withMicromonosporaspecies suggest that these microorganisms have important
beneficial effects in plants (Martínez-Hidalgo 2014 ; Trujillo et al. 2010 , 2015 ).
Due to the fact that culture-dependent methods are very limiting and only target
less than 1% of the existing bacterial universe, culture-independent methods such as
denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment
length polymorphism (T-RFLP) and, more recently, next generation sequencing
techniques, like metagenomics analysis, have become very important tools for the
investigation of the complex microbial communities associated with plants and of
the inherent endophytic population. In particular, metagenomics analysis has
allowed a better understanding of the abundance, diversity, and distribution of
endophytic actinobacteria in a wide variety of plants, including agriculturally
important crops. Using this approach, several studies have shown that endophytic
actinobacteria are well represented in different crops such as grapevine (Vitis
vinifera), olive (Olea europaea), rice (Oryza sativa), potato (Solanum tuberosum),
and lettuce (Lactuca sativa), with the families Corynebacteriaceae,
Kineosporiaceae, Microbacteriaceae, Micrococcaceae, Micromonosporaceae,
Nocardioaceae, and Streptomycetaceae, being amongst the predominant taxa
(Cardinale et al. 2015 ; Manter et al. 2010 ;Müller et al. 2015 ; Okubo et al. 2014 ;
Pinto et al. 2014 ; Trujillo et al. 2015 ). A combination of culture-dependent and
independent methods may be used for a deeper investigation of endophytic com-
munities, with studies suggesting that these two approaches are complementary, as
the microbial communities retrieved by isolation methods are often different from
those obtained through molecular techniques (Garbeva et al. 2001 ; Qin et al. 2011 ,
2012 ).
Despite the accumulating studies suggesting that endophytic actinobacteria are
beneficial to their host plants and contribute to their health, a restricted number of
these microorganisms has been reported to have a pathogenic character, though
when compared with other bacteria these exert a minor role in plant diseases.
Examples of pathogens of agricultural plants include Streptomyces scabies,
S. acidiscabies,S. europaeiscabiei,andS. turgidiscabiesthat cause diverse potato
scab diseases (Bignell et al. 2010 ; Loria et al. 2006 ).S. scabieshas a worldwide
distribution and was thefirst pathogenicStreptomycesdescribed in the literature,
while the other species have a more recent occurrence (Barka et al. 2016 ; Kreuze
et al. 1999 ; Wanner 2006 ). Examples of other pathogenic endophytic actinobacteria
are the speciesCurtobacteriumflaccumfacienswhich cause disease on a variety of
plants such as Phaseolus and Vigna species, sugar beet, etc. (Saddler and
Messenber-Guimaraes 2012 ),Leifsonia xylisubsp.xyliwhich causes the disease
ratoon stunting in sugarcane (Monteiro-Vitorello et al. 2004 ) andClavibacter
michiganensiswhich is pathogenic to alfalfa, maize, potato and wheat, causing
considerable economic losses worldwide (Eichenlaub and Gartemann 2011 ;Flügel
et al. 2012 ; Trujillo et al. 2015 ).
174 M.F. Carvalho et al.