In silico analysis of the 16S rRNA gene of endophytic bacteria, isolated from the aerial parts and seeds of important agricultural crops

Abstract

ABSTRACT. Because of human population growth, increased food production and alternatives to conventional methods of biocontrol and development of plants such as the use of endophytic bacteria and fungi are required. One of the methods used to study microorganism diversity is sequencing of the 16S rRNA gene, which has several advantages, including universality, size, and availability of databases for comparison. The objective of this study was to analyze endophytic bacterial diversity in agricultural crops using published papers, sequence databases, and phylogenetic analysis. Fourteen papers were selected in which the ribosomal 16S rRNA gene was used to identify endophytic bacteria, in important agricultural crops, such as coffee, sugar cane, beans, corn, soybean, tomatoes, and grapes, located in different geographical regions (America, Europe, and Asia). The corresponding 16S rRNA gene sequences were selected from the NCBI database, aligned using the Mega 5.2 program, and phylogenetic analysis was undertaken. The most common orders present in the analyzed cultures were Bacillales, Enterobacteriales, and Actinomycetales and the most frequently observed genera were Bacillus, Pseudomonas, and Microbacterium. Phylogenetic analysis showed that only approximately 1.56% of the total sequences were not properly grouped, demonstrating reliability in the identification of microorganisms. This study identified the main genera found in endophytic bacterial cultures from plants, providing data for future studies on improving plant agriculture, biotechnology, endophytic bacterium prospecting, and to help understand relationships between endophytic bacteria and their interactions with plants.

Characterized non-transient microbiota from stinkbug (Nezara viridula) midgut deactivates soybean chemical defenses

“…The diversity and frequency of NTM were higher in stinkbugs feeding on soybean than in those feeding on secondary hosts (Figs 2 and 3 ). This may be due to diet quality as soybean is a better substrate for enterobacteria [ 60 ]. Also, these bacteria had the ability to remain in the intestine during diapause ( Eucalyptus trees) probably by colonization of midgut epithelium or the lumen ( Fig 3 ).…”

The impact of the endophytic bacterial community on mulberry tree growth in the Three Gorges Reservoir ecosystem, China

“…Taxonomic classification of the bacteria was based on the analysis of 16S rRNA gene sequencing using the universal primers 27F/1492R (Bredow et al ., 2015). Total DNA was extracted from each of the purified isolates using a PrepMan Ultra Sample Preparation Reagent kit (Applied Biosystems, Palo Alto, CA, USA) according to the manufacturer's instructions.…”

RNA applications for endophytic research

“…The 18S nuclear ribosomal small subunit rRNA gene is commonly used in phylogenetic studies, and, although its homolog (16S) is often employed as a species diagnostic paradigm for bacteria (Bredow et al, 2015), 18S has fewer hypervariable domains in fungi. The 28S nuclear ribosomal large subunit rRNA gene sometimes discriminates species alone or with ITS.…”

“…Moreover, 16S rRNA provides trustworthy results for bacterial identification (Bredow et al, 2015). Rhoden et al (2015) identified 16 endophytic bacteria living on leaves of Trichilia elegans (Meliaceae), using sequencing and phylogenetic analyses.…”