Data Dive: How Microbes Handle Poor Nutrition in Tropical Soil

High-performance computing reveals the relationship between DNA and phosphorous uptake.

Forest floor on left with microbe particle flow on right
Using high-performance computing, an Oak Ridge National Laboratory-led research team analyzed how the availability of phosphorous affects microbes’ foraging strategies in a tropical ecosystem. At right, microbial genes encode the production of phytase enzymes that break apart phytate molecules, releasing much needed phosphate for the microbes’ survival.

The Science

The soil in a tropical forest often lacks phosphorus, a vital nutrient for microbes. How do the microbes survive? Using high-performance computing, researchers carried out a detailed investigation of soil microbial genetics to find out. The team sifted through massive amounts of genetic data to analyze how the availability of phosphorous affects microbes’ foraging strategies in such situations. In deficient soils, microbes have significantly more genes involved in pulling in phosphorous. The team’s findings shed light on how certain soil microbes survive in a tropical ecosystem.

The Impact

Microbes play a major role in global nutrient cycles. Improved understanding of the interplay between microbes and soil could help scientists model processes that affect Earth’s climate. For example, scientists could use the soil-microbe interplay to study the carbon cycle. In this cycle, microbes exert influence by breaking down organic carbon and releasing carbon dioxide into the air. The team’s approach could be applied to other ecosystems to study nutrient limitations and inform agriculture and terrestrial biosphere modeling.


Applying metagenomics and metaproteomics techniques along with high-performance computing at the Oak Ridge Leadership Computing Facility, the team compared the genes and proteins from microbes in phosphorous-rich and phosphorous-deficient soils. They discovered several key differences. Among microbes in the phosphorous-deficient soil, the team found more than four times as many genes responsible for encoding enzymes—molecules that accelerate chemical reactions—dedicated to acquiring phosphorous from the environment. The team also identified more than 100 genes among the phosphorous-constrained microbes that work to pull phosphorus from phytate, an organic compound in plant tissue that microbes cannot easily access. Conversely, in the phosphorous-rich environment, the team found that microbes devoted more genes to acquiring other nutrients such as carbon and nitrogen.


Chongle Pan
Oak Ridge National Laboratory  


The research was supported by the Laboratory Directed Research and Development effort at Oak Ridge National Laboratory. Metagenomic sequencing was conducted by the Department of Energy (DOE) Joint Genome Institute, and soil organic matter analyses were performed using Fourier-transform ion cyclotron resonance mass spectrometry at the Environmental Molecular Sciences Laboratory, both DOE Office of Science user facilities. This work also leveraged the Oak Ridge Leadership Computing Facility’s Titan and Rhea supercomputers.


Q. Yao, Z. Li, 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 & Evolution 2 (2018), 499 (2018). [DOI: 10.1038/s41559-017-0463-5]

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Oak Ridge National Laboratory highlight: Researchers reveal how microbes cope in phosphorus-deficient tropical soil

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