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Dove R, Wolfe ER, Stewart NU, Coleman A, Chavez SH, Ballhorn DJ. Root nodules of red alder (Alnus rubra) and sitka alder (Alnus viridis ssp. sinuata) are inhabited by taxonomically diverse cultivable microbial endophytes. Microbiologyopen 2024; 13:e1422. [PMID: 38847331 PMCID: PMC11157421 DOI: 10.1002/mbo3.1422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/10/2024] Open
Abstract
The root nodules of actinorhizal plants are home to nitrogen-fixing bacterial symbionts, known as Frankia, along with a small percentage of other microorganisms. These include fungal endophytes and non-Frankia bacteria. The taxonomic and functional diversity of the microbial consortia within these root nodules is not well understood. In this study, we surveyed and analyzed the cultivable, non-Frankia fungal and bacterial endophytes of root nodules from red and Sitka alder trees that grow together. We examined their taxonomic diversity, co-occurrence, differences between hosts, and potential functional roles. For the first time, we are reporting numerous fungal endophytes of alder root nodules. These include Sporothrix guttuliformis, Fontanospora sp., Cadophora melinii, an unclassified Cadophora, Ilyonectria destructans, an unclassified Gibberella, Nectria ramulariae, an unclassified Trichoderma, Mycosphaerella tassiana, an unclassified Talaromyces, Coniochaeta sp., and Sistotrema brinkmanii. We are also reporting several bacterial genera for the first time: Collimonas, Psychrobacillus, and Phyllobacterium. Additionally, we are reporting the genus Serratia for the second time, with the first report having been recently published in 2023. Pseudomonas was the most frequently isolated bacterial genus and was found to co-inhabit individual nodules with both fungi and bacteria. We found that the communities of fungal endophytes differed by host species, while the communities of bacterial endophytes did not.
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Affiliation(s)
- Robyn Dove
- Portland State University Biology DepartmentPortlandOregonUSA
| | - Emily R. Wolfe
- Portland State University Biology DepartmentPortlandOregonUSA
- Portland State UniversityPortlandOregonUSA
| | - Nathan U. Stewart
- Portland State University Biology DepartmentPortlandOregonUSA
- Portland State UniversityPortlandOregonUSA
| | - Abigail Coleman
- Portland State University Biology DepartmentPortlandOregonUSA
- Oregon Health and Science UniversityPortlandOregonUSA
| | - Sara Herrejon Chavez
- Portland State University Biology DepartmentPortlandOregonUSA
- University of California BerkeleyBerkeleyCaliforniaUSA
| | - Daniel J. Ballhorn
- Portland State University Biology DepartmentPortlandOregonUSA
- Portland State UniversityPortlandOregonUSA
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Mavima L, Beukes CW, Palmer M, De Meyer SE, James EK, Maluk M, Muasya MA, Avontuur JR, Yin Chan W, Venter SN, Steenkamp ET. Delineation of Paraburkholderia tuberum sensu stricto and description of Paraburkholderia podalyriae sp. nov. nodulating the South African legume Podalyria calyptrata. Syst Appl Microbiol 2022; 45:126316. [DOI: 10.1016/j.syapm.2022.126316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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Barrera-Galicia GC, Peniche-Pavía HA, Peña-Cabriales JJ, Covarrubias SA, Vera-Núñez JA, Délano-Frier JP. Metabolic Footprints of Burkholderia Sensu Lato Rhizosphere Bacteria Active against Maize Fusarium Pathogens. Microorganisms 2021; 9:microorganisms9102061. [PMID: 34683382 PMCID: PMC8538949 DOI: 10.3390/microorganisms9102061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Consistent with their reported abundance in soils, several Burkholderia sensu lato strains were isolated from the rhizosphere of maize plants cultivated at different sites in central México. Comparative analysis of their 16S rRNA gene sequences permitted their separation into three distinctive clades, which were further subdivided into six other clusters by their close resemblance to (1) Trinickia dinghuensis; (2) Paraburkholderia kirstenboschensis, P. graminis, P. dilworthii and P. rhynchosiae; (3) B. gladioli; (4) B. arboris; (5) B. contaminans, or (6) B. metallica representative species. Direct confrontation assays revealed that these strains inhibited the growth of pathogenic Fusarium oxysporum f. sp. radicis-lycopersici, and F. verticillioides within a roughly 3-55% inhibition range. The use of a DIESI-based non-targeted mass spectroscopy experimental strategy further indicated that this method is an option for rapid determination of the pathogen inhibitory capacity of Burkholderia sensu lato strains based solely on the analysis of their exometabolome. Furthermore, it showed that the highest anti-fungal activity observed in B. contaminans and B. arboris was associated with a distinctive abundance of certain m/z ions, some of which were identified as components of the ornbactin and pyochelin siderophores. These results highlight the chemical diversity of Burkholderia sensu lato bacteria and suggest that their capacity to inhibit the Fusarium-related infection of maize in suppressive soils is associated with siderophore synthesis.
