Kado (2014) Historical account on gaining insights on the mechanism of crown gall tumorigenesis induced by Agrobacterium tumefaciens. Front Microbiol. 5:340. https://doi.org/10.3389/fmicb.2014.00340
Popoff et al. (1984) Position taxonomique de souches de Agrobacterium d’origine hospitalière. Ann Inst Pasteur Microbiol 135, 427–442. https://doi.org/10.1016/S0769-2609(84)80083-6
Classification of agrobacteria into distinct groups (i.e., genomospecies) based on phenotype and overall genome similarity (DNA-DNA hybridization)
Costechareyre et al. (2010). Rapid and efficient identification of Agrobacterium species by recA allele analysis: Agrobacterium recA diversity. Microb Ecol 60:862–872. https://doi.org/10.1007/s00248-010-9685-7
Lassalle et al. (2011). Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome Biol Evol 3:762–781. https://doi.org/10.1093/gbe/evr070
Use strain C58 (BV1 G8) as the reference, performed microarray hybridization to check presence/absence of specific genomic regions in 25 different strains; strains classified to the same genomospecies are more similar.
G8 named as Agrobacterium fabrum
Shams et al. (2013). Rapid and accurate species and genomic species identification and exhaustive population diversity assessment of Agrobacterium spp. using recA-based PCR. Syst Appl Microbiol 36:351–358. https://doi.org/10.1016/j.syapm.2013.03.002
Lassalle et al. (2017) Ancestral genome estimation reveals the history of ecological diversification in Agrobacterium. Genome Biol Evol 9, 3413–3431. https://doi.org/10.1093/gbe/evx255
Weisberg et al. (2020). Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368:eaba5256. https://doi.org/10.1126/science.aba5256
Large-scale ANI analysis
Chou et al. (2022). Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biol 20:16. https://doi.org/10.1186/s12915-021-01221-y
Genome-scale phylogeny; comparison of divergence based on average nucleotide identity (ANI) and gene content; focused analysis on secretion systems and plasmids
Genome
Goodner et al. (2001) Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294:2323–2328. https://doi.org/10.1126/science.1066803
Goodner et al. (2001) and Wood et al. (2001) are back-to-back papers; first Agrobacterium genome sequence, strain C58
Slater et al. (2009) Genome sequences of three Agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J Bacteriol 191:2501–2511. https://doi.org/10.1128/JB.01779-08
The first genome sequence for BV2 (strain K84) and BV3 (strain S4); 3-way comparison with BV1 (C58)
Model for the evolution of different chromosome/chromid organization among different lineages of ARC
Weisberg et al. (2020). Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368:eaba5256. https://doi.org/10.1126/science.aba5256
Large scale genome sequencing; ??? new assemblies released
Chou et al. (2022). Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biol 20:16. https://doi.org/10.1186/s12915-021-01221-y
Major improvement in the taxon sampling; 14 (nearly) complete assemblies from genomospecies that were poorly characterized
Ramírez-Bahena et al. (2014) Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid. Mol Phylogenet Evol 73:202–207. https://doi.org/10.1016/j.ympev.2014.01.005
Weisberg et al. (2020). Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368:eaba5256. https://doi.org/10.1126/science.aba5256
Weisberg et al. (2022) Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria. Philos Trans R Soc Lond B Biol Sci 377, 20200466. https://doi.org/10.1098/rstb.2020.0466
Type IV Secretion System (T4SS)
Type VI Secretion System (T6SS)
Many, but not all, species within the agrobacteria-rhizobia complex have a conserved gene cluster that encode the T6SS. This system is involved in interbacterial competition.
Lin et al. (2013) Systematic dissection of the Agrobacterium type VI secretion system reveals machinery and secreted components for subcomplex formation. PLOS ONE 8, e67647. https://doi.org/10.1371/journal.pone.0067647
Lin et al. (2014). Fha Interaction with Phosphothreonine of TssL Activates Type VI Secretion in Agrobacterium tumefaciens. PLOS Pathog 10, e1003991. https://doi.org/10.1371/journal.ppat.1003991
Ma et al. (2014) Agrobacterium tumefaciens deploys a superfamily of type VI secretion DNase effectors as weapons for interbacterial competition in planta. Cell Host Microbe 16, 94–104. https://doi.org/10.1016/j.chom.2014.06.002
Wu et al. (2019) Plant-pathogenic Agrobacterium tumefaciens strains have diverse type VI effector-immunity pairs and vary in in-planta competitiveness. Mol Plant Microbe Interact 32, 961–971. https://10.1094/MPMI-01-19-0021-R
Wu et al. (2021) Diversification of the type VI secretion system in agrobacteria. mBio 12, e01927-21. https://10.1128/mBio.01927-21
Chou et al. (2022). Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biol 20:16. https://doi.org/10.1186/s12915-021-01221-y
Molecular evolution of the T6SS genes in BV1; diversity of effector genes.
Transcriptome
Haryono et al. (2019) Differentiations in gene content and expression response to virulence induction between two Agrobacterium strains. Front Microbiol 10, 1554. https://doi.org/10.3389/fmicb.2019.01554
Hwang et al. (2013) Characterization and host range of five tumorigenic Agrobacterium tumefaciens strains and possible application in plant transient transformation assays. Plant Pathol 62, 1384–1397. https://doi.org/10.1111/ppa.12046
Microbiota
Faist et al. (2016) Grapevine (Vitis vinifera) crown galls host distinct microbiota. Appl Environ Microbiol 82, 5542–5552. https://doi.org/10.1128/AEM.01131-16
Wang et al. (2023) Soil inoculation and blocker-mediated sequencing show effects of the antibacterial T6SS on agrobacterial tumorigenesis and gallobiome. mBio 14, e00177-23. https://doi.org/10.1128/mbio.00177-23