Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States
Abstract
Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipid analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, whichmore »
- Authors:
-
- Michigan State Univ., East Lansing, MI (United States); Embrapa Agrobiologia, Rio de Janeiro (Brazil)
- Univ. of Wisconsin, Madison, WI (United States); Chinese Academy of Sciences, Shenyang (China)
- Michigan State Univ., East Lansing, MI (United States)
- Michigan State Univ., East Lansing, MI (United States); Univ. of Toronto, Toronto, ON (Canada)
- Univ. of Wisconsin, Madison, WI (United States)
- Publication Date:
- Research Org.:
- Michigan State Univ., East Lansing, MI (United States); Univ. of Wisconsin, Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1363928
- Alternate Identifier(s):
- OSTI ID: 1401146; OSTI ID: 1438217
- Grant/Contract Number:
- FC02-07ER64494
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Global Change Biology. Bioenergy
- Additional Journal Information:
- Journal Volume: 8; Journal Issue: 2; Journal ID: ISSN 1757-1693
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 09 BIOMASS FUELS; 60 APPLIED LIFE SCIENCES; bacterial communities; biofuel crops; fungal communities; lipid analysis; nifH; pyrosequencing
Citation Formats
Jesus, Ederson da C., Liang, Chao, Quensen, John F., Susilawati, Endang, Jackson, Randall D., Balser, Teresa C., and Tiedje, James M. Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States. United States: N. p., 2015.
Web. doi:10.1111/gcbb.12289.
Jesus, Ederson da C., Liang, Chao, Quensen, John F., Susilawati, Endang, Jackson, Randall D., Balser, Teresa C., & Tiedje, James M. Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States. United States. doi:https://doi.org/10.1111/gcbb.12289
Jesus, Ederson da C., Liang, Chao, Quensen, John F., Susilawati, Endang, Jackson, Randall D., Balser, Teresa C., and Tiedje, James M. Sun .
"Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States". United States. doi:https://doi.org/10.1111/gcbb.12289. https://www.osti.gov/servlets/purl/1363928.
@article{osti_1363928,
title = {Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States},
author = {Jesus, Ederson da C. and Liang, Chao and Quensen, John F. and Susilawati, Endang and Jackson, Randall D. and Balser, Teresa C. and Tiedje, James M.},
abstractNote = {Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipid analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.},
doi = {10.1111/gcbb.12289},
journal = {Global Change Biology. Bioenergy},
number = 2,
volume = 8,
place = {United States},
year = {2015},
month = {6}
}
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Works referenced in this record:
Switchgrass selection as a “model” bioenergy crop: A history of the process
journal, June 2010
- Wright, Lynn; Turhollow, Anthony
- Biomass and Bioenergy, Vol. 34, Issue 6
Life Cycle Analysis of Corn Harvest Strategies for Bioethanol Production
journal, January 2013
- Gao, Juan; Thelen, Kurt D.; Hao, Xinmei
- Agronomy Journal, Vol. 105, Issue 3
Distribution and diversity of Paraglomus spp. in tilled agricultural soils
journal, May 2013
- Gosling, Paul; Proctor, Maude; Jones, Julie
- Mycorrhiza, Vol. 24, Issue 1
Tradeoffs in Biomass and Nutrient Allocation in Prairies and Corn Managed for Bioenergy Production
journal, January 2012
- Jarchow, Meghann E.; Liebman, Matt
- Crop Science, Vol. 52, Issue 3
An alternative approach to indirect land use change: Allocating greenhouse gas effects among different uses of land
journal, November 2012
- Kim, Seungdo; Dale, Bruce E.; Ong, Rebecca G.
- Biomass and Bioenergy, Vol. 46
The Population Frequencies of Species and the Estimation of Population Parameters
journal, January 1953
- Good, I. J.
- Biometrika, Vol. 40, Issue 3-4
Nitrous oxide emissions during establishment of eight alternative cellulosic bioenergy cropping systems in the North Central United States
journal, May 2015
- Oates, Lawrence G.; Duncan, David S.; Gelfand, Ilya
- GCB Bioenergy, Vol. 8, Issue 3
Comparative Biogeochemical Cycles of Bioenergy Crops Reveal Nitrogen-Fixation and Low Greenhouse Gas Emissions in a Miscanthus × giganteus Agro-Ecosystem
journal, December 2009
- Davis, Sarah C.; Parton, William J.; Dohleman, Frank G.
