12
F. M. Romero et al.
diminish or replace the use of agrochemicals, which can result in negative consequences to human health and the environment. In this way, biological control has
attracted the interest of researchers over the last few years as a non-polluting alternative. One of the many strategies is to adopt microbial inoculants since they have
several benefits compared to traditional chemical pest management. Being effective
in small quantities, because they can multiply themselves, and at the same time, the
host and the native microbial community control their spread (Berg 2009). Another
advantage of bioinoculants is that the development of resistance is limited because of
the involvement of different control mechanisms simultaneously. Moreover, microbial inoculants can be used in conventional or integrated pest management (Berg
2009). Thus, it can be achieved by (i) creation of environmental conditions favorable for the action of controlling microorganisms already present in the crops, (ii)
through the genetic improvement of the host’s ability to interact with such microorganisms and (iii) by the genetic manipulation of the controlling microorganisms to
give them advantageous characteristics, or the massive introduction of beneficial
microorganisms into the host during the interaction process.
The first microorganisms receiving attention as potential bioinoculants were those
inhabiting the host-rhizosphere because they were proven to have several traits
regarding plant promotion and antagonistic activity against plant pathogens (Bhattacharyya and Jha 2012). However, the microorganisms able to colonize the inner
cells and tissues of plant hosts also improve plant growth and health and seem to
be excellent candidates as biological control agents (BCAs) as observed by several
workers (Berg and Hallmann 2006; Kloepper and Ryu 2006; Maheshwari 2017).
It is due to endophytic nature which is better protected from harsh environmental
conditions (i.e. extreme temperatures and UV light) and is in closer contact with their
host’s cells and tissues than that of rhizosphere or phyllosphere microbes (Hallmann
et al. 1997; Lindow and Brandl 2003).
A great diversity of microorganisms were reported to exist as endophytes in
cultivation-based studies (Reinhold-Hurek and Hurek 2011; Suryanarayanan 2013).
Among the bacterial endophytes, most isolates belong to the phylum Proteobacteria, even though Firmicutes, Actinobacteria, and Bacteroidetes were also represented (Rosenblueth and Martinez-Romero 2006). However, diversity and richness
of endophytic communities are much greater than those reported in culture-dependent
studies (Dissanayake et al. 2018). In this trend, the use of next-generation sequencing
(NGS) techniques has helped to unravel the structure and composition of endophytic
communities more truly (Bulgarelli et al. 2012; Hong et al. 2019; Romero et al. 2014).
The rapid development and the relative low costs of NGS have contributed to study
microbial communities associated to different plant genotypes and/or growth stages
(Manter et al. 2010; Marques et al. 2014) and is helping to get new insights into
dynamics of plant-endophyte-pathogen interactions (Ardanov et al. 2012; Bulgari
et al. 2014; Tian et al. 2019). Moreover, these culture-independent technologies not
only exhibit the composition of the endophytic communities but also, facilitate the
study of the functions performed by communities in the system. However, the analysis of biological control (BC) related traits in endophyte microbial communities is
F. M. Romero et al.
diminish or replace the use of agrochemicals, which can result in negative consequences to human health and the environment. In this way, biological control has
attracted the interest of researchers over the last few years as a non-polluting alternative. One of the many strategies is to adopt microbial inoculants since they have
several benefits compared to traditional chemical pest management. Being effective
in small quantities, because they can multiply themselves, and at the same time, the
host and the native microbial community control their spread (Berg 2009). Another
advantage of bioinoculants is that the development of resistance is limited because of
the involvement of different control mechanisms simultaneously. Moreover, microbial inoculants can be used in conventional or integrated pest management (Berg
2009). Thus, it can be achieved by (i) creation of environmental conditions favorable for the action of controlling microorganisms already present in the crops, (ii)
through the genetic improvement of the host’s ability to interact with such microorganisms and (iii) by the genetic manipulation of the controlling microorganisms to
give them advantageous characteristics, or the massive introduction of beneficial
microorganisms into the host during the interaction process.
The first microorganisms receiving attention as potential bioinoculants were those
inhabiting the host-rhizosphere because they were proven to have several traits
regarding plant promotion and antagonistic activity against plant pathogens (Bhattacharyya and Jha 2012). However, the microorganisms able to colonize the inner
cells and tissues of plant hosts also improve plant growth and health and seem to
be excellent candidates as biological control agents (BCAs) as observed by several
workers (Berg and Hallmann 2006; Kloepper and Ryu 2006; Maheshwari 2017).
It is due to endophytic nature which is better protected from harsh environmental
conditions (i.e. extreme temperatures and UV light) and is in closer contact with their
host’s cells and tissues than that of rhizosphere or phyllosphere microbes (Hallmann
et al. 1997; Lindow and Brandl 2003).
A great diversity of microorganisms were reported to exist as endophytes in
cultivation-based studies (Reinhold-Hurek and Hurek 2011; Suryanarayanan 2013).
Among the bacterial endophytes, most isolates belong to the phylum Proteobacteria, even though Firmicutes, Actinobacteria, and Bacteroidetes were also represented (Rosenblueth and Martinez-Romero 2006). However, diversity and richness
of endophytic communities are much greater than those reported in culture-dependent
studies (Dissanayake et al. 2018). In this trend, the use of next-generation sequencing
(NGS) techniques has helped to unravel the structure and composition of endophytic
communities more truly (Bulgarelli et al. 2012; Hong et al. 2019; Romero et al. 2014).
The rapid development and the relative low costs of NGS have contributed to study
microbial communities associated to different plant genotypes and/or growth stages
(Manter et al. 2010; Marques et al. 2014) and is helping to get new insights into
dynamics of plant-endophyte-pathogen interactions (Ardanov et al. 2012; Bulgari
et al. 2014; Tian et al. 2019). Moreover, these culture-independent technologies not
only exhibit the composition of the endophytic communities but also, facilitate the
study of the functions performed by communities in the system. However, the analysis of biological control (BC) related traits in endophyte microbial communities is