Frederik Bak: Winner (2019) of a Best Article Award from FEMS Microbiology Ecology
Frederik Bak, Postdoctoral Researcher at the Department of Plant and Environmental Science at the University of Copenhagen (Denmark), is the winner of a 2019 article award from FEMS Microbiology Ecology. He wins the award as the first author of the winning paper: Preferential flow paths shape the structure of bacterial communities in a clayey till depth profile.
You can follow Frederik on Twitter: @Frede_Bak
This is the first time that FEMS Microbiology Ecology has presented such awards and it has selected four top papers to be the winners. The topic of this paper was felt to fit perfectly with the readership of the journal. We interviewed Frederik to find out more about the inspiration behind this paper:
Could you provide a brief, simple overview of the topic your paper covers?
In geology, it is well established that water primarily flows through earthworm burrows and tectonic fractures in clayey till. Hence, the term preferential flow paths. The water transports organic matter and bacteria but also xenobiotics such as pesticides from the top soil layers to the shallow groundwater. Based on this, we hypothesized was that the organic matter and bacteria transported with the water would shape bacterial communities that are different from the adjacent matrix.
In addition, we speculated that in dry periods the preferential flow paths would have a higher amount of oxygen providing good living conditions for aerobic bacteria. We found that bacterial communities in deeper fractures had higher relative abundances of aerobic bacteria and plant decomposers.”
Why is it important for us to learn about how flow paths in subsurface soil shape the structure of bacterial communities?
For example, to come up with better predictions or models of pesticide degradation in soil. Non-degraded pesticides also leach through the flow paths towards the groundwater, so research on bacterial pesticide degradation (or other xenobiotics for that matter) in clayey till and other soils with flow paths would be more appropriate to focus on these bacterial communities instead of bacterial communities in the matrix. In countries where the groundwater is used for drinking water, it is important to understand the fate and transport of pesticides/xenobiotics in soil. Learning about the bacterial communities in flow paths is essential to help us estimate the fate and transport of pesticides and protect the groundwater.
We may also speculate that the rates of nutrient turnover are higher in the preferential flow paths as there are more bacteria per gram of soil. In addition, aerobic conditions extends to greater depths than in the matrix which may lead to faster turnover.
As a microbiologist, I also see the flow paths as an interesting environment. It is dynamic in terms of nutrient inputs, and how do bacteria deal with fluctuating oxygen in a nutrient-poor environment such as a subsurface soil. I think that is an interesting question.”
What encouraged you to perform research in this area of microbiology?
It was my PhD supervisor at the Geological Survey of Denmark and Greenland (GEUS), Jens Aamand, who came up with the idea. I was interested in the complexity of soil as a microbial habitat, but had never heard of preferential flow paths before starting my PhD. The sampling of fractures and earthworm burrows is very laborious and requires a large excavation so it is not something that can be done that often.
My time as a PhD student happened to coincide with more than one of these large excavation giving good opportunities to sample from different locations. I am glad that I got involved in the work, as it has opened up a new world for me.”
What do you see as the next steps in this area of research?
Right now, we are trying to finish a follow up study where we have included the composition of fungal communities, and using metagenomics to investigate the lifestyles of bacteria in preferential flow paths.
A very important step as I see it should be the attempts to isolate subsurface bacteria, whether they are from flow paths or matrix. Studies of subsurface bacteria have shown that there are still a substantial proportion of bacteria that are classified as unknown, containing genes with hitherto uncharaterized functions. In our group, we will increase our focus on isolation in the near future.
With new isolated strains from the subsurface, we can study them in the lab, which will give us a better insight into their ecology. Along with genome sequences of new strains, databases used for gene prediction in metagenomics can be expanded and more useful for subsurface soil.”
Read the 2019 award winning paper: Preferential flow paths shape the structure of bacterial communities in a clayey till depth profile