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van Lill M, Venter SN, Muema EK, Palmer M, Chan WY, Beukes CW, Steenkamp ET. SeqCode facilitates naming of South African rhizobia left in limbo. Syst Appl Microbiol 2024; 47:126504. [PMID: 38593622 DOI: 10.1016/j.syapm.2024.126504] [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: 01/29/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa's current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.
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Affiliation(s)
- Melandré van Lill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Esther K Muema
- Department of Soil Science, Faculty of AgriSciences, Stellenbosch University, South Africa
| | - Marike Palmer
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | | | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
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2
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Li Y, Guo T, Sun L, Wang ET, Young JPW, Tian CF. Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species. BMC Genomics 2024; 25:419. [PMID: 38684951 PMCID: PMC11057113 DOI: 10.1186/s12864-024-10333-y] [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: 01/31/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUD The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated. RESULTS The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40-80.91% and 83.98-86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus. CONCLUSION The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.
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Affiliation(s)
- Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China.
| | - Tingyan Guo
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - Liqin Sun
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, 11340, México
| | - J Peter W Young
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Chang-Fu Tian
- State Key Laboratory of Plant Environmental Resilience, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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3
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Kim I, Chhetri G, So Y, Park S, Jung Y, Woo H, Seo T. Mesorhizobium liriopis sp. nov., isolated from the fermented fruit of Liriope platyphylla a medicinal plant. Int J Syst Evol Microbiol 2023; 73. [PMID: 37801075 DOI: 10.1099/ijsem.0.006086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023] Open
Abstract
A facultative anaerobic and Gram-negative strain, designated RP14T, was isolated from the fruit of Liriope platyphylla fermented for 60 days at 25°C. Strain RP14T showed 98.0 % 16S rRNA similarity to Mesorhizobium huakuii IFO 15243T, but in the phylogenetic tree, Mesorhizobium terrae NIBRBAC000500504T was its closest neighbour. The average nucleotide identity and digital DNA-DNA hybridization values between strain RP14T and 15 genomes of type strains of Mesorhizobium, were 73.8-74.4% and 16.4-20.2 %, respectively, which were lower than the recommended thresholds for species delineation. The strain grew at 25-32°C (optimum, 28°C), at pH 7.0-12.0 (optimum, pH 9.0) and with 0-2% NaCl (optimum, 0 %; w/v). Cells of strain RP14T were catalase-positive, oxidase-negative, rod-shaped and formed yellow-coloured colonies. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major fatty acid were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The DNA G+C content was 62.8 mol%. Based on polyphasic evidence, we propose Mesorhizobium liriopis sp. nov as a novel species within the genus Mesorhizobium. The type strain is RP14T (=KACC 22720T=TBRC 16341T).
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Affiliation(s)
- Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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4
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Colombi E, Hill Y, Lines R, Sullivan JT, Kohlmeier MG, Christophersen CT, Ronson CW, Terpolilli JJ, Ramsay JP. Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer. Microb Genom 2023; 9:mgen000918. [PMID: 36748564 PMCID: PMC9973854 DOI: 10.1099/mgen.0.000918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mesorhizobia are soil bacteria that establish nitrogen-fixing symbioses with various legumes. Novel symbiotic mesorhizobia frequently evolve following horizontal transfer of symbiosis-gene-carrying integrative and conjugative elements (ICESyms) to indigenous mesorhizobia in soils. Evolved symbionts exhibit a wide range in symbiotic effectiveness, with some fixing nitrogen poorly or not at all. Little is known about the genetic diversity and symbiotic potential of indigenous soil mesorhizobia prior to ICESym acquisition. Here we sequenced genomes of 144 Mesorhizobium spp. strains cultured directly from cultivated and uncultivated Australian soils. Of these, 126 lacked symbiosis genes. The only isolated symbiotic strains were either exotic strains used previously as legume inoculants, or indigenous mesorhizobia that had acquired exotic ICESyms. No native symbiotic strains were identified. Indigenous nonsymbiotic strains formed 22 genospecies with phylogenomic diversity overlapping the diversity of internationally isolated symbiotic Mesorhizobium spp. The genomes of indigenous mesorhizobia exhibited no evidence of prior involvement in nitrogen-fixing symbiosis, yet their core genomes were similar to symbiotic strains and they generally lacked genes for synthesis of biotin, nicotinate and thiamine. Genomes of nonsymbiotic mesorhizobia harboured similar mobile elements to those of symbiotic mesorhizobia, including ICESym-like elements carrying aforementioned vitamin-synthesis genes but lacking symbiosis genes. Diverse indigenous isolates receiving ICESyms through horizontal gene transfer formed effective symbioses with Lotus and Biserrula legumes, indicating most nonsymbiotic mesorhizobia have an innate capacity for nitrogen-fixing symbiosis following ICESym acquisition. Non-fixing ICESym-harbouring strains were isolated sporadically within species alongside effective symbionts, indicating chromosomal lineage does not predict symbiotic potential. Our observations suggest previously observed genomic diversity amongst symbiotic Mesorhizobium spp. represents a fraction of the extant diversity of nonsymbiotic strains. The overlapping phylogeny of symbiotic and nonsymbiotic clades suggests major clades of Mesorhizobium diverged prior to introduction of symbiosis genes and therefore chromosomal genes involved in symbiosis have evolved largely independent of nitrogen-fixing symbiosis.