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Affiliation(s)
- Guadalupe C. Barrera-Galicia
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Héctor A. Peniche-Pavía
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Juan José Peña-Cabriales
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Sergio A. Covarrubias
- Área de Ciencias de la Salud, Ciudad Universitaria Campus Siglo XXI, Universidad Autónoma de Zacatecas, Zacatecas 98160, Zacatecas, Mexico; (S.A.C.); (J.A.V.-N.)
| | - José A. Vera-Núñez
- Área de Ciencias de la Salud, Ciudad Universitaria Campus Siglo XXI, Universidad Autónoma de Zacatecas, Zacatecas 98160, Zacatecas, Mexico; (S.A.C.); (J.A.V.-N.)
| | - John P. Délano-Frier
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
- Correspondence: ; Tel.: +52-462-623-9600
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Madhaiyan M, Selvakumar G, Alex TH, Cai L, Ji L. Plant Growth Promoting Abilities of Novel Burkholderia-Related Genera and Their Interactions With Some Economically Important Tree Species. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.618305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A survey of bacterial endophytes associated with the leaves of oil palm and acacias resulted in the isolation of 19 bacterial strains belonging to the genera Paraburkholderia, Caballeronia, and Chitinasiproducens, which are now regarded as distinctively different from the parent genus Burkholderia. Most strains possessed one or more plant growth promotion (PGP) traits although nitrogenase activity was present in only a subset of the isolates. The diazotrophic Paraburkholderia tropica strain S39-2 with multiple PGP traits and the non-diazotrophic Chitinasiproducens palmae strain JS23T with a significant level of 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity were selected to investigate the influence of bacterial inoculation on some economically important tree species. Microscopic examination revealed that P. tropica S39-2 was rhizospheric as well as endophytic while C. palmae JS23T was endophytic. P. tropica strain S39-2 significantly promoted the growth of oil palm, eucalyptus, and Jatropha curcas. Interestingly, the non-diazotrophic, non-auxin producing C. palmae JS23T strain also significantly promoted the growth of oil palm and eucalyptus although it showed negligible effect on J. curcas. Our results suggest that strains belonging to the novel Burkholderia-related genera widely promote plant growth via both N-independent and N-dependent mechanisms. Our results also suggest that the induction of defense response may prevent the colonization of an endophyte in plants.
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Diversity of rhizobial and non-rhizobial bacteria nodulating wild ancestors of grain legume crop plants. Int Microbiol 2021; 24:207-218. [PMID: 33423098 DOI: 10.1007/s10123-020-00158-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/24/2020] [Accepted: 12/29/2020] [Indexed: 10/22/2022]
Abstract
Chickpeas, lentils, and peas are the oldest grain legume species that spread to other regions after their first domestication in Fertile Crescent, and they could reveal the rhizobial evolution in relation to the microsymbionts of wild species in this region. This study investigated the phenotypic and genotypic diversity of the nodule-forming rhizobial bacteria recovered from Pisum sativum subsp., Cicer pinnatifidum, and Lens culinaris subsp. orientalis exhibiting natural distribution in the Gaziantep province of Turkey. PCA analyses of rhizobial isolates, which were tested to be highly resistant to stress conditions, showed that especially pH and salt concentrations had an important effect on these bacteria. Phylogenetic analysis based on 16S rRNA determined that these wild species were nodulated by at least 7 groups including Rhizobium and non-Rhizobium. The largest group comprised of Rhizobium leguminosarum and Rhizobium sp. while R. pusense, which was previously determined as non-symbiotic species, was found to nodulate C. pinnatifidum and L. culinaris subsp. orientalis. In recent studies, Klebsiella sp., which is stated to be able to nodulate different species, strong evidences have been obtained in present study exhibiting that Klebsiella sp. can nodulate C. pinnatifidum and Pseudomonas sp. was able to nodulate C. pinnatifidum and P. sativum subsp. Additionally, L. culinaris subsp. orientalis unlike other plant species, was nodulated by Burkholderia sp. and Serratia sp. associated isolates. Some isolates could not be characterized at the species level since the 16S rRNA sequence similarity rate was low and the fact that they were in a separate group supported with high bootstrap values in the phylogenetic tree may indicate that these isolates could be new species. The REP-PCR fingerprinting provided results supporting the existence of new species nodulating wild ancestors.
