Interview: Jacob Ulzen on the African Mycorrhizal Mapping and Metagenomics Workshop in Kumasi, Ghana

Improving soil microbial sequencing capacity for African researchers: in-depth training on soil fungal DNA extraction

In February, 2024, SPUN and JR Biotek co-hosted the Africa Mycorrhizal Mapping and Metagenomics Workshop in Kumasi, Ghana in partnership with Oxford Nanopore Technologies (ONT) and CSIR - Crops Research Institute. Our aim was to work with these partners to improve soil microbial sequencing capacity for African researchers.

Decentralizing science: DNA sequencing research in Ghana

At present, most biological samples collected in Africa must be sent out of the country or continent for DNA sequencing. We want to help support African scientists to keep these samples in their place of origin from start to finish – part of an effort to decentralize science.

Mycorrhizal fungi identification in hyper-biodiverse regions such as West Africa

Africa is home to many of the most biodiverse regions on Earth, and this is a great opportunity to put capacity and technologies in the hands of local scientists in hyper-biodiverse regions such as West Africa to identify mycorrhizal fungi from these underground ecosystems.

Twelve participants joined us in Ghana from countries like Lesotho, Ghana, Cameroon, Nigeria, and Kenya. Over the course of three days, we provided in-depth training on soil fungal DNA extraction, sequencing using ONT portable sequencing technologies, and downstream data analyses.  The workshop was co-led by Dr. Bethan Manley, who sat down with workshop participant Dr. Jacob Ulzen of University of Ghana to talk about his experience.

Q: It’s great to see you again, Jacob! Could you please introduce yourself?

A: I’m Jacob Ulzen, a research fellow at the University of Ghana. I work on biological nitrogen fixation and integrated soil fertility management to improve crop nutrition.

Theory and extraction of DNA for sequencing from the soil samples in West Africa

Q: Moving on to the workshop: what was covered? How will the results help research in Ghana?

A: The workshop was divided into two sections, the theory and practical sessions. We learned the theory behind DNA sequencing, how to analyze sequencing data, and equipment to be used. Then there was hands-on practical training using the MinION Nanopore and real extraction of DNA from the soil samples.

The researchers from Ghana (myself included) now can isolate fungal DNA from soil on their own, and they understand the equipment needed, reagents to use, and they have a network of people they can ask questions to.

Capacity building for African soil scientists

Q: Why do you think it is important to disseminate this molecular expertise to Africa?

A: If you look at the Global South, the knowledge of arbuscular mycorrhizal fungi (AMF) can be limited on a molecular level, so many people don’t involve these fungi in their studies because the tools aren’t always there, and neither is the theoretical knowledge – most universities don’t teach about these fungi in depth. It is, therefore, important to build capacity in these areas so that African scientists can be the ones leading the research in Africa.

Sequencing DNA and eDNA in order to understand the role of all fungal organisms in ecosystems

Q: Why is it significant to be able to sequence DNA and eDNA?

A: For our work, it is important to know the species of AMF present and what they can do in agriculture or how their ecology works. This is so we can understand the ecosystems we study better, as well as the nutrition of soil. It is valuable to understand the role of all fungal organisms in the ecosystem.

Q: What have your experiences been like doing DNA sequencing in Ghana in the past?

A: The University of Ghana has a biotech center with laboratories and capacity to do molecular work, but no sequencing machines. This is common in many universities around the world, because sequencing machines are expensive and they are difficult to operate without long-term training. Also, there’s usually some difficulty getting equipment and reagents, you have to order from outside Ghana and this means they take a long time to arrive, or we have to pay high shipping fees just to be able to do our molecular work. 

The first project of its kind to map Ghana’s hotspots of AMF

Q: What interests you most the research you are doing with SPUN in Ghana? Most of your career has been focused on agriculture and food production – are you now looking at related scientific subjects?

A: This project will be the first of its kind in trying to map Ghana’s hotspots of AMF. I have worked on bacteria all my life, so expanding to new microbial research is really interesting and helps me grow as a scientist. Considering fungi also gives a more full understanding of soil biodiversity and their contributions to nutrition in agriculture. 

Using AMF to remediate mining soils in Ghana

Q: What are you excited about researching in the future?

A: I like being an early career scientist because there are lots of options ahead of me. I would like to become a leading expert on AMF in Ghana, and I want to see how we can approach and harness AMF in many agricultural systems such as  remediation of degraded mined soils. There is a lot of mining in Ghana (mostly gold) that is very destructive and often illegal (locally called galamsey).  This kind of mining uses a lot of heavy metals such as cadmium, mercury, arsenic, etc.). Thus, destroying the soil biologically.

Climate Change and Food Production in West Africa: Food insecurity

Q: You work a lot with food crops. Do you have any thoughts on the food systems in West Africa?

A: Africa is endowed with land and have capacity to produce a lot to feed its continent, but it is faced with a lot of challenges such as climate change. The effect of climate predicted to be severe in Africa, particularly, West Africa. I do not think that at the moment, West Africa has the capacity to tackle the effect of climate change and therefore, the region at risk of food insecurity. Many funding agencies are supporting this area, but more needs to be done for early career researchers here to do groundbreaking research ourselves.

One of the major challenges we face is a brain drain, where people do not return after their studies due to limited funding and equipment needed to do their work. Also, the conditions of service in most African Universities and research centers are not comparable to those in Europe.

Q: Ok, final question. You were recently featured in Forbes for the work you are doing in Ghana. What did your colleagues say when they saw the article? 

A: They said, “Keep going! Keep going!” A lot of them were really excited for me because they know my story well, but even those I don’t really know were urging me to continue working and doing more to progress as a young scientist and make an impact.

Video: Participants from the African Mycorrhizal Mapping and Metagenomics Workshop in Kumasi, Ghana look to the future, and discuss challenges facing African molecular biologists.

‍

‍