Soil Metagenomics

Soil metagenomics addresses the genetic structural and functional composition of a sample irrespective of whether the microorganisms can be cultured. To date, approximately 3100 culturable species are known. However, this only comprises between 1 to 5 % of the potential microbial genomes in nature. This is due to a lack of knowledge as how to cultivate the unseen microbes with existing traditional culturing techniques that succeed only in recovering the same, well-characterized microbial species. Molecular methodologies such as the polymerase chain reaction (PCR) of select molecular targets can be used to discover genes with useful properties as well as survey the structure and function of the communities. Microbial communities can be profiled and their dynamics monitored using amplicon length heterogeneity (ALH) DNA fingerprinting. Cloning and sequencing of molecular targets such as 16S rDNA will identify indigenous and novel organisms. Our lab will focus on number of projects that utilizes these tools:

1. Soil Metagenomics: As in many regions of the globe, the native habitats of Florida are rapidly disappearing. Florida has been ranked as the state with the greatest degree of risk for loss of biodiversity. Our project goals are to build a microbial inventory of the imperiled sites, to study the microbial functional ecogenomics and to develop a knowledge base of functional microbial biosensors.

2. Novel Antibacterial Compounds: Isolating DNA from soil samples and screening for the production of novel compounds with anti-pseudomonal activity.

3. Surveillance Profiling: Pathogens, both known and emerging, as well as antimicrobial resistance is a real and present danger in the environment. One of our project goals is to develop a suite of surveillance profile assays that will rapidly identify known pathogens and antimicrobial resistance genes found in pristine and impacted sites (i.e, agricultural sites).

Student and post-doctoral fellows involved:

Visiting Scientist 1. Dr. Jim Entry (Sabbatical Visitor)
Collaborator 2. Dr. DeEtta Mills
Graduate Students 3. Mr. Ramakrishna Ruttala
4. Ms. Lilliana Moreno
5. Mr. Todd Crandall

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