LMG 28154T was characterized by a genome wide AT bias that was not due to reduced GC-biased gene conversion or reductive genome evolution, but might have been caused by an altered DNA base excision repair pathway. B. singularis can be differentiated from other Burkholderia species by multilocus sequence analysis, MALDI-TOF mass spectrometry and a distinctive biochemical profile that includes the absence of nitrate reduction, a mucoid appearance on Columbia sheep blood agar, and a slowly positive oxidase reaction. Comparisons with publicly available whole genome sequences demonstrated that strain TSV85, an Australian water isolate, also represents the same species and therefore, to date, B. singularis has been recovered from human or environmental samples on three continents.
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Affiliation(s)
- Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent UniversityGhent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent UniversityGhent, Belgium
| | - Birgit De Smet
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent UniversityGhent, Belgium
| | - Erin P. Price
- Global and Tropical Health Division, Menzies School of Health Research, DarwinNT, Australia
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy DownsQLD, Australia
| | - Derek S. Sarovich
- Global and Tropical Health Division, Menzies School of Health Research, DarwinNT, Australia
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy DownsQLD, Australia
| | - Deborah A. Henry
- Centre for Understanding and Preventing Infection in Children, Department of Pediatrics, University of British Columbia, VancouverBC, Canada
| | - Trevor J. Hird
- Centre for Understanding and Preventing Infection in Children, Department of Pediatrics, University of British Columbia, VancouverBC, Canada
| | - James E. A. Zlosnik
- Centre for Understanding and Preventing Infection in Children, Department of Pediatrics, University of British Columbia, VancouverBC, Canada
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, DarwinNT, Australia
| | - Jeffrey Warner
- College of Public Health, Medical and Veterinary Sciences, Australian Institute of Tropical Health and Medicine, James Cook University, TownsvilleQLD, Australia
| | - Anthony Baker
- Tasmanian Institute of Agriculture, University of Tasmania, HobartTAS, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, DarwinNT, Australia
| | - Aurélien Carlier
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent UniversityGhent, Belgium
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52
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Pratama AA, van Elsas JD. A novel inducible prophage from the mycosphere inhabitant Paraburkholderia terrae BS437. Sci Rep 2017; 7:9156. [PMID: 28831124 PMCID: PMC5567305 DOI: 10.1038/s41598-017-09317-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 07/20/2017] [Indexed: 11/13/2022] Open
Abstract
Bacteriophages constitute key gene transfer agents in many bacteria. Specifically, they may confer gene mobility to Paraburkholderia spp. that dwells in soil and the mycosphere. In this study, we first screened mycosphere and bulk soils for phages able to produce plaques, however found these to be below detection. Then, prophage identification methods were applied to the genome sequences of the mycosphere-derived Paraburkholderia terrae strains BS001, BS007, BS110 and BS437, next to P. phytofirmans strains BS455, BIFAS53, J1U5 and PsJN. These analyses revealed all bacterial genomes to contain considerable amounts [up to 13.3%] of prophage-like sequences. One sequence predicted to encode a complete phage was found in the genome of P. terrae BS437. Using the inducing agent mitomycin C, we produced high-titered phage suspensions. These indeed encompassed the progeny of the identified prophage (denoted ɸ437), as evidenced using phage major capsid gene molecular detection. We obtained the full sequence of phage ɸ437, which, remarkably, had undergone a reshuffling of two large gene blocks. One predicted moron gene was found, and it is currently analyzed to understand the extent of its ecological significance for the host.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands.
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands.
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53
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de Lajudie PM, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the meeting, Budapest, 25 August 2016. Int J Syst Evol Microbiol 2017; 67:2485-2494. [PMID: 28771120 DOI: 10.1099/ijsem.0.002144] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
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54
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Mangalea MR, Plumley BA, Borlee BR. Nitrate Sensing and Metabolism Inhibit Biofilm Formation in the Opportunistic Pathogen Burkholderia pseudomallei by Reducing the Intracellular Concentration of c-di-GMP. Front Microbiol 2017; 8:1353. [PMID: 28790983 PMCID: PMC5524735 DOI: 10.3389/fmicb.2017.01353] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/04/2017] [Indexed: 01/25/2023] Open
Abstract
The opportunistic pathogen Burkholderia pseudomallei is a saprophytic bacterium and the causative agent of melioidosis, an emerging infectious disease associated with high morbidity and mortality. Although melioidosis is most prevalent during the rainy season in endemic areas, domestic gardens and farms can also serve as a reservoir for B. pseudomallei during the dry season, in part due to irrigation and fertilizer use. In the environment, B. pseudomallei forms biofilms and persists in soil near plant root zones. Biofilms are dynamic bacterial communities whose formation is regulated by extracellular cues and corresponding changes in the nearly universal secondary messenger cyclic dimeric GMP. Recent studies suggest B. pseudomallei loads are increased by irrigation and the addition of nitrate-rich fertilizers, whereby such nutrient imbalances may be linked to the transmission epidemiology of this important pathogen. We hypothesized that exogenous nitrate inhibits B. pseudomallei biofilms by reducing the intracellular concentration of c-di-GMP. Bioinformatics analyses revealed B. pseudomallei 1026b has the coding capacity for nitrate sensing, metabolism, and transport distributed on both chromosomes. Using a sequence-defined library of B. pseudomallei 1026b transposon insertion mutants, we characterized the role of denitrification genes in biofilm formation in response to nitrate. Our results indicate that the denitrification pathway is implicated in B. pseudomallei biofilm growth dynamics and biofilm formation is inhibited by exogenous addition of sodium nitrate. Genomics analysis identified transposon insertional mutants in a predicted two-component system (narX/narL), a nitrate reductase (narGH), and a nitrate transporter (narK-1) required to sense nitrate and alter biofilm formation. Additionally, the results presented here show that exogenous nitrate reduces intracellular levels of the bacterial second messenger c-di-GMP. These results implicate the role of nitrate sensing in the regulation of a c-di-GMP phosphodiesterase and the corresponding effects on c-di-GMP levels and biofilm formation in B. pseudomallei 1026b.
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Affiliation(s)
- Mihnea R Mangalea
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort CollinsCO, United States
| | - Brooke A Plumley
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort CollinsCO, United States
| | - Bradley R Borlee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort CollinsCO, United States
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55
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Akita H, Kimura ZI, Yusoff MZM, Nakashima N, Hoshino T. Identification and characterization of Burkholderia multivorans CCA53. BMC Res Notes 2017; 10:249. [PMID: 28683814 PMCID: PMC5501517 DOI: 10.1186/s13104-017-2565-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 06/26/2017] [Indexed: 01/30/2023] Open
Abstract
Objective A lignin-degrading bacterium, Burkholderia sp. CCA53, was previously isolated from leaf soil. The purpose of this study was to determine phenotypic and biochemical features of Burkholderia sp. CCA53. Results Multilocus sequence typing (MLST) analysis based on fragments of the atpD, gltD, gyrB, lepA, recA and trpB gene sequences was performed to identify Burkholderia sp. CCA53. The MLST analysis revealed that Burkholderia sp. CCA53 was tightly clustered with B. multivorans ATCC BAA-247T. The quinone and cellular fatty acid profiles, carbon source utilization, growth temperature and pH were consistent with the characteristics of B. multivorans species. Burkholderia sp. CCA53 was therefore identified as B. multivorans CCA53.
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Affiliation(s)
- Hironaga Akita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.
| | - Zen-Ichiro Kimura
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-2-11 Aga-minami, Kure, Hiroshima, 737-8506, Japan
| | - Mohd Zulkhairi Mohd Yusoff
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.,Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nobutaka Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan.,Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Tamotsu Hoshino
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
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56
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Nguyen TT, Chon TS, Kim J, Seo YS, Heo M. Comparative and bioinformatics analyses of pathogenic bacterial secretomes identified by mass spectrometry in Burkholderia species. J Microbiol 2017; 55:568-582. [PMID: 28664514 DOI: 10.1007/s12275-017-7085-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/02/2017] [Accepted: 06/12/2017] [Indexed: 10/19/2022]
Abstract
Secreted proteins (secretomes) play crucial roles during bacterial pathogenesis in both plant and human hosts. The identification and characterization of secretomes in the two plant pathogens Burkholderia glumae BGR1 and B. gladioli BSR3, which cause diseases in rice such as seedling blight, panicle blight, and grain rot, are important steps to not only understand the disease-causing mechanisms but also find remedies for the diseases. Here, we identified two datasets of secretomes in B. glumae BGR1 and B. gladioli BSR3, which consist of 118 and 111 proteins, respectively, using mass spectrometry approach and literature curation. Next, we characterized the functional properties, potential secretion pathways and sequence information properties of secretomes of two plant pathogens in a comparative analysis by various computational approaches. The ratio of potential non-classically secreted proteins (NCSPs) to classically secreted proteins (CSPs) in B. glumae BGR1 was greater than that in B. gladioli BSR3. For CSPs, the putative hydrophobic regions (PHRs) which are essential for secretion process of CSPs were screened in detail at their N-terminal sequences using hidden Markov model (HMM)-based method. Total 31 pairs of homologous proteins in two bacterial secretomes were indicated based on the global alignment (identity ≥ 70%). Our results may facilitate the understanding of the species-specific features of secretomes in two plant pathogenic Burkholderia species.
