Ecological differences help unlock genomic mysteries

ASU ecologist James Elser is at the leading edge of a research field that focuses on understanding the processing of energy and multiple chemical elements in plants, animals and microbes, and how they sculpt ecosystems, also known as ecological stoichiometry.

Stoichiometry is basically just a formal way of counting carbon, nitrogen and the atoms of other key nutrient elements to study how the lack of limitations in the environment may shape the growth of organisms, Elser says.

“For example, we know that animal biomass is much richer than plant biomass in nutrient elements such as nitrogen (N) or phosphorus (P),” says Elser, a professor with the School of Life Sciences. “Plants just make ‘cheap' biomass, rich in carbon.”

Jim Elser

Sudhir Kumar

Typically, Elser brings this elemental perspective to a wide range of ecosystems around the world: hot springs in Mexico, grasslands in China, and mountain lakes in Colorado and Norway. However, Elser's latest investigations take him deep within the genome to discover if some of those rules that govern ecosystems also apply there.

Elser is at the nexus of a novel partnership with Life Sciences professor Sudhir Kumar, who directs the Center for Evolutionary Functional Genomics at the Biodesign Institute at ASU; fellow scientist Sankar Subramanian; and William Fagan, an ecologist at University of Maryland, College Park. Their goal is to determine whether differences in overall use of the major chemical elements between plants and animals extend down to their proteins.

Thinking that ecological limitations of carbon and nitrogen apply selection pressures affecting the very elements that make up an organism's entire set of proteins (its “proteome”) is relatively new in complex organisms, such as vascular plants and animals.

“Work in microbial systems that showed eco-physiological constraints on amino acid usage inspired us to look for these effects in higher organisms,” Elser says. “We already knew that plant biomass was very low in nitrogen, as compared to animal biomass. And we just asked: is it possible that these differences in nitrogen investment might also be seen at the molecular level rather than just the whole organism level?”

In a recent paper published in the journal Molecular Biology and Evolution and featured as an “Editor's Choice” in Science, Elser and his colleagues in the College of Liberal Arts and Sciences used massive amounts of genomic information to compare the proteomes from animal and plant species. They found that plant proteins have lower nitrogen content than animal proteins and that the largest differences were found in those proteins that were used the most.

Recently, Elser, Kumar and Fagan have been awarded a $1 million grant from the National Science Foundation to further their studies and build an electronic catalog of the frequency of nitrogen, carbon, sulfur and other elements in animal and other proteins accessible through the Internet.

“This community resource will enable scientists to develop and test ecological-genomics hypotheses in a wide range of species,” Kumar says.

“Most of the genomic information that is out there has to do with bacteria or other micro-organisms,” Elser says. “We will also gather more natural history, eco-evolutionary data about animal species that consider what each species is, its trophic level, its feeding strategy, its growth rate, its body size and other sorts of traits that can be entered into the database and aligned with the sequences of genes for animals as they come online.”

With just 10 percent of the species on Earth described, such databases could, over time and with species discovery, evolve into increasingly powerful tools for research.