- Ecosystems, Vol. 13, Issue 1
Impact of different bioenergy crops on N-cycling bacterial and archaeal communities in soil: Impact of bioenergy crops on soil N-cycling archaea and bacteria
journal, August 2012
- Mao, Yuejian; Yannarell, Anthony C.; Davis, Sarah C.
- Environmental Microbiology, Vol. 15, Issue 3
A Comprehensive Evaluation of PCR Primers to Amplify the nifH Gene of Nitrogenase
journal, July 2012
- Gaby, John Christian; Buckley, Daniel H.
- PLoS ONE, Vol. 7, Issue 7
Changes in N-Transforming Archaea and Bacteria in Soil during the Establishment of Bioenergy Crops
journal, September 2011
- Mao, Yuejian; Yannarell, Anthony C.; Mackie, Roderick I.
- PLoS ONE, Vol. 6, Issue 9
Soil Properties and Spatial Processes Influence Bacterial Metacommunities within a Grassland Restoration Experiment: Drivers of Soil Bacterial Communities
journal, July 2014
- Murphy, Cheryl A.; Foster, Bryan L.
- Restoration Ecology, Vol. 22, Issue 5
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007
- Wang, Q.; Garrity, G. M.; Tiedje, J. M.
- Applied and Environmental Microbiology, Vol. 73, Issue 16
Diversity, productivity and landscape-level effects in North American grasslands managed for biomass production
journal, May 2010
- Webster, Christopher R.; Flaspohler, David J.; Jackson, Randall D.
- Biofuels, Vol. 1, Issue 3
Methods of studying soil microbial diversity
journal, August 2004
- Kirk, Jennifer L.; Beaudette, Lee A.; Hart, Miranda
- Journal of Microbiological Methods, Vol. 58, Issue 2
Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment
journal, September 2009
- Iwai, Shoko; Chai, Benli; Sul, Woo Jun
- The ISME Journal, Vol. 4, Issue 2
Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil
journal, January 2001
- Poly, Franck; Monrozier, Lucile Jocteur; Bally, René
- Research in Microbiology, Vol. 152, Issue 1
Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States
journal, October 2013
- Fierer, N.; Ladau, J.; Clemente, J. C.
- Science, Vol. 342, Issue 6158
Ecologically meaningful transformations for ordination of species data
journal, October 2001
- Legendre, Pierre; Gallagher, Eugene D.
- Oecologia, Vol. 129, Issue 2
Soil microbial communities under model biofuel cropping systems in southern Wisconsin, USA: Impact of crop species and soil properties
journal, March 2012
- Liang, Chao; Jesus, Ederson da C.; Duncan, David S.
- Applied Soil Ecology, Vol. 54
Changes in soil Aggregation Associated with Tallgrass Prairie Restoration
journal, November 1987
- Jastrow, J. D.
- American Journal of Botany, Vol. 74, Issue 11
Pyrosequencing enumerates and contrasts soil microbial diversity
journal, July 2007
- Roesch, Luiz F. W.; Fulthorpe, Roberta R.; Riva, Alberto
- The ISME Journal, Vol. 1, Issue 4
Land Clearing and the Biofuel Carbon Debt
journal, February 2008
- Fargione, J.; Hill, J.; Tilman, D.
- Science, Vol. 319, Issue 5867
Changes in Soil Aggregation Associated with Tallgrass Prairie Restoration
journal, November 1987
- Jastrow, J. D.
- American Journal of Botany, Vol. 74, Issue 11
Influence of Phylogeny on Fungal Community Assembly and Ecosystem Functioning
journal, June 2007
- Maherali, H.; Klironomos, J. N.
- Science, Vol. 316, Issue 5832
Functional traits in mycorrhizal ecology: their use for predicting the impact of arbuscular mycorrhizal fungal communities on plant growth and ecosystem functioning
journal, April 2007
- van der Heijden, Marcel G. A.; Scheublin, Tanja R.
