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Title: Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil

Abstract

We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firrnicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Furthermore, microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chlorotlexi, and Planctomycetes.

Authors:
 [1];  [1];  [1];  [2];  [1]
  1. Cornell Univ., Ithaca, NY (United States). School of Integrative Plant Sciences
  2. Butler Univ., Indianapolis, IN (United States). Dept. of Biological Sciences
Publication Date:
Research Org.:
Cornell Univ., Ithaca, NY (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1282112
Alternate Identifier(s):
OSTI ID: 1343031
Report Number(s):
LLNL-JRNL-675821
Journal ID: ISSN 1664-302X
Grant/Contract Number:  
SC0004486; SC0010558; AC52-07NA27344
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; stable isotope probing; carbon cycle; decomposition; verrucomicrobia; cellulose; soil; trophic; dna-sip; microbial community composition; 16s ribosomal-rna; functional-significance; labile carbon; climate-change; bulk soil; bacterial; diversity; nitrogen; tools; 54 ENVIRONMENTAL SCIENCES; stable isotopeprobing; soil trophic

Citation Formats

Pepe-Ranney, Charles, Campbell, Ashley N., Koechli, Chantal N., Berthrong, Sean, and Buckley, Daniel H. Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil. United States: N. p., 2016. Web. doi:10.3389/fmicb.2016.00703.
Pepe-Ranney, Charles, Campbell, Ashley N., Koechli, Chantal N., Berthrong, Sean, & Buckley, Daniel H. Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil. United States. doi:10.3389/fmicb.2016.00703.
Pepe-Ranney, Charles, Campbell, Ashley N., Koechli, Chantal N., Berthrong, Sean, and Buckley, Daniel H. Thu . "Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil". United States. doi:10.3389/fmicb.2016.00703. https://www.osti.gov/servlets/purl/1282112.
@article{osti_1282112,
title = {Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil},
author = {Pepe-Ranney, Charles and Campbell, Ashley N. and Koechli, Chantal N. and Berthrong, Sean and Buckley, Daniel H.},
abstractNote = {We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firrnicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Furthermore, microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chlorotlexi, and Planctomycetes.},
doi = {10.3389/fmicb.2016.00703},
journal = {Frontiers in Microbiology},
number = ,
volume = 7,
place = {United States},
year = {2016},
month = {5}
}

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