# Multi-Year Monitoring of Ecosystem Metabolism in Two Branches of a Cold-Water Stream
## 1 Introduction  
Freshwater biodiversity and ecosystem function are vulnerable to climate change [1, 2, 3, 4]. The major impacts of climate change on stream systems are likely to cause alterations in water temperature, light regime due to shifting phenological patterns in watersheds, and hydrological function because of changing precipitation patterns [5]. These changes are projected to have impacts on water quality [6, 7, 8] and are expected to influence individual organisms, populations, and communities [9], substantially impacting food webs [10]. Since their value in providing ecosystem services (such as nutrient cycling, water purification, carbon sequestration, and recreational opportunities) and the impacts that climate change may have on these resources, there must be long-term monitoring of these systems [11]. Climate change is especially likely to have major effects on cold-water streams [12], with the impact depending on the spatial scale examined [13]. Warming temperatures in cold-water streams may influence stendthermal organisms that often occupy these habitats, potentially resulting in their replacement with more thermally tolerant species [14, 15]. There is a particular concern about the potential loss of cold-water fish species because of their importance for recreational and commercial fisheries [16, 17, 18, 19, 20]. While many cold-water systems are fed by groundwater, climate change may result in increasing groundwater temperatures or a decline in groundwater input leading to increasing stream temperatures [21, 22, 23]. Ecosystem metabolism measures the collective metabolic activity of all of the organisms in an ecosystem [24, 25]. In stream systems, ecosystem metabolism is most often based on changes in the oxygen content of the water related to two metabolic processes: photosynthesis and respiration [26, 27, 28]. [PERSON] et al. [29] provide a series of expected changes to ecosystem metabolism to a range of environmental stressors such as toxic chemicals, channelization and nutrient enrichment, and natural variation. [PERSON] et al. [5] providedan overview of the drivers of ecosystem metabolism, including light, heat, allochthonous inputs, and hydrologic disturbance, and developed a set of recommendations for additional research necessary to better characterize these drivers. Since ecosystem metabolism varies with differences in annual climatic patterns, climate change is also likely to influence stream metabolism [30]. [PERSON] et al. [31] reviewed how climate change could influence aquatic ecosystem metabolism. They suggested that new and more affordable instrumentation will increase our understanding of how processes such as climate change and management actions influence ecosystem metabolism. Using ecosystem metabolism in streams has been suggested as a measure of ecosystem health, since it can be influenced by pollution, eutrophication, alterations of the physical stream habitat, drought, salinization, acidification, and land use [32; 33; 34]. For example, [PERSON] et al. [35] indicated that ecosystem metabolism could be used as a means to measure the response of rivers to changes in minimum environmental flows. Human land use can influence both the level and variability of stream metabolism [36], and stream metabolism has been used to compare agricultural catchments employing different best management practices [37]. Several studies have suggested using stream metabolism measures to better manage stream ecosystems [5; 30; 38]. The components of ecosystem metabolism include gross primary production (GPP), ecosystem respiration (ER), and the balance between these, net ecosystem production (NEP). GPP and ER play a significant role in organic carbon fluxes in stream systems [39]. Warming temperatures associated with climate change are likely to result in streams becoming more heterotrophic and contributing more CO\({}_{2}\) to the atmosphere [40; 41].