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Cianciotto NP. The type II secretion system as an underappreciated and understudied mediator of interbacterial antagonism. Infect Immun 2024:e0020724. [PMID: 38980047 DOI: 10.1128/iai.00207-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024] Open
Abstract
Interbacterial antagonism involves all major phyla, occurs across the full range of ecological niches, and has great significance for the environment, clinical arena, and agricultural and industrial sectors. Though the earliest insight into interbacterial antagonism traces back to the discovery of antibiotics, a paradigm shift happened when it was learned that protein secretion systems (e.g., types VI and IV secretion systems) deliver toxic "effectors" against competitors. However, a link between interbacterial antagonism and the Gram-negative type II secretion system (T2SS), which exists in many pathogens and environmental species, is not evident in prior reviews on bacterial competition or T2SS function. A current examination of the literature revealed four examples of a T2SS or one of its known substrates having a bactericidal activity against a Gram-positive target or another Gram-negative. When further studied, the T2SS effectors proved to be peptidases that target the peptidoglycan of the competitor. There are also reports of various bacteriolytic enzymes occurring in the culture supernatants of some other Gram-negative species, and a link between these bactericidal activities and T2SS is suggested. Thus, a T2SS can be a mediator of interbacterial antagonism, and it is possible that many T2SSs have antibacterial outputs. Yet, at present, the T2SS remains relatively understudied for its role in interbacterial competition. Arguably, there is a need to analyze the T2SSs of a broader range of species for their role in interbacterial antagonism. Such investigation offers, among other things, a possible pathway toward developing new antimicrobials for treating disease.
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Affiliation(s)
- Nicholas P Cianciotto
- Department of Microbiology-Immunology, Northwestern University School of Medicine, Chicago, Illinois, USA
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Taboada-Castro H, Gil J, Gómez-Caudillo L, Escorcia-Rodríguez JM, Freyre-González JA, Encarnación-Guevara S. Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network. Front Microbiol 2022; 13:947678. [PMID: 36312930 PMCID: PMC9611204 DOI: 10.3389/fmicb.2022.947678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
A comparative proteomic study at 6 h of growth in minimal medium (MM) and bacteroids at 18 days of symbiosis of Rhizobium etli CFN42 with the Phaseolus vulgaris leguminous plant was performed. A gene ontology classification of proteins in MM and bacteroid, showed 31 and 10 pathways with higher or equal than 30 and 20% of proteins with respect to genome content per pathway, respectively. These pathways were for energy and environmental compound metabolism, contributing to understand how Rhizobium is adapted to the different conditions. Metabolic maps based on orthology of the protein profiles, showed 101 and 74 functional homologous proteins in the MM and bacteroid profiles, respectively, which were grouped in 34 different isoenzymes showing a great impact in metabolism by covering 60 metabolic pathways in MM and symbiosis. Taking advantage of co-expression of transcriptional regulators (TF’s) in the profiles, by selection of genes whose matrices were clustered with matrices of TF’s, Transcriptional Regulatory networks (TRN´s) were deduced by the first time for these metabolic stages. In these clustered TF-MM and clustered TF-bacteroid networks, containing 654 and 246 proteins, including 93 and 46 TFs, respectively, showing valuable information of the TF’s and their regulated genes with high stringency. Isoenzymes were specific for adaptation to the different conditions and a different transcriptional regulation for MM and bacteroid was deduced. The parameters of the TRNs of these expected biological networks and biological networks of E. coli and B. subtilis segregate from the random theoretical networks. These are useful data to design experiments on TF gene–target relationships for bases to construct a TRN.
