Biology subjects

Mesman, R.

Publications and source records attributed to Mesman, R..

4 recordsLinked to original sources

bioRxiv2026

Streamlining large-scale high-resolution electron tomography with VolWeaver

Researchers using electron microscopy must often balance a trade-off between obtaining high-resolution structural information and preserving sufficient cellular context. At one end of this spectrum, single particle cryo-electron microscopy and cryo-electron tomography provide near-molecular detail but are typically limited to relatively small fields of view. At the other, volume electron microscopy approaches, such as scanning electron microscopy of resin-embedded specimens, capture large cellular volumes but generally at lower resolution. Consequently, linking nanoscale structural information to larger cellular architecture remains a significant challenge. To address this gap, we optimised a transmission electron tomography workflow for resin-embedded malaria parasites that allows us to visualise targeted regions of interest at nanometre-scale resolution while retaining several micrometres of surrounding cellular context. Here, we present our current best-practice pipeline for sample preparation, tomogram acquisition, and reconstruction. In addition, we introduce VolWeaver, a data-processing framework, that integrates high-resolution tomographic datasets into serial section volume reconstructions, enabling the visualisation and interpretation of ultrastructural features within their broader cellular environment.

cell biology↗

bioRxiv2026

The molecular mechanism and activity of Kuenenia stuttgartiensis hydrazine synthase

Anaerobic ammonium-oxidizing (anammox) bacteria convert ammonium and nitrite into dinitrogen gas via the intermediates nitric oxide and hydrazine. To produce hydrazine, anammox bacteria harbor a biochemically unique enzyme: hydrazine synthase. Based on the hydrazine synthase crystal structure it was hypothesized that hydrazine is produced in a two-step mechanism. In this hypothesis, nitric oxide is first reduced to hydroxylamine (first half-reaction), followed by condensation of hydroxylamine with ammonium to hydrazine (second half-reaction). Here, we experimentally investigated the proposed molecular mechanism of hydrazine synthase and characterized and optimized the in vitro activity. First, we optimized the activity of isolated hydrazine synthase from anammox bacterium Kuenenia stuttgartiensis strain MBR1 via an anaerobic isolation method. We further compared hydrazine synthase activity measured via a coupled assay versus that of a newly established direct LC-MS assay. Next, the hypothesized second half-reaction was investigated via the direct LC-MS assay, quantifying biologically produced hydrazine from hydroxylamine and ammonium. Despite variation in hydrazine synthase activity across assays, we determined ammonium and hydroxylamine affinity and investigated product inhibition. Finally, we found that hydrazine synthesis from ammonium and hydroxylamine by isolated hydrazine synthase is oxygen-tolerant, strongly suggesting that the second half-reaction is initiated on an oxidized heme within hydrazine synthase. Taken together, the results corroborate that condensation of ammonium with hydroxylamine to form hydrazine is the second half-reaction of the proposed two-step mechanism for hydrazine synthesis by hydrazine synthase.

microbiology↗

bioRxiv2023

Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea

Anaerobic methanotrophic (ANME) archaea are environmentally important uncultivated microorganisms mitigating the release of the potent greenhouse gas methane. During methane oxidation ANME archaea engage in extracellular electron transfer (EET) with other microorganisms, metal oxides, and electrodes, through a currently unknown mechanism. To shed light on this mechanism, we cultivated ANME-2d archaea (Ca. Methanoperedens) in bioelectrochemical systems and observed strong methane-dependent current (91-93% of total current) associated with high enrichment of Ca. Methanoperedens on the anode (up to 82% of the community) determined by metagenomics and transmission electron microscopy. Electrochemistry and metatranscriptomics indicated that the EET mechanism was similar at various electrode potentials pointing to the involvement of an so far uncharacterized short-range electron transport protein complex and OmcZ nanowires, suggesting a unique EET pathway in all ANME-2 archaea. Our findings furthermore indicate that bioelectrochemical cells might be powerful tools for the cultivation, and possibly isolation, of uncultured electroactive microorganisms.

microbiology↗

bioRxiv2019

Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria

Anaerobic ammonium oxidation (anammox) by anammox bacteria contributes significantly to the global nitrogen cycle, and plays a major role in sustainable wastewater treatment. Anammox bacteria convert ammonium (NH4+) to dinitrogen gas (N2) using nitrite (NO2-) or nitric oxide (NO) as the electron acceptor. In the absence of NO2- or NO, anammox bacteria can couple formate oxidation to the reduction of metal oxides such as Fe(III) or Mn(IV). Their genomes contain homologs of Geobacter and Shewanella cytochromes involved in extracellular electron transfer (EET). However, it is still unknown whether anammox bacteria have EET capability and can couple the oxidation of NH4+ with transfer of electrons to carbon-based insoluble extracellular electron acceptors. Here we show using complementary approaches that in the absence of NO2-, freshwater and marine anammox bacteria couple the oxidation of NH4+ with transfer of electrons to carbon-based insoluble extracellular electron acceptors such as graphene oxide (GO) or electrodes poised at a certain potential in microbial electrolysis cells (MECs). Metagenomics, fluorescence in-situ hybridization and electrochemical analyses coupled with MEC performance confirmed that anammox electrode biofilms were responsible for current generation through EET-dependent oxidation of NH4+. 15N-labelling experiments revealed the molecular mechanism of the EET-dependent anammox process. NH4+ was oxidized to N2 via hydroxylamine (NH2OH) as intermediate when electrode was the terminal electron acceptor. Comparative transcriptomics analysis supported isotope labelling experiments and revealed an alternative pathway for NH4+ oxidation coupled to EET when electrode is used as electron acceptor compared to NO2-as electron acceptor. To our knowledge, our results provide the first experimental evidence that marine and freshwater anammox bacteria can couple NH4+ oxidation with EET, which is a significant finding, and challenges our perception of a key player of anaerobic oxidation of NH4+ in natural environments and engineered systems.

microbiology↗