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Tak N, Bissa G, Gehlot HS. Methods for Isolation and Characterization of Nitrogen-Fixing Legume-Nodulating Bacteria. Methods Mol Biol 2020; 2057:119-143. [PMID: 31595476 DOI: 10.1007/978-1-4939-9790-9_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Symbiotic nitrogen fixation (SNF) is a characteristic feature of nodulating legumes. The wild legumes are comparatively less explored for their SNF ability; hence, it is essential to study nodulation and identify the microsymbiont diversity associated with them. This chapter aims to describe the methodology for nodule hunting; trapping, isolation, and characterization of root nodule bacteria (RNB) at phenotypic, genotypic, and symbiotic levels. The documentation of nodulating native legume species and the rhizobial diversity associated with them in various parts of world has gained attention as this symbiotic association provides fixed nitrogen, improves productivity of plants in an ecofriendly manner. Before field-based applications the symbiotic bacteria need to be assessed for their N fixing ability as well as characterized at molecular level. The phylogeny based on symbiosis-essential genes supplemented with the host-range studies helps in better understanding of the symbiotaxonomy of rhizobia. More efficient symbiotic couples need to be screened by cross-nodulation studies for their application in agricultural practices.
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Affiliation(s)
- Nisha Tak
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur, Rajasthan, India.
| | - Garima Bissa
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur, Rajasthan, India
| | - Hukam S Gehlot
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur, Rajasthan, India
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Rathi S, Tak N, Bissa G, Chouhan B, Ojha A, Adhikari D, Barik SK, Satyawada RR, Sprent JI, James EK, Gehlot HS. Selection of Bradyrhizobium or Ensifer symbionts by the native Indian caesalpinioid legume Chamaecrista pumila depends on soil pH and other edaphic and climatic factors. FEMS Microbiol Ecol 2018; 94:5089966. [DOI: 10.1093/femsec/fiy180] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/01/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Sonam Rathi
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
| | - Nisha Tak
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
| | - Garima Bissa
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
| | - Bhawana Chouhan
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
| | - Archana Ojha
- Department of Botany, North-Eastern Hill University, Shillong-793022, Meghalaya, India
| | - Dibyendu Adhikari
- Department of Botany, North-Eastern Hill University, Shillong-793022, Meghalaya, India
| | - Saroj K Barik
- Department of Botany, North-Eastern Hill University, Shillong-793022, Meghalaya, India
| | - Rama Rao Satyawada
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong-793022, Meghalaya, India
| | - Janet I Sprent
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Hukam S Gehlot
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
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Webb BA, Compton KK, Del Campo JSM, Taylor D, Sobrado P, Scharf BE. Sinorhizobium meliloti Chemotaxis to Multiple Amino Acids Is Mediated by the Chemoreceptor McpU. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:770-777. [PMID: 28745538 DOI: 10.1094/mpmi-04-17-0096-r] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The legume symbiont Sinorhizobium meliloti is chemoattracted to compounds exuded by germinating seeds of its host alfalfa. This response is mainly mediated by the S. meliloti chemoreceptor McpU. McpU also has a prominent contribution in sensing a synthetic amino acid (aa) mixture mimicking the amounts and composition observed in seed exudate. Here, we used the hydrogel capillary assay to quantify chemotactic responses of S. meliloti to individual aa exuded by germinating alfalfa seeds and to define the role of McpU in this behavior. S. meliloti exhibited positive chemotaxis responses to all proteinogenic aa, except for aspartate, and to citrulline, cystine, gamma-aminobutyric acid, and ornithine. Wild-type responses were diverse in intensity, while a strain lacking mcpU displayed strongly diminished responses. Differential scanning fluorimetry demonstrated interaction of the purified periplasmic region of McpU (McpU-PR) with the aa, except glutamate and aspartate. We additionally tested organic acids and sugars, but there were no significant interactions with the McpU ligand-binding domain, except for citrate. Using ligand displacement, we confirmed the interaction of McpU-PR with aa representing strong and weak attractants. Our results show that S. meliloti McpU is a broad-range aa receptor mediating differential responses to individual attractants, which does not bind negatively charged aa.
