101
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Rhizobia: a potential biocontrol agent for soilborne fungal pathogens. Folia Microbiol (Praha) 2017; 62:425-435. [DOI: 10.1007/s12223-017-0513-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 03/02/2017] [Indexed: 01/31/2023]
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102
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Xiao X, Chen W, Zong L, Yang J, Jiao S, Lin Y, Wang E, Wei G. Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments. Mol Ecol 2017; 26:1641-1651. [PMID: 28139080 DOI: 10.1111/mec.14027] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/10/2016] [Accepted: 12/24/2016] [Indexed: 11/28/2022]
Abstract
The microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soya bean and alfalfa were analysed using high-throughput sequencing to investigate the interactions among legume species, microorganisms and soil types. A clear hierarchical filtration of microbiota by plants was observed in the four rhizocompartments - the nodule endosphere, root endosphere, rhizosphere and root zone - as demonstrated by significant variations in the composition of the microbial community in the different compartments. The rhizosphere and root zone microbial communities were largely influenced by soil type, and the nodule and root endophytes were primarily determined by plant species. Diverse microbes inhabited the root nodule endosphere, and the corresponding dominant symbiotic rhizobia belonged to Ensifer for alfalfa and Ensifer-Bradyrhizobium for soya bean. The nonsymbiotic nodule endophytes were mainly Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The variation in root microbial communities was also affected by the plant growth stage. In summary, this study demonstrated that the enrichment process of nodule endophytes follows a hierarchical filtration and that the bacterial communities in nodule endophytes vary according to the plant species.
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Affiliation(s)
- Xiao Xiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Le Zong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jun Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanbing Lin
- 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
| | - 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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103
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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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104
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Draft Genome Sequence of
Cupriavidus
UYMMa02A, a Novel Beta-Rhizobium Species. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01258-16. [PMID: 27834710 PMCID: PMC5105103 DOI: 10.1128/genomea.01258-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
We present the draft genome of
Cupriavidus
UYMMa02A, a rhizobium strain isolated from root nodules of
Mimosa magentea
. The assembly has approximately 8.1 million bp with an average G+C of 64.1%. Symbiotic and metal-resistance genes were identified. The study of this genome will contribute to the understanding of rhizobial evolution.
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105
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Júnior JQDO, Jesus EDC, Lisboa FJ, Berbara RLL, Faria SMD. Nitrogen-fixing bacteria and arbuscular mycorrhizal fungi in Piptadenia gonoacantha (Mart.) Macbr. Braz J Microbiol 2016; 48:95-100. [PMID: 27876549 PMCID: PMC5221347 DOI: 10.1016/j.bjm.2016.10.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 08/31/2016] [Indexed: 11/30/2022] Open
Abstract
The family Leguminosae comprises approximately 20,000 species that mostly form symbioses with arbuscular mycorrhizal fungi (AMF) and nitrogen-fixing bacteria (NFB). This study is aimed at investigating and confirming the dependence on nodulation and biological nitrogen fixation in the specie Piptadenia gonoacantha (Mart.) Macbr., which belongs to the Piptadenia group. Two consecutive experiments were performed in a greenhouse. The experiments were fully randomized with six replicates and a factorial scheme. For the treatments, the two AMF species and three NFB strains were combined to nodulate P. gonoacantha in addition to the control treatments. The results indicate this species' capacity for nodulation without the AMF; however, the AMF+NFB combinations yielded a considerable gain in P. gonoacantha shoot weight compared with the treatments that only included inoculating with bacteria or AMF. The results also confirm that the treatment effects among the AMF+NFB combinations produced different shoot dry weight/root dry weight ratios. We conclude that AMF is not necessary for nodulation and that this dependence improves species development because plant growth increases upon co-inoculation.
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Affiliation(s)
| | | | - Francy Junio Lisboa
- Universidade Federal Rural do Rio de Janeiro (UFRRJ), Departamento de Solos, Laboratório de Biologia do Solo, Seropédica, RJ, Brazil
| | - Ricardo Luis Louro Berbara
- Universidade Federal Rural do Rio de Janeiro (UFRRJ), Departamento de Solos, Laboratório de Biologia do Solo, Seropédica, RJ, Brazil
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106
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Genome Sequence of Paraburkholderia nodosa Strain CNPSo 1341, a N2-Fixing Symbiont of the Promiscuous Legume Phaseolus vulgaris. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01073-16. [PMID: 27811087 PMCID: PMC5095457 DOI: 10.1128/genomea.01073-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Paraburkholderia nodosa CNPSo 1341 is a N2-fixing symbiont of Phaseolus vulgaris isolated from an undisturbed soil of the Brazilian Cerrado. Its draft genome contains 8,614,032 bp and 8,068 coding sequences (CDSs). Nodulation and N2-fixation genes were clustered in the genome that also contains several genes of secretion systems and quorum sensing.
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107
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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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108
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Abstract
In the 1990s several biocontrol agents on that contained Burkholderia strains were registered by the United States Environmental Protection Agency (EPA). After risk assessment these products were withdrawn from the market and a moratorium was placed on the registration of Burkholderia-containing products, as these strains may pose a risk to human health. However, over the past few years the number of novel Burkholderia species that exhibit plant-beneficial properties and are normally not isolated from infected patients has increased tremendously. In this commentary we wish to summarize recent efforts that aim at discerning pathogenic from beneficial Burkholderia strains.
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Affiliation(s)
- Leo Eberl
- Department of Plant and Microbial Biology, University Zürich, Zurich, CH-8008, Switzerland
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Gent, Belgium
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109
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Radkov AD, McNeill K, Uda K, Moe LA. D-Amino Acid Catabolism Is Common Among Soil-Dwelling Bacteria. Microbes Environ 2016; 31:165-8. [PMID: 27169790 PMCID: PMC4912152 DOI: 10.1264/jsme2.me15126] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Soil and rhizosphere environments were examined in order to determine the identity and relative abundance of bacteria that catabolize d- and l-amino acids as the sole source of carbon and nitrogen. All substrates were readily catabolized by bacteria from both environments, with most d-amino acids giving similar CFU counts to their l-amino acid counterparts. CFU count ratios between l- and d-amino acids typically ranged between 2 and 1. Isolates were phylogenetically typed in order to determine the identity of d-amino acid catabolizers. Actinobacteria, specifically the Arthrobacter genus, were abundant along with members of the α- and β-Proteobacteria classes.
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110
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Chriki-Adeeb R, Chriki A. Estimating Divergence Times and Substitution Rates in Rhizobia. Evol Bioinform Online 2016; 12:87-97. [PMID: 27168719 PMCID: PMC4856229 DOI: 10.4137/ebo.s39070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/22/2016] [Accepted: 03/26/2016] [Indexed: 11/05/2022] Open
Abstract
Accurate estimation of divergence times of soil bacteria that form nitrogen-fixing associations with most leguminous plants is challenging because of a limited fossil record and complexities associated with molecular clocks and phylogenetic diversity of root nodule bacteria, collectively called rhizobia. To overcome the lack of fossil record in bacteria, divergence times of host legumes were used to calibrate molecular clocks and perform phylogenetic analyses in rhizobia. The 16S rRNA gene and intergenic spacer region remain among the favored molecular markers to reconstruct the timescale of rhizobia. We evaluate the performance of the random local clock model and the classical uncorrelated lognormal relaxed clock model, in combination with four tree models (coalescent constant size, birth-death, birth-death incomplete sampling, and Yule processes) on rhizobial divergence time estimates. Bayes factor tests based on the marginal likelihoods estimated from the stepping-stone sampling analyses strongly favored the random local clock model in combination with Yule process. Our results on the divergence time estimation from 16S rRNA gene and intergenic spacer region sequences are compatible with age estimates based on the conserved core genes but significantly older than those obtained from symbiotic genes, such as nodIJ genes. This difference may be due to the accelerated evolutionary rates of symbiotic genes compared to those of other genomic regions not directly implicated in nodulation processes.
