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Claassens R, Venter SN, Beukes CW, Stępkowski T, Chan WY, Steenkamp ET. Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa. Syst Appl Microbiol 2023; 46:126452. [PMID: 37634485 DOI: 10.1016/j.syapm.2023.126452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023]
Abstract
A genealogical concordance approach was used to delineate strains isolated from Acacia dealbata and Acacia mearnsii root nodules in South Africa. These isolates form part of Bradyrhizobium based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (atpD, dnaK, glnII, gyrB, recA and rpoB) confirmed that these isolates represent a novel species, while pairwise average nucleotide identity (ANIb) calculations with the closest type strains (B. cosmicum 58S1T, B. betae PL7HG1T, B. ganzhouense CCBAU 51670 T, B. cytisi CTAW11T and B. rifense CTAW71T) resulted in values well below 95-96%. We further performed phenotypic tests which revealed that there are high levels of intraspecies variation, while an additional analysis of the nodA and nifD loci indicated that the symbiotic loci of the strains are closely related to those of Bradyrhizobium isolates with an Australian origin. Strain 14ABT (=LMG 31415 T = SARCC-753 T) is designated as the type strain of the novel species for which we propose the name Bradyrhizobium xenonodulans sp. nov.
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Affiliation(s)
- Ricu Claassens
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa
| | | | - Tomasz Stępkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Poland
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa; Right to Care, Centurion, Gauteng, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa.
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Klonowska A, Ardley J, Moulin L, Zandberg J, Patrel D, Gollagher M, Marinova D, Reddy TBK, Varghese N, Huntemann M, Woyke T, Seshadri R, Ivanova N, Kyrpides N, Reeve W. Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018. Front Microbiol 2023; 14:1082107. [PMID: 36925474 PMCID: PMC10011098 DOI: 10.3389/fmicb.2023.1082107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/24/2023] [Indexed: 03/08/2023] Open
Abstract
Integrated virus genomes (prophages) are commonly found in sequenced bacterial genomes but have rarely been described in detail for rhizobial genomes. Cupriavidus taiwanensis STM 6018 is a rhizobial Betaproteobacteria strain that was isolated in 2006 from a root nodule of a Mimosa pudica host in French Guiana, South America. Here we describe features of the genome of STM 6018, focusing on the characterization of two different types of prophages that have been identified in its genome. The draft genome of STM 6018 is 6,553,639 bp, and consists of 80 scaffolds, containing 5,864 protein-coding genes and 61 RNA genes. STM 6018 contains all the nodulation and nitrogen fixation gene clusters common to symbiotic Cupriavidus species; sharing >99.97% bp identity homology to the nod/nif/noeM gene clusters from C. taiwanensis LMG19424T and "Cupriavidus neocalidonicus" STM 6070. The STM 6018 genome contains the genomes of two prophages: one complete Mu-like capsular phage and one filamentous phage, which integrates into a putative dif site. This is the first characterization of a filamentous phage found within the genome of a rhizobial strain. Further examination of sequenced rhizobial genomes identified filamentous prophage sequences in several Beta-rhizobial strains but not in any Alphaproteobacterial rhizobia.
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Affiliation(s)
- Agnieszka Klonowska
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Julie Ardley
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Lionel Moulin
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Jaco Zandberg
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Delphine Patrel
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Neha Varghese
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rekha Seshadri
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Wayne Reeve
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
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Hernández Guijarro K, De Gerónimo E, Erijman L. Glyphosate Biodegradation Potential in Soil Based on Glycine Oxidase Gene (thiO) from Bradyrhizobium. Curr Microbiol 2021; 78:1991-2000. [PMID: 33797566 DOI: 10.1007/s00284-021-02467-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/16/2021] [Indexed: 11/27/2022]
Abstract
Despite the intensive use of glyphosate (GP) and its ubiquitous presence in the environment, studies addressing the presence of microbial genes involved in glyphosate degradation in natural conditions are scarce. Based on the agronomical importance of Bradyrhizobium genus and its metabolic versatility, we tested the hypothesis that species or genotypes of Bradyrhizobium could be a proxy for GP degrader potential in soil. A quantitative PCR assay was designed to target a specific region of the glycine oxidase gene (thiO), involved in the oxidation of glyphosate to AMPA, from known sequences of Bradyrhizobium species. The abundance of the thiO gene was determined in response to herbicide application in soils with different GP exposure history both under field and microcosm conditions. The gene coding for RNA polymerase subunitB (rpoB) was used as a reference for the abundance of total Bradyrhizobia. The assay using the designed primers was linear over a very large concentration range of the target and showed high efficiency and specificity. In a field experiment, there was a differential response related to the history of glyphosate use and the native Bradyrhizobium genotypes. In a soil without previous exposure to herbicides, thiO gene increased over time after glyphosate application with most genotypes belonging to the B. jicamae and B. elkanni supergroups. Conversely, in an agricultural soil with more than 10 years of continuous glyphosate application, the abundance of thiO gene decreased and most genotypes belonged to B. japonicum supergroup. In a microcosm assay, the amount of herbicide degraded after a single application was positively correlated to the number of thiO copies in different agricultural soils from the Pampean Region. Our results suggest that Bradyrhizobium species are differently involved in glyphosate degradation, denoting the existence of metabolically versatile microorganisms which can be explored for sustainable agriculture practices. The relationship between the abundance of thiO gene and the GP degraded in soil point to the use of thiO gene as a proxy for GP degradation in soil.
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Affiliation(s)
- Keren Hernández Guijarro
- National Institute of Agricultural Technology (INTA), Balcarce Experimental Station, Ruta Nac, 226, Km 73,5, CP 7620 Balcarce, Buenos Aires, Argentina
| | - Eduardo De Gerónimo
- National Institute of Agricultural Technology (INTA), Balcarce Experimental Station, Ruta Nac, 226, Km 73,5, CP 7620 Balcarce, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
| | - Leonardo Erijman
- National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina.
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular - "Dr Héctor N Torres" (INGEBI-CONICET), Vuelta de Obligado 2490, C1428ADN, Buenos Aires, Argentina.
- Department of Physiology, Molecular and Cellular Biology "Prof Héctor Maldonado," School of Sciences, University of Buenos Aires, C1428, Buenos Aires, Argentina.
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Efstathiadou E, Ntatsi G, Savvas D, Tampakaki AP. Genetic characterization at the species and symbiovar level of indigenous rhizobial isolates nodulating Phaseolus vulgaris in Greece. Sci Rep 2021; 11:8674. [PMID: 33883620 PMCID: PMC8060271 DOI: 10.1038/s41598-021-88051-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/31/2021] [Indexed: 11/09/2022] Open
Abstract
Phaseolus vulgaris (L.), commonly known as bean or common bean, is considered a promiscuous legume host since it forms nodules with diverse rhizobial species and symbiovars. Most of the common bean nodulating rhizobia are mainly affiliated to the genus Rhizobium, though strains belonging to Ensifer, Pararhizobium, Mesorhizobium, Bradyrhizobium, and Burkholderia have also been reported. This is the first report on the characterization of bean-nodulating rhizobia at the species and symbiovar level in Greece. The goals of this research were to isolate and characterize rhizobia nodulating local common bean genotypes grown in five different edaphoclimatic regions of Greece with no rhizobial inoculation history. The genetic diversity of the rhizobial isolates was assessed by BOX-PCR and the phylogenetic affiliation was assessed by multilocus sequence analysis (MLSA) of housekeeping and symbiosis-related genes. A total of fifty fast-growing rhizobial strains were isolated and representative isolates with distinct BOX-PCR fingerpriniting patterns were subjected to phylogenetic analysis. The strains were closely related to R. anhuiense, R. azibense, R. hidalgonense, R. sophoriradicis, and to a putative new genospecies which is provisionally named as Rhizobium sp. I. Most strains belonged to symbiovar phaseoli carrying the α-, γ-a and γ-b alleles of nodC gene, while some of them belonged to symbiovar gallicum. To the best of our knowledge, it is the first time that strains assigned to R. sophoriradicis and harbored the γ-b allele were found in European soils. All strains were able to re-nodulate their original host, indicating that they are true microsymbionts of common bean.
