Diversity of endophytic bacteria in the fruits of Coffea canephora

Abstract

Endophytic bacteria colonize the internal tissues of plants without causing infection or negative effects on their hosts. This study investigates the occurrence and diversity of culturable endophytic bacteria in the fruits of Coffea canephora at three developmental stages. Isolation and quantification were performed in R2A culture medium, and the diversity was established using molecular methods and analysis of fatty acid methyl esters (FAME). α-and γ-Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were identified in the investigated community. Kocuria turfanensis and Pantoea vagans were identified as endophytes for the first time. Of the 18 species that were found, the following seven had not been previously described as endophytic in coffee fruits: Bacillus thuringiensis, Bacillus licheniformis, Agrobacterium tumefaciens, Escherichia coli, Enterobacter hormaechei, Chryseobacterium sp., and Ochrobactrum sp. The diversity of endophytic bacteria varied during the three developmental stages that were investigated, and the diversity was greatest in fruits during the green stage, during which Bacillus subtilis predominated. The number of Gram-positive bacteria was larger than the number of Gram-negative bacteria during the two earliest developmental stages, whereas their numbers were similar during the ripe stage. The diversity was lowest during the ripe stage, and Klebsiella oxytoca was the predominant species at this stage, probably due to the higher caffeine and sugar contents in the fruits.

Endophytic microbial diversity in coffee cherries ofCoffea arabicafrom southeastern Brazil

“…More recently, the endophytic microbiota present in coffee plants, and especially in coffee cherries, has received considerable attention, when its diversity and potential contribution to positive attributes of brewed coffee began to be appreciated. Classically, the endophytic microbiota has been profiled by cultural-dependent methods (Sakiyama et al 2001;Vega et al 2005;Silva et al 2008;Miguel et al 2013). However, because the majority of microorganisms are not amenable to cultivation under standard laboratory conditions (Amann et al 1995;Handelsman et al 1998;Handelsman 2005), we anticipate that the real complexity of the endophytic microbiota in coffee cherries is largely underestimated and a phylogenetic description of the endophytes is far from complete.…”

Rhizosphere bacteriome of the medicinal plant Sapindus saponaria L. revealed by pyrosequencing

“…In Brazil, biotechnological research has targeted the diversity of microorganisms because of the potential for discovery of new bioactive compounds or bioprocesses (Schulz and Boyle, 2005;de Oliveira Costa et al, 2012;García et al, 2012b;Rhoden et al, 2012;Miguel et al, 2013;Polonio et al, 2015). Studies on microbiota associated with plants are important to understand and predict the spatial distribution of microbial communities and the ecosystem responses to global climate change (Singh et al, 2010).…”

Identification and characterization of Vietnamese coffee bacterial endophytes displaying in vitro antifungal and nematicidal activities

“…Additionally, the present work provides new insights into the localization of some genera already know to be in endophytic association with coffee. Thus, endophytic genera associated with coffee cherries and seeds (Miguel et al, 2013;Oliveira et al, 2013;Vaughan et al, 2015) were recovered for the first time from the roots including members of Rhizobium, Staphylococcus, and Sphingomonas. Furthermore, members of the Mycobacterium genus already described as coffee root endophytes have never been isolated from the seeds (Teshome et al, 2017).…”

“…roots (Asyiah et al, 2018;Hoang et al, 2020;Jimenez-Salgado et al, 1997;Nair et al, 2002;Nunes and de Melo, 2006;Sakiyama et al, 2001;Shiomi et al, 2006;Teshome et al, 2017;Vaughan et al, 2015;Vega et al, 2005). However, Miguel et al (2013) and Mekete et al (2009), isolated endophytes belonging to the phylum Bacterioidetes from coffee cherries and roots, but the relative abundance of this bacterial phylum was very low with Chryseobacterium as only genus. Recently, Fulthorpe et al (2020) described the C. arabica roots endophytic community with a metabarcoding approach.…”