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Mavima L, Beukes CW, Palmer M, De Meyer SE, James EK, Maluk M, Gross E, Dos Reis Junior FB, Avontuur JR, Chan WY, Venter SN, Steenkamp ET. Paraburkholderia youngii sp. nov. and 'Paraburkholderia atlantica' - Brazilian and Mexican Mimosa-associated rhizobia that were previously known as Paraburkholderia tuberum sv. mimosae. Syst Appl Microbiol 2020; 44:126152. [PMID: 33276286 DOI: 10.1016/j.syapm.2020.126152] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/11/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022]
Abstract
Previous studies have recognized South and Central/Latin American mimosoid legumes in the genera Mimosa, Piptadenia and Calliandra as hosts for various nodulating Paraburkholderia species. Several of these species have been validly named in the last two decades, e.g., P. nodosa, P. phymatum, P. diazotrophica, P. piptadeniae, P. ribeironis, P. sabiae and P. mimosarum. There are still, however, a number of diverse Paraburkholderia strains associated with these legumes that have an unclear taxonomic status. In this study, we focus on 30 of these strains which originate from the root nodules of Brazilian and Mexican Mimosa species. They were initially identified as P. tuberum and subsequently placed into a symbiovar (sv. mimosae) based on their host preferences. A polyphasic approach for the delineation of these strains was used, consisting of genealogical concordance analysis (using atpD, gyrB, acnA, pab and 16S rRNA gene sequences), together with comparisons of Average Nucleotide Identity (ANI), DNA G+C content ratios and phenotypic characteristics with those of the type strains of validly named Paraburkholderia species. Accordingly, these 30 strains were delineated into two distinct groups, of which one is conspecific with 'P. atlantica' CNPSo 3155T and the other new to Science. We propose the name Paraburkholderia youngii sp. nov. with type strain JPY169T (= LMG 31411T; SARCC751T) for this novel species.
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Affiliation(s)
- Lazarus Mavima
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Chrizelle W Beukes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa; School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, United States of America
| | - Sofie E De Meyer
- MALDIID Pty Ltd, Murdoch, Western Australia, Australia; Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Marta Maluk
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Eduardo Gross
- Universidade Estadual de Santa Cruz, km 16 Rodovia Ilhéus - Itabuna, CEP 45662-900 Ilhéus, BA, Brazil
| | | | - Juanita R Avontuur
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa; Biotechnology Platform, Agricultural Research Council Onderstepoort Veterinary Institute (ARC-OVI), Onderstepoort, South Africa
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Wilhelm RC, Cyle KT, Martinez CE, Karasz DC, Newman JD, Buckley DH. Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana. Int J Syst Evol Microbiol 2020; 70:5093-5105. [PMID: 32809929 DOI: 10.1099/ijsem.0.004387] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Two bacterial strains, 1NT and 5NT, were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1NT (0.65×1.85 µm) and 5NT (0.6×1.85 µm) are Gram-stain-negative, aerobic, motile, non-sporulating and exist as single rods, diplobacilli or in chains of varying length. During growth in dilute media (≤0.1× tryptic soy broth; TSB), cells are primarily motile with flagella. At higher concentrations (≥0.3× TSB), cells of both strains increasingly form non-motile chains, and cells of 5NT elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1NT and 5NT occurred at 25-30 °C, pH 6.5-7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1NT and 5NT were distinct from one another and their closest related type strains: Paraburkholderia madseniana RP11T, Paraburkholderia aspalathi LMG 27731T and Paraburkholderia caffeinilytica CF1T. The genomes of 1NT and 5NT had an average nucleotide identity (91.6 and 91.3%) and in silico DNA-DNA hybridization values (45.8%±2.6 and 45.5%±2.5) and differed in functional gene content from their closest related type strains. The composition of fatty acids and patterns of substrate use, including the catabolism of phenolic acids, also differentiated strains 1NT and 5NT from each other and their closest relatives. The only ubiquinone present in strains 1NT and 5NT was Q-8. The major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed features 2 (3OH-C14 : 0 / C16 : 1 iso I), 3 (C16 : 1 ω6c/ω7c) and 8 (C18 : 1 ω7c/ω6c). A third bacterium, strain RL16-012-BIC-B, was isolated from soil associated with shallow roots and was determined to be a strain of P. madseniana (ANI, 98.8%; 16S rRNA gene similarity, 100%). Characterizations of strain RL16-012-BIC-B (DSM 110723=LMG 31706) led to proposed emendments to the species description of P. madseniana. Our polyphasic approach demonstrated that strains 1NT and 5NT represent novel species from the genus Paraburkholderia for which the names Paraburkholderia solitsugae sp. nov. (type strain 1NT=DSM 110721T=LMG 31704T) and Paraburkholderia elongata sp. nov. (type strain 5NT=DSM 110722T=LMG 31705T) are proposed.