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Affiliation(s)
- Thao Thi Nguyen
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea
| | - Tae-Soo Chon
- Department of Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Jaehan Kim
- Department of Food and Nutrition, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.
| | - Muyoung Heo
- Department of Physics, Pusan National University, Busan, 46241, Republic of Korea.
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57
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Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR, van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Blom J, Whitman WB, Venter SN, Steenkamp ET. Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato. Front Microbiol 2017; 8:1154. [PMID: 28694797 PMCID: PMC5483467 DOI: 10.3389/fmicb.2017.01154] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/07/2017] [Indexed: 12/21/2022] Open
Abstract
Although the taxonomy of Burkholderia has been extensively scrutinized, significant uncertainty remains regarding the generic boundaries and composition of this large and heterogeneous taxon. Here we used the amino acid and nucleotide sequences of 106 conserved proteins from 92 species to infer robust maximum likelihood phylogenies with which to investigate the generic structure of Burkholderia sensu lato. These data unambiguously supported five distinct lineages, of which four correspond to Burkholderia sensu stricto and the newly introduced genera Paraburkholderia, Caballeronia, and Robbsia. The fifth lineage was represented by P. rhizoxinica. Based on these findings, we propose 13 new combinations for those species previously described as members of Burkholderia but that form part of Caballeronia. These findings also suggest revision of the taxonomic status of P. rhizoxinica as it is does not form part of any of the genera currently recognized in Burkholderia sensu lato. From a phylogenetic point of view, Burkholderia sensu stricto has a sister relationship with the Caballeronia+Paraburkholderia clade. Also, the lineages represented by P. rhizoxinica and R. andropogonis, respectively, emerged prior to the radiation of the Burkholderia sensu stricto+Caballeronia+Paraburkholderia clade. Our findings therefore constitute a solid framework, not only for supporting current and future taxonomic decisions, but also for studying the evolution of this assemblage of medically, industrially and agriculturally important species.
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Affiliation(s)
- Chrizelle W Beukes
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Puseletso Manyaka
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Wai Y Chan
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Juanita R Avontuur
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Elritha van Zyl
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | | | - Alicia Clum
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Manoj Pillay
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | | | - Neha Varghese
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | | | | | - T B K Reddy
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Chris Daum
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | | | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University GiessenGiessen, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, AthensGA, United States
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
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58
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Dall'Agnol RF, Bournaud C, de Faria SM, Béna G, Moulin L, Hungria M. Genetic diversity of symbiotic Paraburkholderia species isolated from nodules of Mimosa pudica (L.) and Phaseolus vulgaris (L.) grown in soils of the Brazilian Atlantic Forest (Mata Atlântica). FEMS Microbiol Ecol 2017; 93:3045887. [PMID: 28334155 DOI: 10.1093/femsec/fix027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/22/2017] [Indexed: 11/13/2022] Open
Abstract
Some species of the genus Paraburkholderia that are able to nodulate and fix nitrogen in symbiosis with legumes are called β-rhizobia and represent a group of ecological and biotechnological importance. We used Mimosa pudica and Phaseolus vulgaris to trap 427 rhizobial isolates from rhizospheric soil of Mimoseae trees in the Brazilian Atlantic Forest. Eighty-four representative strains were selected according to the 16S rRNA haplotypes and taxonomically characterized using a concatenated 16S rRNA-recA phylogeny. Most strains were assembled in the genus Paraburkholderia, including Paraburkholderia sabiae and Pa. nodosa. Mesorhizobium (α-rhizobia) and Cupriavidus (β-rhizobia) were also isolated, but in smaller proportions. Multilocus sequence analysis and BOX-PCR analyses indicated that six clusters of Paraburkholderia represent potential new species. In the phylogenetic analysis of the nodC gene, the majority of the strains were positioned in the same groups as in the 16S rRNA-recA tree, indicative of stability and vertical inheritance, but we also identified horizontal transfer of nodC in Pa. sabiae. All α- and β-rhizobial species were trapped by both legumes, although preferences of the host plants for specific rhizobial species have been observed.
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Affiliation(s)
- Rebeca Fuzinatto Dall'Agnol
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 231, 86001-970, Londrina, PR, Brazil.,Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 10.011, 86057-970, Londrina, PR, Brazil.,IRD, Cirad, Univ. Montpellier, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet 34398 Montpellier, France
| | - Caroline Bournaud
- IRD, Cirad, Univ. Montpellier, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet 34398 Montpellier, France.,Embrapa Recursos Genéticos e Biotecnologia, LIMPP Laboratory, C.P. 02372, 70770-917, Brasília, DF, Brazil
| | | | - Gilles Béna
- IRD, Cirad, Univ. Montpellier, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet 34398 Montpellier, France.,IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet 34398 Montpellier, France.,IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Mariangela Hungria
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 231, 86001-970, Londrina, PR, Brazil
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Use of Synthetic Hybrid Strains To Determine the Role of Replicon 3 in Virulence of the Burkholderia cepacia Complex. Appl Environ Microbiol 2017; 83:AEM.00461-17. [PMID: 28432094 DOI: 10.1128/aem.00461-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/12/2017] [Indexed: 01/08/2023] Open
Abstract
The Burkholderia cepacia complex (Bcc) displays a wealth of metabolic diversity with great biotechnological potential, but the utilization of these bacteria is limited by their opportunistic pathogenicity to humans. The third replicon of the Bcc, megaplasmid pC3 (0.5 to 1.4 Mb, previously chromosome 3), is important for various phenotypes, including virulence, antifungal, and proteolytic activities and the utilization of certain substrates. Approximately half of plasmid pC3 is well conserved throughout sequenced Bcc members, while the other half is not. To better locate the regions responsible for the key phenotypes, pC3 mutant derivatives of Burkholderia cenocepacia H111 carrying large deletions (up to 0.58 Mb) were constructed with the aid of the FLP-FRT (FRT, flippase recognition target) recombination system from Saccharomyces cerevisiae The conserved region was shown to confer near-full virulence in both Caenorhabditis elegans and Galleria mellonella infection models. Antifungal activity was unexpectedly independent of the part of pC3 bearing a previously identified antifungal gene cluster, while proteolytic activity was dependent on the nonconserved part of pC3, which encodes the ZmpA protease. To investigate to what degree pC3-encoded functions are dependent on chromosomally encoded functions, we transferred pC3 from Burkholderia cenocepacia K56-2 and Burkholderia lata 383 into other pC3-cured Bcc members. We found that although pC3 is highly important for virulence, it was the genetic background of the recipient that determined the pathogenicity level of the hybrid strain. Furthermore, we found that important phenotypes, such as antifungal activity, proteolytic activity, and some substrate utilization capabilities, can be transferred between Bcc members using pC3.IMPORTANCE The Burkholderia cepacia complex (Bcc) is a group of closely related bacteria with great biotechnological potential. Some strains produce potent antifungal compounds and can promote plant growth or degrade environmental pollutants. However, their agricultural potential is limited by their opportunistic pathogenicity, particularly for cystic fibrosis patients. Despite much study, their virulence remains poorly understood. The third replicon, pC3, which is present in all Bcc isolates and is important for pathogenicity, stress resistance, and the production of antifungal compounds, has recently been reclassified from a chromosome to a megaplasmid. In this study, we identified regions on pC3 important for virulence and antifungal activity and investigated the role of the chromosomal background for the function of pC3 by exchanging the megaplasmid between different Bcc members. Our results may open a new avenue for the construction of antifungal but nonpathogenic Burkholderia hybrids. Such strains may have great potential as biocontrol strains for protecting fungus-borne diseases of plant crops.
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60
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Who lives in a fungus? The diversity, origins and functions of fungal endobacteria living in Mucoromycota. ISME JOURNAL 2017; 11:1727-1735. [PMID: 28387771 DOI: 10.1038/ismej.2017.21] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/13/2017] [Accepted: 01/19/2017] [Indexed: 01/07/2023]
Abstract
Bacterial interactions with plants and animals have been examined for many years; differently, only with the new millennium the study of bacterial-fungal interactions blossomed, becoming a new field of microbiology with relevance to microbial ecology, human health and biotechnology. Bacteria and fungi interact at different levels and bacterial endosymbionts, which dwell inside fungal cells, provide the most intimate example. Bacterial endosymbionts mostly occur in fungi of the phylum Mucoromycota and include Betaproteobacteria (Burkhoderia-related) and Mollicutes (Mycoplasma-related). Based on phylogenomics and estimations of divergence time, we hypothesized two different scenarios for the origin of these interactions (early vs late bacterial invasion). Sequencing of the genomes of fungal endobacteria revealed a significant reduction in genome size, particularly in endosymbionts of Glomeromycotina, as expected by their uncultivability and host dependency. Similar to endobacteria of insects, the endobacteria of fungi show a range of behaviours from mutualism to antagonism. Emerging results suggest that some benefits given by the endobacteria to their plant-associated fungal host may propagate to the interacting plant, giving rise to a three-level inter-domain interaction.