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Affiliation(s)
- Hermenegildo Taboada-Castro
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | - Jeovanis Gil
- Division of Oncology, Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden
| | - Leopoldo Gómez-Caudillo
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | - Juan Miguel Escorcia-Rodríguez
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Julio Augusto Freyre-González
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Sergio Encarnación-Guevara
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
- *Correspondence: Sergio Encarnacion Guevara,
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Paulitsch F, Dos Reis FB, Hungria M. Twenty years of paradigm-breaking studies of taxonomy and symbiotic nitrogen fixation by beta-rhizobia, and indication of Brazil as a hotspot of Paraburkholderia diversity. Arch Microbiol 2021; 203:4785-4803. [PMID: 34245357 DOI: 10.1007/s00203-021-02466-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 10/20/2022]
Abstract
Twenty years ago, the first members of the genus Burkholderia capable of nodulating and fixing N2 during symbiosis with leguminous plants were reported. The discovery that β-proteobacteria could nodulate legumes represented a breakthrough event because, for over 100 years, it was thought that all rhizobia belonged exclusively to the α-Proteobacteria class. Over the past 20 years, efforts toward robust characterization of these bacteria with large-scale phylogenomic and taxonomic studies have led to the separation of clinically important and phytopathogenic members of Burkholderia from environmental ones, and the symbiotic nodulating species are now included in the genera Paraburkholderia and Trinickia. Paraburkholderia encompasses the vast majority of β-rhizobia and has been mostly found in South America and South Africa, presenting greater symbiotic affinity with native members of the families Mimosoideae and Papilionoideae, respectively. Being the main center of Mimosa spp. diversity, Brazil is also known as the center of symbiotic Paraburkholderia diversity. Of the 21 symbiotic Paraburkholderia species described to date, 11 have been isolated in Brazil, and others first isolated in different countries have also been found in this country. Additionally, besides the symbiotic N2-fixation capacity of some of its members, Paraburkholderia is considered rich in other beneficial interactions with plants and can promote growth through several direct and indirect mechanisms. Therefore, these bacteria can be considered biological resources employed as environmentally friendly alternatives that could reduce the agricultural dependence on agrochemical inputs.
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Affiliation(s)
- Fabiane Paulitsch
- Embrapa Soja, C.P. 231, Londrina, Paraná, 86001-970, Brazil.,Departamento de Microbiologia, Universidade Estadual de Londrina, C.P. 10011, Londrina, Paraná, 86057-970, Brazil.,Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, Brasília, Distrito Federal, 70040-020, Brazil
| | | | - Mariangela Hungria
- Embrapa Soja, C.P. 231, Londrina, Paraná, 86001-970, Brazil. .,Departamento de Microbiologia, Universidade Estadual de Londrina, C.P. 10011, Londrina, Paraná, 86057-970, Brazil.
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Dias MAM, Bomfim CSG, Rodrigues DR, da Silva AF, Santos JCS, do Nascimento TR, Martins LMV, Dantas BF, Ribeiro PRDA, de Freitas ADS, Fernandes-Júnior PI. Paraburkholderia spp. are the main rhizobial microsymbionts of Mimosa tenuiflora (Willd.) Poir. in soils of the Brazilian tropical dry forests (Caatinga biome). Syst Appl Microbiol 2021; 44:126208. [PMID: 33992956 DOI: 10.1016/j.syapm.2021.126208] [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: 04/22/2020] [Revised: 03/31/2021] [Accepted: 04/14/2021] [Indexed: 02/06/2023]
Abstract
Mimosa tenuiflora (Willd.) Poir. is widespread in southern and central American drylands, but little information is available concerning its associated rhizobia. Therefore, this study aimed to characterize M. tenuiflora rhizobia from soils of the tropical dry forests (Caatinga) in Pernambuco State, Brazil, at the molecular and symbiotic levels. Soil samples of pristine Caatinga areas in four municipalities were used to grow M. tenuiflora. First, the bacteria from root nodules were subjected to nodC/nifH gene amplification, and the bacteria positive for both genes had the 16S rRNA gene sequenced. Then, ten strains were evaluated using recA, gyrB, and nodC gene sequences, and seven of them had their symbiotic efficiency assessed. Thirty-two strains were obtained and 22 of them were nodC/nifH positive. Twenty strains clustered within Paraburkholderia and two within Rhizobium by 16S rRNA gene sequencing. The beta-rhizobia were similar to P. phenoliruptrix (12) and P. diazotrophica (8). Both alpha-rhizobia were closely related to R. miluonense. The recA + gyrB phylogenetic analysis clustered four and five strains within the P. phenoliruptrix and P. diazotrophica branches, respectively, but they were somewhat divergent to the 16S rRNA phylogeny. For Rhizobium sp. ESA 637, the recA + gyrB phylogeny clustered the strain with R. jaguaris. The nodC phylogeny indicated that ESA 626, ESA 629, and ESA 630 probably represented a new symbiovar branch. The inoculation assay showed high symbiotic efficiency for all tested strains. The results indicated high genetic diversity and efficiency of M. tenuiflora rhizobia in Brazilian drylands and included P. phenoliruptrix-like bacteria in the list of efficient beta-rhizobia in the Caatinga biome.
