1
|
Basile LA, Lepek VC. Legume-rhizobium dance: an agricultural tool that could be improved? Microb Biotechnol 2021; 14:1897-1917. [PMID: 34318611 PMCID: PMC8449669 DOI: 10.1111/1751-7915.13906] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/29/2022] Open
Abstract
The specific interaction between rhizobia and legume roots leads to the development of a highly regulated process called nodulation, by which the atmospheric nitrogen is converted into an assimilable plant nutrient. This capacity is the basis for the use of bacterial inoculants for field crop cultivation. Legume plants have acquired tools that allow the entry of compatible bacteria. Likewise, plants can impose sanctions against the maintenance of nodules occupied by rhizobia with low nitrogen-fixing capacity. At the same time, bacteria must overcome different obstacles posed first by the environment and then by the legume. The present review describes the mechanisms involved in the regulation of the entire legume-rhizobium symbiotic process and the strategies and tools of bacteria for reaching the nitrogen-fixing state inside the nodule. Also, we revised different approaches to improve the nodulation process for a better crop yield.
Collapse
Affiliation(s)
- Laura A. Basile
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”Universidad Nacional de San Martín (IIB‐UNSAM‐CONICET)Av. 25 de Mayo y Francia, Gral. San Martín, Provincia de Buenos AiresBuenos AiresB1650HMPArgentina
| | - Viviana C. Lepek
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”Universidad Nacional de San Martín (IIB‐UNSAM‐CONICET)Av. 25 de Mayo y Francia, Gral. San Martín, Provincia de Buenos AiresBuenos AiresB1650HMPArgentina
| |
Collapse
|
2
|
Lindström K, Mousavi SA. Effectiveness of nitrogen fixation in rhizobia. Microb Biotechnol 2020; 13:1314-1335. [PMID: 31797528 PMCID: PMC7415380 DOI: 10.1111/1751-7915.13517] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/01/2022] Open
Abstract
Biological nitrogen fixation in rhizobia occurs primarily in root or stem nodules and is induced by the bacteria present in legume plants. This symbiotic process has fascinated researchers for over a century, and the positive effects of legumes on soils and their food and feed value have been recognized for thousands of years. Symbiotic nitrogen fixation uses solar energy to reduce the inert N2 gas to ammonia at normal temperature and pressure, and is thus today, especially, important for sustainable food production. Increased productivity through improved effectiveness of the process is seen as a major research and development goal. The interaction between rhizobia and their legume hosts has thus been dissected at agronomic, plant physiological, microbiological and molecular levels to produce ample information about processes involved, but identification of major bottlenecks regarding efficiency of nitrogen fixation has proven to be complex. We review processes and results that contributed to the current understanding of this fascinating system, with focus on effectiveness of nitrogen fixation in rhizobia.
Collapse
Affiliation(s)
- Kristina Lindström
- Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiFI‐00014HelsinkiFinland
| | - Seyed Abdollah Mousavi
- Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiFI‐00014HelsinkiFinland
| |
Collapse
|
3
|
Abreu I, Mihelj P, Raimunda D. Transition metal transporters in rhizobia: tuning the inorganic micronutrient requirements to different living styles. Metallomics 2020; 11:735-755. [PMID: 30734808 DOI: 10.1039/c8mt00372f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A group of bacteria known as rhizobia are key players in symbiotic nitrogen fixation (SNF) in partnership with legumes. After a molecular exchange, the bacteria end surrounded by a plant membrane forming symbiosomes, organelle-like structures, where they differentiate to bacteroids and fix nitrogen. This symbiotic process is highly dependent on dynamic nutrient exchanges between the partners. Among these are transition metals (TM) participating as inorganic and organic cofactors of fundamental enzymes. While the understanding of how plant transporters facilitate TMs to the very near environment of the bacteroid is expanding, our knowledge on how bacteroid transporters integrate to TM homeostasis mechanisms in the plant host is still limited. This is significantly relevant considering the low solubility and scarcity of TMs in soils, and the in crescendo gradient of TM bioavailability rhizobia faces during the infection and bacteroid differentiation processes. In the present work, we review the main metal transporter families found in rhizobia, their role in free-living conditions and, when known, in symbiosis. We focus on discussing those transporters which could play a significant role in TM-dependent biochemical and physiological processes in the bacteroid, thus paving the way towards an optimized SNF.
Collapse
Affiliation(s)
- Isidro Abreu
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | | | | |
Collapse
|
4
|
Zou Q, Luo S, Wu H, He D, Li X, Cheng G. A GMC Oxidoreductase GmcA Is Required for Symbiotic Nitrogen Fixation in Rhizobium leguminosarum bv. viciae. Front Microbiol 2020; 11:394. [PMID: 32265862 PMCID: PMC7105596 DOI: 10.3389/fmicb.2020.00394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/26/2020] [Indexed: 11/13/2022] Open
Abstract
GmcA is a FAD-containing enzyme belonging to the GMC (glucose-methanol-choline oxidase) family of oxidoreductases. A mutation in the Rhizobium leguminosarum gmcA gene was generated by homologous recombination. The mutation in gmcA did not affect the growth of R. leguminosarum, but it displayed decreased antioxidative capacity at H2O2 conditions higher than 5 mM. The gmcA mutant strain displayed no difference of glutathione reductase activity, but significantly lower level of the glutathione peroxidase activity than the wild type. Although the gmcA mutant was able to induce the formation of nodules, the symbiotic ability was severely impaired, which led to an abnormal nodulation phenotype coupled to a 30% reduction in the nitrogen fixation capacity. The observation on ultrastructure of 4-week pea nodules showed that the mutant bacteroids tended to start senescence earlier and accumulate poly-β-hydroxybutyrate (PHB) granules. In addition, the gmcA mutant was severely impaired in rhizosphere colonization. Real-time quantitative PCR showed that the gmcA gene expression was significantly up-regulated in all the detected stages of nodule development, and statistically significant decreases in the expression of the redoxin genes katG, katE, and ohrB were found in gmcA mutant bacteroids. LC-MS/MS analysis quantitative proteomics techniques were employed to compare differential gmcA mutant root bacteroids in response to the wild type infection. Sixty differentially expressed proteins were identified including 33 up-regulated and 27 down-regulated proteins. By sorting the identified proteins according to metabolic function, 15 proteins were transporter protein, 12 proteins were related to stress response and virulence, and 9 proteins were related to transcription factor activity. Moreover, nine proteins related to amino acid metabolism were over-expressed.
