Publications
Publications of the subcommittee
Minimal Standards
The subcommittee guidance to be read before writing any rhizobium/agrobacterium taxonomy manuscript!
2019: de Lajudie P et al. Minimal standards for the description of new genera and species of rhizobia and agrobacteria, Int J Syst Evol Microbiol 69:1852-1863; doi:10.1099/ijsem.0.003426.
Minutes of the Subcommittee
2023: Mousavi SA and Young JPW, Int J Syst Evol Microbiol; doi:10.1099/ijsem.0.005856
2022: Mousavi SA and Young JPW, Int J Syst Evol Microbiol; doi:10.1099/ijsem.0.005453
2021: de Lajudie P, Mousavi SA, and Young JPW, Int J Syst Evol Microbiol ; doi:/10.1099/ijsem.0.004784
2020: de Lajudie P and Young JPW, Int J Syst Evol Microbiol ; doi:10.1099/ijsem.0.004157.
2018: de Lajudie P and Young JPW, Int J Syst Evol Microbiol 69:1835-1840; doi:10.1099/ijsem.0.003335.
2017: de Lajudie P and Young JPW, Int J Syst Evol Microbiol 68:3363–3368; doi:10.1099/ijsem.0.002974.
2016: de Lajudie P and Young JPW, Int J Syst Evol Microbiol 67:2485-2494; doi:10.1099/ijsem.0.002144.
2014: de Lajudie P and Martinez-Romero E, Int J Syst Evol Microbiol 67(2):516-520. doi:10.1099/ijsem.0.001597.
2010: Lindström K and Martinez-Romero E, Int J Syst Evol Microbiol 61:3089-3093; doi:10.1099/ijs.0.036913-0.
2008: Lindström K and Young JPW, Int J Syst Evol Microbiol 59:921-922; doi:10.1099/ijs.0.012583-0.
2006: Lindström K and Martinez-Romero E, Int J Syst Evol Microbiol 57:1365-1366; doi:10.1099/ijs.0.65255-0.
2004: Lindström K and Martinez-Romero E, Int J Syst Evol Microbiol 55:1383; doi:10.1099/ijs.0.63744-0.
Publications by subcommittee members or others that are of interest in the field of taxonomy, evolution and physiology of rhizobia and agrobacteria.
Publications relevant to the taxonomy of agrobacteria and rhizobia
2022
Kang M, Seo T. Rhizobium setariae sp. nov., an Indole-3-Acetic Acid-Producing Bacterium Isolated from Green Foxtail, Setaria viridis. Curr Microbiol 79:162; doi:10.1007/s00284-022-02860-2.
Kuzmanović N, Fagorzi C, Mengoni A, Lassalle F, diCenzo G. Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation. Int J Syst Evol Microbiol 72:005243; doi:10.1099/ijsem.0.005243.
Pavima L et al.. Delineation of Paraburkholderia tuberum sensu stricto and description of Paraburkholderia podalyriae sp. nov. nodulating the South African legume Podalyria calyptrata. Syst Appl Microbiol (in press); doi:10.1016/j.syapm.2022.126316.
Rajnovic I et al.. Rhizobium croatiense sp. nov. and Rhizobium redzepovicii sp. nov., two new species isolated from nodules of Phaseolus vulgaris in Croatia. Syst Appl Microbiol (in press); doi:10.1016/j.syapm.2022.126317.
Puławska J, Kuzmanović N, Trzciński P. Agrobacterium vaccinii sp. nov. isolated from galls on blueberry plants (Vaccinium corymbosum). Syst Appl Microbiol (in press); doi:10.1016/j.syapm.2022.126319.
Avontuur JR et al., Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns. Mol Phyl Evol 167:107338; doi:10.1016/j.ympev.2021.107338.
2021
Mafakheri H et al.. Genomics Analyses of Rose Crown Gall-Associated Bacteria Revealed Two New Agrobacterium species: Agrobacterium burrii sp. nov. and Agrobacterium shirazense sp. nov. Phytopathology (in press); doi:10.1094/PHYTO-11-21-0463-SC.
Pedron et al.. Mesorhizobium comanense sp. nov., isolated from groundwater. Int J Syst Evol Microbiol 71(12):005131; doi:10.1099/ijsem.0.005131.
