Optimal Foraging: How Soil Microbes Adapt to Nutrient Constraints

Understanding how microbial communities adjust to nutrient-poor soils at the genomic and proteomic level gives scientists insights into land use and terrestrial biosphere modeling.

The Science

The vital growth nutrient, phosphorus, is scarce in many tropical ecosystems, yet microbes in tropical soils thrive. New research from a team of scientists has now revealed at the genomic and proteomic level how these microbes acquire rare nutrients.

The Impact

This study provides insights into soil microbial communities and how they adapt to different levels of nutrients available in a tropical rainforest. Significant changes in metabolic capabilities, shifts in community structure, and regulation of enzyme abundances revealed how soil microbes adapt to limited nutrients in tropical soils. These findings could have important implications for enhancing agricultural crops and for modeling terrestrial processes and elemental cycles.


A team of scientists set out to determine whether the theory of optimal foraging, which suggests any ecological community will adjust its consumption strategy to balance the distribution of the life-sustaining elements, applied to microorganisms in soils. While the theory had been applied to plants and animals, which can be easily observed, it is more difficult to apply to tiny, unseen microbes. Scientists from Oak Ridge National Laboratory (ORNL) and The University of Tennessee, Knoxville, gathered samples from a 17-year fertilization experiment of the Smithsonian Tropical Research Institute in Panama. Samples included phosphorus-rich and phosphorus-deficient soil. The advanced Fourier-Transform Ion Cyclotron Resonance Mass Spectrometer at the Environmental Molecular Sciences Laboratory (EMSL), a U.S. Department of Energy (DOE) Office of Science user facility, provided the team with spectra that enabled the scientists to look at samples containing soil organic matter in ways that enabled them to understand what organic compounds were available to the microbes. The Joint Genome Institute (JGI), also a DOE Office of Science user facility, helped team members probe microbial genes in the samples, and the scientists used mass spectrometers at ORNL to identify more than 7,000 proteins in each soil sample. What the researchers found closely matched their theories. The microbes in the two types of soils used different foraging strategies and adjusted their allocation of different genes and proteins to make the most of the scarce phosphorus resources in their environment. Scientists also identified differences in genes associated with the use of carbon, nitrogen, and sulfur. These results could help scientists understand how to better model microbial communities, plan for optimal land use, and predict changes in the Earth system.

Principal Investigator(s)

Chongle Pan
Oak Ridge National Laboratory

Related Links


This work was supported by the Office of Biological and Environmental Research, within the U.S. Department of Energy Office of Science, including support of the Environmental Molecular Sciences Laboratory (EMSL) and the Joint Genome Institute (JGI), both DOE Office of Science user facilities, and Laboratory Directed Research and Development funding from Oak Ridge National Laboratory.


Qiuming, Y., L. Zhou, Y. Song, S.J. Wright, X. Guo, S.G. Tringe, M.M. Tfaily, L. Pasa-Tolic, T.C. Hazen, B.L. Turner, M.A. Mayes, and C. Pan. “Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil.”  Nature Ecology and Evolution 2, 499–509 (2018). [DOI:10.1038/s41559-017-0463-5]