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Affiliation(s)
- Rim Chriki-Adeeb
- Département de Biologie, Laboratoire de Génétique, Faculté des Sciences de Bizerte, Jarzouna, Tunisie
| | - Ali Chriki
- Département de Biologie, Laboratoire de Génétique, Faculté des Sciences de Bizerte, Jarzouna, Tunisie
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111
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Genetic diversity of rhizobia nodulating native Vicia spp. in Sweden. Syst Appl Microbiol 2016; 39:203-210. [DOI: 10.1016/j.syapm.2016.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 11/23/2022]
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112
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Borges WL, Prin Y, Ducousso M, Le Roux C, de Faria SM. Rhizobial characterization in revegetated areas after bauxite mining. Braz J Microbiol 2016; 47:314-21. [PMID: 26991294 PMCID: PMC4874681 DOI: 10.1016/j.bjm.2016.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/23/2015] [Indexed: 11/18/2022] Open
Abstract
Little is known regarding how the increased diversity of nitrogen-fixing bacteria contributes to the productivity and diversity of plants in complex communities. However, some authors have shown that the presence of a diverse group of nodulating bacteria is required for different plant species to coexist. A better understanding of the plant symbiotic organism diversity role in natural ecosystems can be extremely useful to define recovery strategies of environments that were degraded by human activities. This study used ARDRA, BOX-PCR fingerprinting and sequencing of the 16S rDNA gene to assess the diversity of root nodule nitrogen-fixing bacteria in former bauxite mining areas that were replanted in 1981, 1985, 1993, 1998, 2004 and 2006 and in a native forest. Among the 12 isolates for which the 16S rDNA gene was partially sequenced, eight, three and one isolate(s) presented similarity with sequences of the genera Bradyrhizobium, Rhizobium and Mesorhizobium, respectively. The richness, Shannon and evenness indices were the highest in the area that was replanted the earliest (1981) and the lowest in the area that was replanted most recently (2006).
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Affiliation(s)
| | - Yves Prin
- CIRAD, UMR 82, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus International de Baillarguet, Montpellier, France
| | - Marc Ducousso
- CIRAD, UMR 82, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus International de Baillarguet, Montpellier, France
| | - Christine Le Roux
- CIRAD, UMR 82, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus International de Baillarguet, Montpellier, France
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113
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Postma A, Slabbert E, Postma F, Jacobs K. Soil bacterial communities associated with natural and commercialCyclopiaspp. FEMS Microbiol Ecol 2016; 92:fiw016. [DOI: 10.1093/femsec/fiw016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2016] [Indexed: 12/16/2022] Open
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114
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Degli Esposti M, Geiger O, Martinez-Romero E. Recent Developments on Bacterial Evolution into Eukaryotic Cells. Evol Biol 2016. [DOI: 10.1007/978-3-319-41324-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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115
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116
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Baymiev AK, Ivanova ES, Gumenko RS, Chubukova OV, Baymiev AK. Analysis of symbiotic genes of leguminous root nodule bacteria grown in the southern urals. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415110034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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117
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Jiao YS, Liu YH, Yan H, Wang ET, Tian CF, Chen WX, Guo BL, Chen WF. Rhizobial Diversity and Nodulation Characteristics of the Extremely Promiscuous Legume Sophora flavescens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1338-1352. [PMID: 26389798 DOI: 10.1094/mpmi-06-15-0141-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In present study, we report our extensive survey on the diversity and biogeography of rhizobia associated with Sophora flavescens, a sophocarpidine (matrine)-containing medicinal legume. We additionally investigated the cross nodulation, infection pattern, light and electron microscopies of root nodule sections of S. flavescens infected by various rhizobia. Seventeen genospecies of rhizobia belonging to five genera with seven types of symbiotic nodC genes were found to nodulate S. flavescens in natural soils. In the cross-nodulation tests, most representative rhizobia in class α-Proteobacteria, whose host plants belong to different cross-nodulation groups, form effective indeterminate nodules, while representative rhizobia in class β-Proteobacteria form ineffective nodules on S. flavescens. Highly host-specific biovars of Rhizobium leguminosarum (bv. trifolii and bv. viciae) and Rhizobium etli bv. phaseoli could establish symbioses with S. flavescens, providing further evidence that S. flavescens is an extremely promiscuous legume and it does not have strict selectivity on either the symbiotic genes or the species-determining housekeeping genes of rhizobia. Root-hair infection is found as the pattern that rhizobia have gained entry into the curled root hairs. Electron microscopies of ultra-thin sections of S. flavescens root nodules formed by different rhizobia show that the bacteroids are regular or irregular rod shape and nonswollen types. Some bacteroids contain poly-β-hydroxybutyrate (PHB), while others do not, indicating the synthesis of PHB in bacteroids is rhizobia-dependent. The extremely promiscuous symbiosis between S. flavescens and different rhizobia provide us a basis for future studies aimed at understanding the molecular interactions of rhizobia and legumes.
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Affiliation(s)
- Yin Shan Jiao
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Yuan Hui Liu
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Hui Yan
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - En Tao Wang
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
- 2 Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, México
| | - Chang Fu Tian
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Wen Xin Chen
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Bao Lin Guo
- 3 Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Wen Feng Chen
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
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118
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Lira MA, Nascimento LRS, Fracetto GGM. Legume-rhizobia signal exchange: promiscuity and environmental effects. Front Microbiol 2015; 6:945. [PMID: 26441880 PMCID: PMC4561803 DOI: 10.3389/fmicb.2015.00945] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/27/2015] [Indexed: 12/29/2022] Open
Abstract
Although signal exchange between legumes and their rhizobia is among the best-known examples of this biological process, most of the more characterized data comes from just a few legume species and environmental stresses. Although a relative wealth of information is available for some model legumes and some of the major pulses such as soybean, little is known about tropical legumes. This relative disparity in current knowledge is also apparent in the research on the effects of environmental stress on signal exchange; cool-climate stresses, such as low-soil temperature, comprise a relatively large body of research, whereas high-temperature stresses and drought are not nearly as well understood. Both tropical legumes and their environmental stress-induced effects are increasingly important due to global population growth (the demand for protein), climate change (increasing temperatures and more extreme climate behavior), and urbanization (and thus heavy metals). This knowledge gap for both legumes and their environmental stresses is compounded because whereas most temperate legume-rhizobia symbioses are relatively specific and cultivated under relatively stable environments, the converse is true for tropical legumes, which tend to be promiscuous, and grow in highly variable conditions. This review will clarify some of this missing information and highlight fields in which further research would benefit our current knowledge.