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Affiliation(s)
- Roland C Wilhelm
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - K Taylor Cyle
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Carmen Enid Martinez
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - David C Karasz
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | | | - Daniel H Buckley
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
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Tapia-García EY, Hernández-Trejo V, Guevara-Luna J, Rojas-Rojas FU, Arroyo-Herrera I, Meza-Radilla G, Vásquez-Murrieta MS, Estrada-de los Santos P. Plant growth-promoting bacteria isolated from wild legume nodules and nodules of Phaseolus vulgaris L. trap plants in central and southern Mexico. Microbiol Res 2020; 239:126522. [DOI: 10.1016/j.micres.2020.126522] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/24/2020] [Accepted: 05/30/2020] [Indexed: 02/07/2023]
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Paraburkholderia lycopersici sp. nov., a nitrogen-fixing species isolated from rhizoplane of Lycopersicon esculentum Mill. var. Saladette in Mexico. Syst Appl Microbiol 2020; 43:126133. [PMID: 32998072 DOI: 10.1016/j.syapm.2020.126133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 01/29/2023]
Abstract
A survey of our in-house bacterial collection identified a group of six strains isolated from the tomato rhizoplane that possessed 16S rRNA gene sequences with 98.2% sequence similarity to Paraburkholderia pallida, suggesting that these strains represented a novel species. Multilocus sequence analysis using gltB, lepA and recA gene sequences showed the clustering of the strains and the BOX-PCR patterns were similar among these strains. The average nucleotide identity and the DNA-DNA virtual hybridization of strain TNe-862T was <89% and <34%, respectively, to the genomes of any sequenced Paraburkholderia species. The genome of strain TNe-862T possessed all the genes necessary for nitrogen fixation and biosynthesis of indoleacetic acid and antimicrobials terpenes, phosphonates and bacteriocins. It also contained genes for metal resistance, xenobiotic degradation, and hydrolytic enzymes such as a putative chitinase and isoamylase. Even though the strain contained potential genes for degradation of cellulose and starch, the bacterium was unable to utilize these substrates in culture medium. The genome encoded flagella and pili as well as multiple chemotaxis systems. In addition, genes encoding for the type I, II, IV, V and VI secretion systems were also present. The strains grow up to 42°C and 5% NaCl. The optimum growth pH was 8. The major cellular fatty acids were C16:0 and C18:1 ω7c. Based on this polyphasic analysis, these strains represent a novel species in the genus Paraburkholderia, for which the name Paraburkholderia lycopersici sp. nov. is proposed. The type strain is TNe-862T (=LMG 26415T=CIP 110323T).
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Singh RK, Singh P, Li HB, Song QQ, Guo DJ, Solanki MK, Verma KK, Malviya MK, Song XP, Lakshmanan P, Yang LT, Li YR. Diversity of nitrogen-fixing rhizobacteria associated with sugarcane: a comprehensive study of plant-microbe interactions for growth enhancement in Saccharum spp. BMC PLANT BIOLOGY 2020; 20:220. [PMID: 32423383 PMCID: PMC7236179 DOI: 10.1186/s12870-020-02400-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 04/21/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Nitrogen is an essential element for sugarcane growth and development and is generally applied in the form of urea often much more than at recommended rates, causing serious soil degradation, particularly soil acidification, as well as groundwater and air pollution. In spite of the importance of nitrogen for plant growth, fewer reports are available to understand the application and biological role of N2 fixing bacteria to improve N2 nutrition in the sugarcane plant. RESULTS In this study, a total of 350 different bacterial strains were isolated from rhizospheric soil samples of the sugarcane plants. Out of these, 22 isolates were selected based on plant growth promotion traits, biocontrol, and nitrogenase activity. The presence and activity of the nifH gene and the ability of nitrogen-fixation proved that all 22 selected strains have the ability to fix nitrogen. These strains were used to perform 16S rRNA and rpoB genes for their identification. The resulted amplicons were sequenced and phylogenetic analysis was constructed. Among the screened strains for nitrogen fixation, CY5 (Bacillus megaterium) and CA1 (Bacillus mycoides) were the most prominent. These two strains were examined for functional diversity using Biolog phenotyping, which confirmed the consumption of diverse carbon and nitrogen sources and tolerance to low pH and osmotic stress. The inoculated bacterial strains colonized the sugarcane rhizosphere successfully and were mostly located in root and leaf. The expression of the nifH gene in both sugarcane varieties (GT11 and GXB9) inoculated with CY5 and CA1 was confirmed. The gene expression studies showed enhanced expression of genes of various enzymes such as catalase, phenylalanine-ammonia-lyase, superoxide dismutase, chitinase and glucanase in bacterial-inoculated sugarcane plants. CONCLUSION The results showed that a substantial number of Bacillus isolates have N-fixation and biocontrol property against two sugarcane pathogens Sporisorium scitamineum and Ceratocystis paradoxa. The increased activity of genes controlling free radical metabolism may at least in part accounts for the increased tolerance to pathogens. Nitrogen-fixation was confirmed in sugarcane inoculated with B. megaterium and B. mycoides strains using N-balance and 15N2 isotope dilution in different plant parts of sugarcane. This is the first report of Bacillus mycoides as a nitrogen-fixing rhizobacterium in sugarcane.
