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Dey S, Awata T, Mitsushita J, Zhang D, Kasai T, Matsuura N, Katayama A. Promotion of biological nitrogen fixation activity of an anaerobic consortium using humin as an extracellular electron mediator. Sci Rep 2021; 11:6567. [PMID: 33753787 PMCID: PMC7985497 DOI: 10.1038/s41598-021-85955-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/05/2021] [Indexed: 11/09/2022] Open
Abstract
Nitrogen fertiliser is manufactured using the industrial Haber–Bosch process, although it is extremely energy-consuming. One sustainable alternative technology is the electrochemical promotion of biological nitrogen fixation (BNF). This study reports the promotion of BNF activity of anaerobic microbial consortia by humin, a solid-phase humic substance, at any pH, functioning as an extracellular electron mediator, to levels of 5.7–11.8 times under nitrogen-deficient conditions. This was evidenced by increased acetylene reduction activity and total nitrogen content of the consortia. Various humins from different origins promoted anaerobic BNF activity, although the degree of promotion differed. The promotion effected by humin differed from the effects of chemical reducing agents and the effects of supplemental micronutrients and vitamins. The promotion of anaerobic BNF activity by only reduced humin without any other electron donor suggested that humin did not serve as organic carbon source but as extracellular electron mediator, for electron donation to the nitrogen-fixing microorganisms. The next generation sequencing (NGS) of partial 16S rRNA genes showed the predominance of Clostridiales (Firmicutes) in the consortia. These findings suggest the effectiveness of humin as a solid-phase extracellular electron mediator for the promotion of anaerobic BNF activity, potentially to serve for the basis for a sustainable technology.
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Affiliation(s)
- Sujan Dey
- Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Takanori Awata
- National Institute for Land and Infrastructure Management, Asahi 1, Tsukuba, Ibaraki, 305-0804, Japan
| | - Jumpei Mitsushita
- Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Dongdong Zhang
- Institute of Materials and Systems for Sustainability, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan.,Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Takuya Kasai
- Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan.,Institute of Materials and Systems for Sustainability, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Norihisa Matsuura
- School of Geosciences and Civil Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Arata Katayama
- Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan. .,Institute of Materials and Systems for Sustainability, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan.
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2
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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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Dall'Agnol RF, Bournaud C, de Faria SM, Béna G, Moulin L, Hungria M. Genetic diversity of symbiotic Paraburkholderia species isolated from nodules of Mimosa pudica (L.) and Phaseolus vulgaris (L.) grown in soils of the Brazilian Atlantic Forest (Mata Atlântica). FEMS Microbiol Ecol 2017; 93:3045887. [PMID: 28334155 DOI: 10.1093/femsec/fix027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/22/2017] [Indexed: 11/13/2022] Open
Abstract
Some species of the genus Paraburkholderia that are able to nodulate and fix nitrogen in symbiosis with legumes are called β-rhizobia and represent a group of ecological and biotechnological importance. We used Mimosa pudica and Phaseolus vulgaris to trap 427 rhizobial isolates from rhizospheric soil of Mimoseae trees in the Brazilian Atlantic Forest. Eighty-four representative strains were selected according to the 16S rRNA haplotypes and taxonomically characterized using a concatenated 16S rRNA-recA phylogeny. Most strains were assembled in the genus Paraburkholderia, including Paraburkholderia sabiae and Pa. nodosa. Mesorhizobium (α-rhizobia) and Cupriavidus (β-rhizobia) were also isolated, but in smaller proportions. Multilocus sequence analysis and BOX-PCR analyses indicated that six clusters of Paraburkholderia represent potential new species. In the phylogenetic analysis of the nodC gene, the majority of the strains were positioned in the same groups as in the 16S rRNA-recA tree, indicative of stability and vertical inheritance, but we also identified horizontal transfer of nodC in Pa. sabiae. All α- and β-rhizobial species were trapped by both legumes, although preferences of the host plants for specific rhizobial species have been observed.
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Affiliation(s)
- Rebeca Fuzinatto Dall'Agnol
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 231, 86001-970, Londrina, PR, Brazil.,Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, C.P. 10.011, 86057-970, Londrina, PR, Brazil.,IRD, Cirad, Univ. Montpellier, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet 34398 Montpellier, France
| | - Caroline Bournaud
- IRD, Cirad, Univ. Montpellier, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet 34398 Montpellier, France.,Embrapa Recursos Genéticos e Biotecnologia, LIMPP Laboratory, C.P. 02372, 70770-917, Brasília, DF, Brazil
| | | | - Gilles Béna
- IRD, Cirad, Univ. Montpellier, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet 34398 Montpellier, France.,IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet 34398 Montpellier, France.,IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Mariangela Hungria
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 231, 86001-970, Londrina, PR, Brazil
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Rhizobium as a Crop Enhancer and Biofertilizer for Increased Non-legume Production. SOIL BIOLOGY 2017. [DOI: 10.1007/978-3-319-64982-5_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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5
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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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6
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De Meyer SE, Parker M, Van Berkum P, Tian R, Seshadri R, Reddy TBK, Markowitz V, Ivanova N, Pati A, Woyke T, Kyrpides N, Howieson J, Reeve W. High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6. Stand Genomic Sci 2015; 10:80. [PMID: 26478786 PMCID: PMC4609095 DOI: 10.1186/s40793-015-0074-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 10/08/2015] [Indexed: 12/20/2022] Open
Abstract
Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata is the only legume described so far to exclusively associates with Cupriavidus symbionts. Moreover, strain AMP6 represents an early-diverging lineage within the symbiotic Cupriavidus group and has the capacity to develop an effective nitrogen-fixing symbiosis with three other species of Mimosa. Therefore, the genome of Cupriavidus sp. strain AMP6 enables comparative analyses of symbiotic trait evolution in this genus and here we describe the general features, together with sequence and annotation. The 7,579,563 bp high-quality permanent draft genome is arranged in 260 scaffolds of 262 contigs, contains 7,033 protein-coding genes and 97 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.
