Aerobic methane-oxidizing bacteria (MOB) substantially reduce methane fluxes from freshwater sediments to the atmosphere. Their metalloenzyme methane monooxygenase (MMO) catalyses the first oxidation step converting methane to methanol. Its most prevalent form is the copper-dependent particulate pMMO, however, some MOB are also able to express the iron-containing, soluble sMMO under conditions of copper scarcity. So far, the link between copper availability in different forms and biological methane consumption in freshwater systems is poorly understood. Here, we present high-resolution profiles of MOB abundance and pMMO and sMMO functional genes in relation to copper, methane and oxygen profiles across the oxic-anoxic boundary of a stratified lake. We show that even at low nanomolar copper concentrations, MOB species containing the gene for pMMO expression are present at high abundance. The findings highlight the importance of copper as a micronutrient for MOB species and the potential usage of copper acquisition strategies, even under conditions of abundant iron, and shed light on the spatial distribution of these microorganisms.

We present a new potentiometric sensor principle and a calibration protocol for in situ profiling of dissolved CO₂ with high temporal and spatial resolution in fresh water lakes. The sensor system is based on the measurement of EMF between two solid-contact ion selective electrodes (SC-ISEs), a hydrogen ion selective and a carbonate selective sensor. Since it relies on SC-ISEs, it is insensitive to changes in pressure, thus suitable for in situ studies. Also, as it offers a response time (t_95%) of <10 s, it allows for profiling applications at high spatial resolution. The proposed optimum in situ protocol accounts for the continuous drift and change in offset that remains a challenge during profiling in natural waters. The fast response resolves features that are usually missed by standard methods like the classical Severinghaus CO₂ probe. In addition, the insensitivity of the presented setup to dissolved sulfide allows also for measurements in anoxic zones of eutrophic systems. Highly resolved CO₂ concentration profiles obtained by the novel and robust SC-ISE setup along with the developed optimum in situ protocol allow investigating hotspots of biogeochemical processes, such as mineralization and primary production in the water column and help improving estimates for CO₂ turnover in freshwater systems.

Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth’s natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870, but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an ‘unusual’ methane monooxygenase (MMO), which was only distantly related to ‘classical’ MMO of gamma-proteobacterial methanotrophs. We now correct this assignment and show that Crenothrix encode a typical gamma-proteobacterial PmoA. Stable isotope labeling in combination swith single-cell imaging mass spectrometry revealed methane-dependent growth of the lacustrine Crenothrix with oxygen as well as under oxygen-deficient conditions. Crenothrix genomes encoded pathways for the respiration of oxygen as well as for the reduction of nitrate to N₂O. The observed abundance and planktonic growth of Crenothrix suggest that these methanotrophs can act as a relevant biological sink for methane in stratified lakes and should be considered in the context of environmental removal of methane.

Tropical inland waters are increasingly recognized for their role in the global carbon cycle, but uncertainty about the effects of such systems on the transported organic matter remains. The seasonal interactions between river, floodplain, and vegetation result in highly dynamic systems, which can exhibit markedly different biogeochemical patterns throughout a flood cycle. In this study, we determined rates and governing processes of organic matter turnover. Multi-probes in the Barotse Plains, a pristine floodplain in the Upper Zambezi River (Zambia), provided a high-resolution data set over the course of a hydrological cycle. The concentrations of oxygen, carbon dioxide, dissolved organic carbon, and suspended particulate matter in the main channel showed clear hysteresis trends with expanding and receding water on the floodplain. Lower oxygen and suspended matter concentrations prevailed at longer travel times of water in the floodplain, while carbon dioxide and dissolved organic carbon concentrations were higher when the water spent more time on the floodplain. Maxima of particulate loads occurred before highest water levels, whereas the maximum in dissolved organic carbon load occurred during the transition of flooding and flood recession. Degradation of terrestrial organic matter occurred mainly on the floodplain at increased floodplain residence times. Our data suggest that floodplains become more intense hotspots at prolonged travel time of the flood pulse over the floodplain.