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Affiliation(s)
- Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
- College of Agriculture, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio resources, Guangxi University, Nanning, 530005, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, 530007, Guangxi, China
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
- College of Agriculture, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio resources, Guangxi University, Nanning, 530005, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, 530007, Guangxi, China
| | - Hai-Bi Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
- College of Agriculture, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio resources, Guangxi University, Nanning, 530005, China
| | - Qi-Qi Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
- College of Agriculture, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio resources, Guangxi University, Nanning, 530005, China
| | - Dao-Jun Guo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
- College of Agriculture, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio resources, Guangxi University, Nanning, 530005, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, 530007, Guangxi, China
| | - Manoj K Solanki
- Department of Food Quality and Safety, Institute for Post-harvest and Food Sciences, The Volcani Center, Agricultural Research Organization, 7528809, Rishon LeZion, Israel
| | - Krishan K Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, 530007, Guangxi, China
| | - Mukesh K Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, 530007, Guangxi, China
| | - Xiu-Peng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
- College of Agriculture, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio resources, Guangxi University, Nanning, 530005, China
| | - Prakash Lakshmanan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, 530007, Guangxi, China
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Li-Tao Yang
- College of Agriculture, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio resources, Guangxi University, Nanning, 530005, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, 530007, Guangxi, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.
- College of Agriculture, State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio resources, Guangxi University, Nanning, 530005, China.
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11
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Wilhelm RC, Murphy SJL, Feriancek NM, Karasz DC, DeRito CM, Newman JD, Buckley DH. Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil. Int J Syst Evol Microbiol 2020; 70:2137-2146. [PMID: 32027304 DOI: 10.1099/ijsem.0.004029] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
RP11T was isolated from forest soil following enrichment with 4-hydroxybenzoic acid. Cells of RP11T are aerobic, non-sporulating, exhibit swimming motility, and are rods (0.8 µm by 1.4 µm) that often occur as diplobacillus or in short chains (3-4 cells). Optimal growth on minimal media containing 4-hydroxybenzoic acid (µ=0.216 hr-1) occurred at 30 °C, pH 6.5 or 7.0 and 0% salinity. Comparative chemotaxonomic, genomic and phylogenetic analyses revealed the isolate was distinct from its closest relative type strains identified as Paraburkholderia aspalathi LMG 27731T, Paraburkholderia fungorum LMG 16225T and Paraburkholderia caffeinilytica CF1T. Strain RP11T is genetically distinct from P. aspalathi, its closest relative, in terms of 16S rRNA gene sequence similarity (98.7%), genomic average nucleotide identity (94%) and in silico DNA-DNA hybridization (56.7 %±2.8). The composition of fatty acids and substrate utilization pattern differentiated strain RP11T from its closest relatives, including growth on phthalic acid. Strain RP11T encoded the greatest number of aromatic degradation genes of all eleven closely related type strains and uniquely encoded a phthalic acid dioxygenase and paralog of the 3-hydroxybenzoate 4-monooxygenase. The only ubiquinone detected in strain RP11T was Q-8, and the major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω7c/ω6c). On the basis of this polyphasic approach, it was determined that strain RP11T represents a novel species from the genus Paraburkholderia for which the name Paraburkholderia madseniana sp. nov. is proposed. The type strain is RP11T (=DSM 110123T=LMG 31517T).
