[1] Methane (CH 4 ) represents a major product of organic matter decomposition in lakes. Once produced in the sediments, CH 4 can be either oxidized or emitted as a greenhouse gas to the atmosphere. Lakes represent an important source of atmospheric CH 4 , but the relative magnitudes of the internal pathways that lead to CH 4 emissions are not yet clear. We quantified internal cycling and methane emissions in three lakes during summer stratification. These methane budgets included: sediment release of CH 4 at different depths; water column transport patterns and methane oxidation; methane storage in the water column; and methane emissions to the atmosphere by diffusion and ebullition. The contribution of CH 4 carbon, via oxidation by methanotrophic bacteria, to pelagic food webs was also estimated. Despite the very low concentration of CH 4 in surface waters, shallow, epilimnetic sediments were major contributors of CH 4 to the atmosphere. While 51-80% of the CH 4 produced in deep sediments was oxidized in the water column, most of the CH 4 released from shallow sediment escaped oxidation and reached the atmosphere. Epilimnetic sediments accounted for 100% of CH 4 emitted during summer stratification, and 14-76% considering the release of CH 4 stored in deep water layers during lake circulation after the stratification period; diffusive emission accounted for 26-48% and ebullition the remainder. These results indicate that it is important to address transport rates of CH 4 from the shallow sediment along with the production-consumption processes when trying to understand methane dynamics and the regulation of lake methane emissions.Citation: Bastviken, D., J. J. Cole, M. L. Pace, and M. C. Van de Bogert (2008), Fates of methane from different lake habitats: Connecting whole-lake budgets and CH 4 emissions,

Ecosystems are supported by organic carbon from two distinct sources. Endogenous carbon is produced by photosynthesis within an ecosystem by autotrophic organisms. Exogenous carbon is produced elsewhere and transported into ecosystems. Consumers may use exogenous carbon with consequent influences on population dynamics, predator-prey relationships and ecosystem processes. For example, exogenous inputs provide resources that may enhance consumer abundance beyond levels supported by within-system primary production. Exogenous fluxes of organic carbon to ecosystems are often large, but this material is recalcitrant and difficult to assimilate, in contrast to endogenously produced organic matter, which is used more easily. Here we show, by the experimental manipulation of dissolved inorganic (13)C in two lakes, that internal primary production is insufficient to support the food webs of these ecosystems. Additions of NaH(13)CO(3) enriched the (13)C content of dissolved inorganic carbon, particulate organic carbon, zooplankton and fish. Dynamics of (13)C indicate that 40-55% of particulate organic carbon and 22-50% of zooplankton carbon are derived from terrestrial sources, showing that there is significant subsidy of these ecosystems by organic carbon produced outside their boundaries.

Organic carbon inputs from outside of ecosystem boundaries potentially subsidize recipient food webs. Four whole-lake additions of dissolved inorganic 13C were made to reveal the pathways of subsidies to lakes from terrestrial dissolved organic carbon (t-DOC), terrestrial particulate organic carbon (t-POC) and terrestrial prey items. Terrestrial DOC, the largest input, was a major subsidy of pelagic bacterial respiration, but little of this bacterial C was passed up the food web. Zooplankton received <2% of their C from the t-DOC to bacteria pathway. Terrestrial POC significantly subsidized the production of both zooplankton and benthic invertebrates, and was passed up the food web to Chaoborus and fishes. This route supplied 33-73% of carbon flow to zooplankton and 20-50% to fishes in non-fertilized lakes. Terrestrial prey, by far the smallest input, provided some fishes with >20% of their carbon. The results show that impacts of cross-ecosystem subsidies depend on characteristics of the imported material, the route of entry into the food web, the types of consumers present, and the productivity of the recipient system.

Significant improvements have been made in estimating gross primary production (GPP), ecosystem respiration (R), and net ecosystem production (NEP) from diel, “free‐water” changes in dissolved oxygen (DO). Here we evaluate some of the assumptions and uncertainties that are still embedded in the technique and provide guidelines on how to estimate reliable metabolic rates from high‐frequency sonde data. True whole‐system estimates are often not obtained because measurements reflect an unknown zone of influence which varies over space and time. A minimum logging frequency of 30 min was sufficient to capture metabolism at the daily time scale. Higher sampling frequencies capture additional pattern in the DO data, primarily related to physical mixing. Causes behind the often large daily variability are discussed and evaluated for an oligotrophic and a eutrophic lake. Despite a 3‐fold higher day‐to‐day variability in absolute GPP rates in the eutrophic lake, both lakes required at least 3 sonde days per week for GPP estimates to be within 20% of the weekly average. A sensitivity analysis evaluated uncertainties associated with DO measurements, piston velocity (k), and the assumption that daytime R equals nighttime R. In low productivity lakes, uncertainty in DO measurements and piston velocity strongly impacts R but has no effect on GPP or NEP. Lack of accounting for higher R during the day underestimates R and GPP but has no effect on NEP. We finally provide suggestions for future research to improve the technique.

We assembled data from a global network of automated lake observatories to test hypotheses regarding the drivers of ecosystem metabolism. We estimated daily rates of respiration and gross primary production (GPP) for up to a full year in each lake, via maximum likelihood fits of a free-water metabolism model to continuous highfrequency measurements of dissolved oxygen concentrations. Uncertainties were determined by a bootstrap analysis, allowing lake-days with poorly constrained rate estimates to be down-weighted in subsequent analyses. GPP and respiration varied considerably among lakes and at seasonal and daily timescales. Mean annual GPP and respiration ranged from 0.1 to 5.0 mg O 2 L 21 d 21 and were positively related to total phosphorus but not dissolved organic carbon concentration. Within lakes, significant day-to-day differences in respiration were common despite large uncertainties in estimated rates on some lake-days. Daily variation in GPP explained 5% to 85% of the daily variation in respiration after temperature correction. Respiration was tightly coupled to GPP at a daily scale in oligotrophic and dystrophic lakes, and more weakly coupled in mesotrophic and eutrophic lakes. Background respiration ranged from 0.017 to 2.1 mg O 2 L 21 d 21 and was positively related to indicators of recalcitrant allochthonous and autochthonous organic matter loads, but was not clearly related to an indicator of the quality of allochthonous organic matter inputs.Gross primary production (GPP) and respiration are perhaps the two most fundamental processes in ecosystems. At the cellular or organismal level, they describe biochemical pathways that make organic carbon molecules and energy available to cells. When these cellular processes are integrated across an entire ecosystem, the result-ecosystemlevel GPP, ecosystem respiration, or collectively ecosystem metabolism-describes biogeochemical and trophic processes occurring at the system level.There is substantial interest in understanding the controls on ecosystem metabolism in aquatic (Mulholland et al.