Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T

Abstract

The type strain of the prospective Bradyrhizobium shewense sp. nov. ERR11T, was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain Bradyrhizobium yuanmingense CCBAU 10071T, was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11T and CCBAU 10071T 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 CCBAU 10071T 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 Bradyrhizobium diazoefficiens USDA110T. 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 Bradyrhizobium arachidis LMG 26795T. The nodulation genes nolYA-nodD2D1YABCSUIJ-nolO-nodZ of ERR11T and CCBAU 10071T are organized in a similar way to the homologous genes identified in the genomes of USDA110T, Bradyrhizobium ottawaense USDA 4 and Bradyrhizobium liaoningense CCBAU 05525. The genomes harbor hupSLCFHK and hypBFDEmore » 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 B. ottawaense branch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11T and closely related sequences revealed that strains belonging to B. ottawaense branch (USDA4 and CCBAU15615), were the closest strains to the strain ERR11T with 95.2% ANI. Type strain ERR11T showed the highest DDH predicted value with CCBAU15615 (58.5%), followed by USDA 4 (53.1%). Nevertheless, the ANI and DDH values obtained between ERR11T and CCBAU 15615 or USDA 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 B. shewense sp. nov. with strain ERR11T (HAMBI 3532T=LMG 30162T) as the type strain.« less

Authors:
 [1];  [2];  [2];  [3];  [1]
+ Show Author Affiliations
  1. Univ. of Helsinki (Finland). Dept. of Environmental Sciences
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Univ. of Georgia, Athens, GA (United States). Dept. of Microbiology, Biological Sciences
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1529250
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Bradyrhizobium shewense sp. nov. ERR11T; Erythrina brucei; Bradyrhizobium yuanmingense CCBAU 10071T; Symbiotic; Ethiopia; Genome average nucleotide identity; Digital DNA-DNA hybridization

Citation Formats

Aserse, Aregu Amsalu, Woyke, Tanja, Kyrpides, Nikos C., Whitman, William B., and Lindström, Kristina. Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T. United States: N. p., 2017. Web. doi:10.1186/s40793-017-0283-x.
Copy to clipboard
Aserse, Aregu Amsalu, Woyke, Tanja, Kyrpides, Nikos C., Whitman, William B., & Lindström, Kristina. Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T. United States. https://doi.org/10.1186/s40793-017-0283-x
Copy to clipboard
Aserse, Aregu Amsalu, Woyke, Tanja, Kyrpides, Nikos C., Whitman, William B., and Lindström, Kristina. Tue . "Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T". United States. https://doi.org/10.1186/s40793-017-0283-x. https://www.osti.gov/servlets/purl/1529250.
Copy to clipboard
@article{osti_1529250,
title = {Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T},
author = {Aserse, Aregu Amsalu and Woyke, Tanja and Kyrpides, Nikos C. and Whitman, William B. and Lindström, Kristina},
abstractNote = {The type strain of the prospective Bradyrhizobium shewense sp. nov. ERR11T, was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain Bradyrhizobium yuanmingense CCBAU 10071T, was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11T and CCBAU 10071T 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 CCBAU 10071T 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 Bradyrhizobium diazoefficiens USDA110T. 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 Bradyrhizobium arachidis LMG 26795T. The nodulation genes nolYA-nodD2D1YABCSUIJ-nolO-nodZ of ERR11T and CCBAU 10071T are organized in a similar way to the homologous genes identified in the genomes of USDA110T, Bradyrhizobium ottawaense USDA 4 and Bradyrhizobium liaoningense CCBAU 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 B. ottawaense branch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11T and closely related sequences revealed that strains belonging to B. ottawaense branch (USDA4 and CCBAU15615), were the closest strains to the strain ERR11T with 95.2% ANI. Type strain ERR11T showed the highest DDH predicted value with CCBAU15615 (58.5%), followed by USDA 4 (53.1%). Nevertheless, the ANI and DDH values obtained between ERR11T and CCBAU 15615 or USDA 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 B. shewense sp. nov. with strain ERR11T (HAMBI 3532T=LMG 30162T) as the type strain.},
doi = {10.1186/s40793-017-0283-x},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 12,
place = {United States},
year = {Tue Dec 05 00:00:00 EST 2017},
month = {Tue Dec 05 00:00:00 EST 2017}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1186/s40793-017-0283-x
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 16 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Disparate origins of Bradyrhizobium symbionts for invasive populations of Cytisus scoparius ( Leguminosae ) in North America
journal, April 2014

