Page 2 Plant-Bacteria Interactions Edited by Iqbal Ahmad, John ...

56j 4 A Review on the Taxonomy and Possible Screening Traits of Plant Growth Promoting Rhizobacteria
in two categories: extracellular PGPR (e-PGPR) and intracellular PGPR (i-PGPR).
The first category, e-PGPR, includes bacteria existing in the rhizosphere, on the
rhizoplane or in the spaces between cells of the root cortex, stimulating plant
growth by producing phytohormones, improving plant disease resistance or improving
mobilization of soil nutrients. Picard and Bosco [6] state that noninvasive
rhizobacteria (e-PGPR) represent the most common plant–microbe interactions in
healthy plants.
i-PGPR are those bacteria that exist inside root cells, generally in specialized
nodular structures where they fix nitrogen. The latter, i-PGPR, are therefore those
bacteria that are also known as rhizobia, a name derived from the genus Rhizobium
[7] and refer to bacteria that induce nodules in legumes and fix atmospheric
nitrogen in symbiosis with them. However, bacteria showing this ability also
belong to genera other than Rhizobium, thus the term legume-nodulating bacteria
(LNB) has been proposed [7]. Notwithstanding, LNB are not the only bacteria able
to fix atmospheric nitrogen in symbiosis as can be seen in Table 4.1.
4.2
Taxonomy of PGPR
The term taxonomy is defined as the science dedicated to the study of relationships
among organisms and has to do with their classification, nomenclature and identification.
The accurate comparison of organisms at different times by different
scientists depends on a reliable taxonomic system that allows a precise classification
of the organisms under study.
Since its beginnings in the late nineteenth century, bacterial taxonomy relied
on phenotypic traits such as cell and colonial morphologies and biochemical,
physiological and immunological tests. Taxonomy was revolutionized thanks to
the discovery of the polymerase chain reaction (PCR) technique in 1983. Since
then, the search for a trait that would be in congruence with the evolutionary
divergence of organisms, that is their phylogeny, was mandatory. This trait was
found in the ribosomal RNA [25], a molecule used by all living cells. The gene
sequences of the 16S subunit of the ribosomal RNA have been used since to
compare evolutionary similitudes among strains. At present, and by correlation
with experimental data obtained in the comparison of total genomic DNA (DNA–
DNA hybridization), it is proposed that a similarity below 98.7–99% on an
UPGMA analysis of the 16S rDNA sequences of two bacterial strains is sufficient
to consider them as belonging to different species [26]. Notwithstanding, it is
possible that two strains showing 16S rDNA sequence similarities above the
98.7% threshold may represent two different species [27]. In these cases, total
genome DNA–DNA hybridizations must be performed and those strains for
which similarities are below 70% are considered to belong to different species.
In this context, and given the fact that no taxonomic technique is absolutely
accurate, the use of a polyphasic approach to taxonomy [28] was implemented
in bacterial taxonomy.