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Affiliation(s)
- Sofie E De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | - Matthew Parker
- Binghamton University, State University of New York, New York, USA
| | - Peter Van Berkum
- Soybean Genomics and improvement laboratory Bldg 006, BARC-West USDA ARS 10300 Baltimore Blvd, Beltsville, MD 20705 USA
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | | | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Western Australia
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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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8
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Gehlot HS, Tak N, Kaushik M, Mitra S, Chen WM, Poweleit N, Panwar D, Poonar N, Parihar R, Tak A, Sankhla IS, Ojha A, Rao SR, Simon MF, dos Reis Junior FB, Perigolo N, Tripathi AK, Sprent JI, Young JPW, James EK, Gyaneshwar P. An invasive Mimosa in India does not adopt the symbionts of its native relatives. ANNALS OF BOTANY 2013; 112:179-96. [PMID: 23712450 PMCID: PMC3690997 DOI: 10.1093/aob/mct112] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 04/05/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS The large monophyletic genus Mimosa comprises approx. 500 species, most of which are native to the New World, with Central Brazil being the main centre of radiation. All Brazilian Mimosa spp. so far examined are nodulated by rhizobia in the betaproteobacterial genus Burkholderia. Approximately 10 Mya, transoceanic dispersal resulted in the Indian subcontinent hosting up to six endemic Mimosa spp. The nodulation ability and rhizobial symbionts of two of these, M. hamata and M. himalayana, both from north-west India, are here examined, and compared with those of M. pudica, an invasive species. METHODS Nodules were collected from several locations, and examined by light and electron microscopy. Rhizobia isolated from them were characterized in terms of their abilities to nodulate the three Mimosa hosts. The molecular phylogenetic relationships of the rhizobia were determined by analysis of 16S rRNA, nifH and nodA gene sequences. KEY RESULTS Both native Indian Mimosa spp. nodulated effectively in their respective rhizosphere soils. Based on 16S rRNA, nifH and nodA sequences, their symbionts were identified as belonging to the alphaproteobacterial genus Ensifer, and were closest to the 'Old World' Ensifer saheli, E. kostiensis and E. arboris. In contrast, the invasive M. pudica was predominantly nodulated by Betaproteobacteria in the genera Cupriavidus and Burkholderia. All rhizobial strains tested effectively nodulated their original hosts, but the symbionts of the native species could not nodulate M. pudica. CONCLUSIONS The native Mimosa spp. in India are not nodulated by the Burkholderia symbionts of their South American relatives, but by a unique group of alpha-rhizobial microsymbionts that are closely related to the 'local' Old World Ensifer symbionts of other mimosoid legumes in north-west India. They appear not to share symbionts with the invasive M. pudica, symbionts of which are mostly beta-rhizobial.
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Affiliation(s)
- Hukam Singh Gehlot
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur-342001, India
| | - Nisha Tak
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur-342001, India
| | - Muskan Kaushik
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur-342001, India
| | - Shubhajit Mitra
- Biological Sciences, University of Wisconsin Milwaukee, 3209 N Maryland Ave, Milwaukee, WI 53211, USA
| | - Wen-Ming Chen
- Laboratory of Microbiology, Dept. of Seafood Science, National Kaohsiung Marine University, Kaohsiung City 811, Taiwan
| | - Nicole Poweleit
- Biological Sciences, University of Wisconsin Milwaukee, 3209 N Maryland Ave, Milwaukee, WI 53211, USA
| | - Dheeren Panwar
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur-342001, India
| | - Neetu Poonar
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur-342001, India
| | - Rashmita Parihar
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur-342001, India
| | - Alkesh Tak
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur-342001, India
| | - Indu Singh Sankhla
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur-342001, India
| | - Archana Ojha
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
| | - Satyawada Rama Rao
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
| | - Marcelo F. Simon
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, 70770-901, DF, Brazil
| | | | - Natalia Perigolo
- Departamento de Botânica, Universidade de Brasília, Brasília, 70910-900, DF, Brazil
| | - Anil K. Tripathi
- School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi-221005, India
| | - Janet I. Sprent
- Division of Plant Sciences, University of Dundee at JHI, Dundee DD2 5DA, UK
| | - J. Peter W. Young
- Department of Biology 3, University of York, PO Box 373, York YO10 5YW, UK
| | - Euan K. James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Prasad Gyaneshwar
- Biological Sciences, University of Wisconsin Milwaukee, 3209 N Maryland Ave, Milwaukee, WI 53211, USA
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Terpolilli JJ, Hood GA, Poole PS. What determines the efficiency of N(2)-fixing Rhizobium-legume symbioses? Adv Microb Physiol 2012; 60:325-89. [PMID: 22633062 DOI: 10.1016/b978-0-12-398264-3.00005-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Biological nitrogen fixation is vital to nutrient cycling in the biosphere and is the major route by which atmospheric dinitrogen (N(2)) is reduced to ammonia. The largest single contribution to biological N(2) fixation is carried out by rhizobia, which include a large group of both alpha and beta-proteobacteria, almost exclusively in association with legumes. Rhizobia must compete to infect roots of legumes and initiate a signaling dialog with host plants that leads to nodule formation. The most common form of infection involves the growth of rhizobia down infection threads which are laid down by the host plant. Legumes form either indeterminate or determinate types of nodules, with these groups differing widely in nodule morphology and often in the developmental program by which rhizobia form N(2) fixing bacteroids. In particular, indeterminate legumes from the inverted repeat-lacking clade (IRLC) (e.g., peas, vetch, alfalfa, medics) produce a cocktail of antimicrobial peptides which cause endoreduplication of the bacterial genome and force rhizobia into a nongrowing state. Bacteroids often become dependent on the plant for provision of key cofactors, such as homocitrate needed for nitrogenase activity or for branched chain amino acids. This has led to the suggestion that bacteroids at least from the IRLC can be considered as ammoniaplasts, where they are effectively facultative plant organelles. A low O(2) tension is critical both to induction of genes needed for N(2) fixation and to the subsequent exchange of nutrient between plants and bacteroids. To achieve high rates of N(2) fixation, the legume host and Rhizobium must be closely matched not only for infection, but for optimum development, nutrient exchange, and N(2) fixation. In this review, we consider the multiple steps of selection and bacteroid development and how these alter the overall efficiency of N(2) fixation.
