Research Trip – Washington, USA

  • Jade O’Leary

Wood decay is brought about by a community of fungi which interact antagonistically with each other, causing the community composition to change. My PhD project explores the interactions of fungi when they are in competition for a wood resource, and the implications of those interactions to wood decay. In March 2016, I travelled to Richland, Washington State, USA for a 3 month period to work on a collaborative project funded by the US Department of Energy (DoE). There, at the Environmental Molecular Sciences Laboratory (EMSL (Fig. 1)), I was able to further my research using cutting edge techniques and equipment not readily available within the UK.

Figure 1. EMSL laboratory facility situated within the Pacific Northwest National Laboratory (PNNL) site in Richland, Washington.

The focal species for this work, Vuilleminia comedens and Biscogniauxia nummularia, are both categorised as primary resource colonisers, i.e. they arrive first to colonise attached branches, and are important because their activities govern the arrival order and identities of their successors. Very little work has been carried out at the molecular level on primary colonisers, and they are overly misrepresented in the DoE-Joint Genome Institute (JGI) fungal database, which catalogues known fungal genetic information. To start to rectify this, DNA isolated from our fungal species was sent to the JGI, California, where their entire genetic code was sequenced and information regarding the specific genes of these fungi recorded. Knowing this information allows us to delve deeper and assess, for example, specific enzymes that are involved in wood decay and during competitive interactions.

At EMSL, 2x2x2 cm beech (Fagus sylvitica) blocks pre-colonised for 3 months with fungi and that had been placed together and allowed to interact for 1 day, 7 days, and 28 days were analysed (Fig. 2). Some of the blocks were ground to sawdust and both proteins and metabolites produced during competitive wood decay extracted. This is still ongoing, but comparison to JGI data will allow us to determine which proteins or metabolites are produced during interactions in wood, and at which stage of the interaction they occur. With the other samples, thin slices (approx. 2mm thick) were cut, and treated with a DNA probe which binds to a specific wood-decay gene within the DNA sequence of the fungi. The probe was labelled with a dye which fluoresces under a confocal, fluorescence lifetime imaging (FLIM) multi-photon fluorescence microscope, allowing us to visualise the exact location of the enzyme encoded by that gene within the fungal hyphae. This technique, called CARD-FISH (catalysed reported deposition-fluorescence in situ hybridization), had a lot of teething problems and is still underway at EMSL after my return to Cardiff.

Figure 1. EMSL laboratory facility situated within the Pacific Northwest National Laboratory (PNNL) site in Richland, Washington.

This ongoing project aims to answer questions relating to competitive wood decay using exciting techniques and equipment that I am privileged to have had necessary training and usage of. Despite having a complaint filed against me regarding the loudness of my keyboard typing (!), I had a fantastic time and learnt a lot of valuable things.

Acknowledgments extend to the British Mycological Society, the Federation of European Microbiological Societies, and the Cardiff University Gillian Powell Memorial Fund for financial support, to Jen Hiscox, Mel Savoury, Will Chrisler, Dehong Hu, Young-Mo Kim and Carrie Nicora for all their lab assistance, and to my supervisors Professor Lynne Boddy, Professor Dan Eastwood and Dr Carsten Müller.