Collapse
Affiliation(s)
- Qian Zou
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Sha Luo
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Hetao Wu
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Donglan He
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Xiaohua Li
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Guojun Cheng
- Hubei Provincial Engineering and Technology Research Center for Resources and Utilization of Microbiology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| |
Collapse
|
5
|
Liang J, Hoffrichter A, Brachmann A, Marín M. Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont. Stand Genomic Sci 2018; 13:36. [PMID: 30534351 PMCID: PMC6280393 DOI: 10.1186/s40793-018-0336-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 11/10/2018] [Indexed: 11/10/2022] Open
Abstract
Rhizobia bacteria engage in nitrogen-fixing root nodule symbiosis, a mutualistic interaction with legume plants in which a bidirectional nutrient exchange takes place. Occasionally, this interaction is suboptimal resulting in the formation of ineffective nodules in which little or no atmospheric nitrogen fixation occurs. Rhizobium leguminosarum Norway induces ineffective nodules in a wide range of Lotus hosts. To investigate the basis of this phenotype, we sequenced the complete genome of Rl Norway and compared it to the genome of the closely related strain R. leguminosarum bv. viciae 3841. The genome comprises 7,788,085 bp, distributed on a circular chromosome containing 63% of the genomic information and five large circular plasmids. The functionally classified bacterial gene set is distributed evenly among all replicons. All symbiotic genes (nod, fix, nif) are located on the pRLN3 plasmid. Whole genome comparisons revealed differences in the metabolic repertoire and in protein secretion systems, but not in classical symbiotic genes.
Collapse
Affiliation(s)
- Juan Liang
- Institute of Genetics, Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Anne Hoffrichter
- Institute of Genetics, Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Andreas Brachmann
- Institute of Genetics, Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Macarena Marín
- Institute of Genetics, Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| |
Collapse
|
6
|
Complete Genome Sequence of the Symbiotic Strain Bradyrhizobium icense LMTR 13 T, Isolated from Lima Bean (Phaseolus lunatus) in Peru. GENOME ANNOUNCEMENTS 2018. [PMID: 29519840 PMCID: PMC5843721 DOI: 10.1128/genomea.00146-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The complete genome sequence of Bradyrhizobium icense LMTR 13T, a root nodule bacterium isolated from the legume Phaseolus lunatus, is reported here. The genome consists of a circular 8,322,773-bp chromosome which codes for a large and novel symbiotic island as well as genes putatively involved in soil and root colonization.
Collapse
|
7
|
Sánchez-Cañizares C, Jorrín B, Durán D, Nadendla S, Albareda M, Rubio-Sanz L, Lanza M, González-Guerrero M, Prieto RI, Brito B, Giglio MG, Rey L, Ruiz-Argüeso T, Palacios JM, Imperial J. Genomic Diversity in the Endosymbiotic Bacterium Rhizobium leguminosarum. Genes (Basel) 2018; 9:E60. [PMID: 29364862 PMCID: PMC5852556 DOI: 10.3390/genes9020060] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/16/2018] [Accepted: 01/22/2018] [Indexed: 12/22/2022] Open
Abstract
Rhizobium leguminosarum bv. viciae is a soil α-proteobacterium that establishes a diazotrophic symbiosis with different legumes of the Fabeae tribe. The number of genome sequences from rhizobial strains available in public databases is constantly increasing, although complete, fully annotated genome structures from rhizobial genomes are scarce. In this work, we report and analyse the complete genome of R. leguminosarum bv. viciae UPM791. Whole genome sequencing can provide new insights into the genetic features contributing to symbiotically relevant processes such as bacterial adaptation to the rhizosphere, mechanisms for efficient competition with other bacteria, and the ability to establish a complex signalling dialogue with legumes, to enter the root without triggering plant defenses, and, ultimately, to fix nitrogen within the host. Comparison of the complete genome sequences of two strains of R. leguminosarum bv. viciae, 3841 and UPM791, highlights the existence of different symbiotic plasmids and a common core chromosome. Specific genomic traits, such as plasmid content or a distinctive regulation, define differential physiological capabilities of these endosymbionts. Among them, strain UPM791 presents unique adaptations for recycling the hydrogen generated in the nitrogen fixation process.
Collapse
Affiliation(s)
- Carmen Sánchez-Cañizares
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
| | - Beatriz Jorrín
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
| | - David Durán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid (UAM), Ciudad Universitaria de Cantoblanco, Calle Francisco Tomás y Valiente 7, 28049 Madrid, Spain
| | - Suvarna Nadendla
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.N.); (M.G.G.)
| | - Marta Albareda
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Laura Rubio-Sanz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Mónica Lanza
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Rosa Isabel Prieto
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Belén Brito
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Michelle G. Giglio
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.N.); (M.G.G.)