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61
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Nguyen TT, Lee HH, Park J, Park I, Seo YS. Computational Identification and Comparative Analysis of Secreted and Transmembrane Proteins in Six Burkholderia Species. THE PLANT PATHOLOGY JOURNAL 2017; 33:148-162. [PMID: 28381962 PMCID: PMC5378436 DOI: 10.5423/ppj.oa.11.2016.0252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/02/2017] [Accepted: 01/05/2017] [Indexed: 05/14/2023]
Abstract
As a step towards discovering novel pathogenesis-related proteins, we performed a genome scale computational identification and characterization of secreted and transmembrane (TM) proteins, which are mainly responsible for bacteria-host interactions and interactions with other bacteria, in the genomes of six representative Burkholderia species. The species comprised plant pathogens (B. glumae BGR1, B. gladioli BSR3), human pathogens (B. pseudomallei K96243, B. cepacia LO6), and plant-growth promoting endophytes (Burkholderia sp. KJ006, B. phytofirmans PsJN). The proportions of putative classically secreted proteins (CSPs) and TM proteins among the species were relatively high, up to approximately 20%. Lower proportions of putative type 3 non-classically secreted proteins (T3NCSPs) (~10%) and unclassified non-classically secreted proteins (NCSPs) (~5%) were observed. The numbers of TM proteins among the three clusters (plant pathogens, human pathogens, and endophytes) were different, while the distribution of these proteins according to the number of TM domains was conserved in which TM proteins possessing 1, 2, 4, or 12 TM domains were the dominant groups in all species. In addition, we observed conservation in the protein size distribution of the secreted protein groups among the species. There were species-specific differences in the functional characteristics of these proteins in the various groups of CSPs, T3NCSPs, and unclassified NCSPs. Furthermore, we assigned the complete sets of the conserved and unique NCSP candidates of the collected Burkholderia species using sequence similarity searching. This study could provide new insights into the relationship among plant-pathogenic, human-pathogenic, and endophytic bacteria.
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Affiliation(s)
- Thao Thi Nguyen
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Hyun-Hee Lee
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Inmyoung Park
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
- Department of Asian Food and Culinary Arts, Youngsan University, Busan 48015,
Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
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Lopes-Santos L, Castro DBA, Ferreira-Tonin M, Corrêa DBA, Weir BS, Park D, Ottoboni LMM, Neto JR, Destéfano SAL. Reassessment of the taxonomic position of Burkholderia andropogonis and description of Robbsia andropogonis gen. nov., comb. nov. Antonie Van Leeuwenhoek 2017; 110:727-736. [PMID: 28190154 DOI: 10.1007/s10482-017-0842-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 02/01/2017] [Indexed: 10/20/2022]
Abstract
The phylogenetic classification of the species Burkholderia andropogonis within the Burkholderia genus was reassessed using 16S rRNA gene phylogenetic analysis and multilocus sequence analysis (MLSA). Both phylogenetic trees revealed two main groups, named A and B, strongly supported by high bootstrap values (100%). Group A encompassed all of the Burkholderia species complex, whi.le Group B only comprised B. andropogonis species, with low percentage similarities with other species of the genus, from 92 to 95% for 16S rRNA gene sequences and 83% for conserved gene sequences. Average nucleotide identity (ANI), tetranucleotide signature frequency, and percentage of conserved proteins POCP analyses were also carried out, and in the three analyses B. andropogonis showed lower values when compared to the other Burkholderia species complex, near 71% for ANI, from 0.484 to 0.724 for tetranucleotide signature frequency, and around 50% for POCP, reinforcing the distance observed in the phylogenetic analyses. Our findings provide an important insight into the taxonomy of B. andropogonis. It is clear from the results that this bacterial species exhibits genotypic differences and represents a new genus described herein as Robbsia andropogonis gen. nov., comb. nov.
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Affiliation(s)
- Lucilene Lopes-Santos
- Laboratório de Bacteriologia Vegetal, Instituto Biológico, Rod. Heitor Penteado KM 3, Campinas, SP, CEP 13092-543, Brazil
| | - Daniel Bedo Assumpção Castro
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas - UNICAMP, Campinas, Brazil
| | - Mariana Ferreira-Tonin
- Laboratório de Bacteriologia Vegetal, Instituto Biológico, Rod. Heitor Penteado KM 3, Campinas, SP, CEP 13092-543, Brazil
| | - Daniele Bussioli Alves Corrêa
- Laboratório de Bacteriologia Vegetal, Instituto Biológico, Rod. Heitor Penteado KM 3, Campinas, SP, CEP 13092-543, Brazil
| | | | - Duckchul Park
- Landcare Research, Private Bag 92170, Auckland, New Zealand
| | | | - Júlio Rodrigues Neto
- Laboratório de Bacteriologia Vegetal, Instituto Biológico, Rod. Heitor Penteado KM 3, Campinas, SP, CEP 13092-543, Brazil
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63
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Beligala DH, Michaels HJ, Devries M, Phuntumart V. Multilocus Sequence Analysis of Root Nodule Bacteria Associated with <i>Lupinus</i> spp. and <i>Glycine max</i>. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/aim.2017.711063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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64
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Evolution of bopA Gene in Burkholderia: A Case of Convergent Evolution as a Mechanism for Bacterial Autophagy Evasion. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6745028. [PMID: 28018913 PMCID: PMC5149610 DOI: 10.1155/2016/6745028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/13/2016] [Accepted: 10/24/2016] [Indexed: 12/20/2022]
Abstract
Autophagy is an important defense mechanism targeting intracellular bacteria to restrict their survival and growth. On the other hand, several intracellular pathogens have developed an antiautophagy mechanism to facilitate their own replication or intracellular survival. Up to now, no information about the origin or evolution of the antiautophagic genes in bacteria is available. BopA is an effector protein secreted by Burkholderia pseudomallei via the type three secretion system, and it has been shown to play a pivotal role in their escape from autophagy. The evolutionary origin of bopA was examined in this work. Sequence similarity searches for BopA showed that no homolog of BopA was detected in eukaryotes. However, eukaryotic linear motifs were detected in BopA. The phylogenetic tree of the BopA proteins in our analysis is congruent with the species phylogeny derived from housekeeping genes. Moreover, there was no obvious difference in GC content values of bopA gene and their respective genomes. Integrated information on the taxonomic distribution, phylogenetic relationships, and GC content of the bopA gene of Burkholderia revealed that this gene was acquired via convergent evolution, not from eukaryotic host through horizontal gene transfer (HGT) event. This work has, for the first time, characterized the evolutionary mechanism of bacterial evasion of autophagy. The results of this study clearly demonstrated the role of convergent evolution in the evolution of how bacteria evade autophagy.
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65
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Palomares‐Rius JE, Archidona‐Yuste A, Cantalapiedra‐Navarrete C, Prieto P, Castillo P. Molecular diversity of bacterial endosymbionts associated with dagger nematodes of the genus
Xiphinema
(Nematoda: Longidoridae) reveals a high degree of phylogenetic congruence with their host. Mol Ecol 2016; 25:6225-6247. [DOI: 10.1111/mec.13904] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 10/07/2016] [Accepted: 10/25/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Juan E. Palomares‐Rius
- Instituto de Agricultura Sostenible (IAS) Consejo Superior de Investigaciones Científicas (CSIC) Avenida Menéndez Pidal s/n 14004 Córdoba Spain
| | - Antonio Archidona‐Yuste
- Instituto de Agricultura Sostenible (IAS) Consejo Superior de Investigaciones Científicas (CSIC) Avenida Menéndez Pidal s/n 14004 Córdoba Spain
| | - Carolina Cantalapiedra‐Navarrete
- Instituto de Agricultura Sostenible (IAS) Consejo Superior de Investigaciones Científicas (CSIC) Avenida Menéndez Pidal s/n 14004 Córdoba Spain
| | - Pilar Prieto
- Instituto de Agricultura Sostenible (IAS) Consejo Superior de Investigaciones Científicas (CSIC) Avenida Menéndez Pidal s/n 14004 Córdoba Spain
| | - Pablo Castillo
- Instituto de Agricultura Sostenible (IAS) Consejo Superior de Investigaciones Científicas (CSIC) Avenida Menéndez Pidal s/n 14004 Córdoba Spain
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66
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Genome Sequence of Paraburkholderia nodosa Strain CNPSo 1341, a N2-Fixing Symbiont of the Promiscuous Legume Phaseolus vulgaris. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01073-16. [PMID: 27811087 PMCID: PMC5095457 DOI: 10.1128/genomea.01073-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Paraburkholderia nodosa CNPSo 1341 is a N2-fixing symbiont of Phaseolus vulgaris isolated from an undisturbed soil of the Brazilian Cerrado. Its draft genome contains 8,614,032 bp and 8,068 coding sequences (CDSs). Nodulation and N2-fixation genes were clustered in the genome that also contains several genes of secretion systems and quorum sensing.