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Affiliation(s)
- Elena Colombi
- Curtin Medical School, Curtin University, Bentley, Western Australia 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia.,Present address: School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Yvette Hill
- Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, 90 South St, Murdoch, Western Australia 6150, Australia
| | - Rose Lines
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Western Australia 6102, Australia
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - MacLean G Kohlmeier
- Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, 90 South St, Murdoch, Western Australia 6150, Australia
| | - Claus T Christophersen
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Western Australia 6102, Australia.,School of Medical & Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia.,Centre for Integrative Metabolomics and Computational Biology, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jason J Terpolilli
- Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, 90 South St, Murdoch, Western Australia 6150, Australia
| | - Joshua P Ramsay
- Curtin Medical School, Curtin University, Bentley, Western Australia 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
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5
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Aquibium microcysteis gen. nov., sp. nov., isolated from a Microcystis aeruginosa culture and reclassification of Mesorhizobium carbonis as Aquibium carbonis comb. nov. and Mesorhizobium oceanicum as Aquibium oceanicum comb. nov. Int J Syst Evol Microbiol 2022. [DOI: 10.1099/ijsem.0.005230 10.1099/ijsem.0.005230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A novel bacterial strain, NIBR3T, was isolated from a
Microcystis aeruginosa
culture. Strain NIBR3T was characterized as Gram-negative, rod-shaped, catalase- and oxidase-positive, and aerobic. The 16S rRNA gene sequence analysis showed that strain NIBR3T was most closely related to
Mesorhizobium carbonis
B2.3T (=KCTC 52461),
Mesorhizobium oceanicum
B7T (=KCTC 42783) and
Mesorhizobium qingshengii
CCBAU 33460T (=HAMBI 3277), at 98.7, 97.2 and 97.2% similarity, respectively. Our phylogenetic analyses revealed that three strains [strain NIBR3T with the previously reported two
Mesorhizobium
species (
M. carbonis
B2.3T and
M. oceanicum
B7T)] formed a distinct cluster from other
Mesorhizobium
type strains. The average nucleotide identity of strain NIBR3T relative to
M. carbonis
B2.3T
, M. oceanicum B7T, and
M. qingshengii
CCBAU 33460T was found to be 84.3, 79.4 and 75.8 %, with average amino-acid identities of 85.1, 74.8 and 64.3 %, and digital DNA–DNA hybridization values of 27.6, 22.6 and 20.7 %, respectively. The genome size and genomic DNA G+C content of NIBR3T were 6.1 Mbp and 67.9 mol%, respectively. Growth of strain NIBR3T was observed at 23–45 °C (optimum, 33 °C), at pH 6–11 (optimum, 8) and in the presence of 0–4 % (w/v) NaCl (optimum, 0 %). The major polar lipids in this novel strain were phosphatidylethanolamine, phosphatidylcholine and phosphatidylmethylethanolamine. The predominant respiratory quinone was Q-10. Summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) was the most abundant cellular fatty acid in strain NIBR3T. Based on genotypic characteristics using our genomic data, strain NIBR3T was identified as a member of new genus, Aquibium gen. nov., with the two aforementioned stains. The type strain f the novel species, Aquibium microcysteis sp. nov., is NIBR3T (=KACC 22092T=HAMBI 3738T). We also reclassified
Mesorhizobium carbonis
and
M. oceanicum
as Aquibium carbonis comb. nov. and A. oceanicum comb. nov., respectively.
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6
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Kim M, Kim W, Park W. Aquibium microcysteis gen. nov., sp. nov., isolated from a Microcystis aeruginosa culture and reclassification of Mesorhizobium carbonis as Aquibium carbonis comb. nov. and Mesorhizobium oceanicum as Aquibium oceanicum comb. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005230] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, NIBR3T, was isolated from a
Microcystis aeruginosa
culture. Strain NIBR3T was characterized as Gram-negative, rod-shaped, catalase- and oxidase-positive, and aerobic. The 16S rRNA gene sequence analysis showed that strain NIBR3T was most closely related to
Mesorhizobium carbonis
B2.3T (=KCTC 52461),
Mesorhizobium oceanicum
B7T (=KCTC 42783) and
Mesorhizobium qingshengii
CCBAU 33460T (=HAMBI 3277), at 98.7, 97.2 and 97.2% similarity, respectively. Our phylogenetic analyses revealed that three strains [strain NIBR3T with the previously reported two
Mesorhizobium
species (
M. carbonis
B2.3T and
M. oceanicum
B7T)] formed a distinct cluster from other
Mesorhizobium
type strains. The average nucleotide identity of strain NIBR3T relative to
M. carbonis
B2.3T
, M. oceanicum B7T, and
M. qingshengii
CCBAU 33460T was found to be 84.3, 79.4 and 75.8 %, with average amino-acid identities of 85.1, 74.8 and 64.3 %, and digital DNA–DNA hybridization values of 27.6, 22.6 and 20.7 %, respectively. The genome size and genomic DNA G+C content of NIBR3T were 6.1 Mbp and 67.9 mol%, respectively. Growth of strain NIBR3T was observed at 23–45 °C (optimum, 33 °C), at pH 6–11 (optimum, 8) and in the presence of 0–4 % (w/v) NaCl (optimum, 0 %). The major polar lipids in this novel strain were phosphatidylethanolamine, phosphatidylcholine and phosphatidylmethylethanolamine. The predominant respiratory quinone was Q-10. Summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) was the most abundant cellular fatty acid in strain NIBR3T. Based on genotypic characteristics using our genomic data, strain NIBR3T was identified as a member of new genus, Aquibium gen. nov., with the two aforementioned stains. The type strain f the novel species, Aquibium microcysteis sp. nov., is NIBR3T (=KACC 22092T=HAMBI 3738T). We also reclassified
Mesorhizobium carbonis
and
M. oceanicum
as Aquibium carbonis comb. nov. and A. oceanicum comb. nov., respectively.