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Affiliation(s)
- Evdoxia Efstathiadou
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855, Athens, Greece
| | - Georgia Ntatsi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855, Athens, Greece
| | - Dimitrios Savvas
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855, Athens, Greece
| | - Anastasia P Tampakaki
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855, Athens, Greece.
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Bünger W, Sarkar A, Grönemeyer JL, Zielinski J, Revermann R, Hurek T, Reinhold-Hurek B. Root Nodule Rhizobia From Undomesticated Shrubs of the Dry Woodlands of Southern Africa Can Nodulate Angolan Teak Pterocarpus angolensis, an Important Source of Timber. Front Microbiol 2021; 12:611704. [PMID: 33584615 PMCID: PMC7876412 DOI: 10.3389/fmicb.2021.611704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/06/2021] [Indexed: 11/17/2022] Open
Abstract
Pterocarpus angolensis, a leguminous tree native to the dry woodlands of Southern Africa, provides valuable timber, but is threatened by land conversion and overharvesting while showing limited natural regeneration. Nitrogen-fixing root nodule symbionts that could improve establishment of young seedlings have not yet been described. Therefore, we investigated the ability of P. angolensis to form nodules with a diverse range of rhizobia. In drought-prone areas under climate change with higher temperatures, inoculants that are heat-tolerant and adapted to these conditions are likely to be of advantage. Sources of bacterial isolates were roots of P. angolensis from nurseries in the Kavango region, other shrubs from this area growing near Pterocarpus such as Indigofera rautanenii, Desmodium barbatum, Chamaecrista sp., or shrubs from drought-prone areas in Namaqualand (Wiborgia monoptera, Leobordea digitata) or Kalahari (Indigofera alternans). Only slight protrusions were observed on P. angolensis roots, from which a non-nodulating Microbacterium sp. was isolated. Rhizobia that were isolated from nodules of other shrubs were affiliated to Bradyrhizobium ripae WR4T, Bradyrhizobium spp. (WR23/WR74/WR93/WR96), or Ensifer/Mesorhizobium (WR41/WR52). As many plant growth-promoting rhizobacteria (PGPR), nodule isolates produced siderophores and solubilized phosphate. Among them, only the Bradyrhizobium strains nodulated P. angolensis under controlled conditions in the laboratory. Isolates were further characterized by multilocus sequence analysis and were found to be distant from known Bradyrhizobium species. Among additional reference species tested for nodulation on P. angolensis, Bradyrhizobium vignae 7-2T and Bradyrhizobium namibiense 5-10T from the Kavango region of Namibia as well as Bradyrhizobium elkanii LMG6234T and Bradyrhizobium yuanmingense LMG21728T induced nitrogen-fixing nodules, while Bradyrhizobium diazoefficiens USDA110T and Bradyrhizobium tropiciagri SEMIA6148T did not. This suggests a broad microsymbiont range from Bradyrhizobium japonicum and B. elkanii lineages. Phylogenetic analysis of nodC genes indicated that nodulating bradyrhizobia did not belong to a specific symbiovar. Also, for I. rautanenii and Wiborgia, nodule isolates B. ripae WR4T or Mesorhizobium sp. WR52, respectively, were authenticated. Characterization of symbionts inducing effective root nodules in P. angolensis and other shrubs from Subsahara Africa (SSA) give insights in their symbiotic partners for the first time and might help in future to develop bioinoculants for young seedlings in nurseries, and for reforestation efforts in Southern Africa.
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Affiliation(s)
- Wiebke Bünger
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Abhijit Sarkar
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Jann Lasse Grönemeyer
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Janina Zielinski
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Rasmus Revermann
- Department of Biodiversity, Ecology and Evolution of Plants, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
- Faculty of Natural Resources and Spatial Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
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Klonowska A, Moulin L, Ardley JK, Braun F, Gollagher MM, Zandberg JD, Marinova DV, Huntemann M, Reddy TBK, Varghese NJ, Woyke T, Ivanova N, Seshadri R, Kyrpides N, Reeve WG. Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil. BMC Genomics 2020; 21:214. [PMID: 32143559 PMCID: PMC7060636 DOI: 10.1186/s12864-020-6623-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/25/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems. RESULTS The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance. CONCLUSIONS STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.
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Affiliation(s)
- Agnieszka Klonowska
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Julie Kaye Ardley
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Florence Braun
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | | | - Jaco Daniel Zandberg
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Dora Vasileva Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, Australia
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, USA
| | | | | | | | - Wayne Gerald Reeve
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
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Characterization of Bradyrhizobium strains indigenous to Western Australia and South Africa indicates remarkable genetic diversity and reveals putative new species. Syst Appl Microbiol 2020; 43:126053. [PMID: 31937424 DOI: 10.1016/j.syapm.2020.126053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 01/01/2023]
Abstract
Bradyrhizobium are N2-fixing microsymbionts of legumes with relevant applications in agricultural sustainability, and we investigated the phylogenetic relationships of conserved and symbiotic genes of 21 bradyrhizobial strains. The study included strains from Western Australia (WA), isolated from nodules of Glycine spp. the country is one genetic center for the genus and from nodules of other indigenous legumes grown in WA, and strains isolated from forage Glycine sp. grown in South Africa. The 16S rRNA phylogeny divided the strains in two superclades, of B. japonicum and B. elkanii, but with low discrimination among the species. The multilocus sequence analysis (MLSA) with four protein-coding housekeeping genes (dnaK, glnII, gyrB and recA) pointed out seven groups as putative new species, two within the B. japonicum, and five within the B. elkanii superclades. The remaining eleven strains showed higher similarity with six species, B. lupini, B. liaoningense, B. yuanmingense, B. subterraneum, B. brasilense and B. retamae. Phylogenetic analysis of the nodC symbiotic gene clustered 13 strains in three different symbiovars (sv. vignae, sv. genistearum and sv. retamae), while seven others might compose new symbiovars. The genetic profiles of the strains evaluated by BOX-PCR revealed high intra- and interspecific diversity. The results point out the high level of diversity still to be explored within the Bradyrhizobium genus, and further studies might confirm new species and symbiovars.
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Estrella MJ, Fontana MF, Cumpa Velásquez LM, Torres Tejerizo GA, Diambra L, Hansen LH, Pistorio M, Sannazzaro AI. Mesorhizobium intechi sp. nov. isolated from nodules of Lotus tenuis in soils of the Flooding Pampa, Argentina. Syst Appl Microbiol 2020; 43:126044. [DOI: 10.1016/j.syapm.2019.126044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/21/2019] [Accepted: 11/04/2019] [Indexed: 01/16/2023]
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Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa. Genes (Basel) 2019; 10:genes10120990. [PMID: 31805640 PMCID: PMC6969944 DOI: 10.3390/genes10120990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 11/17/2022] Open
Abstract
Vavilovia formosa is a relict leguminous plant growing in hard-to-reach habitats in the rocky highlands of the Caucasus and Middle East, and it is considered as the putative closest living relative of the last common ancestor (LCA) of the Fabeae tribe. Symbionts of Vavilovia belonging to Rhizobium leguminosarum bv. viciae compose a discrete group that differs from the other strains, especially in the nucleotide sequences of the symbiotically specialised (sym) genes. Comparison of the genomes of Vavilovia strains with the reference group composed of R. leguminosarum bv. viciae strains isolated from Pisum and Vicia demonstrated that the vavilovia strains have a set of genomic features, probably indicating the important stages of microevolution of the symbiotic system. Specifically, symbionts of Vavilovia (considered as an ancestral group) demonstrated a scattered arrangement of sym genes (>90 kb cluster on pSym), with the location of nodT gene outside of the other nod operons, the presence of nodX and fixW, and the absence of chromosomal fixNOPQ copies. In contrast, the reference (derived) group harboured sym genes as a compact cluster (<60 kb) on a single pSym, lacking nodX and fixW, with nodT between nodN and nodO, and possessing chromosomal fixNOPQ copies. The TOM strain, obtained from nodules of the primitive “Afghan” peas, occupied an intermediate position because it has the chromosomal fixNOPQ copy, while the other features, the most important of which is presence of nodX and fixW, were similar to the Vavilovia strains. We suggest that genome evolution from the ancestral to the derived R. leguminosarum bv. viciae groups follows the “gain-and-loss of sym genes” and the “compaction of sym cluster” strategies, which are common for the macro-evolutionary and micro-evolutionary processes. The revealed genomic features are in concordance with a relict status of the vavilovia strains, indicating that V. formosa coexists with ancestral microsymbionts, which are presumably close to the LCA of R. leguminosarum bv. viciae.
