Source: MICHIGAN STATE UNIV submitted to NRP
MULTI-SCALE CONSEQUENCES OF ROTATIONAL DIVERSITY IN MIDWESTERN AGRICULTURAL SYSTEMS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0219922
Grant No.
2009-65107-05961
Cumulative Award Amt.
$448,500.00
Proposal No.
2009-02672
Multistate No.
(N/A)
Project Start Date
Sep 1, 2009
Project End Date
Aug 31, 2014
Grant Year
2009
Program Code
[94440]- Soil Processes
Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824
Performing Department
Plant, Soil and Microbial Science
Non Technical Summary
The land devoted to maize production in the U.S. is greater now than at any time in the past 50 years. This expansion of maize production, due in large part to demand for feedstock to support the biofuels industry, occurs at the cost of crop rotation length and cropping system diversity. Our overall goal is to examine whether increasing rotational diversity in Midwestern row-crop systems can enhance microbial diversity and function, nutrient cycling, and soil organic matter (SOM) retention. The effects of plant diversity on soil microbial communities and ecosystem processes such as litter decomposition, C sequestration, and trace gas emissions, remain largely unknown. This is especially true for temperate-region row-crop agricultural systems where few studies have been carried out to test the effects of rotational diversity on soil processes. Our specific objectives are to hierarchically examine the effects of cropping system diversity on: 1) soil microbial communities, including denitrifier community structure and function; 2) soil aggregation and the chemistry of inter- and intra-aggregate SOM; 3) plant litter decomposition and the degree to which historical environmental conditions and current litter chemistry influence decomposition in agricultural systems; and 4) soil surface-atmosphere emissions of nitrous oxide and carbon dioxide. Our work will be carried out in a unique long-term agricultural biodiversity study in southwest Michigan where crop diversity is varied from one to six species over a three year rotation cycle. There are no differences in chemical inputs or other management practices that could potentially confound our results. We will use a suite of cutting-edge methods to understand the effects of rotational diversity on soil processes and ecosystem services at multiple spatial scales. Our research will provide new insights into the processes underlying C storage, nutrient cycling and, ultimately, productivity responses to cropping system diversity. Our results will help land managers and policy makers better understand the effects of cropping system diversity on agricultural productivity and ecosystem function.
Animal Health Component
35%
Research Effort Categories
Basic
55%
Applied
35%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1010110100025%
1020120104025%
1330199107025%
2050110200025%
Knowledge Area
133 - Pollution Prevention and Mitigation; 102 - Soil, Plant, Water, Nutrient Relationships; 205 - Plant Management Systems; 101 - Appraisal of Soil Resources;

Subject Of Investigation
0120 - Land; 0110 - Soil; 0199 - Soil and land, general;

Field Of Science
1040 - Molecular biology; 1070 - Ecology; 1000 - Biochemistry and biophysics; 2000 - Chemistry;
Goals / Objectives
Our overall goal is to examine whether increasing plant species diversity in Midwestern row-crop systems can enhance microbial diversity and function, nutrient cycling, and SOM retention. Our work will encompass nano- (spatially explicit isotope analysis of microbes and SOM), micro- (soil structure and microbial communities), and ecosystem-scales (productivity and trace gas emissions) to examine the consequences of rotational diversity in temperate agroecosystems. We will use a suite of cutting-edge methods, including nanometer scale secondary ion mass spectrometry (NanoSIMS), pyrolysis-gas chromatography/mass spectroscopy (py-gc/ms), 13C-nuclear magnetic resonance (NMR) spectroscopy, and nucleic acid based assessments of microbial communities, in a unique long-term biodiversity experiment in Michigan (MI) row-crop systems. Our specific objectives are: 1) examine the effects of cropping system diversity on soil microbial communities, including the structure and function of the denitrifier community; 2) examine the effects of cropping system diversity on soil aggregation and the chemistry and turnover rates of inter- and intra-aggregate SOM; 3) examine the effects of cropping system diversity on: a) plant litter decomposition; and b) the transfer of plant litter to microbial communities and different SOM pools; and 4) examine the effects of cropping system diversity on soil inorganic N availability and soil surface-atmosphere emissions of nitrous oxide and carbon dioxide. This work will advance fundamental scientific understanding but also point the way forward for developing more sustainable agricultural systems. More specifically, the outcomes of this work will include new insights into: 1) fundamental mechanisms underlying C storage, nutrient cycling and, ultimately, productivity responses to plant diversity; 2) links between above and belowground biodiversity and agroecosystem function; 3) relevant spatial scales at which plant diversity alters soil biological processes and ecosystem functions; 4) application of nanoSIMS and other cutting-edge methods to challenges in soil science; and 5) management of biodiversity in Midwestern row-crop systems to enhance productivity and environmental sustainability.
Project Methods
-Objective 1. Examine the effects of cropping system diversity on soil microbial communities, including the structure and function of the denitrifier community. We will assess total bacterial diversity through Tag-sequencing of the16S genes. We will also assess changes in the denitrifier community through molecular surveys of nirK - a central gene in bacterial denitrification. We predict that cropping systems that increase aggregation in soil will support a more diverse and active denitrifier community due to the increased availability of anoxic microenvironments in soil aggregates. -Objective 2. Examine the effects of cropping system diversity on soil aggregation and the chemistry and turnover rates of inter- and intra-aggregate SOM. We will use two complementary methods to analyze SOM chemistry, py-gc/ms and 13C-NMR, and use contemporary and archived soil samples to estimate turnover times using radiocarbon measurements and modeling. We will use standard protocols to separate intra-aggregate SOM from inter-aggregate SOM. Turnover times of the aggregate-associated C fractions in the different treatments analyzed by both py-gc/ms and NMR will be modeled using radiocarbon measurements. -Objective 3. Examine the effects of cropping system diversity on: a) plant litter decomposition; and b) the transfer of plant litter to microbial communities and different SOM pools. We will decompose individual litter types using 400 cm-2 litter bags filled with 9 g of corn, soybean, wheat, red clover, or rye grass litter. We will also look at 3 different litter mixtures with 4.5 g of each residue type: corn-red clover, wheat-red clover and corn-wheat. We will analyze litter chemistry using pyrolysis gc/ms at the beginning of the experiment, the end of the second season (2011), and end of the experiment after the third growing season (2012). A composite sample of initial litter for each species will also be analyzed by 13C-NMR for comparison with py gc/ms and as a reference for the SOM fractions. In each litterbag, we will analyze the activity of 6 enzymes. We will examine differences in the fine-scale redistribution of litter-derived SOM in the soil matrix and uptake by specific microbial groups of corn using a labeled litter decomposition experiment and NanoSIMS. Imaging of biological thin samples of soils and of microbial bodies will be performed with NanoSIMS in collaboration with Dr. Jennifer Pett-Ridge at Lawrence Livermore National Laboratory. -Objective 4. Examine the effects of cropping system diversity on soil inorganic N availability and soil surface-atmosphere emissions of nitrous oxide and carbon dioxide. Gas fluxes will be determined using static PVC chambers (5500 cm-3) located within each plot. Within 48 h of collection carbon dioxide will be analyzed using an infrared gas absorption analyzer (LiCor 820) and nitrous oxide analyzed using a gas chromatograph (Hewlett Packard 5890 Series II, Rolling Meadows, IL, USA) outfitted with a 63Ni electron capture detector. Soil nitrate and ammonium concentrations will be determined spectrophotometrically in a 96 well plate reader. Crop productivity will be measured by the KBS LTER program.

