Metagenomic reconstruction of nitrogen cycling pathways in a CO2-enriched grassland ecosystem

Qichao Tu, Zhili He, Liyou Wu, Kai Xue, Gary Xie, Patrick Chain, Peter B. Reich, Sarah E. Hobbie, Jizhong Zhou

Research output: Contribution to journalArticlepeer-review

28 Scopus citations

Abstract

The nitrogen (N) cycle is a collection of important biogeochemical pathways mediated by microbial communities and is an important constraint in response to elevated CO2 in many terrestrial ecosystems. Previous studies attempting to relate soil N cycling to microbial genetic data mainly focused on a few gene families by PCR, protein assays and functional gene arrays, leaving the taxonomic and functional composition of soil microorganisms involved in the whole N cycle less understood. In this study, 24 soil samples were collected from the long-term experimental site, BioCON, in 2009. A shotgun metagenome sequencing approach was employed to survey the microbial gene families involved in soil N cycle in the grassland that had been exposed to elevated CO2 (eCO2) for >12 years. In addition to evaluating the responses of major N cycling gene families to long-term eCO2, we also aimed to characterize the taxonomic and functional composition of these gene families involved in soil N transformations. At the taxonomic level, organic N metabolism and nitrate reduction had the most diverse microbial species involved. The distinct taxonomic composition of different N cycling processes suggested that the complex N cycle in natural ecosystems was a result of multiple processes by many different microorganisms. Belowground microbial communities that mediate N cycling responded to eCO2 in several different ways, including through stimulated abundances of the gene families related with organic decomposition, dissimilatory nitrate reduction, and N2 fixation, and suppressed abundances of the gene families in glutamine synthesis and anammox. This study provides a genetic basis of the microorganisms involved in key processes in the N cycle in complex ecosystems, and shows that long-term eCO2 selectively affects N cycling pathways instead of tuning up every process.

Original languageEnglish (US)
Pages (from-to)99-108
Number of pages10
JournalSoil Biology and Biochemistry
Volume106
DOIs
StatePublished - Mar 1 2017

Bibliographical note

Funding Information:
This work is supported by the U.S. Department of Agriculture (project 2007-35319-18305) through the NSF-USDA Microbial Observatories Program, by the Department of Energy under contract DE-SC0004601 through Genomics: GTL Foundational Science, Office of Biological and Environmental Research, and by the National Science Foundation (DEB-0716587, DEB-0620652, DEB-1234162, DEB-0218039, DEB-0219104, DEB-0217631, DEB-1120064, DEB-0716587), the DOE Program for Ecosystem Research (DE-FG02-96ER62291), and the Minnesota Environment and Natural Resources Trust Fund (ML 2008, Chap. 367, Sec. 2, Subd. 3(p)).

Keywords

  • Elevated CO
  • Grassland
  • Metagenomic reconstruction
  • Nitrogen cycling
  • Shotgun metagenome sequencing

Fingerprint Dive into the research topics of 'Metagenomic reconstruction of nitrogen cycling pathways in a CO<sub>2</sub>-enriched grassland ecosystem'. Together they form a unique fingerprint.

Cite this