  • Horn, Kevin; Parker, Ingrid M.; Malek, Wanda
  • FEMS Microbiology Ecology, Vol. 89, Issue 1
  • DOI: 10.1111/1574-6941.12335

Characterization of soybean bradyrhizobia for which serogroup affinities have not been identified
journal, June 2001

  • Berkum, Peter van; Fuhrmann, Jeffry J.
  • Canadian Journal of Microbiology, Vol. 47, Issue 6
  • DOI: 10.1139/w01-036

Shifting the genomic gold standard for the prokaryotic species definition
journal, October 2009

  • Richter, Michael; Rosselló-Móra, Ramon
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 45
  • DOI: 10.1073/pnas.0906412106

Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes?
journal, October 2009

  • Masson-Boivin, Catherine; Giraud, Eric; Perret, Xavier
  • Trends in Microbiology, Vol. 17, Issue 10
  • DOI: 10.1016/j.tim.2009.07.004

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
journal, October 2015

  • Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
  • Standards in Genomic Sciences, Vol. 10, Issue 1
  • DOI: 10.1186/s40793-015-0077-y

In Most Bradyrhizobium Groups Sequence Comparison of 16S-23S rDNA Internal Transcribed Spacer Regions Corroborates DNA-DNA Hybridizations
journal, January 2003

  • Willems, Anne; Munive, Antonio; de Lajudie, Philippe
  • Systematic and Applied Microbiology, Vol. 26, Issue 2
  • DOI: 10.1078/072320203322346056

Bradyrhizobium arachidis sp. nov., isolated from effective nodules of Arachis hypogaea grown in China
journal, March 2013

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
journal, February 2014

  • Kim, M.; Oh, H. -S.; Park, S. -C.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2
  • DOI: 10.1099/ijs.0.059774-0

Polyphasic evidence supporting the reclassification of Bradyrhizobium japonicum group Ia strains as Bradyrhizobium diazoefficiens sp. nov.
journal, March 2013

  • Delamuta, J. R. M.; Ribeiro, R. A.; Ormeno-Orrillo, E.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 9
  • DOI: 10.1099/ijs.0.049130-0

The complete denitrification pathway of the symbiotic, nitrogen-fixing bacterium Bradyrhizobium japonicum
journal, February 2005

  • Bedmar, E. J.; Robles, E. F.; Delgado, M. J.
  • Biochemical Society Transactions, Vol. 33, Issue 1
  • DOI: 10.1042/BST0330141

Crotalarieae and Genisteae of the South African Great Escarpment are nodulated by novel Bradyrhizobium species with unique and diverse symbiotic loci
journal, July 2016

  • Beukes, Chrizelle W.; Stępkowski, Tomasz; Venter, Stephanus N.
  • Molecular Phylogenetics and Evolution, Vol. 100
  • DOI: 10.1016/j.ympev.2016.04.011

Mosaic origins of Bradyrhizobium legume symbionts on the Caribbean island of Guadeloupe
journal, August 2014

DNA-DNA Reassociation Methods Applied to Microbial Taxonomy and Their Critical Evaluation
book, January 2006

  • Rosselló-Mora, Ramon
  • Molecular Identification, Systematics, and Population Structure of Prokaryotes
  • DOI: 10.1007/978-3-540-31292-5_2