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67
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Simakov N, Leonard DA, Smith JC, Wymore T, Szarecka A. A Distal Disulfide Bridge in OXA-1 β-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Ω Loop. J Phys Chem B 2016; 121:3285-3296. [PMID: 27668669 DOI: 10.1021/acs.jpcb.6b07884] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Widespread antibiotic resistance, particularly when mediated by broad-spectrum β-lactamases, has major implications for public health. Substitutions in the active site often allow broad-spectrum enzymes to accommodate diverse types of β-lactams. Substitutions observed outside the active site are thought to compensate for the loss of thermal stability. The OXA-1 clade of class D β-lactamases contains a pair of conserved cysteines located outside the active site that forms a disulfide bond in the periplasm. Here, the effect of the distal disulfide bond on the structure and dynamics of OXA-1 was investigated via 4 μs molecular dynamics simulations. The results reveal that the disulfide promotes the preorganized orientation of the catalytic residues and affects the conformation of the functionally important Ω loop. Furthermore, principal component analysis reveals differences in the global dynamics between the oxidized and reduced forms, especially in the motions involving the Ω loop. A dynamical network analysis indicates that, in the oxidized form, in addition to its role in ligand binding, the KTG family motif is a central hub of the global dynamics. As activity of OXA-1 has been measured only in the reduced form, we suggest that accurate assessment of its functional profile would require oxidative conditions mimicking periplasm.
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Affiliation(s)
- Nikolay Simakov
- Carnegie Mellon University , Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania 15213, United States.,Center for Computational Research, SUNY at Buffalo , New York 14203, United States
| | | | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Troy Wymore
- Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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68
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Reclassification of Paraburkholderia panaciterrae (Farh et al. 2015) Dobritsa & Samadpour 2016 as a later synonym of Paraburkholderia ginsengiterrae (Farh et al. 2015) Dobritsa & Samadpour 2016. Int J Syst Evol Microbiol 2016; 66:4085-4087. [DOI: 10.1099/ijsem.0.001314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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69
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Burkholderia pseudomallei: Challenges for the Clinical Microbiology Laboratory. J Clin Microbiol 2016; 54:2866-2873. [PMID: 27654336 DOI: 10.1128/jcm.01636-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Melioidosis is a potentially fatal infection caused by the bacterium Burkholderia pseudomallei Clinical diagnosis of melioidosis can be challenging since there is no pathognomonic clinical syndrome, and the organism is often misidentified by methods used routinely in clinical laboratories. Although the disease is more prevalent in Thailand and northern Australia, sporadic cases may be encountered in areas where it is not endemic, including the United States. Since the organism is considered a tier 1 select agent according to the Centers for Disease Control and Prevention and the U.S. Department of Agriculture Animal and Plant Health Inspection Service, clinical laboratories must be proficient at rapidly recognizing isolates suspicious for B. pseudomallei, be able to safely perform necessary rule-out tests, and to refer suspect isolates to Laboratory Response Network reference laboratories. In this minireview, we report a case of melioidosis encountered at our institution and discuss the laboratory challenges encountered when dealing with clinical isolates suspicious for B. pseudomallei or clinical specimens from suspected melioidosis cases.
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70
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Lv YY, Chen MH, Xia F, Wang J, Qiu LH. Paraburkholderiapallidirosea sp. nov., isolated from a monsoon evergreen broad-leaved forest soil. Int J Syst Evol Microbiol 2016; 66:4537-4542. [PMID: 27499129 DOI: 10.1099/ijsem.0.001387] [Citation(s) in RCA: 16] [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-stain-negative, rod-shaped, aerobic and motile bacterial strain, DHOK13T, was isolated from the forest soils of Dinghushan Biosphere Reserve, Guangdong Province, PR China (112° 31' E, 23° 10' N). It grew optimally at 28-33 °C and pH 7.0-7.5. The main fatty acids were C16 : 0, C17 : 0 cyclo, C19 : 0 cycloω8c, summed feature 2 (C12 : 0 aldehyde and/or unknown 10.9525) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The organism contained ubiquinone Q-8 as the predominant isoprenoid quinone. The total DNA G+C content of strain DHOK13T was 62.0 mol%. Phylogenetic analysis of the 16S rRNA gene, as well as the sequence of the partial housekeeping genes, gyrB and recA, showed consistently that strain DHOK13T formed an independent cluster with Paraburkholderia phenazinium LMG 2247T. DNA-DNA hybridization studies showed relatively low relatedness values (39 %) of strain DHOK13T with P. phenazinium LMG 2247T. The phenotypic, chemotaxonomic and phylogenetic data showed that strain DHOK13T represents a novel species of the genus Paraburkholderia for which the name Paraburkholderia pallidirosea sp. nov. is proposed. The type strain is DHOK13T (=KCTC 42626T=LMG 28846T).
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Affiliation(s)
- Ying-Ying Lv
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Mei-Hong Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Fan Xia
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jia Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Li-Hong Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
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71
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Bolívar-Anillo HJ, Contreras-Zentella ML, Teherán-Sierra LG. Burkholderia tropica UNA BACTERIA CON GRAN POTENCIAL PARA SU USO EN LA AGRICULTURA. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2016. [DOI: 10.1016/j.recqb.2016.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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72
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Draft Genome Sequence of Burkholderia sp. Strain CCA53, Isolated from Leaf Soil. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00630-16. [PMID: 27389268 PMCID: PMC4939785 DOI: 10.1128/genomea.00630-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Burkholderia sp. strain CCA53 was isolated from leaf soil collected in Higashi-Hiroshima City in Hiroshima Prefecture, Japan. Here, we present a draft genome sequence of this strain, which consists of a total of 4 contigs containing 6,647,893 bp, with a G+C content of 67.0% and comprising 9,329 predicted coding sequences.
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73
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Satapute P, Kaliwal B. Biodegradation of propiconazole by newly isolated Burkholderia sp. strain BBK_9. 3 Biotech 2016; 6:110. [PMID: 28330180 PMCID: PMC5398191 DOI: 10.1007/s13205-016-0429-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/26/2016] [Indexed: 10/24/2022] Open
Abstract
The isolation of propiconazole (PCZ) degrading bacterium BBK_9 strain was done from paddy soil, and it was identified as Burkholderia sp. based on the morphological characteristics and biochemical properties combined with 16S rRNA gene sequencing analysis. It has been seen that the factors such as temperature and pH influence the biodegradation process. The role of plasmid was studied in the degradation process by plasmid curing method. The PCZ acts as the sole carbon source and as energy substrate which can be utilized by the strain for its growth in Mineral salt medium and degraded 8.89 µg ml-1 of PCZ at 30 °C and pH 7 within 4 days. During the bioconversion process of PCZ, three metabolite were formed such as 1-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-yl) ethanone, 1-[2-(4-chlorophenyl) ethyl]-1H-1,2,4-triazole and 1-ethyl-1H-1,2,4-triazole. The LD50 value of BBK_9 strain was determined with acridine orange which resulted in 40 µg ml-1 at cell density of 0.243 at 660 nm. Furthermore, plasmid curing was done using LD50 concentration and from that three plasmids got cured in the sixth generation. It was found that, cured strain was able to degrade 7.37 µg ml-1 of PCZ, indicating the plasmid encoded gene were not responsible for the PCZ degradation. On the source of these outcomes, strain BBK_9 can be used as potential strain for bioremediation of contaminated sites.
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74
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Abstract
In the 1990s several biocontrol agents on that contained Burkholderia strains were registered by the United States Environmental Protection Agency (EPA). After risk assessment these products were withdrawn from the market and a moratorium was placed on the registration of Burkholderia-containing products, as these strains may pose a risk to human health. However, over the past few years the number of novel Burkholderia species that exhibit plant-beneficial properties and are normally not isolated from infected patients has increased tremendously. In this commentary we wish to summarize recent efforts that aim at discerning pathogenic from beneficial Burkholderia strains.
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Affiliation(s)
- Leo Eberl
- Department of Plant and Microbial Biology, University Zürich, Zurich, CH-8008, Switzerland
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Gent, Belgium
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75
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Dall'Agnol RF, Plotegher F, Souza RC, Mendes IC, Dos Reis Junior FB, Béna G, Moulin L, Hungria M. Paraburkholderia nodosa is the main N2-fixing species trapped by promiscuous common bean (Phaseolus vulgaris L.) in the Brazilian 'Cerradão'. FEMS Microbiol Ecol 2016; 92:fiw108. [PMID: 27199345 DOI: 10.1093/femsec/fiw108] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2016] [Indexed: 11/14/2022] Open
Abstract
The bacterial genus Burkholderia comprises species occupying several habitats, including a group of symbionts of leguminous plants-also called beta-rhizobia-that has been recently ascribed to the new genus Paraburkholderia We used common bean (Phaseolus vulgaris L.) plants to trap rhizobia from an undisturbed soil of the Brazilian Cerrado under the vegetation type 'Cerradão'. Genetic characterization started with the analyses of 181 isolates by BOX-PCR, where the majority revealed unique profiles, indicating high inter- and intra-species diversity. Restriction fragment length polymorphism-PCR of the 16S rRNA of representative strains of the BOX-PCR groups indicated two main clusters, and gene-sequencing analysis identified the minority (27%) as Rhizobium and the majority (73%) as Paraburkholderia Phylogenetic analyses of the 16S rRNA and housekeeping (recA and gyrB) genes positioned all strains of the second cluster in the species P. nodosa, and the phylogeny of a symbiotic gene-nodC-was in agreement with the conserved genes. All isolates were stable vis-à-vis nodulating common bean, but, in general, with a low capacity for fixing N2, although some effective strains were identified. The predominance of P. nodosa might be associated with the edaphic properties of the Cerrado biome, and might represent an important role in terms of maintenance of the ecosystem, which is characterized by acid soils with high saturation of aluminum and low N2 content.
