Biology subjects

Zopfi, J.

Publications and source records attributed to Zopfi, J..

7 recordsLinked to original sources

bioRxiv2025

Non-canonical reductive nitrous oxide production pathways in a seasonally stratified lake basin

Nitrous oxide (N2O), a potent greenhouse gas and ozone-depleting agent, was detected at high concentrations in the anoxic bottom-waters of a monomictic eutrophic lake basin in Switzerland (Lake Lugano). The observed high site-specific nitrogen (N) isotope preference (SP), was inconsistent with bacterial denitrification, which typically exhibits low SP, thereby challenging its role as the primary N2O source. This pointed to chemo-denitrification and/or fungal denitrification, both characterized by high SP, as possible alternative pathways. We conducted incubation experiments with sediment and bottom-water samples to assess N2O production and reduction dynamics and associated natural-abundance stable isotope signatures. We demonstrate that N2O accumulation predominantly originated from sedimentary production, and that elevated SP values in the bottom water reflected fractional bacterial N2O reduction. Using an isotope mass balance mixing model, we identified bacterial denitrification as the dominant sedimentary process ([~]75%), followed by chemo-denitrification ([~]20%), and fungal denitrification ([~]5%). Additional 15N tracer incubation experiments, combined with selective inhibitors to quantify isolated pathways, confirmed model-estimated contributions. These findings validate the use of literature-based SP values in mixing models, and provide evidence for non-canonical N2O production via chemo- and fungal denitrification, highlighting the need to broaden our understanding of N2O cycling in lakes beyond classical bacterial pathways. SYNOPSISEutrophic lake conditions significantly enhance nitrous oxide production through diverse microbial processes, including non-traditional pathways beyond classical nitrification and denitrification. This study highlights the importance of incorporating chemo- and fungal denitrification when investigating aquatic nitrous oxide cycling. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/670496v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@808806org.highwire.dtl.DTLVardef@626820org.highwire.dtl.DTLVardef@a22bd8org.highwire.dtl.DTLVardef@eca378_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Nitrogen and oxygen isotope effects during enzymatic nitrate reduction in vitro and by natural lake water consortia

Nitrate (NO3-) isotope ratios are useful indicators for nitrogen (N)-transformation processes if the associated isotope effects and their environmental controls are well-constrained. The NO3- isotope effects in natural environments may depend on the type of dissimilatory nitrate reductases involved and the degree of isotopic overprinting via NO3- regeneration. We measured the coupled N and oxygen (O) isotope effects of NO3- reduction in anoxic incubation experiments with laboratory cultures (Pseudomonas sp. and Escherichia coli) harboring different nitrate reductase enzymes (Nar and/or Nap) as well as with natural freshwater consortia from Lake Lugano (Switzerland) and Lake La Cruz (Spain). For comparison, isotope effects were also evaluated through coupled N and O isotope measurements in the redox transition zone of Lake Lugano North Basin. Incubation-based Rayleigh model N isotope effects ({varepsilon}N) were variable, ranging from 9 to 30{per thousand}. In comparison, in situ {varepsilon}N values (5 to 14{per thousand}) estimated by the closed system model were lower, likely due to substrate limitation in the water column. Experiments with Pseudomonas sp. and E. coli cultures possessing Nar yielded N isotope effects of similar magnitudes and, consistent with previous data, robust {Delta}{delta}18O:{Delta}{delta}15N enrichment ratios of [~]0.9 - 1.0. Nitrate reduction by cultures possessing solely Nap led to lower {Delta}{delta}18O:{Delta}{delta}15N of [~]0.7. In anoxic incubations of lake water, where the effect of nitrification could be excluded, {Delta}{delta}18O:{Delta}{delta}15N values between 0.6 and 1.0 suggest "community activity" of both Nar and Nap. Interestingly, stimulation of lithotrophic nitrate reduction in incubations with amended NO3- + sulfide resulted in a {Delta}{delta}18O:{Delta}{delta}15N slope of 0.90 {+/-} 0.03 (standard error, SE), indicating Nar as the more dominant nitrate-reducing enzyme. On the contrary, stimulation of organotrophic nitrate reduction in NO3- + acetate amended incubations resulted in a significantly lower slope of 0.72 {+/-} 0.03 SE, suggesting a greater contribution by Nap. In contrast to the nitrate-reduction incubation experiments, the in situ {Delta}{delta}18O:{Delta}{delta}15N value of 1.36 {+/-} 0.14 SE observed in the Lake Lugano water column was unusually high for a freshwater environment, likely reflecting the superimposed effect of NO3- production by nitrification. Our study thus underscores that both variations in activity of Nar versus Nap during nitrate reduction, as well as isotopic overprinting by nitrate regeneration may impact ecosystem NO3- isotope dynamics in natural denitrifying environments.

microbiology↗

bioRxiv2025

Microbial nitrogen removal versus recycling in the redox transition zone of a meromictic lake and its coupling to sulfur