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Tomás Ruiz-Argüeso
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - José M. Palacios
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 115 bis, 28006 Madrid, Spain
| |
Collapse
|
8
|
Aserse AA, Woyke T, Kyrpides NC, Whitman WB, Lindström K. Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11 T and Bradyrhizobium yuanmingense CCBAU 10071 T. Stand Genomic Sci 2017; 12:74. [PMID: 29225730 PMCID: PMC5717998 DOI: 10.1186/s40793-017-0283-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/21/2017] [Indexed: 01/01/2023] Open
Abstract
The type strain of the prospective 10.1601/nm.30737 sp. nov. ERR11T, was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain 10.1601/nm.1463 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T, was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11T and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T were sequenced by DOE-JGI and deposited at the DOE-JGI genome portal as well as at the European Nucleotide Archive. The genome of ERR11T is 9,163,226 bp in length and has 102 scaffolds, containing 8548 protein-coding and 86 RNA genes. The 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T genome is arranged in 108 scaffolds and consists of 8,201,522 bp long and 7776 protein-coding and 85 RNA genes. Both genomes contain symbiotic genes, which are homologous to the genes found in the complete genome sequence of 10.1601/nm.24498 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+110 T. The genes encoding for nodulation and nitrogen fixation in ERR11T showed high sequence similarity with homologous genes found in the draft genome of peanut-nodulating 10.1601/nm.27386 10.1601/strainfinder?urlappend=%3Fid%3DLMG+26795 T. The nodulation genes nolYA-nodD2D1YABCSUIJ-nolO-nodZ of ERR11T and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T are organized in a similar way to the homologous genes identified in the genomes of 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+110 T, 10.1601/nm.25806 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 and 10.1601/nm.1462 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+05525. The genomes harbor hupSLCFHK and hypBFDE genes that code the expression of hydrogenase, an enzyme that helps rhizobia to uptake hydrogen released by the N2-fixation process and genes encoding denitrification functions napEDABC and norCBQD for nitrate and nitric oxide reduction, respectively. The genome of ERR11T also contains nosRZDFYLX genes encoding nitrous oxide reductase. Based on multilocus sequence analysis of housekeeping genes, the novel species, which contains eight strains formed a unique group close to the 10.1601/nm.25806 branch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11T and closely related sequences revealed that strains belonging to 10.1601/nm.25806 branch (10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615), were the closest strains to the strain ERR11T with 95.2% ANI. Type strain ERR11T showed the highest DDH predicted value with 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615 (58.5%), followed by 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 (53.1%). Nevertheless, the ANI and DDH values obtained between ERR11T and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615 or 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 were below the cutoff values (ANI ≥ 96.5%; DDH ≥ 70%) for strains belonging to the same species, suggesting that ERR11T is a new species. Therefore, based on the phylogenetic analysis, ANI and DDH values, we formally propose the creation of 10.1601/nm.30737 sp. nov. with strain ERR11T (10.1601/strainfinder?urlappend=%3Fid%3DHAMBI+3532 T=10.1601/strainfinder?urlappend=%3Fid%3DLMG+30162 T) as the type strain.
Collapse
Affiliation(s)
- Aregu Amsalu Aserse
- Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | | | - William B Whitman
- Department of Microbiology, Biological Sciences, University of Georgia, Athens, USA
| | - Kristina Lindström
- Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|
9
|
Yan H, Xie JB, Ji ZJ, Yuan N, Tian CF, Ji SK, Wu ZY, Zhong L, Chen WX, Du ZL, Wang ET, Chen WF. Evolutionarily Conserved nodE, nodO, T1SS, and Hydrogenase System in Rhizobia of Astragalus membranaceus and Caragana intermedia. Front Microbiol 2017; 8:2282. [PMID: 29209294 PMCID: PMC5702008 DOI: 10.3389/fmicb.2017.02282] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/06/2017] [Indexed: 02/01/2023] Open
Abstract
Mesorhizobium species are the main microsymbionts associated with the medicinal or sand-fixation plants Astragalus membranaceus and Caragana intermedia (AC) in temperate regions of China, while all the Mesorhizobium strains isolated from each of these plants could nodulate both of them. However, Rhizobium yanglingense strain CCBAU01603 could nodulate AC plants and it's a high efficiency symbiotic and competitive strain with Caragana. Therefore, the common features shared by these symbiotic rhizobia in genera of Mesorhizobium and Rhizobium still remained undiscovered. In order to study the genomic background influencing the host preference of these AC symbiotic strains, the whole genomes of two (M. silamurunense CCBAU01550, M. silamurunense CCBAU45272) and five representative strains (M. septentrionale CCBAU01583, M. amorphae CCBAU01570, M. caraganae CCBAU01502, M. temperatum CCBAU01399, and R. yanglingense CCBAU01603) originally isolated from AC plants were sequenced, respectively. As results, type III secretion systems (T3SS) of AC rhizobia evolved in an irregular pattern, while an evolutionarily specific region including nodE, nodO, T1SS, and a hydrogenase system was detected to be conserved in all these AC rhizobia. Moreover, nodO was verified to be prevalently distributed in other AC rhizobia and was presumed as a factor affecting the nodule formation process. In conclusion, this research interpreted the multifactorial features of the AC rhizobia that may be associated with their host specificity at cross-nodulation group, including nodE, nodZ, T1SS as the possible main determinants; and nodO, hydrogenase system, and T3SS as factors regulating the bacteroid formation or nitrogen fixation efficiency.