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Affiliation(s)
- Marcos André Moura Dias
- Universidade Federal do Vale do São Francisco (Univasf), Colegiado de Farmácia, Petrolina, PE, Brazil
| | | | | | - Aleksandro Ferreira da Silva
- Universidade Federal Rural de Pernambuco (UFRPE), Departamento de Agronomia, Recife, PE, Brazil; Faculdade UniBras, Departamento de Agronomia, Juazeiro, BA, Brazil
| | | | - Tailane Ribeiro do Nascimento
- Universidade do Estado da Bahia (UNEB), Departamento de Tecnologia e Ciências Sociais, R. Edgard Chastinet, s/n, Juazeiro, BA, Brazil
| | - Lindete Míria Vieira Martins
- Universidade do Estado da Bahia (UNEB), Departamento de Tecnologia e Ciências Sociais, R. Edgard Chastinet, s/n, Juazeiro, BA, Brazil
| | | | - Paula Rose de Almeida Ribeiro
- Embrapa Semiárido, Petrolina, PE, Brazil; Fundação de Amparo à Pesquisa do Estado de Pernambuco (Facepe), Recife, PE, Brazil; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, DF, Brazil
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Paulitsch F, Delamuta JRM, Ribeiro RA, da Silva Batista JS, Hungria M. Phylogeny of symbiotic genes reveals symbiovars within legume-nodulating Paraburkholderia species. Syst Appl Microbiol 2020; 43:126151. [PMID: 33171385 DOI: 10.1016/j.syapm.2020.126151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 10/23/2022]
Abstract
Bacteria belonging to the genus Paraburkholderia are capable of establishing symbiotic relationships with plants belonging to the Fabaceae (=Leguminosae) family and fixing the atmospheric nitrogen in specialized structures in the roots called nodules, in a process known as biological nitrogen fixation (BNF). In the nodulation and BNF processes several bacterial symbiotic genes are involved, but the relations between symbiotic, core genes and host specificity are still poorly studied and understood in Paraburkholderia. In this study, eight strains of nodulating nitrogen-fixing Paraburkholderia isolated in Brazil, together with described species and other reference strains were used to infer the relatedness between core (16S rDNA, recA) and symbiotic (nod, nif, fix) genes. The diversity of genes involved in the nodulation (nodAC) and nitrogen fixation (nifH) abilities was investigated. Only two groups, one containing three Paraburkholderia species symbionts of Mimosa, and another one with P. ribeironis strains presented similar phylogenetic patterns in the analysis of core and symbiotic genes. In three other groups events of horizontal gene transfer of symbiotic genes were detected. Paraburkholderia strains with available genomes were used in the complementary analysis of nifHDK and fixABC and confirmed well-defined phylogenetic positions of symbiotic genes. In all analyses of nod, nif and fix genes the strains were distributed into five clades with high bootstrap support, allowing the proposal of five symbiovars in nodulating nitrogen-fixing Paraburkholderia, designated as mimosae, africana, tropicalis, atlantica and piptadeniae. Phylogenetic inferences within each symbiovar are discussed.
