Much of the anthropogenic emissions of greenhouse gases (GHG s) is cycled through the terrestrial biosphere, thereby moving the topic of quantifying the exchange rates between the terrestrial biosphere and the atmosphere of these gases from the margins of traditionally disjointed disciplines such as hydrology, micrometeorology, and plant physiology to a unifying and central research topic in climate science. These fluxes are governed by biophysical processes such as photosynthesis, transpiration, and microbial respiratory processes that have multiple and dynamic drivers such as meteorology, disturbance regimes, and long-term land cover and climate change. These complex processes occur over a broad range of temporal (seconds to decades) and spatial (millimeters to kilometers) scales, complicating efforts to quantify biosphere-atmosphere exchanges over the diverse range of global biomes and necessitating the application of simplifying models to forecast fluxes at the regional and global scales required by climate mitigation and adaptation policymakers.

Over the long history of biophysical research, much progress has been made towards developing appropriate models for the biosphere-atmosphere exchange of GHGs. Many processes are well represented, particularly at the leaf scale. However, many remain poorly understood despite several decades of field measurements, and models still do not perform robustly over coarse spatial scales and long time frames. Indeed, model and parameter uncertainty remains a major contributor to difficulties in constraining the atmospheric budgets of greenhouse gases.

The central objective of this dissertation is to reduce uncertainty in the quantification and up-scaling of the biosphere-atmosphere exchange of greenhouse gases. Naturally, addressing all aspects of this problem remains well beyond the scope of a single dissertation. The compass of this work is to strategically address key research questions through five case studies. In Chapter 1, nocturnal evapotranspiration—a physiological process that had been largely ignored until recent years which is quantified and modeled in three unique ecosystems co-located in central North Carolina, U.S.A. In the second chapter, long-term drivers of evapotranspiration are explored by developing and testing theoretical relationships between plant water use and hydraulic architecture that may be readily incorporated into terrestrial ecosystem models. The third chapter builds on this work by linking key parameters of carbon assimilation models to structural and climatic indices that are well-specified over much of the land surface in an effort to improve model parameterization schemes. The fourth chapter directly addresses questions about the interaction between physiological carbon cycling and disturbance regimes in current and future climates, which are generally poorly represented in terrestrial ecosystem models. And the last chapter explores effluxes of methane and nitrous oxide (which are historically understudied) in addition to CO₂ exchange in a large temperate wetland ecosystem (that is a historically understudied biome). While these five case studies are somewhat distinct investigations in terms of processes and the nature of up-scaling, they are all grounded in the principles of biophysics, are all generally conducted to address exchange rates at the ecosystem scale, and all rely on similar measurement and mathematical modeling techniques.