Response and resilience of microbial functions to global change?

This is a collaborative project funded by the DOE GtL program. Our main collaborators are Steven Allison, Michael Goulden, Jennifer Martiny, Kathleen Treseder (all UCI) and Eoin Brodie (Lawrence Berkely National Laboratory)

Loma Ridge Field Site

 

   

Project goals:The main goal of this project is to connect diverse microbial groups with the extracellular enzyme systems that catalyze the decay of organic material. We will also determine whether different groups of microbes and their enzymes respond to environmental changes, and whether they can recover from such changes. Finally, we will develop mathematical models to predict the responses of microbial communities and their associated functions under new environmental conditions.

Recent technological advances have revealed tremendous genetic and metabolic diversity in microbial communities of bacteria, fungi, and archaea. Microbes play fundamental roles in regulating carbon losses from terrestrial ecosystems by catalyzing the breakdown of dead plant and soil organic material. This process relies on the production of enzymes that act outside of microbial cells to convert complex molecules into available forms. Although these enzymes regulate carbon cycling and sequestration in nearly all terrestrial ecosystems, we do not currently know which microbes produce the diversity of enzymes observed in natural ecosystems. Without this information, we cannot accurately predict how much carbon will be lost from ecosystems under future environmental conditions that may occur with climate change or nutrient pollution.

Our research will take place in a grassland ecosystem in Southern California that hosts an ongoing environmental change experiment funded by DOE. We will assess microbial and enzyme responses to drought and nitrogen addition, two environmental changes likely to affect an increasing number of terrestrial ecosystems locally and globally (Figure 1). High-throughput DNA sequencing will reveal shifts in the composition of the microbial community, and novel gene cloning and expression techniques will link enzymes with specific groups of microbes. We will use this information to construct mathematical models of microbial and enzyme responses to environmental change. Our models will be tested by directly manipulating microbial communities and environmental conditions. The decay rates of specific chemical compounds will be assessed with a new nanotechnological tracer approach. Tracking microbial communities, enzymes, and rates of decay over time will verify if our models are correct and tell us how quickly microbes can recover from environmental perturbations.

The most important scientific impact of this work will be to establish a firm connection between the composition of microbial communities and the enzymatic functions that affect carbon cycling. In addition, our research will generate knowledge and models useful for predicting how ecosystems will store and release plant-derived carbon under future environmental conditions. The enzyme genes and microbes we identify may also have potential industrial applications, such as the processing and synthesis of biofuels.

Several studies have recently been published from this project:

Renaud Berlemont and Adam C. Martiny. Phylogenetic distribution of potential cellulases in bacteria. Appl. Environ. Microbiol. 79:5:1545-54. 2013.

Mari Nyyssönen, Huu M. Tran, Ulas Karaoz, Claudia Weihe, Masood Z. Hadi, Jennifer B. H. Martiny, Adam C. Martiny, Eoin L. Brodie. Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries. Front. Microbiol., 23 September 2013 | doi: 10.3389/fmicb.2013.00282.

Steven D. Allison, Ying Lu, Claudia Weihe, Michael L. Goulden, Adam C. Martiny, Kathleen K. Treseder, Jennifer B. H. Martiny. Microbial abundance and composition influence litter decomposition response to environmental change. Ecology 94:714–725. http://dx.doi.org/10.1890/12-1243.1. 2013.