Collapse
Affiliation(s)
- Hui Yan
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China.,State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian Bo Xie
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhao Jun Ji
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Na Yuan
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chang Fu Tian
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Shou Kun Ji
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhong Yu Wu
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Liang Zhong
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Zheng Lin Du
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico, Mexico
| | - Wen Feng Chen
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China
| |
Collapse
|
10
|
Ormeño-Orrillo E, Rey L, Durán D, Canchaya CA, Rogel MA, Zúñiga-Dávila D, Imperial J, Ruiz-Argüeso T, Martínez-Romero E. Draft genome sequence of Bradyrhizobium paxllaeri LMTR 21 T isolated from Lima bean ( Phaseolus lunatus) in Peru. GENOMICS DATA 2017; 13:38-40. [PMID: 28721334 PMCID: PMC5499027 DOI: 10.1016/j.gdata.2017.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/18/2017] [Accepted: 06/23/2017] [Indexed: 11/30/2022]
Abstract
Bradyrhizobium paxllaeri is a prevalent species in root nodules of the Lima bean (Phaseolus lunatus) in Peru. LMTR 21T is the type strain of the species and was isolated from a root nodule collected in an agricultural field in the Peruvian central coast. Its 8.29 Mbp genome encoded 7635 CDS, 71 tRNAs and 3 rRNAs genes. All genes required to stablish a nitrogen-fixing symbiosis with its host were present. The draft genome sequence and annotation have been deposited at GenBank under the accession number MAXB00000000.
Collapse
Affiliation(s)
- Ernesto Ormeño-Orrillo
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Luis Rey
- Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Spain
| | - David Durán
- Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Spain
| | - Carlos A Canchaya
- Departamento de Bioquímica, Genética e Immunología, Universidad de Vigo, Vigo 36310, Spain
| | - Marco A Rogel
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Doris Zúñiga-Dávila
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Juan Imperial
- Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Spain.,CSIC, Madrid, Spain
| | - Tomás Ruiz-Argüeso
- Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Spain
| | | |
Collapse
|
11
|
Degli Esposti M, Martinez Romero E. A survey of the energy metabolism of nodulating symbionts reveals a new form of respiratory complex I. FEMS Microbiol Ecol 2016; 92:fiw084. [DOI: 10.1093/femsec/fiw084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2016] [Indexed: 01/18/2023] Open
|
12
|
Bretschger O, Carpenter K, Phan T, Suzuki S, Ishii S, Grossi-Soyster E, Flynn M, Hogan J. Functional and taxonomic dynamics of an electricity-consuming methane-producing microbial community. BIORESOURCE TECHNOLOGY 2015; 195:254-264. [PMID: 26178785 DOI: 10.1016/j.biortech.2015.06.129] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 06/04/2023]
Abstract
The functional and taxonomic microbial dynamics of duplicate electricity-consuming methanogenic communities were observed over a 6 months period to characterize the reproducibility, stability and recovery of electromethanogenic consortia. The highest rate of methanogenesis was 0.72 mg-CH4/L/day, which occurred during the third month of enrichment when multiple methanogenic phylotypes and associated Desulfovibrionaceae phylotypes were present in the electrode-associated microbial community. Results also suggest that electromethanogenic microbial communities are very sensitive to electron donor-limiting open-circuit conditions. A 45 min exposure to open-circuit conditions induced an 87% drop in volumetric methane production rates. Methanogenic performance recovered after 4 months to a maximum value of 0.30 mg-CH4/L/day under set potential operation (-700 mV vs Ag/AgCl); however, current consumption and biomass production was variable over time. Long-term functional and taxonomic analyses from experimental replicates provide new knowledge toward understanding how to enrich electromethanogenic communities and operate bioelectrochemical systems for stable and reproducible performance.
Collapse
Affiliation(s)
| | | | - Tony Phan
- J. Craig Venter Institute, La Jolla, CA, USA
| | - Shino Suzuki
- J. Craig Venter Institute, La Jolla, CA, USA; Japan Agency for Marine-Earth Science and Technology, Kochi, Japan
| | - Shun'ichi Ishii
- J. Craig Venter Institute, La Jolla, CA, USA; Japan Agency for Marine-Earth Science and Technology, Kochi, Japan
| | - Elysse Grossi-Soyster
- University Affiliated Research Center, UC Santa Cruz, Moffett Field, CA, USA; Stanford University, Stanford, CA, USA; NASA Ames Research Center, Moffett Field, CA, USA
| | | | - John Hogan
- NASA Ames Research Center, Moffett Field, CA, USA
| |
Collapse
|
13
|
Rogel MA, Bustos P, Santamaría RI, González V, Romero D, Cevallos MÁ, Lozano L, Castro-Mondragón J, Martínez-Romero J, Ormeño-Orrillo E, Martínez-Romero E. Genomic basis of symbiovar mimosae in Rhizobium etli. BMC Genomics 2014; 15:575. [PMID: 25005495 PMCID: PMC4125696 DOI: 10.1186/1471-2164-15-575] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 07/01/2014] [Indexed: 11/25/2022] Open
Abstract
Background Symbiosis genes (nod and nif) involved in nodulation and nitrogen fixation in legumes are plasmid-borne in Rhizobium. Rhizobial symbiotic variants (symbiovars) with distinct host specificity would depend on the type of symbiosis plasmid. In Rhizobium etli or in Rhizobium phaseoli, symbiovar phaseoli strains have the capacity to form nodules in Phaseolus vulgaris while symbiovar mimosae confers a broad host range including different mimosa trees. Results We report on the genome of R. etli symbiovar mimosae strain Mim1 and its comparison to that from R. etli symbiovar phaseoli strain CFN42. Differences were found in plasmids especially in the symbiosis plasmid, not only in nod gene sequences but in nod gene content. Differences in Nod factors deduced from the presence of nod genes, in secretion systems or ACC-deaminase could help explain the distinct host specificity. Genes involved in P. vulgaris exudate uptake were not found in symbiovar mimosae but hup genes (involved in hydrogen uptake) were found. Plasmid pRetCFN42a was partially contained in Mim1 and a plasmid (pRetMim1c) was found only in Mim1. Chromids were well conserved. Conclusions The genomic differences between the two symbiovars, mimosae and phaseoli may explain different host specificity. With the genomic analysis presented, the term symbiovar is validated. Furthermore, our data support that the generalist symbiovar mimosae may be older than the specialist symbiovar phaseoli. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-575) contains supplementary material, which is available to authorized users.