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Affiliation(s)
- Mario A. Lira
- Agronomy Department, Federal Rural University of PernambucoRecife, Brazil
- National Council for Research and Scientific and Technological DevelopmentBrasília, Brazil
| | - Luciana R. S. Nascimento
- Agronomy Department, Federal Rural University of PernambucoRecife, Brazil
- National Council for Research and Scientific and Technological DevelopmentBrasília, Brazil
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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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120
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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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121
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Tariq M, Lum MR, Chong AW, Amirapu AB, Hameed S, Hirsch AM. A reliable method for the selection and confirmation of transconjugants of plant growth-promoting bacteria especially plant-associated Burkholderia spp. J Microbiol Methods 2015; 117:49-53. [PMID: 26187775 DOI: 10.1016/j.mimet.2015.07.008] [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: 04/20/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 11/17/2022]
Abstract
Selectable markers, e.g., antibiotic resistance, for conjugation experiments are not always effective for slow-growing plant growth promoting bacteria such as Burkholderia. We used PCAT medium containing Congo Red for selecting Burkholderia transconjugants. This method allows for the reliable selection of transconjugants of these novel plant growth-promoting bacteria.
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Affiliation(s)
- Mohsin Tariq
- National Institute for Biotechnology & Genetic Engineering, Faisalabad, Pakistan; Government College University Faisalabad, Allama Iqbal Road, Faisalabad, Pakistan
| | - Michelle R Lum
- Department of Biology, Loyola Marymount University, Los Angeles, CA, USA
| | - Allan W Chong
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Anjana B Amirapu
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Sohail Hameed
- National Institute for Biotechnology & Genetic Engineering, Faisalabad, Pakistan
| | - Ann M Hirsch
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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122
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Phylogenetic diversity on housekeeping and symbiotic genes of rhizobial from Sphaerophysa in China. World J Microbiol Biotechnol 2015; 31:1451-9. [PMID: 26149957 DOI: 10.1007/s11274-015-1898-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/03/2015] [Indexed: 10/23/2022]
Abstract
This study explored the diversity and phylogeny of rhizobia collected from nodules of Sphaerophysa salsula in different geographical regions of Northwest China. The 16S rRNA gene sequences divided the strains into the following distinct groups: Mesorhizobium, Rhizobium and Shinella. The phylogenies of recA and atpD genes showed low correlation with nifH and nodA gene in most species, which indicated that, the gene recombination between species and genera might have been exist. To our knowledge, this is the first study using the multilocus sequencing analysis Sphaerophysa rhizobia in order to understand the relation between genetic diversity and ecology.
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123
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Kumar Ghosh P, Kumar Sen S, Kanti Maiti T. Production and metabolism of IAA by Enterobacter spp. (Gammaproteobacteria) isolated from root nodules of a legume Abrus precatorius L. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2015. [DOI: 10.1016/j.bcab.2015.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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124
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Kumar CMS, Mande SC, Mahajan G. Multiple chaperonins in bacteria--novel functions and non-canonical behaviors. Cell Stress Chaperones 2015; 20:555-74. [PMID: 25986150 PMCID: PMC4463927 DOI: 10.1007/s12192-015-0598-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 01/05/2023] Open
Abstract
Chaperonins are a class of molecular chaperones that assemble into a large double ring architecture with each ring constituting seven to nine subunits and enclosing a cavity for substrate encapsulation. The well-studied Escherichia coli chaperonin GroEL binds non-native substrates and encapsulates them in the cavity thereby sequestering the substrates from unfavorable conditions and allowing the substrates to fold. Using this mechanism, GroEL assists folding of about 10-15 % of cellular proteins. Surprisingly, about 30 % of the bacteria express multiple chaperonin genes. The presence of multiple chaperonins raises questions on whether they increase general chaperoning ability in the cell or have developed specific novel cellular roles. Although the latter view is widely supported, evidence for the former is beginning to appear. Some of these chaperonins can functionally replace GroEL in E. coli and are generally indispensable, while others are ineffective and likewise are dispensable. Additionally, moonlighting functions for several chaperonins have been demonstrated, indicating a functional diversity among the chaperonins. Furthermore, proteomic studies have identified diverse substrate pools for multiple chaperonins. We review the current perception on multiple chaperonins and their physiological and functional specificities.
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Affiliation(s)
- C M Santosh Kumar
- Laboratory of Structural Biology, National Centre for Cell Science, Pune, 411007, India,
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125
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Quandt CA, Kohler A, Hesse CN, Sharpton TJ, Martin F, Spatafora JW. Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome. Environ Microbiol 2015; 17:2952-68. [PMID: 25753751 DOI: 10.1111/1462-2920.12840] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/13/2015] [Accepted: 02/28/2015] [Indexed: 01/06/2023]
Abstract
Many obligate symbiotic fungi are difficult to maintain in culture, and there is a growing need for alternative approaches to obtaining tissue and subsequent genomic assemblies from such species. In this study, the genome of Elaphomyces granulatus was sequenced from sporocarp tissue. The genome assembly remains on many contigs, but gene space is estimated to be mostly complete. Phylogenetic analyses revealed that the Elaphomyces lineage is most closely related to Talaromyces and Trichocomaceae s.s. The genome of E. granulatus is reduced in carbohydrate-active enzymes, despite a large expansion in genome size, both of which are consistent with what is seen in Tuber melanosporum, the other sequenced ectomycorrhizal ascomycete. A large number of transposable elements are predicted in the E. granulatus genome, especially Gypsy-like long terminal repeats, and there has also been an expansion in helicases. The metagenome is a complex community dominated by bacteria in Bradyrhizobiaceae, and there is evidence to suggest that the community may be reduced in functional capacity as estimated by KEGG pathways. Through the sequencing of sporocarp tissue, this study has provided insights into Elaphomyces phylogenetics, genomics, metagenomics and the evolution of the ectomycorrhizal association.
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Affiliation(s)
- C Alisha Quandt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Annegret Kohler
- Institut National de la Recherché Agronomique, Centre de Nancy, Champenoux, France
| | - Cedar N Hesse
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA.,Department of Statistics, Oregon State University, Corvallis, OR, 97331, USA
| | - Francis Martin
- Institut National de la Recherché Agronomique, Centre de Nancy, Champenoux, France
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
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126
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Quain MD, Makgopa ME, Cooper JW, Kunert KJ, Foyer CH. Ectopic phytocystatin expression increases nodule numbers and influences the responses of soybean (Glycine max) to nitrogen deficiency. PHYTOCHEMISTRY 2015; 112:179-87. [PMID: 25659749 DOI: 10.1016/j.phytochem.2014.12.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 12/16/2014] [Accepted: 12/23/2014] [Indexed: 05/04/2023]
Abstract
Cysteine proteases and cystatins have many functions that remain poorly characterised, particularly in crop plants. We therefore investigated the responses of these proteins to nitrogen deficiency in wild-type soybeans and in two independent transgenic soybean lines (OCI-1 and OCI-2) that express the rice cystatin, oryzacystatin-I (OCI). Plants were grown for four weeks under either a high (5 mM) nitrate (HN) regime or in the absence of added nitrate (LN) in the absence or presence of symbiotic rhizobial bacteria. Under the LN regime all lines showed similar classic symptoms of nitrogen deficiency including lower shoot biomass and leaf chlorophyll. However, the LN-induced decreases in leaf protein and increases in root protein tended to be smaller in the OCI-1 and OCI-2 lines than in the wild type. When LN-plants were grown with rhizobia, OCI-1 and OCI-2 roots had significantly more crown nodules than wild-type plants. The growth nitrogen regime had a significant effect on the abundance of transcripts encoding vacuolar processing enzymes (VPEs), LN-dependent increases in VPE2 and VPE3 transcripts in all lines. However, the LN-dependent increases of VPE2 and VPE3 transcripts were significantly lower in the leaves of OCI-1 and OCI-2 plants than in the wild type. These results show that nitrogen availability regulates the leaf and root cysteine protease, VPE and cystatin transcript profiles in a manner that is in some cases influenced by ectopic OCI expression. Moreover, the OCI-dependent inhibition of papain-like cysteine proteases favours increased nodulation and enhanced tolerance to nitrogen limitation, as shown by the smaller LN-dependent decreases in leaf protein observed in the OCI-1 and OCI-2 plants relative to the wild type.