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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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Avontuur JR, Palmer M, Beukes CW, Chan WY, Coetzee MPA, Blom J, Stępkowski T, Kyrpides NC, Woyke T, Shapiro N, Whitman WB, Venter SN, Steenkamp ET. Genome-informed Bradyrhizobium taxonomy: where to from here? Syst Appl Microbiol 2019; 42:427-439. [PMID: 31031014 DOI: 10.1016/j.syapm.2019.03.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 02/06/2023]
Abstract
Bradyrhizobium is thought to be the largest and most diverse rhizobial genus, but this is not reflected in the number of described species. Although it was one of the first rhizobial genera recognised, its taxonomy remains complex. Various contemporary studies are showing that genome sequence information may simplify taxonomic decisions. Therefore, the growing availability of genomes for Bradyrhizobium will likely aid in the delineation and characterization of new species. In this study, we addressed two aims: first, we reviewed the availability and quality of available genomic resources for Bradyrhizobium. This was achieved by comparing genome sequences in terms of sequencing technologies used and estimated level of completeness for inclusion in genome-based phylogenetic analyses. Secondly, we utilized these genomes to investigate the taxonomic standing of Bradyrhizobium in light of its diverse lifestyles. Although genome sequences differed in terms of their quality and completeness, our data indicate that the use of these genome sequences is adequate for taxonomic purposes. By using these resources, we inferred a fully resolved, well-supported phylogeny. It separated Bradyrhizobium into seven lineages, three of which corresponded to the so-called supergroups known for the genus. Wide distribution of key lifestyle traits such as nodulation, nitrogen fixation and photosynthesis revealed that these traits have complicated evolutionary histories. We present the first robust Bradyrhizobium species phylogeny based on genome sequence information for investigating the evolution of this important assemblage of bacteria. Furthermore, this study provides the basis for using genome sequence information as a resource to make important taxonomic decisions, particularly at the species and genus levels.
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Affiliation(s)
- Juanita R Avontuur
- 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
| | - Chrizelle W Beukes
- 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 0110, South Africa
| | - Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Poland
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - 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. http://emma.steenkamp.up.ac.za
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12
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Goss-Souza D, Mendes LW, Borges CD, Rodrigues JLM, Tsai SM. Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept. FEMS Microbiol Ecol 2019; 95:fiz009. [PMID: 30715365 DOI: 10.1093/femsec/fiz009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/31/2019] [Indexed: 12/17/2023] Open
Abstract
The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due to liming and fertilization in long-term no-till cropping. Data revealed that long-term no-till cropping culminated in a decrease in Acidobacteria, Actinobacteria and Proteobacteria abundances. However, α- and β-Proteobacteria abundances were higher in the rhizosphere than in bulk soil, regardless of the time after forest-to-agriculture conversion. Changes in functional potential occurred predominantly in bulk soil, with decreases in functions related to potassium metabolism and virulence, disease and defense, while functions related to nucleic acids metabolism increased. Functions in the soybean rhizosphere remained stable, except for those related to potassium metabolism, which decreased after 20-year no-till cropping. Together, our results show that the soybean root system selects microbial taxa via trade-offs, to maintain functional resilience in the rhizosphere microbiome over time.
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Affiliation(s)
- Dennis Goss-Souza
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400-970, Brazil
- Department of Land, Air and Water Resources, University of California - Davis, Davis, CA 95616, USA
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, SC 88523-000, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Clovis Daniel Borges
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400-970, Brazil
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jorge L M Rodrigues
- Department of Land, Air and Water Resources, University of California - Davis, Davis, CA 95616, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400-970, Brazil
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13
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Kumar H, Dubey R, Maheshwari D. Rhizobial genetic diversity in root nodules of Trigonella foenum-graecum cultivated in sub-himalayan region of Uttarakhand. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Tong W, Li X, Huo Y, Zhang L, Cao Y, Wang E, Chen W, Tao S, Wei G. Genomic insight into the taxonomy of Rhizobium genospecies that nodulate Phaseolus vulgaris. Syst Appl Microbiol 2018; 41:300-310. [PMID: 29576402 DOI: 10.1016/j.syapm.2018.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 10/17/2022]
Abstract
Due to the wide cultivation of bean (Phaseolus vulgaris L.), rhizobia associated with this plant have been isolated from many different geographical regions. In order to investigate the species diversity of bean rhizobia, comparative genome sequence analysis was performed in the present study for 69 Rhizobium strains mainly isolated from root nodules of bean and clover (Trifolium spp.). Based on genome average nucleotide identity, digital DNA:DNA hybridization, and phylogenetic analysis of 1,458 single-copy core genes, these strains were classified into 28 clusters, consistent with their species definition based on multilocus sequence analysis (MLSA) of atpD, glnII, and recA. The bean rhizobia were found in 16 defined species and nine putative novel species; in addition, 35 strains previously described as Rhizobium etli, Rhizobium phaseoli, Rhizobium vallis, Rhizobium gallicum, Rhizobium leguminosarum and Rhizobium spp. should be renamed. The phylogenetic patterns of symbiotic genes nodC and nifH were highly host-specific and inconsistent with the genomic phylogeny. Multiple symbiovars (sv.) within the Rhizobium species were found as a common feature: sv. phaseoli, sv. trifolii and sv. viciae in Rhizobium anhuiense; sv. phaseoli and sv. mimosae in Rhizobium sophoriradicis/R. etli/Rhizobium sp. III; sv. phaseoli and sv. trifolii in Rhizobium hidalgonense/Rhizobium acidisoli; sv. phaseoli and sv. viciae in R. leguminosarum/Rhizobium sp. IX; sv. trifolii and sv. viciae in Rhizobium laguerreae. Thus, genomic comparison revealed great species diversity in bean rhizobia, corrected the species definition of some previously misnamed strains, and demonstrated the MLSA a valuable and simple method for defining Rhizobium species.
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Affiliation(s)
- Wenjun Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangchen Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunyun Huo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Cao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D.F., Mexico
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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15
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Stępkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP. Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae. Genes (Basel) 2018. [PMID: 29538303 PMCID: PMC5867884 DOI: 10.3390/genes9030163] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The legume tribe Genisteae comprises 618, predominantly temperate species, showing an amphi-Atlantic distribution that was caused by several long-distance dispersal events. Seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species. Bradyrhizobium predominates among rhizobia nodulating Genisteae legumes. Bradyrhizobium strains that infect Genisteae species belong to both the Bradyrhizobium japonicum and Bradyrhizobium elkanii superclades. In symbiotic gene phylogenies, Genisteae bradyrhizobia are scattered among several distinct clades, comprising strains that originate from phylogenetically distant legumes. This indicates that the capacity for nodulation of Genisteae spp. has evolved independently in various symbiotic gene clades, and that it has not been a long-multi-step process. The exception is Bradyrhizobium Clade II, which unlike other clades comprises strains that are specialized in nodulation of Genisteae, but also Loteae spp. Presumably, Clade II represents an example of long-lasting co-evolution of bradyrhizobial symbionts with their legume hosts.