Collapse
|
14
|
Ormeño-Orrillo E, Menna P, Almeida LGP, Ollero FJ, Nicolás MF, Pains Rodrigues E, Shigueyoshi Nakatani A, Silva Batista JS, Oliveira Chueire LM, Souza RC, Ribeiro Vasconcelos AT, Megías M, Hungria M, Martínez-Romero E. Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.). BMC Genomics 2012; 13:735. [PMID: 23270491 PMCID: PMC3557214 DOI: 10.1186/1471-2164-13-735] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 12/15/2012] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 are α-Proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. These strains are broadly used in commercial inoculants for application to common bean (Phaseolus vulgaris) in South America and Africa. Both strains display intrinsic resistance to several abiotic stressful conditions such as low soil pH and high temperatures, which are common in tropical environments, and to several antimicrobials, including pesticides. The genetic determinants of these interesting characteristics remain largely unknown. RESULTS Genome sequencing revealed that CIAT 899 and PRF 81 share a highly-conserved symbiotic plasmid (pSym) that is present also in Rhizobium leucaenae CFN 299, a rhizobium displaying a similar host range. This pSym seems to have arisen by a co-integration event between two replicons. Remarkably, three distinct nodA genes were found in the pSym, a characteristic that may contribute to the broad host range of these rhizobia. Genes for biosynthesis and modulation of plant-hormone levels were also identified in the pSym. Analysis of genes involved in stress response showed that CIAT 899 and PRF 81 are well equipped to cope with low pH, high temperatures and also with oxidative and osmotic stresses. Interestingly, the genomes of CIAT 899 and PRF 81 had large numbers of genes encoding drug-efflux systems, which may explain their high resistance to antimicrobials. Genome analysis also revealed a wide array of traits that may allow these strains to be successful rhizosphere colonizers, including surface polysaccharides, uptake transporters and catabolic enzymes for nutrients, diverse iron-acquisition systems, cell wall-degrading enzymes, type I and IV pili, and novel T1SS and T5SS secreted adhesins. CONCLUSIONS Availability of the complete genome sequences of CIAT 899 and PRF 81 may be exploited in further efforts to understand the interaction of tropical rhizobia with common bean and other legume hosts.
Collapse
Affiliation(s)
- Ernesto Ormeño-Orrillo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pâmela Menna
- Embrapa Soja, C. P. 231, Londrina, Paraná, 86001-970, Brazil
| | - Luiz Gonzaga P Almeida
- Laboratório Nacional de Computação Científica (LNCC), Avenida Getúlio Vargas 333, Petrópolis, Rio de Janeiro, Brazil
| | | | - Marisa Fabiana Nicolás
- Laboratório Nacional de Computação Científica (LNCC), Avenida Getúlio Vargas 333, Petrópolis, Rio de Janeiro, Brazil
| | | | | | | | | | - Rangel Celso Souza
- Laboratório Nacional de Computação Científica (LNCC), Avenida Getúlio Vargas 333, Petrópolis, Rio de Janeiro, Brazil
| | | | - Manuel Megías
- Universidad de Sevilla, Apdo Postal 874, Sevilla, 41080, Spain
| | | | | |
Collapse
|
15
|
Kaneko T, Maita H, Hirakawa H, Uchiike N, Minamisawa K, Watanabe A, Sato S. Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T. Genes (Basel) 2011; 2:763-87. [PMID: 24710291 PMCID: PMC3927601 DOI: 10.3390/genes2040763] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 10/11/2011] [Accepted: 10/12/2011] [Indexed: 12/03/2022] Open
Abstract
The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.