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Affiliation(s)
- Marian D Quain
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, Leeds LS2 9JT, UK; Council for Scientific and Industrial Research, Crops Research Institute, P.O. Box 3785, Kumasi, Ghana
| | - Matome E Makgopa
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, Leeds LS2 9JT, UK; Forestry and Agricultural Biotechnology Institute, Plant Science Department, University of Pretoria, Pretoria 0002, South Africa
| | - James W Cooper
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Karl J Kunert
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, Leeds LS2 9JT, UK; Forestry and Agricultural Biotechnology Institute, Plant Science Department, University of Pretoria, Pretoria 0002, South Africa
| | - Christine H Foyer
- Centre for Plant Sciences, Faculty of Biology, University of Leeds, Leeds LS2 9JT, UK.
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127
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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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128
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Aeron A, Chauhan PS, Dubey RC, Maheshwari DK, Bajpai VK. Root nodule bacteria fromClitoria ternateaL. are putative invasive nonrhizobial endophytes. Can J Microbiol 2015; 61:131-42. [DOI: 10.1139/cjm-2014-0483] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, bacteria (8 species and 5 genera) belonging to the classes Betaproteobacteria, Gammaproteobacteria, and Sphingobacteria were isolated from root nodules of the multipurpose legume Clitoria ternatea L. and identified on the basis of partial 16S rRNA sequencing. The root nodule bacteria were subjected to phenotypic clustering and diversity studies using biochemical kits, including Hi-Media Carbokit™, Enterobacteriaceae™ identification kit, ERIC–PCR, and 16S ARDRA. All the strains showed growth on Ashby’s N-free media over 7 generations, indicative of presumptive nitrogen fixation and further confirmed by amplification of the nifH gene. None of the strains showed the capability to renodulate the host plant, neither alone nor in combination with standard rhizobial strains, which was further confirmed by the absence of nodC bands in PCR assay. The results clearly indicate the common existence of nonrhizobial microflora inside the root nodules of legumes, which were thought to be colonized only by rhizobia and were responsible for N2fixation in leguminous crops. However, with the recent discovery of nodule endophytes from a variety of legumes, as also observed here, it can be assumed that symbiotic rhizobia are not all alone and that these invasive endophytes belonging to various bacterial genera are more than just opportunistic colonizers of specialized nodule niche.
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Affiliation(s)
- Abhinav Aeron
- Department of Botany and Microbiology, Faculty of Life Sciences, Gurukul Kangri Vishwavidhyalaya, Haridwar 249-404, Uttarakhand, India
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Knowledge Park 3, Greater Noida (NCR, Delhi) 201-306, Uttar Pradesh, India
| | - Puneet Singh Chauhan
- Division of Plant Microbe Interactions, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226-001, Uttar Pradesh, India
| | - Ramesh Chand Dubey
- Department of Botany and Microbiology, Faculty of Life Sciences, Gurukul Kangri Vishwavidhyalaya, Haridwar 249-404, Uttarakhand, India
| | - Dinesh Kumar Maheshwari
- Department of Botany and Microbiology, Faculty of Life Sciences, Gurukul Kangri Vishwavidhyalaya, Haridwar 249-404, Uttarakhand, India
| | - Vivek K. Bajpai
- Department of Applied Microbiology and Biotechnology, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
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129
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Martins PGS, Junior MAL, Fracetto GGM, da Silva MLRB, Vincentin RP, de Lyra MDCCP. Mimosa caesalpiniifolia rhizobial isolates from different origins of the Brazilian Northeast. Arch Microbiol 2015; 197:459-69. [DOI: 10.1007/s00203-014-1078-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/05/2014] [Accepted: 12/26/2014] [Indexed: 11/30/2022]
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130
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Maymon M, Martínez-Hidalgo P, Tran SS, Ice T, Craemer K, Anbarchian T, Sung T, Hwang LH, Chou M, Fujishige NA, Villella W, Ventosa J, Sikorski J, Sanders ER, Faull KF, Hirsch AM. Mining the phytomicrobiome to understand how bacterial coinoculations enhance plant growth. FRONTIERS IN PLANT SCIENCE 2015; 6:784. [PMID: 26442090 PMCID: PMC4585168 DOI: 10.3389/fpls.2015.00784] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/10/2015] [Indexed: 05/02/2023]
Abstract
In previous work, we showed that coinoculating Rhizobium leguminosarum bv. viciae 128C53 and Bacillus simplex 30N-5 onto Pisum sativum L. roots resulted in better nodulation and increased plant growth. We now expand this research to include another alpha-rhizobial species as well as a beta-rhizobium, Burkholderia tuberum STM678. We first determined whether the rhizobia were compatible with B. simplex 30N-5 by cross-streaking experiments, and then Medicago truncatula and Melilotus alba were coinoculated with B. simplex 30N-5 and Sinorhizobium (Ensifer) meliloti to determine the effects on plant growth. Similarly, B. simplex 30N-5 and Bu. tuberum STM678 were coinoculated onto Macroptilium atropurpureum. The exact mechanisms whereby coinoculation results in increased plant growth are incompletely understood, but the synthesis of phytohormones and siderophores, the improved solubilization of inorganic nutrients, and the production of antimicrobial compounds are likely possibilities. Because B. simplex 30N-5 is not widely recognized as a Plant Growth Promoting Bacterial (PGPB) species, after sequencing its genome, we searched for genes proposed to promote plant growth, and then compared these sequences with those from several well studied PGPB species. In addition to genes involved in phytohormone synthesis, we detected genes important for the production of volatiles, polyamines, and antimicrobial peptides as well as genes for such plant growth-promoting traits as phosphate solubilization and siderophore production. Experimental evidence is presented to show that some of these traits, such as polyamine synthesis, are functional in B. simplex 30N-5, whereas others, e.g., auxin production, are not.
