You are here

Bacteria confused with rhizobia, including Agrobacterium taxonomy

Updated 27 April 2013

This page lists bacteria that could be confused with 'true' rhizobia, such as non-nodulating Rhizobium species, and invalid names.

I define 'rhizobia' as "nitrogen-fixing bacteria capable of forming symbiotic root nodules on legumes, mediated by nod genes", other researcher's definitions will differ. Naturally this is a continual work in progress. As well as the categories below there are many diverse species of bacteria that can fix nitrogen, but in a free living state — not in root nodules. A few examples of these are Rhodopseudomonas palustris, Azospirillum sp., Azotobacter sp. and many more.

Agrobacterium

Species in the Agrobacterium genus (including the type species) has been placed into synonymy with the Rhizobium genus (Young et al., 2001), they are listed below, with their new names. See the LPSN for more information on the Agrobacterium. These generally do not form symbiotic root nodules, unless they harbour a Sym plasmid or other transposable element with nodulation genes. In this case, I would define them as rhizobia. Other Agrobacterium species have been reclassified as Stappia, Ruegeria, and Pseudorhodobacter. There has been some controversy over 'losing' the name Agrobacterium, but it is a valid taxonomic change, I have written more about this reclassification here. The word 'agrobacteria' can be used to describe tumour and gall forming Rhizobium species, in the same way that 'rhizobia' is used for nitrogen-fixing root nodule bacteria.

The former pathogenic Agrobacterium species
Former name Current Name Symptoms
Agrobacterium larrymoorei Rhizobium larrymoorei (Young et al., 2001) aerial tumours
Agrobacterium radiobacter = A. tumefaciens Rhizobium radiobacter (Young et al., 2001) crown gall
Agrobacterium rhizogenes Rhizobium rhizogenes (Young et al., 2001) hairy-root disease
Agrobacterium rubi Rhizobium rubi (Young et al., 2001) cane gall
Agrobacterium vitis Rhizobium vitis (Young et al., 2001) crown gall



Bacteria that are not rhizobia in 'rhizobia genera'

These may have names that suggest that they are rhizobia, but have not been shown to form symbiotic root nodules.

Rhizobium selenitireducens Selenite-reducing, isolated from bioreactor (invalid name was: R. selenireducens) (Hunter et al., 2008)
Rhizobium soli Does not have nodD and nifH genes and does not nodulate the tested legumes (Yoon et al., 2010)
Rhizobium borbori aniline-degrading bacteria isolated from activated sludge (Zhang et al., 2011)
Rhizobium rosettiformans isolated from hexachlorocyclohexane (HCH)-contaminated groundwater (Kaur et al., 2011), but is involved in (non-nodule) root-associated nitrogen fixation with sugarcane and spruce (Burbano et al., 2011)
Rhizobium aggregatum formerly Blastobacter aggregatus, no NifH (Kaur et al., 2011)
Burkholderia unamae N2 fixing but does not form root nodules (Caballero-Mellado et al., 2004)
Bradyrhizobium betae Tumour forming bacteria (Rivas et al., 2004)
Mesorhizobium thiogangeticum Sulfur oxidising, nodulation unknown (Ghosh and Roy, 2006)
Cohnella phaseoli Isolated from nodules, but cannot form root nodules (Garcia-Fraile et al., 2008)
Herbaspirillum lusitanum Previously I have included this a a nodulating species, however although it has been isolated from nodules, it has not been shown to induce nodulation.
Rhizobium taibaishanense No strains were able to induce any nodule or tumour formation on plants, and nodA, nifH, and virC were absent by PCR (Yao et al. 2012)
Devosia yakushimensis Isolated from nodules of Pueraria lobata; no nodulation reported. (Bautista et al. 2010)
Rhizobium skierniewicense Isolated from tumours on chrysanthemum and cherry plum (Puławska et al. 2012), previously this would have been called an Agrobacterium species.



Names that have not been validly published or are no longer valid

These include names that have been submitted to the NCBI database but not yet published, and names that were never formally published. It also includes some names that were vaild, but are no longer valid.

Rhizobium massiliae not rhizobia, unpublished (link to NCBI)
Rhizobium arachis not valid (link to NCBI)
Bradyrhizobium lupini not valid (link to NCBI)
Blastobacter denitrificans not valid name is now Bradyrhizobium denitrificans (link to NCBI)
Agrobacterium agile not valid (link to NCBI)
Mesorhizobium alexandrii not valid. Name is now Hoeflea alexandrii (link to NCBI)
Rhizobium taeanense not valid (link to NCBI)
Mesorhizobium aestuarii not valid. Name is now Aliihoeflea aestuarii (link to NCBI)
Rhizobium trifolii a later synonym of R. leguminosarum (IJSEM paper)