Collapse
Affiliation(s)
- Takakazu Kaneko
- Faculty of Engineering, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.
| | - Hiroko Maita
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
| | - Nobukazu Uchiike
- Faculty of Engineering, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
| | - Akiko Watanabe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
| |
Collapse
|
16
|
Brito B, Prieto RI, Cabrera E, Mandrand-Berthelot MA, Imperial J, Ruiz-Argüeso T, Palacios JM. Rhizobium leguminosarum hupE encodes a nickel transporter required for hydrogenase activity. J Bacteriol 2010; 192:925-35. [PMID: 20023036 PMCID: PMC2812973 DOI: 10.1128/jb.01045-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 12/07/2009] [Indexed: 02/04/2023] Open
Abstract
Synthesis of the hydrogen uptake (Hup) system in Rhizobium leguminosarum bv. viciae requires the function of an 18-gene cluster (hupSLCDEFGHIJK-hypABFCDEX). Among them, the hupE gene encodes a protein showing six transmembrane domains for which a potential role as a nickel permease has been proposed. In this paper, we further characterize the nickel transport capacity of HupE and that of the translated product of hupE2, a hydrogenase-unlinked gene identified in the R. leguminosarum genome. HupE2 is a potential membrane protein that shows 48% amino acid sequence identity with HupE. Expression of both genes in the Escherichia coli nikABCDE mutant strain HYD723 restored hydrogenase activity and nickel transport. However, nickel transport assays revealed that HupE and HupE2 displayed different levels of nickel uptake. Site-directed mutagenesis of histidine residues in HupE revealed two motifs (HX(5)DH and FHGX[AV]HGXE) that are required for HupE functionality. An R. leguminosarum double mutant, SPF22A (hupE hupE2), exhibited reduced levels of hydrogenase activity in free-living cells, and this phenotype was complemented by nickel supplementation. Low levels of symbiotic hydrogenase activity were also observed in SPF22A bacteroid cells from lentil (Lens culinaris L.) root nodules but not in pea (Pisum sativum L.) bacteroids. Moreover, heterologous expression of the R. leguminosarum hup system in bacteroid cells of Rhizobium tropici and Mesorhizobium loti displayed reduced levels of hydrogen uptake in the absence of hupE. These data support the role of R. leguminosarum HupE as a nickel permease required for hydrogen uptake under both free-living and symbiotic conditions.
Collapse
Affiliation(s)
- Belén Brito
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Rosa-Isabel Prieto
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Ezequiel Cabrera
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Marie-Andrée Mandrand-Berthelot
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Juan Imperial
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Tomás Ruiz-Argüeso
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - José-Manuel Palacios
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40, km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain, Université Lyon, F-69622 Lyon, Université Lyon 1, Villeurbanne, INSA de Lyon, F-69621 Villeurbanne, and CNRS UMR5240 Microbiologie, Adaptation et Pathogénie, Lyon, France, Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| |
Collapse
|
17
|
Salinero KK, Keller K, Feil WS, Feil H, Trong S, Di Bartolo G, Lapidus A. Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation. BMC Genomics 2009; 10:351. [PMID: 19650930 PMCID: PMC2907700 DOI: 10.1186/1471-2164-10-351] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Accepted: 08/03/2009] [Indexed: 12/24/2022] Open
Abstract
Background Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for this microbe. It is considered to be a free-living organism. Results The a priori prediction that the D. aromatica genome would contain previously characterized "central" enzymes to support anaerobic aromatic degradation of benzene proved to be false, suggesting the presence of novel anaerobic aromatic degradation pathways in this species. These missing pathways include the benzylsuccinate synthase (bssABC) genes (responsible for fumarate addition to toluene) and the central benzoyl-CoA pathway for monoaromatics. In depth analyses using existing TIGRfam, COG, and InterPro models, and the creation of de novo HMM models, indicate a highly complex lifestyle with a large number of environmental sensors and signaling pathways, including a relatively large number of GGDEF domain signal receptors and multiple quorum sensors. A number of proteins indicate interactions with an as yet unknown host, as indicated by the presence of predicted cell host remodeling enzymes, effector enzymes, hemolysin-like proteins, adhesins, NO reductase, and both type III and type VI secretory complexes. Evidence of biofilm formation including a proposed exopolysaccharide complex and exosortase (epsH) are also present. Annotation described in this paper also reveals evidence for several metabolic pathways that have yet to be observed experimentally, including a sulphur oxidation (soxFCDYZAXB) gene cluster, Calvin cycle enzymes, and proteins involved in nitrogen fixation in other species (including RubisCo, ribulose-phosphate 3-epimerase, and nif gene families, respectively). Conclusion Analysis of the D. aromatica genome indicates there is much to be learned regarding the metabolic capabilities, and life-style, for this microbial species. Examples of recent gene duplication events in signaling as well as dioxygenase clusters are present, indicating selective gene family expansion as a relatively recent event in D. aromatica's evolutionary history. Gene families that constitute metabolic cycles presumed to create D. aromatica's environmental 'foot-print' indicate a high level of diversification between its predicted capabilities and those of its close relatives, A. aromaticum str EbN1 and Azoarcus BH72.
Collapse
|
18
|
Lee KB, De Backer P, Aono T, Liu CT, Suzuki S, Suzuki T, Kaneko T, Yamada M, Tabata S, Kupfer DM, Najar FZ, Wiley GB, Roe B, Binnewies TT, Ussery DW, D'Haeze W, Herder JD, Gevers D, Vereecke D, Holsters M, Oyaizu H. The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571. BMC Genomics 2008; 9:271. [PMID: 18522759 PMCID: PMC2443382 DOI: 10.1186/1471-2164-9-271] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 06/04/2008] [Indexed: 11/17/2022] Open
Abstract
Background Biological nitrogen fixation is a prokaryotic process that plays an essential role in the global nitrogen cycle. Azorhizobium caulinodans ORS571 has the dual capacity to fix nitrogen both as free-living organism and in a symbiotic interaction with Sesbania rostrata. The host is a fast-growing, submergence-tolerant tropical legume on which A. caulinodans can efficiently induce nodule formation on the root system and on adventitious rootlets located on the stem. Results The 5.37-Mb genome consists of a single circular chromosome with an overall average GC of 67% and numerous islands with varying GC contents. Most nodulation functions as well as a putative type-IV secretion system are found in a distinct symbiosis region. The genome contains a plethora of regulatory and transporter genes and many functions possibly involved in contacting a host. It potentially encodes 4717 proteins of which 96.3% have homologs and 3.7% are unique for A. caulinodans. Phylogenetic analyses show that the diazotroph Xanthobacter autotrophicus is the closest relative among the sequenced genomes, but the synteny between both genomes is very poor. Conclusion The genome analysis reveals that A. caulinodans is a diazotroph that acquired the capacity to nodulate most probably through horizontal gene transfer of a complex symbiosis island. The genome contains numerous genes that reflect a strong adaptive and metabolic potential. These combined features and the availability of the annotated genome make A. caulinodans an attractive organism to explore symbiotic biological nitrogen fixation beyond leguminous plants.
