By Emma Sage, Coffee Science Manager
This summer, arguably one of the most significant advances in coffee science in recent years occurred, and passed quietly by, (that is, if you don’t frequently peruse scientific journals). In fact, in Scientific Reports, published by Nature Publishing Group, a study was published to announce the draft genome of Hypothenemus hampei (Ferrari) (Vega and others 2015b). Who, pray tell, is this Hypothenemus? None other than the most globally devastating insect to coffee: the coffee berry borer. A parallel study was released in Nature Communications the same month on the discovery of the key role played by gut microbiota within the coffee berry borer (Ceja-Navarro and others 2015). Now I will explain just why this research is so critical for the coffee industry.
For those of you who have not encountered a coffee berry borer in person, they are tiny beetles (approximately 2 millimeters long) hardly distinguishable to the naked eye. As often is the case with insects, the females drive the business of the species, with a 10:1 female to male sex ratio (Vega and others 2009). They find a nice red coffee fruit to bore into and deposit their cache of eggs safely inside the coffee seeds (Ortiz and others 2004; Vega and others 2015a). Later, when the eggs hatch into larvae, low and behold there is a lot to eat, which is how the seed damage occurs (Vega and others 2009). Inside the coffee bean, those babies get to work eating and mating, as animals tend to do. The cycle starts again when the males expire and the females eat their way to the outside world, where they fly to another perfect yet vulnerable nearby coffee fruit. If this life cycle sounds impressively efficient to you, your inner biologist is showing.
The reason that this is truly exceptional, from a biological standpoint, is that generally caffeine in plants is supposed to serve as a protection against herbivory (Nathanson 1984). In fact, the coffee berry borer is the only animal that can feed exclusively on coffee seeds. Biology is not “supposed” to work this way, which is a key reason that this insect has been so elusive to management. Current defense strategies investigated by research labs and practiced in the field include trapping (Fernandes and others 2015), biological control (Vega and others 2009; Rojas and others 2006; Damon 2000), and cultural control via agronomic farm management (Vega and others 2015a). None of these have provided a perfect or very effective solution to this hungry, devastating insect. Scientists have yet to find the “Achilles heel” of the coffee berry borer. With climate change imminent, and the coffee berry borer expected to become an even greater threat (Jaramillo and others 2011), we live in a critical time for understanding the biology of this devastating coffee-munching pest.
For us on the consuming-side of the coffee industry, we often see evidence of coffee berry borers through a small hole in the end of green coffee beans, or in cases of severe infestations, black or brown discoloring around it. This is a defect and definitely affects the quality of coffee. Because of this, more often than not, these are cleaned out before they are exported. However, you may be surprised to learn that the United States Department of Agriculture (USDA) has been studying the insect in an attempt to develop novel pest management strategies that can be adopted by coffee growing families worldwide. Dr. Fernando E. Vega of the USDA Sustainable Perennial Crops Laboratory in Beltsville, Maryland, was a key author on both of these new studies, and is a world-renowned expert on the pest.
Having the full draft genome of the coffee berry borer is a major breakthrough in coffee research. These two studies not only tell the world that the coffee berry borer is a formidable pest and explain some the major reasons why and create a platform for future study. The coffee berry borer is without a doubt the most economically important coffee pest of coffee worldwide. In Brazil alone, yearly losses caused by the insect are estimated at US$215-358 million (Oliveira 2013). Therefore, understanding more of its biology, genetics, and strengths and weaknesses thereof, will allow researchers and private companies alike develop smarter defense strategies to combat it. According to Dr. Vega, “The publication of the genome presents in-depth information of many basic biological mechanisms that can theoretically be exploited to manage the insect.”
In this study, the researchers not only reported on the genome, but discovered ten cases of horizontal gene transfer, which means they identified those 10 genes as being more closely related to bacteria than to insects. That means, over evolutionary time, the coffee berry borers have actually “acquired” some genetic material from bacteria, maybe from bacteria found within the guts. The term “horizontal gene transfer” simply means that the genes were transferred in a way other than through reproduction, but the mechanism for these transfers are not fully understood. No one would say that this was purposeful “acquiring” on the part of the coffee berry borer, but genes that provide an advantage tend to stick around. In the case of the coffee berry borer and its ten bacterially-originating genes, these are linked to easier digestion through enzymatic activity. These genes now live permanently in their genome and allow them to digest some key carbohydrates found in coffee seeds.
