Aerobic and Anaerobic Oxidation of Methane in Sediments of Lake Constance

Abstract

In this study, methane oxidation in Lake Constance and the respective microorganisms were investigated using a broad range of methods. High-resolution methane and oxygen profiles combined with molecular techniques (FISH, qPCR) were used to identify the distribution of methane oxidation activity and methanotrophic bacteria in the sediment column. Methaneoxidizing bacteria (MOB) were found to be evenly distributed in the sediment column of profundal sediments, and methane oxidation took place only in the narrow zone where methane and oxygen met at low concentrations. In littoral sediments, however, a maximum of MOB abundance and methane oxidation activity was detected at 1 to 4 cm sediment depth where oxygen was absent. The latter finding indicated either substantial mixing of the upper sediment layers of littoral sediments in-situ or a zone of anaerobic methane oxidation.Because of these indications for AOM in littoral sediments, tracer experiments were performed to test this hypothesis. These experiments revealed the potential for nitratedependent AOM in sediments of oligotrophic Lake Constance, but could not detect sulfatedependent AOM. Furthermore, NC10 bacteria related to candidatus “Methylomirabilis oxyfera”, which catalyses AOM coupled to denitrification, were detected using 16S rRNA gene clone libraries. For the first time, pmoA gene sequences related to those of M. oxyfera were retrieved from environmental samples and support the presence of NC10 bacteria able to oxidize methane with nitrate or nitrite as electron acceptor in these sediments. AOM coupled to denitrification appears to depend on stable gradient systems and was found mainly in profundal but not in mixed littoral sediments.To gain further insights into the methane-oxidizing communities from Lake Constance sediments opposing gradients of methane and oxygen were used to cultivate MOB, thus mimicking the low substrate concentrations they experience in-situ. This approach finally allowed the isolation of a novel oxygen-sensitive methanotroph (strain KoM1) from profundal sediment. Strain KoM1 represents a new species and genus and is distantly related to Methylosoma, which was previously isolated from Lake Constance.In addition to the distinct environments of littoral and profundal sediments, active methane seeps, called pockmarks, were investigated in Eastern Lake Constance. High methane oxidation potentials as well as high MOB abundance designated littoral pockmark sediments as “hot spots” of methane oxidation in an otherwise oligotrophic environment. This was also reflected by the distinctly different MOB community at these sites compared to those in the surrounding sediments.Altogether, this study demonstrates that methane oxidation occurs mainly at low oxygen concentrations in-situ and could even play a role under anoxic conditions. In line with previous studies, it was shown that MOB communities differ significantly even in different parts of the same lake, thus encouraging further research on the adaptations of MOB strains to different ecological niches.