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Affiliation(s)
- Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
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7
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Pedron R, Luchi E, Albiac MA, Di Cagno R, Catorci D, Esposito A, Bianconi I, Losa D, Cristofolini M, Guella G, Jousson O. Mesorhizobium comanense sp. nov., isolated from groundwater. Int J Syst Evol Microbiol 2021; 71. [PMID: 34870580 DOI: 10.1099/ijsem.0.005131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain 3P27G6T was isolated from an artesian well connected to the thermal water basin of Comano Terme, Province of Trento, Italy. In phylogenetic analyses based on multilocus sequence analysis, strain 3P27G6T clustered together with Mesorhizobium australicum WSM2073T. Genome sequencing produced a 99.51 % complete genome, with a length of 7 363 057 bp and G+C content of 63.53 mol%, containing 6897 coding sequences, 55 tRNA and three rRNA. Average nucleotide identity analysis revealed that all distances calculated between strain 3P27G6T and the other Mesorhizobium genomes were below 0.9, indicating that strain 3P27G6T represents a new species. Therefore, we propose the name Mesorhizobium comanense sp. nov. with the type strain 3P27G6T (=DSM 110654T=CECT 30067T). Strain 3P27G6T is a Gram-negative, rod-shaped, aerobic bacterium. Growth condition, antibiotic susceptibility, metabolic and fatty acid-methyl esters profiles of the strain were determined. Only few nodulation and nitrogen fixation genes were found in the genome, suggesting that this strain may not be specialized in nodulation or in nitrogen fixation.
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Affiliation(s)
- Renato Pedron
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Elena Luchi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Marta Acin Albiac
- Faculty of Sciences and Technology, Libera Università di Bolzano, 39100 Bolzano, Italy
| | - Raffaella Di Cagno
- Faculty of Sciences and Technology, Libera Università di Bolzano, 39100 Bolzano, Italy
| | - Daniele Catorci
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy.,Department of Physics, University of Trento, 38123 Trento, Italy
| | - Alfonso Esposito
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Irene Bianconi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Davide Losa
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | | | - Graziano Guella
- Department of Physics, University of Trento, 38123 Trento, Italy
| | - Olivier Jousson
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
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8
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Muleta A, Tesfaye K, Assefa F, Greenlon A, Riely BK, Carrasquilla-Garcia N, Gai Y, Haileslassie T, Cook DR. Genomic diversity and distribution of Mesorhizobium nodulating chickpea (Cicer arietinum L.) from low pH soils of Ethiopia. Syst Appl Microbiol 2021; 45:126279. [PMID: 34839036 DOI: 10.1016/j.syapm.2021.126279] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 10/26/2021] [Accepted: 11/09/2021] [Indexed: 10/19/2022]
Abstract
Chickpea is the third most important grain legume worldwide. This is due in part to its high protein content that results from its ability to acquire bioavailable nitrogen when colonized by diverse, nitrogen fixing Mesorhizobium species. However, the diversity and distribution of mesorhizobia communities may depend on their adaptation to soil conditions. Therefore, this study was initiated in order to isolate and investigate the diversity and taxonomic identities of chickpea-nodulating Mesorhizobium species from low pH soils of Ethiopia. A total of 81 rhizobia strains were isolated from chickpea nodules harvested from low pH soils throughout Ethiopia, and their genomes were sequenced and assembled. Considering a representative set of the best-sequenced 81 genomes, the average sequence depth was 30X, with estimated average genome sizes of approximately 7 Mbp. Annotation of the assembled genome predicted an average of 7,453 protein-coding genes. Concatenation of 400 universal PhyloPhlAn conserved genes present in the genomes of all 81 strains allowed detailed phylogenetic analysis, from which eight well-supported species were identified, including M.opportunistum, M.australicum, Mesorhizobium sp. LSJC280BOO, M.wenxiniae, M.amorphae, M.loti and M.plurifarium, as well as a novel species. Phylogenetic reconstructions based on the symbiosis-related (nodC and nifH) genes were different from the core genes and consistent with horizontal transfer of the symbiotic island. The two major genomic groups, M.plurifarium and M.loti, were widely distributed in almost all the sites. The geographic pattern of genomic diversity indicated there was no relationship between geographic and genetic distance (r = 0.01, p > 0.01). In conclusion, low pH soils in Ethiopia harbored a diverse group of Mesorhizobium species, several of which were not previously known to nodulate chickpea.
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Affiliation(s)
- Atsede Muleta
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia.
| | - Kassahun Tesfaye
- Institutes of Biotechnology, Addis Ababa University, P.O Box 1176, Addis Ababa, Ethiopia; Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Fassil Assefa
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Alex Greenlon
- Department of Plant Pathology, University of California Davis, One Shields Ave, Davis, CA, United States
| | - Brendan K Riely
- Department of Plant Pathology, University of California Davis, One Shields Ave, Davis, CA, United States
| | - Noelia Carrasquilla-Garcia
- Department of Plant Pathology, University of California Davis, One Shields Ave, Davis, CA, United States
| | - Yunpeng Gai
- Department of Plant Pathology, University of California Davis, One Shields Ave, Davis, CA, United States
| | | | - Douglas R Cook
- Department of Plant Pathology, University of California Davis, One Shields Ave, Davis, CA, United States
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9
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Abstract
AbstractLegume genotype (GL) x rhizobium genotype (GR) interaction in chickpea was studied using a genetically diverse set of accessions and rhizobium strains in modified Leonard Jars. A subset of effective GL x GR combinations was subsequently evaluated in a pot experiment to identify combinations of chickpea genotypes and rhizobium strains with stable and superior symbiotic performance. A linear mixed model was employed to analyse the occurrence of GL x GR interaction and an additive main effects and multiplicative interaction (AMMI) model was used to study patterns in the performance of genotype-strain combinations. We found statistically significant interaction in jars in terms of symbiotic effectiveness that was entirely due to the inclusion of one of the genotypes, ICC6263. No interaction was found in a subsequent pot experiment. The presence of two genetic groups (Kabuli and Desi genepools) did not affect interaction with Mesorhizobium strains. With the exception of a negative interaction with genotype ICC6263 in the jar experiment, the type strain Mesorhizobium ciceri LMG 14989 outperformed or equalled other strains on all chickpea genotypes in both jar and pot experiments. Similar to earlier reports in common bean, our results suggest that efforts to find more effective strains may be more rewarding than aiming for identification of superior combinations of strains and genotypes.