- New Phytologist, Vol. 174, Issue 2
Bouncing Back: Plant-Associated Soil Microbes Respond Rapidly to Prairie Establishment
journal, December 2014
- Herzberger, Anna J.; Duncan, David S.; Jackson, Randall D.
- PLoS ONE, Vol. 9, Issue 12
Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes
journal, December 2011
- Liu, Kuan-Liang; Porras-Alfaro, Andrea; Kuske, Cheryl R.
- Applied and Environmental Microbiology, Vol. 78, Issue 5
Biofuels and Biodiversity: Principles for Creating Better Policies for Biofuel Production
journal, June 2008
- Groom, Martha J.; Gray, Elizabeth M.; Townsend, Patricia A.
- Conservation Biology, Vol. 22, Issue 3
Experimental factors affecting PCR-based estimates of microbial species richness and evenness
journal, January 2010
- Engelbrektson, Anna; Kunin, Victor; Wrighton, Kelly C.
- The ISME Journal, Vol. 4, Issue 5
Perennial grasslands enhance biodiversity and multiple ecosystem services in bioenergy landscapes
journal, January 2014
- Werling, B. P.; Dickson, T. L.; Isaacs, R.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 4
Distance-Based Tests for Homogeneity of Multivariate Dispersions
journal, October 2005
- Anderson, Marti J.
- Biometrics, Vol. 62, Issue 1
Soil texture affects soil microbial and structural recovery during grassland restoration
journal, December 2010
- Bach, Elizabeth M.; Baer, Sara G.; Meyer, Clinton K.
- Soil Biology and Biochemistry, Vol. 42, Issue 12
Fungal-to-bacterial ratios in soils investigated for enhanced C sequestration
journal, July 2002
- Bailey, V. L.; Smith, J. L.; Bolton, H.
- Soil Biology and Biochemistry, Vol. 34, Issue 7
Nitrogen conservation decreases with fertilizer addition in two perennial grass cropping systems for bioenergy
journal, June 2015
- Jach-Smith, Laura C.; Jackson, Randall D.
- Agriculture, Ecosystems & Environment, Vol. 204
FunGene: the functional gene pipeline and repository
journal, January 2013
- Fish, Jordan A.; Chai, Benli; Wang, Qiong
- Frontiers in Microbiology, Vol. 4
Evaluation of PCR primers for universal nifH gene targeting and for assessment of transcribed nifH pools in roots of Oryza longistaminata with and without low nitrogen input: DGGE analysis of nifH
journal, August 2008
- Demba Diallo, Moudjahidou; Reinhold-Hurek, Barbara; Hurek, Thomas
- FEMS Microbiology Ecology, Vol. 65, Issue 2
Ecological Patterns of nifH Genes in Four Terrestrial Climatic Zones Explored with Targeted Metagenomics Using FrameBot, a New Informatics Tool
journal, September 2013
- Wang, Qiong; Quensen, John F.; Fish, Jordan A.
- mBio, Vol. 4, Issue 5
Filamentous Fungi: the Indeterminate Lifestyle and Microbial Ecology
journal, March 2004
- Klein, D. A.; Paschke, M. W.
- Microbial Ecology, Vol. 47, Issue 3
Mycorrhizal-mediated nitrogen acquisition in switchgrass under elevated temperatures and N enrichment
journal, October 2011
- Schroeder-Moreno, Michelle S.; Greaver, Tara L.; Wang, Shuxin
- GCB Bioenergy, Vol. 4, Issue 3
Biodiversity and ecosystem services in agricultural landscapes—are we asking the right questions?
journal, September 2004
- Swift, M. J.; Izac, A. -M. N.; van Noordwijk, M.
