Metagenomics workflow analysis of endophytic bacteria from oil palm fruits

Agricultural and Other Biotechnological Applications Resulting from Trophic Plant-Endophyte Interactions

“…The Next-Generation Sequencing (NGS) technology is one of the most important techniques for microbiological research [13,[15][16][17][18]. It has contributed to the emergence of metagenomics, i.e., an analysis of the genome of microorganisms by only DNA extraction without the necessity of cultivating microorganisms on artificial media [16,18,19]. Dijk et al [20] and Wolińska et al [21] suggested that the NGS technique contributed to overcoming the shortages and limitations that are connected with detection of only the most abundant and cultivated genera.…”

“…Three basic platforms can be distinguished in NGS: Roche 454-pyrosequencing, Ion Torrent, and Illumina sequencing. They differ in the average length of the base pair reading (Roche 454-500 base pairs, Ion Torrent~200-300 base pairs, Illumina~120-150 for SR200, and 250-300 base pairs for v2 250PE and v3 300 PE, respectively) [16,18,25]. The Ion Torrent and the Illumina rely on a slightly different mechanism of detection of nucleotide sequences.…”

“…A list of the most recent metagenomic studies [11][12][13][14][15][16][17]23,24,[32][33][34][35][36][37][38][39][40] has been prepared to summarize endophyte strains that can be potentially employed for specific plants and properties that have been enhanced (Table 1). It was demonstrated that plant growth promoting (PGP) abilities and biological nitrogen fixation, followed by the production of secondary metabolites and bioactive compounds, synthesis of fungicides and bactericides, and protection against environmental stresses are the most important benefits that are provided to plants by endophytes (Table 1).…”

“…In turn, Annapurna et al [33] analyzed the genome of the KMS80 strain Bacillus paralicheniformis while using the NGS technique, which made it possible to understand the process of endophytic nitrogen fixation and the positive effect on plant growth and crop yields. Many studies recently published studies used NGS for the determination of the plant growth promoting properties of endophytes [13,16,17,32,33]. NGS evidenced that endophytic representatives of the following bacterial genera: Bacillus, Paenibacillus, Rhizobium, Duganella, Serratia, Klebsiella, Agrobacterium, Microbacterium, Sphingobacterium, Erwinia, Herbaspirillum, etc.…”

“…Plant growth promoting bacteria (PGPB) can be defined as representatives of biota that can stimulate the growth of the host, for example, rhizobacteria, when they grow in association with host plants [13,43,44]. Endophytic organisms can stimulate and intensify plant growth through the following mechanisms [16,17,24]:…”