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Affiliation(s)
- Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Joanna Banasiewicz
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Camille E Granada
- Universidade do Vale do Taquari-UNIVATES, Rua Avelino Tallini, 171, 95900-000 Lajeado, RS, Brazil.
| | - Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil.
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16
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Sánchez-Cañizares C, Jorrín B, Durán D, Nadendla S, Albareda M, Rubio-Sanz L, Lanza M, González-Guerrero M, Prieto RI, Brito B, Giglio MG, Rey L, Ruiz-Argüeso T, Palacios JM, Imperial J. Genomic Diversity in the Endosymbiotic Bacterium Rhizobium leguminosarum. Genes (Basel) 2018; 9:E60. [PMID: 29364862 PMCID: PMC5852556 DOI: 10.3390/genes9020060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/16/2018] [Accepted: 01/22/2018] [Indexed: 12/22/2022] Open
Abstract
Rhizobium leguminosarum bv. viciae is a soil α-proteobacterium that establishes a diazotrophic symbiosis with different legumes of the Fabeae tribe. The number of genome sequences from rhizobial strains available in public databases is constantly increasing, although complete, fully annotated genome structures from rhizobial genomes are scarce. In this work, we report and analyse the complete genome of R. leguminosarum bv. viciae UPM791. Whole genome sequencing can provide new insights into the genetic features contributing to symbiotically relevant processes such as bacterial adaptation to the rhizosphere, mechanisms for efficient competition with other bacteria, and the ability to establish a complex signalling dialogue with legumes, to enter the root without triggering plant defenses, and, ultimately, to fix nitrogen within the host. Comparison of the complete genome sequences of two strains of R. leguminosarum bv. viciae, 3841 and UPM791, highlights the existence of different symbiotic plasmids and a common core chromosome. Specific genomic traits, such as plasmid content or a distinctive regulation, define differential physiological capabilities of these endosymbionts. Among them, strain UPM791 presents unique adaptations for recycling the hydrogen generated in the nitrogen fixation process.
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Affiliation(s)
- Carmen Sánchez-Cañizares
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
| | - Beatriz Jorrín
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
| | - David Durán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid (UAM), Ciudad Universitaria de Cantoblanco, Calle Francisco Tomás y Valiente 7, 28049 Madrid, Spain
| | - Suvarna Nadendla
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.N.); (M.G.G.)
| | - Marta Albareda
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Laura Rubio-Sanz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Mónica Lanza
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Rosa Isabel Prieto
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Belén Brito
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Michelle G. Giglio
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.N.); (M.G.G.)
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Tomás Ruiz-Argüeso
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - José M. Palacios
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 115 bis, 28006 Madrid, Spain
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17
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Porter SS, Faber-Hammond JJ, Friesen ML. Co-invading symbiotic mutualists of Medicago polymorpha retain high ancestral diversity and contain diverse accessory genomes. FEMS Microbiol Ecol 2017; 94:4705886. [DOI: 10.1093/femsec/fix168] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/29/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
- Stephanie S Porter
- School of Biological Sciences, Washington State University, 14204 NE Salmon Creek Ave, Vancouver, WA 98686, USA
| | - Joshua J Faber-Hammond
- School of Biological Sciences, Washington State University, 14204 NE Salmon Creek Ave, Vancouver, WA 98686, USA
| | - Maren L Friesen
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
- Department of Plant Pathology, Washington State University, P.O. Box 646430 Pullman, WA 99164, USA
- Department of Crop and Soil Sciences, Washington State University, P.O. Box 646420 Pullman, WA 99164, USA
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18
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Osman WAM, van Berkum P, León-Barrios M, Velázquez E, Elia P, Tian R, Ardley J, Gollagher M, Seshadri R, Reddy TBK, Ivanova N, Woyke T, Pati A, Markowitz V, Baeshen MN, Baeshen NN, Kyrpides N, Reeve W. High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain. Stand Genomic Sci 2017; 12:58. [PMID: 28975015 PMCID: PMC5613336 DOI: 10.1186/s40793-017-0270-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 09/14/2017] [Indexed: 11/26/2022] Open
Abstract
10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 T, 10.1601/nm.1334 A 321T and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 T, based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata-nodulating 10.1601/nm.1328 strains, but ≤93% with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic recombination between strain Mlalz-1 and 10.1601/nm.1334 and the horizontal gene transfer of lpiA-acvB.
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Affiliation(s)
| | - Peter van Berkum
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Tenerife, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genetica and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - Patrick Elia
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Amrita Pati
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Mohamed N. Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | | | | | - Wayne Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
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Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
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20
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Reeve W, van Berkum P, Ardley J, Tian R, Gollagher M, Marinova D, Elia P, Reddy TBK, Pillay M, Varghese N, Seshadri R, Ivanova N, Woyke T, Baeshen MN, Baeshen NA, Kyrpides N. High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76 T, isolated from Glycine max (L.) Merr. Stand Genomic Sci 2017; 12:26. [PMID: 28270909 PMCID: PMC5336687 DOI: 10.1186/s40793-017-0238-2] [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: 10/14/2016] [Accepted: 02/21/2017] [Indexed: 11/10/2022] Open
Abstract
Bradyrhizobium elkanii USDA 76T (INSCD = ARAG00000000), the type strain for Bradyrhizobium elkanii, is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Glycine max (L. Merr) grown in the USA. Because of its significance as a microsymbiont of this economically important legume, B. elkanii USDA 76T was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria sequencing project. Here the symbiotic abilities of B. elkanii USDA 76T are described, together with its genome sequence information and annotation. The 9,484,767 bp high-quality draft genome is arranged in 2 scaffolds of 25 contigs, containing 9060 protein-coding genes and 91 RNA-only encoding genes. The B. elkanii USDA 76T genome contains a low GC content region with symbiotic nod and fix genes, indicating the presence of a symbiotic island integration. A comparison of five B. elkanii genomes that formed a clique revealed that 356 of the 9060 protein coding genes of USDA 76T were unique, including 22 genes of an intact resident prophage. A conserved set of 7556 genes were also identified for this species, including genes encoding a general secretion pathway as well as type II, III, IV and VI secretion system proteins. The type III secretion system has previously been characterized as a host determinant for Rj and/or rj soybean cultivars. Here we show that the USDA 76T genome contains genes encoding all the type III secretion system components, including a translocon complex protein NopX required for the introduction of effector proteins into host cells. While many bradyrhizobial strains are unable to nodulate the soybean cultivar Clark (rj1), USDA 76T was able to elicit nodules on Clark (rj1), although in reduced numbers, when plants were grown in Leonard jars containing sand or vermiculite. In these conditions, we postulate that the presence of NopX allows USDA 76T to introduce various effector molecules into this host to enable nodulation.
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Affiliation(s)
- Wayne Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | - Peter van Berkum
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | - Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Patrick Elia
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Manoj Pillay
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Mohamed N Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA USA.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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21
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Klonowska A, López-López A, Moulin L, Ardley J, Gollagher M, Marinova D, Tian R, Huntemann M, Reddy T, Varghese N, Woyke T, Markowitz V, Ivanova N, Seshadri R, Baeshen MN, Baeshen NA, Kyrpides N, Reeve W. High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia. Stand Genomic Sci 2017; 12:7. [PMID: 28116041 PMCID: PMC5240323 DOI: 10.1186/s40793-016-0212-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 11/26/2016] [Indexed: 11/12/2022] Open
Abstract
Rhizobium mesoamericanum STM6155 (INSCD = ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155 was isolated in 2009 from a nodule of the trap host M. pudica grown in nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project. Here we describe the symbiotic properties of R. mesoamericanum STM6155, together with its genome sequence information and annotation. The 6,927,906 bp high-quality draft genome is arranged into 147 scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved in these strains and the type strain of Rhizobium grahamii CCGE501T. Within the STM6155 genome, we have identified a chr chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate.