Progress 09/01/09 to 08/31/14

Outputs
Target Audience: 1. Scientists interested in soil organic matter dynamics, C sequestration, and soil N cycling, particularly in the context of plant community diversity. Our work is advancing understanding of the basic mechanisms regulating SOM formation and persistence, N cycling dynamics and their relationship to microbial communities, which is an area of active international research. 2. Land managers that are concerned about soil quality, soil N dynamics, and their relationship to cropping system diversity. There continues to be uncertainty over the mechanisms that form and stabilize soil organic matter, and understanding these mechanisms is critical to developing sustainable agricultural systems. Our research is also advancing understanding of N cycling management, which is a key economic and environmental concern of land managers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This project has provided training and professional development for early career scientists in agroecosystem science, microbial genomics, soil organic matter dynamics, agronomy, and soil biogeochemistry. Graduate student Cynthia Kallenbach received the Francis and Evelyn Clark Soil Biology Scholarship, awarded to an outstanding graduate student in soil biology by the Soil Science Society of America, an NSF Doctoral Dissertation Improvement Grant, and a two-year USDA graduate fellowship for her proposal titled, ‘Microbial Ecophysiology as an Explanation for Observed Differences in Soil Carbon Concentrations between an Organic and Conventional Agricultural System’. Postdoc Kyle Wickings recently accepted an assistant professorship at Cornell University, and Lisa Tiemann an assistant professorship at Michigan State University. Faculty Jeffrey Bird, Associate Professor, City University of New York Gordan Bonan, Scientist, National Center for Atmospheric Research A. Stuart Grandy, Associate Professor, University of New Hampshire Erika Marin-Spiotta, Associate Professor, University of Wisconsin Jennifer Pett-Ridge, Career Staff Scientist, Lawrence Livermore National Lab Tom Schmidt, Professor, University of Michigan Mike Weintraub, University of Toledo Postdoctoral Scholars Heli Juottonen, Postdoc, Michigan State University Marshall McDaniel, Postdoc, University of New Hampshire Tracy Teal, Postdoctoral Fellow, Michigan State University Lisa Tiemann, Postdoc, University of New Hampshire K. Wickings, Postdoc, University of New Hampshire PhD Students Emily Atkinson, Graduate Student, University of Wisconsin Cynthia Kallenbach, Graduate Student, University of New Hampshire Brendan O'Neil, Graduate Student, Michigan State University Zachary Rinkes, Graduate Student, University of Toledo Undergraduates Ryan MacWilliams, Undergraduate Technician, Michigan State University Michael Casazza, Undergraduate Technician, University of New Hampshire Jesse Dick, Undergraduate Technician, University of New Hampshire Anthony Guidice, Undergraduate Technician, University of New Hampshire Sophie Trusty, Undergraduate Technician, University of New Hampshire How have the results been disseminated to communities of interest? 1) Results have been shared with the scientific community through the publications and presentations listed herein. 2) Results have been shared with producers and other stakeholders through these presentations. Increased microbial efficiency and growth drive soil organic matter increases in organic cropping systems. 02/2015, Organic Agriculture Research Symposium, La Crosse, WI. Microbes drive soil organic matter accumulation in organic cropping systems, 01/2015, Organic Growers Association Meeting, Concord, NH. Nitrogen Management in Organic Production Systems: Is it Time for a New Approach?, 03/2012, Organic Growers Association Meeting, Concord, NH. Managing Trace Gas Emissions in Agroecosystems, 01/2011, In-Service Training for Agricultural Service Providers, University of Maine Cooperative Extension, Portsmouth, NH. Get your Harness and Use your Spurs: Putting Soil Microbes to Work, 11/2011, New England Vegetable Conference, Manchester, NH. Managing Microbes to Build Soil Organic Matter, 10/2011, Maine Organic Farmer and Gardener’s Association Farmer to Farmer Conference, Camden, ME. Soil Organic Matter: It’s More than Just Trash. Farmer to Farmer Conference, Maine Organic Farmers and Gardeners Association. November 4-6th. Northport, ME 3) Results and new knowledge generated have been incorporated into A.S. Grandy’s classes in Soil Biology, Environmental Soil Chemistry, and Soil Biogeochemistry. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Impact statement: Biodiversity loss is arguably the most prominent and poorly understood consequence of agricultural intensification, leading to reductions in the efficiency and stability of agroecosystem functions and services. Increasing crop diversity through rotation may alleviate these negative consequences by restoring positive interactions between plants and soil microorganisms. However, positive impacts of aboveground biodiversity on belowground communities and processes have primarily been observed in natural systems and it remains unclear if similar patterns apply in managed ecosystems. Using field and lab experiments and meta analyses examining crop biodiversity, we show that as crop diversity increases, distinctive soil microbial communities are related to increases in soil aggregation,organic carbon and total nitrogen stocks, microbial activity, accelerated rates of nutrient cycling, and the ratio of carbon to nitrogen acquiring enzyme activities. By increasing the quantity, quality and complexity of crop residues, high diversity rotations can sustain soil biological communities, with positive effects on soil organic matter accrual, soil fertility, and crop yield. Objective one. Examine the effects of cropping system diversity on soil microbial communities, in particular denitrifier community structure and function. CO2 increases linearly with increasing plant number in rotation, and nitrous oxide flux in cover cropped treatments is more than twice that of non-cover cropped treatments. This is due in part to differences in the soil microbial