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Testing Insights into Microorganisms

Source:  Dan Hawkes

Figure 5. (A) Emergent self-organizing map (ESOM) of the sequences from the positive clones. The map was generated based on tetranucleotide frequencies calculated from contigs fragmented to 2 Kbp
The structure and functionality of microbial communities plays a key role in the resilience and functioning of ecosystems. Understanding the relationship between microbial contributions to ecosystem processes may be key to predicting how ecosystems respond to environmental change. However, relating the composition of mostly uncultured microbial communities to functional traits, and further to ecosystem functioning, is challenging.

In response to this challenge, ESD microbiologists Mari Nyyssönen, Ulas Karaoz and Eoin Brodie recently led a team of scientists in developing high-throughput screening assays for function-based characterization of activities involved in plant-polymer decomposition from environmental metagenomic libraries. Their work builds on new genome-sequencing technologies, which have generated new predictions and hypotheses about the functional roles of environmental microorganisms. Shotgun sequencing of metagenomic DNA isolated from environmental microbial communities has advanced understanding of their functional diversity, evolution, and role in ecosystem functioning. Reconstructing genomes from environmental sequence data has been particularly valuable in studying the metabolic potential housed in the genomes of uncultured microbes. In addition, large-scale sequencing efforts geared toward the prediction of microbial processes and their response to environmental change are currently under way.

Yet until predictions resulting from these advances can be tested at a scale that matches the ability to generate them, most of them will remain as hypotheses. Function-based mining of metagenomic libraries can provide direct linkages between genes, metabolic traits, and microbial taxa, and thus bridge this gap between sequence data generation and functional predictions. In an attempt to bridge that gap, ESD microbiologists Nyyssönen, Karaoz and Brodie worked with scientists at the Joint BioEnergy Institute and at the University of California, Irvine to develop a high-throughput robotic screening platform that directly determines the activity of hundreds to thousands of key genes. Overall, their results demonstrate how functional screening of metagenomic libraries can be used to connect microbial functionality to community composition and, as a result, complement large-scale metagenomic sequencing efforts.

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Citation: Nyyssönen, M., H.M. Tran, U. Karaoz, C. Weihe, M.Z. Hadi, J.B.H. Martiny, A.C. Martiny, and E.L. Brodie (2013), Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries. Frontiers in Microbiology, DOI: 10.3389/fmicb.2013.00282.

Funding: BER Biological Systems Sciences Division under the Genomic Sciences program