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Affiliation(s)
- Agnieszka Klonowska
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | - Aline López-López
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | | | - T.B.K. Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | | | - Mohamed N. Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Nabih A. Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA USA
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
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22
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Le Quéré A, Tak N, Gehlot HS, Lavire C, Meyer T, Chapulliot D, Rathi S, Sakrouhi I, Rocha G, Rohmer M, Severac D, Filali-Maltouf A, Munive JA. Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts. BMC Genomics 2017; 18:85. [PMID: 28088165 PMCID: PMC5237526 DOI: 10.1186/s12864-016-3447-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 12/20/2016] [Indexed: 02/06/2023] Open
Abstract
Background Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined. Results Draft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced. Genome based species delineation tools demonstrated that they belong to a new species of Ensifer. Comparison of its core genome with those of E. meliloti, E. medicae and E. fredii enabled the identification of a species conserved gene set. Predicted functions of associated proteins and pathway reconstruction revealed notably the presence of transport systems for octopine/nopaline and inositol phosphates. Phenotypic characterization of this new desert rhizobium species showed that it was capable to utilize malonate, to grow at 48 °C or under high pH while NaCl tolerance levels were comparable to other Ensifer species. Analysis of accessory genomes and plasmid profiling demonstrated the presence of large plasmids that varied in size from strain to strain. As symbiotic functions were found in the accessory genomes, the differences in symbiotic interactions between strains may be well related to the difference in plasmid content that could explain the different legumes with which they can develop the symbiosis. Conclusions The genomic analysis performed here confirms that the selected rhizobial strains isolated from desert regions in three continents belong to a new species. As until now only recovered from such harsh environment, we propose to name it Ensifer aridi. The presented genomic data offers a good basis to explore adaptations and functionalities that enable them to adapt to alkalinity, low water potential, salt and high temperature stresses. Finally, given the original phylogeographic distribution and the different hosts with which it can develop a beneficial symbiotic interaction, Ensifer aridi may provide new biotechnological opportunities for degraded land restoration initiatives in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3447-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antoine Le Quéré
- Laboratoire de Microbiologie et Biologie Moléculaire, Université Mohammed V, Av Ibn Batouta BP 1014, Rabat, Morocco. .,IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes UMR113, IRD/INRA/CIRAD/Montpellier SupAgro/Université de Montpellier, TA A82/J, Campus International de Baillarguet, 34398, Montpellier, Cedex 5, France.
| | - Nisha Tak
- BNF & Microbial Genomics Lab, Department of Botany, Jai Narain Vyas University, Jodhpur, 342001, India
| | - Hukam Singh Gehlot
- BNF & Microbial Genomics Lab, Department of Botany, Jai Narain Vyas University, Jodhpur, 342001, India
| | - Celine Lavire
- Université de Lyon, F69622, Lyon, France.,CNRS, UMR5557, Ecologie Microbienne and INRA, UMR1418, Université Lyon 1, Villeurbanne, France
| | - Thibault Meyer
- Université de Lyon, F69622, Lyon, France.,CNRS, UMR5557, Ecologie Microbienne and INRA, UMR1418, Université Lyon 1, Villeurbanne, France
| | - David Chapulliot
- Université de Lyon, F69622, Lyon, France.,CNRS, UMR5557, Ecologie Microbienne and INRA, UMR1418, Université Lyon 1, Villeurbanne, France
| | - Sonam Rathi
- BNF & Microbial Genomics Lab, Department of Botany, Jai Narain Vyas University, Jodhpur, 342001, India
| | - Ilham Sakrouhi
- Laboratoire de Microbiologie et Biologie Moléculaire, Université Mohammed V, Av Ibn Batouta BP 1014, Rabat, Morocco
| | - Guadalupe Rocha
- Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. IC10, Ciudad Universitaria, Col. San Manuel, CP 72570, Puebla, Mexico
| | - Marine Rohmer
- Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, Montpellier, Cedex, 34 094, France
| | - Dany Severac
- Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, Montpellier, Cedex, 34 094, France
| | - Abdelkarim Filali-Maltouf
- Laboratoire de Microbiologie et Biologie Moléculaire, Université Mohammed V, Av Ibn Batouta BP 1014, Rabat, Morocco
| | - Jose-Antonio Munive
- Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. IC10, Ciudad Universitaria, Col. San Manuel, CP 72570, Puebla, Mexico
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23
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Tian R, Heiden S, Osman WAM, Ardley JK, James EK, Gollagher MM, Tiwari R, Seshadri R, Kyrpides NC, Reeve WG. Evolution of a multi-step phosphorelay signal transduction system in Ensifer: recruitment of the sigma factor RpoN and a novel enhancer-binding protein triggers acid-activated gene expression. Mol Microbiol 2016; 103:829-844. [PMID: 27935141 DOI: 10.1111/mmi.13592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2016] [Indexed: 11/29/2022]
Abstract
Most Ensifer strains are comparatively acid sensitive, compromising their persistence in low pH soils. In the acid-tolerant strain Ensifer medicae WSM419, the acid-activated expression of lpiA is essential for enhancing survival in lethal acidic conditions. Here we characterise a multi-step phosphorelay signal transduction pathway consisting of TcsA, TcrA, FsrR, RpoN and its cognate enhancer-binding protein EbpA, which is required for the induction of lpiA and the downstream acvB gene. The fsrR, tcrA, tcsA and rpoN genes were constitutively expressed, whereas lpiA and acvB were strongly acid-induced. RACE mapping revealed that lpiA/acvB were co-transcribed as an operon from an RpoN promoter. In most Ensifer species, lpiA/acvB is located on the chromosome and the sequence upstream of lpiA lacks an RpoN-binding site. Nearly all Ensifer meliloti strains completely lack ebpA, tcrA, tcsA and fsrR regulatory loci. In contrast, E. medicae strains have lpiA/acvB and ebpA/tcrA/tcsA/fsrR co-located on the pSymA megaplasmid, with lpiA/acvB expression coupled to an RpoN promoter. Here we provide a model for the expression of lpiA/acvB in E. medicae. This unique acid-activated regulatory system provides insights into an evolutionary process which may assist the adaptation of E. medicae to acidic environmental niches.
