Summary: Recent advances in the partitioning of autotrophic from heterotrophic respiration processes in soils in conjunction with new high temporal resolution soil respiration data sets offer insights into biotic and environmental controls of respiration. Besides temperature, many emerging controlling factors have not yet been incorporated into ecosystem‐scale models. We synthesize recent research that has partitioned soil respiration into its process components to evaluate effects of nitrogen, temperature and photosynthesis on autotrophic flux from soils at the ecosystem level. Despite the widely used temperature dependence of root respiration, gross primary productivity (GPP) can explain most patterns of ecosystem root respiration (and to some extent heterotrophic respiration) at within‐season time‐scales. Specifically, heterotrophic respiration is influenced by a seasonally variable supply of recent photosynthetic products in the rhizosphere. The contribution of stored root carbon (C) to root respiratory fluxes also varied seasonally, partially decoupling the proportion of photosynthetic C driving root respiration. In order to reflect recent insights, new hierarchical models, which incorporate root respiration as a primary function of GPP and which respond to environmental variables by modifying C allocation belowground, are needed for better prediction of future ecosystem C sequestration.

Pest and pathogen disturbances are ubiquitous across forest ecosystems, impacting their species composition, structure, and function. Whereas severe abiotic disturbances (e.g., clear-cutting and fire) largely reset successional trajectories, pest and pathogen disturbances cause diffuse mortality, driving forests into nonanalogous system states. Biotic perturbations that disrupt forest carbon dynamics either reduce or enhance net primary production (NPP) and carbon storage, depending on pathogen type. Relative to defoliators, wood borers and invasive pests have the largest negative impact on NPP and the longest recovery time. Forest diversity is an important contributing factor to productivity: NPP is neutral, marginally enhanced, or reduced in high-diversity stands in which a small portion of the canopy is affected (temperate deciduous or mixed forests) but very negative in low-diversity stands in which a large portion of the canopy is affected (western US forests). Pests and pathogens reduce forest structural and functional redundancy, affecting their resilience to future climate change or new outbreaks. Therefore, pests and pathogens can be considered biotic forcing agents capable of causing consequences of similar magnitude to climate forcing factors.