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Klonowska A, Ardley J, Moulin L, Zandberg J, Patrel D, Gollagher M, Marinova D, Reddy TBK, Varghese N, Huntemann M, Woyke T, Seshadri R, Ivanova N, Kyrpides N, Reeve W. Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018. Front Microbiol 2023; 14:1082107. [PMID: 36925474 PMCID: PMC10011098 DOI: 10.3389/fmicb.2023.1082107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/24/2023] [Indexed: 03/08/2023] Open
Abstract
Integrated virus genomes (prophages) are commonly found in sequenced bacterial genomes but have rarely been described in detail for rhizobial genomes. Cupriavidus taiwanensis STM 6018 is a rhizobial Betaproteobacteria strain that was isolated in 2006 from a root nodule of a Mimosa pudica host in French Guiana, South America. Here we describe features of the genome of STM 6018, focusing on the characterization of two different types of prophages that have been identified in its genome. The draft genome of STM 6018 is 6,553,639 bp, and consists of 80 scaffolds, containing 5,864 protein-coding genes and 61 RNA genes. STM 6018 contains all the nodulation and nitrogen fixation gene clusters common to symbiotic Cupriavidus species; sharing >99.97% bp identity homology to the nod/nif/noeM gene clusters from C. taiwanensis LMG19424T and "Cupriavidus neocalidonicus" STM 6070. The STM 6018 genome contains the genomes of two prophages: one complete Mu-like capsular phage and one filamentous phage, which integrates into a putative dif site. This is the first characterization of a filamentous phage found within the genome of a rhizobial strain. Further examination of sequenced rhizobial genomes identified filamentous prophage sequences in several Beta-rhizobial strains but not in any Alphaproteobacterial rhizobia.
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Affiliation(s)
- Agnieszka Klonowska
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Julie Ardley
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Lionel Moulin
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Jaco Zandberg
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Delphine Patrel
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Neha Varghese
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rekha Seshadri
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Wayne Reeve
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
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Klonowska A, Moulin L, Ardley JK, Braun F, Gollagher MM, Zandberg JD, Marinova DV, Huntemann M, Reddy TBK, Varghese NJ, Woyke T, Ivanova N, Seshadri R, Kyrpides N, Reeve WG. Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil. BMC Genomics 2020; 21:214. [PMID: 32143559 PMCID: PMC7060636 DOI: 10.1186/s12864-020-6623-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/25/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems. RESULTS The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance. CONCLUSIONS STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.
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Affiliation(s)
- Agnieszka Klonowska
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Julie Kaye Ardley
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Florence Braun
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | | | - Jaco Daniel Zandberg
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Dora Vasileva Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, Australia
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, USA
| | | | | | | | - Wayne Gerald Reeve
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
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De Meyer SE, Ruthrof KX, Edwards T, Hopkins AJ, Hardy G, O’Hara G, Howieson J. Diversity of endemic rhizobia on Christmas Island: Implications for agriculture following phosphate mining. Syst Appl Microbiol 2018; 41:641-649. [DOI: 10.1016/j.syapm.2018.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/31/2018] [Accepted: 07/31/2018] [Indexed: 11/26/2022]
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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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Baraúna AC, Rouws LFM, Simoes-Araujo JL, Dos Reis Junior FB, Iannetta PPM, Maluk M, Goi SR, Reis VM, James EK, Zilli JE. Rhizobium altiplani sp. nov., isolated from effective nodules on Mimosa pudica growing in untypically alkaline soil in central Brazil. Int J Syst Evol Microbiol 2016; 66:4118-4124. [PMID: 27453319 DOI: 10.1099/ijsem.0.001322] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Root nodule bacteria were isolated from nodules on Mimosa pudica L. growing in neutral-alkaline soils from the Distrito Federal in central Brazil. The 16S rRNA gene sequence analysis of 10 strains placed them into the genus Rhizobium with the closest neighbouring species (each with 99 % similarity) being Rhizobium grahamii, Rhizobium cauense, Rhizobium mesoamericanum and Rhizobium tibeticum. This high similarity, however, was not confirmed by multi-locus sequence analysis (MLSA) using three housekeeping genes (recA, glnII and rpoB), which revealed R. mesoamericanum CCGE 501T to be the closest type strain (92 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [with majority being C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c)], DNA G+C content (57.6 mol%), and carbon compound utilization patterns supported the placement of the novel strains in the genus Rhizobium. Results of average nucleotide identity (ANI) differentiated the novel strains from the closest species of the genus Rhizobium, R. mesoamericanum, R. grahamii and R. tibeticum with 89.0, 88.1 and 87.8 % similarity, respectively. The symbiotic genes essential for nodulation (nodC) and nitrogen fixation (nifH) were most similar (99-100 %) to those of R. mesoamericanum, another Mimosa-nodulating species. Based on the current data, these 10 strains represent a novel species of the genus Rhizobium for which the name Rhizobium altiplani sp. nov. is proposed. The type strain is BR 10423T (=HAMBI 3664T).
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Affiliation(s)
- Alexandre C Baraúna
- Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23890-000, Brazil
| | - Luc F M Rouws
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Jean L Simoes-Araujo
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | | | | | - Marta Maluk
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Silvia R Goi
- Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23890-000, Brazil
| | - Veronica M Reis
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jerri E Zilli
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
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Novel Cupriavidus Strains Isolated from Root Nodules of Native Uruguayan Mimosa Species. Appl Environ Microbiol 2016; 82:3150-3164. [PMID: 26994087 DOI: 10.1128/aem.04142-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/11/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The large legume genus Mimosa is known to be associated with both alphaproteobacterial and betaproteobacterial symbionts, depending on environment and plant taxonomy, e.g., Brazilian species are preferentially nodulated by Burkholderia, whereas those in Mexico are associated with alphaproteobacterial symbionts. Little is known, however, about the symbiotic preferences of Mimosa spp. at the southern subtropical limits of the genus. In the present study, rhizobia were isolated from field-collected nodules from Mimosa species that are native to a region in southern Uruguay. Phylogenetic analyses of sequences of the 16S rRNA, recA, and gyrB core genome and the nifH and nodA symbiosis-essential loci confirmed that all the isolates belonged to the genus Cupriavidus However, none were in the well-described symbiotic species C. taiwanensis, but instead they were closely related to other species, such as C. necator, and to species not previously known to be symbiotic (or diazotrophic), such as C. basilensis and C. pinatubonensis Selection of these novel Cupriavidus symbionts by Uruguayan Mimosa spp. is most likely due to their geographical separation from their Brazilian cousins and to the characteristics of the soils in which they were found. IMPORTANCE With the aim of exploring the diversity of rhizobia associated with native Mimosa species, symbionts were isolated from root nodules on five Mimosa species that are native to a region in southern Uruguay, Sierra del Abra de Zabaleta. In contrast to data obtained in the major centers of diversification of the genus Mimosa, Brazil and Mexico, where it is mainly associated with Burkholderia and Rhizobium/Ensifer, respectively, the present study has shown that all the isolated symbiotic bacteria belonged to the genus Cupriavidus Interestingly, none of nodules contained bacteria belonging to the well-described symbiotic species C. taiwanensis, but instead they were related to other Cupriavidus species such as C. necator and C. pinatubonensis These data suggest the existence of a higher diversity within beta-rhizobial Cupriavidus than was previously suspected, and that Mimosa spp. from Sierra del Abra de Zabaleta, may be natural reservoirs for novel rhizobia.
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