In the parallel and elegant study published in Nature Communications, scientists gave coffee berry borers caffeine and analyzed their dung for the leftovers of the compound. In normal borers, they found almost no caffeine left over, which means that it was being digested. They then treated the borers with antibiotics (to knock out their gut microbiota) and fed them caffeine again. This time, the treated beetles had plenty of caffeine in their dung, and on top of that, they could hardly function. This effect was so severe that the coffee berry borers who got the antibiotics were unable to reproduce successfully. Just to check their hypothesis, they re-inoculated those beetles with a certain type of bacteria, and once again, the beetles digested the caffeine. This all is a very simple and nice way of supporting the hypothesis that in fact, the beetles are not doing the digesting, but their friendly local gut microorganisms are. We hear a lot about the human gut microbiome in the popular press lately (for example, here and here). It makes a lot of sense that insects would have one too, but it is very impressive (from an evolutionary standpoint) that it is doing so much for the coffee berry borer. Dr. Vega explained, “The presence of these bacteria is what allows the insect to survive on a food source rich in caffeine, an alkaloid that has been shown to be toxic to other insects. When these bacteria are eliminated, there are severe detrimental effects on insect fitness.” So, basically, the coffee berry borer microbiota enable it to eat coffee seeds, and if they did not have those bacteria, they could die from caffeine toxicity.
We now have a greater understanding of how bacteria have helped the coffee berry borer in at least two ways – through gene transfer so that they can digest specific carbohydrates found in coffee seeds, as well as though digesting the caffeine currently found in coffee seeds to that the insects can survive and reproduce. In biology, we might call this an obligate symbiosis, which means a win-win for the coffee berry borer and its gut-dwelling free riding bacteria. The key for us humans (who enjoy coffee) will be to now understand how we can disable this relationship in a way that is detrimental to the pests.
So what’s next? The genome publication is the first step in paving the way for lots of new advances in research on the coffee berry borer. For Dr. Vega, studying the coffee berry borer is a life’s work. He says, “Even though the insect has been studied for more than 100 years, we keep finding fascinating aspects of its biology that have not been previously reported.” Vega says that the USDA will continue to work on the defense against the coffee berry borer, including a promising repellent that will enter field trials soon.
Ceja-Navarro JA, Vega FE, Karaoz U, Hao Z, Jenkins S, Lim HC, Kosina P, Infante F, Northen TR, Brodie EL. 2015. Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee. Nature Communications 6.
Damon A. 2000. A review of the biology and control of the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae). Bulletin of Entomological Research 90(06):453-65.
Fernandes FL, Picanço MC, Fernandes MES, Dângelo RAC, Souza FF, Guedes RNC. 2015. A new and highly effective sampling plan using attractant-baited traps for the coffee berry borer (Hypothenemus hampei). Journal of Pest Science 88(2):289-99.
Jaramillo J, Muchugu E, Vega FE, Davis A, Borgemeister C, Chabi-Olaye A. 2011. Some Like It Hot: The Influence and Implications of Climate Change on Coffee Berry Borer (Hypothenemus hampei) and Coffee Production in East Africa. PLoS ONE 6(9).
Nathanson J. 1984. Caffeine and related methylxanthines: possible naturally occurring pesticides. Science 226(4671):184-7.
Oliveira CM, Auad, A. M., Mendes, S. M., and Frizzas, M. R. 2013. Economic impact of exotic insect pests in Brazilian agriculture. Journal of Applied Entomology 137(1-2):1-15.
Ortiz A, Ortiz A, Vega FE, Posada F. 2004. Volatile Composition of Coffee Berries at Different Stages of Ripeness and Their Possible Attraction to the Coffee Berry Borer Hypothenemus hampei (Coleoptera: Curculionidae). J. Agric. Food Chem. 52(19):5914-8.
Rojas JC, Castillo A, Virgen A. 2006. Chemical cues used in host location by Phymastichus coffea, a parasitoid of coffee berry borer adults, Hypothenemus hampei. Biological Control 37(2):141-7.
Vega F, Infante F, Johnson A. 2015a. The genus Hypothenemus, with emphasis on H. hampei, the coffee berry borer. In: Vega FE, Hofstetter RW, editors. Bark Beetles: Biology and Ecology of Native and Invasive Species. San Diego: Academic Press. p. 427-94.
Vega FE, Brown SM, Chen H, Shen E, Nair MB, Ceja-Navarro JA, Brodie EL, Infante F, Dowd PF, Pain A. 2015b. Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei. Scientific Reports 5:12525.
Vega FE, Infante F, Castillo A, Jaramillo J. 2009. The coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae): a short review, with recent findings and future research directions. Terrestrial Arthropod Reviews 2(2):129-47.