Endophytic microbial diversity in coffee cherries ofCoffea arabicafrom southeastern Brazil

Abstract

The microbiota associated with coffee plants may play a critical role in the final expression of coffee quality. However, the microbial diversity in coffee cherries is still poorly characterized. Here, we investigated the endophytic diversity in cherries of Coffea arabica by using culture-independent approaches to identify the associated microbes, ultimately to better understand their ecology and potential role in determining coffee quality. Group-specific 16S rRNA and 26S rRNA genes polymerase chain reaction - denaturing gradient gel electrophoresis and clone library sequencing showed that the endophytic community is composed of members of the 3 domains of life. Bacterial sequences showing high similarity with cultured and uncultured bacteria belonged to the Betaproteobacteria, Gammaproteobacteria, and Firmicutes phyla. Phylogenetic analyses of cloned sequences from Firmicutes revealed that most sequences fell into 3 major genera: Bacillus, Staphylococcus, and Paenibacillus. Archaeal sequences revealed the presence of operational taxonomic units belonging to Euryarchaeota and Crenarchaeota phyla. Sequences from endophytic yeast were not recovered, but various distinct sequences showing high identity with filamentous fungi were found. There was no obvious correlation between the microbial composition and cultivar or geographic location of the coffee plant. To the best of our knowledge, this is the first report demonstrating internal tissue colonization of plant fruits by members of the Archaea domain. The finding of archaeal small-subunit rRNA in coffee cherries, although not sufficient to indicate their role as active endophytes, certainly expands our perspectives toward considering members of this domain as potential endophytic microbes.

Diversity and distribution of the endophytic fungal community in eucalyptus leaves

“…Next, the material w as immersed tw ice in distilled w ater and phosphate buffer (0.05 mmol·L -1 ), pH 7, immersed in 70% ethanol (v/v) for one minute, kept in a container filled w ith sodium hypochlorite (5%) + 0.05% (v/v) Tw een-80 for five minutes, and then immersed for 30 s in 70% ethanol (v/v) before being immersed again in sodium hypochlorite + Tw een-80 for 15 min (Miguel et al, , 2016Oliveira et al, 2013). This process w as repeated once.…”

“…Microbial diversity can also be studied by analyzing the total DNA of the microbiota extracted directly from the plant for processing using electrophoretic techniques . Studies using these techniques have contributed to a better understanding of the microbial community structure and have led to new perspectives and advances in ecological studies (Hoshino and Matsumoto, 2007;Oliveira et al, 2013;Da Silva et al, 2014). Thus, the present study aimed at evaluating the composition and diversity of the endophytic fungal community in eucalyptus leaves at the onset of the rainy period and during the rainy and dry periods.…”

Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees

“…Archaea represent the so-called third domain of life, and have only recently been described as important component of the moderate environment and the human microbiome (Probst et al, 2013). A few very recent publications have mentioned internal plant tissue colonization by members of the Archaea (Ma et al, 2013; Oliveira et al, 2013), but their distribution, significance, function, and activity remains unclear. In addition, the endophytic microbiota of trees has undergone less investigation and nothing is known about the associated microorganisms within olive trees.…”

Endophyte community composition is associated with dieback occurrence in an invasive tree

“…These results extend current thinking, that multiple organisms within multiple taxonomic domains may be involved in the onset of disease or disease suppression in plants (Coats and Rumpho 2014). Most studies on microbial endophyte communities and dieback investigate one specific microbial taxon, typically fungi (Wilson and Pitkethley 1992;Diplock et al 2006;Kowalski and Holdenrieder 2009;Haque et al 2012;Ismail et al 2012;Sacdalan et al 2012), although there are exceptions (Mendes et al 2011;Knief et al 2012;Ma et al 2013;Oliveira et al 2013;Ruppel et al 2013). Our study found a very diverse microbial community (as assessed using OTUs) whose structure differed with plant health status.…”