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10
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Jung YJ, Kim HJ, Hur M. Mesorhizobium terrae sp. nov., a novel species isolated from soil in Jangsu, Korea. Antonie van Leeuwenhoek 2020; 113:1279-1287. [PMID: 32564274 DOI: 10.1007/s10482-020-01435-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
Abstract
A gram-negative, white-pigmented, aerobic, rod-shaped bacterium, designated as strain NIBRBAC000500504T, was isolated from soil in Jangsu, Korea. Optimal growth of this strain was observed at 25 °C, pH 7.0, and in the presence of 0% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NIBRBAC000500504T belonged to the genus Mesorhizobium and was closely related to Mesorhizobium shangrilense LMG 24762T (98.3% sequence similarity), Mesorhizobium australicum LMG 24608T (98.2%), Mesorhizobium qingshengii LMG 26793T (98.1%), Mesorhizobium ciceri ATCC 51585T (98.0%), Mesorhizobium loti DSM 2626T (98.0%), Mesorhizobium sophorae LMG 28223T (97.9%), Mesorhizobium waitakense LMG 28227T (97.8%), and Mesorhizobium cantuariense LMG 28225T (97.8%). Next-generation sequencing analysis indicated that the genome of strain NIBRBAC000500504T comprised a circular chromosome (5,731,152 bp, G+C content: 63.26%) and a plasmid (293,638 bp, G+C content: 61.39%) with 5672 coding sequences, 50 tRNAs, and 6 rRNAs. The major respiratory isoprenoid quinone was Q10; the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine; the major fatty acids were summed feature 8 (comprising C18:1 ω7c/C18:1 ω6c), C19:0 cyclo ω8c, C16:0, and C18:1 ω7c 11-methyl; and the G+C content of the genomic DNA was 62.9 mol%. The DNA-DNA relatedness values between NIBRBAC000500504T and its closest type strains were low. On the basis of these polyphasic taxonomic data, it is proposed that strain NIBRBAC000500504T represents a novel species of the genus Mesorhizobium, with the type strain being NIBRBAC000500504T (= KCTC 72278T = JCM 33432T).
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Affiliation(s)
- You-Jung Jung
- Biological Resources Utilization Department, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Hyun-Joong Kim
- Department of Food Engineering, Mokpo National University, Muan, 58554, Republic of Korea
| | - Moonsuk Hur
- Biological Resources Utilization Department, National Institute of Biological Resources, Incheon, 22689, Republic of Korea.
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Ferraz Helene LC, Dall’Agnol RF, Delamuta JRM, Hungria M. Mesorhizobium atlanticum sp. nov., a new nitrogen-fixing species from soils of the Brazilian Atlantic Forest biome. Int J Syst Evol Microbiol 2019; 69:1800-1806. [DOI: 10.1099/ijsem.0.003397] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Luisa Caroline Ferraz Helene
- 1Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- 2Department of Biotechnology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
- 3Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, BlocoL, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, Brazil
| | - Rebeca Fuzinatto Dall’Agnol
- 3Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, BlocoL, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, Brazil
| | - Jakeline Renata Marçon Delamuta
- 1Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- 4Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 ConjuntoB, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
| | - Mariangela Hungria
- 2Department of Biotechnology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
- 1Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- 4Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 ConjuntoB, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
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Camacho M, Medina C, Rodríguez-Navarro DN, Temprano Vera F. Biodiversity of rhizobia present in plant nodules of Biserrula pelecinus across Southwest Spain. Syst Appl Microbiol 2019; 42:415-421. [PMID: 30952451 DOI: 10.1016/j.syapm.2019.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 11/29/2022]
Abstract
Biodiversity studies of native Mesorhizobium spp. strains able to nodulate the annual herbaceous legume Biserrula pelecinus L. in soils from Southwest Spain have been carried out. One or two isolates per plant, 30 in total, were randomly selected for further characterization. There was no association between the presence of mesorhizobia nodulating-B. pelecinus and the chemical or textural properties of the soils. The isolates were tested for their symbiotic effectiveness on this forage legume under greenhouse conditions and characterized on the basis of physiological parameters: carbon source utilisation (API 50CH), 16S rRNA sequencing and ERIC-PCR, lipopolysaccharide, protein and plasmid profiles. Our results show that in spite of the great diversity found among the native isolates, most of them belong to the genus Mesorhizobium, the exception being strain B24 which sequence matches 97.52% with Neorhizobium huautlense; this is the first description of a Neorhizobium strain effectively nodulating-biserrula plants. Results of a field trial indicated that some of these isolates could be recommended as inoculants for this legume. B24=DSM 28743=CECT 8815; ENA (HF955513) 16S rRNA sequences of isolates B13, B18, B26, B30 and B1 are deposited at ENA under numbers LS999402 to LS999406, respectively.
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Affiliation(s)
- María Camacho
- IFAPA Centro Las Torres Tomejil, Ctra Sevilla-Cazalla Km 12, 2. 41200 Seville, Spain.
| | - Carlos Medina
- Department of Microbiology, Faculty of Biology, University of Seville, Avda. Reina Mercedes 6, 41012 Seville, Spain
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traG Gene Is Conserved across Mesorhizobium spp. Able to Nodulate the Same Host Plant and Expressed in Response to Root Exudates. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3715271. [PMID: 30834262 PMCID: PMC6374801 DOI: 10.1155/2019/3715271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/09/2019] [Indexed: 11/22/2022]
Abstract
Evidences for an involvement of the bacterial type IV secretion system (T4SS) in the symbiotic relationship between rhizobia and legumes have been pointed out by several recent studies. However, information regarding this secretion system in Mesorhizobium is still very scarce. The aim of the present study was to investigate the phylogeny and expression of the traG gene, which encodes a substrate receptor of the T4SS. In addition, the occurrence and genomic context of this and other T4SS genes, namely, genes from tra/trb and virB/virD4 complexes, were also analyzed in order to unveil the structural and functional organization of T4SS in mesorhizobia. The location of the T4SS genes in the symbiotic region of the analyzed rhizobial genomes, along with the traG phylogeny, suggests that T4SS genes could be horizontally transferred together with the symbiosis genes. Regarding the T4SS structural organization in Mesorhizobium, the virB/virD4 genes were absent in all chickpea (Cicer arietinum L.) microsymbionts and in the Lotus symbiont Mesorhizobium japonicum MAFF303099T. Interestingly, the presence of genes belonging to another secretion system (T3SS) was restricted to these strains lacking the virB/virD4 genes. The traG gene expression was detected in M. mediterraneum Ca36T and M. ciceri LMS-1 strains when exposed to chickpea root exudates and also in the early nodules formed by M. mediterraneum Ca36T, but not in older nodules. This study contributes to a better understanding of the importance of T4SS in mutualistic symbiotic bacteria.
