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

doi:10.3389/fmicb.2021.644768

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

Front Microbiol. 2021 Apr 6:12:644768. doi: 10.3389/fmicb.2021.644768. eCollection 2021.

Authors

Affiliations

¹ Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States.
² Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States.
³ U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States.
⁴ Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, United States.
⁵ Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.
⁶ El Colegio de la Frontera Sur (ECOSUR), Tapachula, Mexico.
⁷ Department of Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States.

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.

Keywords: Coffea; Coleoptera (beetles); Hypothenemus hampei; bark beetle; broca del café; coffee; symbiosis; symbiotes.