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Affiliation(s)
- Jason J Terpolilli
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
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10
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Klonowska A, Chaintreuil C, Tisseyre P, Miché L, Melkonian R, Ducousso M, Laguerre G, Brunel B, Moulin L. Biodiversity of Mimosa pudica rhizobial symbionts (Cupriavidus taiwanensis, Rhizobium mesoamericanum) in New Caledonia and their adaptation to heavy metal-rich soils. FEMS Microbiol Ecol 2012; 81:618-35. [DOI: 10.1111/j.1574-6941.2012.01393.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/06/2012] [Accepted: 04/09/2012] [Indexed: 11/30/2022] Open
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Andrus AD, Andam C, Parker MA. American origin of Cupriavidus bacteria associated with invasive Mimosa legumes in the Philippines. FEMS Microbiol Ecol 2012; 80:747-50. [PMID: 22381032 DOI: 10.1111/j.1574-6941.2012.01342.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 02/20/2012] [Accepted: 02/20/2012] [Indexed: 11/26/2022] Open
Abstract
To identify the origins of Cupriavidus nodule symbionts associated with two invasive Mimosa species in the Philippines, 22 isolates were sequenced for portions of three chromosomal genes and two symbiotic plasmid loci. Eleven isolates were identical at all gene loci (2713 bp) to a lineage found in Central America. Four other Philippine isolates were identical to a second Cupriavidus lineage distributed both in Central America and in the Caribbean. None of the remaining Philippine strains had more than 0.6% sequence divergence from American Cupriavidus lineages. These results imply that the Philippine population was founded by multiple introductions from the native range of their Mimosa hosts.
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Affiliation(s)
- Alexis D Andrus
- Department of Biological Sciences, State University of New York, Binghamton, NY, USA
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12
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Taulé C, Zabaleta M, Mareque C, Platero R, Sanjurjo L, Sicardi M, Frioni L, Battistoni F, Fabiano E. New betaproteobacterial Rhizobium strains able to efficiently nodulate Parapiptadenia rigida (Benth.) Brenan. Appl Environ Microbiol 2012; 78:1692-700. [PMID: 22226956 PMCID: PMC3298154 DOI: 10.1128/aem.06215-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 12/23/2011] [Indexed: 11/20/2022] Open
Abstract
Among the leguminous trees native to Uruguay, Parapiptadenia rigida (Angico), a Mimosoideae legume, is one of the most promising species for agroforestry. Like many other legumes, it is able to establish symbiotic associations with rhizobia and belongs to the group known as nitrogen-fixing trees, which are major components of agroforestry systems. Information about rhizobial symbionts for this genus is scarce, and thus, the aim of this work was to identify and characterize rhizobia associated with P. rigida. A collection of Angico-nodulating isolates was obtained, and 47 isolates were selected for genetic studies. According to enterobacterial repetitive intergenic consensus PCR patterns and restriction fragment length polymorphism analysis of their nifH and 16S rRNA genes, the isolates could be grouped into seven genotypes, including the genera Burkholderia, Cupriavidus, and Rhizobium, among which the Burkholderia genotypes were the predominant group. Phylogenetic studies of nifH, nodA, and nodC sequences from the Burkholderia and the Cupriavidus isolates indicated a close relationship of these genes with those from betaproteobacterial rhizobia (beta-rhizobia) rather than from alphaproteobacterial rhizobia (alpha-rhizobia). In addition, nodulation assays with representative isolates showed that while the Cupriavidus isolates were able to effectively nodulate Mimosa pudica, the Burkholderia isolates produced white and ineffective nodules on this host.
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Affiliation(s)
- Cecilia Taulé
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Unidad Asociada a la Facultad de Ciencias, Montevideo, Uruguay
| | - María Zabaleta
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Unidad Asociada a la Facultad de Ciencias, Montevideo, Uruguay
| | - Cintia Mareque
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Unidad Asociada a la Facultad de Ciencias, Montevideo, Uruguay
| | - Raúl Platero
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Unidad Asociada a la Facultad de Ciencias, Montevideo, Uruguay
| | - Lucía Sanjurjo
- Laboratorio de Microbiología, Facultad de Agronomía, UdelaR, Montevideo, Uruguay
| | - Margarita Sicardi
- Laboratorio de Microbiología del Suelo, Facultad de Ciencias-CIN, UdelaR, Montevideo, Uruguay
| | - Lillian Frioni
- Laboratorio de Microbiología, Facultad de Agronomía, UdelaR, Montevideo, Uruguay
| | - Federico Battistoni
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Unidad Asociada a la Facultad de Ciencias, Montevideo, Uruguay
| | - Elena Fabiano
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Unidad Asociada a la Facultad de Ciencias, Montevideo, Uruguay
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13
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da Silva K, Florentino LA, da Silva KB, de Brandt E, Vandamme P, de Souza Moreira FM. Cupriavidus necator isolates are able to fix nitrogen in symbiosis with different legume species. Syst Appl Microbiol 2012; 35:175-82. [PMID: 22361568 DOI: 10.1016/j.syapm.2011.10.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 11/25/2022]
Abstract
The aim of the present study was to identify a collection of 35 Cupriavidus isolates at the species level and to examine their capacity to nodulate and fix N(2). These isolates were previously obtained from the root nodules of two promiscuous trap species, Phaseolus vulgaris and Leucaena leucocephala, inoculated with soil samples collected near Sesbania virgata plants growing in Minas Gerais (Brazil) pastures. Phenotypic and genotypic methods applied for this study were SDS-PAGE of whole-cell proteins, and 16S rRNA and gyrB gene sequencing. To confirm the ability to nodulate and fix N(2), the presence of the nodC and nifH genes was also determined, and an experiment was carried out with two representative isolates in order to authenticate them as legume nodule symbionts. All 35 isolates belonged to the betaproteobacterium Cupriavidus necator, they possessed the nodC and nifH genes, and two representative isolates were able to nodulate five different promiscuous legume species: Mimosa caesalpiniaefolia, L. leucocephala, Macroptilium atropurpureum, P. vulgaris and Vigna unguiculata. This is the first study to demonstrate that C. necator can nodulate legume species.