community. Community structure of 16S rRNA bacterial genes is more similar between cropping systems with higher complexity, but it is not strong and or significant. At this level, this indicates significant differences in gas fluxes are due to abundance and activity rather than shifts in community. However targeted analysis reveals more altered nitrogen cycling process under cover crops. A sub-set of nitrite reductase genes (nirK) show a significantly higher proportion of nirK associated with ammonia oxidizing bacteria (than from heterotrophic denitrifies) under cover crops – indicating higher nitrification potential and possible nitrifier denitrification. Furthermore, while nitrous oxide flux is higher under cover crops, denitrification enzyme assays (DEA) show that a significantly higher proportion of N is completely denitrified to dinitrogen gas under cover cropped treatments. Objective two. Examine the effects of cropping system diversity on soil aggregation and the chemistry of inter- and intra-aggregate SOM, In order to examine soil C dynamics related to aggregation, we used six treatments from the Biodiversity Gradient experiment ranging in diversity from one to five species consisting of continuous corn with no cover crop or one cover crop, a corn-soy rotation and corn-soy-wheat rotations with no cover, one cover or two cover crop species. We collected soils from four replicate plots of each of these treatments and separated soils into four different size fractions using two fractionation methods,and within each fraction measured permanganate oxidizable C, extracellular enzyme activities, C chemistry, and microbial community structure. With increased rotational diversity, we observed a 33% increase in soil C compared to monocultures at this site, with increasing rotational diversity fundamentally changing microbial community structure and activity, with positive impacts on aggregate formation and SOM accrual. As crop diversity increased we found increases in the stability of mega-aggregates, with indications of increasing soil organic C and total N concentrations. Based on enzyme activity levels and SOC mineralization rates, the increases in crop diversity appear to have stimulated microbial activity in the mega-aggregates. This increase in microbial activity is likely responsible for the increase in aggregate stability through the production of soil binding agents, such as fungal hyphae, glomalin and polysaccharides. While we observed no differences in microbial biomass among treatments, higher enzyme activities and faster decomposition of labile residues suggest that crop diversification accelerated microbial metabolism in micro- and macro-aggregates. Given that microbial by-products are thought to be the primary components of stable SOM, increasing microbial crop residue processing, growth rates and biomass turnover may be driving SOM increases. In this study, we provide insight into the mechanisms controlling soil system responses to crop diversity. As crop diversity increased through multiple species rotations, we observed significant gains in soil organic matter that were driven by changes in soil and microbial community structure. Objective three. Examine the effects of cropping system diversity on plant litter decomposition and the degree to which historical environmental conditions and current litter chemistry influence decomposition in agricultural systems, and We examined how crop rotational diversity alters the decomposition dynamics of newly-added residues inputs. In a year-long laboratory incubation, we examined the decomposition of four crop residues in agricultural soils managed for over a decade with five different corn-based crop rotations. Combining rotations varying in diversity from one to five crops over a three-year period with different litter combinations allows us to test the longer-term rotation effects on processing of newly-added crop residues. We showed that crop rotations induce changes in the microbe-SOM interactions that regulate soil C and N availability, and that such changes shape the processing of new residue inputs varying in chemistry. More specifically, our results point to monocultures bringing about suppressed microbial activity. Eleven years of crop rotations influenced basal soil respiration, microbial biomass N, and extracellular enzyme activities, with 125% greater C respired in the four crop rotation compared to corn monoculture. Our research highlights the importance of crop rotations as a viable means to increase aboveground biodiversity while enhancing soil functioning. Although all of the soils used in our experiment were under the same crop (corn) for the year, crop rotation history strongly influenced how contemporary residues were processed. While the rotation effect is typically attributed to declines in weed or insect pest pressure, enhanced retention of N in microbial biomass decomposing high quality residues, more rapid decomposition of low-quality residues, and overall higher microbial activity point to more tightly coupled crop-soil-microbe relationships in biodiverse cropping systems, which likely feedback to influence plant productivity. 4) Examine the effects of cropping system diversity on soil surface-atmosphere emissions of N2O and CO2. Denitrifier communities in the monocultures differed from the multiple-crop rotation. This treatment showed the highest relative abundance of Betaproteobacteria based on both nirK sequences and 16S rRNA gene tags. Nitrous oxide flux and denitrification potential were distinctly higher in the multiple-crop rotation than in any other treatment, including single crop rotation and fallow soils. The high denitrification in the multiple-crop rotation most likely resulted from the additional plant matter and legume nitrogen provided by cover crops. Higher resources may also explain the increased occurrence of Betaproteobacteria, often prominent under such conditions. Our results suggest that plant inputs in the multiple-crop rotation led to increased denitrification. Further, the annual change of crop species with rotation cycle was sufficient to differentiate the bacterial communities of the crop rotations from monocultures.