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Diep P, Mahadevan R, Yakunin AF. Heavy Metal Removal by Bioaccumulation Using Genetically Engineered Microorganisms. Front Bioeng Biotechnol 2018; 6:157. [PMID: 30420950 PMCID: PMC6215804 DOI: 10.3389/fbioe.2018.00157] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/09/2018] [Indexed: 11/25/2022] Open
Abstract
Wastewater effluents from mines and metal refineries are often contaminated with heavy metal ions, so they pose hazards to human and environmental health. Conventional technologies to remove heavy metal ions are well-established, but the most popular methods have drawbacks: chemical precipitation generates sludge waste, and activated carbon and ion exchange resins are made from unsustainable non-renewable resources. Using microbial biomass as the platform for heavy metal ion removal is an alternative method. Specifically, bioaccumulation is a natural biological phenomenon where microorganisms use proteins to uptake and sequester metal ions in the intracellular space to utilize in cellular processes (e.g., enzyme catalysis, signaling, stabilizing charges on biomolecules). Recombinant expression of these import-storage systems in genetically engineered microorganisms allows for enhanced uptake and sequestration of heavy metal ions. This has been studied for over two decades for bioremediative applications, but successful translation to industrial-scale processes is virtually non-existent. Meanwhile, demands for metal resources are increasing while discovery rates to supply primary grade ores are not. This review re-thinks how bioaccumulation can be used and proposes that it can be developed for bioextractive applications-the removal and recovery of heavy metal ions for downstream purification and refining, rather than disposal. This review consolidates previously tested import-storage systems into a biochemical framework and highlights efforts to overcome obstacles that limit industrial feasibility, thereby identifying gaps in knowledge and potential avenues of research in bioaccumulation.
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Affiliation(s)
| | | | - Alexander F. Yakunin
- BioZone - Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
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15
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Rodrigues RR, Rodgers NC, Wu X, Williams MA. COREMIC: a web-tool to search for a niche associated CORE MICrobiome. PeerJ 2018; 6:e4395. [PMID: 29473009 PMCID: PMC5816963 DOI: 10.7717/peerj.4395] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/30/2018] [Indexed: 02/01/2023] Open
Abstract
Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool “COREMIC” meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com or http://core-mic.com), developed using Google App Engine, to help in the process of database mining to identify the “core microbiome” associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (five environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val <0.05% for Fisher’s exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software.
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Affiliation(s)
- Richard R Rodrigues
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.,Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, United States of America
| | - Nyle C Rodgers
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Xiaowei Wu
- Department of Statistics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Mark A Williams
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.,School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
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Andrews M, Andrews ME. Specificity in Legume-Rhizobia Symbioses. Int J Mol Sci 2017; 18:E705. [PMID: 28346361 PMCID: PMC5412291 DOI: 10.3390/ijms18040705] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N₂) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis (Neorhizobium galegeae sv. officinalis), Galega orientalis (Neorhizobium galegeae sv. orientalis), Hedysarum coronarium (Rhizobium sullae), Medicago laciniata (Ensifer meliloti sv. medicaginis), Medicago rigiduloides (Ensifer meliloti sv. rigiduloides) and Trifolium ambiguum (Rhizobium leguminosarum sv. trifolii). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils. Strain-specific legume rhizobia symbioses can develop in particular habitats.
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Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
| | - Morag E Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
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Shamseldin A, Abdelkhalek A, Sadowsky MJ. Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review. Symbiosis 2016. [DOI: 10.1007/s13199-016-0462-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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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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Bohu T, Santelli CM, Akob DM, Neu TR, Ciobota V, Rösch P, Popp J, Nietzsche S, Küsel K. Characterization of pH dependent Mn(II) oxidation strategies and formation of a bixbyite-like phase by Mesorhizobium australicum T-G1. Front Microbiol 2015; 6:734. [PMID: 26236307 PMCID: PMC4505141 DOI: 10.3389/fmicb.2015.00734] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/03/2015] [Indexed: 01/09/2023] Open
Abstract
Despite the ubiquity of Mn oxides in natural environments, there are only a few observations of biological Mn(II) oxidation at pH < 6. The lack of low pH Mn-oxidizing bacteria (MOB) isolates limits our understanding of how pH influences biological Mn(II) oxidation in extreme environments. Here, we report that a novel MOB isolate, Mesorhizobium australicum strain T-G1, isolated from an acidic and metalliferous uranium mining area, can oxidize Mn(II) at both acidic and neutral pH using different enzymatic pathways. X-ray diffraction, Raman spectroscopy, and scanning electron microscopy with energy dispersive X-ray spectroscopy revealed that T-G1 initiated bixbyite-like Mn oxide formation at pH 5.5 which coincided with multi-copper oxidase expression from early exponential phase to late stationary phase. In contrast, reactive oxygen species (ROS), particularly superoxide, appeared to be more important for T-G1 mediated Mn(II) oxidation at neutral pH. ROS was produced in parallel with the occurrence of Mn(II) oxidation at pH 7.2 from early stationary phase. Solid phase Mn oxides did not precipitate, which is consistent with the presence of a high amount of H2O2 and lower activity of catalase in the liquid culture at pH 7.2. Our results show that M. australicum T-G1, an acid tolerant MOB, can initiate Mn(II) oxidation by varying its oxidation mechanisms depending on the pH and may play an important role in low pH manganese biogeochemical cycling.