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Affiliation(s)
- Roland C Wilhelm
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Sean J L Murphy
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Nicole M Feriancek
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - David C Karasz
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Christopher M DeRito
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY, 14853, USA
| | | | - Daniel H Buckley
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
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12
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Shamseldin A, Velázquez E. The promiscuity of Phaseolus vulgaris L. (common bean) for nodulation with rhizobia: a review. World J Microbiol Biotechnol 2020; 36:63. [PMID: 32314065 DOI: 10.1007/s11274-020-02839-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/09/2020] [Indexed: 11/24/2022]
Abstract
Phaseolus vulgaris L. (common bean) is a legume indigenous to American countries currently cultivated in all continents, which is nodulated by different rhizobial species and symbiovars. Most of species able to nodulate this legume worldwide belong to the genus Rhizobium, followed by those belonging to the genera Ensifer (formerly Sinorhizobium) and Pararhizobium (formerly Rhizobium) and minority by species of the genus Bradyrhizobium. All these genera belong to the phylum alpha-Proteobacteria, but the nodulation of P. vulgaris has also been reported for some species belonging to Paraburkholderia and Cupriavidus from the beta-Proteobacteria. Several species nodulating P. vulgaris were originally isolated from nodules of this legume in American countries and are linked to the symbiovars phaseoli and tropici, which are currently present in other continents probably because they were spread in their soils together with the P. vulgaris seeds. In addition, this legume can be nodulated by species and symbiovars originally isolated from nodules of other legumes due its high promiscuity, a concept currently related with the ability of a legume to be nodulated by several symbiovars rather than by several species. In this article we review the species and symbiovars able to nodulate P. vulgaris in different countries and continents and the challenges on the study of the P. vulgaris endosymbionts diversity in those countries where they have not been studied yet, that will allow to select highly effective rhizobial strains in order to guarantee the success of P. vulgaris inoculation.
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Affiliation(s)
- Abdelaal Shamseldin
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, New Borg El-Arab, Alexandria, Egypt.
| | - Encarna Velázquez
- Departamento de Microbiología Y Genética and CIALE, Universidad de Salamanca, Salamanca, Spain.,Unidad Asociada Grupo de Interacción Planta-Microorganismo (Universidad de Salamanca-IRNASA-CSIC), Salamanca, Spain
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13
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Draft Genome Sequence of Paraburkholderia sp. UYCP14C, a Rhizobium Strain Isolated from Root Nodules of Calliandra parvifolia. Microbiol Resour Announc 2019; 8:8/16/e00173-19. [PMID: 31000547 PMCID: PMC6473141 DOI: 10.1128/mra.00173-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Here, we present the draft genome sequence of strain UYCP14C, a rhizobium isolated from Calliandra parvifolia nodules. The assembled genome size was around 9.8 million bp, containing 9,031 predicted protein-coding sequences, including several symbiotic and nitrogen fixation genes. Here, we present the draft genome sequence of strain UYCP14C, a rhizobium isolated from Calliandra parvifolia nodules. The assembled genome size was around 9.8 million bp, containing 9,031 predicted protein-coding sequences, including several symbiotic and nitrogen fixation genes. UYCP14C appears to be a novel species of the plant growth-promoting Paraburkholderia genus.
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14
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Mannaa M, Park I, Seo YS. Genomic Features and Insights into the Taxonomy, Virulence, and Benevolence of Plant-Associated Burkholderia Species. Int J Mol Sci 2018; 20:E121. [PMID: 30598000 PMCID: PMC6337347 DOI: 10.3390/ijms20010121] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/24/2018] [Accepted: 12/24/2018] [Indexed: 11/17/2022] Open
Abstract
The members of the Burkholderia genus are characterized by high versatility and adaptability to various ecological niches. With the availability of the genome sequences of numerous species of Burkholderia, many studies have been conducted to elucidate the unique features of this exceptional group of bacteria. Genomic and metabolic plasticity are common among Burkholderia species, as evidenced by their relatively large multi-replicon genomes that are rich in insertion sequences and genomic islands and contain a high proportion of coding regions. Such unique features could explain their adaptability to various habitats and their versatile lifestyles, which are reflected in a multiplicity of species including free-living rhizospheric bacteria, plant endosymbionts, legume nodulators, and plant pathogens. The phytopathogenic Burkholderia group encompasses several pathogens representing threats to important agriculture crops such as rice. Contrarily, plant-beneficial Burkholderia have also been reported, which have symbiotic and growth-promoting roles. In this review, the taxonomy of Burkholderia is discussed emphasizing the recent updates and the contributions of genomic studies to precise taxonomic positioning. Moreover, genomic and functional studies on Burkholderia are reviewed and insights are provided into the mechanisms underlying the virulence and benevolence of phytopathogenic and plant-beneficial Burkholderia, respectively, on the basis of cutting-edge knowledge.
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Affiliation(s)
- Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea.
| | - Inmyoung Park
- Department of Oriental Food and Culinary Arts, Youngsan University, Busan 48015, Korea.
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea.