Castellano-Hinojosa A et al.. Agrobacterium leguminum sp. nov., isolated from nodules of Phaseolus vulgaris in Spain. Int J Syst Evol Microbiol 71(12):005120; doi:10.1099/ijsem.0.005120.
Thin KK et al.. Rhizobium rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants in China. Curr Microbiol 78:830–836; doi:10.1007/s00284-020-02323-6.
Su XJ, Liu GP, Zhang L, Zhou XY, Qiao WJ, Jiang JD. Rhizobium flavescens sp. nov., Isolated from a Chlorothalonil-Contaminated Soil. Curr Microbiol 78:2165–2172; doi:10.1007/s00284-021-02462-4.
Singh NK, Lavire C, Nesme J, Vial L, Nesme X, Mason CE, Lassalle F, Venkateswaran K. Comparative genomics of novel Agrobacterium G3 strains isolated from the International Space Station and description of Agrobacterium tomkonis sp. nov.. Front Microbiol 12:3369; doi:10.3389/fmicb.2021.765943.
Bromfield ESP and Cloutier S. Bradyrhizobium septentrionale sp. nov. (sv. septentrionale) and Bradyrhizobium quebecense sp. nov. (sv. septentrionale) associated with legumes native to Canada possess rearranged symbiosis genes and numerous insertion sequences. Int J Syst Evol Microbiol 71(6):004831; doi:10.1099/ijsem.0.004831.
Rahi P et al., Peteryoungia gen. nov. with four new species combinations and description of Peteryoungia desertarenae sp. nov., and taxonomic revision of the genus Ciceribacter based on phylogenomics of Rhizobiaceae. Arch Microbiol (in press); doi:10.1007/s00203-021-02349-9.
Klepa SM, Ferraz Helene FC, O'Hara G and Hungria M. Bradyrhizobium agreste sp. nov., Bradyrhizobium glycinis sp. nov. and Bradyrhizobium diversitatis sp. nov., isolated from a biodiversity hotspot of the genus Glycine in Western Australia. Int J Syst Evol Microbiol 71(3):004742 ; doi:10.1099/ijsem.0.004742.
Su XJ, Liu Gp, Zhang, L, Zhou XY, Qiao WJ and Jian JD. Rhizobium flavescens sp. nov., Isolated from a Chlorothalonil-Contaminated Soil. Curr Microbiol 78:2165–2172; doi:10.1007/s00284-021-02462-4.
Young JPW et al., Defining the Rhizobium leguminosarum Species Complex. Genes 12(1):111; doi:10.3390/genes12010111.
Lassalle F et al., Phylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus. Syst Appl Microbiol 44(1):126165; doi:10.1016/j.syapm.2020.126165.
2020
Menéndez E, Flores-Félix JD, Ramírez-Bahena MH, Igual JM, García-Fraile P, Peix A, Velázquez E. Genome Analysis of Endobacterium cerealis, a Novel Genus and Species Isolated from Zea mays Roots in North Spain. Microorganisms 8:939; doi:10.3390/microorganisms8060939.
Mavima L, Beukes CW, Palmer M, De Meyer SE, James EK et al. Paraburkholderia youngii sp. nov. and ‘Paraburkholderia atlantica’ – Brazilian and Mexican Mimosa-associated rhizobia that were previously known as Paraburkholderia tuberum sv. mimosae. Syst Appl Microbiol 44(1):126152; doi:10.1016/j.syapm.2020.126152.
Velázquez E, Flores-Félix JD, Sánchez-Juanes F, Igual JM and Peix A. Strain ATCC 4720T is the authentic type strain of Agrobacterium tumefaciens, which is not a later heterotypic synonym of Agrobacterium radiobacter. Int J Syst Evol Microbiol 70(9):5172-5176; doi:10.1099/ijsem.0.004443.
Jorrin B, Palacios JM, Peix A and Imperial J, Rhizobium ruizarguesonis sp. nov., isolated from nodules of Pisum sativum L. Syst Appl Microbiol 43(4):126090; doi:10.1016/j.syapm.2020.126090.
Rahi P et al., Rhizobium indicum sp. nov., isolated from root nodules of pea (Pisum sativum) cultivated in the Indian trans-Himalayas. Syst Appl Microbiol 43(5):126127; doi:10.1016/j.syapm.2020.126127.
Delamuta JRM et al., Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov. Int J Syst Evol Microbiol 70(7) (in press); doi:10.1099/ijsem.0.004278.