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Affiliation(s)
- Rebeca F Dall'Agnol
- Embrapa Soja, Soil Biotechnology Laboratory, C.P. 231, 86001-970, Londrina, PR, Brazil Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, PR, Brazil
| | - Fábio Plotegher
- Embrapa Soja, Soil Biotechnology Laboratory, C.P. 231, 86001-970, Londrina, PR, Brazil
| | - Renata C Souza
- Embrapa Soja, Soil Biotechnology Laboratory, C.P. 231, 86001-970, Londrina, PR, Brazil Department of Microbiology, Universidade Federal do Paraná, C.P. 19031, 81531-990, Curitiba, PR, Brazil
| | - Iêda C Mendes
- Department of Soil Microbiology, Embrapa Cerrados, C.P. 08223, 73301-970, Planaltina, DF, Brazil
| | - Fábio B Dos Reis Junior
- Department of Soil Microbiology, Embrapa Cerrados, C.P. 08223, 73301-970, Planaltina, DF, Brazil
| | - Gilles Béna
- IRD, Cirad, University of Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, University of Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Mariangela Hungria
- Embrapa Soja, Soil Biotechnology Laboratory, C.P. 231, 86001-970, Londrina, PR, Brazil Department of Microbiology, Universidade Federal do Paraná, C.P. 19031, 81531-990, Curitiba, PR, Brazil
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76
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Akita H, Kimura ZI, Mohd Yusoff MZ, Nakashima N, Hoshino T. Isolation and characterization of Burkholderia sp. strain CCA53 exhibiting ligninolytic potential. SPRINGERPLUS 2016; 5:596. [PMID: 27247892 PMCID: PMC4864794 DOI: 10.1186/s40064-016-2237-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/26/2016] [Indexed: 12/04/2022]
Abstract
Microbial degradation of lignin releases fermentable sugars, effective utilization of which could support biofuel production from lignocellulosic biomass. In the present study, a lignin-degrading bacterium was isolated from leaf soil and identified as Burkholderia sp. based on 16S rRNA gene sequencing. This strain was named CCA53, and its lignin-degrading capability was assessed by observing its growth on medium containing alkali lignin or lignin-associated aromatic monomers as the sole carbon source. Alkali lignin and at least eight lignin-associated aromatic monomers supported growth of this strain, and the most effective utilization was observed for p-hydroxybenzene monomers. These findings indicate that Burkholderia sp. strain CCA53 has fragmentary activity for lignin degradation.
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Affiliation(s)
- Hironaga Akita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Sciences and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046 Japan
| | - Zen-Ichiro Kimura
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-2-11 Aga-minami, Kure, Hiroshima 737-8506 Japan
| | - Mohd Zulkhairi Mohd Yusoff
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Sciences and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046 Japan ; Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Nobutaka Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan ; Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan
| | - Tamotsu Hoshino
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Sciences and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046 Japan ; Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan
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77
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Fernández-González E, Bakioui S, Gomes MC, O'Callaghan D, Vergunst AC, Sangari FJ, Llosa M. A Functional oriT in the Ptw Plasmid of Burkholderia cenocepacia Can Be Recognized by the R388 Relaxase TrwC. Front Mol Biosci 2016; 3:16. [PMID: 27200362 PMCID: PMC4853378 DOI: 10.3389/fmolb.2016.00016] [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: 03/11/2016] [Accepted: 04/14/2016] [Indexed: 12/14/2022] Open
Abstract
Burkholderia cenocepacia is both a plant pathogen and the cause of serious opportunistic infections, particularly in cystic fibrosis patients. B. cenocepacia K56-2 harbors a native plasmid named Ptw for its involvement in the Plant Tissue Watersoaking phenotype. Ptw has also been reported to be important for survival in human cells. Interestingly, the presence of PtwC, a homolog of the conjugative relaxase TrwC of plasmid R388, suggests a possible function for Ptw in conjugative DNA transfer. The ptw region includes Type IV Secretion System genes related to those of the F plasmid. However, genes in the adjacent region shared stronger homology with the R388 genes involved in conjugative DNA metabolism. This region included the putative relaxase ptwC, a putative coupling protein and accessory nicking protein, and a DNA segment with high number of inverted repeats and elevated AT content, suggesting a possible oriT. Although we were unable to detect conjugative transfer of the Ptw resident plasmid, we detected conjugal mobilization of a co-resident plasmid containing the ptw region homologous to R388, demonstrating the cloned ptw region contains an oriT. A similar plasmid lacking ptwC could not be mobilized, suggesting that the putative relaxase PtwC must act in cis on its oriT. Remarkably, we also detected mobilization of a plasmid containing the Ptw oriT by the R388 relaxase TrwC, yet we could not detect PtwC-mediated mobilization of an R388 oriT-containing plasmid. Our data unambiguously show that the Ptw plasmid harbors DNA transfer functions, and suggests the Ptw plasmid may play a dual role in horizontal DNA transfer and eukaryotic infection.
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Affiliation(s)
- Esther Fernández-González
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria, UC-SODERCAN-Consejo Superior de Investigaciones Científicas Santander, Spain
| | - Sawsane Bakioui
- Institut National de la Santé et de la Recherche Médicale, U1047Nimes, France; UFR de Médecine Site de Nimes, U1047, Université de MontpellierFrance
| | - Margarida C Gomes
- Institut National de la Santé et de la Recherche Médicale, U1047Nimes, France; UFR de Médecine Site de Nimes, U1047, Université de MontpellierFrance
| | - David O'Callaghan
- Institut National de la Santé et de la Recherche Médicale, U1047Nimes, France; UFR de Médecine Site de Nimes, U1047, Université de MontpellierFrance
| | - Annette C Vergunst
- Institut National de la Santé et de la Recherche Médicale, U1047Nimes, France; UFR de Médecine Site de Nimes, U1047, Université de MontpellierFrance
| | - Félix J Sangari
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria, UC-SODERCAN-Consejo Superior de Investigaciones Científicas Santander, Spain
| | - Matxalen Llosa
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria, UC-SODERCAN-Consejo Superior de Investigaciones Científicas Santander, Spain
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Guentas L, Gensous S, Cavaloc Y, Ducousso M, Amir H, De Georges de Ledenon B, Moulin L, Jourand P. Burkholderia novacaledonica sp. nov. and B. ultramafica sp. nov. isolated from roots of Costularia spp. pioneer plants of ultramafic soils in New Caledonia. Syst Appl Microbiol 2016; 39:151-159. [DOI: 10.1016/j.syapm.2016.03.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/09/2016] [Accepted: 03/18/2016] [Indexed: 11/28/2022]
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Burkholderia: an update on taxonomy and biotechnological potential as antibiotic producers. Appl Microbiol Biotechnol 2016; 100:5215-29. [PMID: 27115756 DOI: 10.1007/s00253-016-7520-x] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 03/29/2016] [Accepted: 03/31/2016] [Indexed: 02/02/2023]
Abstract
Burkholderia is an incredibly diverse and versatile Gram-negative genus, within which over 80 species have been formally named and multiple other genotypic groups likely represent new species. Phylogenetic analysis based on the 16S rRNA gene sequence and core genome ribosomal multilocus sequence typing analysis indicates the presence of at least three major clades within the genus. Biotechnologically, Burkholderia are well-known for their bioremediation and biopesticidal properties. Within this review, we explore the ability of Burkholderia to synthesise a wide range of antimicrobial compounds ranging from historically characterised antifungals to recently described antibacterial antibiotics with activity against multiresistant clinical pathogens. The production of multiple Burkholderia antibiotics is controlled by quorum sensing and examples of quorum sensing pathways found across the genus are discussed. The capacity for antibiotic biosynthesis and secondary metabolism encoded within Burkholderia genomes is also evaluated. Overall, Burkholderia demonstrate significant biotechnological potential as a source of novel antibiotics and bioactive secondary metabolites.