Organotrophic denitrification is an important nitrogen (N) removal process in lakes, but alternative N reduction processes such as lithotrophic sulfur (S)-oxidizing denitrification may be greatly underappreciated. We studied the redox transition zone (RTZ) in the meromictic water column of the North Basin of Lake Lugano (Switzerland) to characterize N transformation pathways coupled to the S and carbon (C) cycles. Incubations with 15N-labeled and unlabeled nitrate showed low denitrification rates and a general limitation of organic electron donors. The most accessible fractions of exported primary production biomass may have been largely consumed in the oxic water column during sedimentation, and did not reach the RTZ at [~]100 m. Conversely, sulfide (H2S) and methane (CH4), major end products of anaerobic degradation of the more recalcitrant organic matter fractions in the sediment, represent a continuous source of energy to the RTZ, fostering the establishment of a community of S- and CH4-dependent nitrate reducers, dominated by Sulfuritalea and Candidatus Methylomirabilis over several years of observation. Anoxic incubation experiments with H2S amendments revealed a strong stimulation of dissimilatory nitrate reduction to ammonium (DNRA), but not denitrification. High relative abundances of the archaeal ammonia oxidizer Candidatus Nitrosopumilus and bacterial nitrifiers indicate intense nitrate regeneration by nitrification in the upper RTZ. The potential interaction between nitrification and S-driven DNRA is unclear. However, their importance in close proximity suggests that, at least under conditions of carbon limitation, N recycling between the nitrate and ammonium pools, predominates over N removal via complete denitrification in the Lake Lugano North Basin.

microbiology↗

bioRxiv2024

Methanotrophic flexibility of Ca. Methanoperedens and its interactions with sulfate-1 reducing bacteria in the sediment of meromictic Lake Cadagno

The greenhouse gas methane is an important contributor to global warming, with freshwater sediments representing important potential methane sources. Anaerobic methane-oxidizing archaea mitigate methane release into the atmosphere by coupling the oxidation of methane to the reduction of extracellular electron acceptors or through interspecies electron transfer with microbial partners. Understanding their metabolic flexibility and microbial interactions is crucial to assess their role in global methane cycling. Here, we investigated anoxic sediments of the meromictic freshwater Lake Cadagno (Switzerland), where Ca. Methanoperedens and sulfate-reducing bacteria co-occur, with metagenomics and long-term incubations. Incubations were performed with different electron acceptors, revealing that manganese oxides supported highest CH4 oxidation potential but enriched for Ca. Methanoperedens phylotypes that were hardly present in the inoculum. Combining data from the inoculum and incubations, we obtained five Ca. Methanoperedens genomes, each harboring different extracellular electron transfer pathways. In a reconstructed Desulfobacterota QYQD01 genome we observed large multi-heme cytochromes, type IV pili, and a putative loss of hydrogenases, suggesting facultative syntrophic interactions with Ca. Methanoperedens. We also screened for putative extrachromosomal elements in the Ca. Methanoperedens genomes, including BORGs. This research deepens our understanding of the metabolic flexibility and potential interspecific interactions of Ca. Methanoperedens in freshwater lakes.

microbiology↗

bioRxiv2021

Multiple groups of methanotrophic bacteria mediate methane oxidation in anoxic lake sediments

Freshwater lakes represent an important source of the potent greenhouse gas methane (CH4) to the atmosphere. Methane emissions are regulated to large parts by aerobic (MOx) and anaerobic (AOM) oxidation of methane that are important sinks in lakes. In contrast to marine benthic environments, our knowledge about the modes of AOM and the related methanotrophic microorganisms in anoxic lake sediments is still rudimentary. Here we demonstrate the occurrence of AOM in the anoxic sediments of Lake Sempach (Switzerland), with maximum in situ AOM rates observed within the surface sediment layers in presence of multiple groups of methanotrophic bacteria and various oxidants known to support AOM. However, substrate-amended incubations (with NO2-, NO3-, SO42-, Fe3+ and Mn4+) revealed that none of the electron acceptors previously reported to support AOM enhanced methane turnover in Lake Sempach sediments under anoxic conditions. In contrast, the addition of oxygen to the anoxic sediments resulted in an approximately tenfold increase in methane oxidation relative to the anoxic incubations. Phylogenetic and isotopic evidence indicate that both Type I and Type II aerobic methanotrophs were growing on methane under both oxic and anoxic conditions, although methane assimilation rates were an order of magnitude higher under oxic conditions. While the anaerobic electron acceptor responsible for AOM could not be identified, these findings expand our understanding of the metabolic versatility of canonically aerobic methanotrophs under anoxic conditions, with important implications for future investigations to identify methane oxidation processes. Bacterial AOM by facultative aerobic methane oxidizers might be of much larger environmental significance in reducing methane emissions than previously thought.

microbiology↗

bioRxiv2020

Comprehensive dataset of shotgun metagenomes from stratified freshwater lakes and ponds

Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.

ecology↗

bioRxiv2019

Manganese/iron-supported sulfate-dependent anaerobic oxidation of methane by archaea in lake sediments

Anaerobic oxidation of methane (AOM) by methanotrophic archaea is an important sink of this greenhouse gas in marine sediments. However, evidence for AOM in freshwater habitats is rare, and little is known about the pathways, electron acceptors and microbes involved. Here, we show that AOM occurs in anoxic sediments of a lake in southern Switzerland (Lake Cadagno). Combined AOM-rate and 16S rRNA gene-sequencing data suggest that Candidatus Methanoperedens archaea are responsible for the observed methane oxidation. Members of the Methanoperedenaceae family were previously reported to conduct nitrate- or iron/manganese-dependent AOM. However, we demonstrate for the first time that the methanotrophic archaea do not necessarily rely upon these oxidants as terminal electron acceptors directly, but mainly perform canonical sulfate-dependent AOM, which under sulfate-starved conditions can be supported by metal (Mn, Fe) oxides through oxidation of reduced sulfur species to sulfate. The correspondence of high abundances of Desulfobulbaceae and Candidatus Methanoperedens at the same sediment depth confirm the interdependence of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria. The relatively high abundance and widespread distribution of Candidatus Methanoperedens in lake sediments highlight their potentially important role in mitigating methane emissions from terrestrial freshwater environments to the atmosphere, analogous to ANME-1, -2 and -3 in marine settings.

microbiology↗