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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:
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Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1439692
Report Number(s):
PNNL-SA-131384
Journal ID: ISSN 2397-334X; 50001; 49740; KP1704020
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nature Ecology and Evolution; Journal Volume: 2; Journal Issue: 3
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

Yao, Qiuming, Li, Zhou, Song, Yang, Wright, S. Joseph, Guo, Xuan, Tringe, Susannah G., Tfaily, Malak M., Paša-Tolić, Ljiljana, Hazen, Terry C., Turner, Benjamin L., 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, S. Joseph, Guo, Xuan, Tringe, Susannah G., Tfaily, Malak M., Paša-Tolić, Ljiljana, Hazen, Terry C., Turner, Benjamin L., 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, S. Joseph, Guo, Xuan, Tringe, Susannah G., Tfaily, Malak M., Paša-Tolić, Ljiljana, Hazen, Terry C., Turner, Benjamin L., Mayes, Melanie A., and Pan, Chongle. Mon . "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_1439692,
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, S. Joseph and Guo, Xuan and Tringe, Susannah G. and Tfaily, Malak M. and Paša-Tolić, Ljiljana and Hazen, Terry C. and Turner, Benjamin L. 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 and Evolution},
number = 3,
volume = 2,
place = {United States},
year = {Mon Jan 22 00:00:00 EST 2018},
month = {Mon Jan 22 00:00:00 EST 2018}
}