Collapse
Affiliation(s)
- Kyung-Bum Lee
- Laboratory of Plant Biotechnology, Biotechnology Research Center, University of Tokyo, Tokyo 113-8657, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains. ISME JOURNAL 2008; 2:158-70. [DOI: 10.1038/ismej.2007.105] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
20
|
Ishii S, Shimoyama T, Hotta Y, Watanabe K. Characterization of a filamentous biofilm community established in a cellulose-fed microbial fuel cell. BMC Microbiol 2008; 8:6. [PMID: 18186940 PMCID: PMC2254626 DOI: 10.1186/1471-2180-8-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Accepted: 01/10/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial fuel cells (MFCs) are devices that exploit microorganisms to generate electric power from organic matter. Despite the development of efficient MFC reactors, the microbiology of electricity generation remains to be sufficiently understood. RESULTS A laboratory-scale two-chamber microbial fuel cell (MFC) was inoculated with rice paddy field soil and fed cellulose as the carbon and energy source. Electricity-generating microorganisms were enriched by subculturing biofilms that attached onto anode electrodes. An electric current of 0.2 mA was generated from the first enrichment culture, and ratios of the major metabolites (e.g., electric current, methane and acetate) became stable after the forth enrichment. In order to investigate the electrogenic microbial community in the anode biofilm, it was morphologically analyzed by electron microscopy, and community members were phylogenetically identified by 16S rRNA gene clone-library analyses. Electron microscopy revealed that filamentous cells and rod-shaped cells with prosthecae-like filamentous appendages were abundantly present in the biofilm. Filamentous cells and appendages were interconnected via thin filaments. The clone library analyses frequently detected phylotypes affiliated with Clostridiales, Chloroflexi, Rhizobiales and Methanobacterium. Fluorescence in-situ hybridization revealed that the Rhizobiales population represented rod-shaped cells with filamentous appendages and constituted over 30% of the total population. CONCLUSION Bacteria affiliated with the Rhizobiales constituted the major population in the cellulose-fed MFC and exhibited unique morphology with filamentous appendages. They are considered to play important roles in the cellulose-degrading electrogenic community.
Collapse
Affiliation(s)
- Shun'ichi Ishii
- Marine Biotechnology Institute, Heita, Kamaishi, Iwate 026-000, Japan.
| | | | | | | |
Collapse
|
21
|
Maimaiti J, Zhang Y, Yang J, Cen YP, Layzell DB, Peoples M, Dong Z. Isolation and characterization of hydrogen-oxidizing bacteria induced following exposure of soil to hydrogen gas and their impact on plant growth. Environ Microbiol 2007; 9:435-44. [PMID: 17222141 DOI: 10.1111/j.1462-2920.2006.01155.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In many legumes, the nitrogen fixing root nodules produce H2 gas that diffuses into soil. It has been demonstrated that such exposure of soil to H2 can promote plant growth. To assess whether this may be due to H2-oxidizing microorganisms, bacteria were isolated from soil treated with H2 under laboratory conditions and from soils collected adjacent to H2 producing soybean nodules. Nineteen isolates of H2-oxidizing bacteria were obtained and all exhibited a half-saturation coefficient (Ks) for H2 of about 1 ml l(-1). The isolates were identified as Variovorax paradoxus, Flavobacterium johnsoniae and Burkholderia spp. using conventional microbiological tests and 16S rRNA gene sequence analysis. Seventeen of the isolates enhanced (57-254%) root elongation of spring wheat seedlings. Using an Arabidopsis thaliana bioassay, plant biomass was increased by 11-27% when inoculated by one of four isolates of V. paradoxus or one isolate of Burkholderia that were selected for evaluation. The isolates of V. paradoxus found in both H2-treated soil and in soil adjacent to soybean nodules had the greatest impact on plant growth. The results are consistent with the hypothesis that H2-oxidizing bacteria in soils have plant growth promoting properties.
Collapse
Affiliation(s)
- Jiamila Maimaiti
- Department of Biology, St. Mary's University, Halifax, NS, Canada, B3H 3C3
| | | | | | | | | | | | | |
Collapse
|
22
|
Baginsky C, Brito B, Imperial J, Ruiz-Argüeso T, Palacios JM. Symbiotic hydrogenase activity in Bradyrhizobium sp. (Vigna) increases nitrogen content in Vigna unguiculata plants. Appl Environ Microbiol 2005; 71:7536-8. [PMID: 16269797 PMCID: PMC1287714 DOI: 10.1128/aem.71.11.7536-7538.2005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium sp. (Lupinus) and Bradyrhizobium sp. (Vigna) mutants in which hydrogenase (hup) activity was affected were constructed and analyzed. Vigna unguiculata plants inoculated with the Bradyrhizobium sp. (Vigna) hup mutant showed reduced nitrogenase activity and also a significant decrease in nitrogen content, suggesting a relevant contribution of hydrogenase activity to plant yield.
