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Title: Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil

Despite the central role of soil microbial communities in global carbon (C) cycling, little is known about soil microbial community structure and even less about their metabolic pathways. Efforts to characterize soil communities often focus on identifying differences in gene content across environmental gradients, but an alternative question is what genes are similar in soils. These genes may indicate critical species or potential functions that are required in all soils. Here we identified the “core” set of C cycling sequences widely present in multiple soil metagenomes from a fertilized prairie (FP). Of 226,887 sequences associated with known enzymes involved in the synthesis, metabolism, and transport of carbohydrates, 843 were identified to be consistently prevalent across four replicate soil metagenomes. This core metagenome was functionally and taxonomically diverse, representing five enzyme classes and 99 enzyme families within the CAZy database. Though it only comprised 0.4% of all CAZy-associated genes identified in FP metagenomes, the core was found to be comprised of functions similar to those within cumulative soils. The FP CAZy-associated core sequences were present in multiple publicly available soil metagenomes and most similar to soils sharing geographic proximity. As a result, in soil ecosystems, where high diversity remains a keymore » challenge for metagenomic investigations, these core genes represent a subset of critical functions necessary for carbohydrate metabolism, which can be targeted to evaluate important C fluxes in these and other similar soils.« less
Authors:
 [1] ;  [1] ;  [1] ;  [2] ;  [3] ;  [4]
  1. Iowa State Univ., Ames, IA (United States)
  2. Argonne National Lab. (ANL), Argonne, IL (United States)
  3. Iowa State Univ., Ames, IA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  4. Loyola Univ., Chicago, IL (United States)
Publication Date:
Grant/Contract Number:
AC02-06CH11357; SC0010775
Type:
Published Article
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 11; Journal Issue: 11; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Research Org:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; metagenomics; physical geography; agricultural soil science; sequence databases; sequence alignment; actinobacteria; soil ecology; phylogenetic analysis
OSTI Identifier:
1338428
Alternate Identifier(s):
OSTI ID: 1411035

Howe, Adina, Yang, Fan, Williams, Ryan J., Meyer, Folker, Hofmockel, Kirsten S., and Kelly, John J.. Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil. United States: N. p., Web. doi:10.1371/journal.pone.0166578.
Howe, Adina, Yang, Fan, Williams, Ryan J., Meyer, Folker, Hofmockel, Kirsten S., & Kelly, John J.. Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil. United States. doi:10.1371/journal.pone.0166578.
Howe, Adina, Yang, Fan, Williams, Ryan J., Meyer, Folker, Hofmockel, Kirsten S., and Kelly, John J.. 2016. "Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil". United States. doi:10.1371/journal.pone.0166578.
@article{osti_1338428,
title = {Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil},
author = {Howe, Adina and Yang, Fan and Williams, Ryan J. and Meyer, Folker and Hofmockel, Kirsten S. and Kelly, John J.},
abstractNote = {Despite the central role of soil microbial communities in global carbon (C) cycling, little is known about soil microbial community structure and even less about their metabolic pathways. Efforts to characterize soil communities often focus on identifying differences in gene content across environmental gradients, but an alternative question is what genes are similar in soils. These genes may indicate critical species or potential functions that are required in all soils. Here we identified the “core” set of C cycling sequences widely present in multiple soil metagenomes from a fertilized prairie (FP). Of 226,887 sequences associated with known enzymes involved in the synthesis, metabolism, and transport of carbohydrates, 843 were identified to be consistently prevalent across four replicate soil metagenomes. This core metagenome was functionally and taxonomically diverse, representing five enzyme classes and 99 enzyme families within the CAZy database. Though it only comprised 0.4% of all CAZy-associated genes identified in FP metagenomes, the core was found to be comprised of functions similar to those within cumulative soils. The FP CAZy-associated core sequences were present in multiple publicly available soil metagenomes and most similar to soils sharing geographic proximity. As a result, in soil ecosystems, where high diversity remains a key challenge for metagenomic investigations, these core genes represent a subset of critical functions necessary for carbohydrate metabolism, which can be targeted to evaluate important C fluxes in these and other similar soils.},
doi = {10.1371/journal.pone.0166578},
journal = {PLoS ONE},
number = 11,
volume = 11,
place = {United States},
year = {2016},
month = {11}
}