Hördt et al., Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 11:468; doi:10.3389/fmicb.2020.00468
Liu L, Liang L, Xu L, Chi M, Zhang X, Li L. Rhizobium deserti sp. nov. Isolated from Biological Soil Crusts Collected at Mu Us Sandy Land, China. Curr Microbiol 77(2):327-333; doi:10.1007/s00284-019-01831-4.
Ruan Z et al., Rhizobium terrae sp. nov., Isolated from an Oil-Contaminated Soil in China. Curr Microbiol 77:1117–1124; doi:10.1007/s00284-020-01889-5.
2019
Flores-Félix JD et al., History and current taxonomic status of genus Agrobacterium. Syst Appl Microbiol doi:10.1016/j.syapm.2019.126046.
Ormeño-Orrillo E and Martinez-Romero E. A Genomotaxonomy View of the Bradyrhizobium Genus. Front Microbiol 10:1334; doi:10.3389/fmicb.2019.01334.
González V et al., Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters. Front Microbiol 10:910; doi:10.3389/fmicb.2019.00910.
Avontuur JR et al., Genome-informed Bradyrhizobium taxonomy: where to from here? Syst Appl Microbiol 42(4):427-439; doi:10.1016/j.syapm.2019.03.006.
2018
Manaa M, Park I and Seo Y-S, Genomic Features and Insights into the Taxonomy, Virulence, and Benevolence of Plant-Associated Burkholderia Species. Int J Mol Sci 2019, 20(1):121; doi:10.3390/ijms20010121.
Gan HM and Savka MA, One More Decade of Agrobacterium Taxonomy. In: . Current Topics in Microbiology and Immunology. Springer, Berlin, Heidelberg. doi:10.1007/82_2018_81.
Kuzmanović N et al., Rhizobium tumorigenes sp. nov., a novel plant tumorigenic bacterium isolated from cane gall tumors on thornless blackberry. Sci Rep 8:9051; doi:10.1038/s41598-018-27485-z.
Zahradník J et al., Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in central Bohemia. Syst Appl Microbiol 41:184-190; doi:10.1016/j.syapm.2018.01.003.
Yan J et al., Agrobacterium deltaense sp. nov., an endophytic bacteria isolated from nodule of Sesbania cannabina. Arch Microbiol 199:1003-1009; doi:10.1007/s00203-017-1367-0.
Kuzmanović N. et al. (2018) Agrobacterium rosae sp. nov., isolated from galls on different agricultural crops. Syst Appl Microbiol 41(3):191-197 doi.org/10.1016/j.syapm.2018.01.004
2017
Yan J et al., Agrobacterium salinitolerans sp. nov., a saline–alkaline-tolerant bacterium isolated from root nodule of Sesbania cannabina. Int J Syst Evol Microbiol 67:1906–1911; doi:10.1099/ijsem.0.001885.
2015
Ormeño-Orrillo E et al., Taxonomy of rhizobia and agrobacteria from the Rhizobiaceae family in light of genomics. Syst Appl Microbiol 38:287-291; doi:10.1016/j.syapm.2014.12.002.
Moussavi SA et al., Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. Syst Appl Microbiol 38:84-90; doi:10.1016/j.syapm.2014.12.003.
Kuzmanović N. et al. (2015) Agrobacterium arsenijevicii sp. nov., isolated from crown gall tumors on raspberry and cherry plum. Syst Appl Microbiol 38: 373–378. doi:10.1016/j.syapm.2015.06.001
Other publications relevant to the study of the diversity of rhizobia and agrobacteria
2022
Khairnar M, Hagir A, Parmar K, Sayyed RZ, James EK, Rahi P. Phylogenetic diversity and plant growth-promoting activities of rhizobia nodulating fenugreek (Trigonella foenum-graecum Linn.) cultivated in different agroclimatic regions of India. FEMS Microbiol Ecol, fiac014, doi:10.1093/femsec/fiac014.
2021
Dlamini ST, Jaiswal SK, Mohammed M et al. Studies of Phylogeny, Symbiotic Functioning and Ecological Traits of Indigenous Microsymbionts Nodulating Bambara Groundnut (Vigna subterranea L. Verdc) in Eswatini . Microb Ecol. doi:10.1007/s00248-021-01684-0.