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Affiliation(s)
- Tsing Bohu
- Department of Aquatic Geomicrobiology, Friedrich Schiller University JenaJena, Germany
| | - Cara M. Santelli
- Department of Mineral Sciences, Smithsonian InstitutionWashington, DC, USA
| | - Denise M. Akob
- National Research Program, United States Geological SurveyReston, VA, USA
| | - Thomas R. Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research-UFZMagdeburg, Germany
| | - Valerian Ciobota
- Institute of Physical Chemistry and Abbe School of Photonics, Friedrich Schiller University JenaJena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe School of Photonics, Friedrich Schiller University JenaJena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe School of Photonics, Friedrich Schiller University JenaJena, Germany
- Leibniz Institute of Photonic TechnologiesJena, Germany
| | - Sándor Nietzsche
- Centre of Electron Microscopy, University Hospital Jena, Friedrich Schiller University JenaJena, Germany
| | - Kirsten Küsel
- Department of Aquatic Geomicrobiology, Friedrich Schiller University JenaJena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
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Mesorhizobium soli sp. nov., a novel species isolated from the rhizosphere of Robinia pseudoacacia L. in South Korea by using a modified culture method. Antonie van Leeuwenhoek 2015; 108:301-10. [DOI: 10.1007/s10482-015-0481-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/13/2015] [Indexed: 10/23/2022]
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Diouf F, Diouf D, Klonowska A, Le Queré A, Bakhoum N, Fall D, Neyra M, Parrinello H, Diouf M, Ndoye I, Moulin L. Genetic and genomic diversity studies of Acacia symbionts in Senegal reveal new species of Mesorhizobium with a putative geographical pattern. PLoS One 2015; 10:e0117667. [PMID: 25658650 PMCID: PMC4319832 DOI: 10.1371/journal.pone.0117667] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/29/2014] [Indexed: 11/29/2022] Open
Abstract
Acacia senegal (L) Willd. and Acacia seyal Del. are highly nitrogen-fixing and moderately salt tolerant species. In this study we focused on the genetic and genomic diversity of Acacia mesorhizobia symbionts from diverse origins in Senegal and investigated possible correlations between the genetic diversity of the strains, their soil of origin, and their tolerance to salinity. We first performed a multi-locus sequence analysis on five markers gene fragments on a collection of 47 mesorhizobia strains of A. senegal and A. seyal from 8 localities. Most of the strains (60%) clustered with the M. plurifarium type strain ORS 1032T, while the others form four new clades (MSP1 to MSP4). We sequenced and assembled seven draft genomes: four in the M. plurifarium clade (ORS3356, ORS3365, STM8773 and ORS1032T), one in MSP1 (STM8789), MSP2 (ORS3359) and MSP3 (ORS3324). The average nucleotide identities between these genomes together with the MLSA analysis reveal three new species of Mesorhizobium. A great variability of salt tolerance was found among the strains with a lack of correlation between the genetic diversity of mesorhizobia, their salt tolerance and the soils samples characteristics. A putative geographical pattern of A. senegal symbionts between the dryland north part and the center of Senegal was found, reflecting adaptations to specific local conditions such as the water regime. However, the presence of salt does not seem to be an important structuring factor of Mesorhizobium species.
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Affiliation(s)
- Fatou Diouf
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
- IRD-Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet, Montpellier, France
| | - Diegane Diouf
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
| | - Agnieszka Klonowska
- IRD-Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet, Montpellier, France
| | - Antoine Le Queré
- Laboratoire Mixte International Biotechnologie Microbienne et Végétale (LBMV), Rabat, Morocco
| | - Niokhor Bakhoum
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
| | - Dioumacor Fall
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal
- Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
| | - Marc Neyra
- Irstea, UR MALY, centre de Lyon-Villeurbanne, Villeurbanne, France
| | - Hugues Parrinello
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Mayecor Diouf
- Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
| | - Ibrahima Ndoye
- Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
| | - Lionel Moulin
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
- IRD-Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet, Montpellier, France
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Lemaire B, Dlodlo O, Chimphango S, Stirton C, Schrire B, Boatwright JS, Honnay O, Smets E, Sprent J, James EK, Muasya AM. Symbiotic diversity, specificity and distribution of rhizobia in native legumes of the Core Cape Subregion (South Africa). FEMS Microbiol Ecol 2014; 91:1-17. [DOI: 10.1093/femsec/fiu024] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Pérez-Yépez J, Armas-Capote N, Velázquez E, Pérez-Galdona R, Rivas R, León-Barrios M. Evaluation of seven housekeeping genes for multilocus sequence analysis of the genus Mesorhizobium: Resolving the taxonomic affiliation of the Cicer canariense rhizobia. Syst Appl Microbiol 2014; 37:553-9. [DOI: 10.1016/j.syapm.2014.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/02/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022]
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Nandasena K, Yates R, Tiwari R, O’Hara G, Howieson J, Ninawi M, Chertkov O, Detter C, Tapia R, Han S, Woyke T, Pitluck S, Nolan M, Land M, Liolios K, Pati A, Copeland A, Kyrpides N, Ivanova N, Goodwin L, Meenakshi U, Reeve W. Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271(T)). Stand Genomic Sci 2014; 9:462-72. [PMID: 25197432 PMCID: PMC4148989 DOI: 10.4056/sigs.4458283] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mesorhizobium ciceri bv. biserrulae strain WSM1271(T) was isolated from root nodules of the pasture legume Biserrula pelecinus growing in the Mediterranean basin. Previous studies have shown this aerobic, motile, Gram negative, non-spore-forming rod preferably nodulates B. pelecinus - a legume with many beneficial agronomic attributes for sustainable agriculture in Australia. We describe the genome of Mesorhizobium ciceri bv. biserrulae strain WSM1271(T) consisting of a 6,264,489 bp chromosome and a 425,539 bp plasmid that together encode 6,470 protein-coding genes and 61 RNA-only encoding genes.
