Managing Agroecosystems for Soil Microbial Carbon Use Efficiency: Ecological Unknowns, Potential Outcomes, and a Path Forward

Abstract

Agricultural systems are increasingly managed for improving soil carbon (C) accumulation. However, there are limits to C returns in agricultural systems that constrain soil C accumulation capacity. Increasing the efficiency of how soil microbes process C is gaining interest as an important management strategy for increasing soil C and is a key feature of soil C dynamics in many new microbial-explicit models. A higher microbial C use efficiency (CUE) may increase C storage while reducing C system losses and is a fundamental trait affecting community assembly dynamics and nutrient cycling. However, the numerous ecological unknowns influencing CUE limit our ability to effectively manage CUE in agricultural soils for greater soil C storage. In this perspective, we consider three complex drivers of agroecosystem CUE that need to be resolved to develop effective C sequestration management practices in the future: (1) the environment as an individual trait moderator versus a filter, (2) microbial community competitive and faciliatory interactions, and (3) spatiotemporal dynamics through the soil profile and across the microbial lifecycle. We highlight ways that amendments, crop rotations, and tillage practices might affect microbial CUE conditions and the variable outcomes of these practices. We argue that to resolve some of the unknowns of CUE dynamics, we need to include more mechanistic, trait-based approaches that capitalize on advanced methods and innovative field research designs within an agroecosystem-specific context. By identifying the management-level determinants of CUE expression, we will be better positioned to optimize CUE to increase soil C storage in agricultural systems.

Keywords: CUE; agriculture; carbon sequestration; crop diversity; microbial biomass; soil ecology; tillage.

Figure 1

Trait moderating and trait filtering across a changing environment. Environmental change influences CUE by (1) modifying the existing community (trait modification) and/or (2) by selecting for a new community with different life histories (trait filtering). The community CUE response depends on whether trait moderating or filtering occurs [Panel (A)]. As an example, high-quality (1/C:N) inputs such as poultry manure may increase the intrinsic CUE of all community members (trait moderating) but may also shift the community toward one dominated by inefficient members (Species B) (trait filtering) [Panel (B)]. At the other end of the resource quality spectrum, applications of high C:N resources such as corn stover might shift the community toward more efficient microbes (Species A). Yet this community may still be C or N limited and thus have a lower CUE relative to its maximum potential. A community-level CUE “sweet spot” may exist in the middle that enhances the efficiency of all members without over-selecting for inefficient microbes or creating resource limitations.

Figure 2

Theoretical temporal dynamics of CUE under different resource inputs and timing. Single additions (arrows) of high-quality (low C:N) inputs early in the season result in a higher initial CUE but faster decomposition rate [Panel (A)]. Without replenishment, the microbial community will experience C limitations more quickly, reducing CUE, biomass production, and increasing biomass recycling [Panels (A,B)]. Such a decline in off-season microbial biomass production counteracts the benefits of a relatively higher early-season CUE associated with higher quality residues. This potentially reduces the overall annual amount of C inputs ending up as microbial stable C. Alternatively, a lower quality input results in a lower initial CUE but continues to provide a C source longer due to slower decomposition. Thus, annual cumulative CUE and biomass production may be relatively greater with lower quality inputs [Panels (A,B)]. Perennial or cover crop systems (repeated inputs) provide a more constant resource, effectively alleviating C limitations throughout the year, allowing microbes to delay metabolic dormancy and maintain a relatively higher CUE.