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Affiliation(s)
- Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Stephan Heiden
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Wan A M Osman
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Julie K Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Margaret M Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - Ravi Tiwari
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | | | | | - Wayne G Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
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24
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Torres Tejerizo G, Rogel MA, Ormeño-Orrillo E, Althabegoiti MJ, Nilsson JF, Niehaus K, Schlüter A, Pühler A, Del Papa MF, Lagares A, Martínez-Romero E, Pistorio M. Rhizobium favelukesii sp. nov., isolated from the root nodules of alfalfa (Medicago sativa L). Int J Syst Evol Microbiol 2016; 66:4451-4457. [DOI: 10.1099/ijsem.0.001373] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gonzalo Torres Tejerizo
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
- CeBiTec, Bielefeld Universität, Bielefeld, Germany
| | - Marco Antonio Rogel
- Centro de Ciencias Genómicas Av. Universidad 1001, Col. Chamilpa. 62210 Cuernavaca, Universidad Nacional Autónoma de México, Morelos, Mexico
| | - Ernesto Ormeño-Orrillo
- Centro de Ciencias Genómicas Av. Universidad 1001, Col. Chamilpa. 62210 Cuernavaca, Universidad Nacional Autónoma de México, Morelos, Mexico
| | - María Julia Althabegoiti
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Juliet Fernanda Nilsson
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | | | | | | | - María Florencia Del Papa
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Antonio Lagares
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas Av. Universidad 1001, Col. Chamilpa. 62210 Cuernavaca, Universidad Nacional Autónoma de México, Morelos, Mexico
| | - Mariano Pistorio
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
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Assembly and transfer of tripartite integrative and conjugative genetic elements. Proc Natl Acad Sci U S A 2016; 113:12268-12273. [PMID: 27733511 DOI: 10.1073/pnas.1613358113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Integrative and conjugative elements (ICEs) are ubiquitous mobile genetic elements present as "genomic islands" within bacterial chromosomes. Symbiosis islands are ICEs that convert nonsymbiotic mesorhizobia into symbionts of legumes. Here we report the discovery of symbiosis ICEs that exist as three separate chromosomal regions when integrated in their hosts, but through recombination assemble as a single circular ICE for conjugative transfer. Whole-genome comparisons revealed exconjugants derived from nonsymbiotic mesorhizobia received three separate chromosomal regions from the donor Mesorhizobium ciceri WSM1271. The three regions were each bordered by two nonhomologous integrase attachment (att) sites, which together comprised three homologous pairs of attL and attR sites. Sequential recombination between each attL and attR pair produced corresponding attP and attB sites and joined the three fragments to produce a single circular ICE, ICEMcSym1271 A plasmid carrying the three attP sites was used to recreate the process of tripartite ICE integration and to confirm the role of integrase genes intS, intM, and intG in this process. Nine additional tripartite ICEs were identified in diverse mesorhizobia and transfer was demonstrated for three of them. The transfer of tripartite ICEs to nonsymbiotic mesorhizobia explains the evolution of competitive but suboptimal N2-fixing strains found in Western Australian soils. The unheralded existence of tripartite ICEs raises the possibility that multipartite elements reside in other organisms, but have been overlooked because of their unusual biology. These discoveries reveal mechanisms by which integrases dramatically manipulate bacterial genomes to allow cotransfer of disparate chromosomal regions.
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De Meyer SE, Briscoe L, Martínez-Hidalgo P, Agapakis CM, de-Los Santos PE, Seshadri R, Reeve W, Weinstock G, O'Hara G, Howieson JG, Hirsch AM. Symbiotic Burkholderia Species Show Diverse Arrangements of nif/fix and nod Genes and Lack Typical High-Affinity Cytochrome cbb3 Oxidase Genes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:609-619. [PMID: 27269511 DOI: 10.1094/mpmi-05-16-0091-r] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Genome analysis of fourteen mimosoid and four papilionoid beta-rhizobia together with fourteen reference alpha-rhizobia for both nodulation (nod) and nitrogen-fixing (nif/fix) genes has shown phylogenetic congruence between 16S rRNA/MLSA (combined 16S rRNA gene sequencing and multilocus sequence analysis) and nif/fix genes, indicating a free-living diazotrophic ancestry of the beta-rhizobia. However, deeper genomic analysis revealed a complex symbiosis acquisition history in the beta-rhizobia that clearly separates the mimosoid and papilionoid nodulating groups. Mimosoid-nodulating beta-rhizobia have nod genes tightly clustered in the nodBCIJHASU operon, whereas papilionoid-nodulating Burkholderia have nodUSDABC and nodIJ genes, although their arrangement is not canonical because the nod genes are subdivided by the insertion of nif and other genes. Furthermore, the papilionoid Burkholderia spp. contain duplications of several nod and nif genes. The Burkholderia nifHDKEN and fixABC genes are very closely related to those found in free-living diazotrophs. In contrast, nifA is highly divergent between both groups, but the papilionoid species nifA is more similar to alpha-rhizobia nifA than to other groups. Surprisingly, for all Burkholderia, the fixNOQP and fixGHIS genes required for cbb3 cytochrome oxidase production and assembly are missing. In contrast, symbiotic Cupriavidus strains have fixNOQPGHIS genes, revealing a divergence in the evolution of two distinct electron transport chains required for nitrogen fixation within the beta-rhizobia.
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Affiliation(s)
- Sofie E De Meyer
- 1 Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Leah Briscoe
- 2 Dept. of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA, U.S.A
| | | | - Christina M Agapakis
- 2 Dept. of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA, U.S.A
| | - Paulina Estrada de-Los Santos
- 3 Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas. Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, México
| | | | - Wayne Reeve
- 1 Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - George Weinstock
- 5 The Jackson Laboratory for Genomic Medicine, Farmington, CT, U.S.A; and
| | - Graham O'Hara
- 1 Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John G Howieson
- 1 Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ann M Hirsch
- 2 Dept. of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA, U.S.A
- 6 The Molecular Biology Institute, UCLA, Los Angeles, CA, U.S.A
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Gehlot HS, Ardley J, Tak N, Tian R, Poonar N, Meghwal RR, Rathi S, Tiwari R, Adnawani W, Seshadri R, Reddy TBK, Pati A, Woyke T, Pillay M, Markowitz V, Baeshen MN, Al-Hejin AM, Ivanova N, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India. Stand Genomic Sci 2016; 11:43. [PMID: 27340511 PMCID: PMC4918122 DOI: 10.1186/s40793-016-0157-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 05/18/2016] [Indexed: 11/17/2022] Open
Abstract
Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume P. cineraria (L.) Druce (Khejri), which is a keystone species that grows in arid and semi-arid regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as species of mimosoid trees and shrubs. Here we describe the features of Ensifer sp. PC2, together with genome sequence information and its annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into 171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.
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Affiliation(s)
- Hukam Singh Gehlot
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Julie Ardley
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Nisha Tak
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Rui Tian
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Neetu Poonar
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Raju R Meghwal
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Sonam Rathi
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Ravi Tiwari
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Wan Adnawani
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Rekha Seshadri
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Manoj Pillay
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California USA
| | - Mohammed N Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M Al-Hejin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California USA ; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
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28
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Ardley J, Tian R, O'Hara G, Seshadri R, Reddy TBK, Pati A, Woyke T, Markowitz V, Ivanova N, Kyrpides N, Howieson J, Reeve W. High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil. Stand Genomic Sci 2015; 10:126. [PMID: 26664655 PMCID: PMC4674904 DOI: 10.1186/s40793-015-0119-5] [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: 09/04/2015] [Accepted: 11/03/2015] [Indexed: 11/12/2022] Open
Abstract
Ensifer medicae WSM244 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago species. WSM244 was isolated in 1979 from a nodule recovered from the roots of the annual Medicago polymorpha L. growing in alkaline soil (pH 8.0) in Tel Afer, Iraq. WSM244 is the only acid-sensitive E. medicae strain that has been sequenced to date. It is effective at fixing nitrogen with M. polymorpha L., as well as with more alkaline-adapted Medicago spp. such as M. littoralis Loisel., M. scutellata (L.) Mill., M. tornata (L.) Mill. and M. truncatula Gaertn. This strain is also effective with the perennial M. sativa L. Here we describe the features of E. medicae WSM244, together with genome sequence information and its annotation. The 6,650,282 bp high-quality permanent draft genome is arranged into 91 scaffolds of 91 contigs containing 6,427 protein-coding genes and 68 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.
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Affiliation(s)
- Julie Ardley
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | - Graham O'Hara
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | | | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA USA ; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
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29
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De Meyer SE, Tian R, Seshadri R, Ivanova N, Pati A, Markowitz V, Woyke T, Yates R, Howieson J, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556T. Stand Genomic Sci 2015; 10:64. [PMID: 26388968 PMCID: PMC4575442 DOI: 10.1186/s40793-015-0048-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 07/22/2015] [Indexed: 11/24/2022] Open
Abstract
Burkholderia dilworthii strain WSM3556T is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected near Grotto Bay Nature Reserve, in the Western Cape of South Africa, in October 2004. This plant persists in infertile and deep sandy soils with acidic pH, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. WSM3556T thus represents a potential inoculant quality strain for L. ambigua for which we describe the general features, together with genome sequence and annotation. The 7,679,067 bp high-quality permanent draft genome is arranged in 140 scaffolds of 141 contigs, contains 7,059 protein-coding genes and 64 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.
