Pyrophilous (fire-loving) microbes
The frequency of large, high severity wild fires is increasing in the western US and in regions around the world due to long-term fire suppression strategies and climate change. These fires have direct, negative effects on soil carbon stocks through combustion, but they have indirect and potentially positive effects on soil carbon stocks through the production of pyrogenic organic matter (PyOM) that has a long residence time and constitutes a major pool of C in fire-prone ecosystems. Soil microbes are likely to be involved with the degradation of all of these compounds, yet little is currently known about the organisms or metabolic processes involved. In a DOE-funded grant with Tom Bruns (UC Berkeley), Matt Traxler (UC Berkeley), and Igor Grigoriev (JGI), we are dissecting the effects of microbes on post-fire soil carbon dynamics by using a systems biology approach that couples small experimental “pyrocosms”, highly controlled production of 13C-labeled pyrolyzed substrates, genomics, transcriptomics, stable isotope techniques, and mass spectrometry to address the following objectives:
- Develop improved genomic and other -omic resources for the dominant microbes of fire-affected soils
- Determine the temporal response of soil microbes to fire and to PyOM additions
- Characterize the temporal patterns of degradation of different sub-fractions of PyOM
Our team’s work on this project includes isolating and characterizing bacteria that can use PyOM as their sole C source and tracing PyOM through soil microbial communities using stable isotope flux tracing and stable isotope probing of DNA (DNA-SIP). Some of the fun things we are building in order to carry out this research include a13C labeling chamber to grow labelled biomass, which will be pyrolyzed in a custom-built “charcoalator” that allows for highly-controlled production of PyOM, and an automated custom gas-sampling “multiplexer” connected to a cavity ringdown spectrometer, through which we can measure the efflux and isotopic composition of microbially-respired CO2. Team members on this project include Dr. Tim Berry, Nayela Zeba, and some of our undergrads.
Fire effects on soil microbial communities
Boreal forest soils are among the richest stocks of terrestrial carbon (C) in the world, primarily as a result of their low temperatures and slow decomposition rates. The fate of these large C stocks in the face of climate change is an area of critical concern, particularly when considered in the context of predictions of increasing wildfire. Although soil microbes are the core drivers of the soil organic C cycle, the effects of wildfire on boreal soil microbial communities remain poorly characterized.
The 2014 fires in the Northwest Territories were exceptional: they were the largest recorded burn in a single fire season, with some fires burning unusually intensely, leaving essentially no living vegetation, and others resulting in “fire refugia” of unburned or only lightly burned areas. We are collaborating with researchers from the Canadian Forest Service and the University of Alberta, who, in addition to linking remote-sensing data to a comprehensive on-the-ground site characterization and measurements of burn severity, will also collect an unprecedented set of soil samples from these fires. Characterizing the microbiome of these soils will offer us a profound level of insight into the effects of fire on soil microbial communities, and leverage an extensive field campaign to bridge the scale from satellites to microbes.
Microbial ecology of microhabitats
Despite the billions of microbial cells found in a gram of soil, soil microbes are estimated to inhabit only 1% of total soil volume, and are unevenly distributed, forming colonies and biofilms. Thus, the biogeochemical processes driven by these microbes are often limited to relatively small volumes of soil, or “hotspots”. The different soil conditions that develop in each microhabitat support different microbial communities – e.g., rhizosphere vs. bulk soil; microaggregate interiors vs. whole aggregates; micropores vs. macropores; detritosphere (decomposing organic matter) vs. bulk soil. However, the genetic and ecological mechanisms driving these differences in microbial community composition across different microhabitats are not well understood, nor are their implications for soil microbial diversity and functioning. In addition, the prevalence of each microhabitat changes over time and under different soil management strategies, so the relative importance of these mechanisms would also be expected to change over time. Understanding how soil microhabitats structure soil microbial communities will allow us to better predict how changes to the environment will affect the soil microbial community and its biogeochemical functioning.