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Affiliation(s)
- Fabiane Paulitsch
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil; Departamento de Microbiologia, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, Brazil.
| | - Jakeline Renata Marçon Delamuta
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil; Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil.
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil.
| | - Jesiane Stefania da Silva Batista
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Avenida General Carlos Cavalcanti, 4748 - Uvaranas, C.P. 6001, Ponta Grossa, PR 84030‑900, Brazil.
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil; Departamento de Microbiologia, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil; Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil.
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Maquia IS, Fareleira P, Videira e Castro I, Brito DRA, Soares R, Chaúque A, Ferreira-Pinto MM, Lumini E, Berruti A, Ribeiro NS, Marques I, Ribeiro-Barros AI. Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion. Microorganisms 2020; 8:E1291. [PMID: 32846974 PMCID: PMC7563409 DOI: 10.3390/microorganisms8091291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 01/19/2023] Open
Abstract
(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions.
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Affiliation(s)
- Ivete Sandra Maquia
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
- TropiKMan Doctoral Program, Nova School of Business & Economics (Nova SBE), 2775-405 Carcavelos, Portugal
- Biotechnology Center, Eduardo Mondlane University, CP 257 Maputo, Mozambique;
| | - Paula Fareleira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Isabel Videira e Castro
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Denise R. A. Brito
- Biotechnology Center, Eduardo Mondlane University, CP 257 Maputo, Mozambique;
| | - Ricardo Soares
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Aniceto Chaúque
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, CP 257 Maputo, Mozambique; (A.C.); (N.S.R.)
| | - M. Manuela Ferreira-Pinto
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| | - Erica Lumini
- Institute for Sustainable Plant Protection, National Research Council, I-10135 Turin, Italy; (E.L.); (A.B.)
| | - Andrea Berruti
- Institute for Sustainable Plant Protection, National Research Council, I-10135 Turin, Italy; (E.L.); (A.B.)
| | - Natasha S. Ribeiro
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, CP 257 Maputo, Mozambique; (A.C.); (N.S.R.)
| | - Isabel Marques
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| | - Ana I. Ribeiro-Barros
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
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Effects of Selected Functional Bacteria on Maize Growth and Nutrient Use Efficiency. Microorganisms 2020; 8:microorganisms8060854. [PMID: 32517011 PMCID: PMC7356773 DOI: 10.3390/microorganisms8060854] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 01/09/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR), which include isolates from genera Paraburkholderia, Burkholderia and Serratia, have received attention due to their numerous plant growth-promoting mechanisms such as their ability to solubilize insoluble phosphates and nitrogen-fixation. However, there is a dearth of information on the potential plant growth-promoting effects of these three groups of bacteria on non-legumes such as maize. This study determined the influences of the aforementioned strains on soil properties, maize growth, nutrient uptake and nutrient use efficiency. A pot trial using maize as a test crop was done using a randomized complete block design with 7 treatments each replicated 7 times. The treatments used in this study were: Control (no fertilizer), chemical fertilizer (CF), organic-chemical fertilizers combination without inoculum (OCF) and with inocula consisting of single strains [cellulolytic bacteria (TC), organic fertilizer and chemical fertilizer with N-fixing bacteria (TN), organic fertilizer and chemical fertilizer with P-solubilizing bacteria (TP)) and three-strain inocula (TCNP), respectively. The variables measured included plant growth and nutrient content, soil nutrient content and functional rhizospheric bacterial populations. Paraburkholderia nodosa NB1 and Burkholderia cepacia PB3 showed comparable effects on maize biomass and also improved N and P use efficiencies when compared to full chemical fertilization. Nitrogen-fixing rhizobacteria had a positive effect on above-ground biomass of maize. Paraburkholderia nodosa NB1 improved soil total C and organic matter contents, besides being the only bacterial treatment that improved K use efficiency compared to OCF. The results suggest that P. nodosa NB1 and B. cepacia PB3 have potential usage in bio-fertilizers. In contrast, treatments with Serratia nematodiphila C46d and consortium strains showed poorer maize nutrient uptake and use efficiency than the other single strain treatments. Bacterial treatments generally showed comparable or higher overall N and P use efficiencies than full chemical fertilization. These findings suggest that at least half the amounts of N and P fertilizers could be reduced through the use of combined fertilization together with beneficial bacteria.
