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1. Simulating measurable ecosystem carbon and nitrogen dynamics with the mechanistically defined MEMS 2.0 model

   https://doi.org/10.5194/bg-18-3147-2021  

   Zhang, Yao; Lavallee, Jocelyn M.; Robertson, Andy D.; Even, Rebecca; Ogle, Stephen M.; Paustian, Keith; Cotrufo, M. Francesca (January 2021, Biogeosciences)

   null (Ed.)

   Abstract. For decades, predominant soil biogeochemical models have used conceptual soil organic matter (SOM) pools and only simulated them to a shallow depthin soil. Efforts to overcome these limitations have prompted the development of the new generation SOM models, including MEMS 1.0, which representsmeasurable biophysical SOM fractions, over the entire root zone, and embodies recent understanding of the processes that govern SOM dynamics. Herewe present the result of continued development of the MEMS model, version 2.0. MEMS 2.0 is a full ecosystem model with modules simulating plantgrowth with above- and belowground inputs, soil water and temperature by layer, decomposition of plant inputs and SOM, and mineralization andimmobilization of nitrogen (N). The model simulates two commonly measured SOM pools – particulate and mineral-associated organic matter (POM andMAOM, respectively). We present results of calibration and validation of the model with several grassland sites in the US. MEMS 2.0 generallycaptured the soil carbon (C) stocks (R2 of 0.89 and 0.6 for calibration and validation, respectively) and their distributions between POM andMAOM throughout the entire soil profile. The simulated soil N matches measurements but with lower accuracy (R2 of 0.73 and 0.31 for calibrationand validation of total N in SOM, respectively) than for soil C. Simulated soil water and temperature were compared with measurements, and theaccuracy is comparable to the other commonly used models. The seasonal variation in gross primary production (GPP; R2 = 0.83), ecosystemrespiration (ER; R2 = 0.89), net ecosystem exchange (NEE; R2 = 0.67), and evapotranspiration (ET; R2 = 0.71) was wellcaptured by the model. We will further develop the model to represent forest and agricultural systems and improve it to incorporate newunderstanding of SOM decomposition. 

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2. Simulating Global Terrestrial Carbon and Nitrogen Biogeochemical Cycles With Implicit and Explicit Representations of Soil Microbial Activity

   https://doi.org/10.1029/2023MS004156  

   Wieder, William_R; Hartman, Melannie_D; Kyker‐Snowman, Emily; Eastman, Brooke; Georgiou, Katerina; Pierson, Derek; Rocci, Katherine_S; Grandy, A_Stuart (June 2024, Journal of Advances in Modeling Earth Systems)

   Abstract Nutrient limitation is widespread in terrestrial ecosystems. Accordingly, representations of nitrogen (N) limitation in land models typically dampen rates of terrestrial carbon (C) accrual, compared with C‐only simulations. These previous findings, however, rely on soil biogeochemical models that implicitly represent microbial activity and physiology. Here we present results from a biogeochemical model testbed that allows us to investigate how an explicit versus implicit representation of soil microbial activity, as represented in the MIcrobial‐MIneral Carbon Stabilization (MIMICS) and Carnegie‐Ames‐Stanford Approach (CASA) soil biogeochemical models, respectively, influence plant productivity, and terrestrial C and N fluxes at initialization and over the historical period. When forced with common boundary conditions, larger soil C pools simulated by the MIMICS model reflect longer inferred soil organic matter (SOM) turnover times than those simulated by CASA. At steady state, terrestrial ecosystems experience greater N limitation when using the MIMICS‐CN model, which also increases the inferred SOM turnover time. Over the historical period, however, warming‐induced acceleration of SOM decomposition over high latitude ecosystems increases rates of N mineralization in MIMICS‐CN. This reduces N limitation and results in faster rates of vegetation C accrual. Moreover, as SOM stoichiometry is an emergent property of MIMICS‐CN, we highlight opportunities to deepen understanding of sources of persistent SOM and explore its potential sensitivity to environmental change. Our findings underscore the need to improve understanding and representation of plant and microbial resource allocation and competition in land models that represent coupled biogeochemical cycles under global change scenarios. 

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3. Bridging 20 Years of Soil Organic Matter Frameworks: Empirical Support, Model Representation, and Next Steps

   https://doi.org/10.1029/2023JG007964  

   Rocci, Katherine_S; Cotrufo, M_Francesca; Ernakovich, Jessica; Foster, Erika; Frey, Serita; Georgiou, Katerina; Grandy, A_Stuart; Malhotra, Avni; Reich, Peter_B; Schlerman, Else_P; et al (June 2024, Journal of Geophysical Research: Biogeosciences)

