## 3 Monitoring of C and Water Cycling in Terrestrial Ecosystems
### CO\({}_{2}\) Concentration Measurements, Data Assimilation and CarbonTracker  
Observations of CO\({}_{2}\) over the continent within the atmospheric boundary layer reflect exchange processes occurring at the surface at a regional scale (10\({}^{2}\)-10\({}^{5}\) km\({}^{2}\)). The flux information contained in CO\({}_{2}\) concentration data represents footprints of up to 10\({}^{5}\) km\({}^{2}\)[75, 76, 77], which is several orders of magnitude larger than the direct EC-flux footprint. These measurements form a record of integrated net CO\({}_{2}\) exchange from multiple processes, geographic areas, and times [78]. CO\({}_{2}\) concentration measurements are made from tall towers [79-81] or balloons that reach the top of the planetary boundary layer (PBL) of the Earth. These measurements therefore provide significant information to upscale from site to region. Moreover, the number of CO\({}_{2}\) concentration measurements above the land surface, made by either tower or aircraft, is steadily increasing. Data are collected by numerous agencies around the world, for instance, the National Oceanic and Atmospheric Administration's (NOAA's) Earth System Research Laboratory (ESRL) monitors CO\({}_{2}\) in the atmosphere as a contribution to the North American Carbon Program (NACP) [82]. In addition, [PERSON] _et al._[78] suggest that direct satellite observations of CO\({}_{2}\) are available already for the upper troposphere, whereas near-surface CO\({}_{2}\) from space will become available within several years to augment the current efforts.  
Previous efforts to interpret the signal of regional CO\({}_{2}\) exchange making use of tower concentration data have focused on simple one-dimensional PBL budgets that rely on gradients in CO\({}_{2}\) concentrations between the PBL and the free troposphere [77,79,83-85]. These methods are limited to monthly resolution because of the need to smooth and average over several synoptic events [86].  
The atmosphere integrates surface fluxes over many temporal and spatial scales and links scalar sources and sinks with concentrations and fluxes. This principle has been successfully used to develop inverse models to estimate annual carbon budgets [87-90]. However, due to model limitations and paucity of continental CO\({}_{2}\) observations these studies have yielded carbon fluxes only at coarse resolution, over large spatial regions (i.e., at continental scale, [91]). Recently, [PERSON] [89] and [PERSON] [90] showed that a large set of atmospheric inverse model results were inconsistent with free troposphere CO\({}_{2}\) concentration. Transport biases are one of the largest unknown sources of error in flux inversions [88].  
A powerful way to use all these CO\({}_{2}\) data is in a data assimilation system, which combines diverse data and models into a unified description of a physical/biogeochemical system consistent with observations [13]. Such a new data assimilation system called CarbonTracker, has been built in the NOAA ESRL, using a state-of-the-art atmospheric transport model coupled to an ensemble Kalman filter [78]. The first release of CarbonTracker marks a significant step in our ability to monitor monthly-month surface sources and sinks of CO\({}_{2}\)[78],with all results, data and code of CarbonTracker freely available from NOAA ERSL's CarbonTracker web site, [[http://carbontracker.noaa.gov](http://carbontracker.noaa.gov)]([http://carbontracker.noaa.gov](http://carbontracker.noaa.gov)).