Cyanobacteria, the most ancient and abundant photoautotrophs on Earth, produce the greenhouse gas methane during photosynthesis.

The prevailing paradigm in aquatic science is that microbial methanogenesis happens primarily in anoxic environments. Here, we used multiple complementary approaches to show that microbial methane production could and did occur in the well-oxygenated water column of an oligotrophic lake (Lake Stechlin, Germany). Oversaturation of methane was repeatedly recorded in the well-oxygenated upper 10 m of the water column, and the methane maxima coincided with oxygen oversaturation at 6 m. Laboratory incubations of unamended epilimnetic lake water and inoculations of photoautotrophs with a lake-enrichment culture both led to methane production even in the presence of oxygen, and the production was not affected by the addition of inorganic phosphate or methylated compounds. Methane production was also detected by in-lake incubations of lake water, and the highest production rate was 1.8–2.4 nM⋅h ⁻¹ at 6 m, which could explain 33–44% of the observed ambient methane accumulation in the same month. Temporal and spatial uncoupling between methanogenesis and methanotrophy was supported by field and laboratory measurements, which also helped explain the oversaturation of methane in the upper water column. Potentially methanogenic Archaea were detected in situ in the oxygenated, methane-rich epilimnion, and their attachment to photoautotrophs might allow for anaerobic growth and direct transfer of substrates for methane production. Specific PCR on mRNA of the methyl coenzyme M reductase A gene revealed active methanogenesis. Microbial methane production in oxygenated water represents a hitherto overlooked source of methane and can be important for carbon cycling in the aquatic environments and water to air methane flux.

The competition between sulfate reducing bacteria and methanogens over common substrates has been proposed as a critical control for methane production. In this study, we examined the co-existence of methanogenesis and sulfate reduction with shared substrates over a large range of sulfate concentrations and rates of sulfate reduction in estuarine systems, where these processes are the key terminal sink for organic carbon. Incubation experiments were carried out with sediment samples from the sulfate-methane transition zone of the Yarqon (Israel) estuary with different substrates and inhibitors along a sulfate concentrations gradient from 1 to 10 mM. The results show that methanogenesis and sulfate reduction can co-exist while the microbes share substrates over the tested range of sulfate concentrations and at sulfate reduction rates up to 680 µmol L-1 day-1. Rates of methanogenesis were two orders of magnitude lower than rates of sulfate reduction in incubations with acetate and lactate, suggesting a higher affinity of sulfate reducing bacteria for the available substrates. The co-existence of both processes was also confirmed by the isotopic signatures of δ34S in the residual sulfate and that of δ13C of methane and dissolved inorganic carbon. Copy numbers of dsrA and mcrA genes supported the dominance of sulfate reduction over methanogenesis, while showing also the ability of methanogens to grow under high sulfate concentration and in the presence of active sulfate reduction.

In lakes and reservoirs with variable water level, gas ebullition can play a substantial role in methane transport in the water column and to the atmosphere. However, measuring methane ebullition from sediment is difficult as releases are highly heterogeneous and intermittent on macro‐ and micro‐scales. In contrast to conventional gas traps and optical methods, hydroacoustic technology allows rapid scanning over large volumes of the water column synoptically to quantify gas bubble abundance. A 120‐kHz dual beam downward‐looking echosounder was used to measure the size distributions of bubbles that do not resonate at the sonar frequency. Data obtained with this sonar permit accurate calculation and evaluation of ebullition flux from the bottom. A robust relationship was established between gas volumes and backscattering cross‐section of individual bubbles in experimental conditions, and rise velocities of bubbles were precisely measured. The volume backscattering coefficient was shown to be a good gauge of the total volume of bubbles per cubic meter of water, allowing the use of a single‐beam sonar for measuring volumetric bubble concentrations. Data obtained from hydroacoustic surveys on Lake Kinneret, where gaseous methane is emitted from randomly dispersed sediment sources, indicated that ~90% of bubbles escaping from soft sediments ranged from 1.3 mm to 4.5 mm and ~50% ranged from 2.0 mm to 3.2 mm in equivalent radius. In summer‐fall 2001, the gaseous methane fluxes from hypolimnetic sediments was ~10 mmol m⁻² d⁻¹, accounting for one‐third of the observed methane accumulation in the hypolimnion. This relatively high ebullition rate could be attributed to the gradual decreasing of the mean water level in preceding years.