Lab to Landscape: Costco-PAm Scholar Rodney Richardson and Pollen Metabarcoding

Photo Courtesy of Drew Spacht

 “Pollen metabarcoding is a way that we can enable larger questions to be answered, and larger scientific studies to be conducted more cost efficiently.”  – Rodney Richardson, PhD Candidate, Ohio State University

Rodney Richardson is a Costco-PAm Scholar and a PhD Candidate studying under Reed Johnson at The Ohio State University Department of Entomology.  Since childhood Rodney has had an interest in honey bees and even kept a few colonies of his own while growing up on an Indiana farm.  
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Today,  Rodney’s interests are focused on honey bee research.  One of the many projects he is currently working on is the molecular identification (or metabarcoding) of pollen. 

We know that bee colonies need pollen to survive, but what difference does it make how we identify the pollen?

Richardson says that, “in order to really take on the perspective of a colony, you have to understand honey bees as a super-organism comprised of 20,000 to 60,000 individuals at any given point in time.  A typical honey bee colony has about half the metabolic requirement of a human being and consumes a massive amount of resources from the environment – something like 300 pounds of nectar and pollen per year just to survive.” 

“We often don’t think about that sort of scale of resource use by a colony, but it is why habitat is so important.  Honey bees forage on a landscape-wide scale to exploit floral resources within the environment.  Often people have the best of intentions to create habitat for pollinators but getting the concept of the scale can be difficult because while a 4’x4’ plot of pollinator garden is a great supplement and a worthy venture, a colony needs acre upon acre of forage-able land. If the 4’x4’ plot of flowers is good, seeding your whole lawn with Dutch clover is the bees knees.”

So, as pollinator habitat is lost to agricultural advances and urban development, it becomes more pressing for us to understand the relationship between the land and honey bees.  Molecular identification of pollen is a powerful research tool to help us understand this relationship using technology that makes it faster and more accurate. 

Figure 1: During molecular analysis of pollen, DNA is extracted from samples of bee-collected corbicular pollen and specific sections of the plant genome, termed genetic markers, are sequenced. Using reference sequences of known taxonomic identity, sequence variations can be used to infer the types of plants present in the original pollen sample. Since no individual genetic marker performs perfectly, we sequence multiple markers per sample and average the results. ‘Measure twice, cut once’ as they say. Overall, this enables us to catalog colony foraging habits with much greater sample sizes than are achievable through traditional microscopy.

The “very simple process” Richardson uses to make an inference or identification of a pollen source is called metabarcoding.  In short, metabarcoding includes grinding up a sample of pollen, extracting DNA and amplifying a specific regions of the genome using Polymerase Chain Reaction, a reaction which involves copying a genetic region millions of times.  The resulting products are then sequenced to produce tens of millions of DNA sequences, which can be compared to a reference database of sequences of known plant species identity.

Not only is Richardson using this process, he is also working on refining and assessing the building blocks of the process.  One of these building blocks includes identifying new genetic markers which yield more accurate and precise results.  Another, is his contribution to the software and databases used throughout this process, which will be a valuable resource for research in the future. 
While there are already researchers using molecular identification to analyze honey and pollen, the more common method has been using microscopes to identify whole pollen grains,  which is generally performed by a palynologist with years of experience identifying pollen by size, shape, and color.  This process of microscopy is valuable, and Richardson works with palynologist Chia Hua-Lin to help check the accuracy of his metabarcoding techniques.

Microscopy is labor intensive, and somewhat subjective.  It also takes years to develop the skills needed to become an expert – of which there are few - and even the best palynologists are generally limited to specific geographic regions.  Metabarcoding, on the other hand, is a standardized process which can be easily implemented by lab technicians. It allows for much larger sample sizes with fewer resources, and the confidence of research findings can be objectively assessed.

Richardson noted that “molecular identification can take pressure off of people – if you don’t have to spend two years identifying all of your pollen samples under a microscope, maybe you can spend more time collecting samples to have a larger sample size, or doing other analyses that you wouldn't have had time to do if you didn’t have this technology.”
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While his current focus is on developing improved methods for metabarcoding pollen, Rodney is also actively using the technology to help with research projects and is teaching other researchers how to utilize it as well.  

Collage 1: Honey bees foraging on borage, mustard (turnip), Helenium and buckwheat.

Some of these projects which demonstrate possible impacts of Rodney’s contribution to research include:

Analyzing honey samples in Ohio for the presence and quantity of soybean pollen which could ultimately help beekeepers advocate for more pollinator friendly farming practices and policies.  This project could also help scientists and beekeepers have a better understanding of colony inputs which relates to the bigger picture of the health and productivity of honey bees.  

Rodney is also collaborating with Dr. Douglas Sponsler at the Penn State University Department of Entomology, who is working on several projects which look at honey bee foraging ecology across urban-rural gradients, and how honey bee foraging changes across landscapes where there is a lot of variation in forage composition and availability.

We often think of honey bee habitat as intentional, designed plantings, but of course the full picture includes crops, trees, and other floral resources which are available as nutrition sources for bees.  Understanding the relationship between bees and the landscapes in which they live more fully is an important key to understanding the bigger picture of honey bee health.  

Richardson envisions that future applications of this technology could include things like broader and more accurate studies about cover crop competition in orchards and farmlands, providing a larger base of information with which to make observations about what bees are foraging on during bloom times.  And other bee nutrition and forage researchers like Costco-Pam PhD Scholar Morgan-Carr-Markell at the University of Minnesota Department of Entomology are already utilizing the technology to enhance the scope of their research.

Photo Courtesy of Drew Spacht

Richardson says that “with the help of technological advances like this, we could have weight data, pollen data, nectar data, parasite loads, and pathogen data on 1,000 colonies and have a very complete picture of what’s going on at these large scales, which is what you really need to make highly generalizable conclusions.” 

Developing these technologies and understanding their accuracy and efficacy is very important to increasing the capacity we have for investigating honey bee health issues.  Richardson’s research in the lab and beyond is helping to usher in a new, more efficient, and effective era of honey bee research.   
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While much of Rodney’s time is spent in the lab and in front of computers, he often has the opportunity to get outside, working with beekeepers and managing university apiaries.  These connections keep Rodney inspired to work for the benefit of not only scientific understanding and knowledge, but for the health of honey bee colonies and the prosperity of those who make a living from them. 

Rodney Richardson is a Ph.D. Candidate working in the laboratory of Dr. Reed Johnson at The Ohio State University. Rodney’s goal is to apply DNA sequencing technology and the power of high-performance computers to illuminate which habitats and floral communities most positively affect bee health. In his spare time, Rodney enjoys long-distance running, making experimental crosses of landrace corn varieties and watching the diverse assortment of pollinators attracted to his backyard garden in central Ohio. Married to Sandra Salcedo Richardson, Rodney also spends a lot of time trying to justify why the whole yard should be a garden.

Click Here for a list of Rodney's scientific publications. 

Author

Sharah Yaddaw
Communications Director
Project Apis m.