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Misra HS, Maurya GK, Kota S, Charaka VK. Maintenance of multipartite genome system and its functional significance in bacteria. J Genet 2018; 97:1013-1038. [PMID: 30262715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacteria are unicellular organisms that do not show compartmentalization of the genetic material and other cellular organelles as seen in higher organisms. Earlier, bacterial genomes were defined as single circular chromosome and extrachromosomal plasmids. Recently, many bacteria were found harbouringmultipartite genome system and the numbers of copies of genome elements including chromosomes vary from one to several per cell. Interestingly, it is noticed that majority of multipartite genome-harbouring bacteria are either stress tolerant or pathogens. Further, it is observed that the secondary genomes in these bacteria encode proteins that are involved in bacterial genome maintenance and also contribute to higher stress tolerance, and pathogenicity in pathogenic bacteria. Surprisingly, in some bacteria the genes encoding the proteins of classical homologous recombination pathways are present only on the secondary chromosomes, and some do not have either of the classical homologous recombination pathways. This review highlights the presence of ploidy and multipartite genomes in bacterial system, the underlying mechanisms of genome maintenance and the possibilities of these features contributing to higher abiotic and biotic stress tolerance in these bacteria.
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Affiliation(s)
- Hari Sharan Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
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Misra HS, Maurya GK, Kota S, Charaka VK. Maintenance of multipartite genome system and its functional significance in bacteria. J Genet 2018. [DOI: 10.1007/s12041-018-0969-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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10
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Investigation on the Evolutionary Relation of Diverse Polyhydroxyalkanoate Gene Clusters in Betaproteobacteria. J Mol Evol 2018; 86:470-483. [PMID: 30062554 DOI: 10.1007/s00239-018-9859-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
Products of numerous genes (phaC, phaA, phaB, phaP, phaR, and phaZ) are involved in the synthesis and degradation processes of the ubiquitous prokaryotic polyhydroxyalkanoate (PHA) intracellular reserve storage system. In this study, we performed a bioinformatics analysis to identify PHA-related genes and proteins in the genome of 66 selected organisms (class: Betaproteobacteria) that occur in various habitats; besides, evolutionary trajectories of the PHA system are reported here. The identified PHA-related genes were organized into clusters, and the gene arrangement was highly diverse. The occurrence and distribution of PHA-related clusters revealed that a single cluster was primarily segmented into small gene groups among various genomes, which were further reorganized as novel clusters based on various functional genes. The individual phylogenies of gene and protein sequences supported that the clusters were assembled through the relocation of native orthologous genes that underwent insertion, deletion, and elongation events. Furthermore, the neighboring genes provided valuable evolutionary and functional cues regarding the conservation and maintenance of PHA-related genes in the genome. Overall, the aforementioned results strongly indicate the influence of horizontal gene transfer on the organization of PHA-related gene clusters. Therefore, our results reveal new insights into the organization, evolutionary history, and cluster conservation of the PHA-related gene inventories among Betaproteobacterial organisms.