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14
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Liu X, Wei S, Wang F, James EK, Guo X, Zagar C, Xia LG, Dong X, Wang YP. Burkholderia and Cupriavidus spp. are the preferred symbionts of Mimosa spp. in Southern China. FEMS Microbiol Ecol 2012; 80:417-26. [DOI: 10.1111/j.1574-6941.2012.01310.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 01/03/2012] [Accepted: 01/07/2012] [Indexed: 11/27/2022] Open
Affiliation(s)
| | - Shuang Wei
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province; College of Life Sciences; Hebei University; Baoding; China
| | - Fang Wang
- Key Laboratory of Biodiversity Conservation in Southwest China; SFA; Southwest Forestry University; Kunming; China
| | | | - XiaoYe Guo
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province; College of Life Sciences; Hebei University; Baoding; China
| | - Catherine Zagar
- Department of English; Faculty of Humanities; McMaster University; Hamilton; ON; Canada
| | - Liu Gui Xia
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province; College of Life Sciences; Hebei University; Baoding; China
| | - Xin Dong
- Key Laboratory of Biodiversity Conservation in Southwest China; SFA; Southwest Forestry University; Kunming; China
| | - Yi Peng Wang
- Key Laboratory of Biodiversity Conservation in Southwest China; SFA; Southwest Forestry University; Kunming; China
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15
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Mishra RPN, Tisseyre P, Melkonian R, Chaintreuil C, Miché L, Klonowska A, Gonzalez S, Bena G, Laguerre G, Moulin L. Genetic diversity of Mimosa pudica rhizobial symbionts in soils of French Guiana: investigating the origin and diversity of Burkholderia phymatum and other beta-rhizobia. FEMS Microbiol Ecol 2011; 79:487-503. [PMID: 22093060 DOI: 10.1111/j.1574-6941.2011.01235.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 10/14/2011] [Accepted: 10/19/2011] [Indexed: 12/01/2022] Open
Abstract
The genetic diversity of 221 Mimosa pudica bacterial symbionts trapped from eight soils from diverse environments in French Guiana was assessed by 16S rRNA PCR-RFLP, REP-PCR fingerprints, as well as by phylogenies of their 16S rRNA and recA housekeeping genes, and by their nifH, nodA and nodC symbiotic genes. Interestingly, we found a large diversity of beta-rhizobia, with Burkholderia phymatum and Burkholderia tuberum being the most frequent and diverse symbiotic species. Other species were also found, such as Burkholderia mimosarum, an unnamed Burkholderia species and, for the first time in South America, Cupriavidus taiwanensis. The sampling site had a strong influence on the diversity of the symbionts sampled, and the specific distributions of symbiotic populations between the soils were related to soil composition in some cases. Some alpha-rhizobial strains taxonomically close to Rhizobium endophyticum were also trapped in one soil, and these carried two copies of the nodA gene, a feature not previously reported. Phylogenies of nodA, nodC and nifH genes showed a monophyly of symbiotic genes for beta-rhizobia isolated from Mimosa spp., indicative of a long history of interaction between beta-rhizobia and Mimosa species. Based on their symbiotic gene phylogenies and legume hosts, B. tuberum was shown to contain two large biovars: one specific to the mimosoid genus Mimosa and one to South African papilionoid legumes.
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16
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Gyaneshwar P, Hirsch AM, Moulin L, Chen WM, Elliott GN, Bontemps C, Estrada-de Los Santos P, Gross E, Dos Reis FB, Sprent JI, Young JPW, James EK. Legume-nodulating betaproteobacteria: diversity, host range, and future prospects. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1276-88. [PMID: 21830951 DOI: 10.1094/mpmi-06-11-0172] [Citation(s) in RCA: 207] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Rhizobia form specialized nodules on the roots of legumes (family Fabaceae) and fix nitrogen in exchange for carbon from the host plant. Although the majority of legumes form symbioses with members of genus Rhizobium and its relatives in class Alphaproteobacteria, some legumes, such as those in the large genus Mimosa, are nodulated predominantly by betaproteobacteria in the genera Burkholderia and Cupriavidus. The principal centers of diversity of these bacteria are in central Brazil and South Africa. Molecular phylogenetic studies have shown that betaproteobacteria have existed as legume symbionts for approximately 50 million years, and that, although they have a common origin, the symbiosis genes in both subclasses have evolved separately since then. Additionally, some species of genus Burkholderia, such as B. phymatum, are highly promiscuous, effectively nodulating several important legumes, including common bean (Phaseolus vulgaris). In contrast to genus Burkholderia, only one species of genus Cupriavidus (C. taiwanensis) has so far been shown to nodulate legumes. The recent availability of the genome sequences of C. taiwanensis, B. phymatum, and B. tuberum has paved the way for a more detailed analysis of the evolutionary and mechanistic differences between nodulating strains of alpha- and betaproteobacteria. Initial analyses of genome sequences have suggested that plant-associated Burkholderia spp. have lower G+C contents than Burkholderia spp. that are opportunistic human pathogens, thus supporting previous suggestions that the plant- and human-associated groups of Burkholderia actually belong in separate genera.