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Affiliation(s)
- Kemanthi Nandasena
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ron Yates
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
- Department of Agriculture and Food, Western Australia, Australia
| | - Ravi Tiwari
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Graham O’Hara
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Mohamed Ninawi
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Chris Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Shunseng Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Miriam Land
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Uma Meenakshi
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
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Wang S, Hao B, Li J, Gu H, Peng J, Xie F, Zhao X, Frech C, Chen N, Ma B, Li Y. Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics. BMC Genomics 2014; 15:440. [PMID: 24906389 PMCID: PMC4072884 DOI: 10.1186/1471-2164-15-440] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 05/20/2014] [Indexed: 11/10/2022] Open
Abstract
Background Evidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between Mesorhizobium strain MAFF303099 and M. huakuii. To define underlying causes for the rather striking difference in host specificity between M. huakuii strain 7653R and MAFF303099, several probable determinants also require comparison at the genomic level. An improved understanding of mobile genetic elements that can be integrated into the main chromosomes of Mesorhizobium to form genomic islands would enrich our knowledge of how genome dynamics may contribute to Mesorhizobium evolution in general. Results In this study, we sequenced the complete genome of 7653R and compared it with five other Mesorhizobium genomes. Genomes of 7653R and MAFF303099 were found to share a large set of orthologs and, most importantly, a conserved chromosomal backbone and even larger perfectly conserved synteny blocks. We also identified candidate molecular differences responsible for the different host specificities of these two strains. Finally, we reconstructed an ancestral Mesorhizobium genomic island that has evolved into diverse forms in different Mesorhizobium species. Conclusions Our ortholog and synteny analyses firmly establish MAFF303099 as a strain of M. huakuii. Differences in nodulation factors and secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host specificities of 7653R and MAFF303099 strains. The plasmids of 7653R may have arisen by excision of the original genomic island from the 7653R chromosome. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-440) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nansheng Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, P, R, China.
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Armas-Capote N, Pérez-Yépez J, Martínez-Hidalgo P, Garzón-Machado V, del Arco-Aguilar M, Velázquez E, León-Barrios M. Core and symbiotic genes reveal nine Mesorhizobium genospecies and three symbiotic lineages among the rhizobia nodulating Cicer canariense in its natural habitat (La Palma, Canary Islands). Syst Appl Microbiol 2014; 37:140-8. [DOI: 10.1016/j.syapm.2013.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 07/30/2013] [Accepted: 08/03/2013] [Indexed: 11/16/2022]
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Laranjo M, Alexandre A, Oliveira S. Legume growth-promoting rhizobia: An overview on the Mesorhizobium genus. Microbiol Res 2014; 169:2-17. [DOI: 10.1016/j.micres.2013.09.012] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/16/2013] [Accepted: 09/21/2013] [Indexed: 11/24/2022]
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28
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Reeve W, Nandasena K, Yates R, Tiwari R, O’Hara G, Ninawi M, Chertkov O, Goodwin L, Bruce D, Detter C, Tapia R, Han S, Woyke T, Pitluck S, Nolan M, Land M, Copeland A, Liolios K, Pati A, Mavromatis K, Markowitz V, Kyrpides N, Ivanova N, Goodwin L, Meenakshi U, Howieson J. Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075(T.). Stand Genomic Sci 2013; 9:294-303. [PMID: 24976886 PMCID: PMC4062634 DOI: 10.4056/sigs.4538264] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Mesorhizobium opportunistum strain WSM2075(T) was isolated in Western Australia in 2000 from root nodules of the pasture legume Biserrula pelecinus that had been inoculated with M. ciceri bv. biserrulae WSM1271. WSM2075(T) is an aerobic, motile, Gram negative, non-spore-forming rod that has gained the ability to nodulate B. pelecinus but is completely ineffective in N2 fixation with this host. This report reveals that the genome of M. opportunistum strain WSM2075(T) contains a chromosome of size 6,884,444 bp, encoding 6,685 protein-coding genes and 62 RNA-only encoding genes. The genome contains no plasmids, but does harbor a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene.
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Affiliation(s)
- Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Kemanthi Nandasena
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ron Yates
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
- Department of Agriculture and Food, Western Australia, Australia
| | - Ravi Tiwari
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Graham O’Hara
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Mohamed Ninawi
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - David Bruce
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Chris Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Shunseng Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Miriam Land
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Uma Meenakshi
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
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Reeve W, Nandasena K, Yates R, Tiwari R, O’Hara G, Ninawi M, Gu W, Goodwin L, Detter C, Tapia R, Han C, Copeland A, Liolios K, Chen A, Markowitz V, Pati A, Mavromatis K, Woyke T, Kyrpides N, Ivanova N, Howieson J. Complete genome sequence of Mesorhizobium australicum type strain (WSM2073T). Stand Genomic Sci 2013. [DOI: 10.4056/sigs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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30
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Reeve W, Nandasena K, Yates R, Tiwari R, O'Hara G, Ninawi M, Gu W, Goodwin L, Detter C, Tapia R, Han C, Copeland A, Liolios K, Chen A, Markowitz V, Pati A, Mavromatis K, Woyke T, Kyrpides N, Ivanova N, Howieson J. Complete genome sequence of Mesorhizobium australicum type strain (WSM2073(T)). Stand Genomic Sci 2013; 9:410-9. [PMID: 24976896 PMCID: PMC4062642 DOI: 10.4056/sigs.4568282] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mesorhizobium australicum strain WSM2073T was isolated from root nodules on the pasture legume Biserrula pelecinus growing in Australia in 2000. This aerobic, motile, gram negative, non-spore-forming rod is poorly effective in N2 fixation on B. pelecinus and has gained the ability to nodulate B. pelecinus following in situ lateral transfer of a symbiosis island from the original inoculant strain for this legume, Mesorhizobium ciceri bv. biserrulae WSM1271. We describe that the genome size of M. australicum strain WSM2073T is 6,200,534 bp encoding 6,013 protein-coding genes and 67 RNA-only encoding genes. This genome does not contain any plasmids but has a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene.