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Affiliation(s)
- Maskit Maymon
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Pilar Martínez-Hidalgo
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Stephen S. Tran
- Bioinformatics, University of California, Los AngelesLos Angeles, CA, USA
| | - Tyler Ice
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Karena Craemer
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Teni Anbarchian
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Tiffany Sung
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Lin H. Hwang
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Semel Institute for Neuroscience and Human Behavior, University of California, Los AngelesLos Angeles, CA, USA
| | - Minxia Chou
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Nancy A. Fujishige
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - William Villella
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los AngelesLos Angeles, CA, USA
| | - Jérôme Ventosa
- Biotechnology, Plants, and Microorganisms Biology, University of Montpellier IIMontpellier, France
| | - Johannes Sikorski
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHBraunschweig, Germany
| | - Erin R. Sanders
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los AngelesLos Angeles, CA, USA
| | - Kym F. Faull
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Semel Institute for Neuroscience and Human Behavior, University of California, Los AngelesLos Angeles, CA, USA
- Molecular Biology Institute, University of California, Los AngelesLos Angeles, CA, USA
| | - Ann M. Hirsch
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
- Molecular Biology Institute, University of California, Los AngelesLos Angeles, CA, USA
- *Correspondence: Ann M. Hirsch, Departments of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, 621 Charles Young Drive South, Los Angeles, CA 90095-1606, USA
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131
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García-Fraile P, Menéndez E, Rivas R. Role of bacterial biofertilizers in agriculture and forestry. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.3.183] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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132
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Remigi P, Capela D, Clerissi C, Tasse L, Torchet R, Bouchez O, Batut J, Cruveiller S, Rocha EPC, Masson-Boivin C. Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer. PLoS Biol 2014; 12:e1001942. [PMID: 25181317 PMCID: PMC4151985 DOI: 10.1371/journal.pbio.1001942] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 07/25/2014] [Indexed: 11/22/2022] Open
Abstract
Stress-responsive error-prone DNA polymerase genes transferred along with key symbiotic genes ease the evolution of a soil bacterium into a legume endosymbiont by accelerating adaptation of the recipient bacterial genome to its new plant host. Horizontal gene transfer (HGT) is an important mode of adaptation and diversification of prokaryotes and eukaryotes and a major event underlying the emergence of bacterial pathogens and mutualists. Yet it remains unclear how complex phenotypic traits such as the ability to fix nitrogen with legumes have successfully spread over large phylogenetic distances. Here we show, using experimental evolution coupled with whole genome sequencing, that co-transfer of imuABC error-prone DNA polymerase genes with key symbiotic genes accelerates the evolution of a soil bacterium into a legume symbiont. Following introduction of the symbiotic plasmid of Cupriavidus taiwanensis, the Mimosa symbiont, into pathogenic Ralstonia solanacearum we challenged transconjugants to become Mimosa symbionts through serial plant-bacteria co-cultures. We demonstrate that a mutagenesis imuABC cassette encoded on the C. taiwanensis symbiotic plasmid triggered a transient hypermutability stage in R. solanacearum transconjugants that occurred before the cells entered the plant. The generated burst in genetic diversity accelerated symbiotic adaptation of the recipient genome under plant selection pressure, presumably by improving the exploration of the fitness landscape. Finally, we show that plasmid imuABC cassettes are over-represented in rhizobial lineages harboring symbiotic plasmids. Our findings shed light on a mechanism that may have facilitated the dissemination of symbiotic competency among α- and β-proteobacteria in natura and provide evidence for the positive role of environment-induced mutagenesis in the acquisition of a complex lifestyle trait. We speculate that co-transfer of complex phenotypic traits with mutagenesis determinants might frequently enhance the ecological success of HGT. Horizontal gene transfer has an extraordinary impact on microbe evolution and diversification, by allowing exploration of new niches such as higher organisms. This is the case for rhizobia, a group of phylogenetically diverse bacteria that form a nitrogen-fixing symbiotic relationship with most leguminous plants. While these arose through horizontal transfer of symbiotic plasmids, this in itself is usually unproductive, and full expression of the acquired traits needs subsequent remodeling of the genome to ensure the ecological success of the transfer. Here we uncover a mechanism that accelerates the evolution of a soil bacterium into a legume symbiont. We show that key symbiotic genes are co-transferred with genes encoding stress-responsive error-prone DNA polymerases that transiently elevate the mutation rate in the recipient genome. This burst in genetic diversity accelerates the symbiotic evolution process under selection pressure from the host plant. A more widespread involvement of plasmid mutagenesis cassettes in rhizobium evolution is supported by their overrepresentation in rhizobia-containing lineages. Our findings provide evidence for the role of environment-induced mutagenesis in the acquisition of a complex lifestyle trait and predict that co-transfer of complex phenotypic traits with mutagenesis determinants might help successful horizontal gene transfer.
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Affiliation(s)
- Philippe Remigi
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Delphine Capela
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Camille Clerissi
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Léna Tasse
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Rachel Torchet
- CNRS-UMR 8030 and Commissariat à l'Energie Atomique CEA/DSV/IG/Genoscope LABGeM, Evry, France
| | - Olivier Bouchez
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
| | - Jacques Batut
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Stéphane Cruveiller
- CNRS-UMR 8030 and Commissariat à l'Energie Atomique CEA/DSV/IG/Genoscope LABGeM, Evry, France
| | - Eduardo P C Rocha
- CNRS UMR3525, Paris, France; Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
| | - Catherine Masson-Boivin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
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133
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Diversity of endophytic bacteria associated with nodules of two indigenous legumes at different altitudes of the Qilian Mountains in China. Syst Appl Microbiol 2014; 37:457-65. [DOI: 10.1016/j.syapm.2014.05.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 05/05/2014] [Accepted: 05/07/2014] [Indexed: 11/22/2022]
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134
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Marchetti M, Jauneau A, Capela D, Remigi P, Gris C, Batut J, Masson-Boivin C. Shaping bacterial symbiosis with legumes by experimental evolution. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:956-964. [PMID: 25105803 DOI: 10.1094/mpmi-03-14-0083-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nitrogen-fixing symbionts of legumes have appeared after the emergence of legumes on earth, approximately 70 to 130 million years ago. Since then, symbiotic proficiency has spread to distant genera of α- and β-proteobacteria, via horizontal transfer of essential symbiotic genes and subsequent recipient genome remodeling under plant selection pressure. To tentatively replay rhizobium evolution in laboratory conditions, we previously transferred the symbiotic plasmid of the Mimosa symbiont Cupriavidus taiwanensis in the plant pathogen Ralstonia solanacearum, and selected spontaneous nodulating variants of the chimeric Ralstonia sp. using Mimosa pudica as a trap. Here, we pursued the evolution experiment by submitting two of the rhizobial drafts to serial ex planta-in planta (M. pudica) passages that may mimic alternating of saprophytic and symbiotic lives of rhizobia. Phenotyping 16 cycle-evolved clones showed strong and parallel evolution of several symbiotic traits (i.e., nodulation competitiveness, intracellular infection, and bacteroid persistence). Simultaneously, plant defense reactions decreased within nodules, suggesting that the expression of symbiotic competence requires the capacity to limit plant immunity. Nitrogen fixation was not acquired in the frame of this evolutionarily short experiment, likely due to the still poor persistence of final clones within nodules compared with the reference rhizobium C. taiwanensis. Our results highlight the potential of experimental evolution in improving symbiotic proficiency and for the elucidation of relationship between symbiotic capacities and elicitation of immune responses.
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135
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Estrada-de los Santos P, Solano-Rodríguez R, Matsumura-Paz LT, Vásquez-Murrieta MS, Martínez-Aguilar L. Cupriavidus plantarum sp. nov., a plant-associated species. Arch Microbiol 2014; 196:811-7. [DOI: 10.1007/s00203-014-1018-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/13/2014] [Accepted: 07/15/2014] [Indexed: 11/25/2022]
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136
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Draft Genome Sequence of a Symbiotic Bacterium, Rhizobium vignae CCBAU 05176T. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00657-14. [PMID: 25081255 PMCID: PMC4118058 DOI: 10.1128/genomea.00657-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Rhizobium vignae strain CCBAU 05176T was isolated from a root nodule of Astragalus dahuricus grown in Hebei Province, China. It grows on yeast mannitol agar (YMA) supplemented with 0 to 2% (wt/vol) NaCl. We report the annotated genome sequence of this strain in a 6.34-Mb scaffold.