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Affiliation(s)
- Benjamin A Webb
- 1 Virginia Tech, Department of Biological Sciences, Life Sciences I, Blacksburg, VA 24061, U.S.A.; and
| | - K Karl Compton
- 1 Virginia Tech, Department of Biological Sciences, Life Sciences I, Blacksburg, VA 24061, U.S.A.; and
| | | | - Doris Taylor
- 1 Virginia Tech, Department of Biological Sciences, Life Sciences I, Blacksburg, VA 24061, U.S.A.; and
| | - Pablo Sobrado
- 2 Virginia Tech, Department of Biochemistry, Fralin Life Science Institute
| | - Birgit E Scharf
- 1 Virginia Tech, Department of Biological Sciences, Life Sciences I, Blacksburg, VA 24061, U.S.A.; and
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Tampakaki AP, Fotiadis CT, Ntatsi G, Savvas D. A novel symbiovar (aegeanense) of the genus Ensifer nodulates Vigna unguiculata. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:4314-4325. [PMID: 28220509 DOI: 10.1002/jsfa.8281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/10/2017] [Accepted: 02/16/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND Cowpea (Vigna unguiculata) forms nitrogen-fixing root nodules with diverse symbiotic bacteria, mainly slow-growing rhizobial species belonging to the genus Bradyrhizobium, although a few studies have reported the isolation of fast-growing rhizobia under laboratory and field conditions. Although much research has been done on cowpea-nodulating bacteria in various countries around the world, very limited information is available on cowpea rhizobia in European soils. The aim of this study was to study the genetic and phenotypic diversity of indigenous cowpea-nodulating rhizobia in Greece. RESULTS The genetic diversity of indigenous rhizobia associated with cowpea was investigated through a polyphasic approach. ERIC-PCR based fingerprinting analysis grouped the isolates into three groups. Based on the analysis of the 16S rRNA genes, IGS and on the concatenation of six housekeeping genes (recA, glnII, gyrB, truA, thrA and SMc00019), rhizobial isolates were classified within the species Ensifer fredii. However, symbiotic gene phylogenies, based on nodC, nifH and rhcRST genes, showed that the Ensifer isolates are markedly diverged from type and reference strains of E. fredii and formed one clearly separate cluster. The E. fredii strains were able to nodulate and fix nitrogen in cowpea but not in soybean and common bean. CONCLUSION The present study showed that cowpea is nodulated under field conditions by fast-growing rhizobia belonging to the species E. fredii. Based on the phylogenies, similarity levels of symbiotic genes and the host range, the Ensifer isolates may constitute a new symbiovar for which the name 'aegeanense' is proposed. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Anastasia P Tampakaki
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Christos T Fotiadis
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Georgia Ntatsi
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Savvas
- Laboratory of Vegetable Production, Department of Crop Science, Agricultural University of Athens, Athens, Greece
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Le Quéré A, Tak N, Gehlot HS, Lavire C, Meyer T, Chapulliot D, Rathi S, Sakrouhi I, Rocha G, Rohmer M, Severac D, Filali-Maltouf A, Munive JA. Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts. BMC Genomics 2017; 18:85. [PMID: 28088165 PMCID: PMC5237526 DOI: 10.1186/s12864-016-3447-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 12/20/2016] [Indexed: 02/06/2023] Open
Abstract
Background Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined. Results Draft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced. Genome based species delineation tools demonstrated that they belong to a new species of Ensifer. Comparison of its core genome with those of E. meliloti, E. medicae and E. fredii enabled the identification of a species conserved gene set. Predicted functions of associated proteins and pathway reconstruction revealed notably the presence of transport systems for octopine/nopaline and inositol phosphates. Phenotypic characterization of this new desert rhizobium species showed that it was capable to utilize malonate, to grow at 48 °C or under high pH while NaCl tolerance levels were comparable to other Ensifer species. Analysis of accessory genomes and plasmid profiling demonstrated the presence of large plasmids that varied in size from strain to strain. As symbiotic functions were found in the accessory genomes, the differences in symbiotic interactions between strains may be well related to the difference in plasmid content that could explain the different legumes with which they can develop the symbiosis. Conclusions The genomic analysis performed here confirms that the selected rhizobial strains isolated from desert regions in three continents belong to a new species. As until now only recovered from such harsh environment, we propose to name it Ensifer aridi. The presented genomic data offers a good basis to explore adaptations and functionalities that enable them to adapt to alkalinity, low water potential, salt and high temperature stresses. Finally, given the original phylogeographic distribution and the different hosts with which it can develop a beneficial symbiotic interaction, Ensifer aridi may provide new biotechnological opportunities for degraded land restoration initiatives in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3447-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antoine Le Quéré
- Laboratoire de Microbiologie et Biologie Moléculaire, Université Mohammed V, Av Ibn Batouta BP 1014, Rabat, Morocco. .,IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes UMR113, IRD/INRA/CIRAD/Montpellier SupAgro/Université de Montpellier, TA A82/J, Campus International de Baillarguet, 34398, Montpellier, Cedex 5, France.
