ESM 2022 poster: Patterns of bacterial-fungal co-occurrence in European beech (Fagus sylvatica L.) deadwood

For those that were not able to attend the Ecology of Soil Microorganisms 2022 conference (which ran from 19-23 July in Prague, Czech Republic) I got permission to upload the poster which I presented. Being a scientist can also mean doing a bit of public speaking and graphic design. Below, you will find the abstract and poster.

Patterns of bacterial-fungal co-occurrence in European beech (Fagus sylvatica L.) deadwood

Jason Bosch, Ema Némethová, Vojtěch Tláskal, Vendula Brabcová, Petr Baldrian

Deadwood represents an important nutrient source and microbial habitat in forest ecosystems. Its decomposition is one of the key processes of global carbon turnover considering that European natural forests can contain up to 1200 m3 of deadwood per hectare. This deadwood is primarily decomposed by saprotrophic fungi but bacteria also have a role to play, particularly in the provision of nitrogen. Previous work has shown that the first fungi to become established will physically prevent further colonisation by other fungi. As bacteria and fungi can interact in both synergistic and antagonistic ways, we expect that these fungal zones of control will also influence the bacterial community composition at local scales.

We investigated the patterns of microbial diversity and co-occurrence in 1 cm3 blocks of European beech (Fagus sylvatica L.) deadwood collected from the Žofínský prales National Nature Reserve in the Czech Republic, using 16S and ITS amplicon sequencing. Compared to previously-collected “whole log” communities, the small-scale communities showed less diversity both individually and in combination. By correlating fungal and bacterial species, we were able to expand on previous work which showed that fungi influence bacterial community composition. As small-scale microbial communities collected from the same log can differ dramatically from one another, we advise caution when interpreting “whole log” microbial community data as the results may not reflect the actual interactions which take place in the deadwood.

If you would like to cite the poster, you can use the abstract book citation:

Piché Choquette S., Slaninová Kyselková M., Pospíšek M., Baldrian P. (Eds.), 2022. Ecology of Soil Microorganisms – Book of Abstracts, Prague, June 19 – 23, 2022.

Final papers from my PhD

I am happy to report that the last two papers from my PhD are now available for everyone to read!

Two Is Better Than One: Studying Ustilago bromivora–Brachypodium Compatibility by Using a Hybrid Pathogen

This, along with the U. bromivora genome paper,  is probably the most important paper from my PhD. Those two papers formed the basis of my thesis. Although I did not manage to fully answer the question I set out to answer, this is a paper where most of the experiments, most of the analysis and most of the writing was done by me, so it is special to me. It’s also quite interesting! If you want to know exactly what we learned, you can read the paper itself but I will give you a brief summary of what we were trying to learn.

We knew there were two very closely-related fungal species which could infect different host plants. This told us that although they were very similar, there was something important about them that was different; we wanted to know what that was. Even more exciting, we could create a hybrid between the two fungi that was still able to infect one of the host plants. What I was trying to do was take the hybrid and breed it over and over again with the parent that couldn’t infect while making sure that the hybrid could infect. After enough generations, we should then find the hybrid would be genetically almost identical to the non-infecting parent but with just a tiny bit of the infecting parent inside it. That would tell us what the difference between them was and we could then try to figure out how that part of the genome led to interactions with the plant. Continue reading

My paper on a new plant pathogen system

elife-20522-fig4-v1

Different accessions of Brachypodium infected with Ustilago bromivora. The fungus is the black material in the spikelet. (Source: My new paper!)

I finally have the first publication from my PhD out! It’s quite a nice paper too which took a lot longer than expected. And it’s also open access so everyone can read it! If you do, you’ll learn about a new system we have set up for understanding plant pathogen interactions with the fungus Ustilago bromivora and the grass Brachypodium distachyon.

My contribution to this is almost entirely in bioinformatics. The genome assembly had been performed before I joined the group, but I did the genome analysis and comparative genomics, starting off visiting some collaborators in Munich. This was quite nice; going in a direction which is becoming more and more important and taking things further than I had before. Continue reading