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Title: Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil

Abstract

Phosphorus (P) is a scarce nutrient in many tropical ecosystems, yet how soil microbial communities cope with growth-limiting P deficiency at the gene and protein levels remains unknown. Here we report a metagenomic and metaproteomic comparison of microbial communities in P-deficient and P-rich soils in a 17-year fertilization experiment in a tropical forest. The large-scale proteogenomics analyses provided extensive coverage of many microbial functions and taxa in the complex soil communities. A >4-fold increase in the gene abundance of 3-phytase was the strongest response of soil communities to P deficiency. Phytase catalyzes the release of phosphate from phytate, the most recalcitrant P-containing compound in soil organic matter. Genes and proteins for the degradation of P-containing nucleic acids and phospholipids as well as the decomposition of labile carbon and nitrogen were also enhanced in the P-deficient soils. In contrast, microbial communities in the P-rich soils showed increased gene abundances for the degradation of recalcitrant aromatic compounds, the transformation of nitrogenous compounds, and the assimilation of sulfur. Overall, these results demonstrate the adaptive allocation of genes and proteins in soil microbial communities in response to shifting nutrient constraints.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6]; ORCiD logo [7];  [7];  [8];  [9];  [1];  [1]
  1. OAK RIDGE NATIONAL LAB
  2. Oak RIdge National Laboratory
  3. Oak Ridge National Laboratory
  4. Smithsonian Tropical Research Institute
  5. University of Tennessee
  6. Joint Genome Institute
  7. BATTELLE (PACIFIC NW LAB)
  8. Oak Ridge National Labratory
  9. UNKNOWN
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1511464
Report Number(s):
PNNL-SA-131384
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Nature Ecology & Evolution
Additional Journal Information:
Journal Volume: 2; Journal Issue: 3
Country of Publication:
United States
Language:
English

Citation Formats

Yao, Qiuming, Li, Zhou, Song, Yang, Wright, Joseph, Guo, Xuan, Tringe, Susannah G., Tfaily, Malak M., Pasa Tolic, Ljiljana, Hazen, Terry, Turner, Benjamin, Mayes, Melanie A., and Pan, Chongle. Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil. United States: N. p., 2018. Web. doi:10.1038/s41559-017-0463-5.
Yao, Qiuming, Li, Zhou, Song, Yang, Wright, Joseph, Guo, Xuan, Tringe, Susannah G., Tfaily, Malak M., Pasa Tolic, Ljiljana, Hazen, Terry, Turner, Benjamin, Mayes, Melanie A., & Pan, Chongle. Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil. United States. doi:10.1038/s41559-017-0463-5.
Yao, Qiuming, Li, Zhou, Song, Yang, Wright, Joseph, Guo, Xuan, Tringe, Susannah G., Tfaily, Malak M., Pasa Tolic, Ljiljana, Hazen, Terry, Turner, Benjamin, Mayes, Melanie A., and Pan, Chongle. Thu . "Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil". United States. doi:10.1038/s41559-017-0463-5.
@article{osti_1511464,
title = {Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil},
author = {Yao, Qiuming and Li, Zhou and Song, Yang and Wright, Joseph and Guo, Xuan and Tringe, Susannah G. and Tfaily, Malak M. and Pasa Tolic, Ljiljana and Hazen, Terry and Turner, Benjamin and Mayes, Melanie A. and Pan, Chongle},
abstractNote = {Phosphorus (P) is a scarce nutrient in many tropical ecosystems, yet how soil microbial communities cope with growth-limiting P deficiency at the gene and protein levels remains unknown. Here we report a metagenomic and metaproteomic comparison of microbial communities in P-deficient and P-rich soils in a 17-year fertilization experiment in a tropical forest. The large-scale proteogenomics analyses provided extensive coverage of many microbial functions and taxa in the complex soil communities. A >4-fold increase in the gene abundance of 3-phytase was the strongest response of soil communities to P deficiency. Phytase catalyzes the release of phosphate from phytate, the most recalcitrant P-containing compound in soil organic matter. Genes and proteins for the degradation of P-containing nucleic acids and phospholipids as well as the decomposition of labile carbon and nitrogen were also enhanced in the P-deficient soils. In contrast, microbial communities in the P-rich soils showed increased gene abundances for the degradation of recalcitrant aromatic compounds, the transformation of nitrogenous compounds, and the assimilation of sulfur. Overall, these results demonstrate the adaptive allocation of genes and proteins in soil microbial communities in response to shifting nutrient constraints.},
doi = {10.1038/s41559-017-0463-5},
journal = {Nature Ecology & Evolution},
number = 3,
volume = 2,
place = {United States},
year = {2018},
month = {3}
}