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Symbiotic and non-symbiotic Paraburkholderia isolated from South African Lebeckia ambigua root nodules and the description of Paraburkholderia fynbosensis sp. nov. Int J Syst Evol Microbiol 2018; 68:2607-2614. [DOI: 10.1099/ijsem.0.002884] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Lee JW, Kim YE, Park SJ. Burkholderia alba sp. nov., isolated from a soil sample on Halla mountain in Jeju island. J Microbiol 2018; 56:312-316. [PMID: 29721827 DOI: 10.1007/s12275-018-8034-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 11/29/2022]
Abstract
A rod-shaped, round and white colony-forming strain AD18T was isolated from the soil on Halla mountain in Jeju Island, Republic of Korea. Comparative analysis of 16S rRNA gene sequence revealed that this strain was closely related to Burkholderia oklahomensis C6786T (98.8%), Burkholderia thailandensis KCTC 23190T (98.5%). DNA-DNA relatedness (14.6%) indicated that the strain AD18T represents a distinct species that is separate from B. oklahomensis C6786T. The isolate grew at pH 5.0-9.0 (optimum, pH 7.0), 0-3% (w/v) NaCl (optimum, 0%), and temperature 10-40°C (optimum 35°C). The sole quinone of the strain was Q-8, and the predominant fatty acids were C16:0, C17:0 cyclo, and C19:0 cyclo ω8c. The genomic DNA G + C content of AD18T was 65.6 mol%. Based on these findings, strain AD18T is proposed to be a novel species in the genus Burkholderia, for which the name Burkholderia alba sp. nov. is proposed (= KCCM 43268T = JCM 32403T). The type strain is AD18T.
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Affiliation(s)
- Jae-Won Lee
- Department of Biology, Jeju National University, Jeju, 63243, Republic of Korea
| | - Ye-Eun Kim
- Department of Biology, Jeju National University, Jeju, 63243, Republic of Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju, 63243, Republic of Korea.
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17
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Draft genome of Paraburkholderia caballeronis TNe-841 T, a free-living, nitrogen-fixing, tomato plant-associated bacterium. Stand Genomic Sci 2017; 12:80. [PMID: 29255574 PMCID: PMC5732367 DOI: 10.1186/s40793-017-0294-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/05/2017] [Indexed: 11/16/2022] Open
Abstract
10.1601/nm.26956
caballeronis is a plant-associated bacterium. Strain TNe-841T was isolated from the rhizosphere of tomato (Solanum lycopersicum L. var. lycopersicum) growing in Nepantla Mexico State. Initially this bacterium was found to effectively nodulate Phaseolus vulgaris L. However, from an analysis of the genome of strain TNe-841T and from repeat inoculation experiments, we found that this strain did not nodulate bean and also lacked nodulation genes, suggesting that the genes were lost. The genome consists of 7,115,141 bp with a G + C content of 67.01%. The sequence includes 6251 protein-coding genes and 87 RNA genes.
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18
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Lardi M, Liu Y, Purtschert G, Bolzan de Campos S, Pessi G. Transcriptome Analysis of Paraburkholderia phymatum under Nitrogen Starvation and during Symbiosis with Phaseolus Vulgaris. Genes (Basel) 2017; 8:genes8120389. [PMID: 29244728 PMCID: PMC5748707 DOI: 10.3390/genes8120389] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 01/31/2023] Open
Abstract
Paraburkholderia phymatum belongs to the β-subclass of proteobacteria. It has recently been shown to be able to nodulate and fix nitrogen in symbiosis with several mimosoid and papilionoid legumes. In contrast to the symbiosis of legumes with α-proteobacteria, very little is known about the molecular determinants underlying the successful establishment of this mutualistic relationship with β-proteobacteria. In this study, we performed an RNA-sequencing (RNA-seq) analysis of free-living P. phymatum growing under nitrogen-replete and -limited conditions, the latter partially mimicking the situation in nitrogen-deprived soils. Among the genes upregulated under nitrogen limitation, we found genes involved in exopolysaccharides production and in motility, two traits relevant for plant root infection. Next, RNA-seq data of P. phymatum grown under free-living conditions and from symbiotic root nodules of Phaseolus vulgaris (common bean) were generated and compared. Among the genes highly upregulated during symbiosis, we identified—besides the nif gene cluster—an operon encoding a potential cytochrome o ubiquinol oxidase (Bphy_3646-49). Bean root nodules induced by a cyoB mutant strain showed reduced nitrogenase and nitrogen fixation abilities, suggesting an important role of the cytochrome for respiration inside the nodule. The analysis of mutant strains for the RNA polymerase transcription factor RpoN (σ54) and its activator NifA indicated that—similar to the situation in α-rhizobia—P. phymatum RpoN and NifA are key regulators during symbiosis with P. vulgaris.
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Affiliation(s)
- Martina Lardi
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
| | - Yilei Liu
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
| | - Gabriela Purtschert
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
| | | | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, CH-8057 Zurich, Switzerland.