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80
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Dobritsa AP, Samadpour M. Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia. Int J Syst Evol Microbiol 2016; 66:2836-2846. [PMID: 27054671 DOI: 10.1099/ijsem.0.001065] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been proposed to split the genus Burkholderia into two genera according to phylogenetic clustering: (1) a genus retaining this name and consisting mainly of animal and plant pathogens and (2) the genus Paraburkholderia including so-called environmental bacteria. The latter genus name has been validly published recently. During the period between the effective and valid publications of the genus name Paraburkholderia, 16 novel species of the genus Burkholderiawere described, but only two of them can be classified as members of this genus based on the emended genus description. Analysis of traits and phylogenetic positions of the other 11 species shows that they belong to the genus Paraburkholderia, and we propose to transfer them to this genus. The reclassified species names are proposed as Paraburkholderia dipogonis comb. nov., Paraburkholderia ginsengiterrae comb. nov., Paraburkholderia humisilvae comb. nov., Paraburkholderia insulsa comb. nov., Paraburkholderia kirstenboschensis comb. nov., Paraburkholderia metalliresistens comb. nov., Paraburkholderia monticola comb. nov., Paraburkholderia panaciterrae comb. nov., Paraburkholderia rhizosphaerae comb. nov., Paraburkholderia solisilvae comb. nov. and Paraburkholderia susongensis comb. nov. The remaining three species are transferred to the new genus Caballeronia gen. nov. proposed to accommodate twelve species of the genera Burkholderia and Paraburkholderia forming a distinctive clade in phylogenetic trees. The new genus members are Caballeronia choica comb. nov., Caballeronia cordobensis comb. nov., Caballeronia glathei comb. nov., Caballeronia grimmiae comb. nov., Caballeronia humi comb. nov., Caballeronia megalochromosomata comb. nov., Caballeronia jiangsuensis comb. nov., Caballeronia sordidicola comb. nov., Caballeronia telluris comb. nov., Caballeronia terrestris comb. nov., Caballeronia udeis comb. nov., and Caballeronia zhejiangensis comb. nov.
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Affiliation(s)
- Anatoly P Dobritsa
- Institute for Environmental Health, Inc, 15300 Bothell Way NE, Lake Forest Park, WA 98155, USA
| | - Mansour Samadpour
- Institute for Environmental Health, Inc, 15300 Bothell Way NE, Lake Forest Park, WA 98155, USA
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81
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Asselin JAE, Bonasera JM, Beer SV. PCR Primers for Detection of Pantoea ananatis, Burkholderia spp., and Enterobacter sp. from Onion. PLANT DISEASE 2016; 100:836-846. [PMID: 30688614 DOI: 10.1094/pdis-08-15-0941-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacterial decays of onion bulbs cause sporadic and sometimes serious losses to onion (Allium cepa). In New York, three groups of bacteria were identified as problematic: Burkholderia spp., Pantoea ananatis, and Enterobacter spp. To aid in efficient detection and diagnosis of these pathogens, pairs of specific polymerase chain reaction primers were designed and validated, based on a strategy that utilized various genome sequences now available in public databases. Primer pairs were tested against numerous strains of target bacteria, closely related bacteria, and other onion-pathogenic bacteria. Each primer pair yielded a single, apparently highly specific amplicon from aqueous suspensions of the target bacteria. Minimum sensitivities were approximately 103 CFU per 25-μl reaction mixture for all three primer pairs.
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Affiliation(s)
- Jo Ann E Asselin
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca NY 14853
| | - Jean M Bonasera
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca NY 14853
| | - Steven V Beer
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca NY 14853
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82
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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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83
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Wang X, Liu A, Guerrero A, Liu J, Yu X, Deng P, Ma L, Baird S, Smith L, Li X, Lu S. Occidiofungin is an important component responsible for the antifungal activity of Burkholderia pyrrocinia
strain Lyc2. J Appl Microbiol 2016; 120:607-18. [DOI: 10.1111/jam.13036] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/18/2015] [Accepted: 12/14/2015] [Indexed: 11/29/2022]
Affiliation(s)
- X.Q. Wang
- Department of Plant Pathology; College of Plant Protection; Shandong Agricultural University; Tai'an Shandong China
- Collaborative Innovation Centre for Annually High Yield and High Efficiency Production of Wheat and Corn; Shandong Agricultural University Tai'an Shandong China
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology; Mississippi State University; Mississippi State MS USA
| | - A.X. Liu
- Department of Plant Pathology; College of Plant Protection; Shandong Agricultural University; Tai'an Shandong China
| | - A. Guerrero
- Department of Biology; Texas A&M University; College Station TX USA
| | - J. Liu
- Department of Plant Pathology; College of Plant Protection; Shandong Agricultural University; Tai'an Shandong China
- Collaborative Innovation Centre for Annually High Yield and High Efficiency Production of Wheat and Corn; Shandong Agricultural University Tai'an Shandong China
| | - X.Q. Yu
- Department of Plant Pathology; College of Plant Protection; Shandong Agricultural University; Tai'an Shandong China
| | - P. Deng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology; Mississippi State University; Mississippi State MS USA
| | - L. Ma
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology; Mississippi State University; Mississippi State MS USA
| | - S.M. Baird
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology; Mississippi State University; Mississippi State MS USA
| | - L. Smith
- Department of Biology; Texas A&M University; College Station TX USA
| | - X.D. Li
- Department of Plant Pathology; College of Plant Protection; Shandong Agricultural University; Tai'an Shandong China
- Collaborative Innovation Centre for Annually High Yield and High Efficiency Production of Wheat and Corn; Shandong Agricultural University Tai'an Shandong China
| | - S.E. Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology; Mississippi State University; Mississippi State MS USA
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84
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Castanheira N, Dourado A, Kruz S, Alves P, Delgado-Rodríguez A, Pais I, Semedo J, Scotti-Campos P, Sánchez C, Borges N, Carvalho G, Barreto Crespo M, Fareleira P. Plant growth-promoting Burkholderia
species isolated from annual ryegrass in Portuguese soils. J Appl Microbiol 2016; 120:724-39. [DOI: 10.1111/jam.13025] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/25/2015] [Accepted: 12/09/2015] [Indexed: 02/05/2023]
Affiliation(s)
- N. Castanheira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P.; Oeiras Portugal
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
| | - A.C. Dourado
- iBET-Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
| | - S. Kruz
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
- iBET-Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
| | - P.I.L. Alves
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
- iBET-Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
| | | | - I. Pais
- Instituto Nacional de Investigação Agrária e Veterinária, I.P.; Oeiras Portugal
| | - J. Semedo
- Instituto Nacional de Investigação Agrária e Veterinária, I.P.; Oeiras Portugal
| | - P. Scotti-Campos
- Instituto Nacional de Investigação Agrária e Veterinária, I.P.; Oeiras Portugal
| | - C. Sánchez
- Instituto Nacional de Investigação Agrária e Veterinária, I.P.; Oeiras Portugal
| | - N. Borges
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
| | - G. Carvalho
- UCBIO; REQUIMTE; Department of Chemistry; Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Caparica Portugal
| | - M.T. Barreto Crespo
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
- iBET-Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
| | - P. Fareleira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P.; Oeiras Portugal
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85
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Leung HTC, Maas KR, Wilhelm RC, Mohn WW. Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils. THE ISME JOURNAL 2016; 10:363-75. [PMID: 26274049 PMCID: PMC4737928 DOI: 10.1038/ismej.2015.118] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 11/09/2022]
Abstract
Forest ecosystems need to be sustainably managed, as they are major reservoirs of biodiversity, provide important economic resources and modulate global climate. We have a poor knowledge of populations responsible for key biomass degradation processes in forest soils and the effects of forest harvesting on these populations. Here, we investigated the effects of three timber-harvesting methods, varying in the degree of organic matter removal, on putatively hemicellulolytic bacterial and fungal populations 10 or more years after harvesting and replanting. We used stable-isotope probing to identify populations that incorporated (13)C from labeled hemicellulose, analyzing (13)C-enriched phospholipid fatty acids, bacterial 16 S rRNA genes and fungal ITS regions. In soil microcosms, we identified 104 bacterial and 52 fungal hemicellulolytic operational taxonomic units (OTUs). Several of these OTUs are affiliated with taxa not previously reported to degrade hemicellulose, including the bacterial genera Methylibium, Pelomonas and Rhodoferax, and the fungal genera Cladosporium, Pseudeurotiaceae, Capronia, Xenopolyscytalum and Venturia. The effect of harvesting on hemicellulolytic populations was evaluated based on in situ bacterial and fungal OTUs. Harvesting treatments had significant but modest long-term effects on relative abundances of hemicellulolytic populations, which differed in strength between two ecozones and between soil layers. For soils incubated in microcosms, prior harvesting treatments did not affect the rate of incorporation of hemicellulose carbon into microbial biomass. In six ecozones across North America, distributions of the bacterial hemicellulolytic OTUs were similar, whereas distributions of fungal ones differed. Our work demonstrates that diverse taxa in soil are hemicellulolytic, many of which are differentially affected by the impact of harvesting on environmental conditions. However, the hemicellulolytic capacity of soil communities appears resilient.
