Characterization of desert microbes

Over 70% of the geography of the Emirate of Abu Dhabi is composed of desert and arid lands. These harsh soils are characterized by their low organic substances and water sources, large annual variation in temperature, and the exposure to high levels of radiation. In spite of these extreme conditions, these soils harbor a diverse microbial community. To date, there are few reports that that identify microbial populations in the UAE and Abu Dhabi. This project is identifying the diverse microbial desert community and isolating novel microorganisms from this extreme desert environment.

Microbes are essential to all biogeochemical processes. It has been shown that microbial community structure employ secondary metabolites as signaling and microcidal agent sources. These small molecules guide cellular processes, mediate response to environmental stresses, provide inter and intra species communication, and are emerging as key players in mediating microbial population dynamics and maintenance of community stability. In addition, these secondary metabolites, and their derivatives, form the basis of most antibiotics in use today. Recent genomic sequencing studies have identified many unknown secondary metabolite pathways present in microbes that have remained silent under current cultivation methods. In spite of this significance, an overwhelming majority of microbial species cannot be cultivated, thus limiting our understanding of the basis of molecular interactions between microbes in the environment. Having a laboratory model system capable of cultivating and sustaining microbial communities is crucial for identifying and characterizing novel secondary metabolite pathways. The herein proposed research agenda will:

1. Develop a model system to cultivate and sustain previously uncultured microbial communities.

Environmental microbial samples will be (1) cell sorted and stored for identification and genomic sequencing and (2) cultivated in micro-bioreactors under defined growth conditions to establish multimember communities. Samples of local soil will be extracted, analyzed for nutrient content and chemical composition, and used as growth media for both environmental isolates and microbial type strains. Cultivated communities will be evaluated using 16S rRNA sequencing for identification of community members and monitored over time until a stable microbial community consortia is achieved. In addition, known microbial type strains, such as members of the genus Streptomyces, Bacillus, or Actinomyces, with silent or ‘cryptic’ metabolite pathways will be subjected to soil extracts to stimulate production of secondary metabolites.

2. Isolate and characterize metabolites excreted by novel organisms and use high throughput sequencing to investigate metabolic potential of community isolates.

Metabolites from microbial isolates will be extracted and characterized using liquid chromatography/mass spectroscopy (LC/MS) and gas chromatography/mass spectroscopy (GC/MS) or other appropriate techniques to identify compounds excreted by microbial isolates. Isolated microbes from both cell sorting and cultivation efforts will undergo genome sequencing using Illumina sequencing technology. The genomic information will allow for a database of members of the microbial community. Bioinformatics tools will be used to mine known microbial genomes for molecular pathways involved in production of metabolites identified in samples. This database will allow for identification of potential metabolic pathways involved in substrate degradation, small molecule utilization, and environmental interactions.

3. Characterize structure and function of interspecies interactions measuring change in community response to molecular signaling events.

Microbial communities isolated and type strains characterized in aims 1 and 2 will be exposed to various primary and secondary metabolites to study the significance of these molecules on physiology and ecology of microbial communities. Substrate utilization networks and secondary metabolite synthesis will be monitored using radio labeled small molecule substrates.  These data will allow for the quantitative determination of community response to a diverse set of metabolic substrates.

We plan to integrate high throughput molecular approaches such as meta-genomics, meta-transcriptomics, metabolomics, and computational systems biology to investigate how microbial communities sustain life under mixed environments. In addition, these communities will be exposed to various primary and secondary metabolites to study the significance of these molecules on physiology and ecology of microbial communities. The combination of these two approaches will allow for the development of ecological models that help predict interactions between members of environmentally sensitive microbial communities.

Overall we have a limited understanding of the microbial interactions that occur in the natural environment. Recent work has identified complex mixed microbial communities capable of carrying out diverse and multifaceted chemical reactions that have environmental and industrial application. Understanding how these systems maintain equilibrium and community structure will allow us to model alternate systems to address current and emerging challenges facing society.