184
H. B. Slama et al.
sciences, Microbiology, Mycology, Biotechnology, Ecology, and Agronomy. The
publication rate was doubled during last 5 years suggesting that the field is more
and more attractive to researchers. USA, China, Germany, and India are the main
countries for such scientific research.
8.4 Endophyte Taxonomic Affinities
Endophyte taxonomic affinity is constantly updated by the huge mass of sequences
that are being deposited in databases. In this report, we checked the taxonomic affinity
of endophytes by monitoring bacterial 16S-rDNA and fungal ITS-rDNA sequences
in GenBank. Two taxonomic divisions have been checked the phylum and the genus
levels.
a. Bacterial endophytes taxonomic affinities
Our analysis documented that bacterial endophyte communities are dominated by
proteobacteria (57.24%). This is in line with the results reported by Santoyo et al.
(2016) and Belbahri et al. (2017). α, β, γ, and δ proteobacteria represented respectively 17.67, 22.94, 16.6, and 0.03% of the reported bacterial endophyte community in
GenBank. Less abundant phyla were represented by Firmicutes (18.38%), Actinobacteria (13.89%), and Enterobacteria (8.74%). Remaining phyla represent all together
lesser than 2% of the endophytic bacterial communities (Fig. 8.2). Similar results
have also been reported in many endophytes targeted studies (Cheffi et al. 2019;
Cherif-Silini et al. 2019; Slama et al. 2018, 2019). The most commonly reported
endophytic genera are Burkholderia (16.88%), Bacillus (15.13%), Methylorubrum
(12.04%), Enterobacter (6.02%), Herbaspirillum (5.94%), Streptomyces (5.43%),
Pseudomonas (5.41%), and Pantoea (4.37%). (Alenezi et al. 2016; Slama et al. 2018,
2019).
b. Fungal endophytes taxonomic affinities
Our survey of fungal endophyte ITS-rDNA attested that belongs to Ascomycota
(96.82%). Basidiomycetes represented 3.06% and Glomeromycota represented only
0.12%. These results corroborate earlier findings (Mefteh et al. 2017, 2018, 2019;
White et al. 2019; Haro and Benito 2019). At the genus level Ustilago (13.42%),
Fusarium (5.82%), Gibberella (5.7%), Colletotrichum (4.96%), Alternaria (4.48%),
and Diaporthe (4.47%) dominated fungal endophyte communities (Fig. 8.3).
8.5 Endophyte Lifestyle
The host-associated microbial communities are classified into obligate and facultative
endophytes. Obligate endophytes are culture-independent and are revealed through
molecular approaches, whereas facultative endophytes are culture-dependent and
H. B. Slama et al.
sciences, Microbiology, Mycology, Biotechnology, Ecology, and Agronomy. The
publication rate was doubled during last 5 years suggesting that the field is more
and more attractive to researchers. USA, China, Germany, and India are the main
countries for such scientific research.
8.4 Endophyte Taxonomic Affinities
Endophyte taxonomic affinity is constantly updated by the huge mass of sequences
that are being deposited in databases. In this report, we checked the taxonomic affinity
of endophytes by monitoring bacterial 16S-rDNA and fungal ITS-rDNA sequences
in GenBank. Two taxonomic divisions have been checked the phylum and the genus
levels.
a. Bacterial endophytes taxonomic affinities
Our analysis documented that bacterial endophyte communities are dominated by
proteobacteria (57.24%). This is in line with the results reported by Santoyo et al.
(2016) and Belbahri et al. (2017). α, β, γ, and δ proteobacteria represented respectively 17.67, 22.94, 16.6, and 0.03% of the reported bacterial endophyte community in
GenBank. Less abundant phyla were represented by Firmicutes (18.38%), Actinobacteria (13.89%), and Enterobacteria (8.74%). Remaining phyla represent all together
lesser than 2% of the endophytic bacterial communities (Fig. 8.2). Similar results
have also been reported in many endophytes targeted studies (Cheffi et al. 2019;
Cherif-Silini et al. 2019; Slama et al. 2018, 2019). The most commonly reported
endophytic genera are Burkholderia (16.88%), Bacillus (15.13%), Methylorubrum
(12.04%), Enterobacter (6.02%), Herbaspirillum (5.94%), Streptomyces (5.43%),
Pseudomonas (5.41%), and Pantoea (4.37%). (Alenezi et al. 2016; Slama et al. 2018,
2019).
b. Fungal endophytes taxonomic affinities
Our survey of fungal endophyte ITS-rDNA attested that belongs to Ascomycota
(96.82%). Basidiomycetes represented 3.06% and Glomeromycota represented only
0.12%. These results corroborate earlier findings (Mefteh et al. 2017, 2018, 2019;
White et al. 2019; Haro and Benito 2019). At the genus level Ustilago (13.42%),
Fusarium (5.82%), Gibberella (5.7%), Colletotrichum (4.96%), Alternaria (4.48%),
and Diaporthe (4.47%) dominated fungal endophyte communities (Fig. 8.3).
8.5 Endophyte Lifestyle
The host-associated microbial communities are classified into obligate and facultative
endophytes. Obligate endophytes are culture-independent and are revealed through
molecular approaches, whereas facultative endophytes are culture-dependent and