Publications

  • Type: Journal Articles Status: Under Review Year Published: 2014 Citation: Tiemann, L., A.S. Grandy, E.E. Atkinson, E. Marin-Spiotta, and M.D. McDaniel. Crop rotational diversity enhances belowground communities and functions in an agroecosystem, Ecology Letters, in review
  • Type: Journal Articles Status: Under Review Year Published: 2014 Citation: Wieder, W.R., A.S. Grandy, C.M. Kallenbach, P.G. Taylor, and G.B. Bonan. Representing life in the Earth system by considering soil microbial functional traits, Proceedings of the National academy of Sciences, in review
  • Type: Journal Articles Status: Under Review Year Published: 2014 Citation: McDaniel, M.D. and A.S. Grandy. Cropping biodiversity and season affect soil microbial biomass and functioning in a long-term crop rotation experiment, Soil Biology and Chemistry, in review.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2014 Citation: Wieder, W.R., A.S. Grandy, C.M. Kallenbach, and G.B. Bonan. Integrating microbial physiology and physiochemical principles in soils with the Microbial Mineral Carbon Stabilization (MIMICS) model, Biogeosciences, in press.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: McDaniel, M.D., A.S. Grandy, L.K. Tiemann, and M.N. Weintraub. Crop rotation complexity regulates the decomposition of high and low quality residues. Soil Biology & Biochemistry, 78:243-254.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: McDaniel, M., L. Tiemann, and A.S. Grandy. 2014. Does agricultural crop diversity enhance soil microbial biomass and organic matter dynamics? a meta-analysis. Ecological Applications, 24:560570.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Grandy, A.S., D.S. Salam, K. Wickings, M. McDaniel, S.W. Culman, S.S. Snapp. 2013. Soil respiration and litter decomposition responses to nitrogen fertilization rate in no-till corn systems. Agriculture, Ecosystems, and Environment, 179: 35-40.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Rinkes, Z.L., M.N. Weintraub, J.L. DeForest, A.S. Grandy, and D.L. Moorehead. 2014. Interactions between leaf litter quality, particle size, and microbial community during the earliest stage of decay. Biogeochemistry, 117:153-168
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wickings, K. and A.S. Grandy. 2013. Management intensity interacts with litter chemistry and climate to drive temporal patterns in arthropod communities during decomposition, Pedobiologia, 56:105-112
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Rinkes, Z.L., R.L. Sinsabaugh, D.L. Moorhead, A.S. Grandy, and M.N. Weintraub. Field and lab conditions alter microbial enzyme and biomass driving decomposition of the same leaf litter. Frontiers in Terrestrial Microbiology, 4:1-14.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Organizer (with graduate students C. Kallenbach and L. Atwood), Contributed Session, Ecological society of America Meeting, 2014, Rhizosphere interactions: An Exploration of Patterns Across Systems
  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: ONeill, B., T. Schmidt, and A.S,. Grandy. Enhanced belowground nutrient cycling under gradient of increasing crop diversity. Soil Science Society of America annual Meeting, Long Beach, CA, 11/2014
  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Grandy, A.S., W. Wieder, and C.M. Kallenbach. Integrating data and experiments with the MIcrobial MIneral Carbon Stabilization Model (MIMICS) to understand soil carbon responses to agricultural plant diversity. Sixth International Workshop on Soil and Sedimentary Organic Matter Stabilization and Destabilization, Kiawah Island, SC, 10/2014.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Invited: Microbial Ecophysiology Explains Agricultural Soil Carbon Responses to Changes in Plant Communities. Soil Science Society of America Annual Meeting, Long beach, CA, 11/2014
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Wickings, K., A.S. Grandy, S. Reed, and C. Cleveland. 2012. The origin of litter chemical complexity during decomposition, Ecology Letters, 15:1180-1188.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Wickings, K., and A.S. Grandy. 2011. The oribatid mite Scheloribates moestus (Acari: Oribatida) alters litter chemistry and nutrient cycling during decomposition. Soil Biology & Biochemistry, 43:351-358.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Wickings, K., A.S. Grandy, S. Reed, and C. Cleveland. 2011. Management intensity alters decomposition via biological pathways. Biogeochemistry, 104:365-379.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Wieder, W.R., A.S. Grandy, C. Kallenbach, E.S. Hinckley, and G. Bonan. Merging microbial traits and soil physiochemical interactions with the MIMICS (MIcrobial-MIneral Carbon Stabilization) model. Ecological Society of America Meeting, Sacramento, CA, 07/2014
