The University of Texas at Arlington :: Department Biology :: Microbiology :: Genome Biology Group

Projects

amazon
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.

Collaborators: Dr. Brendan Bohannan (Univ. of Oregon), Dr. Brigitte Feigl (Univ. of Sao Paulo), Dr. Klaus Nüsslein (Univ. Massachusetts), Dr. Vivian Pellizari (Univ. of Sao Paulo), and Dr. James M. Tiedje (Michigan State University).


2012 NEWS! The ARMO project received a DOE/JGI grant for sequencing of 1 Tbase of Metagenomic data. It will be the first biogeographical study applied to metagenomic information.

2013 NEWS! The ARMO project received a DOE/JGI grant for sequencing of 2 Tbases of Metatranscriptome Data.

See the following publications:

Mirza and Rodrigues (2012) Appl. Environ. Microbiol.
Rodrigues et al. (2013) Proc. Natl. Acad. Sci. USA
Mirza et al. (2014) Appl. Environ. Microbiol.
Muller et al. (2014) The ISME J.
Paula et al (2014) under review
Ranjan et al. (2014) under review


Systems Biology at Population Level.
amazon
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) J. Bacteriol.
Wertz et al. (2012) Appl. Environ. Microbiol.
Rodrigues and Isanapong (2013) The Prokaryotes.

Isanapong et al. (2013) The ISME J. 

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