Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

Pepe-Ranney, Charles; Campbell, Ashley N.; Koechli, Chantal N.; Berthrong, Sean; Buckley, Daniel H.

doi:10.3389/fmicb.2016.00703

Title: Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

Journal Article · Thu May 12 00:00:00 EDT 2016 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2016.00703· OSTI ID:1864330

Pepe-Ranney, Charles ^[1]; Campbell, Ashley N. ^[1]; Koechli, Chantal N. ^[1]; Berthrong, Sean ^[2]; Buckley, Daniel H. ^[1]

Cornell Univ., Ithaca, NY (United States)
Butler Univ., Indianapolis, IN (United States)

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.

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Research Organization:: Cornell Univ., Ithaca, NY (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0016364; SC0004486; SC0010558; AC52-07NA27344

OSTI ID:: 1864330

Alternate ID(s):: OSTI ID: 1282112; OSTI ID: 1343031

Report Number(s):: LLNL-JRNL-675821

Journal Information:: Frontiers in Microbiology, Vol. 7; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 111 works

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New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes Kroeger, Marie E.; Delmont, Tom O.; Eren, A. M. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01635	journal	July 2018
Embracing the unknown: disentangling the complexities of the soil microbiome Fierer, Noah Nature Reviews Microbiology, Vol. 15, Issue 10 https://doi.org/10.1038/nrmicro.2017.87	journal	August 2017
Resource Partitioning between Bacteria, Fungi, and Protists in the Detritusphere of an Agricultural Soil Kramer, Susanne; Dibbern, Dörte; Moll, Julia Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01524	journal	September 2016
There's no harm in having too much: A comprehensive toolbox of methods in trophic ecology Majdi, Nabil; Hette-Tronquart, Nicolas; Auclair, Etienne Food Webs, Vol. 17 https://doi.org/10.1016/j.fooweb.2018.e00100	journal	December 2018
Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing Coskun, Ömer K.; Pichler, Monica; Vargas, Sergio Applied and Environmental Microbiology, Vol. 84, Issue 18 https://doi.org/10.1128/aem.01083-18	journal	July 2018
DNA Stable-Isotope Probing Delineates Carbon Flows from Rice Residues into Soil Microbial Communities Depending on Fertilization Kong, Yali; Kuzyakov, Yakov; Ruan, Yang Applied and Environmental Microbiology, Vol. 86, Issue 7 https://doi.org/10.1128/aem.02151-19	journal	January 2020
Advancing Genome-Resolved Metagenomics beyond the Shotgun Malmstrom, Rex R.; Eloe-Fadrosh, Emiley A. mSystems, Vol. 4, Issue 3 https://doi.org/10.1128/msystems.00118-19	journal	June 2019
Long-Term Enrichment of Stress-Tolerant Cellulolytic Soil Populations following Timber Harvesting Evidenced by Multi-Omic Stable Isotope Probing Wilhelm, Roland C.; Cardenas, Erick; Leung, Hilary Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00537	journal	April 2017
Resource Legacies of Organic and Conventional Management Differentiate Soil Microbial Carbon Use Arcand, Melissa M.; Levy-Booth, David J.; Helgason, Bobbi L. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02293	journal	November 2017
Managing Agroecosystems for Soil Microbial Carbon Use Efficiency: Ecological Unknowns, Potential Outcomes, and a Path Forward Kallenbach, Cynthia M.; Wallenstein, Matthew D.; Schipanksi, Meagan E. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01146	journal	May 2019
Sowing Methods Influence Soil Bacterial Diversity and Community Composition in a Winter Wheat-Summer Maize Rotation System on the Loess Plateau Huang, Chunguo; Han, Xiaoli; Yang, Zhenping Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.00192	journal	February 2020

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