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19
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de León-Martínez JA, Yañez-Ocampo G, Wong-Villarreal A. Burkholderia species associated with legumes of Chiapas, Mexico, exhibit stress tolerance and growth in aromatic compounds. Rev Argent Microbiol 2017; 49:394-401. [PMID: 28864228 DOI: 10.1016/j.ram.2017.04.009] [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: 05/24/2016] [Revised: 02/09/2017] [Accepted: 04/20/2017] [Indexed: 11/18/2022] Open
Abstract
Leguminous plants have received special interest for the diversity of β-proteobacteria in their nodules and are promising candidates for biotechnological applications. In this study, 15 bacterial strains were isolated from the nodules of the following legumes: Indigofera thibaudiana, Mimosa diplotricha, Mimosa albida, Mimosa pigra, and Mimosa pudica, collected in 9 areas of Chiapas, Mexico. The strains were grouped into four profiles of genomic fingerprints through BOX-PCR and identified based on their morphology, API 20NE biochemical tests, sequencing of the 16S rRNA, nifH and nodC genes as bacteria of the Burkholderia genus, genetically related to Burkholderia phenoliruptrix, Burkholderia phymatum, Burkholderia sabiae, and Burkholderia tuberum. The Burkholderia strains were grown under stress conditions with 4% NaCl, 45°C, and benzene presence at 0.1% as the sole carbon source. This is the first report on the isolation of these nodulating species of the Burkholderia genus in legumes in Mexico.
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Affiliation(s)
- José A de León-Martínez
- Instituto de Biociencias, Universidad Autónoma de Chiapas, C.P. 30700 Tapachula, Chiapas, Mexico
| | - Gustavo Yañez-Ocampo
- Laboratorio de Edafología y Ambiente Universidad Autónoma del Estado de México, Instituto Literario 100, C.P. 50000 Toluca, Mexico
| | - Arnoldo Wong-Villarreal
- División Agroalimentaria, Universidad Tecnológica de la Selva, C.P. 29950 Ocosingo, Chiapas, Mexico.
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20
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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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21
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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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22
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Bournaud C, Moulin L, Cnockaert M, Faria SD, Prin Y, Severac D, Vandamme P. Paraburkholderia piptadeniae sp. nov. and Paraburkholderia ribeironis sp. nov., two root-nodulating symbiotic species of Piptadenia gonoacantha in Brazil. Int J Syst Evol Microbiol 2017; 67:432-440. [DOI: 10.1099/ijsem.0.001648] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Caroline Bournaud
- Present address: Embrapa Genetic Resources and Biotechnology, Pest-Plant Molecular Interaction Laboratory, Brasilia, Distrito Federal, Brazil
- Cirad, IRD, Univ. Montpellier, SupAgro, Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
- Cirad, IRD, Univ. Montpellier, SupAgro, Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier, France
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Sergio de Faria
- EMBRAPA-Agrobiologia, Km 47 Seropedica, 23851-970 Rio de Janeiro, Brazil
| | - Yves Prin
- Cirad, IRD, Univ. Montpellier, SupAgro, Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier, France
| | - Dany Severac
- Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094 Montpellier Cedex, France
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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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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24
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25
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Burkholderia kirstenboschensis sp. nov. nodulates papilionoid legumes indigenous to South Africa. Syst Appl Microbiol 2015; 38:545-54. [DOI: 10.1016/j.syapm.2015.09.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 09/08/2015] [Accepted: 09/11/2015] [Indexed: 11/17/2022]
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26
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De Meyer SE, Fabiano E, Tian R, Van Berkum P, Seshadri R, Reddy T, Markowitz V, Ivanova N, Pati A, Woyke T, Howieson J, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413. Stand Genomic Sci 2015. [PMID: 26203342 PMCID: PMC4511699 DOI: 10.1186/s40793-015-0018-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A survey of symbionts of P. rigida in Uruguay demonstrated that this species is nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this host. Currently, the only other sequenced isolate to fix with this host is Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was selected for sequencing on the basis of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the GEBA-RNB project. Here we describe the features of Burkholderia sp. strain UYPR1.413, together with sequence and annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only encoding genes.
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Affiliation(s)
- Sofie E De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA, Australia
| | - Elena Fabiano
- Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA, Australia
| | - Peter Van Berkum
- Soybean Genomics and improvement laboratory Bldg 006, BARC-West USDA ARS, 10300 Baltimore Blvd, Beltsville 20705, MD, USA
| | | | - Tbk Reddy
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA, Australia
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA, Australia
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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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28
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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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29
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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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30
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2014. [DOI: 10.1099/ijs.0.064402-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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