  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Kallenbach, C., and A.S. Grandy. Microbially-derived soil carbon: Experimental evidence links accumulation rates with microbial response to resource quality. Ecological Society of America Meeting, Sacramento, CA, 07/2014
  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Grandy, A.S., W. Wieder, C.M. Kallenbach. Integrating plant-microbe interactions to understand soil C stabilization with the MIcrobial-MIneral Carbon Stabilization model (MIMICS). European Geophysical Union Annual Meeting, Vienna, Austria, 05/2014. Winner of Outstanding Poster in Soil System Sciences.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: McDaniel, M.D., and A.S. Grandy. Cropping biodiversity effects on decomposition of dual-labeled (13C and 15N) wheat residue. Ecological Society of America Meeting, Minneapolis, MN, 08/2013.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Grandy, A.S., M.D. McDaniel*, L.K. Tiemann*, C.M. Kallenbach*, and K. Wickings*. One plant, two plants, three plants, four: in agricultural soils does it really matter if we increase diversity by one plant more? Soil Ecology Society Annual Meeting, Camden, NJ, 07/2013.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: McDaniel, M.D. and A.S. Grandy. Does crop biodiversity through time alter belowground function? Soil Ecology Society Annual Meeting, Camden, NJ, 07/2013
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Kallenbach, C.M. L. Tiemann, A.S. Grandy. 2013. Do new conceptual models of soil organic matter alter how we think about soil carbon management? Soil Ecology Society Annual Meeting, Camden, NJ, 07/2013
  • Type: Conference Papers and Presentations Status: Other Year Published: 2012 Citation: Tiemann, L. K., S. A. Grandy, E. E. Atkinson and E. Marin-Spiotta. Mechanisms for increased soil C storage with increasing temporal and spatial plant diversity in Agroecosystems. American Geophysical Union. AGU, San Francisco, CA, 12/2012. Contributed poster.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2012 Citation: McDaniel, M. and A.S. Grandy. Does Crop Rotation Influence Soil Microbial Function? LTER All Scientists Meeting, YMCA of the Rockies, Estes Park, CO, 09/2012.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2011 Citation: Grandy, A.S., H. Juottonen, B. O'Neill, and T. Schmidt. Relationships between plant diversity and soil ecosystem health and function in agricultural systems. Soil Science Society of America, San Antonio, TX, 10/2011.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2011 Citation: Wickings, K.G., A.S. Grandy, S. Reed, and C. Cleveland. Litter quality explains the effects of biology and management on litter chemistry during decomposition. Ecological Society of America, Austin, TX, 08/2011
  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Invited: One plant, two plants, three plants, four: the belowground effects of increasing agricultural diversity by one plant more. University of Vermont, Burlington, VT, 03/2014
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Invited: One plant, two plants, three plants, four: the belowground effects of increasing agricultural diversity by one plant more. American Geophysical Union, San Francisco, CA, 12/2013
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Invited: Biological Controls on Decomposition in Agroecosystems, Ecological Society of America Annual Meeting, Minneapolis, MN, 7/2013 (presented by postdoc Kyle Wickings).
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Invited: New Insights into the Plant Litter-Soil Organic Matter Interface, University of Massachusetts, Amherst, MA, 02/2013.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2012 Citation: Wickings, K.G. and A.S. Grandy. Management intensity and litter chemistry interact to determine microarthropod succession patterns during decomposition. LTER All Scientists Meeting, YMCA of the Rockies, Estes Park, CO, 09/2012.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2012 Citation: O'Neill, B., A.S. Grandy, and T. Schmidt. Cover crops have the greatest influence on belowground ecosystem processes along a gradient of cropping system diversity. LTER All Scientists Meeting, YMCA of the Rockies, Estes Park, CO, 09/2012.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2012 Citation: Wickings, K., A.S. Grandy, S.C. Reed, and C.C. Cleveland. The origin of chemical complexity during plant litter decomposition. Ecological Society of America Annual Meeting, Portland, OR 08/2012.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2012 Citation: McDaniel, M.D. and A.S. Grandy. Cropping biodiversity effects on soil organic matter dynamics and microbial function. Ecological Society of America Annual Meeting, Portland, OR 08/2012.