High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010

  • Gnerre, S.; MacCallum, I.; Przybylski, D.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
  • DOI: 10.1073/pnas.1017351108

Solexa Ltd
journal, June 2004

Class I. Alphaproteobacteria class. nov.
book, January 2005

  • Garrity, George M.; Bell, Julia A.; Lilburn, Timothy
  • Bergey’s Manual® of Systematic Bacteriology
  • DOI: 10.1007/0-387-29298-5_1

Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

Influence of moisture stress on growth, dry matter yield and allocation, water use and water-use efficiency of four Indigofera species
journal, March 2007

  • Hassen, A.; Rethman, Nfg; Apostolides, Z.
  • African Journal of Range & Forage Science, Vol. 24, Issue 1
  • DOI: 10.2989/102201107780178195

Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations
journal, March 2015

  • Mousavi, Seyed Abdollah; Willems, Anne; Nesme, Xavier
  • Systematic and Applied Microbiology, Vol. 38, Issue 2
  • DOI: 10.1016/j.syapm.2014.12.003

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990

  • Woese, C. R.; Kandler, O.; Wheelis, M. L.
  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
  • DOI: 10.1073/pnas.87.12.4576

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997

Genome sequence-based species delimitation with confidence intervals and improved distance functions
journal, January 2013

  • Meier-Kolthoff, Jan P.; Auch, Alexander F.; Klenk, Hans-Peter
  • BMC Bioinformatics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2105-14-60

Cowpea and peanut in southern Africa are nodulated by diverse Bradyrhizobium strains harboring nodulation genes that belong to the large pantropical clade common in Africa
journal, September 2008

  • Steenkamp, Emma T.; Stępkowski, Tomasz; Przymusiak, Anna
  • Molecular Phylogenetics and Evolution, Vol. 48, Issue 3
  • DOI: 10.1016/j.ympev.2008.04.032

Complete genome sequence of the salmonella enterica serovar enteritidis bacteriophages fSE1C and fSE4C isolated from food matrices
journal, January 2017

  • Santander, Javier; Vasquez, Jose I.; Segovia, Cristopher
  • Standards in Genomic Sciences, Vol. 12, Issue 1
  • DOI: 10.1186/s40793-016-0218-y

Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010

IMG 4 version of the integrated microbial genomes comparative analysis system
journal, October 2013

  • Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt963

Microbial species delineation using whole genome sequences
journal, July 2015

  • Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia
  • Nucleic Acids Research, Vol. 43, Issue 14
  • DOI: 10.1093/nar/gkv657

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008

Bradyrhizobium subterraneum sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of groundnuts
journal, October 2015

  • Reinhold-Hurek, Barbara; Chimwamurombe, Percy; Grönemeyer, Jann Lasse
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 10
  • DOI: 10.1099/ijsem.0.000403

The global nitrogen cycle: changes and consequences
journal, January 1998

Bradyrhizobium huanghuaihaiense sp. nov., an effective symbiotic bacterium isolated from soybean (Glycine max L.) nodules
journal, October 2011

  • Zhang, Y. M.; Li, Y.; Chen, W. F.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue Pt 8
  • DOI: 10.1099/ijs.0.034546-0

Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains
journal, May 2015

  • Whitman, William B.; Woyke, Tanja; Klenk, Hans-Peter
  • Standards in Genomic Sciences, Vol. 10, Issue 1
  • DOI: 10.1186/s40793-015-0017-x

Diversity Among Fibrobacter Isolates: Towards a Phylogenetic Classification
journal, February 1992

EDGAR 2.0: an enhanced software platform for comparative gene content analyses
journal, April 2016

  • Blom, Jochen; Kreis, Julian; Spänig, Sebastian
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw255

Bradyrhizobium manausense sp. nov., isolated from effective nodules of Vigna unguiculata grown in Brazilian Amazonian rainforest soils
journal, April 2014