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Affiliation(s)
- Prasad Gyaneshwar
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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17
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Dos Reis FB, Simon MF, Gross E, Boddey RM, Elliott GN, Neto NE, de Fatima Loureiro M, de Queiroz LP, Scotti MR, Chen WM, Norén A, Rubio MC, de Faria SM, Bontemps C, Goi SR, Young JPW, Sprent JI, James EK. Nodulation and nitrogen fixation by Mimosa spp. in the Cerrado and Caatinga biomes of Brazil. THE NEW PHYTOLOGIST 2010; 186:934-946. [PMID: 20456044 DOI: 10.1111/j.1469-8137.2010.03267.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
*An extensive survey of nodulation in the legume genus Mimosa was undertaken in two major biomes in Brazil, the Cerrado and the Caatinga, in both of which there are high degrees of endemicity of the genus. *Nodules were collected from 67 of the 70 Mimosa spp. found. Thirteen of the species were newly reported as nodulating. Nodules were examined by light and electron microscopy, and all except for M. gatesiae had a structure typical of effective Mimosa nodules. The endosymbiotic bacteria in nodules from all of the Mimosa spp. were identified as Burkholderia via immunolabelling with an antibody against Burkholderia phymatum STM815. *Twenty of the 23 Mimosa nodules tested were shown to contain nitrogenase by immunolabelling with an antibody to the nitrogenase Fe- (nifH) protein, and using the delta(15)N ((15)N natural abundance) technique, contributions by biological N(2) fixation of up to 60% of total plant N were calculated for Caatinga Mimosa spp. *It is concluded that nodulation in Mimosa is a generic character, and that the preferred symbionts of Brazilian species are Burkholderia. This is the first study to demonstrate N(2) fixation by beta-rhizobial symbioses in the field.
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Affiliation(s)
| | | | - Eduardo Gross
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, km 16, Ilhéus 45662-900 BA, Brazil
| | - Robert M Boddey
- Embrapa Agrobiologia, km 47, Seropédica, 23851-970, RJ, Brazil
| | | | - Nicolau E Neto
- Faculdade de Agronomia, Universidade Federal de Mato Grosso, Cuiabá, 78060-900, MT, Brazil
| | - M de Fatima Loureiro
- Faculdade de Agronomia, Universidade Federal de Mato Grosso, Cuiabá, 78060-900, MT, Brazil
| | - Luciano P de Queiroz
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana 44031-460 BA, Brazil
| | - Maria Rita Scotti
- Departamento de Botânica, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung City 811, Taiwan
| | - Agneta Norén
- Department of Biochemistry & Biophysics, Stockholm University, S-106 91 Sweden
| | - Maria C Rubio
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, 50080 Zaragoza, Spain
| | | | - Cyril Bontemps
- UMR1128 Génétique et Microbiologie, Nancy-Université, INRA, Boulevard des Aiguillettes BP70239, 54506 Vandoeuvre-lès-Nancy Cedex, France
| | - Silvia R Goi
- Department of Biology 3, University of York, PO Box 373, York YO10 5YW, UK
| | - J Peter W Young
- Departamento de Ciências Ambientais, Instituto de Florestas, Universidade Federal Rural do Rio de Janeiro, Seropédica, 23890-000, RJ, Brazil
| | - Janet I Sprent
- Division of Plant Sciences, University of Dundee at SCRI, DD2 5DA, UK
| | - Euan K James
- College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Present address: Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
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18
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Hoque MS, Broadhurst LM, Thrall PH. Genetic characterization of root-nodule bacteria associated with Acacia salicina and A. stenophylla (Mimosaceae) across south-eastern Australia. Int J Syst Evol Microbiol 2010; 61:299-309. [PMID: 20228207 DOI: 10.1099/ijs.0.021014-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Symbiotic relationships between legumes and nitrogen-fixing soil micro-organisms are of ecological importance in plant communities worldwide. For example, nutrient-poor Australian soils are often dominated by shrubby legumes (e.g. species of Acacia). However, relatively few studies have quantified patterns of diversity, host-specificity and effectiveness of these ecologically important plant-microbe interactions. In this study, 16S rRNA gene sequence and PCR-RFLP analyses were used to examine bacterial strains isolated from the root nodules of two widespread south-eastern Australian legumes, Acacia salicina and Acacia stenophylla, across nearly 60 sites. The results showed that there was extensive genetic diversity in microbial populations, including a broad range of novel genomic species. While previous studies have suggested that most native Australian legumes nodulate primarily with species of the genus Bradyrhizobium, our results indicate significant associations with members of other root-nodule-forming bacterial genera, including Rhizobium, Ensifer, Mesorhizobium, Burkholderia, Phyllobacterium and Devosia. Genetic analyses also revealed a diverse suite of non-nodulating bacterial endophytes, only a subset of which have been previously recorded. Although the ecological roles of these endosymbionts are not well understood, they may play both direct and indirect roles in promoting plant growth, nodulation and disease suppression.
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Affiliation(s)
| | | | - Peter H Thrall
- CSIRO Plant Industry, PO Box 1600, Canberra ACT 2601 Australia
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19
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Elliott GN, Chou JH, Chen WM, Bloemberg GV, Bontemps C, Martínez-Romero E, Velázquez E, Young JPW, Sprent JI, James EK. Burkholderia spp. are the most competitive symbionts of Mimosa, particularly under N-limited conditions. Environ Microbiol 2008; 11:762-78. [PMID: 19040456 DOI: 10.1111/j.1462-2920.2008.01799.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria isolated from Mimosa nodules in Taiwan, Papua New Guinea, Mexico and Puerto Rico were identified as belonging to either the alpha- or beta-proteobacteria. The beta-proteobacterial Burkholderia and Cupriavidus strains formed effective symbioses with the common invasive species Mimosa diplotricha, M. pigra and M. pudica, but the alpha-proteobacterial Rhizobium etli and R. tropici strains produced a range of symbiotic phenotypes from no nodulation through ineffective to effective nodulation, depending on Mimosa species. Competition studies were performed between three of the alpha-proteobacteria (R. etli TJ167, R. tropici NGR181 and UPRM8021) and two of the beta-rhizobial symbionts (Burkholderia mimosarum PAS44 and Cupriavidus taiwanensis LMG19424) for nodulation of these invasive Mimosa species. Under flooded conditions, B. mimosarum PAS44 out-competed LMG19424 and all three alpha-proteobacteria to the point of exclusion. This advantage was not explained by initial inoculum levels, rates of bacterial growth, rhizobia-rhizobia growth inhibition or individual nodulation rate. However, the competitive domination of PAS44 over LMG19424 was reduced in the presence of nitrate for all three plant hosts. The largest significant effect was for M. pudica, in which LMG19424 formed 57% of the nodules in the presence of 0.5 mM potassium nitrate. In this host, ammonium also had a similar, but lesser, effect. Comparable results were also found using an N-containing soil mixture, and environmental N levels are therefore suggested as a factor in the competitive success of the bacterial symbiont in vivo.
