Cultivation and Genome Sequencing of Bacteria Isolated From the Coffee Berry Borer (Hypothenemus hampei), With Emphasis on the Role of Caffeine Degradation.

Fernando E Vega,Jonathan Shao,Sayaka Aoki,Jude E Maul,Sarah Emche,Ryan M Summers,Ann Simpkins,Francisco Infante,Meredith B Mock,Dieter Ebert

doi:10.3389/fmicb.2021.644768

Abstract

The coffee berry borer, the most economically important insect pest of coffee worldwide, is the only insect capable of feeding and reproducing solely on the coffee seed, a food source containing the purine alkaloid caffeine. Twenty-one bacterial species associated with coffee berry borers from Hawai’i, Mexico, or a laboratory colony in Maryland (Acinetobacter sp. S40, S54, S55, Bacillus aryabhattai, Delftia lacustris, Erwinia sp. S38, S43, S63, Klebsiella oxytoca, Ochrobactrum sp. S45, S46, Pantoea sp. S61, Pseudomonas aeruginosa, P. parafulva, and Pseudomonas sp. S30, S31, S32, S37, S44, S60, S75) were found to have at least one of five caffeine N-demethylation genes (ndmA, ndmB, ndmC, ndmD, ndmE), with Pseudomonas spp. S31, S32, S37, S60 and P. parafulva having the full complement of these genes. Some of the bacteria carrying the ndm genes were detected in eggs, suggesting possible vertical transmission, while presence of caffeine-degrading bacteria in frass, e.g., P. parafulva (ndmABCDE) and Bacillus aryabhattai (ndmA) could result in horizontal transmission to all insect life stages. Thirty-five bacterial species associated with the insect (Acinetobacter sp. S40, S54, S55, B. aryabhattai, B. cereus group, Bacillus sp. S29, S70, S71, S72, S73, D. lacustris, Erwinia sp. S38, S43, S59, S63, K. oxytoca, Kosakonia cowanii, Ochrobactrum sp. S45, S46, Paenibacillus sp. S28, Pantoea sp. S61, S62, P. aeruginosa, P. parafulva, Pseudomonas sp. S30, S31, S32, S37, S44, S60, S75, Stenotrophomonas sp. S39, S41, S48, S49) might contribute to caffeine breakdown using the C-8 oxidation pathway, based on presence of genes required for this pathway. It is possible that caffeine-degrading bacteria associated with the coffee berry borer originated as epiphytes and endophytes in the coffee plant microbiota.

Highlights

80 plant species synthesize purine alkaloids (Ashihara and Crozier, 1999)
The detection of genes involved in the two mechanisms for bacterial metabolism of caffeine, i.e., N-demethylation and C8 oxidation, has revealed the complexity of culturable bacterial symbiotes of the coffee berry borer
The isolation and identification of culturable bacteria for an assessment of caffeinebreakdown capabilities would be useful in understanding the coffee berry borer microbial diversity in various coffeegrowing regions as well as various coffee- growing regimes such as Arabica vs robusta and shaded coffee vs coffee grown at full sun

Summary

Introduction

80 plant species synthesize purine alkaloids (Ashihara and Crozier, 1999). Among these species, coffee, tea (Camellia spp.), and cacao (Theobroma cacao) are well known for the presence of the purine alkaloid 1,3,7-trimethylxanthine, commonly known as caffeine, which is widely used for its stimulant effects (Cappelletti et al, 2015). Of 125 species in the genus Coffea (Rubiaceae) (Davis et al, 2006, 2011), only three are commercially traded: Coffea arabica, C. canephora ( known as robusta coffee), and C. liberica. Several studies have confirmed a negative effect of caffeine on insects (see Vega et al, 2003 and references therein). An exception is the coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae: Scolytinae), which has evolved an extreme adaptation to caffeine and is the only insect that feeds solely on seeds within the coffee fruit (Vega et al, 2015)

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Conclusion