| | - Nisha Tak
- BNF & Microbial Genomics Lab, Department of Botany, Jai Narain Vyas University, Jodhpur, 342001, India
| | - Hukam Singh Gehlot
- BNF & Microbial Genomics Lab, Department of Botany, Jai Narain Vyas University, Jodhpur, 342001, India
| | - Celine Lavire
- Université de Lyon, F69622, Lyon, France.,CNRS, UMR5557, Ecologie Microbienne and INRA, UMR1418, Université Lyon 1, Villeurbanne, France
| | - Thibault Meyer
- Université de Lyon, F69622, Lyon, France.,CNRS, UMR5557, Ecologie Microbienne and INRA, UMR1418, Université Lyon 1, Villeurbanne, France
| | - David Chapulliot
- Université de Lyon, F69622, Lyon, France.,CNRS, UMR5557, Ecologie Microbienne and INRA, UMR1418, Université Lyon 1, Villeurbanne, France
| | - Sonam Rathi
- BNF & Microbial Genomics Lab, Department of Botany, Jai Narain Vyas University, Jodhpur, 342001, India
| | - Ilham Sakrouhi
- Laboratoire de Microbiologie et Biologie Moléculaire, Université Mohammed V, Av Ibn Batouta BP 1014, Rabat, Morocco
| | - Guadalupe Rocha
- Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. IC10, Ciudad Universitaria, Col. San Manuel, CP 72570, Puebla, Mexico
| | - Marine Rohmer
- Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, Montpellier, Cedex, 34 094, France
| | - Dany Severac
- Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, Montpellier, Cedex, 34 094, France
| | - Abdelkarim Filali-Maltouf
- Laboratoire de Microbiologie et Biologie Moléculaire, Université Mohammed V, Av Ibn Batouta BP 1014, Rabat, Morocco
| | - Jose-Antonio Munive
- Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. IC10, Ciudad Universitaria, Col. San Manuel, CP 72570, Puebla, Mexico
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Multi locus sequence analysis and symbiotic characterization of novel Ensifer strains nodulating Tephrosia spp. in the Indian Thar Desert. Syst Appl Microbiol 2016; 39:534-545. [DOI: 10.1016/j.syapm.2016.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 11/23/2022]
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Gehlot HS, Ardley J, Tak N, Tian R, Poonar N, Meghwal RR, Rathi S, Tiwari R, Adnawani W, Seshadri R, Reddy TBK, Pati A, Woyke T, Pillay M, Markowitz V, Baeshen MN, Al-Hejin AM, Ivanova N, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India. Stand Genomic Sci 2016; 11:43. [PMID: 27340511 PMCID: PMC4918122 DOI: 10.1186/s40793-016-0157-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 05/18/2016] [Indexed: 11/17/2022] Open
Abstract
Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume P. cineraria (L.) Druce (Khejri), which is a keystone species that grows in arid and semi-arid regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as species of mimosoid trees and shrubs. Here we describe the features of Ensifer sp. PC2, together with genome sequence information and its annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into 171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.
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Affiliation(s)
- Hukam Singh Gehlot
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Julie Ardley
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Nisha Tak
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Rui Tian
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Neetu Poonar
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Raju R Meghwal
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Sonam Rathi
- BNF and Stress Biology Lab., Department of Botany, J.N. Vyas University, Jodhpur, 342001 India
| | - Ravi Tiwari
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Wan Adnawani
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
| | - Rekha Seshadri
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California USA
| | - Manoj Pillay
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California USA
| | - Mohammed N Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M Al-Hejin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California USA ; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- Centre for Studies, Murdoch University, Murdoch, Western Australia Australia
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Sakrouhi I, Belfquih M, Sbabou L, Moulin P, Bena G, Filali-Maltouf A, Le Quéré A. Recovery of symbiotic nitrogen fixing acacia rhizobia from Merzouga Desert sand dunes in South East Morocco – Identification of a probable new species of Ensifer adapted to stressed environments. Syst Appl Microbiol 2016; 39:122-31. [DOI: 10.1016/j.syapm.2016.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 11/17/2015] [Accepted: 01/14/2016] [Indexed: 10/22/2022]
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Terpolilli J, Garau G, Hill Y, Tian R, Howieson J, Bräu L, Goodwin L, Han J, Liolios K, Huntemann M, Pati A, Woyke T, Mavromatis K, Markowitz V, Ivanova N, Kyrpides N, Reeve W. Genome sequence of Ensifer medicae strain WSM1369; an effective microsymbiont of the annual legume Medicago sphaerocarpos. Stand Genomic Sci 2013; 9:420-30. [PMID: 24976897 PMCID: PMC4062641 DOI: 10.4056/sigs.4838624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ensifer medicae WSM1369 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago. WSM1369 was isolated in 1993 from a nodule recovered from the roots of Medicago sphaerocarpos growing at San Pietro di Rudas, near Aggius in Sardinia (Italy). WSM1369 is an effective microsymbiont of the annual forage legumes M. polymorpha and M. sphaerocarpos. Here we describe the features of E. medicae WSM1369, together with genome sequence information and its annotation. The 6,402,557 bp standard draft genome is arranged into 307 scaffolds of 307 contigs containing 6,656 protein-coding genes and 79 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
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Affiliation(s)
- Jason Terpolilli
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Giovanni Garau
- Dipartimento di Agraria, S.T.A.A., University of Sassari, Italy
| | - Yvette Hill
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Lambert Bräu
- School of Life and Environmental Sciences, Deakin University, Victoria, Australia
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Konstantinos Mavromatis
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
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