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What sort of science is envisioned?

An April 2012 iBiosphere white paper envisioned a grand opportunity for UA to implement a new science we here call ‘Ecosystem Genomics’. The EGI seeks to realize the key iBiosphere goal to “Discover the emergent properties and processes of ecosystems through 'top down' analysis of communities, populations and organisms, and 'bottom up' analysis of genomes, transcriptomes and metabolomes.”

Microbial communities in natural systems offer an immediate means for investigating such ecosystem-level science as it is now possible to characterize the genes, transcripts, proteins and metabolites of a community (a recent and large advance!). However, understanding and making predictions across levels of organization ranging from the gene to the ecosystem is proving non-trivial and requires a unified framework within which hierarchical investigations could be networked to reveal cross-scale connectivity and ultimately ecosystem function. In this vision, “ecosystem function” ranges from carbon cycle response to climate change in globally critical biomes, to human microbiome response to disease with initial projects as follows:

1. Global Change Ecogenomics, pioneering the study of the integrated roles of microbial and viral ecology in global climate.  This example poses such questions as: 

a - Can we better predict the carbon-cycle feedback to climate from thawing permafrost, if we use genomic tools to include microbial community ecology in coupled carbon-climate models?

b - How do vegetation-microbial community interactions structure functional ecosystem response to landscape scale changes?  (Biosphere 2’s LEO provides ideal opportunities for experimental investigation integrating plant ecology, hydrology, and microbial metagenomics)

c - Fungal relationships in driving leaf and root function 

2. Viral Ecosystem science, pioneering the study of viruses in cellular ‘ecosystems’ and in macroscale biomes, from terrestrial hillslopes to marine waters.  A key question is: 

Are there viral species?  -- and if so, will that enable a new science of population ecology and evolution of viral communities that enhances predictive understanding of viral roles across diverse ecosystems ranging from thawing permafrosts and oceans to humans and industrial fermenters? 

3. Biomedical metagenomics 

At UA, these ideas coalesce with the stated priorities of multiple biological science departments, as well as the Biosphere 2 and iPlant Cyberinfrastructure. Such microbe-focused Ecosystem Genomics science is initially being piloted in recent awards to EGI co-founders Saleska-/Rich (DOE Systems Biology/C Cycling grant to study microbial communities in thawing permafrost), Sullivan (Gordon and Betty Moore Foundation Investigator Award to enable technologies that ‘see’ viruses in nature), Hurwitz  (also Macrosystems), Arnold (NSF Macrosystems?) and others (to be updated) . In these “shovel ready” opportunities, microbial communities are the focus, since they are of immense importance in environmental, human and manmade systems, and are an ideal model for coupling of reductionist, mechanistic understanding with large-scale system-level approaches.