2020
Teulet A et al., Phylogenetic distribution and evolutionary dynamics of nod and T3SS genes in the genus Bradyrhizobium. Microbial Genomics 6(9):e000407; doi:10.1099/mgen.0.000407.
Youseif SH, Abd El-Megeed FH, Mohamed AH, Ageez A, Veliz E, Martínez-Romero E. Diverse Rhizobium strains isolated from root nodules of Trifolium alexandrinum in Egypt and symbiovars. Syst Appl Microbiol 44(1):126156; doi:10.1016/j.syapm.2020.126156.
Boivin S et al., Host‐specific competitiveness to form nodules in Rhizobium leguminosarum symbiovar viciae. New Phytologist 226(2):555-568; doi:10.1111/nph.16392.
Cavassim MIA et al., Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex. Microbial Genomics 6(4):e000351; doi:10.1099/mgen.0.000351.
Weisberg AJ et al., Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368(6495):eaba5256. doi: 10.1126/science.aba5256
Nuccio EE et al. Niche differentiation is spatially and temporally regulated in the rhizosphere. ISME J. doi:10.1038/s41396-019-0582-x
2019
Kuzmanović N et al. A novel group of Rhizobium tumorigenes-like agrobacteria associated with crown gall disease of rhododendron and blueberry. Phytopathology. doi:10.1094/PHYTO-05-19-0167-R.
Mafakheri H et al. Two Novel Genomospecies in the Agrobacterium tumefaciens Species Complex Associated with Rose Crown Gall. Phytopathology. doi:10.1094/PHYTO-05-19-0178-R.
Kuzmanović N and Puławska J. Evolutionary Relatedness and Classification of Tumour-Inducing and Opine-Catabolic Plasmids in Three Rhizobium rhizogenes Strains Isolated from the Same Crown Gall Tumour. Genome Biol Evol 11(6):1525-1540; doi:10.1093/gbe/evz091.
2018
Garrido-Oter R. et al. Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia. Cell Host & Microbe 24(1):155-167.e5; doi:10.1016/j.chom.2018.06.006.
2017
Lassalle F et al. Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium. Genome Biol Evol 9 (12):3413-3431; doi:10.1093/gbe/evx255.
Eardly B, Elia P, Brockwell J, Golemboski D, and van Berkum P. Biogeography of a novel clade of Ensifer meliloti associated with the Australian legume Trigonella suavissima. Appl Env Microbiol 83(10):e03446-16; doi:10.1128/AEM.03446-16.
Le Quéré A et al. Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts. BMC Genomics 18:85; doi:10.1186/s12864-016-3447-y
2014
Aujoulat F et al. Rhizobium pusense is the main human pathogen in the genus Agrobacterium/Rhizobium. Clin Microbiol Infect 21:472.e1–472.e5; doi:10.1016/j.cmi.2014.12.005.
Other publication of general interest for bacterial taxonomy, and the (potential) evolution of the taxonomic framework
2021
Rahi P. Regulating access can restrict participation in reporting new species and taxa. Nature Microbiology ; doi:10.1038/s41564-021-01002-x.
2020
Murray A et al., Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology 5:987-994; doi:10.1038/s41564-020-0733-x.
Parks et al., A complete domain-to-species taxonomy for Bacteria and Archaea. Nature Biotechnol ; doi:10.1038/s41587-020-0501-8.
Barco et al. A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index. mBio 11(1):02475-19; doi:10.1128/mBio.02475-19.
2019
Stackebrandt E and Smith D. Paradigm shift in species description: the need to move towards a tabular format. Arch Microbiol 201(2):143–145; doi:10.1007/s00203-018-1609-9.
Parker CT, Tindall, BJ and Garrity GM. International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 69: S1-S111; doi:10.1099/ijsem.0.000778.
2018
Chun J et al., Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68(1):461-466; doi:10.1099/ijsem.0.002516.
Parks et al., A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnol 36:996–1004; doi:10.1038/nbt.4229.
Publications relevant to host plant specificity in legume nodulation, crown gall infection, or commensal rhizosphere colonization
2018
Ben Gharsa H et al., Evaluation of the interspecific competition within Agrobacterium spp. in the soil and rhizosphere of tomato and maize. J Plant Pathol 100:505; doi:10.1007/s42161-018-0114-y.
2017
Andrews M and Andrews ME. Specificity in legume-rhizobia symbioses. Int J Mol Sci. 18(4):705; doi:10.3390/ijms18040705.