Biology subjects

Schouten, S.

Publications and source records attributed to Schouten, S..

5 recordsLinked to original sources

bioRxiv2025

Adaptation and response of verrucomicrobial methanotrophs to heat and acidity

Acidophilic microorganisms thrive in environments where the external pH is orders of magnitude lower than their intracellular pH. Verrucomicrobial methanotrophs of the family Methylacidiphilaceae, including Methylacidiphilum and Methylacidimicrobium, inhabit extremely acidic geothermal environments and can grow at a pH < 1.0 and temperatures up to 65 {degrees}C. We analyzed and compared their membrane fatty acid compositions at pH 3.0 across strains with different temperature optima. Thermophilic Methylacidiphilum strains almost exclusively contain saturated fatty acids, while mesophilic Methylacidimicrobium strains incorporate 16-47% unsaturated fatty acids. Notably, the thermophile Methylacidiphilum fumariolicum SolV increases unsaturated fatty acid content in response to a 10 {degrees}C temperature decrease. Genomic analysis revealed a conserved fatty acid biosynthesis pathway. Despite constitutive expression of predicted pH homeostasis genes, SolV did not upregulate them upon changing the pH from 3.0 to 1.7. However, genes involved in methane oxidation were strongly upregulated, suggesting a potential metabolic adaptation to extreme acidity.

microbiology↗

bioRxiv2025

Substantial contribution of in-situ produced bacterial lipids to the sedimentary lipidome

The sedimentary lipid pool is comprised of a myriad of individual components. Due to their importance for organic carbon sequestration and their application in paleoclimatic and geobiological reconstructions, its composition has been studied for many decades with targeted approaches but an overall view on its composition is still lacking. In part this uncertainty relates to the different sources of sedimentary lipids, they can be both delivered from the overlying water column by sedimentation, but also produced in-situ by sediment dwelling organisms. Another uncertainty relates to the differing degree of preservation, both between lipid groups and relative to other organic matters. Here we conduct an untargeted analysis of the sedimentary lipidome in the Black Sea using high resolution mass spectrometry. Besides commonly reported phytoplankton-derived fossil lipids, a diverse and abundant set of sphingolipids was discovered, accounting for [~]20% of the sedimentary lipidome. These sphingolipids are produced in situ by sedimentary anaerobic bacteria, which probably used sphingolipids instead of phospholipids, likely because of the deficiency of phosphate in the anoxic sediments. Our results suggest that while phytoplankton-derived lipids contribute 50-60% of the sedimentary lipidome, the importance of bacterial lipids, particularly in-situ produced sphingolipids, may have been overlooked.

microbiology↗

bioRxiv2020

Reconstructing the diet, trophic level, and migration pattern of Mysticete whales based on baleen isotopic composition.

Baleen from mysticete whales is a well-preserved proteinaceous material that can be used to identify migrations and feeding habits for species whose migration pathways are unknown. Analysis of {delta}13C and {delta}15N from bulk baleen has been used to infer migration patterns for individuals. However, this approach has fallen short of identifying migrations between regions as it is difficult to determine variations in isotopic shifts without temporal sampling of prey items. Here we apply analysis of {delta}15N values of amino acids to five baleen plates belonging to three species, revealing novel insights on trophic position, metabolic state, and migration between regions. Humpback and minke whales had higher reconstructed trophic levels than fin whales (3.4-3.5 versus 2.7-2.9, respectively) as expected due to different feeding specialization. Isotopic niche areas between baleen minima and maxima were well separated, indicating regional resource use for individuals during migration that aligned with isotopic gradients in Atlantic Ocean particulate organic matter. {delta}15N values from phenylalanine confirmed regional separation between the niche areas for two fin whales as migrations occurred and elevated glycine and threonine {delta}15N values revealed physiological changes due to fasting. Simultaneous resolution of trophic level and physiological changes allow for identification of regional migrations in mysticetes.

ecology↗

bioRxiv2019

Practical considerations for improved reliability and precision during compound specific analysis of δ15N in amino acids using a single combined oxidation-reduction reactor.

RATIONALEThere has been increased interest in the analysis for {delta}15N in amino acids to gain simultaneous insight into both trophic relationships and source producers within ecosystems. New developments in gas chromatography combustion isotope ratio mass spectrometry equipment has led to variable outcomes in performance due to limited information about best practices for new systems.\n\nMETHODSPrecision for {delta}15N in amino acids using the single combined oxidation-reduction reactor is improved across a sequence of analyses if the reactor is oxidized for a substantial period (2 h), immediately followed with a conditioning run of alkanes prior to analysis for N, and the liquid N2 CO2 trap is left immersed throughout. A five point calibration curve using amino acids with a range of {delta}15N values from -2.4{per thousand} to +61.5{per thousand} was used in combination with a 13 amino acid mixture to correct for offsets during derivatization.\n\nRESULTSCombining the improved setup with normalization techniques using both internal and external standards allows for a reliable throughput of ~25 samples per week. It allowed for a reproducible level of error of <{+/-}0.5{per thousand} within standards repeated 10 times across each sequence and a sample error of ({+/-}0.18{per thousand}), which is lower than analytical error typically associated with {delta}15N-amino acid analysis ({+/-}1{per thousand}).\n\nCONCLUSIONSA few practical considerations regarding oxidation and conditioning of the combustion reactor allow for increased sequence capacity with the single combined oxidation-reduction reactor. These considerations combined with normalization techniques result in a higher throughput and reduced analytical error during analysis of {delta}15N in amino acids.

ecology↗

bioRxiv2019

ANME-2d anaerobic methanotrophic archaea differ from other ANME archaea in lipid composition and carbon source

The anaerobic oxidation of methane (AOM) is a microbial process present in marine and freshwater environments. AOM is important for reducing the emission of the second most important greenhouse gas methane. In marine environments anaerobic methanotrophic archaea (ANME) are involved in sulfate-reducing AOM. In contrast, Ca. Methanoperedens of the ANME-2d cluster carries out nitrate AOM in freshwater ecosystems. Despite the importance of those organisms for AOM in non-marine environments not much is known about their lipid composition or carbon sources. To close this gap, we analyzed the lipid composition of ANME-2d archaea and found that they mainly synthesize archaeol and hydroxyarchaeol as well as different (hydroxy-) glycerol dialkyl glycerol tetraethers, albeit in much lower amounts. Abundant lipid headgroups were dihexose, monomethyl-phosphatidyl ethanolamine and phosphatidyl hexose. Moreover, a monopentose was detected as a lipid headgroup which is rare among microorganisms. Batch incubations with 13C labelled bicarbonate and methane showed that methane is the main carbon source of ANME-2d archaea varying from ANME-1 archaea which primarily assimilate dissolved inorganic carbon (DIC). ANME-2d archaea also assimilate DIC, but to a lower extent than methane. The lipid characterization and analysis of the carbon source of Ca. Methanoperedens facilitates distinction between ANME-2d and other ANMEs.

microbiology↗