40
A. Dahiya et al.
log cfu) as compared to pathogenic bacteria (7–10 log cfu) (Zinniel et al. 2002).
Hence, the endophytic presence of bacteria is determined by genetic determinants that
enable bacterial-plant crosstalk, leading to an active endophytic colonization process
(Hardoim et al. 2008). The plant host also plays a critical role in selecting an endophytic partner where secretion of specific root exudates and a selective plant defense
response are considered important factors in the selection of suitable endophytes
(Rosenblueth and Martínez-Romero 2006).
3.3.2 Colonization of Aerial Plant Tissues
After entry into the roots, the endophytic bacteria can spread systemically to colonize
above-ground tissues. These can establish stem and leaf population densities between
10
3 and 10
4 cfu under natural conditions (Compant et al. 2010). The final sink for
these specialized endophytic bacteria is leaf tissue wherein they gain entry into the
leaves from the phyllosphere via leaf stomata (Senthilkumar et al. 2011).
3.4 Occurrence and Diversity of Bacterial Endophytes
The earth planet has been reported to contain about 300,000 species of plants.
The endophytes (bacteria and fungi) have been documented in the vast majority
of plants that have been analyzed so far (Smith and Read 2008). Partida-Martínez
and Heil (2011) stated that an endophyte-free plant is a rare exception and such a
plant without endophytes would be more susceptible to phytopathogens and environmental stress conditions (Timmusk et al. 2011). Endophytic bacterial diversity
has been reported for several plant species. The population estimates of endophytic
bacteria in plants may also vary depending on the type of growth media used for
isolation, growth conditions of the host plant, and method used for sterilization of
plant tissue (Lodewyckx et al. 2002; Eevers et al. 2015). Moreover, cultivationdependent methods can also strongly underestimate the number of bacteria present
in plant tissues (Bogas et al. 2015) because culturable bacteria usually represents
only 0.001–1% of the actual endophyte counts (Torsvik and Øvreås 2002; Alain and
Querellou 2009). Therefore, culture-independent methods (metagenomics) which
mostly rely on the total bacterial genomic DNA extraction from plant tissues, tend to
be less biased in analyzing the true endophytic diversity. The emergence of molecular techniques in microbial ecology has validated more comprehensive studies of
endophyte abundance, community composition, and function using genetic analysis.
A broad-spectrum of endophytic bacteria have been detected from plant tissues by
using culture-independent molecular biological techniques, which assess the diversity and composition of uncovering endophytes with obligate host associations such
as RFLP analysis and sequencing of rDNA or rRNA. Techniques like fluorescence
in situ hybridization (FISH) have also allowed studying the endophytic bacteria in
A. Dahiya et al.
log cfu) as compared to pathogenic bacteria (7–10 log cfu) (Zinniel et al. 2002).
Hence, the endophytic presence of bacteria is determined by genetic determinants that
enable bacterial-plant crosstalk, leading to an active endophytic colonization process
(Hardoim et al. 2008). The plant host also plays a critical role in selecting an endophytic partner where secretion of specific root exudates and a selective plant defense
response are considered important factors in the selection of suitable endophytes
(Rosenblueth and Martínez-Romero 2006).
3.3.2 Colonization of Aerial Plant Tissues
After entry into the roots, the endophytic bacteria can spread systemically to colonize
above-ground tissues. These can establish stem and leaf population densities between
10
3 and 10
4 cfu under natural conditions (Compant et al. 2010). The final sink for
these specialized endophytic bacteria is leaf tissue wherein they gain entry into the
leaves from the phyllosphere via leaf stomata (Senthilkumar et al. 2011).
3.4 Occurrence and Diversity of Bacterial Endophytes
The earth planet has been reported to contain about 300,000 species of plants.
The endophytes (bacteria and fungi) have been documented in the vast majority
of plants that have been analyzed so far (Smith and Read 2008). Partida-Martínez
and Heil (2011) stated that an endophyte-free plant is a rare exception and such a
plant without endophytes would be more susceptible to phytopathogens and environmental stress conditions (Timmusk et al. 2011). Endophytic bacterial diversity
has been reported for several plant species. The population estimates of endophytic
bacteria in plants may also vary depending on the type of growth media used for
isolation, growth conditions of the host plant, and method used for sterilization of
plant tissue (Lodewyckx et al. 2002; Eevers et al. 2015). Moreover, cultivationdependent methods can also strongly underestimate the number of bacteria present
in plant tissues (Bogas et al. 2015) because culturable bacteria usually represents
only 0.001–1% of the actual endophyte counts (Torsvik and Øvreås 2002; Alain and
Querellou 2009). Therefore, culture-independent methods (metagenomics) which
mostly rely on the total bacterial genomic DNA extraction from plant tissues, tend to
be less biased in analyzing the true endophytic diversity. The emergence of molecular techniques in microbial ecology has validated more comprehensive studies of
endophyte abundance, community composition, and function using genetic analysis.
A broad-spectrum of endophytic bacteria have been detected from plant tissues by
using culture-independent molecular biological techniques, which assess the diversity and composition of uncovering endophytes with obligate host associations such
as RFLP analysis and sequencing of rDNA or rRNA. Techniques like fluorescence
in situ hybridization (FISH) have also allowed studying the endophytic bacteria in