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20
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Chen WM, de Faria SM, Chou JH, James EK, Elliott GN, Sprent JI, Bontemps C, Young JPW, Vandamme P. Burkholderia sabiae sp. nov., isolated from root nodules of Mimosa caesalpiniifolia. Int J Syst Evol Microbiol 2008; 58:2174-9. [PMID: 18768625 DOI: 10.1099/ijs.0.65816-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
MESH Headings
- Bacterial Proteins/analysis
- Bacterial Typing Techniques
- Brazil
- Burkholderia/classification
- Burkholderia/genetics
- Burkholderia/isolation & purification
- Burkholderia/physiology
- Cluster Analysis
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Electrophoresis, Gel, Pulsed-Field
- Fatty Acids/analysis
- Genes, rRNA
- Mimosa/microbiology
- Molecular Sequence Data
- Nitrogen Fixation
- Nucleic Acid Hybridization
- Phylogeny
- Plant Roots/microbiology
- Proteome/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan.
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21
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Andam CP, Mondo SJ, Parker MA. Monophyly of nodA and nifH genes across Texan and Costa Rican populations of Cupriavidus nodule symbionts. Appl Environ Microbiol 2007; 73:4686-90. [PMID: 17526782 PMCID: PMC1932833 DOI: 10.1128/aem.00160-07] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
nodA and nifH phylogenies for Cupriavidus nodule bacteria from native legumes in Texas and Costa Rica grouped all strains into a single clade nested among neotropical Burkholderia strains. Thus, Cupriavidus symbiotic genes were not acquired independently in different regions and are derived from other Betaproteobacteria rather than from alpha-rhizobial donors.
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Affiliation(s)
- Cheryl P Andam
- Department of Biological Sciences, State University of New York, Binghamton, NY 13902-6000, USA
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22
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Miller TR, Franklin MP, Halden RU. Bacterial community analysis of shallow groundwater undergoing sequential anaerobic and aerobic chloroethene biotransformation. FEMS Microbiol Ecol 2007; 60:299-311. [PMID: 17386036 DOI: 10.1111/j.1574-6941.2007.00290.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
At Department of Energy Site 300, beneficial hydrocarbon cocontaminants and favorable subsurface conditions facilitate sequential reductive dechlorination of trichloroethene (TCE) and rapid oxidation of the resultant cis-dichloroethene (cis-DCE) upon periodic oxygen influx. We assessed the geochemistry and microbial community of groundwater from across the site. Removal of cis-DCE was shown to coincide with oxygen influx in hydrocarbon-containing groundwater near the source area. Principal component analysis of contaminants and inorganic compounds showed that monitoring wells could be differentiated based upon concentrations of TCE, cis-DCE, and nitrate. Structurally similar communities were detected in groundwater from wells containing cis-DCE, high TCE, and low nitrate levels. Bacteria identified by sequencing 16S rRNA genes belonged to seven phylogenetic groups, including Alpha-, Beta-, Gamma- and Deltaproteobacteria, Nitrospira, Firmicutes and Cytophaga-Flexibacter-Bacteroidetes (CFB). Whereas members of the Burkholderiales and CFB group were abundant in all wells (10(4)-10(9) 16S rRNA gene copies L(-1)), quantitative PCR showed that Alphaproteobacteria were elevated (>10(6) L(-1)) only in wells containing hydrocarbon cocontaminants. The study shows that bacterial community structure is related to groundwater geochemistry and that Alphaproteobacteria are enriched in locales where cis-DCE removal occurs.
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MESH Headings
- Aerobiosis
- Anaerobiosis
- Bacteria/classification
- Bacteria/genetics
- Bacteria/metabolism
- Biodegradation, Environmental
- California
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- Dichloroethylenes/chemistry
- Dichloroethylenes/metabolism
- Ecosystem
- Electrophoresis
- Fresh Water/microbiology
- Gas Chromatography-Mass Spectrometry
- Geography
- Hydrocarbons, Chlorinated/chemistry
- Hydrocarbons, Chlorinated/metabolism
- Molecular Sequence Data
- Nitrates/chemistry
- Nitrates/metabolism
- Oxygen/chemistry
- Oxygen/metabolism
- Phylogeny
- Polymerase Chain Reaction
- Principal Component Analysis
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Trichloroethylene/chemistry
- Trichloroethylene/metabolism
- Water Microbiology
- Water Pollutants, Chemical/chemistry
- Water Pollutants, Chemical/metabolism
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Affiliation(s)
- Todd R Miller
- Department of Environmental Health Sciences, Center for Water and Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, USA
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23
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Chen WM, de Faria SM, James EK, Elliott GN, Lin KY, Chou JH, Sheu SY, Cnockaert M, Sprent JI, Vandamme P. Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella. Int J Syst Evol Microbiol 2007; 57:1055-1059. [PMID: 17473258 DOI: 10.1099/ijs.0.64873-0] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains, Br3437T, Br3461 and Br3470, were isolated from nitrogen-fixing nodules on the roots of Mimosa scabrella (Br3437T) and Mimosa bimucronata (Br3461, Br3470), both of which are woody legumes native to Brazil. On the basis of 16S rRNA gene sequence similarities, all the strains were shown previously to belong to the genus Burkholderia. A polyphasic approach, including DNA–DNA hybridizations, PFGE of whole-genome DNA profiles, whole-cell protein analyses, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains further; the strains are here classified within a novel species, for which the name Burkholderia nodosa sp. nov. is proposed. The type strain, Br3437T (=LMG 23741T=BCRC 17575T), was isolated from nodules of M. scabrella.