  • Silva, F. V.; De Meyer, S. E.; Simoes-Araujo, J. L.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 7
  • DOI: 10.1099/ijs.0.061259-0

Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of Crotalaria spp., Indigofera spp., Erythrina brucei and Glycine max growing in Ethiopia
journal, November 2012

  • Aserse, Aregu Amsalu; Räsänen, Leena A.; Aseffa, Fassil
  • Molecular Phylogenetics and Evolution, Vol. 65, Issue 2
  • DOI: 10.1016/j.ympev.2012.07.008

Bradyrhizobium daqingense sp. nov., isolated from soybean nodules
journal, April 2012

  • Wang, J. Y.; Wang, R.; Zhang, Y. M.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 2
  • DOI: 10.1099/ijs.0.034280-0

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
journal, November 2007

  • Pruesse, E.; Quast, C.; Knittel, K.
  • Nucleic Acids Research, Vol. 35, Issue 21
  • DOI: 10.1093/nar/gkm864

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species
journal, May 2015

  • Wang, Yi; Coleman-Derr, Devin; Chen, Guoping
  • Nucleic Acids Research, Vol. 43, Issue W1
  • DOI: 10.1093/nar/gkv487

Biosynthesis of the Iron-Molybdenum Cofactor of Nitrogenase
journal, October 2008

Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium)
journal, January 2008

  • Martens, M.; Dawyndt, P.; Coopman, R.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 1
  • DOI: 10.1099/ijs.0.65392-0

Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations
journal, May 2012

  • Tian, C. F.; Zhou, Y. J.; Zhang, Y. M.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 22
  • DOI: 10.1073/pnas.1120436109

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
journal, January 2010

  • Auch, Alexander F.; Klenk, Hans-Peter; Göker, Markus
  • Standards in Genomic Sciences, Vol. 2, Issue 1
  • DOI: 10.4056/sigs.541628

Expression of nir, nor and nos denitrification genes from Bradyrhizobium japonicum in soybean root nodules
journal, February 2004

The minimum information about a genome sequence (MIGS) specification
journal, May 2008

  • Field, Dawn; Garrity, George; Gray, Tanya
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1360

Phylogeny of the Rhizobium–Allorhizobium–Agrobacterium clade supports the delineation of Neorhizobium gen. nov.
journal, May 2014

  • Mousavi, Seyed Abdollah; Österman, Janina; Wahlberg, Niklas
  • Systematic and Applied Microbiology, Vol. 37, Issue 3
  • DOI: 10.1016/j.syapm.2013.12.007

Involvement of Bradyrhizobium japonicum denitrification in symbiotic nitrogen fixation by soybean plants subjected to flooding
journal, January 2011

Distinct Bradyrhizbium communities nodulate legumes native to temperate and tropical monsoon Australia
journal, May 2012

  • Stępkowski, Tomasz; Watkin, Elizabeth; McInnes, Alison
  • Molecular Phylogenetics and Evolution, Vol. 63, Issue 2
  • DOI: 10.1016/j.ympev.2011.12.020

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members
journal, October 2008

  • Itakura, Manabu; Saeki, Kazuhiko; Omori, Hirofumi
  • The ISME Journal, Vol. 3, Issue 3
  • DOI: 10.1038/ismej.2008.88

Phylogenetic clustering of Bradyrhizobium symbionts on legumes indigenous to North America
journal, April 2012

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
journal, January 2010

  • Auch, Alexander F.; von Jan, Mathias; Klenk, Hans-Peter
  • Standards in Genomic Sciences, Vol. 2, Issue 1
  • DOI: 10.4056/sigs.531120

List of new names and new combinations previously effectively, but not validly, published
journal, September 2015

  • Oren, Aharon; Garrity, George M.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 9
  • DOI: 10.1099/ijsem.0.000464

IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009

Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T
journal, October 2011

  • Kaneko, Takakazu; Maita, Hiroko; Hirakawa, Hideki
  • Genes, Vol. 2, Issue 4
  • DOI: 10.3390/genes2040763

