Linking C and N Cycling to Microbial Community Function in Cover Crop Systems

Project Overview

Project Type: Graduate Student
Funds awarded in 2006: $9,995.00
Projected End Date: 12/31/2008
Region: Western
State: California
Graduate Student:

Annual Reports


  • Agronomic: corn


  • Crop Production: cover crops, nutrient cycling, organic fertilizers
  • Education and Training: demonstration, display
  • Production Systems: agroecosystems
  • Soil Management: green manures, organic matter, soil analysis, nutrient mineralization


    In this study, we sought to link short-term cover crop C and N cycling to microbial-mediated turnover and subsequent stabilization of below- and aboveground cover crop inputs across various soil microenvironments, operationally defined as soil organic matter (SOM) fractions. Few differences were found in the 13C-PLFA community profiles and bacterial abundances across the three cropping systems and among the microenvironments. Results from this study corroborate the hypothesis that belowground C input plays a larger role than residue C in SOM stabilization; but the hypothesis that both residue and root C are preferentially stabilized in microaggregates by enhanced microbial processing was not corroborated.


    To promote the long-term management of agroecosystems as carbon (C) sinks for anthropogenic emissions of CO2, mechanisms of C sequestration need to be better understood and subsequently managed. For example, definitive estimates of the relative contributions of roots versus residues to soil organic C pools in cropping systems are still lacking. Aboveground and belowground plant decomposition dynamics are fundamentally distinct in terms of soil conditions (e.g., temperature and moisture) and interactions with soil microbial systems (Rasse et al. 2005). The influence of roots on soil organic C pools could be relatively greater than the influence of aboveground C inputs because active roots are continuously releasing a range of organic compounds (i.e., mainly carbohydrates, carboxylic acids, and amino acids) into the rhizosphere (Oades 1978; Michulnas et al., 1985). Yet, belowground inputs are generally assumed to parallel aboveground net primary productivity. Recent papers have shown roots to contribute more to soil C and have suggested that roots decay in soil slower than aboveground plant parts, due to the intrinsic biochemical composition and/or conditions for decomposition for belowground biomass (Balesdent and Balabane 1996; Puget and Drinkwater 2001).
    Plant roots also influence soil organic matter (SOM) stabilization via their role in soil aggregate dynamics. In the rhizosphere, roots physically enmesh soil particles, while exudates stimulate microbial biomass that in turn synthesizes polymers that act as binding agents (Tisdall and Oades, 1979; Jastrow et al., 1998). Gale et al. (2000) and Puget and Drinkwater (2001) have reported the potential importance of plant roots and exudates to the stabilization of aggregate-associated SOM. Still, few studies have investigated the mechanisms of residue- versus root-derived C stabilization in situ mainly because of the difficulties involved in quantifying belowground biomass production, turnover, and exudation.
    Many studies have demonstrated that the soil microbial community is a key regulator of soil C and N cycling. Plant roots, exudates, and sloughed off root material, which are major sources of C and N input to soil, are readily available C and N sources for microorganisms. Microbial immobilization of rhizodeposit-derived C and N, followed by the release of microbial biomass C and N with cell death, and subsequent release of mineral N is an ongoing process during cover crop growth (Coleman et al. 1978). Hence, microorganisms preferentially colonize the rhizosphere, making the rhizosphere an area of intense activity with specific biological, chemical, and physical characteristics (Lynch 1990).
    Recently, soil microaggregates-within-macroaggregates have been shown to be microenvironments within the soil structure, where SOM is preferentially stabilized (Denef et al. 2004; Kong et al. 2005). The physico-chemical characteristics of soil aggregates, especially microaggregates, in conjunction with the high concentration of C and N in the rhizosphere determine the distribution and activity of microbial populations. In turn, as the abundance of microorganisms utilizing rhizodeposits increases during cover crop growth, different microenvironments form as a result of interactions between minerals and microbial-processed rhizodeposits (Harris et al. 1963). This perpetuating cycle is expected to facilitate greater microbial C turnover and stabilization as well as more efficient N cycling (i.e., greater mineral N availability and reduced N loss) in the microaggregate of the rhizosphere. Furthermore, changes in physical and chemical soil properties that occur as a result of agricultural management, and subsequent changes in microbial community composition, in turn, influence soil processes (Schimel 1995).

    Project objectives:

    Few studies have elucidated the underlying mechanisms of the short- and long-term effects of cover crops on the relationship between soil structural properties, nutrient cycling, and microbial community structure and function. Hence, the main objectives of this study were:

    Objective1: To elucidate the role of aggregates in stabilizing residue-derived C compared to root-derived C across different cropping systems.

    Objective2: To identify and quantify the microbial communities (e.g., nitrifying and denitrifying populations) associated with overall C stabilization and N cycling within soil microenvironments across different cropping systems.

    Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.