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Gramibactin is a bacterial siderophore with a diazeniumdiolate ligand system. Nat Chem Biol 2018; 14:841-843. [DOI: 10.1038/s41589-018-0101-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/08/2018] [Indexed: 02/01/2023]
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12
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Uroz S, Oger P. Caballeronia mineralivorans sp. nov., isolated from oak- Scleroderma citrinum mycorrhizosphere. Syst Appl Microbiol 2017; 40:345-351. [DOI: 10.1016/j.syapm.2017.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 10/19/2022]
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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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Oyehan TA, Al-Thukair AA. Isolation and characterization of PAH-degrading bacteria from the Eastern Province, Saudi Arabia. MARINE POLLUTION BULLETIN 2017; 115:39-46. [PMID: 27912917 DOI: 10.1016/j.marpolbul.2016.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 10/25/2016] [Accepted: 11/06/2016] [Indexed: 06/06/2023]
Abstract
Contaminated sediment samples were collected from the Eastern Province, Saudi Arabia for isolation of pyrene- and phenanthrene-degrading bacteria by enrichment method. Four isolates were morphologically characterized as Gram-negative rod strains and 16S rRNA sequence analysis revealed the isolates as closely related to Pseudomonas aeruginosa, P. citronellolis, Ochrobactrum intermedium and Cupriavidus taiwanensis. Degradation of the polycyclic aromatic hydrocarbons (PAHs) by the latter three strains was investigated in liquid cultures. Results of concentration reduction analyzed with gas chromatography show that P. citronellolis_LB was efficient in removing phenanthrene, degrading 94% of 100ppm in 15days while O. intermedium_BC1 was more efficient in pyrene-removal, degrading 62% in 2weeks. Furthermore, bacterial growth assessment using optical density and population counts revealed the latter as more suitable for microbial growth analysis in PAH-containing cultures. In conclusion, the isolated bacterial strains could be further developed for efficient use in biodegradation of PAH.
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Affiliation(s)
- Tajudeen A Oyehan
- Environmental Sciences Program of Earth Sciences Dept., King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
| | - Assad A Al-Thukair
- Life Sciences Dept., King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia.
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15
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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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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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Babujia LC, Silva AP, Nakatani AS, Cantão ME, Vasconcelos ATR, Visentainer JV, Hungria M. Impact of long-term cropping of glyphosate-resistant transgenic soybean [Glycine max (L.) Merr.] on soil microbiome. Transgenic Res 2016; 25:425-40. [PMID: 26873023 DOI: 10.1007/s11248-016-9938-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/04/2016] [Indexed: 01/21/2023]
Abstract
The transgenic soybean [Glycine max (L.) Merrill] occupies about 80 % of the global area cropped with this legume, the majority comprising the glyphosate-resistant trait (Roundup Ready(®), GR or RR). However, concerns about possible impacts of transgenic crops on soil microbial communities are often raised. We investigated soil chemical, physical and microbiological properties, and grain yields in long-term field trials involving conventional and nearly isogenic RR transgenic genotypes. The trials were performed at two locations in Brazil, with different edaphoclimatic conditions. Large differences in physical, chemical and classic microbiological parameters (microbial biomass of C and N, basal respiration), as well as in grain production were observed between the sites. Some phyla (Proteobacteria, Actinobacteria, Acidobacteria), classes (Alphaproteobacteria, Actinomycetales, Solibacteres) and orders (Rhizobiales, Burkholderiales, Myxococcales, Pseudomonadales), as well as some functional subsystems (clustering-based subsystems, carbohydrates, amino acids and protein metabolism) were, in general, abundant in all treatments. However, bioindicators related to superior soil fertility and physical properties at Londrina were identified, among them a higher ratio of Proteobacteria:Acidobacteria. Regarding the transgene, the metagenomics showed differences in microbial taxonomic and functional abundances, but lower in magnitude than differences observed between the sites. Besides the site-specific differences, Proteobacteria, Firmicutes and Chlorophyta were higher in the transgenic treatment, as well as sequences related to protein metabolism, cell division and cycle. Although confirming effects of the transgenic trait on soil microbiome, no differences were recorded in grain yields, probably due to the buffering capacity associated with the high taxonomic and functional microbial diversity observed in all treatments.
