Dissecting the Effects of Fire on Soil Microbial Communities in Northern California Mixed Conifer Forests

The overall goal of my scientific pursuits has been to understand how the environment influences ecological systems and organismal biology and vice versa. Over the past two centuries humans have placed unprecedented demands on the Earth’s natural resources. As a result of these pressures, we have witnessed an accelerated loss of biodiversity and a dramatic alteration of ecological patterns and processes. These changes have potentially devastating consequences in the long-term and are a cause for instigating novel scientific investigation and ecological mediation. Thus, the aim of my doctoral research was to understand community dynamics and primary metabolisms of soil-dwelling microbes following a fire disturbance./nPrescribed fire is a critical strategy for mitigating the effects of catastrophic wildfires. While the above-ground response to fire has been well-documented, fewer studies have addressed the effect of prescribed fire on soil microorganisms. As documented in Chapter 2, we set out to understand how soil microbial communities respond to prescribed fire. For this work we extensively sampled four plots (two burned, two controls) for 17 months in a mixed conifer forest in northern California, USA. Using amplicon sequencing, we found that prescribed fire significantly altered both fungal and bacterial community structure. We found that most differentially abundant fungal taxa had a positive fold-change, while differentially abundant bacterial taxa generally had a negative fold-change in burned plots. We tested the null hypothesis that these communities assembled due to neutral processes (i.e., drift and/or dispersal), finding that >90% of taxa fit this neutral prediction. However, a dynamic subcommunity composed of burn-associated indicator taxa that were positively differentially abundant was enriched for non-neutral ASVs, suggesting assembly via deterministic processes. In synthesizing these results, we identified 15 pyrophilous taxa with a significant and positive response to prescribed burns. Together, these results lay the foundation for building a process-driven understanding of microbial community assembly in the context of the classical disturbance regime of fire./nFires have a significant impact on soil carbon stocks because combustion transforms carbon into either CO2 or in the production of recalcitrant pyrogenic organic matter (PyOM). PyOM is chemically heterogeneous and composed of a spectrum of fixed organic carbon (C), ranging from living plant biomass to completely charred material and soot. Pyrogenic carbon can modify microbial activity via promotion of microbial metabolism of PyOM as an energy or nutrient source, alteration of physical and chemical properties of the soil, or by interference of microbial signaling. As documented in Chapter 3, we were interested in bacterial species whose metabolic activities were promoted by the PyOM generated by fire. We targeted and isolated post-fire bacteria which can utilize the complex carbon compounds, found in PyOM, from fire-affected soils collected from wildfire sites across Northern California, in addition to soil collected from our prescribed burn sites. We find two bacterial genera, Streptomyces sp. and Paraburkholderia sp., were the dominate species in our post-fire isolate collection, suggesting they have the metabolic potential to utilize carbon substrates found in PyOM. Further, preliminary experiments reveal that a post-fire isolate from our prescribed burn sites, Paraburkholderia caledonica F3, can grow on aromatic carbon substrates in the lab. Finally, genomic analyses reveal that Paraburkholderia caledonica F3 possess the metabolic potential to degrade a variety of complex aromatic carbon compounds found in PyOM. These findings provide an exciting and promising outlook for the application of these post-fire bacteria for bioremediation efforts following fire./nBioremediation utilizes the naturally occurring abilities of microorganisms (or plants) to break down harmful compounds and detoxify a polluted environment. Many of these organisms are native to these ecosystems, thus researchers are particularly interested in uncovering who these microorganisms are and how they can metabolically catabolize toxic compounds, such as aromatics and PAHs. While isolating organisms which are native to environments of interest poses its own challenges, we are still able to strategically and successful isolated these specialists in the laboratory. The arduous task arises in interpreting gene functions which have a phenotype under laboratory conditions. However, recent innovations in high-throughput analysis of mutant phenotypes have improved the rate at which researchers can predict gene functions. As documented in Chapter 4, we applied Random-Barcoded Transposon Sequencing to characterize the functional pathways of aromatic degradation in our laboratory isolate, Paraburkholderia caledonica F3. Here we validate the success of the generation of our Paraburkholderia caledonica F3 barcoded transposon insertion mutant library and propose fitness experiments with compounds of interest which are to follow.

Advisor: Traxler, Matthew F
Fischer, Monika S