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

Abstract

The endophytic bacteria were isolated from coffee roots and seeds in Vietnam and identified with 16S rDNA sequencing as belonging to the Actinobacteria, Firmicutes and Proteobacteria phyla with the Nocardia, Bacillus and Burkholderia as dominant genera, respectively. Out of the thirty genera recovered from Coffea canephora and Coffea liberica, twelve were reported for the first time in endophytic association with coffee including members of the genera Brachybacterium, Caballeronia, Kitasatospora, Lechevalieria, Leifsonia, Luteibacter, Lysinibacillus, Mycolicibacterium, Nakamurella, Paracoccus, Sinomonas and Sphingobium. A total of eighty bacterial endophytes were characterized in vitro for several plant growth promoting and biocontrol traits including: the phosphate solubilization, the indolic compounds, siderophores, HCN, esterase, lipase, gelatinase and chitinase production. A subset of fifty selected bacteria were tested for their potential as biocontrol agents with in vitro confrontations with the fungal pathogen Fusarium oxysporum as well as the coffee parasitic nematodes Radopholus duriophilus and Pratylenchus coffeae. The three most efficient isolates on F. oxysporum belonging to the Bacillus, Burkholderia, and Streptomyces genera displayed a growth inhibition rate higher than 40%. Finally, five isolates from the Bacillus genus were able to lead to 100% of mortality in 24 h on both R. duriophilus and P. coffeae.

Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review

“…The endosphere is the most studied compartment of the indigenous coffee microbiota. We reviewed the content of 71 publications dealing with coffee endophytes, among which 65 employed a culture-dependent method to isolate bacterial and fungal endophytes from various C. arabica, C. canephora, and C. liberica tissues including cherries (Sakiyama et al, 2001;Vega et al, 2008;Miguel et al, 2013), leaves (Santamaría and Bayman, 2005;Bongiorno et al, 2016), roots (Raviraja et al, 1996;Jimenez-Salgado et al, 1997;Vega et al, 2006;Hoang et al, 2020;Duong et al, 2021), seeds (Vega et al, 2006;Duong et al, 2021), and stems (Vega et al, 2005(Vega et al, , 2010. Basic culture-independent strategies were used in three studies to identify archaea, bacteria, and fungi including AMF inside the C. arabica roots and cherries (Oliveira et al, 2013;Mahdhi et al, 2017;Prates Júnior et al, 2019).…”

“…To this end, the capacity to solubilize the phosphorus has been demonstrated not only for numerous bacterial species associated with C. arabica, C. canephora, and C. liberica roots and seeds, belonging to the genera Acinetobacter, Aeromonas, Alcaligenes, Arthrobacter, Bacillus, Brachybacterium, Burkholderia, Caballeronia, Cellulomonas, Chromobacterium, Chryseobacterium, Chryseomonas, Citrobacter, Curtobacterium, Enterobacter, Gordonia, Kocuria, Luteibacter, Mycolicibacterium, Nocardia, Paenibacillus, Paraburkholderia, Pasteurella, Pseudomonas, Rhodococcus, Sphingomonas, Staphylococcus, Stenotrophomonas, and Vibrio (Baon et al, 2012;Muleta et al, 2013;Teshome et al, 2017;Duong et al, 2021) and also for some fungi from the genera Aspergillus, Chaetomium, Cladosporium, Cylindrocarpon, Fusarium, Humicola, Paecilomyces, and Penicillium (Posada et al, 2013;Perea Rojas et al, 2019). Another capacity is the iron mobilization through the production of siderophores as displayed by the bacterial genera Acinetobacter, Bacillus, Burkholderia, Caballeronia, Cellulomonas, Enterobacter, Escherichia, Luteibacter, Mycolicibacterium, Paraburkholderia, Lechevalieria, Mycobacterium, Pseudomonas, Nocardia, Paenibacillus, and Rhizobium associated with roots, leaves and seeds of C. arabica, C. canephora, and C. liberica (Silva et al, 2012;Kejela et al, 2016;Duong et al, 2021). Finally, the production of phytohormones (e.g., auxins) or regulators (e.g., the ACC deaminase enzyme able to lower ethylene level) was established for some members of the genera Bacillus, Brachybacterium, Burkholderia, Erwinia, Escherichia, Kocuria, Luteibacter, Methylobacterium, Mycobacterium, Mycolicibacterium, Nocardia, Ochrobactrum, Paenibacillus, Paracoccus, Pseudomonas, Rhizobium, Serratia, Sinomonas, and Sphingobium (Muleta et al, 2009;Baon et al, 2012;Silva et al, 2012;Kejela et al, 2016;Duong et al, 2021).…”

“…Another capacity is the iron mobilization through the production of siderophores as displayed by the bacterial genera Acinetobacter, Bacillus, Burkholderia, Caballeronia, Cellulomonas, Enterobacter, Escherichia, Luteibacter, Mycolicibacterium, Paraburkholderia, Lechevalieria, Mycobacterium, Pseudomonas, Nocardia, Paenibacillus, and Rhizobium associated with roots, leaves and seeds of C. arabica, C. canephora, and C. liberica (Silva et al, 2012;Kejela et al, 2016;Duong et al, 2021). Finally, the production of phytohormones (e.g., auxins) or regulators (e.g., the ACC deaminase enzyme able to lower ethylene level) was established for some members of the genera Bacillus, Brachybacterium, Burkholderia, Erwinia, Escherichia, Kocuria, Luteibacter, Methylobacterium, Mycobacterium, Mycolicibacterium, Nocardia, Ochrobactrum, Paenibacillus, Paracoccus, Pseudomonas, Rhizobium, Serratia, Sinomonas, and Sphingobium (Muleta et al, 2009;Baon et al, 2012;Silva et al, 2012;Kejela et al, 2016;Duong et al, 2021).…”

“…Microorganisms colonizing several coffee plant compartments have been examined for their potential use as biocontrol agents including bacteria and fungi isolated from the rhizosphere (Mulaw et al, 2010;Kejela et al, 2016), the episphere (Haddad et al, 2014;Leong et al, 2014), and the endosphere (Silva et al, 2012;Hoang et al, 2020;Duong et al, 2021).…”

“…As for the plant growth-promoting agents, several in vitro screenings of potential biocontrol capacities were employed. For example, it was successfully demonstrated that numerous bacterial isolates (from the genera: Acinetobacter, Aeromonas, Alcaligenes, Bacillus, Brachybacterium, Brevibacillus, Burkholderia, Cedecea, Caballeronia, Cellulomonas, Chromobacterium, Chryseobacterium, Chryseomonas, Curtobacterium, Enterobacter, Erwinia, Escherichia, Flavobacterium, Herbaspirillum, Kitasatospora, Lechevalieria, Leifsonia, Luteibacter, Microbacterium, Micrococcus, Mycobacterium, Mycolicibacterium, Nocardia, Ochrobactrum, Paenibacillus, Paraburkholderia, Pasteurella, Pectobacterium, Pseudomonas, Rhizobium, Salmonella, Serratia, Sinomonas, Streptomyces, and Vibrio) were able to produce some enzymes including chitinases, gelatinases, lipases, and proteases (Muleta et al, 2009;Tiru et al, 2013;Kejela et al, 2016;Asyiah et al, 2018;Hoang et al, 2020;Duong et al, 2021) as well as some other active compounds like HCN and siderophores (Muleta et al, 2007;Silva et al, 2012;Tiru et al, 2013;Duong et al, 2021), already known to be involved in the biocontrol mechanisms (Compant et al, 2005;Saraf et al, 2014;Köhl et al, 2019).…”