A team led by the Department of Energy's Oak Ridge National Laboratory has uncovered how certain soil microbes cope in a phosphorus-poor environment to survive in a tropical ecosystem. Their novel approach could be applied in other ecosystems to study various nutrient limitations and inform agriculture and terrestrial biosphere modeling.
Phosphorus is a critical nutrient for global biological processes, such as collecting the sun's energy during photosynthesis and degrading plant debris and soil organic matter. Most tropical ecosystems endure long-term weathering that leaches phosphorus from soil.
An Oak Ridge National Laboratory-led research team found genes for production of phytase enzymes that would be released by tropical soil microbes. Phytase enzymes will attack phytate molecules, releasing much needed phosphate molecules for the microbes' survival. The soil samples were collected in phosphorus-rich and -poor experimental sites at the Smithsonian Tropical Research Institute in the Republic of Panama.
Credit: Melanie Mayes and Andy Sproles/Oak Ridge National Laboratory, U.S. Dept. of Energy
The ORNL-led team set out to discover how soil microbial communities respond to the lack of phosphorus and other nutrient deficiencies at the molecular level.
They collected soil samples at the Smithsonian Tropical Research Institute in the Republic of Panama, an experimental field site with phosphorus-rich plots and unfertilized control plots.
"This was the perfect place to test the optimal foraging theory, which is a model that helps predict an organism's behavior when searching for resources," said Chongle Pan, ORNL senior staff scientist and joint associate professor at the University of Tennessee. "We learned how this theory plays out when applied to microbial communities as they compete for nutrients."
The team analyzed the behaviors of many genes and proteins, and in the phosphorus-deficient, untreated soil, they found an increased number of genes responsible for producing phosphorus-acquiring enzymes. They also discovered more than 100 genes that work to pull phosphorus from phytate, which is a complex organic compound found in plant tissue.
"Finding so many genes to break apart and transport such a complex molecule tells us that microbes are hungry for phosphorus in untreated soil," said Melanie Mayes, an ORNL senior staff scientist who studies multi-scale environmental processes.
Conversely, she noted that when phosphorus was plentiful, more genes needed to acquire complex carbon compounds were present. "The microbial community prioritizes the breakdown of the most needed nutrients, focusing efforts on the most limiting element to balance their overall nutritional needs," she said.
The team ran each soil sample through a series of rigorous and comprehensive analyses. The DOE Joint Genome Institute conducted deep sequencing of the soils' metagenomes, or genetic material recovered directly from the soil. ORNL then used mass spectrometry and metaproteomics to identify more than 7,000 proteins in each sample.
ORNL's Titan supercomputer quickly analyzed the large amounts of metagenomics and metaproteomics data, comparing microbial activities in phosphorus-rich and -poor soils. Environmental Molecular Sciences Laboratory scientists further characterized the soils' organic matter at Pacific Northwest National Laboratory.
These unique tools working together enabled one of the deepest proteogenomics studies done on soil microbial communities, according to Pan.
The ORNL-led team plans to continue their research to characterize the ecology and evolution of soil microbial communities in nutrient-poor environments, which has applications in agriculture and terrestrial biosphere modeling worldwide. Additionally, Mayes and her team are incorporating metagenomics information into nutrient cycling models under a DOE Early Career Research Program Award.
Results from their three-year study titled, "Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil," were published in Nature Ecology & Evolution.
The paper's coauthors included Qiuming Yao, Zhou Li, Yang Song, Melanie A. Mayes and Chongle Pan of ORNL; S. Joseph Wright and Benjamin L. Turner of the Smithsonian Tropical Research Institute; Terry C. Hazen, University of Tennessee-ORNL Governor's Chair for Environmental Biotechnology; Xuan Guo of UT; Susannah G. Tringe of the DOE Joint Genome Institute; and Malak M. Tfaily and Ljiljana Paša-Tolic of Pacific Northwest National Laboratory.
The research was supported by the Laboratory Directed Research and Development program at ORNL. Metagenomic sequencing was conducted by the DOE Joint Genome Institute and soil organic matter analyses were performed using Fourier-transform ion cyclotron resonance mass spectrometry by PNNL's Environmental Molecular Sciences Laboratory, both DOE Office of Science User Facilities. This work also leveraged the Oak Ridge Leadership Computing Facility, a DOE Office of Science User Facility.
ORNL is managed by UT-Battelle for DOE's Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit http://science.
Sara Shoemaker | EurekAlert!
New research calculates capacity of North American forests to sequester carbon
16.07.2018 | University of California - Santa Cruz
Scientists discover Earth's youngest banded iron formation in western China
12.07.2018 | University of Alberta
For the first time ever, scientists have determined the cosmic origin of highest-energy neutrinos. A research group led by IceCube scientist Elisa Resconi, spokesperson of the Collaborative Research Center SFB1258 at the Technical University of Munich (TUM), provides an important piece of evidence that the particles detected by the IceCube neutrino telescope at the South Pole originate from a galaxy four billion light-years away from Earth.
To rule out other origins with certainty, the team led by neutrino physicist Elisa Resconi from the Technical University of Munich and multi-wavelength...
For the first time a team of researchers have discovered two different phases of magnetic skyrmions in a single material. Physicists of the Technical Universities of Munich and Dresden and the University of Cologne can now better study and understand the properties of these magnetic structures, which are important for both basic research and applications.
Whirlpools are an everyday experience in a bath tub: When the water is drained a circular vortex is formed. Typically, such whirls are rather stable. Similar...
Physicists working with Roland Wester at the University of Innsbruck have investigated if and how chemical reactions can be influenced by targeted vibrational excitation of the reactants. They were able to demonstrate that excitation with a laser beam does not affect the efficiency of a chemical exchange reaction and that the excited molecular group acts only as a spectator in the reaction.
A frequently used reaction in organic chemistry is nucleophilic substitution. It plays, for example, an important role in in the synthesis of new chemical...
Optical spectroscopy allows investigating the energy structure and dynamic properties of complex quantum systems. Researchers from the University of Würzburg present two new approaches of coherent two-dimensional spectroscopy.
"Put an excitation into the system and observe how it evolves." According to physicist Professor Tobias Brixner, this is the credo of optical spectroscopy....
Ultra-short, high-intensity X-ray flashes open the door to the foundations of chemical reactions. Free-electron lasers generate these kinds of pulses, but there is a catch: the pulses vary in duration and energy. An international research team has now presented a solution: Using a ring of 16 detectors and a circularly polarized laser beam, they can determine both factors with attosecond accuracy.
Free-electron lasers (FELs) generate extremely short and intense X-ray flashes. Researchers can use these flashes to resolve structures with diameters on the...
13.07.2018 | Event News
12.07.2018 | Event News
03.07.2018 | Event News
18.07.2018 | Materials Sciences
18.07.2018 | Life Sciences
18.07.2018 | Health and Medicine