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MESH Headings
- Bacterial Proteins/analysis
- Bacterial Typing Techniques
- Brazil
- Burkholderia/chemistry
- Burkholderia/classification
- Burkholderia/isolation & purification
- Burkholderia/physiology
- Cluster Analysis
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Electrophoresis, Gel, Pulsed-Field
- Fatty Acids/analysis
- Genes, rRNA
- Mimosa/microbiology
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- Plant Roots/microbiology
- Proteome/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Sergio M de Faria
- EMBRAPA-Agrobiologia, km 47, Seropedica, 23851-970 Rio de Janeiro, Brazil
| | - Euan K James
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Kuan-Yin Lin
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Jui-Hsing Chou
- Department of Soil Environmental Science, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - M Cnockaert
- Laboratorium voor Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Janet I Sprent
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Peter Vandamme
- Laboratorium voor Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
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24
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Elliott GN, Chen WM, Chou JH, Wang HC, Sheu SY, Perin L, Reis VM, Moulin L, Simon MF, Bontemps C, Sutherland JM, Bessi R, de Faria SM, Trinick MJ, Prescott AR, Sprent JI, James EK. Burkholderia phymatum is a highly effective nitrogen-fixing symbiont of Mimosa spp. and fixes nitrogen ex planta. THE NEW PHYTOLOGIST 2007; 173:168-80. [PMID: 17176403 DOI: 10.1111/j.1469-8137.2006.01894.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
* The ability of Burkholderia phymatum STM815 to effectively nodulate Mimosa spp., and to fix nitrogen ex planta, was compared with that of the known Mimosa symbiont Cupriavidus taiwanensis LMG19424. * Both strains were equally effective symbionts of M. pudica, but nodules formed by STM815 had greater nitrogenase activity. STM815 was shown to have a broader host range across the genus Mimosa than LMG19424, nodulating 30 out of 31 species, 21 of these effectively. LMG19424 effectively nodulated only nine species. GFP-marked variants were used to visualise symbiont presence within nodules. * STM815 gave significant acetylene reduction assay (ARA) activity in semisolid JMV medium ex planta, but no ARA activity was detected with LMG19424. 16S rDNA sequences of two isolates originally from Mimosa nodules in Papua New Guinea (NGR114 and NGR195A) identified them as Burkholderia phymatum also, with nodA, nodC and nifH genes of NGR195A identical to those of STM815. * B. phymatum is therefore an effective Mimosa symbiont with a broad host range, and is the first reported beta-rhizobial strain to fix nitrogen in free-living culture.
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25
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Chen WM, James EK, Coenye T, Chou JH, Barrios E, de Faria SM, Elliott GN, Sheu SY, Sprent JI, Vandamme P. Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America. Int J Syst Evol Microbiol 2006; 56:1847-1851. [PMID: 16902019 DOI: 10.1099/ijs.0.64325-0] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fourteen strains were isolated from nitrogen-fixing nodules on the roots of plants of the genus Mimosa growing in Taiwan, Brazil and Venezuela. On the basis of 16S rRNA gene sequence similarities, all of the strains were previously shown to be closely related to each other and to belong to the genus Burkholderia. A polyphasic approach, including DNA–DNA reassociation, whole-cell protein analysis, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains: all 14 strains were classified as representing a novel species, for which the name Burkholderia mimosarum sp. nov. is proposed. The type strain, PAS44T (=LMG 23256T =BCRC 17516T), was isolated from Mimosa pigra nodules in Taiwan.
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Affiliation(s)
- Wen-Ming Chen
- Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Road, Nan-Tzu, Kaohsiung City 811, Taiwan
| | - Euan K James
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Tom Coenye
- Laboratorium voor Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Jui-Hsing Chou
- Department of Soil Environmental Science, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Edmundo Barrios
- Tropical Soil Biology and Fertility Institute of Centro Internacional de Agricultura Tropical (TSBF-CIAT), A.A. 6713, Cali, Colombia
| | - Sergio M de Faria
- EMBRAPA-Agrobiologia, km 47, Seropedica, 23851-970 Rio de Janeiro, Brazil
| | | | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - Janet I Sprent
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Peter Vandamme
- Laboratorium voor Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
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26
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Barrett CF, Parker MA. Coexistence of Burkholderia, Cupriavidus, and Rhizobium sp. nodule bacteria on two Mimosa spp. in Costa Rica. Appl Environ Microbiol 2006; 72:1198-206. [PMID: 16461667 PMCID: PMC1392967 DOI: 10.1128/aem.72.2.1198-1206.2006] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
rRNA gene sequencing and PCR assays indicated that 215 isolates of root nodule bacteria from two Mimosa species at three sites in Costa Rica belonged to the genera Burkholderia, Cupriavidus, and Rhizobium. This is the first report of Cupriavidus sp. nodule symbionts for Mimosa populations within their native geographic range in the neotropics. Burkholderia spp. predominated among samples from Mimosa pigra (86% of isolates), while there was a more even distribution of Cupriavidus, Burkholderia, and Rhizobium spp. on Mimosa pudica (38, 37, and 25% of isolates, respectively). All Cupriavidus and Burkholderia genotypes tested formed root nodules and fixed nitrogen on both M. pigra and M. pudica, and sequencing of rRNA genes in strains reisolated from nodules verified identity with inoculant strains. Inoculation tests further indicated that both Cupriavidus and Burkholderia spp. resulted in significantly higher plant growth and nodule nitrogenase activity (as measured by acetylene reduction assays) relative to plant performance with strains of Rhizobium. Given the prevalence of Burkholderia and Cupriavidus spp. on these Mimosa legumes and the widespread distribution of these plants both within and outside the neotropics, it is likely that both beta-proteobacterial genera are more ubiquitous as root nodule symbionts than previously believed.
