182
H. B. Slama et al.
Keywords Rhizosphere · Genomics · Omics · Endophytes · Bioremediation
8.1 Introduction
Since last decade, microbial endophytes have attracted attention. They are occupying
a considerable position due to their ubiquitous association with almost all plants (Nair
and Padmavathy 2014; Hardoim et al. 2015; Selim et al. 2017; Sharma et al. 2018;
Goulart et al. 2019). Therefore, extensive studies have provided information about
their endless potentialities in promotion of plant growth (Jasim et al. 2014; Cheffi
et al. 2019; Slama et al. 2019) and inhibition of phytopathogens (Mefteh et al. 2017;
Slama et al. 2018; Cherif-Silini et al. 2019). In addition to that, endophytes have
been exploited in several other fields such as medicine, industry, pharmacology,
bioremediation, and phytoremediation of pollutants (Eevers et al. 2015; Wani et al.
2015; Ma et al. 2016; Kumar and Verma 2018; Paramanantham et al. 2019). Modern
next-generation sequencing involving genomic, proteomic, metabolomics, and metatranscriptomic technologies, have given deep learning of endophytic potentialities as
well as mechanisms and metabolic pathways of secondary metabolites (Fakruddin
and Mannan 2013; Finkel et al. 2019; Hong et al. 2019; Srivastava et al. 2019). Based
on account of informations, this paper first attempts to define endophytes, followed
by a brief insight into bacterial and fungal classification and taxonomic diversity. This
chapter is also an account on role of endophytes in plant growth-promoting activities
via direct and indirect ways. Their widespread environment-friendly applications
in biotic and abiotic stress alleviation, in medicinal, industrial, and environmental
applications have also been described. An overall overview of the advanced “omic”
tools that could be used to get complete informations about endophytic genome and
proteome functions and their interactions with hosts, potentialities, and secondary
metabolites.
8.2 Definition of Endophytes
Microbial endophytes have been known for more than a century, they mainly include
fungi, bacteria, and actinomycetes. Their definition changed over time, in 1866 the
term “endophyte” was first introduced by de Bary, it was originated from the Greek
words endon: within and phyte: plant (Bary 1866). In 1926 endophytic behavior
was defined as a particular stage (symbiotic mutualism) in the bacterial life cycle
(Perotti 1926). From that moment, endophytes were defined as microorganisms being
isolated from host plants after surface sterilization (Henning and Villforth 1940).
Hollis defined endophytes more accurately as being microorganisms existing inside
plant organs without causing disease symptoms (Hollis 1951). Several other definitions, differing from one another, were attributed to the term endophyte. Quispel
H. B. Slama et al.
Keywords Rhizosphere · Genomics · Omics · Endophytes · Bioremediation
8.1 Introduction
Since last decade, microbial endophytes have attracted attention. They are occupying
a considerable position due to their ubiquitous association with almost all plants (Nair
and Padmavathy 2014; Hardoim et al. 2015; Selim et al. 2017; Sharma et al. 2018;
Goulart et al. 2019). Therefore, extensive studies have provided information about
their endless potentialities in promotion of plant growth (Jasim et al. 2014; Cheffi
et al. 2019; Slama et al. 2019) and inhibition of phytopathogens (Mefteh et al. 2017;
Slama et al. 2018; Cherif-Silini et al. 2019). In addition to that, endophytes have
been exploited in several other fields such as medicine, industry, pharmacology,
bioremediation, and phytoremediation of pollutants (Eevers et al. 2015; Wani et al.
2015; Ma et al. 2016; Kumar and Verma 2018; Paramanantham et al. 2019). Modern
next-generation sequencing involving genomic, proteomic, metabolomics, and metatranscriptomic technologies, have given deep learning of endophytic potentialities as
well as mechanisms and metabolic pathways of secondary metabolites (Fakruddin
and Mannan 2013; Finkel et al. 2019; Hong et al. 2019; Srivastava et al. 2019). Based
on account of informations, this paper first attempts to define endophytes, followed
by a brief insight into bacterial and fungal classification and taxonomic diversity. This
chapter is also an account on role of endophytes in plant growth-promoting activities
via direct and indirect ways. Their widespread environment-friendly applications
in biotic and abiotic stress alleviation, in medicinal, industrial, and environmental
applications have also been described. An overall overview of the advanced “omic”
tools that could be used to get complete informations about endophytic genome and
proteome functions and their interactions with hosts, potentialities, and secondary
metabolites.
8.2 Definition of Endophytes
Microbial endophytes have been known for more than a century, they mainly include
fungi, bacteria, and actinomycetes. Their definition changed over time, in 1866 the
term “endophyte” was first introduced by de Bary, it was originated from the Greek
words endon: within and phyte: plant (Bary 1866). In 1926 endophytic behavior
was defined as a particular stage (symbiotic mutualism) in the bacterial life cycle
(Perotti 1926). From that moment, endophytes were defined as microorganisms being
isolated from host plants after surface sterilization (Henning and Villforth 1940).
Hollis defined endophytes more accurately as being microorganisms existing inside
plant organs without causing disease symptoms (Hollis 1951). Several other definitions, differing from one another, were attributed to the term endophyte. Quispel