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Affiliation(s)
- Letícia Carlos Babujia
- Department of Chemistry, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, 87020-900, Brazil
- Embrapa Soja, C.P. 231, Londrina, Paraná, 86001-970, Brazil
| | | | | | | | | | - Jesuí Vergilio Visentainer
- Department of Chemistry, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, 87020-900, Brazil
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Deng P, Wang X, Baird SM, Showmaker KC, Smith L, Peterson DG, Lu S. Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis. Microbiologyopen 2016; 5:353-69. [PMID: 26769582 PMCID: PMC4905989 DOI: 10.1002/mbo3.333] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/22/2015] [Accepted: 12/03/2015] [Indexed: 11/13/2022] Open
Abstract
Burkholderia contaminans MS14 shows significant antimicrobial activities against plant and animal pathogenic fungi and bacteria. The antifungal agent occidiofungin produced by MS14 has great potential for development of biopesticides and pharmaceutical drugs. However, the use of Burkholderia species as biocontrol agent in agriculture is restricted due to the difficulties in distinguishing between plant growth-promoting bacteria and the pathogenic bacteria. The complete MS14 genome was sequenced and analyzed to find what beneficial and virulence-related genes it harbors. The phylogenetic relatedness of B. contaminans MS14 and other 17 Burkholderia species was also analyzed. To research MS14's potential virulence, the gene regions related to the antibiotic production, antibiotic resistance, and virulence were compared between MS14 and other Burkholderia genomes. The genome of B. contaminans MS14 was sequenced and annotated. The genomic analyses reveal the presence of multiple gene sets for antimicrobial biosynthesis, which contribute to its antimicrobial activities. BLAST results indicate that the MS14 genome harbors a large number of unique regions. MS14 is closely related to another plant growth-promoting Burkholderia strain B. lata 383 according to the average nucleotide identity data. Moreover, according to the phylogenetic analysis, plant growth-promoting species isolated from soils and mammalian pathogenic species are clustered together, respectively. MS14 has multiple antimicrobial activity-related genes identified from the genome, but it lacks key virulence-related gene loci found in the pathogenic strains. Additionally, plant growth-promoting Burkholderia species have one or more antimicrobial biosynthesis genes in their genomes as compared with nonplant growth-promoting soil-isolated Burkholderia species. On the other hand, pathogenic species harbor multiple virulence-associated gene loci that are not present in nonpathogenic Burkholderia species. The MS14 genome as well as Burkholderia species genome show considerable diversity. Multiple antimicrobial agent biosynthesis genes were identified in the genome of plant growth-promoting species of Burkholderia. In addition, by comparing to nonpathogenic Burkholderia species, pathogenic Burkholderia species have more characterized homologs of the gene loci known to contribute to pathogenicity and virulence to plant and animals.
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Affiliation(s)
- Peng Deng
- Departments of Biochemistry, Molecular BiologyEntomology and Plant PathologyMississippi State UniversityMississippi stateMississippi
| | - Xiaoqiang Wang
- Departments of Biochemistry, Molecular BiologyEntomology and Plant PathologyMississippi State UniversityMississippi stateMississippi
| | - Sonya M. Baird
- Departments of Biochemistry, Molecular BiologyEntomology and Plant PathologyMississippi State UniversityMississippi stateMississippi
| | - Kurt C. Showmaker
- Institute for GenomicsBiocomputing and BiotechnologyMississippi State UniversityMississippi stateMississippi
| | - Leif Smith
- Department of BiologyTexas A&M UniversityCollege StationTexas
| | - Daniel G. Peterson
- Institute for GenomicsBiocomputing and BiotechnologyMississippi State UniversityMississippi stateMississippi
| | - Shien Lu
- Departments of Biochemistry, Molecular BiologyEntomology and Plant PathologyMississippi State UniversityMississippi stateMississippi
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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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Lee SY, Kim GH, Yun SH, Choi CW, Yi YS, Kim J, Chung YH, Park EC, Kim SI. Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24. PLoS One 2016; 11:e0154233. [PMID: 27124467 PMCID: PMC4849787 DOI: 10.1371/journal.pone.0154233] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/11/2016] [Indexed: 11/19/2022] Open
Abstract
Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs), including benzene, toluene, and xylene (BTX), as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX.
