University of California - Davis :: Department of Land, Air, and Water Resources

1. Amazon Rainforest Microbial Observatory:  Functional Diversity, Taxonomic  Diversity, and Response to Ecosystem Conversion.
The Amazon Forest is the largest terrestrial ecosystem on Earth, yet the least understood regarding its microbial diversity. The increasing demand for food, fiber, and biofuels has caused a shift in forest to agriculture. This is the largest land use change going on around the world and expected to cause
ecosystem level changes that will threaten biodiversity and modify Earth's biogeochemical cycles.

In this research project, we ask the following questions:

(1) What are the bacterial taxa present in the Amazon rainforest soils?

(2) How are microbial communities organized in space and time in tropical systems? 

(3) What are the functional and taxonomic alterations caused by forest-to-agriculture conversion?

A combination of high throughput sequencing of the 16S rRNA gene, functional genes, and cultivation of microorganisms has been used to study the impact of land use change in microbial communities and their ecosystem services. Our lab has been particularly interested in the role of nitrogen fixers in maintaining a steady N supply in the forest. This has important ecosystem consequences as effective C sequestration depends on the N content.

ARMO and Amazon PIRE teams will join forces to study microbial communities associated with the methane cycle in the Amazon, a NSF Dimensions of Biodiversity award.
Collaborators: Dr. Brendan Bohannan (Univ. of Oregon), Dr. Klaus Nüsslein (Univ. Massachusetts), Drs. Scott Saleska and Joost van Haren (University of Arizona), and Dr. Siu Mui Tsai (CENA/University of Sao Paulo) and Dr. Fernando Andreote (ESALQ - University of Sao Paulo).

Funds: National Science Foundation - Dimensions of Biodiversity, USDA, DOE/JGI

See the following publications:

Mirza and Rodrigues (2012) Applied and Environmental Microbiology
Rodrigues et al. (2013) Proc. National Academy of Sciences of USA
Mirza et al. (2014) Applied and Environmental Microbiology
Muller et al. (2014) The ISME Journal
Paula et al (2014) Molecular Ecololgy
Ranjan et al. (2015) Frontiers in Microbiology
Navarette et al. (2016) Frontiers in Microbiology
Mueller et al. (2016) Functional Ecology
Hamanoui et al. (2016) Applied Soil Ecology
Pylro et al (2016) Trends in Microbiology
Meyer et al. (2017) Molecular Ecology
Khan et al. (2018) (under review)

2. Systems Biology at Population Level.
Wood-feeding termites are model bioconverters, harboring an entire microbial community orchestrated to transform cellulose, hemicellulose and lignin into soluble oligosaccharides, H2, and methane, among other intermediates of interest for biofuel production. Among the many bacterial species found in the termite hindgut, members of phylum Verrucomicrobia are always observed in molecular surveys of the 16S rRNA gene, but rarely captured in isolation studies. Our laboratory has maintained a small population of Verrucomicrobia isolates and has been using a combination of physiological studies and 'omics tools to understand their ecological attributes and functional roles in the termite gut. We hypothesize that intraspecies variation is as an essential component of ecotypic differences and a stabilizing force in ecosystem resilience. The genomes of the Termite Associated Verrucomicrobia (TAV) strains have been sequenced, whole genome expression profiles have been contrasted and their proteomes measured. In addition, we are interested in identifying whole cell regulatory networks involded in gene expression under low O2 concentration.

See the following publications:

Isanapong et al. (2012) Journal of Bacteriology
Wertz et al. (2012) Applied and Environmental Microbiology
Isanapong et al. (2013) The ISME Journal
Rodrigues and Isanapong (2013) The Prokaryotes
Kotak et al. (2015) Genome Announcements
Kotak et al. (2018) (under review)
Isanapong et al. (2018) (in preparation)

Funds: US Department of Energy/Joint Genome Institute

3. Climate Change in California dairy - forage systems.
One of the many challenges in dairy - forage farms in California is the generation of massive amounts of manure.  The application of animal waste to soil has been linked to increases in greenhouse gases emissions, but the reasons remain elusive. At the heart of greenhouse gas emissions lies microbial communities responsible for different steps of multiple biogeochemical cycles. We aim to understand the effects of manure fertilization on microbial communities during plant growth.

Collaborators: Drs. Kate Scow and Amelie Gaudin (UC-Davis)
Funds: US Department of Agriculture

4. Microbial and Plant Indicators of Soil Health

2018 NEWS! Soil health is defined as the capacity for soil to function as a vital living system to sustain biological productivity, maintain environmental quality and promote plant, animal, and human health. Our central hypothesis is that poor soil health resuls in the increase of plant and microbial stresses, similar to human health metrics. Theses stresses can be quantified as biological indicators. We will use metagenomics to identify and quantify genes associated with environmental stresses in agricultural intensive conditions.

Collaborators: Drs. Daniel Geisseler and Maeli Melotto (UC-Davis)
Funds: US Department of Agriculture

 Plant and Environmental Sciences Building, room 3308, University of California - Davis, CA, 95616