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Affiliation(s)
- Craig F Barrett
- Department of Biological Sciences, State University of New York, Binghamton, NY 13902, USA
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27
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Singh RK, Mishra RPN, Jaiswal HK, Kumar V, Pandey SP, Rao SB, Annapurna K. Isolation and identification of natural endophytic rhizobia from rice (Oryza sativa L.) through rDNA PCR-RFLP and sequence analysis. Curr Microbiol 2006; 52:345-9. [PMID: 16586025 DOI: 10.1007/s00284-005-0138-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Accepted: 11/14/2005] [Indexed: 11/24/2022]
Abstract
Three novel endophytic rhizobial strains (RRE3, RRE5, and RRE6) were isolated from naturally growing surface-sterilized rice roots. These isolates had the ability to nodulate common bean (Phaseolus vulgaris). Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and sequencing of 16S rDNA of these isolates revealed that RRE3 and RRE5 are phylogenetically very close to Burkholderia cepacia complex, whereas RRE6 has affinity with Rhizobium leguminosarum bv. phaseoli. Plant infection test using gusA reporter gene-tagged construct of these isolates indicated that bacterial cells can go inside and colonize the rice root interiors. A significant increase in biomass and grain yield was also recorded in greenhouse-grown rice plants inoculated with these isolates.
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Affiliation(s)
- Ramesh K Singh
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India.
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28
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Singh RK, Mishra RPN, Jaiswal HK, Kumar V, Pandey SP, Rao SB, Annapurna K. Isolation and Identification of Natural Endophytic Rhizobia from Rice (Oryza sativa L.) Through rDNA PCR-RFLP and Sequence Analysis. Curr Microbiol 2006; 52:117-22. [PMID: 16450073 DOI: 10.1007/s00284-005-0136-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 09/30/2005] [Indexed: 10/25/2022]
Abstract
Three novel endophytic rhizobial strains (RRE3, RRE5, and RRE6) were isolated from naturally growing surface sterilized rice roots. These isolates had the ability to nodulate common bean (Phaseolus vulgaris). Polymerase chain reaction-restriction fragment length polymorphism and sequencing of 16S rDNA of these isolates revealed that RRE3 and RRE5 are phylogenetically very close to Burkholderia cepacia complex, whereas RRE6 has affinity with Rhizobium leguminosarum bv. phaseoli. Plant infection test using gusA reporter gene tagged construct of these isolates indicated that bacterial cells can go inside and colonize the rice root interiors. A significant increase in biomass and grain yield was also recorded in greenhouse-grown rice plants inoculated with these isolates.
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Affiliation(s)
- Ramesh K Singh
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India.
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29
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Chen WM, de Faria SM, Straliotto R, Pitard RM, Simões-Araùjo JL, Chou JH, Chou YJ, Barrios E, Prescott AR, Elliott GN, Sprent JI, Young JPW, James EK. Proof that Burkholderia strains form effective symbioses with legumes: a study of novel Mimosa-nodulating strains from South America. Appl Environ Microbiol 2005; 71:7461-71. [PMID: 16269788 PMCID: PMC1287612 DOI: 10.1128/aem.71.11.7461-7471.2005] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twenty Mimosa-nodulating bacterial strains from Brazil and Venezuela, together with eight reference Mimosa-nodulating rhizobial strains and two other beta-rhizobial strains, were examined by amplified rRNA gene restriction analysis. They fell into 16 patterns and formed a single cluster together with the known beta-rhizobia, Burkholderia caribensis, Burkholderia phymatum, and Burkholderia tuberum. The 16S rRNA gene sequences of 15 of the 20 strains were determined, and all were shown to belong to the genus Burkholderia; four distinct clusters could be discerned, with strains isolated from the same host species usually clustering very closely. Five of the strains (MAP3-5, Br3407, Br3454, Br3461, and Br3469) were selected for further studies of the symbiosis-related genes nodA, the NodD-dependent regulatory consensus sequences (nod box), and nifH. The nodA and nifH sequences were very close to each other and to those of B. phymatum STM815, B. caribensis TJ182, and Cupriavidus taiwanensis LMG19424 but were relatively distant from those of B. tuberum STM678. In addition to nodulating their original hosts, all five strains could also nodulate other Mimosa spp., and all produced nodules on Mimosa pudica that had nitrogenase (acetylene reduction) activities and structures typical of effective N2-fixing symbioses. Finally, both wild-type and green fluorescent protein-expressing transconjugant strains of Br3461 and MAP3-5 produced N2-fixing nodules on their original hosts, Mimosa bimucronata (Br3461) and Mimosa pigra (MAP3-5), and hence this confirms strongly that Burkholderia strains can form effective symbioses with legumes.
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Affiliation(s)
- Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung City, Taiwan
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30
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Chen WM, James EK, Chou JH, Sheu SY, Yang SZ, Sprent JI. Beta-rhizobia from Mimosa pigra, a newly discovered invasive plant in Taiwan. THE NEW PHYTOLOGIST 2005; 168:661-75. [PMID: 16313648 DOI: 10.1111/j.1469-8137.2005.01533.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A total of 191 rhizobial isolates from the root nodules of three geographically separate populations of the invasive plant Mimosa pigra in Taiwan were examined using amplified rDNA restriction analysis, 16S rDNA sequences, protein profiles and ELISA. Of these, 96% were identified as Burkholderia and 4% as Cupriavidus taiwanensis. The symbiosis-essential genes nodA and nifH were present in two strains of Burkholderia (PAS44 and PTK47), and in one of C. taiwanensis (PAS15). All three could nodulate M. pigra. Light and electron microscopy studies with a green fluorescent protein transconjugant variant of strain PAS44 showed the presence of fluorescent bacteroids in M. pigra nodules. These bacteroids expressed the nifH protein, hence this is the first confirmation that Burkholderia is a genuine symbiont of legume nodules. The predominance of Burkholderia in Taiwanese M. pigra suggests that this species may have brought its symbionts from its native South America, rather than entering into association with the Taiwanese Mimosa symbiont C. taiwanensis which so successfully nodulates Mimosa pudica and Mimosa diplotricha.
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Affiliation(s)
- Wen-Ming Chen
- Department of Seafood Science, National Kaohsiung Marine University, 142 Hai-Chuan Road, Nan-Tzu, Kaohsiung City 811, Taiwan.
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