How does long-term climate warming affect microbial feedbacks to climate change?

Soils store a significant portion of global carbon as soil organic matter (SOM), most of which tend to resist decomposition under current environmental conditions. It is likely that SOM decay will change as climate warms, but how is not clear. Two decades of warming have revealed decidedly non-linear trends in warming-accelerated CO2 emissions from soils. In addition to an observed loss of soil carbon, we have observed changing microbial communities with increased diversity in warmed plots compared to controls. While the mechanisms of soil C loss are not yet understood, preliminary data strongly implicates microbial adaptation in the loss of soil C. We are using next generation sequencing to understand the microbial ecology of altered C cycling in the temperate forests of the Harvard Forest LTER with respect to warming, as well as targeted cultivation of taxa that are affected by long-term warming for comparative genomics and physiology. This includes detailed measurements of community and functional dynamics measured six times during the growing season, over two years.

This project is partially supported by a user grant from the DOE Joint Genome Institute's Community Sequencing Program; co-PIs on this grant include Jerry Melillo (MBL), Jeff Blanchard (UMass), Linda van Diepen and Serita Frey (UNH). This project will also be supported by a grant awarded by the TES section of the DOE to myself, Jerry Melillo and Jeff Blanchard.

Harvard Forest, Prospect Hill, Winter 2014, Image courtesy Audrey Barker-Plotkin

What is the nature of anaerobic lignin degradation in tropical forest soils?

With rapid turnover of carbon pools, tropical forest soils exhibit some of the highest decomposition rates in the world. However, they are accompanied by low or rapidly fluctuating redox driven by high precipitation and high biological oxygen demand. The limitation of oxygen in tropical forest soils coupled to high rates of decomposition suggests that anaerobic or nimble facultative decomposing microorganisms must be prevalent in these soils. Additionally, iron is highly abundant in these highly-weathered soils, and the abiotic re-oxidation of reduced iron creates a regenerating cycle of iron-catalyzed decomposition that could fuel abundant carbon mineralization. Fast rates of decomposition in highly active and biodiverse tropical forest soils could be informative for improving lignocellulose deconstruction in development of next generation biofuels, where bacterial dominance in anaerobic lignin and cellulose degradation could provide insight into plant-based biodiesel development. As part of this project we are characterizing bacteria isolated based on their ability to grow anaerobically with lignin as the sole carbon source.

This project is partially funded by collaboration with the Joint BioEnergy Institute in Emeryville, CA, and an in kind award from the Environmental Molecular Sciences Lab (EMSL). This work is also being conducted with the intention of applying lignin-degrading enzymes to advancing efficiency of lignocellulose biofuels production.

Luquillo, Short Cloud Forest, SCF, BisR, BisV, Puerto Rico

How and to what extent do soil microorganisms store energy and carbon in natural ecosystems?

A wide diversity of bacteria produce carbon storage compounds such as polyhydroxyalkanoates (PHAs) or polyhydroxybutyrates (PHBs) under stressful conditions in culture, though the extent to which they are made in nature is not well understood. Microbial carbon storage in the rhizosphere represents a possible large, though transient, pool of carbon which impacts plant health, productivity and disease by modulating rhizosphere bacterial activity in times of stress. I hypothesize that increased granule formation in the rhizosphere is a mechanism of competition in an environment of limited carbon. To test this,the diversity of the granulated rhizosphere microbial population will be determined, as will how it differs from that in bulk soil. Functional cell sorting based on differential staining will produce four sub-populations: rhizosphere and bulk soil, granulated and non-granulated cells, which we will then analyze using community phylogenetic, metagenomic and single-cell genomic sequencing. The proposed work is a first step towards evaluating the extent to which microbes store carbon as granules in rhizosphere soil, and will define the diversity of these organisms. In addition to exploring an underrepresented branch of soil carbon storage, polymerization of energy-storing carbon molecules will provide a template for new biofuels and fuel storage mechanisms.

The sequencing portions of this project, including community analysis, metagenomes of the functionally sorted sub-populations, and single-cell sequencing of granule-containing bacteria, are funded by the Community Sequencing Program (CSP) at the Joint Genome Institute.

PHB, carbon storage granules

How can new technology deepen our understanding of natural systems?

Myriad new tools are under development that will open windows into the internal mechanisms of nature. Methods strongly dictate conclusions; therefore, I dedicate part of my research towards using, evaluating and developing new tools. The degree to which we can recover, read, and interpret the information encoded in biological molecules is the limiting factor for understanding the identity and behavior of organisms in their natural environments. Therefore, a long-term goal of my research program is to continue laboratory and computational methods development to improve the study of microbial communities with better fidelity, using techniques such as emulsion PCR and high-throughput sequencing. Three relatively new directions for my lab include applying technology to classical physiology, linking microbes with functions, ecosystem modeling. With an undergraduate in the lab, we are building a 2D bioprinter that will allow us to test more interaction and growth conditions of wild isolates. Most microbial and ecological studies rest their conclusions on correlation, but methods like stable isotope probing (SIP) are powerful tools for attributing functions to specific taxa. Likewise, models like the trait-based models can be used to question assumptions about microbial interactions and environmental requirements for microbial function and feedbacks. My long-term goal is to incorporate the results from the trait-based model and growth parameters of co-cultures and isolates into ecosystem and global models.

This proposed work coincides with a project that was recently funded by the DOE Terrestrial Ecosystems Sciences Program (PIs Melillo, DeAngelis & Blanchard, through 2016). Development of these molecular and modeling methods will greatly benefit my students and our science.

Kristen DeAngelis, Daniel Burkhardt