Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil
Abstract
Here, 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 also 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 Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. Furthermore, 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. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi, and Planctomycetes.
- Authors:
-
- Cornell Univ., Ithaca, NY (United States)
- Butler Univ., Indianapolis, IN (United States)
- Publication Date:
- Research Org.:
- Cornell Univ., Ithaca, NY (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1864330
- Alternate Identifier(s):
- OSTI ID: 1282112; OSTI ID: 1343031
- Report Number(s):
- LLNL-JRNL-675821
Journal ID: ISSN 1664-302X
- Grant/Contract Number:
- SC0016364; 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; 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. https://doi.org/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. https://doi.org/10.3389/fmicb.2016.00703. https://www.osti.gov/servlets/purl/1864330.
@article{osti_1864330,
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 = {Here, 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 also 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 Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. Furthermore, 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. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi, and Planctomycetes.},
doi = {10.3389/fmicb.2016.00703},
journal = {Frontiers in Microbiology},
number = ,
volume = 7,
place = {United States},
year = {Thu May 12 00:00:00 EDT 2016},
month = {Thu May 12 00:00:00 EDT 2016}
}
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