Integrating microbial ecology into ecosystem models: challenges and priorities

Abstract

Microbial communities can potentially mediate feedbacks between global change and ecosystem function, owing to their sensitivity to environmental change and their control over critical biogeochemical processes. Numerous ecosystem models have been developed to predict global change effects, but most do not consider microbial mechanisms in detail. In this idea paper, we examine the extent to which incorporation of microbial ecology into ecosystem models improves predictions of carbon (C) dynamics under warming, changes in precipitation regime, and anthropogenic nitrogen (N) enrichment. We focus on three cases in which this approach might be especially valuable: temporal dynamics in microbial responses to environmental change, variation in ecological function within microbial communities, and N effects on microbial activity. Four microbially-based models have addressed these scenarios. In each case, predictions of the microbial-based models differ-sometimes substantially-from comparable conventional models. However, validation and parameterization of model performance is challenging. We recommend that the development of microbial-based models must occur in conjunction with the development of theoretical frameworks that predict the temporal responses of microbial communities, the phylogenetic distribution of microbial functions, and the response of microbes to N enrichment.

Microbial dormancy improves development and experimental validation of ecosystem model

“…Although the importance of microbial community composition may vary with spatiotemporal scales (Schimel and Schaeffer, 2012), the inclusion of microbial physiology is essential to confidently project feedbacks between climate change and carbon cycle (Bradford, 2013). Continued development is needed to bring microbial physiology into global climate and ecosystem models (Todd-Brown et al, 2012;Treseder et al, 2012;Schimel, 2013).…”

“…Microbially controlled SOM decomposition is increasingly represented in ecosystem models (Treseder et al, 2012). Other vital common evolutionary traits, however, such as microbial dormancy and community shifts are not yet represented (Jones and Lennon, 2010;Weedon et al, 2013).…”

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

“…Extensive bodies of work have provided detailed insights into the mechanism(s) on the transformation of soil C pools by extracellular enzymes excreted into the soil by microbes, thus allowing researchers to develop enzyme-driven ESMs that provide a better fit to observations, especially in changing environments (Allison et al, 2010;Treseder et al, 2012;Wieder et al, 2013;Hararuk et al, 2015). Processlevel analyses such as respiration and enzymatic transformation of added substrate are used as a proxy of microbial function, which gives valuable insight into overall microbial-mediated transformations in soils.…”

Microbial community modeling using reliability theory

“…In ecosystem models, microbial activity is often approached as a 'black box' (for example, a single rate for decomposition), despite continuing evidence supporting the need for more detail (for example, Schimel, 2001;Allison and Martiny, 2008;Treseder et al, 2012). The range of scales (micrometer to global) and the magnitude of microbial diversity present challenges to the development of more detailed models, but the evidence for differences in microorganisms' responses to disturbances suggest that these challenges must be met.…”