58
A. Dahiya et al.
3.8 The Genetics Involved in Endophytic Behavior
and Phosphate Solubilization
The genomic analysis could help to understand the mechanisms involved in decisionmaking regarding the influence of bacteria to act as endophyte because the capacity
to penetrate and survive inside plant tissues are multifactorial. Moreover, rhizospheric bacteria colonize tissues inside plants, so that both lifestyles share a variety
of mechanisms. In addition to testing of individual biochemical/genetic mechanisms
involved in the interaction of a bacterial endophyte with a plant, it is possible to use
a bioinformatics approach to predict some of the key features that distinguish endophyte from rhizospheric PGPB (Ali et al. 2014). The genomic DNA sequences of
rhizospheric and endophytic PGPB (both Burkholderia spp.) were compared and the
genes encoded by the rhizospheric strain were subtracted from the endophytic strain.
Then, the remaining, putative endophytic genes, were compared with the complete
genomes of eight different endophytic PGPB (B. phytofirmans PsJN, Burkholderia
spp. strain JK006, A. lipoferum 4B, E. cloacae ENHKU01, K. pneumoniae 342, P.
putida W619, Enterobacter spp. 638, Azoarcus spp. BH72, and S. proteamaculans
568). Genes that were common to all of these strains were considered to be potentially involved in endophytic behavior, including genes encoding transporter proteins,
secretion and delivery systems, plant polymer degradation or modification, transcriptional regulation, detoxification, redox potential maintenance, unknown functions,
and functions like 2-isopropylmalate synthase and diaminopimelate decarboxylase.
Most of the (~40) genes identified by this procedure encode functions previously
suggested by separate biochemical/genetic studies involved in endophytic behavior.
Most of the genetic studies have been carried out on B. phytofirmans strain
PsJN, a model endophytic bacterium, with the ability to competently colonize (both
rhizosphere and endosphere) and promote the growth of a variety of different plant
hosts, including A. thaliana, grape, maize, potato, switchgrass, tomato, and wheat
(Sessitsch et al. 2005; Sheibani-Tezerji et al. 2015). Moreover, strain PsJN also
increases tolerance of host plants to abiotic stress such as chilling and drought
(Barka et al. 2006, Naveed et al. 2014), and biotic stress like inhibition of fungal
phytopathogens (Sharma and Nowak 1998; Barka et al. 2006). Strain PsJN has been
shown to require IAA degradation, ACC deaminase, and quorum sensing to colonize
host plants and produce beneficial effects (Sun et al. 2009; Zuniga et al. 2013). Moreover, in planta gene expression profiling revealed that, during its growth inside host
plants, the bacterium expresses several different traits related to cellular homeostasis,
cell redox homeostasis, energy production, general metabolism (amino acids, lipids,
nucleotides, sugars), and transcription regulation (Sheibani-Tezerji et al. 2015).
The nitrogen-fixing endophyte Azocarus sp. was reported to infect plants through
the emergence points of lateral roots and root tips via the action of bacterial endoglucanase (Rheinhold-Hurek et al. 2006). Also, transposon mutants lacking the activity
of this endoglucanase colonized rice plants to a significantly lesser extent. This
group subsequently showed that deletion mutants of the pilT and pilA genes in this
A. Dahiya et al.
3.8 The Genetics Involved in Endophytic Behavior
and Phosphate Solubilization
The genomic analysis could help to understand the mechanisms involved in decisionmaking regarding the influence of bacteria to act as endophyte because the capacity
to penetrate and survive inside plant tissues are multifactorial. Moreover, rhizospheric bacteria colonize tissues inside plants, so that both lifestyles share a variety
of mechanisms. In addition to testing of individual biochemical/genetic mechanisms
involved in the interaction of a bacterial endophyte with a plant, it is possible to use
a bioinformatics approach to predict some of the key features that distinguish endophyte from rhizospheric PGPB (Ali et al. 2014). The genomic DNA sequences of
rhizospheric and endophytic PGPB (both Burkholderia spp.) were compared and the
genes encoded by the rhizospheric strain were subtracted from the endophytic strain.
Then, the remaining, putative endophytic genes, were compared with the complete
genomes of eight different endophytic PGPB (B. phytofirmans PsJN, Burkholderia
spp. strain JK006, A. lipoferum 4B, E. cloacae ENHKU01, K. pneumoniae 342, P.
putida W619, Enterobacter spp. 638, Azoarcus spp. BH72, and S. proteamaculans
568). Genes that were common to all of these strains were considered to be potentially involved in endophytic behavior, including genes encoding transporter proteins,
secretion and delivery systems, plant polymer degradation or modification, transcriptional regulation, detoxification, redox potential maintenance, unknown functions,
and functions like 2-isopropylmalate synthase and diaminopimelate decarboxylase.
Most of the (~40) genes identified by this procedure encode functions previously
suggested by separate biochemical/genetic studies involved in endophytic behavior.
Most of the genetic studies have been carried out on B. phytofirmans strain
PsJN, a model endophytic bacterium, with the ability to competently colonize (both
rhizosphere and endosphere) and promote the growth of a variety of different plant
hosts, including A. thaliana, grape, maize, potato, switchgrass, tomato, and wheat
(Sessitsch et al. 2005; Sheibani-Tezerji et al. 2015). Moreover, strain PsJN also
increases tolerance of host plants to abiotic stress such as chilling and drought
(Barka et al. 2006, Naveed et al. 2014), and biotic stress like inhibition of fungal
phytopathogens (Sharma and Nowak 1998; Barka et al. 2006). Strain PsJN has been
shown to require IAA degradation, ACC deaminase, and quorum sensing to colonize
host plants and produce beneficial effects (Sun et al. 2009; Zuniga et al. 2013). Moreover, in planta gene expression profiling revealed that, during its growth inside host
plants, the bacterium expresses several different traits related to cellular homeostasis,
cell redox homeostasis, energy production, general metabolism (amino acids, lipids,
nucleotides, sugars), and transcription regulation (Sheibani-Tezerji et al. 2015).
The nitrogen-fixing endophyte Azocarus sp. was reported to infect plants through
the emergence points of lateral roots and root tips via the action of bacterial endoglucanase (Rheinhold-Hurek et al. 2006). Also, transposon mutants lacking the activity
of this endoglucanase colonized rice plants to a significantly lesser extent. This
group subsequently showed that deletion mutants of the pilT and pilA genes in this