Progress 09/01/12 to 08/31/13

Outputs
Target Audience: 1. Scientists interested in soil organic matter dynamics, C sequestration, and soil N cycling, particularly in the context of plant community diversity. Our work is advancing understanding of the basic mechanisms regulating SOM formation and persistence, N cycling dynamics and their relationship to microbial communities, which is an area of active international research. 2. Land managers that are concerned about soil quality, soil N dynamics, and their relationship to cropping system diversity. There continues to be uncertainty over the mechanisms that form and stabilize soil organic matter, and understanding these mechanisms is critical to developing sustainable agricultural systems. Our research is also advancing understanding of N cycling management, which is a key economic and environmental concern of land managers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? In the past year the following undergraduate and graduate students and postdocs have been involved with the project: 1. Michael Casazza, undergraduate technician, University of New Hampshire 2. Sophie Trusty, undergraduate techician, University of New Hampshire 3. Emily Atkinson, graduate student, University of Wisconsin 4. Brendan O'Neil, graduate student, Michigan State University 5. Marshall McDaniel, postdoc, University of New Hampshire 6. Lisa Tiemann, postdoc, University of New Hampshire All of the above postdocs and graduate students have been directly invloved with presentations related to the project. How have the results been disseminated to communities of interest? Results have been shared with the scientifc community through the publications and presentations listed herein. What do you plan to do during the next reporting period to accomplish the goals? We are focused this year on the publication of 3-5 additional papers and of the labeled litter decomposition experiment and Nano-SIMS analysis outlined in the original proposal. This is a key element of the proposal designed to track labeled wheat litter decomposing in different agroecosystems through microbial communities and ultimately its long-term stabilization on mineral surfaces. The combination of Nano-SIMS with a long-term litter decomposition experiment will provide new insights into soil C stabilization dynamics, but is still ongoing.

Impacts
What was accomplished under these goals? Overview. In the last year we have used a multi-tiered approach that includes meta-analysis, observations, and field manipulations to address questions related to belowground diversity and ecosystem function. In our meta-analysis (McDaniel et al. 2013 in press, Ecological Applications), we examined how rotation crop type and management practices influence C and N dynamics in different climates and soil types. We found that adding one or more crops in rotation to a monoculture increased total soil C by 3.6% but when rotations included a cover crop (i.e. crops that are not harvested but produced to enrich the soil and capture inorganic N), total C increased by 8.5%. Further, rotations substantially increased the soil microbial biomass C (20.7%) and N (26.1%) pools. These results are supported by field observations at the W.K. Kellogg Biological Station in Michigan. In a recent published paper (Wickings and Grandy 2011, Soil Biology and Biochemistry) and in multiple publications in preparation, we show that decomposer community structure and function, SOM dynamics, and nutrient cycling are all strongly influenced by cropping system diversity. Thus, our research shows that enhancing cropping system diversity enhances soil C, N and microbial biomass and even two-crop rotations, especially those including a cover crop, are far better for sustaining soils than monocultures, making crop rotations a cornerstone for sustainable agroecosystems. Below I cover the major experimental activities. Aggregate-associated soil C (postdoc Lisa Tiemann). We used six treatments from the Biodiversity Gradient experiment ranging in diversity from one to five species consisting of continuous corn with no cover crop or one cover crop, a corn-soy rotation and corn-soy-wheat rotations with no cover, one cover or two cover crop species. We collected soils from four replicate plots of each of these treatments and separated soils into four different size fractions using two fractionation methods, wet and dry sieving. In both sets of aggregates (wet or dry sieved) we measured the distribution and C and N concentrations in of the mega- (>2 mm), macro- (0.25–2 mm), and micro- (0.053-0.25 mm) aggregates. Also, within each dry sieved aggregate size class, we measured permanganate oxidizable C (POXC), extracellular enzyme activities (EEA), SOM chemistry via pyrolysis-GC/MS and microbial community structure with phospholipid fatty acid (PLFA) analysis. In a manuscript currently in preparation, we use these data to address the impacts of both rotational and cover crop diversity on soil physical structure, associated microbial community structure and activity and soil C storage. We are currently in the process of measuring C and N content in the wet-sieved aggregates, and have designed a sequential SOM extraction procedure. This sequential extraction procedure will first separate soils into particle size fractions (clay, silt and sand), then using sodium pyrophosphate we will extract mineral associated SOM molecules > 3500 Dalton. The molecular structure of this mineral associated SOM will be qualitatively assessed using 13C-NMR and pyrolysis-GC/MS. These data will provide insights into SOM chemistry across range of vegetation and levels of diversity that will help us build a better understanding of SOM dynamics. In particular, these data will illuminate the chemical structure and origins of the most stable SOM and how this might change with different levels of cropping diversity. Crop biodiversity and belowground C cycling (postdoc M. McDaniel). McDaniel has lead the data collection and analysis of Objective 3 - Examine the effects of cropping system diversity on: a) plant litter decomposition; and b) the transfer of plant litter to microbial communities and different SOM pools. This objective was primarily addressed with a dual-labeled (13C and 15N stable isotopes) wheat residue incubation in the field. This 2-year incubation has just finished and the samples are currently being processed. Co-I E. Marin-Spiotta is also working on analyzing these samples for 13C-PLFA, in order to examine which members of the microbial community are most involved in processing newly added residue. Furthermore, collaborator J. Pett-Ridge is analyzing these samples with nano- Secondary Ion Mass Spectrometry in order to determine the distribution at the sub-micron scale of the 13C and 15N being stabilized in the soil organic matter. Additionally, to supplement the experiment(s) addressing Objective 3, M. McDaniel has used a soil+crop residue incubation approach to look at interactions between crop rotation history and residue quality and diversity. These results show that crop rotations alter how soils process newly-added residues. He has also used a community-level physiological profile (CLPP) method to test the effect of cropping diversity on soil microbial biomass and functioning at three points over a growing season. Both season and crop rotation alter the soil substrates available to soil microbes over the year, and the microbial catabolic potential. The publications from these two experiments will be published within the next year. M. McDaniel and the authors of this proposal are also collaborating with B. O’Neill, K. Wickings, and A. Peralta on a collaborative, intensive effort to assess the effects of crop rotational biodiversity on multiple measures of belowground diversity. This “multi-trophic” analysis of soil diversity is the first of its kind to involve assessing the soil organic matter complexity, microbial biodiversity, functional diversity (CLPP), and soil faunal diversity at one time point but on nine different crop rotations. Microbial communities and trace gas emissions (graduate student B. O’Neil). Over the past year we have completed a third and final year of targeted sequencing of 16S bacterial rRNA from across the KBS-LTER Biodiversity Gradient. In addition, we have designed a unique set of primers for fungal 18S rRNA surveys, and begun optimizing methods for carrying out this sequencing. The same three years’ of soil samples used for bacteria will be assayed for the fungal community to complete a fuller picture of overall microbial diversity across the gradient. In the past year the data collected thus far have contributed to a poster presentation at the national meeting of the Soil Science Society of America and a seminar as the Kellogg Biological Station. These presentations included data from three manuscripts currently in preparation. The first is an analysis of biogeochemical factors across the biodiversity gradient, including nitrogen carbon and nitrogen pools, trace gas flux and enzyme activities. The second study describes the effect of cropping system diversity on the belowground microbial community dynamics, both bacterial and fungal after sequencing is completed. The third targets changes in denitrification across the gradient, and relating in-field N2O flux rates, denitrification potential and targeted gene surveys in the denitrification pathway. All of these results reveal changing soil processes and microbial community structure across the gradient of cropping complexity, but with cover crops having the greatest effect along the diversity gradient. In addition, the degree of potential soil carbon and nitrogen mineralization is particularly treatment sensitive across the gradient. This past season we measured soil mineralization potentials in conjunction maize chlorophyll content as critical factors related to crop productivity. The results from monitoring soil C and N mineralization potential have also led directly to talks with extension staff and faculty about how to integrate these measures into soil testing in ways that will be meaningful for growers for better management of soil health and quality.