   Abstract In the past few decades, there has been an evolution in our understanding of soil organic matter (SOM) dynamics from one of inherent biochemical recalcitrance to one deriving from plant‐microbe‐mineral interactions. This shift in understanding has been driven, in part, by influential conceptual frameworks which put forth hypotheses about SOM dynamics. Here, we summarize several focal conceptual frameworks and derive from them six controls related to SOM formation, (de)stabilization, and loss. These include: (a) physical inaccessibility; (b) organo‐mineral and ‐metal stabilization; (c) biodegradability of plant inputs; (d) abiotic environmental factors; (e) biochemical reactivity and diversity; and (f) microbial physiology and morphology. We then review the empirical evidence for these controls, their model representation, and outstanding knowledge gaps. We find relatively strong empirical support and model representation of abiotic environmental factors but disparities between data and models for biochemical reactivity and diversity, organo‐mineral and ‐metal stabilization, and biodegradability of plant inputs, particularly with respect to SOM destabilization for the latter two controls. More empirical research on physical inaccessibility and microbial physiology and morphology is needed to deepen our understanding of these critical SOM controls and improve their model representation. The SOM controls are highly interactive and also present some inconsistencies which may be reconciled by considering methodological limitations or temporal and spatial variation. Future conceptual frameworks must simultaneously refine our understanding of these six SOM controls at various spatial and temporal scales and within a hierarchical structure, while incorporating emerging insights. This will advance our ability to accurately predict SOM dynamics. 

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4. Clarifying the evidence for microbial‐ and plant‐derived soil organic matter, and the path toward a more quantitative understanding

   https://doi.org/10.1111/gcb.16413  

   Whalen, Emily D.; Grandy, A. Stuart; Sokol, Noah W.; Keiluweit, Marco; Ernakovich, Jessica; Smith, Richard G.; Frey, Serita D. (December 2022, Global Change Biology)

   Abstract Predicting and mitigating changes in soil carbon (C) stocks under global change requires a coherent understanding of the factors regulating soil organic matter (SOM) formation and persistence, including knowledge of the direct sources of SOM (plants vs. microbes). In recent years, conceptual models of SOM formation have emphasized the primacy of microbial‐derived organic matter inputs, proposing that microbial physiological traits (e.g., growth efficiency) are dominant controls on SOM quantity. However, recent quantitative studies have challenged this view, suggesting that plants make larger direct contributions to SOM than is currently recognized by this paradigm. In this review, we attempt to reconcile these perspectives by highlighting that variation across estimates of plant‐ versus microbial‐derived SOM may arise in part from methodological limitations. We show that all major methods used to estimate plant versus microbial contributions to SOM have substantial shortcomings, highlighting the uncertainty in our current quantitative estimates. We demonstrate that there is significant overlap in the chemical signatures of compounds produced by microbes, plant roots, and through the extracellular decomposition of plant litter, which introduces uncertainty into the use of common biomarkers for parsing plant‐ and microbial‐derived SOM, especially in the mineral‐associated organic matter (MAOM) fraction. Although the studies that we review have contributed to a deeper understanding of microbial contributions to SOM, limitations with current methods constrain quantitative estimates. In light of recent advances, we suggest that now is a critical time to re‐evaluate long‐standing methods, clearly define their limitations, and develop a strategic plan for improving the quantification of plant‐ and microbial‐derived SOM. From our synthesis, we outline key questions and challenges for future research on the mechanisms of SOM formation and stabilization from plant and microbial pathways. 

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5. Can switchgrass increase carbon accrual in marginal soils? The importance of site selection

   https://doi.org/10.1111/gcbb.12777  

   Kasanke, Christopher P.; Zhao, Qian; Bell, Sheryl; Thompson, Allison M.; Hofmockel, Kirsten S. (December 2020, GCB Bioenergy)

   Abstract Most soil carbon (C) is in the form of soil organic matter (SOM), the composition of which is controlled by the plant–microbe–soil continuum. The extent to which plant and microbial inputs contribute to persistent SOM has been linked to edaphic properties such as mineralogy and aggregation. However, it is unknown how variation in plant inputs, microbial community structure, and soil physical and chemical attributes interact to influence the chemical classes that comprise SOM pools. We used two long‐term biofuel feedstock field experiments to test the influence of cropping systems (corn and switchgrass) and soil characteristics (sandy and silty loams) on microbial selection and SOM chemistry. Cropping system had a strong influence on water‐extractable organic C chemistry with perennial switchgrass generally having a higher chemical richness than the annual corn cropping system. Nonetheless, cropping system was a less influential driver of soil microbial community structure and overall C chemistry than soil type. Soil type was especially influential on fungal community structure and the chemical composition of the chloroform‐extractable C. Although plant inputs strongly influence the substrates available for decomposition and SOM formation, total C and nitrogen (N) did not differ between cropping systems within either site. We conclude this is likely due to enhanced microbial activity under the perennial cropping system. Silty soils also had a higher activity of phosphate and C liberating enzymes. After 8 years, silty loams still contained twice the total C and N as sandy loams, with no significant response to biofuel cropping system inputs. Together, these results demonstrate that initial site selection is critical to plant–microbe interactions and substantially impacts the potential for long‐term C accrual in soils under biofuel feedstock production. 

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