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

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  1 , Sarah Emche  2 , Jonathan Shao  3 , Ann Simpkins  1 , Ryan M Summers  4 , Meredith B Mock  4 , Dieter Ebert  5 , Francisco Infante  6 , Sayaka Aoki  7 , Jude E Maul  2
Affiliations

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 et al. Front Microbiol. .

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.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Metabolic pathways for caffeine degradation by bacteria. N-demethylation is indicated by red arrows. C-8 oxidation is indicated by the blue arrow.
FIGURE 2
FIGURE 2
Consensus gene clusters containing N-demethylase genes from bacterial isolates in this work. (A) ndmABCDE cluster from Pseudomonas sp. S31, S32, S37, S60, and Pseudomonas parafulva. (B) ndmAD cluster from Erwinia sp. S38, S43. (C) ndmA cluster from Bacillus aryabhattai. (D) ndmC gene cluster from Acinetobacter sp. S40, S54, S55. (E) ndmD gene cluster from Acinetobacter sp. S40, S54, S55. (F) ndmE gene cluster from Ochrobactrum sp. S45, S46. (G) ndmD gene cluster from Pseudomonas aeruginosa. (H) ndmE gene cluster from Pseudomonas aeruginosa. (I) ndmE gene cluster from Pseudomonas sp. S30, S75. (J) ndmD gene cluster from Erwinia sp. S63. (K) ndmD gene cluster from Pseudomonas sp. S44. (L) ndmE gene cluster from Pseudomonas sp. S44. (M) ndmA gene cluster from Delftia lacustris. (N) ndmD gene cluster from D. lacustris. (O) ndmE gene cluster from D. lacustris. Genes in each cluster are listed in Supplementary Table 4.
FIGURE 3
FIGURE 3
Venn diagram showing genes involved in the caffeine N-demethylation pathway shared among Acinetobacter sp. S40, S54, S55, Bacillus aryabhattai, Delftia lacustris, Erwinia sp. S38, S43, S63, Klebsiella oxytoca, Ochrobactrum sp. S45, S46, Pantoea sp. S61, Pseudomonas sp. S30, S31, S32, S37, S44, S60, S75, P. aeruginosa, and P. parafulva.
See this image and copyright information in PMC

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