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Affiliation(s)
- Sang-Yeop Lee
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Gun-Hwa Kim
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Sung Ho Yun
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Chi-Won Choi
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yoon-Sun Yi
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
- Department of Food Science and Technology, Chungnam National University, Daejeon, 305–764, Republic of Korea
| | - Jonghyun Kim
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Young-Ho Chung
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Edmond Changkyun Park
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Seung Il Kim
- Drug & Disease Target Team, Korea Basic Science Institute, 169–148 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
- Bio-Analysis Science, University of Science & Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
- * E-mail:
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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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Lemaire B, Van Cauwenberghe J, Chimphango S, Stirton C, Honnay O, Smets E, Muasya AM. Recombination and horizontal transfer of nodulation and ACC deaminase (acdS) genes within Alpha- and Betaproteobacteria nodulating legumes of the Cape Fynbos biome. FEMS Microbiol Ecol 2015; 91:fiv118. [PMID: 26433010 DOI: 10.1093/femsec/fiv118] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2015] [Indexed: 11/14/2022] Open
Abstract
The goal of this work is to study the evolution and the degree of horizontal gene transfer (HGT) within rhizobial genera of both Alphaproteobacteria (Mesorhizobium, Rhizobium) and Betaproteobacteria (Burkholderia), originating from South African Fynbos legumes. By using a phylogenetic approach and comparing multiple chromosomal and symbiosis genes, we revealed conclusive evidence of high degrees of horizontal transfer of nodulation genes among closely related species of both groups of rhizobia, but also among species with distant genetic backgrounds (Rhizobium and Mesorhizobium), underscoring the importance of lateral transfer of symbiosis traits as an important evolutionary force among rhizobia of the Cape Fynbos biome. The extensive exchange of symbiosis genes in the Fynbos is in contrast with a lack of significant events of HGT among Burkholderia symbionts from the South American Cerrado and Caatinga biome. Furthermore, homologous recombination among selected housekeeping genes had a substantial impact on sequence evolution within Burkholderia and Mesorhizobium. Finally, phylogenetic analyses of the non-symbiosis acdS gene in Mesorhizobium, a gene often located on symbiosis islands, revealed distinct relationships compared to the chromosomal and symbiosis genes, suggesting a different evolutionary history and independent events of gene transfer. The observed events of HGT and incongruence between different genes necessitate caution in interpreting topologies from individual data types.
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Affiliation(s)
- Benny Lemaire
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium
| | - Jannick Van Cauwenberghe
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Samson Chimphango
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Charles Stirton
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Olivier Honnay
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium
| | - Erik Smets
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium Naturalis Biodiversity Center, Leiden University, 2300 RA Leiden, the Netherlands
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
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Sayavedra L, Kleiner M, Ponnudurai R, Wetzel S, Pelletier E, Barbe V, Satoh N, Shoguchi E, Fink D, Breusing C, Reusch TBH, Rosenstiel P, Schilhabel MB, Becher D, Schweder T, Markert S, Dubilier N, Petersen JM. Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. eLife 2015; 4:e07966. [PMID: 26371554 PMCID: PMC4612132 DOI: 10.7554/elife.07966] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/14/2015] [Indexed: 01/06/2023] Open
Abstract
Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable 'arsenal' of TRGs.
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Affiliation(s)
| | - Manuel Kleiner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ruby Ponnudurai
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Silke Wetzel
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Eric Pelletier
- Genoscope - Centre National de Séquençage, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
- Metabolic Genomics Group, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
- University of Évry-Val d'Essonne, Evry, France
| | - Valerie Barbe
- Genoscope - Centre National de Séquençage, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Dennis Fink
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Corinna Breusing
- Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Thorsten BH Reusch
- Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | | | - Dörte Becher
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- University of Bremen, Bremen, Germany
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