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Affiliation(s)
- Hilary T C Leung
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kendra R Maas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Roland C Wilhelm
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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86
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Yang L, Poles MA, Fisch GS, Ma Y, Nossa C, Phelan JA, Pei Z. HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria. AIDS 2016; 30:19-29. [PMID: 26731752 DOI: 10.1097/qad.0000000000000935] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVES To evaluate the impact of HIV infection on colonization resistance in the proximal gut. DESIGN It was a case-control study. METHODS We contrasted microbiota composition between eight HIV-1-infected patients and eight HIV-negative controls to characterize community alteration and detect exogenous bacteria in the esophagus, stomach, and duodenum, as well as the mouth using a universal 16s ribosomal RNA gene survey and correlated the findings with HIV serostatus and peripheral blood T-cell counts. RESULTS HIV infection was associated with an enrichment of Proteobacteria (P=0.020) and depletion of Firmicutes (P = 0.005) in the proximal gut. In particular, environmental species Burkholderia fungorum and Bradyrhizobium pachyrhizi colonized the duodenum of HIV patients who had abnormal blood CD4 T-cell counts but were absent in HIV-negative controls or HIV patients whose CD4 cell counts were normal. The two species coexisted and exhibited a decreasing trend proximally toward the stomach and esophagus and were virtually absent in the mouth. B. fungorum always outnumbered B. pachyrhizi in a ratio of approximately 15 to 1 regardless of the body sites (P < 0.0001, r = 0.965). Their abundance was inversely correlated with CD4 cell counts (P = 0.004) but not viral load. Overgrowth of potential opportunistic pathogens for example, Prevotella, Fusobacterium, and Ralstonia and depletion of beneficial bacteria, for example, Lactobacillus was also observed in HIV patients. CONCLUSIONS The colonization of the duodenum by environmental bacteria reflects loss of colonization resistance in HIV infection. Their correlation with CD4 cell counts suggests that compromised immunity could be responsible for the observed invasion by exogenous microbes.
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87
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Lee J, Park J, Kim S, Park I, Seo YS. Differential regulation of toxoflavin production and its role in the enhanced virulence of Burkholderia gladioli. MOLECULAR PLANT PATHOLOGY 2016; 17:65-76. [PMID: 25845410 PMCID: PMC6638467 DOI: 10.1111/mpp.12262] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Burkholderia gladioli is a causal agent of bacterial panicle blight and sheath/grain browning in rice in many countries. Many strains produce the yellow pigment toxoflavin, which is highly toxic to plants, fungi, animals and microorganisms. Although there have been several studies on the toxoflavin biosynthesis system of B. glumae, it is still unclear how B. gladioli activates toxoflavin biosynthesis. In this study, we explored the genomic organization of the toxoflavin system of B. gladioli and its biological functions using comparative genomic analysis between toxoflavin-producing strains (B. glumae BGR1 and B. gladioli BSR3) and a strain not producing toxoflavin (B. gladioli KACC11889). The latter exhibits normal physiological characteristics similar to other B. gladioli strains. Burkholderia gladioli KACC11889 possesses all the genes involved in toxoflavin biosynthesis, but lacks the quorum-sensing (QS) system that functions as an on/off switch for toxoflavin biosynthesis. These data suggest that B. gladioli has evolved to use the QS signalling cascade of toxoflavin production (TofI/TofR of QS → ToxJ or ToxR → tox operons) similar to that in B. glumae. However, some strains may have evolved to eliminate toxoflavin production through deletion of the QS genes. In addition, we demonstrate that the toxoflavin biosynthetic system enhances the virulence of B. gladioli. These findings provide another line of evidence supporting the differential regulation of the toxoflavin system in Burkholderia strains.
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Affiliation(s)
- Jongyun Lee
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
| | - Sunyoung Kim
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
| | - Inmyoung Park
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
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88
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89
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Perrin E, Fondi M, Maida I, Mengoni A, Chiellini C, Mocali S, Cocchi P, Campana S, Taccetti G, Vaneechoutte M, Fani R. Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers. J Microbiol Methods 2015; 117:108-12. [PMID: 26235543 DOI: 10.1016/j.mimet.2015.07.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/29/2015] [Accepted: 07/29/2015] [Indexed: 12/21/2022]
Abstract
The growing number of available microbial genomes offers the possibility to identify features that could be used for identification. In this work, the possibility to exploit overlapping genes to develop a simple PCR based method of identification, was explored. Using the Burkholderia cepacia complex as a model, genomic analyses were performed to check the phylogenetic distribution of an overlap between marC and hisH genes and then, a PCR specific for Burkholderia was designed, set up and tested on a panel of strains and on DNA extracted from the sputum of cystic fibrosis patients. Results obtained revealed the usefulness of this approach, which could then be used to develop PCR for the identification of specific bacteria species or genera.
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Affiliation(s)
- Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy.
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy.
| | - Isabel Maida
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy.
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy.
| | - Carolina Chiellini
- CRA-ABP Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per l'Agrobiologia e la Pedologia, Piazza M. D'Azeglio 30, 50121 Firenze, FI, Italy.
| | - Stefano Mocali
- CRA-ABP Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per l'Agrobiologia e la Pedologia, Piazza M. D'Azeglio 30, 50121 Firenze, FI, Italy.
| | - Priscilla Cocchi
- Department of Paediatric Medicine, Anna Meyer Children's University Hospital, Viale G. Pieraccini, 24, 50141 Florence, Italy.
| | - Silvia Campana
- Department of Paediatric Medicine, Anna Meyer Children's University Hospital, Viale G. Pieraccini, 24, 50141 Florence, Italy.
| | - Giovanni Taccetti
- Department of Paediatric Medicine, Anna Meyer Children's University Hospital, Viale G. Pieraccini, 24, 50141 Florence, Italy.
| | - Mario Vaneechoutte
- Ghent University, Laboratory of Bacteriology Research, De Pintelaan 185 BA-3/4, 9000 Ghent, Belgium.
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy.
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Draft Genome Sequence of Broad-Spectrum Antifungal Bacterium Burkholderia gladioli Strain NGJ1, Isolated from Healthy Rice Seeds. GENOME ANNOUNCEMENTS 2015. [PMID: 26205861 PMCID: PMC4513155 DOI: 10.1128/genomea.00803-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We report here the draft genome sequence of Burkholderia gladioli strain NGJ1. The strain was isolated from healthy rice seeds and exhibits broad-spectrum antifungal activity against several agriculturally important pathogens, including Rhizoctonia solani, Magnaporthe oryzae, Venturia inaequalis, and Fusarium oxysporum.
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91
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Review of Risk Status of Groundwater Supply Wells by Tracing the Source of Coliform Contamination. WATER 2015. [DOI: 10.3390/w7073878] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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92
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Tago K, Kikuchi Y, Nakaoka S, Katsuyama C, Hayatsu M. Insecticide applications to soil contribute to the development of Burkholderia mediating insecticide resistance in stinkbugs. Mol Ecol 2015; 24:3766-78. [PMID: 26059639 DOI: 10.1111/mec.13265] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 11/30/2022]
Abstract
Some soil Burkholderia strains are capable of degrading the organophosphorus insecticide, fenitrothion, and establish symbiosis with stinkbugs, making the host insects fenitrothion-resistant. However, the ecology of the symbiotic degrading Burkholderia adapting to fenitrothion in the free-living environment is unknown. We hypothesized that fenitrothion applications affect the dynamics of fenitrothion-degrading Burkholderia, thereby controlling the transmission of symbiotic degrading Burkholderia from the soil to stinkbugs. We investigated changes in the density and diversity of culturable Burkholderia (i.e. symbiotic and nonsymbiotic fenitrothion degraders and nondegraders) in fenitrothion-treated soil using microcosms. During the incubation with five applications of pesticide, the density of the degraders increased from less than the detection limit to around 10(6)/g of soil. The number of dominant species among the degraders declined with the increasing density of degraders; eventually, one species predominated. This process can be explained according to the competitive exclusion principle using V(max) and K(m) values for fenitrothion metabolism by the degraders. We performed a phylogenetic analysis of representative strains isolated from the microcosms and evaluated their ability to establish symbiosis with the stinkbug Riptortus pedestris. The strains that established symbiosis with R. pedestris were assigned to a cluster including symbionts commonly isolated from stinkbugs. The strains outside the cluster could not necessarily associate with the host. The degraders in the cluster predominated during the initial phase of degrader dynamics in the soil. Therefore, only a few applications of fenitrothion could allow symbiotic degraders to associate with their hosts and may cause the emergence of symbiont-mediated insecticide resistance.
