3 Microbial Endophytes: Sustainable Approach …
41
the natural habitat (Picollo et al. 2010). The application of molecular techniques
will continue to enable extensive research on environmental factors that shape endophyte communities (Gaiero et al. 2013). Combinatorial approaches, combining both
culture-dependent and culture-independent methods can increase the possibility of
complete structural and functional analysis of the endophytic bacterial community
of a plant (Sessitsch et al. 2004; Hallmann and Berg 2006).
Sessitsch et al. (2012) observed rice’s endorhizosphere using the metagenomics
approach and deciphered many traits shared by the endophytic inhabitants that
might be crucial in their competence and success. The 16S-rRNA pyrosequencing
approach was used in determining the composition of endophytic bacterial communities in tomato leaves (Romero et al. 2001). The endophyte communities were
mainly comprised of five phyla, with Proteobacteria as the most highly represented
(90%), including the classes α-, β-, and γ-Proteobacteria and later is the most
diverse and dominant (Miliute et al. 2015;). Other phyla detected were Actinobacteria (1.5%), Planctomycetes (1.4%), Verrucomicrobia (1.1%), and Acidobacteria
(0.5%) (Santoyo et al. 2016). However, a predominance of these phyla can vary
with the type of host plant species (Bodenhausen et al. 2013; Ding and Melcher
2016). Among the most commonly isolated endophytes, bacterial genera were
Bacillus, Burkholderia, Microbacterium, Micrococcus, Pantoea, Pseudomonas, and
Stenotrophomonas, where Bacillus and Pseudomonas are the predominant genera
(Hallmann et al. 1997; Romeo et al. 2014; Chaturvedi et al. 2016).
Using PCR-based Illumina pyrosequencing, the dynamics of endophytic bacterial communities of sugar beet (Beta vulgaris L.) was analyzed with different
plant genotypes and their growth stages (Shi et al. 2014). The greatest numbers
of OTUs (Operational Taxonomic Units) were detected during tuber growth and
rosette formation, respectively. Interestingly, 43 OTUs were common to all analyzed
periods. Proteobacteria was the most abundant division, with 98% of the total microbial endophyte community being composed of Enterobacteriales, Pseudomonadales,
Xanthomonadales, Rhizobiales, Sphingomonadales, Burkholderiales, Actinomycetales, and Flavobacteriales. All of them were common inhabitants of the rhizosphere
and therefore, suggested that the endophyte microbiome may be a subpopulation of
the rhizosphere inhabiting bacteria (Marquez-Santacruz et al. 2010; Germida et al.
1998).
The occurrence of Acinetobacter sp. along with Bacillus sp. was reported in the
medicinal plant Echinacea (Lata et al. 2018). Bacillus sp. such as B. pumilus, B.
subtilis, and B. megaterium were isolated from the roots of medicinal plant Chlorophytum borivilianum (Safed musli) and demonstrated as the major contributors to the
endophytic bacterial diversity in medicinal plants (Panchal and Ingle 2011). Apart
from medicinal plants, the endophytic occurrence of Acinetobacter and Bacillus
species have also been reported in other crops like soybean (Li et al. 2008), sugarcane (Velázquez et al. 2008), the grapevine (Trotel-Aziz et al. 2008), sweet corn, and
cotton (McInroy and Kloepper 1995; Joe et al. 2016). Gagne-Bourgue et al. (2013)
41
the natural habitat (Picollo et al. 2010). The application of molecular techniques
will continue to enable extensive research on environmental factors that shape endophyte communities (Gaiero et al. 2013). Combinatorial approaches, combining both
culture-dependent and culture-independent methods can increase the possibility of
complete structural and functional analysis of the endophytic bacterial community
of a plant (Sessitsch et al. 2004; Hallmann and Berg 2006).
Sessitsch et al. (2012) observed rice’s endorhizosphere using the metagenomics
approach and deciphered many traits shared by the endophytic inhabitants that
might be crucial in their competence and success. The 16S-rRNA pyrosequencing
approach was used in determining the composition of endophytic bacterial communities in tomato leaves (Romero et al. 2001). The endophyte communities were
mainly comprised of five phyla, with Proteobacteria as the most highly represented
(90%), including the classes α-, β-, and γ-Proteobacteria and later is the most
diverse and dominant (Miliute et al. 2015;). Other phyla detected were Actinobacteria (1.5%), Planctomycetes (1.4%), Verrucomicrobia (1.1%), and Acidobacteria
(0.5%) (Santoyo et al. 2016). However, a predominance of these phyla can vary
with the type of host plant species (Bodenhausen et al. 2013; Ding and Melcher
2016). Among the most commonly isolated endophytes, bacterial genera were
Bacillus, Burkholderia, Microbacterium, Micrococcus, Pantoea, Pseudomonas, and
Stenotrophomonas, where Bacillus and Pseudomonas are the predominant genera
(Hallmann et al. 1997; Romeo et al. 2014; Chaturvedi et al. 2016).
Using PCR-based Illumina pyrosequencing, the dynamics of endophytic bacterial communities of sugar beet (Beta vulgaris L.) was analyzed with different
plant genotypes and their growth stages (Shi et al. 2014). The greatest numbers
of OTUs (Operational Taxonomic Units) were detected during tuber growth and
rosette formation, respectively. Interestingly, 43 OTUs were common to all analyzed
periods. Proteobacteria was the most abundant division, with 98% of the total microbial endophyte community being composed of Enterobacteriales, Pseudomonadales,
Xanthomonadales, Rhizobiales, Sphingomonadales, Burkholderiales, Actinomycetales, and Flavobacteriales. All of them were common inhabitants of the rhizosphere
and therefore, suggested that the endophyte microbiome may be a subpopulation of
the rhizosphere inhabiting bacteria (Marquez-Santacruz et al. 2010; Germida et al.
1998).
The occurrence of Acinetobacter sp. along with Bacillus sp. was reported in the
medicinal plant Echinacea (Lata et al. 2018). Bacillus sp. such as B. pumilus, B.
subtilis, and B. megaterium were isolated from the roots of medicinal plant Chlorophytum borivilianum (Safed musli) and demonstrated as the major contributors to the
endophytic bacterial diversity in medicinal plants (Panchal and Ingle 2011). Apart
from medicinal plants, the endophytic occurrence of Acinetobacter and Bacillus
species have also been reported in other crops like soybean (Li et al. 2008), sugarcane (Velázquez et al. 2008), the grapevine (Trotel-Aziz et al. 2008), sweet corn, and
cotton (McInroy and Kloepper 1995; Joe et al. 2016). Gagne-Bourgue et al. (2013)