Bacterial and Fungal Contributions to Carbon Sequestration in Agroecosystems

This paper reviews the current knowledge of microbial processes affecting C sequestration in agroecosystems. The microbial contribution to soil C storage is directly related to microbial community dynamics and the balance between formation and degradation of microbial byproducts. Soil microbes also indirectly influence C cycling by improving soil aggregation, which physically protects soil organic matter (SOM). Consequently, the microbial contribution to C sequestration is governed by the interactions between the amount of microbial biomass, microbial community structure, microbial byproducts, and soil properties such as texture, clay mineralogy, pore-size distribution, and aggregate dynamics. The capacity of a soil to protect microbial biomass and microbially derived organic matter (MOM) is directly and/or indirectly (i.e., through physical protection by aggregates) related to the reactive properties of clays. However, the stabilization of MOM in the soil is also related to the efficiency with which microorganisms utilize substrate C and the chemical nature of the byproducts they produce. Crop rotations, reduced or no-tillage practices, organic farming, and cover crops increase total microbial biomass and shift the community structure toward a more fungal-dominated community, thereby enhancing the accumulation of MOM. A quantitative and qualitative improvement of SOM is generally observed in agroecosystems favoring a fungal-dominated community, but the mechanisms leading to this improvement are not completely understood. Gaps within our knowledge on MOM-C dynamics and how they are related to soil properties and agricultural practices are identified. GREATER THAN two-thirds of the organic C stored in terrestrial ecosystems is contained in SOM, with the net flux of C from soils to the atmosphere being on the order of 60 Pg C yr (Schlesinger, 1997). The historical loss of soil C due to intensive cultivation is estimated to be about 55 Pg C or 25% of the original C present in virgin, uncultivated soils, and has contributed significantly to CO2 release to the atmosphere on a global scale (Cole et al., 1997). The potential for agricultural soils to regain some of this lost C is being evaluated as a means to improve soil fertility, reduce erosion, and mitigate CO2 emissions. Increasing the potential for agricultural soils to sequester C requires a thorough understanding of the underlying processes and mechanisms controlling soil C levels, for which a great deal of knowledge already exists. Previous reviews have examined the relationships between microbial communities and SOM decomposition (Scow, 1997), management controls on soil C (Paustian et al., 1997), and the macromolecular composition of SOM (Kogel-Knabner, 2002). Here, we focus specifically on how soil bacteria and fungi may differentially influence the formation and stabilization of different SOM components in agricultural soils via differences in metabolism, the recalcitrance of microbial products, and interactions with soil physical properties (i.e., texture, mineralogy, and structure). Soil C levels are fundamentally determined by the balance between organic matter inputs, primarily as plant residues, roots, and root exudates, and organic matter losses due to decomposition, erosion, and leaching. Bacteria and fungi generally comprise .90% of the total soil microbial biomass, and they are responsible for the majority of SOM decomposition. Since soil microbial communities are key regulators of SOM dynamics and nutrient availability, shifts in microbial community composition and function (e.g., substrate utilization) in response to different agricultural management practices may play an important role in determining rates of C loss from the soil. The ratio of fungal:bacterial biomass has been shown to be particularly sensitive to soil disturbance, with lower ratios associated with increased intensity of cultivation (Bailey et al., 2002; Beare et al., 1992; Frey et al., 1999), increased grazing pressure (Bardgett et al., 1996, 1998), and increased N fertilization inputs (Bardgett and McAlister, 1999; Bardgett et al., 1996, 1999; Frey et al., 2004). In addition, fungal: bacterial biomass ratios were found to increase with successional age in a semiarid grassland community (Klein et al., 1996) and along an Alaskan forest chronosequence (Ohtonen et al., 1999). Substrate quality also alters fungal:bacterial ratios, with low quality substrates (high C/N) favoring fungi and high quality (low C/N) substrates favoring bacteria (Bossuyt et al., 2001). Organic C taken up by the microbial biomass is partitioned between microbial cell biomass production, metabolite excretion, and respiration (Fig. 1). The degree to which MOM accumulates in soil depends on a balance between production and decomposition of microbial products, that is: (1) the microbial growth efficiency (MGE), the efficiency with which substrates are incorporated into bacterial and fungal biomass and byproducts, (2) the degree of protection of microbial biomass in the soil structure, and (3) the rate at which bacterial and fungal byproducts are decomposed by other microorganisms. The proportion of substrate C retained as biomass versus respired as CO2 depends on MGE and the degree of protection of microbial biomass; the lower the MGE or the less protected the biomass, the more MOM-C is lost as CO2 (Fig. 1, Step I). Substrate C can J. Six and K.M. Batten, Dep. of Plant Sciences, Univ. of California, Davis, CA 95616; S.D. Frey and R.K. Thiet, Dep. of Natural Resources, Univ. of New Hampshire, Durham, NH 03824. Received 1 Nov. 2004. *Corresponding author ( jwsix@ucdavis.edu). Published in Soil Sci. Soc. Am. J. 70:555–569 (2006). Soil Biology & Biochemistry doi:10.2136/sssaj2004.0347 a Soil Science Society of America 677 S. Segoe Rd., Madison, WI 53711 USA Abbreviations: CT, conventional tillage; LF, light fraction; MAP, mean annual precipitation; MAT, mean annual temperature; MGE, microbial growth efficiency; MOM, microbially derived organic matter; MT, minimum tillage; NT, no-tillage; POM, plant-derived organic matter; SOM, soil organic matter. R e p ro d u c e d fr o m S o il S c ie n c e S o c ie ty o f A m e ri c a J o u rn a l. P u b lis h e d b y S o il S c ie n c e S o c ie ty o f A m e ri c a . A ll c o p y ri g h ts re s e rv e d . 555 Published online February 27, 2006