Have you ever sat in an airport lounge, gazing out at the runway, and found yourself marvelling at just how quickly the world can change? That was precisely my mood yesterday at Heathrow as I prepared to depart for Kenya. My companions and I, from Kenyatta University, are about to embark on an exciting endeavour—using environmental DNA (eDNA) techniques to track mango and avocado pollinators and link their vital role to improved crop productivity.
It is a moment that reminds me of a similar journey a little over a decade ago when I was at Cambridge University. Back then, eDNA was still in its infancy, though its foundational technologies—like virus metagenomics—were already showing promise. I remember the thrill of my first real foray into genomics and the sheer power of high-throughput sequencing, even if it did feel rather like peering into a crystal ball.
Fifty-two weeks ago, I set out to share my readings on biodiversity research, initially with a focus on the Global South but gradually spanning the entire globe. Throughout this series, eDNA has taken centre stage—especially when paired with high-throughput sequencing and artificial intelligence—offering a treasure trove of insights: monitoring biodiversity at scale, tracking pests and diseases in crops and livestock, managing invasive species, verifying the authenticity of biological products, unravelling the interactions between plants and insects, and even ensuring safe drinking water. The past 52 weeks have been a constant reminder to me, and perhaps the reader of this newsletter, that the well-being of our planet and ourselves is inextricably linked.
This is the 52nd entry in the series, and in many respects, it feels like I have come full circle—right back to where the story started, ready to begin the next chapter.
November 2014.
My PhD mentor, Professor John Carr and I were raring to go. It would be our first fieldwork experience since I began my PhD at the University of Cambridge in the Molecular Virology Lab. We were on a virus discovery mission and primarily looking to catch viruses transmitted by aphids. We already knew that aphids were responsible for spreading most plant viruses affecting crops, including beans. This mission was to investigate whether aphids flying around in fields carry and transmit multiple plant-infecting viruses. The thought that aphids could serve as ‘dirty hypodermic needles’ is a scary prospect for farmers and researchers. We were keen to know the diversity of aphid species in the field and the viruses they spread. At Heathrow Airport, John turned to me and said, ‘Look, Francis, it is going to be a long flight with dodgy aeroplane food; we may as well have a champagne breakfast before bingeing on movies.’ I could not agree faster.
Our hosts in Kenya were scientists at the Biosciences Eastern and Central Africa Hub (BecA-ILRI) at the International Livestock Research Institute (ILRI). I had worked at ILRI as a research assistant before joining Cambridge University. James Wainaina, then a research assistant working on aflatoxins, joined John and me for the fieldwork. He had the social capital we needed. Over time he had forged strong connections with the Kenya Agricultural and Livestock Research Organization and a host of farmers who grew beans. James was about to leave for his PhD studies in Australia. His research interest was whiteflies on beans, which created a perfect convergence of our scientific interests.
Our journey took us to Katumani and into the bean fields. However, we were two weeks early. There were hardly any aphids in the area. Usually, aphids accumulate on beans as they flower and pod. At times, they can be found in younger plants, but this was not the case at Katumani. Curiously, whiteflies were all over the place, which was great for James’ work. With not much to find, we headed for Kaiti in Makueni- a richly agricultural county in Eastern Kenya. Beans and cowpeas (Vigna unguiculata and locally called ‘kunde’) were plentiful. There were no aphids on the bean crop there, either. Instead, in our wandering through cowpea plots, we found plenty of other closely related species of aphid (the cowpea aphid), which was not what we wanted, save for scientific curiosity. It was a brutal initiation into fieldwork for John and I.
The following morning, we set out for the highlands of Kiambu to a farmer called Njiiri, where his wife received us. It was a smallholder farm in the classic sense, optimised to produce as much crop variety as possible. Sweet potato, maize, kale, tree tomato, and the occasional beehive thrived alongside bean plots. Aphids were all over the place. Though we were happy to find aphids, Njiiri’s wife was not pleased. From the level of aphid infestation, it was apparent that she was not keen to spray to kill the aphids. Some of the plants showed signs of disease. It may have been that either the pesticides were financially inaccessible or undesirable environmentally. Notably, part of her farmland was leased to other farmers who also did not use pesticides and whose cultivated plots would continue to be a source of aphids and infection. As we were about to leave, she asked us in the precise way that farmers always speak, ‘Will I harvest anything on those bean plots, or do I just uproot everything?’.
It was a poignant moment. Our next words were chosen carefully. We could tell the crop was lost to both disease and aphid infestation but had to hedge our words and actions to blunt the sharp edge of our assessment. So we said, ‘Look, we have trampled all over your shamba, mama. Surely, anything you would have harvested here is almost gone. We are more than happy to compensate you in cash for allowing us to work in your bean plots’. Her smile indicated to us that she understood what we implied. She would buy fresh seed and have another go the following season. Over that week, we found similar success in trapping aphids in smallholder farms in Oloirien and Oloolua in Kajiado. We also found despondency in farmers caused by insect and virus burdens- their efforts would not translate into bumper harvests.
Back at the Beca-ILRI hub, we prepared the samples for High Throughput Sequencing on the Illumina Platform. Like all ‘clever-thinking’ scientists, we had a fair expectation of what we would get, but nature is full of surprises. I was back in the UK when the findings came through.
Yes, insect-vectored plant viruses were detected, but plenty of sequences were annotated as ‘Aphid lethal paralysis virus’ and ‘Big Sioux River virus’. We had found dicistroviruses.
Dicistroviruses are remarkable insect-infecting viruses; they use plants as reservoirs to infect their insect hosts. They can, in some cases, kill aphids, decrease their reproduction, or cause confusion, which predisposes aphids to attacks by predators and parasitoids. Concurrently, another researcher based in the UK detected similar and related viruses in maise while searching for components for maise lethal necrosis disease, which at the time was wreaking havoc for maize farmers in East and Central Africa. This finding of dicistroviruses was the first report of these viruses in the black bean aphid globally.
I would go on to design research to explore the use of these potentially beneficial dicistroviruses for crop protection (bio-control). Funded through a Royal Society FLAIR Fellowship, I hoped to put a halt to aphid infestation and secure better yields for farmers by protecting crops without wrecking the environment. The work began in June 2019 at the International Centre of Insect Physiology and Ecology (icipe) in Nairobi, Kenya. icipe is a storied, one-of-a-kind organisation with a rich history of research in entomology to address grower challenges. I was looking to dig for the long haul, build collaborations, establish a research group, make discoveries, and translate those into solutions.
Then, suddenly, the covid pandemic struck, and the world stopped.
When we re-emerged, the world was different; the cost of sustaining the research proved a mile too far for the funding agency. John would carry on the research at Cambridge. I moved to the UK and joined Niab as a Research Leader In Entomology.
Niab is very big on applied entomology, and I quickly noticed that my skillsets could help advance the fortunes of growers, especially with pest identification and monitoring. Identification of cryptic insects using traditional methods is difficult, fault-prone for non-specialists, tedious and very difficult to scale. DNA-based tools are a modern and efficient solution. Pretty soon, this has gravitated to environmental DNA as an important tool for this work. The more I study the eDNA method, the more I am fascinated by its versatility in answering questions across different spheres, be it plant health, biodiversity, one health, pests, diseases, or plant-insect interactions.
So here we are.
In the coming weeks, I will share more about the eDNA project in Kenya as well as other exciting advancements in the 52 Science Stories space. Stay in touch for the next ‘52’.
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