- Agriculture, Ecosystems & Environment, Vol. 104, Issue 1
Carbon sequestration in perennial bioenergy, annual corn and uncultivated systems in southern Quebec
journal, August 2001
- Zan, Claudia S.; Fyles, James W.; Girouard, Patrick
- Agriculture, Ecosystems & Environment, Vol. 86, Issue 2
Mechanical soil disturbance as a determinant of arbuscular mycorrhizal fungal communities in semi-natural grassland
journal, July 2010
- Schnoor, Tim Krone; Lekberg, Ylva; Rosendahl, Søren
- Mycorrhiza, Vol. 21, Issue 3
Changes in Soil Microbial Community Structure in a Tallgrass Prairie Chronosequence
journal, January 2005
- Allison, Victoria J.; Miller, R. Michael; Jastrow, Julie D.
- Soil Science Society of America Journal, Vol. 69, Issue 5
Contribution of nitrogen fixation to first year Miscanthus × giganteus
journal, July 2013
- Keymer, Daniel P.; Kent, Angela D.
- GCB Bioenergy, Vol. 6, Issue 5
Variations in microbial community composition through two soil depth profiles
journal, January 2003
- Fierer, Noah; Schimel, Joshua P.; Holden, Patricia A.
- Soil Biology and Biochemistry, Vol. 35, Issue 1
Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties
journal, October 2011
- Jangid, Kamlesh; Williams, Mark A.; Franzluebbers, Alan J.
- Soil Biology and Biochemistry, Vol. 43, Issue 10
Nitrogenase activity associated with some wisconsin prairie grasses
journal, August 1976
- Tjepkema, J. D.; Burris, R. H.
- Plant and Soil, Vol. 45, Issue 1
Energy Crops and Their Implications on Soil and Environment
journal, January 2010
- Blanco-Canqui, Humberto
- Agronomy Journal, Vol. 102, Issue 2
Bacterial Communities in the Rhizosphere of Biofuel Crops Grown on Marginal Lands as Evaluated by 16S rRNA Gene Pyrosequences
journal, January 2010
- da C. Jesus, Ederson; Susilawati, Endang; Smith, Stephanie L.
- BioEnergy Research, Vol. 3, Issue 1
Diversity and dynamics of microbial communities in soils from agro-ecosystems
journal, June 2003
- Buckley, Daniel H.; Schmidt, Thomas M.
- Environmental Microbiology, Vol. 5, Issue 6
Fungal Diversity in Permafrost and Tallgrass Prairie Soils under Experimental Warming Conditions
journal, September 2013
- Penton, C. Ryan; StLouis, Derek; Cole, James R.
- Applied and Environmental Microbiology, Vol. 79, Issue 22
Carbon-Negative Biofuels from Low-Input High-Diversity Grassland Biomass
journal, December 2006
- Tilman, D.; Hill, J.; Lehman, C.
- Science, Vol. 314, Issue 5805
Plant species composition and biofuel yields of conservation grasslands
journal, December 2009
- Adler, Paul R.; Sanderson, Matt A.; Weimer, Paul J.
- Ecological Applications, Vol. 19, Issue 8
Microbial Biomass and Community Structure in a Sequence of Soils with Increasing Fertility and Changing Land Use
journal, August 2000
- Yao, H.; He, Z.; Wilson, M. J.
- Microbial Ecology, Vol. 40, Issue 3
Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii.
journal, January 1989
- Zehr, J. P.; McReynolds, L. A.
- Applied and Environmental Microbiology, Vol. 55, Issue 10
Works referencing / citing this record:
Indications of shifting microbial communities associated with growing biomass crops on marginal lands in Southern Ontario
journal, October 2019
- Mafa-Attoye, Tolulope G.; Thevathasan, Naresh V.; Dunfield, Kari E.
- Agroforestry Systems, Vol. 94, Issue 3
Lignocellulosic-based bioenergy and water quality parameters: a review
journal, May 2018
- Acharya, Bharat Sharma; Blanco-Canqui, Humberto
- GCB Bioenergy, Vol. 10, Issue 8
Linking microbial community analysis and ecosystem studies: A rapid lipid analysis protocol for high throughput
journal, June 2019
- Balser, Teri C.; Liang, Chao; Gutknecht, Jessica L. M.
- Soil Ecology Letters, Vol. 1, Issue 1-2
Microbial spatial footprint as a driver of soil carbon stabilization
journal, July 2019
- Kravchenko, A. N.; Guber, A. K.; Razavi, B. S.