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Affiliation(s)
- Kanako Tago
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences (NIAES), 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, Hokkaido Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan.,Graduate School of Agriculture, Hokkaido University, Kita 8, Nishi 5, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Sinji Nakaoka
- Laboratory for Mathematical Modeling of Immune System, RIKEN Center for Integrative Medical Science Center (IMS-RCAI), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Chie Katsuyama
- Graduate School of Integrated Arts and Sciences, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8521, Japan
| | - Masahito Hayatsu
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences (NIAES), 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
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Rurangwa E, Sipkema D, Kals J, Ter Veld M, Forlenza M, Bacanu GM, Smidt H, Palstra AP. Impact of a novel protein meal on the gastrointestinal microbiota and the host transcriptome of larval zebrafish Danio rerio. Front Physiol 2015; 6:133. [PMID: 25983694 PMCID: PMC4415425 DOI: 10.3389/fphys.2015.00133] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/14/2015] [Indexed: 01/06/2023] Open
Abstract
Larval zebrafish was subjected to a methodological exploration of the gastrointestinal microbiota and transcriptome. Assessed was the impact of two dietary inclusion levels of a novel protein meal (NPM) of animal origin (ragworm Nereis virens) on the gastrointestinal tract (GIT). Microbial development was assessed over the first 21 days post egg fertilization (dpf) through 16S rRNA gene-based microbial composition profiling by pyrosequencing. Differentially expressed genes in the GIT were demonstrated at 21 dpf by whole transcriptome sequencing (mRNAseq). Larval zebrafish showed rapid temporal changes in microbial colonization but domination occurred by one to three bacterial species generally belonging to Proteobacteria and Firmicutes. The high iron content of NPM may have led to an increased relative abundance of bacteria that were related to potential pathogens and bacteria with an increased iron metabolism. Functional classification of the 328 differentially expressed genes indicated that the GIT of larvae fed at higher NPM level was more active in transmembrane ion transport and protein synthesis. mRNAseq analysis did not reveal a major activation of genes involved in the immune response or indicating differences in iron uptake and homeostasis in zebrafish fed at the high inclusion level of NPM.
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Affiliation(s)
- Eugene Rurangwa
- Institute for Marine Resources and Ecosystem Studies, Wageningen University and Research Centre Yerseke, Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Jeroen Kals
- Institute for Marine Resources and Ecosystem Studies, Wageningen University and Research Centre Yerseke, Netherlands
| | - Menno Ter Veld
- Aquaculture and Fisheries Group, Wageningen University Wageningen, Netherlands
| | - Maria Forlenza
- Cell Biology and Immunology Group, Wageningen University Wageningen, Netherlands
| | - Gianina M Bacanu
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Arjan P Palstra
- Institute for Marine Resources and Ecosystem Studies, Wageningen University and Research Centre Yerseke, Netherlands
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94
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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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95
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96
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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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97
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Tago K, Itoh H, Kikuchi Y, Hori T, Sato Y, Nagayama A, Okubo T, Navarro R, Aoyagi T, Hayashi K, Hayatsu M. A fine-scale phylogenetic analysis of free-living Burkholderia species in sugarcane field soil. Microbes Environ 2014; 29:434-7. [PMID: 25410730 PMCID: PMC4262370 DOI: 10.1264/jsme2.me14122] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The diversity and abundance of Burkholderia species in sugarcane field soils were investigated by a 16S rRNA gene-based approach using genus-specific primers. A total of 365,721 sequences generated by the Illumina MiSeq platform were assigned to the genus Burkholderia. Nearly 58% of these sequences were placed in a previously defined cluster, including stinkbug symbionts. Quantitative PCR analysis revealed a consistent number of 16S rRNA gene copies for Burkholderia species (107 g−1 soil) across the sampled fields. C/N, pH, and nitrate concentrations were important factors shaping the Burkholderia community structure; however, their impacts were not significant considering the overall genus size.
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Affiliation(s)
- Kanako Tago
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences
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98
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Campisano A, Antonielli L, Pancher M, Yousaf S, Pindo M, Pertot I. Bacterial endophytic communities in the grapevine depend on pest management. PLoS One 2014; 9:e112763. [PMID: 25387008 PMCID: PMC4227848 DOI: 10.1371/journal.pone.0112763] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 10/16/2014] [Indexed: 01/26/2023] Open
Abstract
Microbial plant endophytes are receiving ever-increasing attention as a result of compelling evidence regarding functional interaction with the host plant. Microbial communities in plants were recently reported to be influenced by numerous environmental and anthropogenic factors, including soil and pest management. In this study we used automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and pyrosequencing of 16S rDNA to assess the effect of organic production and integrated pest management (IPM) on bacterial endophytic communities in two widespread grapevines cultivars (Merlot and Chardonnay). High levels of the dominant Ralstonia, Burkholderia and Pseudomonas genera were detected in all the samples We found differences in the composition of endophytic communities in grapevines cultivated using organic production and IPM. Operational taxonomic units (OTUs) assigned to the Mesorhizobium, Caulobacter and Staphylococcus genera were relatively more abundant in plants from organic vineyards, while Ralstonia, Burkholderia and Stenotrophomonas were more abundant in grapevines from IPM vineyards. Minor differences in bacterial endophytic communities were also found in the grapevines of the two cultivars.
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Affiliation(s)
- Andrea Campisano
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy
- * E-mail:
| | - Livio Antonielli
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy
- Austrian Institute of Technology GmbH, Department of Health & Environment, Bioresources Unit, Tulln, Austria
| | - Michael Pancher
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy
| | - Sohail Yousaf
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy
- Department of Environmental Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy
| | - Ilaria Pertot
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige (TN), Italy
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99
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Rusch A, Islam S, Savalia P, Amend JP. Burkholderia insulsa sp. nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system. Int J Syst Evol Microbiol 2014; 65:189-194. [PMID: 25323596 DOI: 10.1099/ijs.0.064477-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-April(T). Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-April(T) grew at temperatures between 4 °C and 40 °C (optimum 30-37 °C), at pH 3.5 to 8.3 (optimum pH 5-6) and in the presence of up to 2.7% NaCl (optimum 0-1.0%). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-April(T) was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-April(T) belongs to the genus Burkholderia and shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum (99.8%), Burkholderia phytofirmans (98.8%), Burkholderia caledonica (98.4%) and Burkholderia sediminicola (98.4%). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA-DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia, for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-April(T) ( = DSM 28142(T) = LMG 28183(T)).
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Affiliation(s)
- Antje Rusch
- Center for Ecology, Southern Illinois University Carbondale, 1125 Lincoln Drive, Carbondale, IL 62901, USA.,Department of Microbiology, Southern Illinois University Carbondale, 1125 Lincoln Drive, Carbondale, IL 62901, USA
| | - Shaer Islam
- Department of Microbiology, Southern Illinois University Carbondale, 1125 Lincoln Drive, Carbondale, IL 62901, USA
| | - Pratixa Savalia
- Department of Earth Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
| | - Jan P Amend
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA.,Department of Earth Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
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100
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Liu XY, Li CX, Luo XJ, Lai QL, Xu JH. Burkholderia jiangsuensis sp. nov., a methyl parathion degrading bacterium, isolated from methyl parathion contaminated soil. Int J Syst Evol Microbiol 2014; 64:3247-3253. [PMID: 24981326 DOI: 10.1099/ijs.0.064444-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A methyl parathion (MP) degrading bacterial strain, designated MP-1(T), was isolated from a waste land where pesticides were formerly manufactured in Jiangsu province, China. Polyphasic taxonomic studies showed that MP-1(T) is a Gram-stain-negative, non-spore-forming, rod-shaped and motile bacterium. The bacterium could grow at salinities of 0-1 % (w/v) and temperatures of 15-40 °C. Strain MP-1(T) could reduce nitrate to nitrite, utilize d-glucose and l-arabinose, but not produce indole, or hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that MP-1(T) belongs to the genus Burkholderia, showing highest sequence similarity to Burkholderia grimmiae DSM 25160(T) (98.5 %), and similar strains including Burkholderia zhejiangensis OP-1(T) (98.2 %), Burkholderia choica LMG 22940(T) (97.5 %), Burkholderia glathei DSM 50014(T) (97.4 %), Burkholderia terrestris LMG 22937(T) (97.2 %) and Burkholderia telluris LMG 22936(T) (97.0 %). In addition, the gyrB and recA gene segments of strain MP-1(T) exhibited less than 89.0 % and 95.1 % similarities with the most highly-related type strains indicated above. The G+C content of strain MP-1(T) was 62.6 mol%. The major isoprenoid quinone was ubiquinone Q-8. The predominant polar lipids comprised phosphatidyl ethanolamine, phosphatidyl glycerol, aminolipid and phospholipid. The principal fatty acids in strain MP-1(T) were C18 : 1ω7c/C18 : 1ω6c (23.3 %), C16 : 0 (16.8 %), cyclo-C17 : 0 (15.0 %), C16 : 1ω7c/C16 : 1ω6 (8.5 %), cyclo-C19 : 0ω8c (8.1 %), C16 : 1 iso I/C14 : 0 3-OH (5.7 %), C16 : 0 3-OH (5.6 %) and C16 : 02-OH (5.1 %). The DNA-DNA relatedness values between strain MP-1(T) and the three type strains (B. grimmiae DSM 25160(T), B. zhejiangensis OP-1(T) and B. glathei DSM 50014(T)) ranged from 24.6 % to 37.4 %. In accordance with phenotypic and genotypic characteristics, strain MP-1(T) represents a novel species of the genus Burkholderia, for which the name Burkholderia jiangsuensis sp. nov. is proposed, the type strain is MP-1(T) (LMG 27927(T) = MCCC 1K00250(T)).
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Affiliation(s)
- Xu-Yun Liu
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Chun-Xiu Li
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Xiao-Jing Luo
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Qi-Liang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Jian-He Xu
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
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