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30
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Discovery of Novel Plant Interaction Determinants from the Genomes of 163 Root Nodule Bacteria. Sci Rep 2015; 5:16825. [PMID: 26584898 PMCID: PMC4653623 DOI: 10.1038/srep16825] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/20/2015] [Indexed: 12/11/2022] Open
Abstract
Root nodule bacteria (RNB) or "rhizobia" are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. In this study, we sequenced the genomes of 110 RNB from diverse hosts and biogeographical regions, and undertook a global exploration of all available RNB genera with the aim of identifying novel genetic determinants of symbiotic association and plant growth promotion. Specifically, we performed a subtractive comparative analysis with non-RNB genomes, employed relevant transcriptomic data, and leveraged phylogenetic distribution patterns and sequence signatures based on known precepts of symbiotic- and host-microbe interactions. A total of 184 protein families were delineated, including known factors for nodulation and nitrogen fixation, and candidates with previously unexplored functions, for which a role in host-interaction, -regulation, biocontrol, and more, could be posited. These analyses expand our knowledge of the RNB purview and provide novel targets for strain improvement in the ultimate quest to enhance plant productivity and agricultural sustainability.
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31
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Eshraghi L, De Meyer SE, Tian R, Seshadri R, Ivanova N, Pati A, Markowitz V, Woyke T, Kyrpides NC, Tiwari R, Yates R, Howieson J, Reeve W. High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia. Stand Genomic Sci 2015; 10:87. [PMID: 26512312 PMCID: PMC4623297 DOI: 10.1186/s40793-015-0073-2] [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] [Received: 12/09/2014] [Accepted: 10/08/2015] [Indexed: 11/10/2022] Open
Abstract
Bradyrhizobium sp. strain WSM1743 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of an Indigofera sp. WSM1743 was isolated from a nodule recovered from the roots of an Indigofera sp. growing 20 km north of Carnarvon in Australia. It is slow growing, tolerates up to 1 % NaCl and is capable of growth at 37 °C. Here we describe the features of Bradyrhizobium sp. strain WSM1743, together with genome sequence information and its annotation. The 8,341,956 bp high-quality permanent draft genome is arranged into 163 scaffolds and 167 contigs, contains 7908 protein-coding genes and 75 RNA-only encoding genes and was sequenced as part of the Root Nodule Bacteria chapter of the Genomic Encyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Leila Eshraghi
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia ; Centre for Phytophthora Science and Management (CPSM), Murdoch University, Murdoch, Western Australia
| | - Sofie E De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | | | | | - Amrita Pati
- DOE Join Genome Institute, Walnut Creek, CA USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Tanja Woyke
- DOE Join Genome Institute, Walnut Creek, CA USA
| | - Nikos C Kyrpides
- DOE Join Genome Institute, Walnut Creek, CA USA ; Department of Biological Sciences, King Abdulaziz, Jeddah, Saudia Arabia
| | - Ravi Tiwari
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | - Ron Yates
- Department of Agriculture and Food, South Perth, Western Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
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32
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De Meyer SE, Parker M, Van Berkum P, Tian R, Seshadri R, Reddy TBK, Markowitz V, Ivanova N, Pati A, Woyke T, Kyrpides N, Howieson J, Reeve W. High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6. Stand Genomic Sci 2015; 10:80. [PMID: 26478786 PMCID: PMC4609095 DOI: 10.1186/s40793-015-0074-1] [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] [Received: 11/26/2014] [Accepted: 10/08/2015] [Indexed: 12/20/2022] Open
Abstract
Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata is the only legume described so far to exclusively associates with Cupriavidus symbionts. Moreover, strain AMP6 represents an early-diverging lineage within the symbiotic Cupriavidus group and has the capacity to develop an effective nitrogen-fixing symbiosis with three other species of Mimosa. Therefore, the genome of Cupriavidus sp. strain AMP6 enables comparative analyses of symbiotic trait evolution in this genus and here we describe the general features, together with sequence and annotation. The 7,579,563 bp high-quality permanent draft genome is arranged in 260 scaffolds of 262 contigs, contains 7,033 protein-coding genes and 97 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.
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Affiliation(s)
- Sofie E De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | - Matthew Parker
- Binghamton University, State University of New York, New York, USA
| | - Peter Van Berkum
- Soybean Genomics and improvement laboratory Bldg 006, BARC-West USDA ARS 10300 Baltimore Blvd, Beltsville, MD 20705 USA
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | | | - T B K 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, Western Australia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
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33
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De Meyer SE, Tian R, Seshadri R, Reddy T, Markowitz V, Ivanova N, Pati A, Woyke T, Kyrpides N, Yates R, Howieson J, Reeve W. High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176. Stand Genomic Sci 2015; 10:79. [PMID: 26478785 PMCID: PMC4609093 DOI: 10.1186/s40793-015-0072-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 10/08/2015] [Indexed: 12/20/2022] Open
Abstract
Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected in Nieuwoudtville, Western Cape of South Africa, in October 2007. This plant persists in infertile, acidic and deep sandy soils, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. Here we describe the features of Burkholderia sp. strain WSM4176, which represents a potential inoculant quality strain for L. ambigua, together with sequence and annotation. The 9,065,247 bp high-quality-draft genome is arranged in 13 scaffolds of 65 contigs, contains 8369 protein-coding genes and 128 RNA-only encoding genes, and is part of the GEBA-RNB project proposal (Project ID 882).
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Affiliation(s)
- Sofie E De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA Australia
| | | | - 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
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ron Yates
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA Australia ; Department of Agriculture and Food, Western Australia, Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA Australia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA Australia
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Tian R, Parker M, Seshadri R, Reddy T, Markowitz V, Ivanova N, Pati A, Woyke T, Baeshen M, Baeshen N, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of Bradyrhizobium sp. Ai1a-2; a microsymbiont of Andira inermis discovered in Costa Rica. Stand Genomic Sci 2015; 10:33. [PMID: 26380037 PMCID: PMC4571121 DOI: 10.1186/s40793-015-0007-z] [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] [Received: 02/13/2015] [Accepted: 04/16/2015] [Indexed: 11/30/2022] Open
Abstract
Bradyrhizobium sp. Ai1a-2 is is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen fixing root nodule of Andira inermis collected from Tres Piedras in Costa Rica. In this report we describe, for the first time, the genome sequence information and annotation of this legume microsymbiont. The 9,029,266 bp genome has a GC content of 62.56% with 247 contigs arranged into 246 scaffolds. The assembled genome contains 8,482 protein-coding genes and 102 RNA-only encoding genes. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.
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Affiliation(s)
- Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | - Matthew Parker
- Binghamton University, State University of New York, New York, USA
| | - Rekha Seshadri
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Tbk Reddy
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California USA
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Mohammed Baeshen
- Center of Nanotechnology, King Abdulaziz University, Jeddah, Saudi Arabia ; Department of Biological Sciences, Faculty of Science, Jeddah University, Jeddah, Saudi Arabia
| | - Nabih Baeshen
- Center of Nanotechnology, King Abdulaziz University, Jeddah, Saudi Arabia ; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California USA ; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
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35
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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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36
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De Meyer SE, Fabiano E, Tian R, Van Berkum P, Seshadri R, Reddy T, Markowitz V, Ivanova NN, Pati A, Woyke T, Howieson J, Kyrpides NC, Reeve W. High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512. Stand Genomic Sci 2015. [PMID: 26203327 PMCID: PMC4511410 DOI: 10.1186/1944-3277-10-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cupriavidus sp. strain UYPR2.512 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida grown in soils from a native forest of Uruguay. Here we describe the features of Cupriavidus sp. strain UYPR2.512, together with sequence and annotation. The 7,858,949 bp high-quality permanent draft genome is arranged in 365 scaffolds of 369 contigs, contains 7,411 protein-coding genes and 76 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.