- Nature Communications, Vol. 10, Issue 1
Effect of LSU and ITS genetic markers and reference databases on analyses of fungal communities
journal, November 2018
- Xue, Chao; Hao, Yuewen; Pu, Xiaowei
- Biology and Fertility of Soils, Vol. 55, Issue 1
Ammonia‐oxidizing bacteria are the primary N 2 O producers in an ammonia‐oxidizing archaea dominated alkaline agricultural soil
journal, June 2018
- Meinhardt, Kelley A.; Stopnisek, Nejc; Pannu, Manmeet W.
- Environmental Microbiology, Vol. 20, Issue 6
Ammonia‐oxidizing bacteria are the primary N 2 O producers in an ammonia‐oxidizing archaea dominated alkaline agricultural soil
journal, June 2018
- Meinhardt, Kelley A.; Stopnisek, Nejc; Pannu, Manmeet W.
- Environmental Microbiology, Vol. 20, Issue 6
Associative nitrogen fixation (ANF) in switchgrass (Panicum virgatum) across a nitrogen input gradient
journal, June 2018
- Roley, Sarah S.; Duncan, David S.; Liang, Di
- PLOS ONE, Vol. 13, Issue 6
The impacts of four potential bioenergy crops on soil carbon dynamics as shown by biomarker analyses and DRIFT spectroscopy
journal, May 2018
- Zhu, Xuefeng; Liang, Chao; Masters, Michael D.
- GCB Bioenergy, Vol. 10, Issue 7
Cellulosic biofuel contributions to a sustainable energy future: Choices and outcomes
journal, June 2017
- Robertson, G. Philip; Hamilton, Stephen K.; Barham, Bradford L.
- Science, Vol. 356, Issue 6345
Soil microbial community structure and enzymatic activity responses to nitrogen management and landscape positions in switchgrass ( Panicum virgatum L.)
journal, January 2019
- Sekaran, Udayakumar; McCoy, Cameron; Kumar, Sandeep
- GCB Bioenergy, Vol. 11, Issue 7
Community-Level Physiological Profiles of Microorganisms from Different Types of Soil That are Characteristic to Poland—a Long-Term Microplot Experiment
journal, December 2018
- Grządziel, Jarosław; Furtak, Karolina; Gałązka, Anna
- Sustainability, Vol. 11, Issue 1
Community structure of soil fungi in a novel perennial crop monoculture, annual agriculture, and native prairie reconstruction
journal, January 2020
- McKenna, Thomas P.; Crews, Timothy E.; Kemp, Laura
- PLOS ONE, Vol. 15, Issue 1
Associative nitrogen fixation (ANF) in switchgrass (Panicum virgatum) across a nitrogen input gradient
journal, June 2018
- Roley, Sarah S.; Duncan, David S.; Liang, Di
- PLOS ONE, Vol. 13, Issue 6
Linking microbial community analysis and ecosystem studies: A rapid lipid analysis protocol for high throughput
journal, June 2019
- Balser, Teri C.; Liang, Chao; Gutknecht, Jessica L. M.
- Soil Ecology Letters, Vol. 1, Issue 1-2
X-ray computed tomography to predict soil N 2 O production via bacterial denitrification and N 2 O emission in contrasting bioenergy cropping systems
journal, September 2018
- Kravchenko, Alexandra N.; Guber, Andrey K.; Quigley, Michelle Y.
- GCB Bioenergy, Vol. 10, Issue 11
Litter quantity, litter chemistry, and soil texture control changes in soil organic carbon fractions under bioenergy cropping systems of the North Central U.S.
journal, April 2019
- von Haden, Adam C.; Kucharik, Christopher J.; Jackson, Randall D.
- Biogeochemistry, Vol. 143, Issue 3
Impact of newly introduced perennial bioenergy crops on soil quality parameters at three different locations in W-Germany
journal, October 2017
- Emmerling, Christoph; Schmidt, Axel; Ruf, Thorsten
- Journal of Plant Nutrition and Soil Science, Vol. 180, Issue 6