Biology subjects

Lehmann, M. F.

Publications and source records attributed to Lehmann, M. F..

6 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

Batch culture and species effects modulate the decoupling between diatom frustule-bound and biomass nitrogen isotope signatures

The stable nitrogen (N) isotope composition of organic matter encapsulated in diatom silica frustules ({delta}15NDB) from sedimentary records has been used as a proxy for reconstructing N consumption dynamics in the ocean over geologic timescales. This proxy relies on the assumption that {delta}15NDB tracks biomass {delta}15N without being affected by internal N-isotope fractionation. However, recent ground-truthing efforts have shown that {delta}15NDB can diverge from biomass {delta}15N values, though the extent and mechanisms behind this decoupling remain unclear. In this study, we cultured two freshwater and two marine diatom species in batch cultures to test whether {delta}15NDB (1) is subject to species-dependent internal 15N fractionation, and (2) reflects the {delta}15N of source nitrate to the same extent as biomass {delta}15N values, assessing potential asynchronous integration of the N isotope signal. We monitored the N-isotope systematics during diatom growth by measuring {delta}15N values of nitrate, bulk biomass and frustule-bound organic N throughout batch culture progression. We found that {delta}15NDB did not follow typical Rayleigh fractionation dynamics and remained relatively stable, while biomass {delta}15N increased predictably with progressive fractional nitrate consumption. The observed divergence could only be partially explained by asynchronous integration of source-nitrate {delta}15N values into biomass versus frustule-bound organic N (i.e., delayed incorporation into frustule-bound material), as newly formed frustules predominantly recorded the {delta}15N of 15N-labeled nitrate added during growth. This demonstrates that {delta}15NDB values capture the isotopic signature of newly assimilated nitrate rather than N derived from internal, or legacy, pools. We hypothesize that shifts in growth conditions during batch culture progression alter the coupling between carbon and nitrogen metabolism, leading to physiologically driven variation in internal 15N fractionation and corresponding offsets between {delta}15NDB and biomass {delta}15N. Such sensitivity to internal isotope fractionation during biosynthesis implies that the interpretation of sedimentary {delta}15NDB records is more intricate than previously assumed.

plant biology↗

bioRxiv2025

Long-term euxinia hinders microbial ammonium removal in brackish coastal waters

Anthropogenic activities are key drivers of eutrophication and deoxygenation in coastal marine ecosystems. This stimulates the anaerobic degradation of organic matter and the release of reduced products, such as ammonium, methane, and hydrogen sulfide, which may, in turn, exacerbate eutrophication and deoxygenation. In this study, using a combination of chemical and microbial analyses, we assess the nitrogen dynamics in the water column of a eutrophic coastal system (Stockholm Archipelago) at three sites with contrasting redox conditions (oxic to long-term euxinic). At the oxic site, counter gradients of ammonium and oxygen in the water column, low nitrate {delta}15N values in bottom waters, and the 16S rRNA gene-based presence of nitrifiers indicate nitrification near the sediment-water interface. At the seasonally and long-term euxinic sites, nitrification, as inferred from the water column oxygen and nutrient profiles and the relative abundance of nitrifiers, primarily occurred near the oxycline. At these two sites, nitrate was removed below the oxycline through denitrification linked to sulfide oxidation by Sulfurimonas. Nitrous oxide emissions from surface waters in the archipelago reached up to 40 {micro}mol m-2 d-1 and were not directly related to water column redox conditions, indicating that multiple factors control coastal emissions of this greenhouse gas to the atmosphere. The relative abundance of 16S rRNA genes and of N-cycle genes in metagenomes was highest at the seasonally euxinic site. Importantly, nitrifiers were significantly less abundant at the long-term euxinic site. Our results highlight that prolonged euxinia promotes recycling of ammonium over its removal, likely due to sulfide inhibition of nitrification, which sustains eutrophication and deoxygenation of coastal systems.

microbiology↗

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↗

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↗