Research Overview

Microorganisms are ubiquitous and play key roles in geochemical cycles, human and animal health. They also represent a valuable source of enzymes that can be used to produce food, biofuel, pharmaceuticals and other natural products.

The research of the Hess Lab centers on the multi-scale (from molecule to cell to population to ecosystem) understanding of microbial systems. We utilize traditional and recent cutting-edge Molecular Biology and Microbiology techniques in combination with bioinformatics to:

1. understand how microbial systems respond to environmental changes and how they affect their habitats
2. identify and characterize new microbes, microbial enzymes and microbial products of industrial relevance from complex biological systems
3. develop industrial processes that utilize microorganisms or microbial enzymes and that are more sustainable than current processes

Animal Health/Animal Microbiology

Microbes play a key part in the health and productivity of animals. The long-term goal of our research is to enhance our understanding of microbe-microbe and microbe-host interaction to ensure the well-being of the host organisms. Our current main focus is the microbiome of ruminants.

Climate Change/Carbon and Nitrogen Cycling

Microbial communities associated with agricultural systems are major sources of greenhouse gases such as N2O and CO2. The Hess Lab studies how microbial communities in these systems can be manipulated to reduce greenhouse gas emission. Currently we are developing strategies to mitigate greenhouse gas emission from ruminants, manure, and agricultural soils.

Natural Products

Microorganisms are a potent source of fine and bulk chemicals. In the past, discovery and reconstruction of the genes and pathways involved in the synthesis of the final product was hindered by the recalcitrance of most microbes (~95-99% of all microbes) to isolation and cultivation. In our Lab we utilize a combination of different cultivation-independent approaches (e.g. single-cell technologies, phylogenomics, metagenomics, metatranscriptomics, metaproteomics and metametabolomics) to overcome this recalcitrance to cultivation. Recently we have been screening microbial communities from diverse ecosystems for carbohydrate and hydrocarbon active enzymes and for microbial products that have antimicrobial activity.

Research Focus Areas

Microbe-Host Interaction

The Hess lab is dedicated to enhance our understanding of the interaction between microorganisms and animals, specifically ruminants. We are collaborating with several U.S. National Laboratories (i.e. Lawrence Berkeley National Laboratory and Pacific Northwest National Laboratory) and utilize a variety of omics approaches (i.e. metagenomics, metatranscriptomics, metaproteomics and metabolomics) to study the molecular mechanisms involved in the degradation of plant material in the cow’s digestive system and the subsequent generation and emission of methane, a highly potent greenhouse gas.

Identification and characterization of novel biocatalysts/antimicrobial peptides from microbial communities

Microbes and microbial enzymes are sustainable alternatives to chemical catalysts and have been used for centuries for the synthesis of commodity products such as beer, bread, cheese and wine. More recently microorganisms have been discovered as a source for enzymes that allow the sustainable production of fine chemical and pharmaceuticals. The Hess Lab uses various cultivation independent approaches to screen extreme environments for novel microbial enzymes that might improve and render current agricultural, industrial and medical processes more sustainable. Currently we are screening microbial communities capable of carbon and nitrogen fixation, and microbial consortia that degrade lignocellulose and complex natural hydrocarbons for novel enzymes with industrial value.

Biological strategies to reduce greenhouse gas emission from agriculture

Ruminants and manure are significant sources of greenhouse gases, specifically of CH4 and N2O. The Hess Laboratory studies microbial communities associated with ruminants and their manure to develop improved strategies for the mitigation of greenhouse gases and for reducing the nitrogen load of agricultural soils. Currently we are studying microbial co-cultures capable of carbon and nitrogen fixation and their potential of being utilized in agricultural systems to decrease their carbon and nitrogen footprint.

Tools for Omics Data Analysis

Our projects utilize various omics platforms (e.g. phylogenomics, metagenomics, metatranscriptomics, metaproteomics and metametabolomics) and we are working together with scientists from Lawrence Berkeley National Laboratory and Pacific Northwest National Laboratory to develop algorithms that allow the integration and analysis of these different and complex data.