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137
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Zuleta LFG, Cunha CDO, de Carvalho FM, Ciapina LP, Souza RC, Mercante FM, de Faria SM, Baldani JI, Straliotto R, Hungria M, de Vasconcelos ATR. The complete genome of Burkholderia phenoliruptrix strain BR3459a, a symbiont of Mimosa flocculosa: highlighting the coexistence of symbiotic and pathogenic genes. BMC Genomics 2014; 15:535. [PMID: 24972629 PMCID: PMC4101177 DOI: 10.1186/1471-2164-15-535] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 06/05/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Burkholderia species play an important ecological role related to xenobiosis, the promotion of plant growth, the biocontrol of agricultural diseases, and symbiotic and non-symbiotic biological nitrogen fixation. Here, we highlight our study as providing the first complete genome of a symbiotic strain of B. phenoliruptrix, BR3459a (=CLA1), which was originally isolated in Brazil from nodules of Mimosa flocculosa and is effective in fixing nitrogen in association with this leguminous species. RESULTS Genomic comparisons with other pathogenic and non-pathogenic Burkholderia strains grouped B. phenoliruptrix BR3459a with plant-associated beneficial and environmental species, although it shares a high percentage of its gene repertoire with species of the B. cepacia complex (Bcc) and "pseudomallei" group. The genomic analyses showed that the bce genes involved in exopolysaccharide production are clustered together in the same genomic region, constituting part of the Group III cluster of non-pathogenic bacteria. Regarding environmental stresses, we highlight genes that might be relevant in responses to osmotic, heat, cold and general stresses. Furthermore, a number of particularly interesting genes involved in the machinery of the T1SS, T2SS, T3SS, T4ASS and T6SS secretion systems were identified. The xenobiotic properties of strain BR3459a were also investigated, and some enzymes involved in the degradation of styrene, nitrotoluene, dioxin, chlorocyclohexane, chlorobenzene and caprolactam were identified. The genomic analyses also revealed a large number of antibiotic-related genes, the most important of which were correlated with streptomycin and novobiocin. The symbiotic plasmid showed high sequence identity with the symbiotic plasmid of B. phymatum. Additionally, comparative analysis of 545 housekeeping genes among pathogenic and non-pathogenic Burkholderia species strongly supports the definition of a new genus for the second branch, which would include BR3459a. CONCLUSIONS The analyses of B. phenoliruptrix BR3459a showed key property of fixing nitrogen that together with genes for high tolerance to environmental stresses might explain a successful strategy of symbiosis in the tropics. The strain also harbours interesting sets of genes with biotechnological potential. However, the resemblance of certain genes to those of pathogenic Burkholderia raise concerns about large-scale applications in agriculture or for bioremediation.
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138
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Willems A, Tian R, Bräu L, Goodwin L, Han J, Liolios K, Huntemann M, Pati A, Woyke T, Mavrommatis K, Markowitz V, Ivanova N, Kyrpides N, Reeve W. Genome sequence of Burkholderia mimosarum strain LMG 23256(T), a Mimosa pigra microsymbiont from Anso, Taiwan. Stand Genomic Sci 2014; 9:484-94. [PMID: 25197434 PMCID: PMC4148967 DOI: 10.4056/sigs.4848627] [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: 11/20/2022] Open
Abstract
Burkholderia mimosarum strain LMG 23256(T) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Mimosa pigra (giant sensitive plant). LMG 23256(T) was isolated from a nodule recovered from the roots of the M. pigra growing in Anso, Taiwan. LMG 23256(T) is highly effective at fixing nitrogen with M. pigra. Here we describe the features of B. mimosarum strain LMG 23256(T), together with genome sequence information and its annotation. The 8,410,967 bp high-quality-draft genome is arranged into 268 scaffolds of 270 contigs containing 7,800 protein-coding genes and 85 RNA-only encoding genes, and is one of 100 rhizobial genomes 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)
- Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Begium
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Lambert Bräu
- School of Life and Environmental Sciences, Deakin University, Victoria, Australia
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - James Han
- 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
| | - Konstantinos Mavrommatis
- 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
| | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
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139
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Moulin L, Klonowska A, Caroline B, Booth K, Vriezen JA, Melkonian R, James EK, Young JPW, Bena G, Hauser L, Land M, Kyrpides N, Bruce D, Chain P, Copeland A, Pitluck S, Woyke T, Lizotte-Waniewski M, Bristow J, Riley M. Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species. Stand Genomic Sci 2014; 9:763-74. [PMID: 25197461 PMCID: PMC4148976 DOI: 10.4056/sigs.4861021] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815(T), was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp).
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Affiliation(s)
- Lionel Moulin
- IRD, UMR-LSTM, Campus de Baillarguet 34398 Montpellier cedex 5; France
| | | | - Bournaud Caroline
- IRD, UMR-LSTM, Campus de Baillarguet 34398 Montpellier cedex 5; France
| | | | | | - Rémy Melkonian
- IRD, UMR-LSTM, Campus de Baillarguet 34398 Montpellier cedex 5; France
| | | | | | - Gilles Bena
- IRD, UMR-LSTM, Campus de Baillarguet 34398 Montpellier cedex 5; France
| | - Loren Hauser
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Miriam Land
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - David Bruce
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | | | - Sam Pitluck
- Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Jim Bristow
- Joint Genome Institute, Walnut Creek, CA, USA
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140
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Abstract
Most ecosystems are populated by a large number of diversified microorganisms, which interact with one another and form complex interaction networks. In addition, some of these microorganisms may colonize the surface or internal parts of plants and animals, thereby providing an additional level of interaction complexity. These microbial relations range from intraspecific to interspecific interactions, and from simple short-term interactions to intricate long-term ones. They have played a key role in the formation of plant and animal kingdoms, often resulting in coevolution; they control the size, activity level, and diversity patterns of microbial communities. Therefore, they modulate trophic networks and biogeochemical cycles, regulate ecosystem productivity, and determine the ecology and health of plant and animal partners. A better understanding of these interactions is needed to develop microbe-based ecological engineering strategies for environmental sustainability and conservation, to improve environment-friendly approaches for feed and food production, and to address health challenges posed by infectious diseases. The main types of biotic interactions are presented: interactions between microorganisms, interactions between microorganisms and plants, and interactions between microorganisms and animals.
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141
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Mavengere NR, Ellis AG, Le Roux JJ. Burkholderia aspalathi sp. nov., isolated from root nodules of the South African legume Aspalathus abietina Thunb. Int J Syst Evol Microbiol 2014; 64:1906-1912. [PMID: 24599894 DOI: 10.1099/ijs.0.057067-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study to investigate the diversity of rhizobia associated with native legumes in South Africa's Cape Floristic Region, a Gram-negative bacterium designated VG1C(T) was isolated from the root nodules of Aspalathus abietina Thunb. Based on phylogenetic analyses of the 16S rRNA and recA genes, VG1C(T) belongs to the genus Burkholderia, with the highest degree of sequence similarity to the type strain of Burkholderia sediminicola (98.5% and 98%, respectively). The DNA G+C content of strain VG1C(T) was 60.1 mol%, and DNA-DNA relatedness values to the type strain of closely related species were found to be substantially lower than 70%. As evidenced by results of genotypic, phenotypic and chemotaxonomic tests provided here, we conclude that isolate VG1C(T) represents a novel rhizosphere-associated species in the genus Burkholderia, for which the name Burkholderia aspalathi sp. nov. is proposed, with the type strain VG1C(T) ( = DSM 27239(T) = LMG 27731(T)).
