BackgroundLake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments.MethodsWe analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137Cs dating and was sectioned into layers 1–4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota.ResultsCommunity β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5–14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions.ConclusionsBy including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper “replacement horizon” is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower “depauperate horizon” is characterized by low taxonomic richness, more stable “low-energy” conditions, and a dominance of enigmatic Archaea.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-017-0255-9) contains supplementary material, which is available to authorized users.

Global warming is expected to raise temperatures in freshwater lakes, which have been acknowledged to contribute up to 10% of the atmospheric methane concentrations. Increasing temperature enhances methane production and oxidation rates, but few studies have considered the balance between both processes at experimentally higher temperatures within lake sediments. The temperature dependence of methane concentrations, methane production rates, and methanogenic (mcrA) and methanotrophic (pmoA) community size was investigated in intact sediment cores incubated with aerobic hypolimnion water at 4, 8, and 12°C over 3 weeks. Sediment cores of 25 cm length were collected at two temperate lakes—Lake Stechlin (Germany; mesotrophic‐oligotrophic, maximum depth 69.5 m) and Lake Geneva (France/Switzerland; mesotrophic, maximum depth 310 m). While methane production rates in Lake Stechlin sediments did not change with increasing temperatures, methane concentrations decreased significantly. In contrast, methane production rates increased in 20–25 cm in Lake Geneva sediments with increasing temperatures, but methane concentrations did not differ. Real‐time PCR demonstrated the methanogenic and methanotrophic community size remained stable independently of the incubation temperature. Methane concentrations as well as community sizes were 1–2 orders of magnitude higher in Lake Stechlin than in Lake Geneva, while potential methane production rates after 24 h were similar in both lakes, with on average 2.5 and 1.9 nmol g−1 DW h−1, respectively. Our results suggest that at higher temperatures methane oxidation could balance, and even exceed, methane production. This suggests that anaerobic methane oxidation could be involved in the methane balance at a more important rate than previously anticipated.

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WGA-prodrug targeting offers new perspectives for site-specific, cytoinvading drug delivery in colon cancer chemotherapy.

Rationale Carbon isotope ratio analysis using cavity ring‐down spectroscopy (CRDS) offers insight into methanogenic activity. In livestock buildings, measuring 13CH4/12CH4 by CRDS is challenging and prone to errors, due to cross‐interference from NH3. Therefore, an interference‐corrected and improved approach to monitor methanogenic pathways with CRDS was developed and described in this study. Methods Cross‐interference from NH3 and other livestock gases on 13CH4/12CH4 was measured using CRDS. The removal efficiency of livestock gases was quantified using proton transfer reaction mass spectrometry. The linearity of the cavity ring‐down spectrometer was tested by dilution of a 13CH4 standard up to 15.6 atom % in CH4. 13C isotope‐labeled acetate was utilized to elucidate the methanogenic pathway contribution in swine manure using a stoichiometric model. Results Significant NH3 cross‐interference on 13CH4/12CH4 was observed, and correction factors were calculated. Cross‐interfering gases were effectively removed using a copper scrubber and a Nafion tube. The instrument responded linearly with 13/12C ratios up to 7.6 atom % in CH4. Isotope‐labeled experiments suggested that hydrogenotrophic methanogenesis was dominant and acetate‐derived CH4 was limited in the studied swine manure. The observations were cross‐validated and consistent with measurements of the natural isotope signatures. Conclusion NH3 cross‐interference leads to major errors in isotope ratios and therefore in evaluating the relative methanogenic pathway activity. We present methodological approaches, which are crucial to apply in livestock‐related uses where NH3 is abundant. This methodology provides a considerable benefit to advance the understanding and reduction of methane emissions in the livestock sector.

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