The Science

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

The Impact

This study offers insights into how microbial communities in the soil adapt to different levels of nutrients in a tropical rainforest. These findings could have far-reaching effects on agricultural crops that rely on these microbes. Also, the results could affect models of terrestrial processes and knowledge of how elements, such as carbon, cycle through the environment.


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 life-sustaining elements, applied to microorganisms in soils. While scientists have applied the theory 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 and the University of Tennessee, Knoxville gathered samples from a 17-year fertilization experiment. The Smithsonian Tropical Research Institute conducted the experiment 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 Department of Energy (DOE) Office of Science user facility, provided the team with spectra. The spectra enabled the scientists to determine what organic compounds were available to the microbes. The Joint Genome Institute, also a DOE Office of Science user facility, helped team members probe microbial genes in the samples, and the scientists used mass spectrometers at Oak Ridge National Laboratory 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.


This work was supported by the Department of Energy’s (DOE’s) Office of Science, Office of Biological and Environmental Research, including support of the Environmental Molecular Sciences Laboratory, Oak Ridge Leadership Computing Facility, and the Joint Genome Institute, all DOE Office of Science user facilities, and Laboratory Directed Research and Development funding from Oak Ridge National Laboratory.


Y. Qiuming, L. Zhou, Y. Song, S.J. Wright, X. Guo, S.G. Tringe, M.M. Tfaily, L. Paša-Tolić, 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 (2018). [DOI: 10.1038/s41559-017-0463-5]

Journal Link: Nature Ecology and Evolution 2, 499 (2018). [DOI: 10.1038/s41559-017-0463-5]