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Affiliation(s)
- Natasha R Mavengere
- Centre for Invasion Biology, Department of Botany and Zoology, Natural Sciences Building, Private Bag X1, Stellenbosch University, Matieland 7602, Western Cape, South Africa
| | - Allan G Ellis
- Department of Botany and Zoology, Natural Sciences Building, Private Bag X1, Stellenbosch University, Matieland 7602, Western Cape, South Africa
| | - Johannes J Le Roux
- Centre for Invasion Biology, Department of Botany and Zoology, Natural Sciences Building, Private Bag X1, Stellenbosch University, Matieland 7602, Western Cape, South Africa
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142
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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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143
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Sharma S, Gaur RK, Choudhary DK. Phenetic and functional characterization of endophytic root-nodule bacteria isolated from chickpea (Cicer arietinum L.) and mothbean (Vigna aconitifolia l.) of arid-and semi-arid regions of Rajasthan, India. Pak J Biol Sci 2013; 15:889-94. [PMID: 24205759 DOI: 10.3923/pjbs.2012.889.894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In the present study we recovered endophytic root-nodule bacteria from chickpea (Cicer arietinumi L.) and mothbean (Vigna aconitifolia L.). Phenotypic and genotypic characterization of isolates was performed by employing biochemical and genetic approaches. Sequencing data showed that most isolates belonged to genus, Pseudomonas spp. being a dominant species. They also showed similarity with Rhizobium, Agrobacterium and Erwinia spp. Isolates were screened functionally for indole-3-acetic acid, siderophore production and inorganic phosphorus (Pi) solubilization. All isolates showed Pi solubilization except CJS-2. Nine isolates (CSS-1, CBS-1, CLS-3, CCS-1, CHS-1, VS-1, VL-1, VN-1, VN-2) were found positive for IAA production and eight isolates (CBS-1, CCS-1, CHS-2, CKS-2, CNS-2, VS-1, VJ-1) exhibited positive results for siderophore production. An understanding of the phonetic and functional diversity of these microbes that interact with plants will be worthwhile to fully achieve the biotechnological potential of efficient plant-microbe partnerships for a range of applications.
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Affiliation(s)
- Saroj Sharma
- Department of Science, Faculty of Arts, Science and Commerce (FASC), Mody Institute of Technology and Science (MITS), Lakshmangarh-332311, Sikar, Rajasthan, India
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144
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De Meyer SE, Cnockaert M, Ardley JK, Trengove RD, Garau G, Howieson JG, Vandamme P. Burkholderia rhynchosiae sp. nov., isolated from Rhynchosia ferulifolia root nodules. Int J Syst Evol Microbiol 2013; 63:3944-3949. [DOI: 10.1099/ijs.0.048751-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of Gram-stain-negative, rod-shaped bacteria were isolated from root nodules of the South African legume Rhynchosia ferulifolia and authenticated on this host. Based on phylogenetic analysis of the 16S rRNA gene, strains WSM3930 and WSM3937T belonged to the genus
Burkholderia
, with the highest degree of sequence similarity to
Burkholderia terricola
(98.84 %). Additionally, the housekeeping genes gyrB and recA were analysed since 16S rRNA gene sequences are highly similar between closely related species of the genus
Burkholderia
. The results obtained for both housekeeping genes, gyrB and recA, showed the highest degree of sequence similarity of the novel strains towards
Burkholderia caledonica
LMG 19076T (94.2 % and 94.5 %, respectively). Chemotaxonomic data, including fatty acid profiles and respiratory quinone data supported the assignment of strains WSM3930 and WSM3937T to the genus
Burkholderia
. DNA–DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains WSM3930 and WSM3937T from the most closely related species of the genus
Burkholderia
with validly published names. We conclude, therefore, that these strains represent a novel species for which the name Burkholderia rhynchosiae sp. nov. is proposed, with strain WSM3937T ( = LMG 27174T = HAMBI 3354T) as the type strain.
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Affiliation(s)
- Sofie E. De Meyer
- Centre for Rhizobium Studies, Murdoch University, Western Australia 6150, Australia
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Julie K. Ardley
- Centre for Rhizobium Studies, Murdoch University, Western Australia 6150, Australia
| | - Robert D. Trengove
- Separation Science and Metabolomics Laboratory, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Giovanni Garau
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agro-Alimentari (DiSAABA), University of Sassari, Italy
| | - John G. Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia 6150, Australia
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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145
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Melkonian R, Moulin L, Béna G, Tisseyre P, Chaintreuil C, Heulin K, Rezkallah N, Klonowska A, Gonzalez S, Simon M, Chen WM, James EK, Laguerre G. The geographical patterns of symbiont diversity in the invasive legume Mimosa pudica can be explained by the competitiveness of its symbionts and by the host genotype. Environ Microbiol 2013; 16:2099-111. [PMID: 24131520 DOI: 10.1111/1462-2920.12286] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/04/2013] [Accepted: 09/12/2013] [Indexed: 01/23/2023]
Abstract
Variations in the patterns of diversity of symbionts have been described worldwide on Mimosa pudica, a pan-tropical invasive species that interacts with both α and β-rhizobia. In this study, we investigated if symbiont competitiveness can explain these variations and the apparent prevalence of β- over α-rhizobia. We developed an indirect method to measure the proportion of nodulation against a GFP reference strain and tested its reproducibility and efficiency. We estimated the competitiveness of 54 strains belonging to four species of β-rhizobia and four of α-rhizobia, and the influence of the host genotype on their competitiveness. Our results were compared with biogeographical patterns of symbionts and host varieties. We found: (i) a strong strain effect on competitiveness largely explained by the rhizobial species, with Burkholderia phymatum being the most competitive species, followed by B. tuberum, whereas all other species shared similar and reduced levels of competitiveness; (ii) plant genotype can increase the competitiveness of Cupriavidus taiwanensis. The latter data support the likelihood of the strong adaptation of C. taiwanensis with the M. pudica var. unijuga and help explain its prevalence as a symbiont of this variety over Burkholderia species in some environments, most notably in Taiwan.
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Affiliation(s)
- Rémy Melkonian
- IRD, UMR LSTM, Campus de Baillarguet, 34398, Montpellier cedex 5, France
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146
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Júnior PIF, de Lima AA, Passos SR, Tuão Gava CA, de Oliveira PJ, Rumjanek NG, Xavier GR. Phenotypic diversity and amylolytic activity of fast growing rhizobia from pigeonpea [Cajanus cajan (L.) Millsp]. Braz J Microbiol 2013; 43:1604-12. [PMID: 24031992 PMCID: PMC3769046 DOI: 10.1590/s1517-838220120004000045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 06/07/2012] [Indexed: 11/22/2022] Open
Abstract
This study evaluated 26 pigeonpea rhizobial isolates according to their cultural characteristics, intrinsic antibiotic resistance, salt and temperature tolerance, carbon source utilization and amylolytic activity. The cultural characterization showed that the majority of them presented the ability to acidify the YMA. Among the 27 isolates evaluated, 25 were able to grow when incubated at 42° C and 11 showed tolerance to 3% (w/v) of NaCl in YMA medium. The patterns of carbon sources utilization was very diverse among the isolates. It was observed the capacity of three strains to metabolize all the carbon sources evaluated and a total of 42% of the bacterial isolates was able to grow in the culture medium supplemented with at least, six carbon sources. The carbon sources mannitol (control) and sucrose were metabilized by all isolates evaluated. The profile of intrinsic resistance to antibiotics showed that the isolates were mostly resistant to streptomycin and ampicillin, but susceptible to kanamycin and chloranphenicol. High amylolytic activity of, at least, four isolates was also demonstrated, especially for isolated 47.3b, which showed the highest enzymatic index. These results indicate the metabolic versatility of the pigeonpea rhizobia, and indicates the isolate 47.3b to further studies regarding the amylase production and characterization.