Publications

  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Wickings, K., A.S. Grandy, S. Reed, and C. Cleveland. 2012. The origin of litter chemical complexity during decomposition. Ecology Letters, 15:1180-1188.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: McDaniel, M.D., and A.S. Grandy. 2013. Does crop biodiversity through time alter belowground functioning? Soil Ecology Society meeting in Camden, NJ.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wickings, K. and A.S. Grandy. Management intensity interacts with litter chemistry and climate to drive temporal patterns in arthropod communities during decomposition. Pedobiologia, 56:105-112.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Grandy, A.S., D.S. Salam, K. Wickings, M. McDaniel*, S.W. Culman, S.S. Snapp. Soil respiration and litter decomposition responses to nitrogen fertilization rate in no-till corn systems. Agriculture, Ecosystems, and Environment, 179: 35-40
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: McDaniel, M., L. Tiemann, and A.S. Grandy. Does agricultural crop diversity enhance soil microbial biomass and organic matter dynamics? a meta-analysis. Ecological Applications, in press.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Invited: Biological Controls on Decomposition in Agroecosystems, Ecological Society of America Annual Meeting, Minneapolis, MN, 7/2013 (presented by postdoc Kyle Wickings).
  • Type: Conference Papers and Presentations Status: Other Year Published: 2013 Citation: Invited: New Insights into the Plant Litter-Soil Organic Matter Interface, University of Massachusetts, Amherst, MA, 02/2013.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: Invited: Invertebrate-Microbe Interactions during Plant Litter Decomposition, Entomological Society of America Annual Meeting, Knoxville, TN, 11/2012 (presented by postdoc Kyle Wickings).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: McDaniel, M. and A.S. Grandy. Does Crop Rotation Influence Soil Microbial Function? LTER All Scientists Meeting, YMCA of the Rockies, Estes Park, CO, 09/2012.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: O'Neill, B., A.S. Grandy, and T. Schmidt. Cover crops have the greatest influence on belowground ecosystem processes along a gradient of cropping system diversity. LTER All Scientists Meeting, YMCA of the Rockies, Estes Park, CO, 09/2012.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Grandy, A.S., M.D. McDaniel, L.K. Tiemann, C.M. Kallenbach, and K. Wickings. One plant, two plants, three plants, four: in agricultural soils does it really matter if we increase diversity by one plant more? Soil Ecology Society Annual Meeting, Camden, NJ, 07/2013
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Grandy, A.S. One plant, two plants, three plants, four: in agricultural soils does it really matter if we increase diversity by one plant more? NIFA project directors annual meeting, Annapolis, MD, 08/2013
  • Type: Conference Papers and Presentations Status: Published Year Published: 2012 Citation: Tiemann, L. K., S. A. Grandy, E. E. Atkinson and E. Marin-Spiotta. Mechanisms for increased soil C storage with increasing temporal and spatial plant diversity in Agroecosystems. AGU Meeting, San Francisco, CA, December 3-7, 2012. Contributed poster.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: McDaniel, M.D., and A.S. Grandy. 2013. Cropping biodiversity effects on decomposition of dual-labeled (13C and 15N) wheat residue. Ecological Society of America meeting in Minneapolis, MN.


