Freshwaters inextricably link flows of carbon between the land, oceans, and atmosphere. Resulting carbon dioxide supersaturation relative to the atmosphere in most of the world’s lakes and rivers has long been assumed to come from aerobic respiration. Although carbon dioxide also comes from the oxidation of anaerobically produced methane, this has been largely ignored within freshwaters. Here, we use stable carbon isotopes of carbon dioxide and methane to show that a nontrivial proportion of the total dissolved carbon dioxide in a tropical flood pulse lake comes from methane oxidation. Seasonal pulses of flooding are common in the tropics, suggesting that coupled methane production and oxidation likely contribute more broadly to flows of carbon between the land, understudied tropical freshwaters, and atmosphere.

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Large river systems, particularly those shared by developing nations in the tropics, exemplify the interconnected and thorny challenges of achieving sustainability with respect to food, energy, and water. Numerous countries in South America, Africa, and Asia have committed to hydropower as a means to supply affordable energy with net-zero emissions by 2050. The placement, size, and number of dams within each river basin network have enormous consequences for not only the ability to produce electricity but also how they affect people whose livelihoods depend on the local river systems.

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Stream/river carbon dioxide (CO₂) emission has significant spatial and seasonal variations critical for understanding its macroecosystem controls and plumbing of the terrestrial carbon budget. We relied on direct fluvial CO₂ partial pressure measurements and seasonally varying gas transfer velocity and river network surface area estimates to resolve reach-level seasonal variations of the flux at the global scale. The percentage of terrestrial primary production (GPP) shunted into rivers that ultimately contributes to CO₂ evasion increases with discharge across regions, due to a stronger response in fluvial CO₂ evasion to discharge than GPP. This highlights the importance of hydrology, in particular water throughput, in terrestrial–fluvial carbon transfers and the need to account for this effect in plumbing the terrestrial carbon budget.

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Headwater streams are critical for freshwater ecosystems. Global and continental studies consistently show major dams as dominant sources of hydrological stress threatening biodiversity in the world’s major rivers, but cumulative impacts from small artificial impoundments (SAIs) concentrated in headwater streams have rarely been acknowledged. Using the Murray Darling River basin (Australia) and the Arkansas River basin (US) as case studies, we examined the hydrological impacts of SAIs. The extent of their influence is considerable, altering hydrology in 280–380% more waterways as compared to major dams. Hydrological impacts are concentrated in smaller streams (catchment area <100 km²), raising concerns that the often diverse and highly endemic biota found in these systems may be under threat. Adjusting existing biodiversity planning and management approaches to address the cumulative effects of many small and widely distributed artificial impoundments presents a rapidly emerging challenge for ecologically sustainable water management.

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Freshwater ecosystems are facing a deepening biodiversity crisis. Developing robust indicators to assess ecological integrity across large spatial scales and identifying the specific threats and pathways of impairment are thus critically needed if we are to inform freshwater conservation strategies. This paper presents the first comprehensive threat assessment across the Colorado River Basin – one of the largest and most endangered river basins in North America – using a spatial framework accounting for the wide range of human activities (land uses, transportation infrastructure, exploitative activities, water withdrawals), pathways (local footprint, overland runoff, upstream cumulative effects), and spatial extent of influence (valley bottom, catchment and river network) known to affect the ecological integrity of riverine ecosystems. In addition to its implications for the conservation and management of the highly imperiled Colorado River Basin, this case study illustrates how multi-faceted threat mapping can be used to assess the ecological integrity of riverine ecosystems in the absence of spatially extensive in situ measurements.

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