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Affiliation(s)
- Sofie E De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | - Elena Fabiano
- Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | - Peter Van Berkum
- Soybean Genomics and improvement laboratory Bldg 006, BARC-West USDA ARS 10300 Baltimore Blvd, Beltsville, MD 20705, 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, Western Australia
| | - Nikos C 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, Western Australia
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37
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Yates R, Howieson J, De Meyer SE, Tian R, Seshadri R, Pati A, Woyke T, Markowitz V, Ivanova N, Kyrpides N, Loi A, Nutt B, Garau G, Sulas L, Reeve W. High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy. Stand Genomic Sci 2015; 10:44. [PMID: 26380632 PMCID: PMC4572446 DOI: 10.1186/s40793-015-0020-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/19/2015] [Indexed: 11/22/2022] Open
Abstract
Rhizobium sullae strain WSM1592 is an aerobic, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N2) fixing root nodule formed on the short-lived perennial legume Hedysarum coronarium (also known as Sulla coronaria or Sulla). WSM1592 was isolated from a nodule recovered from H. coronarium roots located in Ottava, bordering Sassari, Sardinia in 1995. WSM1592 is highly effective at fixing nitrogen with H. coronarium, and is currently the commercial Sulla inoculant strain in Australia. Here we describe the features of R. sullae strain WSM1592, together with genome sequence information and its annotation. The 7,530,820 bp high-quality permanent draft genome is arranged into 118 scaffolds of 118 contigs containing 7.453 protein-coding genes and 73 RNA-only encoding genes. This rhizobial genome is sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
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Affiliation(s)
- Ron Yates
- Department of Agriculture and Food, Western Australia, Australia ; Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Sofie E De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia Australia
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut, Creek, CA USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut, Creek, CA USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut, Creek, CA USA ; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Angelo Loi
- Department of Agriculture and Food, Western Australia, Australia
| | - Brad Nutt
- Department of Agriculture and Food, Western Australia, Australia
| | - Giovanni Garau
- Department of Agriculture, University of Sassari, Sardinia, Italy
| | - Leonardo Sulas
- Institute for the Animal Production System in the Mediterranean Environment (ISPAAM), National Research Council (CNR), Sassari, Italy
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia Australia
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38
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Mazur A, De Meyer SE, Tian R, Wielbo J, Zebracki K, Seshadri R, Reddy TBK, Markowitz V, Ivanova NN, Pati A, Woyke T, Kyrpides NC, Reeve W. High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland. Stand Genomic Sci 2015; 10:36. [PMID: 26221417 PMCID: PMC4517663 DOI: 10.1186/s40793-015-0029-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/05/2015] [Indexed: 11/20/2022] Open
Abstract
Rhizobium leguminosarum bv. viciae GB30 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Pisum sativum. GB30 was isolated in Poland from a nodule recovered from the roots of Pisum sativum growing at Janow. GB30 is also an effective microsymbiont of the annual forage legumes vetch and pea. Here we describe the features of R. leguminosarum bv. viciae strain GB30, together with sequence and annotation. The 7,468,464 bp high-quality permanent draft genome is arranged in 78 scaffolds of 78 contigs containing 7,227 protein-coding genes and 75 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.
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Affiliation(s)
- Andrzej Mazur
- />Department of Genetics and Microbiology, Maria Curie Sklodowska University, Lublin, Poland
| | - Sofie E. De Meyer
- />Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | - Rui Tian
- />Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | - Jerzy Wielbo
- />Department of Genetics and Microbiology, Maria Curie Sklodowska University, Lublin, Poland
| | - Kamil Zebracki
- />Department of Genetics and Microbiology, Maria Curie Sklodowska University, Lublin, Poland
| | - Rekha Seshadri
- />DOE Joint Genome Institute, Walnut Creek, California USA
| | - TBK Reddy
- />DOE Joint Genome Institute, Walnut Creek, California USA
| | - Victor Markowitz
- />Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California USA
| | | | - Amrita Pati
- />DOE Joint Genome Institute, Walnut Creek, California USA
| | - Tanja Woyke
- />DOE Joint Genome Institute, Walnut Creek, California USA
| | - Nikos C. Kyrpides
- />DOE Joint Genome Institute, Walnut Creek, California USA
- />Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- />Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
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39
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Mhamdi R, Ardley J, Tian R, Seshadri R, Reddy T, Pati A, Woyke T, Markowitz V, Ivanova N, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris. Stand Genomic Sci 2015; 10:34. [PMID: 26380038 PMCID: PMC4571125 DOI: 10.1186/s40793-015-0005-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/15/2015] [Indexed: 11/10/2022] Open
Abstract
Ensifer meliloti 4H41 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of common bean (Phaseolus vulgaris). Strain 4H41 was isolated in 2002 from root nodules of P. vulgaris grown in South Tunisia from the oasis of Rjim-Maatoug. Strain 4H41 is salt- and drought-tolerant and highly effective at fixing nitrogen with P. vulgaris. Here we describe the features of E. meliloti 4H41, together with genome sequence information and its annotation. The 6,795,637 bp high-quality permanent draft genome is arranged into 47 scaffolds of 47 contigs containing 6,350 protein-coding genes and 72 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.
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Affiliation(s)
- Ridha Mhamdi
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cedria, BP 901, Hammam-Lif, 2050 Tunisia
| | - Julie Ardley
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA Australia
| | | | - T.B.K. Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA USA
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA Australia
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40
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Tian R, Parker M, Seshadri R, Reddy TBK, Markowitz V, Ivanova N, Pati A, Woyke T, Baeshen MN, Baeshen NA, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of Bradyrhizobium sp. Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of Panama. Stand Genomic Sci 2015; 10:27. [PMID: 26203338 PMCID: PMC4511254 DOI: 10.1186/s40793-015-0006-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/16/2015] [Indexed: 11/28/2022] Open
Abstract
Bradyrhizobiumsp. Tv2a.2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Tachigali versicolor collected in Barro Colorado Island of Panama. Here we describe the features of Bradyrhizobiumsp. Tv2a.2, together with high-quality permanent draft genome sequence information and annotation. The 8,496,279 bp high-quality draft genome is arranged in 87 scaffolds of 87 contigs, contains 8,109 protein-coding genes and 72 RNA-only encoding genes. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
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Affiliation(s)
- Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | - Matthew Parker
- Binghamton University, State University of New York, New York, USA
| | - Rekha Seshadri
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - TBK Reddy
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Mohammed N Baeshen
- Center of Nanotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, Jeddah University, Jeddah, Saudi Arabia
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
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41
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Tian R, Parker M, Seshadri R, Reddy TBK, Markowitz V, Ivanova N, Pati A, Woyke T, Baeshen MN, Baeshen NA, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of Bradyrhizobium sp. Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York. Stand Genomic Sci 2015; 10:24. [PMID: 26203336 PMCID: PMC4511635 DOI: 10.1186/s40793-015-0008-y] [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] [Received: 02/13/2015] [Accepted: 04/16/2015] [Indexed: 11/10/2022] Open
Abstract
Bradyrhizobium sp. Th.b2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Amphicarpaea bracteata collected in Johnson City, New York. Here we describe the features of Bradyrhizobium sp. Th.b2, together with high-quality permanent draft genome sequence information and annotation. The 10,118,060 high-quality draft genome is arranged in 266 scaffolds of 274 contigs, contains 9,809 protein-coding genes and 108 RNA-only encoding genes. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
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Affiliation(s)
- Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
| | - Matthew Parker
- Binghamton University, State University of New York, New York, USA
| | - Rekha Seshadri
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - TBK Reddy
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Mohammed N Baeshen
- Center of Nanotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, Jeddah University, Jeddah, Saudi Arabia
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Nanotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Australia
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