Progress 09/01/09 to 08/31/13

Outputs
OUTPUTS: In 2010 our project, which employed a graduate student, postdoc, and undergraduate technician, focused on establishing baseline measurements of cropping system diversity effects on soil ecosystem functions. We also evaluated the impact of cropping system diversity on overall bacterial communities and more specifically on denitrifiers and their activity as nitrous oxide producers. Of the seven examined treatments in the KBS LTER Biodiversity plots, five were in the corn phase of the rotation, one was continuous soybean and one was a continuous fallow with only spring cultivation. The five corn rotations ranged from continuous corn, to corn-soybean-wheat monoculture, to mixed cover-cropped treatments including up to six plant species. From June to November, soil cores were taken from each of the seven plots and examined for moisture, pH, mineral nitrogen (ammonium and nitrate) and a series of soil enzyme activities. Over the same period, trace gas samples were taken from in situ chambers and soil flux rates determined for carbon dioxide and nitrous oxide. Total bacterial communities were evaluated by 454-pyrosequenced 16S rRNA gene tags and denitrifiers by clone libraries for the nitrite reductase gene nirK. Denitrification activity was measured as field nitrous oxide fluxes and as denitrifier enzyme activity measured with and without acetylene inhibition to assess nitrous oxide reduction to dinitrogen. Along with these research activities, a meeting was held at MSU with project participants, including Erika Marin-Spiotta from the University of Wisconsin, to discuss progress on different components of the project. PARTICIPANTS: Jeffrey Bird, assistant professor, City University of New York; Stuart Grandy, assistant professor, Michigan State University; Heli Juttonen, postdoctoral scholar, Michigan State University; Ryan MacWilliams, undergraduate technician, Michigan State University; Erika Marin-Spiotta, assistant professor, University of Wisconsin; Brendan O'Neill, graduate fellow, Michigan State University; Jennifer Pett-Ridge, career staff scientist, Lawrence Livermore National Lab; Tom Schmidt, professor, Michigan State University; Tracy Teal, postdoctoral fellow, Michigan State University TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Over the course of the growing season, soil N levels remained higher in the most diverse, intercropped rotations and continuous soybean treatment, compared to other plots, especially monocultures. Notably, by late September, soil nitrate concentrations were significantly higher in the soybean treatment and the most diverse cropping treatments which included a legume species. Soil gas flux rates for both carbon dioxide and nitrous oxide were consistently lower in soybean plots compared to all other rotations, while fallow plots maintained a comparatively higher carbon dioxide flux and lower nitrous oxide flux than other plots. For corn phase rotations, all monocultures tended to group together, and differed from the two most diverse, inter-cropped treatments which generally had higher nitrous oxide flux rates than other treatments. Soil enzyme results showed a similar trend, with enzyme activities in the most diverse plots tending to group together compared to monoculture rotations. This was particularly clear for beta-1,4-cellobisidase (BG) and beta-1,4-N-acetyl-glucosaminidase (NAG) activities which were significantly higher at most time points for the most species-rich rotations compared to monocultures. Other soil enzyme activities did not exhibit consistent differences between treatments. Over the winter, archived soil samples from the 2010 season will be used to measure C:N and soil respiration followed by microbial biomass extraction. The Biodiversity Plot field data from 2010 indicate discernible differences in ecosystem function between the most plant-diverse rotations, compared to all other monoculture rotations. In particular, the data indicate that nitrogen cycling differs between these two types of cropping systems. With regards to soil communities, monocultures unexpectedly showed higher bacterial diversity than crop rotations and fallow soil. The community composition of corn and soybean monocultures was also distinct from more diverse cropping systems. Similarly, denitrifier communities in the monocultures differed from the multiple-crop rotation. This treatment showed the highest relative abundance of Betaproteobacteria based on both nirK sequences and 16S rRNA gene tags. Nitrous oxide flux and denitrification potential were distinctly higher in the multiple-crop rotation than in any other treatment, including single crop rotation and fallow soils. The high denitrification in the multiple-crop rotation most likely resulted from the additional plant matter and legume nitrogen provided by cover crops. Higher resources may also explain the increased occurrence of Betaproteobacteria, often prominent under such conditions. Our results suggest that plant inputs in the multiple-crop rotation led to increased denitrification. Further, the annual change of crop species with rotation cycle was sufficient to differentiate the bacterial communities of the crop rotations from monocultures.

Publications

  • Juottonen H, Gomez-Alvarez V, Teal TK, Grandy AS, Schmidt TM. 2010. Effect of fertilization and plant diversity on denitrifier and bacterial communities in agricultural soil. 13th International Symposium on Microbial Ecology, Seattle, USA, 22-27 August 2010.
  • Juottonen H, Gomez-Alvarez V, Teal TK, Grandy AS, Schmidt TM. 2010. Disentangling the effects of fertilization and plants on denitrifier and bacterial communities in agricultural soil. USDA Annual Project Director Meeting, Washington, D.C.