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147
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Aoki S, Ito M, Iwasaki W. From β- to α-proteobacteria: the origin and evolution of rhizobial nodulation genes nodIJ. Mol Biol Evol 2013; 30:2494-508. [PMID: 24030554 DOI: 10.1093/molbev/mst153] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Although many α- and some β-proteobacterial species are symbiotic with legumes, the evolutionary origin of nitrogen-fixing nodulation remains unclear. We examined α- and β-proteobacteria whose genomes were sequenced using large-scale phylogenetic profiling and revealed the evolutionary origin of two nodulation genes. These genes, nodI and nodJ (nodIJ), play key roles in the secretion of Nod factors, which are recognized by legumes during nodulation. We found that only the nodulating β-proteobacteria, including the novel strains isolated in this study, possess both nodIJ and their paralogous genes (DRA-ATPase/permease genes). Contrary to the widely accepted scenario of the α-proteobacterial origin of rhizobia, our exhaustive phylogenetic analysis showed that the entire nodIJ clade is included in the clade of Burkholderiaceae DRA-ATPase/permease genes, that is, the nodIJ genes originated from gene duplication in a lineage of the β-proteobacterial family. After duplication, the evolutionary rates of nodIJ were significantly accelerated relative to those of homologous genes, which is consistent with their novel function in nodulation. The likelihood analyses suggest that this accelerated evolution is not associated with changes in either nonsynonymous/synonymous substitution rates or transition/transversion rates, but rather, in the GC content. Although the low GC content of the nodulation genes has been assumed to reflect past horizontal transfer events from donor rhizobial genomes with low GC content, no rhizobial genome with such low GC content has yet been found. Our results encourage a reconsideration of the origin of nodulation and suggest new perspectives on the role of the GC content of bacterial genes in functional adaptation.
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Affiliation(s)
- Seishiro Aoki
- Department of General Systems Studies, Graduate School of Arts and Sciences, the University of Tokyo, Meguro-ku, Tokyo, Japan
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148
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Stopnisek N, Bodenhausen N, Frey B, Fierer N, Eberl L, Weisskopf L. Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations. Environ Microbiol 2013; 16:1503-12. [PMID: 23945027 DOI: 10.1111/1462-2920.12211] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/04/2013] [Accepted: 07/10/2013] [Indexed: 11/30/2022]
Abstract
Bacteria belonging to the genus Burkholderia are highly versatile with respect to their ecological niches and lifestyles, ranging from nodulating tropical plants to causing melioidosis and fatal infections in cystic fibrosis patients. Despite the clinical importance and agronomical relevance of Burkholderia species, information about the factors influencing their occurrence, abundance and diversity in the environment is scarce. Recent findings have demonstrated that pH is the main predictor of soil bacterial diversity and community structure, with the highest diversity observed in neutral pH soils. As many Burkholderia species have been isolated from low pH environments, we hypothesized that acid tolerance may be a general feature of this genus, and pH a good predictor of their occurrence in soils. Using a combination of environmental surveys at trans-continental and local scales, as well as in vitro assays, we show that, unlike most bacteria, Burkholderia species have a competitive advantage in acidic soils, but are outcompeted in alkaline soils. Physiological assays and diversity analysis based on 16S rRNA clone libraries demonstrate that pH tolerance is a general phenotypic trait of the genus Burkholderia. Our results provide a basis for building a predictive understanding of the biogeographical patterns exhibited by Burkholderia sp.
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Affiliation(s)
- Nejc Stopnisek
- Institute of Plant Biology, University of Zurich, Zürich, CH-8008, Switzerland; Swiss Federal Research Station for Agronomy and Nature, Agroscope Reckenholz-Tänikon, Zürich, CH-8046, Switzerland
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149
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Diversity and symbiotic effectiveness of beta-rhizobia isolated from sub-tropical legumes of a Brazilian Araucaria Forest. World J Microbiol Biotechnol 2013; 29:2335-42. [PMID: 23861038 DOI: 10.1007/s11274-013-1400-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/06/2013] [Indexed: 10/26/2022]
Abstract
While the occurrence of Betaproteobacteria occupying the nodules of tropical legumes has been shown, little is known about subtropical areas. Araucaria Forest is a subtropical endangered ecosystem, and a better understanding of the legume-rhizobial symbionts may allow their use in land reclamation. The 16S rRNA gene of bacteria isolated from nine leguminous species was sequenced and their nodulation tested in Mimosa scabrella and Phaseolus vulgaris. 196 isolates were identified as eight genotypes: Pantoea, Pseudomonas, Bradyrhizobium sp1-2, Rhizobium, and Burkholderia sp1-3. The majority of the isolates from native plants (87 %) were taxonomically related to β-rhizobia, namely Burkholderia, however the legumes Galactia crassifolia and Collea speciosa were nodulated by both α and β-rhizobia, and Acacia dealbata, an exotic plant, only by α-rhizobia. The nifH genes of some isolates were sequenced and N-fixing potential shown by the acetylene reduction test. Most of the isolates nodulated the test plants, some were effective in M. scabrella, but all presented low efficiency in the exotic promiscuous legume P. vulgaris. Pantoea and Pseudomonas did not nodulate and probably are endophytic bacteria. The presented data shows diversity of α, β and γ-Proteobacteria in nodules of subtropical legumes, and suggests host specificity with β-rhizobia. Potential isolates were found for M. scabrella, indicating that a high N-fixing strain may be further inoculated in plants for use in reforestation.
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150
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South african papilionoid legumes are nodulated by diverse burkholderia with unique nodulation and nitrogen-fixation Loci. PLoS One 2013; 8:e68406. [PMID: 23874611 PMCID: PMC3708930 DOI: 10.1371/journal.pone.0068406] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 05/29/2013] [Indexed: 11/20/2022] Open
Abstract
The root-nodule bacteria of legumes endemic to the Cape Floristic Region are largely understudied, even though recent reports suggest the occurrence of nodulating Burkholderia species unique to the region. In this study, we considered the diversity and evolution of nodulating Burkholderia associated with the endemic papilionoid tribes Hypocalypteae and Podalyrieae. We identified distinct groups from verified rhizobial isolates by phylogenetic analyses of the 16S rRNA and recA housekeeping gene regions. In order to gain insight into the evolution of the nodulation and diazotrophy of these rhizobia we analysed the genes encoding NifH and NodA. The majority of these 69 isolates appeared to be unique, potentially representing novel species. Evidence of horizontal gene transfer determining the symbiotic ability of these Cape Floristic Region isolates indicate evolutionary origins distinct from those of nodulating Burkholderia from elsewhere in the world. Overall, our findings suggest that Burkholderia species associated with fynbos legumes are highly diverse and their symbiotic abilities have unique ancestries. It is therefore possible that the evolution of these bacteria is closely linked to the diversification and establishment of legumes characteristic of the Cape Floristic Region.
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