P>1. The tropical Cerrado savannah, the second-largest South American biome, is undergoing the most rapid land-use change in South America, including a wholesale shift from native vegetation to pasture and cropland. However, the consequences of this development for aquatic ecosystem functioning remain unclear. In this study, we investigated how agriculture affects chemical, physical and biological characteristics of headwater streams in the Brazilian Cerrado, and how these changes relate to an important ecosystem function, i.e. ecosystem metabolism. 2. Three paired samplings of pristine and agricultural streams were conducted considering the most abundant morphotypes of Cerrado streams. Nutrient concentrations, stream morphometry and hydrodynamics, sediment transport, as well as benthic microbial biomass (BMB), and its chlorophyll a (Chl-a) content were measured. In parallel, whole-stream gross primary production (GPP) and community respiration (CR) were estimated using a diel open-channel dissolved O-2 change technique. 3. Agricultural streams had consistently higher nutrient concentrations, less variability in channel morphology, smaller channel cross-sectional areas, smaller transient storage zones, higher current velocities and higher boundary shear stresses than pristine streams. At base flow, agricultural streams exhibited a midstream band of shifting sediments, while pristine streams had stable sediments. Both agricultural and pristine streams were dominated by thick microbial mats. Due to differences in hydrodynamics and sediment stability, these microbial mats covered the entire stream bed in pristine streams, but were restricted to the stream margins in agricultural streams. 4. As a result, BMB of agricultural streams was diminished by a factor of 7.5 compared to pristine streams. Interestingly, CR of agricultural streams was diminished only by a factor of 2.0, because higher BMB-specific respiration efficiencies, potentially due to increased nutrient availability, compensated for lower BMB due to physical stress. Similarly, the 3.3-fold elevated GPP in agricultural compared to pristine streams was only to a minor degree due to increased benthic Chl-a, but mainly a result of 2.4-fold higher Chl-a-specific primary production efficiencies, potentially due to increased nutrient availability. 5. In conclusion, agriculture impacted the studied Cerrado streams through two antagonistic mechanisms: physical stress resulted in decreased BMB and whole-stream CR by preventing BMB accrual in the central streambed, but higher nutrient availability led to increased primary production and respiration efficiencies in marginal zones, as well as higher whole-stream GPP. Finally, measures of whole-stream metabolism were useful indicators of stream ecosystem health and allowed for the differential assessment of the effects of physical stress and eutrophication.
