8.4 Identification and Diversity of Endophytic
Actinobacteria in Agricultural Plants
Plants may host a wide range of actinobacteria genera within their inner tissues.
Identification of actinobacterial endophytes is often based in a polyphasic approach
consisting of several morphological, biochemical and molecular studies.
Morphological studies often consist in colony characterization on agar plates, which
include examination of aerial and substrate mycelia colors and spore mass color,
analysis of spores and hyphae morphology (usually observed in a scanning electron
microscope), as well as inspection for the production and color of diffusible soluble
pigments. Biochemical tests may comprise analysis of melanin production, pres-
ence of various enzymes, and utilization of a range of carbon sources, cell wall
composition, whole-cell sugar distribution, cellular phospholipid composition, and
menaquinone type (Barka et al. 2016 ; Labeda 1987 ; Shirling and Gottlieb 1966 ).
Molecular analyses are based on the sequencing of the 16S rRNA gene and
DNA–DNA hybridization, and are strictly necessary for the identification of new
species (Barka et al. 2016 ).
Diversity of endophytic actinobacteria seems to be higher in woody than in
herbaceous plants, with roots having the highest number and diversity, followed by
stems and leaves (Kekuda 2016 ). The ecological environment of the plant also
influences actinobacterial diversity (Sheil 1999 ). Endophytic actinobacteria have
been isolated from various crop plants, such as maize, wheat, tomato, rice, citrus,
potato, Aloe vera, etc. (Araújo et al. 2000 , 2001 ; Coombs and Franco 2003 ;de
Oliveira et al. 2010 ; Garbeva et al. 2001 ; Prakash et al. 2014 ; Thanaboripat et al.
2015 ; Tian et al. 2007 ), with the most frequently isolated genus beingStreptomyces
(Kampapongsa and Kaewkla 2016 ; Sardi et al. 1992 ; Taechowisan et al. 2003 ; Tian
et al. 2004 ). Other common isolated genera areMicromonospora,Microbispora,
andNocardia(Table8.1). Recent studies on the diversity of endophytic acti-
nobacteria in various plants have also allowed the identification of more than 40
new taxa, namely of the generaActinoallomurus,Actinophytocola,Jishengella,
Phytohabitans,Saccharopolyspora,Streptosporangium,Plantactinospora, among
others (Masand et al. 2015 ; Qin et al. 2011 ).
Studies revealed that in addition to roots, stems, and leaves, nitrogen-fixing
nodules also harbor endophytic actinobacteria, and exhibited the isolation of the
genera Streptomyces, Agromyces, Curtobacterium, Micromonospora, and
Microbacteriumfrom the nodules of different leguminous and actinorhizal plants
(Carro et al. 2012 ; Deng et al. 2011 ; Trujillo et al. 2006 , 2007 ). The two latter
genera were found to be particularly predominant in plant nodules, with several
new species ofMicromonosporabeing isolated from these tissues (Carro et al.
2013 ; Garcia et al. 2010 ; Trujillo et al. 2006 , 2007 , 2015 ). The role of these
microorganisms in plant growth promotion in not completely known, but studies
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