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010

  • Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia
  • Nature Methods, Vol. 7, Issue 6
  • DOI: 10.1038/nmeth.1457

Nitrate-Dependent N 2 O Emission from Intact Soybean Nodules via Denitrification by Bradyrhizobium japonicum Bacteroids
journal, October 2011

  • Hirayama, Junta; Eda, Shima; Mitsui, Hisayuki
  • Applied and Environmental Microbiology, Vol. 77, Issue 24
  • DOI: 10.1128/AEM.06262-11

Cell biology and molecular basis of denitrification.
journal, January 1997

Class I. Alphaproteobacteria class. nov.
book, January 2005

Biosynthesis of the Iron-Molybdenum Cofactor of Nitrogenase
journal, March 2013

List of new names and new combinations previously effectively, but not validly, published
journal, April 2015

  • Oren, Aharon; Garrity, George M.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue Pt_4
  • DOI: 10.1099/ijs.0.000178

Alcohol pretreatment of stools effect on culturomics
journal, March 2020

List of new names and new combinations previously effectively, but not validly, published
journal, March 2020

  • Oren, Aharon; Garrity, George
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 3
  • DOI: 10.1099/ijsem.0.003991

List of new names and new combinations previously effectively, but not validly, published
journal, November 2017

  • Oren, Aharon; Garrity, George M.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 67, Issue 11
  • DOI: 10.1099/ijsem.0.002415

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
journal, May 2014

  • Kim, M.; Oh, H. -S.; Park, S. -C.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 5
  • DOI: 10.1099/ijs.0.064931-0

List of new names and new combinations previously effectively, but not validly, published
journal, July 2019

  • Oren, Aharon; Garrity, George M.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 7
  • DOI: 10.1099/ijsem.0.003452

List of new names and new combinations previously effectively, but not validly, published
journal, September 2013

  • Oren, Aharon; Garrity, George M.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 63, Issue Pt_9
  • DOI: 10.1099/ijs.0.056101-0

Involvement of Bradyrhizobium japonicum denitrification in symbiotic nitrogen fixation by soybean plants subjected to flooding
journal, January 2011

Bradyrhizobium arachidis sp. nov., isolated from effective nodules of Arachis hypogaea grown in China
journal, March 2013

Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes?
journal, October 2009

  • Masson-Boivin, Catherine; Giraud, Eric; Perret, Xavier
  • Trends in Microbiology, Vol. 17, Issue 10
  • DOI: 10.1016/j.tim.2009.07.004

Cowpea and peanut in southern Africa are nodulated by diverse Bradyrhizobium strains harboring nodulation genes that belong to the large pantropical clade common in Africa
journal, September 2008

  • Steenkamp, Emma T.; Stępkowski, Tomasz; Przymusiak, Anna
  • Molecular Phylogenetics and Evolution, Vol. 48, Issue 3
  • DOI: 10.1016/j.ympev.2008.04.032

Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of Crotalaria spp., Indigofera spp., Erythrina brucei and Glycine max growing in Ethiopia
journal, November 2012

  • Aserse, Aregu Amsalu; Räsänen, Leena A.; Aseffa, Fassil
  • Molecular Phylogenetics and Evolution, Vol. 65, Issue 2
  • DOI: 10.1016/j.ympev.2012.07.008

Molecular characterization of nosRZDFYLX genes coding for denitrifying nitrous oxide reductase of Bradyrhizobium japonicum
journal, April 2004

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members
journal, October 2008

  • Itakura, Manabu; Saeki, Kazuhiko; Omori, Hirofumi
  • The ISME Journal, Vol. 3, Issue 3
  • DOI: 10.1038/ismej.2008.88

The minimum information about a genome sequence (MIGS) specification
journal, May 2008

  • Field, Dawn; Garrity, George; Gray, Tanya
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1360

Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments
journal, June 2021

  • Pérez Castro, Sherlynette; Borton, Mikayla A.; Regan, Kathleen
  • The ISME Journal, Vol. 15, Issue 12
  • DOI: 10.1038/s41396-021-01026-5

Dietary palmitic acid promotes a prometastatic memory via Schwann cells
journal, November 2021

Shifting the genomic gold standard for the prokaryotic species definition
journal, October 2009

  • Richter, Michael; Rosselló-Móra, Ramon
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 45
  • DOI: 10.1073/pnas.0906412106

High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010

  • Gnerre, S.; MacCallum, I.; Przybylski, D.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
  • DOI: 10.1073/pnas.1017351108

Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations
journal, May 2012

  • Tian, C. F.; Zhou, Y. J.; Zhang, Y. M.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 22
  • DOI: 10.1073/pnas.1120436109

In Most Bradyrhizobium Groups Sequence Comparison of 16S-23S rDNA Internal Transcribed Spacer Regions Corroborates DNA-DNA Hybridizations
journal, January 2003

  • Willems, Anne; Munive, Antonio; de Lajudie, Philippe
  • Systematic and Applied Microbiology, Vol. 26, Issue 2
  • DOI: 10.1078/072320203322346056

IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
journal, November 2007

  • Pruesse, E.; Quast, C.; Knittel, K.
  • Nucleic Acids Research, Vol. 35, Issue 21
  • DOI: 10.1093/nar/gkm864

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species
journal, May 2015

  • Wang, Yi; Coleman-Derr, Devin; Chen, Guoping
  • Nucleic Acids Research, Vol. 43, Issue W1
  • DOI: 10.1093/nar/gkv487

Microbial species delineation using whole genome sequences
journal, July 2015

  • Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia
  • Nucleic Acids Research, Vol. 43, Issue 14
  • DOI: 10.1093/nar/gkv657

Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology.
journal, May 2002

  • Garrity, George M.; Trüper, Hans G.; Whitman, William B.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 3
  • DOI: 10.1099/00207713-52-3-1043

Characterization of rhizobia that nodulate legume species of the genus Lespedeza and description of Bradyrhizobium yuanmingense sp. nov.
journal, November 2002

  • Yao, Zhu Yun; Kan, Feng Ling; Wang, En Tao
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 6
  • DOI: 10.1099/00207713-52-6-2219

Polyphasic evidence supporting the reclassification of Bradyrhizobium japonicum group Ia strains as Bradyrhizobium diazoefficiens sp. nov.
journal, March 2013

  • Delamuta, J. R. M.; Ribeiro, R. A.; Ormeno-Orrillo, E.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 9
  • DOI: 10.1099/ijs.0.049130-0

Bradyrhizobium manausense sp. nov., isolated from effective nodules of Vigna unguiculata grown in Brazilian Amazonian rainforest soils
journal, April 2014

  • Silva, F. V.; De Meyer, S. E.; Simoes-Araujo, J. L.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 7
  • DOI: 10.1099/ijs.0.061259-0

Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada
journal, June 2014

  • Yu, X.; Cloutier, S.; Tambong, J. T.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 9
  • DOI: 10.1099/ijs.0.065540-0

Bradyrhizobium subterraneum sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of groundnuts
journal, October 2015

  • Reinhold-Hurek, Barbara; Chimwamurombe, Percy; Grönemeyer, Jann Lasse
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 10
  • DOI: 10.1099/ijsem.0.000403

List of new names and new combinations previously effectively, but not validly, published
journal, March 2018

  • Oren, Aharon; Garrity, George M.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 3
  • DOI: 10.1099/ijsem.0.002570

Phylogenetic clustering of Bradyrhizobium symbionts on legumes indigenous to North America
journal, April 2012

Expression of nir, nor and nos denitrification genes from Bradyrhizobium japonicum in soybean root nodules
journal, February 2004