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Affiliation(s)
- Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Kemanthi Nandasena
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ron Yates
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia ; Department of Agriculture and Food, Western Australia, Australia
| | - Ravi Tiwari
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Graham O'Hara
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Mohamed Ninawi
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Wei Gu
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Chris Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Cliff Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Amy Chen
- 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
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
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Laranjo M, Young JPW, Oliveira S. Multilocus sequence analysis reveals multiple symbiovars within Mesorhizobium species. Syst Appl Microbiol 2012; 35:359-67. [DOI: 10.1016/j.syapm.2012.06.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/07/2012] [Accepted: 06/09/2012] [Indexed: 10/28/2022]
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Degefu T, Wolde-Meskel E, Liu B, Cleenwerck I, Willems A, Frostegård Å. Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees. Int J Syst Evol Microbiol 2012; 63:1746-1753. [PMID: 22941297 DOI: 10.1099/ijs.0.044032-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 18 strains, representing members of the genus Mesorhizobium, obtained from root nodules of woody legumes growing in Ethiopia, have been previously shown, by multilocus sequence analysis (MLSA) of five housekeeping genes, to form three novel genospecies. In the present study, the phylogenetic relationship between representative strains of these three genospecies and the type strains of their closest phylogenetic neighbours Mesorhizobium plurifarium, Mesorhizobium amorphae, Mesorhizobium septentrionale and Mesorhizobium huakuii was further evaluated using a polyphasic taxonomic approach. In line with our earlier MLSA of other housekeeping genes, the phylogenetic trees derived from the atpD and glnII genes grouped the test strains into three well-supported, distinct lineages that exclude all defined species of the genus Mesorhizobium. The DNA-DNA relatedness between the representative strains of genospecies I-III and the type strains of their closest phylogenetic neighbours was low (≤59 %). They differed from each other and from their closest phylogenetic neighbours by the presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon and nitrogen sources. The strains belonging to genospecies I, II and III therefore represent novel species for which we propose the names Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov. The isolates AC39a(T) ( = LMG 26966(T) = HAMBI 3295(T)), AC99b(T) ( = LMG 26968(T) = HAMBI 3301(T)) and AC98c(T) ( = LMG 26967(T) = HAMBI 3306(T)) are proposed as type strains for the respective novel species.
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Affiliation(s)
- Tulu Degefu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Endalkachew Wolde-Meskel
- School of Plant and Horticultural Sciences, Hawassa University, PO Box 5, Hawassa, Ethiopia.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Binbin Liu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Anne Willems
- Laboratory of Microbiology (WE10), Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
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Ramírez-Bahena MH, Hernández M, Peix Á, Velázquez E, León-Barrios M. Mesorhizobial strains nodulating Anagyris latifolia and Lotus berthelotii in Tamadaya ravine (Tenerife, Canary Islands) are two symbiovars of the same species, Mesorhizobium tamadayense sp. nov. Syst Appl Microbiol 2012; 35:334-41. [DOI: 10.1016/j.syapm.2012.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/25/2012] [Accepted: 05/06/2012] [Indexed: 10/28/2022]
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Molecular and phenotypic characterization of strains nodulating Anthyllis vulneraria in mine tailings, and proposal of Aminobacter anthyllidis sp. nov., the first definition of Aminobacter as legume-nodulating bacteria. Syst Appl Microbiol 2012; 35:65-72. [DOI: 10.1016/j.syapm.2011.11.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 11/14/2011] [Accepted: 11/30/2011] [Indexed: 11/18/2022]
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Lorite MJ, Donate-Correa J, del Arco-Aguilar M, Pérez Galdona R, Sanjuán J, León-Barrios M. Lotus endemic to the Canary Islands are nodulated by diverse and novel rhizobial species and symbiotypes. Syst Appl Microbiol 2010; 33:282-90. [PMID: 20447791 DOI: 10.1016/j.syapm.2010.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/09/2010] [Accepted: 03/11/2010] [Indexed: 10/19/2022]
Abstract
Genetic and symbiotic characterization of 34 isolates from several Lotus species endemic to the Canary Islands showed extraordinary diversity, with bacteria belonging to different species of the genera Mesorhizobium (17 isolates), Sinorhizobium (12 isolates) and Rhizobium/Agrobacterium (5 isolates). In a previous report, we showed that the Sinorhizobium isolates mostly belonged to S. meliloti. Here, we focused on the remaining isolates. The Lotus mesorhizobial strains were distributed in the rrs tree within six poorly resolved branches. Partial sequences from atpD and recA genes produced much better resolved phylogenies that were, with some exceptions, congruent with the ribosomal phylogeny. Thus, up to six different mesorhizobial species were detected, which matched with or were sister species of M. ciceri, M. alhagi, M. plurifarium or M. caraganae, and two represented new lineages that did not correspond to any of the currently recognized species. Neither M. loti nor Bradyrhizobium sp. (Lotus), recognized as the typical Lotus-symbionts, were identified among the Canarian Lotus isolates, although their nodulation genes were closely related to M. loti. However, several subbranches of mesorhizobia nodulating Lotus spp. could be differentiated in a nodC tree, with the isolates from the islands distributed in two of them (A1 and A3). Subbranch A1 included reference strains of M. loti and a group of isolates with a host range compatible with biovar loti, whereas A3 represented a more divergent exclusive subbranch of isolates with a host range almost restricted to endemic Lotus and it could represent a new biovar among the Lotus rhizobia.
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Affiliation(s)
- Ma José Lorite
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Granada, Spain
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