Collapse
Affiliation(s)
- Cecilia Baginsky
- Laboratory of Microbiology, Department of Biotechnology, E.T.S. Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | | | | | | | | |
Collapse
|
23
|
Fernández D, Toffanin A, Palacios JM, Ruiz-Argüeso T, Imperial J. Hydrogenase genes are uncommon and highly conserved in Rhizobium leguminosarum bv. viciae. FEMS Microbiol Lett 2005; 253:83-8. [PMID: 16216440 DOI: 10.1016/j.femsle.2005.09.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 09/14/2005] [Accepted: 09/14/2005] [Indexed: 11/30/2022] Open
Abstract
A screening for hydrogen uptake (hup) genes in Rhizobium leguminosarum bv. viciae isolates from different locations within Spain identified no Hup+ strains, confirming the scarcity of the Hup trait in R. leguminosarum. However, five new Hup+ strains were isolated from Ni-rich soils from Italy and Germany. The hup gene variability was studied in these strains and in six available strains isolated from North America. Sequence analysis of three regions within the hup cluster showed an unusually high conservation among strains, with only 0.5-0.6% polymorphic sites, suggesting that R. leguminosarum acquired hup genes de novo in a very recent event.
Collapse
Affiliation(s)
- Domingo Fernández
- Laboratorio de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, s/n, 28040 Madrid, Spain
| | | | | | | | | |
Collapse
|
24
|
Brito B, Baginsky C, Palacios JM, Cabrera E, Ruiz-Argüeso T, Imperial J. Biodiversity of uptake hydrogenase systems from legume endosymbiotic bacteria. Biochem Soc Trans 2005; 33:33-5. [PMID: 15667257 DOI: 10.1042/bst0330033] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Uptake hydrogenases in legume endosymbiotic bacteria recycle hydrogen produced during the nitrogen fixation process in legume nodules. Despite the described beneficial effect on plant productivity, the hydrogen oxidation capability is not widespread in the Rhizobiaceae family. Characterization of hydrogenase gene clusters in strains belonging to Rhizobium, Bradyrhizobium and Azorhizobium reveals a similar overall genetic organization along with important differences in gene regulation. In addition, phylogenetic analysis of hup genes indicates distinct evolutionary origins for hydrogenase genes in Rhizobia.
Collapse
Affiliation(s)
- B Brito
- Laboratorio de Microbiología, E.T.S. Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | | | | | | | | | | |
Collapse
|
25
|
Root-based N2-fixing symbioses: Legumes, actinorhizal plants, Parasponia sp. and cycads. PLANT ECOPHYSIOLOGY 2005. [DOI: 10.1007/1-4020-4099-7_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
26
|
Parro V, Moreno-Paz M. Nitrogen fixation in acidophile iron-oxidizing bacteria: The nif regulon of Leptospirillum ferrooxidans. Res Microbiol 2004; 155:703-9. [PMID: 15501646 DOI: 10.1016/j.resmic.2004.05.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Accepted: 05/26/2004] [Indexed: 10/26/2022]
Abstract
The Gram-negative iron-oxidizing bacterium Leptospirillum ferrooxidans contains all genes necessary for nitrogen fixation, from genes encoding the Mo-Fe nitrogenase, the specific regulator (nifA), global regulators like glnB and ntrC like genes, to other sensors and transport systems somehow related to nitrogen assimilation. We review current knowledge about the nif regulon and its connection with other metabolic functions in L. ferrooxidans.
Collapse
Affiliation(s)
- Víctor Parro
- Laboratorio de Ecología Molecular, Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain.
| | | |
Collapse
|
27
|
Baginsky C, Palacios JM, Imperial J, Ruiz-Argüeso T, Brito B. Molecular and functional characterization of the Azorhizobium caulinodans ORS571 hydrogenase gene cluster. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09723.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
28
|
Parro V, Moreno-Paz M. Gene function analysis in environmental isolates: the nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans. Proc Natl Acad Sci U S A 2003; 100:7883-8. [PMID: 12808145 PMCID: PMC164682 DOI: 10.1073/pnas.1230487100] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A random genomic library from an environmental isolate of the Gram-negative bacterium Leptospirillum ferrooxidans has been printed on a microarray. Gene expression analysis was carried out with total RNA extracted from L. ferrooxidans cultures in the presence or absence of ammonium as nitrogen source under aerobic conditions. Although practically nothing is known about the genome sequence of this bacterium, this approach allowed us the selection and sequencing of only those clones bearing genes that showed an altered expression pattern. By sequence comparison, we have identified most of the genes of nitrogen fixation regulon in L. ferrooxidans, like the nifHDKENX operon, encoding the structural components of Mo-Fe nitrogenase; nifSU-hesB-hscBA-fdx operon, for Fe-S cluster assembly; the amtB gene (ammonium transporter); modA (molybdenum ABC type transporter); some regulatory genes like ntrC, nifA (the specific activator of nif genes); or two glnB-like genes (encoding the PII regulatory protein). Our results show that shotgun DNA microarrays are very powerful tools to accomplish gene expression studies with environmental bacteria whose genome sequence is still unknown, avoiding the time and effort necessary for whole genome sequencing projects.
Collapse
Affiliation(s)
- Victor Parro
- Laboratorio de Ecología Molecular, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial Esteban Terradas, Madrid, Spain.
| | | |
Collapse
|