Diversity and Evolution of Hydrogenase Systems in Rhizobia
journal, October 2002

Cell biology and molecular basis of denitrification
journal, December 1997

Characterization of soybean bradyrhizobia for which serogroup affinities have not been identified
journal, June 2001

  • Berkum, Peter van; Fuhrmann, Jeffry J.
  • Canadian Journal of Microbiology, Vol. 47, Issue 6
  • DOI: 10.1139/w01-036

Biosynthesis of the Iron-Molybdenum Cofactor of Nitrogenase
journal, October 2008

Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010

Genome sequence-based species delimitation with confidence intervals and improved distance functions
journal, January 2013

  • Meier-Kolthoff, Jan P.; Auch, Alexander F.; Klenk, Hans-Peter
  • BMC Bioinformatics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2105-14-60

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
journal, October 2015

  • Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
  • Standards in Genomic Sciences, Vol. 10, Issue 1
  • DOI: 10.1186/s40793-015-0077-y

Complete genome sequence of the salmonella enterica serovar enteritidis bacteriophages fSE1C and fSE4C isolated from food matrices
journal, January 2017

  • Santander, Javier; Vasquez, Jose I.; Segovia, Cristopher
  • Standards in Genomic Sciences, Vol. 12, Issue 1
  • DOI: 10.1186/s40793-016-0218-y

Influence of moisture stress on growth, dry matter yield and allocation, water use and water-use efficiency of four Indigofera species
journal, March 2007

  • Hassen, A.; Rethman, Nfg; Apostolides, Z.
  • African Journal of Range & Forage Science, Vol. 24, Issue 1
  • DOI: 10.2989/102201107780178195

Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T
journal, October 2011

  • Kaneko, Takakazu; Maita, Hiroko; Hirakawa, Hideki
  • Genes, Vol. 2, Issue 4
  • DOI: 10.3390/genes2040763

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
journal, January 2010

  • Auch, Alexander F.; von Jan, Mathias; Klenk, Hans-Peter
  • Standards in Genomic Sciences, Vol. 2, Issue 1
  • DOI: 10.4056/sigs.531120

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
journal, January 2010

  • Auch, Alexander F.; Klenk, Hans-Peter; Göker, Markus
  • Standards in Genomic Sciences, Vol. 2, Issue 1
  • DOI: 10.4056/sigs.541628
    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Minimal standards for the description of new genera and species of rhizobia and agrobacteria
    journal, July 2019

    • de Lajudie, Philippe M.; Andrews, Mitchell; Ardley, Julie
    • International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 7
    • DOI: 10.1099/ijsem.0.003426

    Description and complete genome sequence of Bradyrhizobium amphicarpaeae sp. nov., harbouring photosystem and nitrogen-fixation genes
    journal, September 2019

    • Bromfield, Eden S. P.; Cloutier, Sylvie; Nguyen, Hai D. T.
    • International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 9
    • DOI: 10.1099/ijsem.0.003569

    Bradyrhizobium niftali sp. nov., an effective nitrogen-fixing symbiont of partridge pea [Chamaecrista fasciculata (Michx.) Greene], a native caesalpinioid legume broadly distributed in the USA
    journal, November 2019

    • Klepa, Milena Serenato; Urquiaga, Maria Clara de Oliveira; Somasegaran, Padma
    • International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 11
    • DOI: 10.1099/ijsem.0.003640

    Diversity of Bradyrhizobia in Subsahara Africa: A Rich Resource
    journal, September 2018

    Widespread Distribution of Highly Adapted Bradyrhizobium Species Nodulating Diverse Legumes in Africa
    journal, February 2019

    Diversity of Bradyrhizobia in Subsahara Africa: A Rich Resource
    journal, September 2018

    Widespread Distribution of Highly Adapted Bradyrhizobium Species Nodulating Diverse Legumes in Africa
    journal, February 2019

      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections:

      Other research related to this record: