Biology subjects

Schleheck, D.

Publications and source records attributed to Schleheck, D..

9 recordsLinked to original sources

bioRxiv2026

Seasonal succession of nano- and picoplankton communities in Lake Constance: conserved dynamics despite compositional shifts under contrasting mixing and oxygen regimes

Lake Constance is a pre-Alpine, monomictic, oligotrophic lake situated at the southern end of Germany composed of two main water bodies: deep, oligotrophic Upper Lake Constance (ULC) and the shallow, more mesotrophic Lower Lake Constance (LLC). To date, no sequencing-based study exists of the seasonal succession of the microbial plankton in Lake Constance. Over one-year, microbial plankton communities were sampled biweekly from the top 20 m of the water column in both sites and separated into nanoplankton (NP) and picoplankton (PP). Communities were analysed using rDNA amplicon sequencing: NP samples were analysed by 18S rDNA, and PP samples by 18S and 16S rDNA sequencing. Temporal community diversity was compared between sites and the effect of two major environmental perturbations, winter vertical mixing in ULC and oxygen depletion of the bottom-water layer in LLC, on the community was examined. Despite strong environmental contrasts, microbial plankton communities exhibited conserved seasonal temporal dynamics across basins. In contrast, pronounced compositional shifts occurred during mixing and oxygen depletion events. Approximately 20% of detected taxa were positively associated with these events, with log fold changes reaching 9.82, reflecting rare or undetectable taxa outside these periods. Taxa favoured by these perturbations commonly exhibited high metabolic flexibility, including mixotrophy, fermentation, or anaerobic respiration, or possessed functional traits conferring tolerance to altered redox and mixing regimes. Our results suggest that the temporal dynamics of freshwater microbial plankton communities are driven by deterministic processes and highlight the profound impact of large, and less known, environmental changes on these communities.

ecology↗

bioRxiv2025

A Family VIII Esterase with Dual Activities: Bioplastic Depolymerization and Beta-Lactam Antibiotics Hydrolysis

Microorganisms in the plastisphere are associated with plastic degradation, as well as with an unusually high occurrence of antibiotic resistance genes (ARGs), suggesting plastic debris as a potential vector for antibiotic-resistant microorganisms. In this study, we investigated microbial communities associated with the degradation of aliphatic long-chain polyester (LCAP) bioplastics in forest soil. Sequencing analysis revealed a family VIII esterase with structural similarity to type C {beta}-lactamases. Structural modeling and substrate docking analysis indicated catalytically favorable binding of both LCAP and {beta}-lactam antibiotics. Heterologous expression and in-vitro activity testing confirmed its dual functionality as plastic depolymerase and {beta}-lactam hydrolase. Sequence-based predictions identify the enzyme as a membrane-associated lipoprotein, with suggested further secretion via outer-membrane vesicles (OMVs), offering potential ecological benefits in competitive plastisphere environments. These findings highlight an enzyme with a rare substrate spectrum, bridging plastic and antibiotics degradation and suggesting an intriguing biochemical connection that warrants further investigation of microbial evolution in the plastisphere and its potential implications for the spread of antibiotic resistance.

microbiology↗

bioRxiv2025

Extensive richness and novel taxa of sulfoquinovose-degrading bacteria in the cow rumen

Sulfoquinovose (SQ), a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol (SQDG), is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release SQ from SQDG. Despite its ecological importance, the diversity and functional roles of SQ-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments, including marine sediments and the mammalian gut. We revealed particularly high richness of yihQ-containing microorganisms in cow rumen, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of SQ metabolism in ruminant digestion. Anaerobic microcosm experiments with SQ-amended rumen fluid revealed cooperative microbial degradation of SQ to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics identified novel uncultured SQ-degrading taxa, including members of Caproiciproducens (Acutalibacteraceae), Limivicinus (Oscillospiraceae), and Sphaerochaetaceae, which encode the sulfo-transketolase pathway, along with Mailhella (Desulfovibrionaceae), a likely isethionate-respiring bacterium. This study presents the first functional gene-based assay for tracking environmental yihQ diversity, highlights SQ degradation as a central metabolic process in the cow rumen, describes novel SQ-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.

microbiology↗

bioRxiv2025

Microbial sedimentary DNA from a cultural landscape disentangles the impacts of humans and nature over the past 13.5 thousand years

Bacteria and archaea are currently under-characterised in palaeoecological studies, despite their ubiquity, high diversity and tight integration with the biotic and abiotic environment and human activity. The complexity of their assemblages, and the difficulties in separating living- from paleo-prokaryotes renders analyses challenging. Here we present an ancient prokaryote metagenomic time-series from a sediment core of Lake Constance, a large and deep perialpine lake from temperate Europe, spanning the last 13,500 years of natural and anthropogenic impact. We mapped DNA to reference genomes and estimated the DNA damage of taxa, which displayed a monotonic relationship with time. By constructing co-abundance networks we recognize major microbial assemblages, containing both ancient and living microbes, that show specific dynamics. Short-term and often low-abundance assemblages are linked to the Pleistocene-Holocene transition, floods and human activities. Noticeably, certain lineages harbouring microbes common in human-impacted environments expanded during the Middle Ages and Modern time. Some abundant taxa that were linked to various freshwater and soil environments persisted through millennia. By extricating various sources and trajectories of change, we demonstrate the power of prokaryotic sedimentary DNA in revealing long-term eco-evolutionary outcomes caused by both nature- and humans.

ecology↗

bioRxiv2025

Sulfoquinovose is differently degraded by the mouse and human gut microbiota and not metabolized by the host

BackgroundSulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for few human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism. Results13CO2 breath tests with germ-free C57BL/6 mice gavaged with 13C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of Agathobacter rectalis and Bilophila wadsworthia in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the mouse gut. Escherichia coli and Enterocloster clostridioformis were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some E. clostridioformis genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived E. clostridioformis strain. ConclusionsOur findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health.

microbiology↗

bioRxiv2022

A novel taurine-respiring murine gut bacterium contributes to colonization resistance against enteropathogens

Taurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and genomic-ecophysiological characterization of the first taurine-respiring mouse gut bacterium. Taurinivorans muris represents a new widespread species with protective capacity against pathogens and differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism and host distribution. Despite alternative physiologies, taurine respiration was the main in vivo lifestyle of T. muris independent of mouse diet and genotype. In gnotobiotic mice, T. muris selectively enhanced the activity of a sulfur metabolism gene-encoding prophage and provided slightly increased colonization resistance against Salmonella Typhimurium, which showed reduced expression of galactonate catabolism genes. We identified T. muris as the dominant sulfidogen of a mouse microbiota that conferred H2S-mediated protection against Klebsiella pneumoniae in a previous study. Together, we revealed the realized physiological niche of a key murine gut sulfidogen and its impact on pathogen and phage gene expression. One sentence summaryOur work identified and characterized a new core member of the murine gut microbiota, revealed sulfidogenic taurine respiration as its predominant in vivo lifestyle, and emphasizes its protective function in pathogen colonization.

microbiology↗

bioRxiv2021

Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia

BackgroundBilophila wadsworthia, a strictly anaerobic, sulfite-reducing bacterium and common member of the human gut microbiota, has been associated with diseases such as appendicitis and colitis. It is specialized on organosulfonate respiration for energy conservation, i.e., utilization of dietary and host-derived organosulfonates, such as taurine (2-aminoethansulfonate), as sulfite donors for sulfite respiration, producing hydrogen sulfide (H2S), an important intestinal metabolite that may have beneficial as well as detrimental effects on the colonic environment. Its taurine desulfonation pathway involves a glycyl radical enzyme (GRE), isethionate sulfite-lyase (IslAB), which cleaves isethionate (2-hydroxyethane sulfonate) into acetaldehyde and sulfite. ResultsWe demonstrate that taurine metabolism in B. wadsworthia 3.1.6 involves bacterial microcompartments (BMCs). First, we confirmed taurine-inducible production of BMCs by proteomic, transcriptomic and ultra-thin sectioning and electron-microscopical analyses. Then, we isolated BMCs from taurine-grown cells by density-gradient ultracentrifugation and analyzed their composition by proteomics as well as by enzyme assays, which suggested that the GRE IslAB and acetaldehyde dehydrogenase are located inside of the BMCs. Finally, we are discussing the recycling of cofactors in the IslAB-BMCs and a potential shuttling of electrons across the BMC shell by a potential ironsulfur (FeS) cluster-containing shell protein identified by sequence analysis. ConclusionsWe characterized a novel subclass of BMCs and broadened the spectrum of reactions known to take place enclosed in BMCs, which is of biotechnological interest. We also provided more details on the energy metabolism of the opportunistic pathobiont B. wadsworthia and on microbial H2S production in the human gut.

microbiology↗

bioRxiv2019

SiaABCD - A threonine phosphorylation pathway that controls biofilm formation in Pseudomonas aeruginosa

The critical role of bacterial biofilms in chronic human infections calls for novel anti-biofilm strategies targeting the regulation of biofilm development. However, the regulation of biofilm development is very complex and can include multiple, highly interconnected signal transduction/response pathways, which are incompletely understood. We demonstrated previously that in the opportunistic, human pathogen P. aeruginosa, the PP2C-like protein phosphatase SiaA and the di-guanylate cyclase SiaD control the formation of macroscopic cellular aggregates, a type of suspended biofilms, in response to surfactant stress. In this study, we demonstrate that the SiaABC proteins represent a signal response pathway that functions through a partner switch mechanism to control biofilm formation. We also demonstrate that SiaABCD functionality is dependent on carbon substrate availability for a variety of substrates, and that upon carbon starvation, SiaB mutants show impaired dispersal, in particular with the primary fermentation product ethanol. This suggests that carbon availability is at least one of the key environmental cues integrated by the SiaABCD system. Further, our biochemical, physiological and crystallographic data reveals that the phosphatase SiaA and its kinase counterpart SiaB balance the phosphorylation status of their target protein SiaC at threonine 68 (T68). Crystallographic analysis of the SiaA-PP2C domain shows that SiaA is present as a dimer. Dynamic modelling of SiaA with SiaC suggested that SiaA interacts strongly with phosphorylated SiaC and dissociates rapidly upon dephosphorylation of SiaC. Further, we show that the known phosphatase inhibitor fumonisin inhibits SiaA mediated phosphatase activity in vitro. In conclusion, the present work improves our understanding of how P. aeuruginosa integrates specific environmental conditions, such as carbon availability and surfactant stress, to regulate cellular aggregation and biofilm formation. With the biochemical and structural characterization of SiaA, initial data on the catalytic inhibition of SiaA, and the interaction between SiaA and SiaC, our study identifies promising targets for the development of biofilm-interference drugs to combat infections of this aggressive opportunistic pathogen. Author SummaryPseudomonas aeruginosa is a Gram-negative bacterium that is feared within clinical environments due to its potential to cause life-threatening acute and chronic infections. One cornerstone of its success is the ability to form and disperse from biofilms, which are self-made, multicellular structures that protect the individual cell from the human immune system and antibiotic treatment. As such, therapies that combine a biofilm-interference strategy and the use of antimicrobial drugs represent one of the promising strategies to tackle infections of this organism. With the current study, we gain a deeper understanding of the SiaABCD mediated biofilm formation in response to clinically relevant environmental conditions. Further, our structural and biochemical characterization of the PP2C-type protein-phosphatase SiaA and the partner switch protein SiaC suggest that both represent promising novel targets for the development of future anti-biofilms drugs based on a signal interference strategy.

microbiology↗

bioRxiv2019

Organohalide-respiring Desulfoluna species isolated from marine environments

The genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1{top} and D. butyratoxydans MSL71{top} of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third member of this genus from marine intertidal sediment, designed D. spongiiphila strain DBB. All three Desulfoluna strains harbour three reductive dehalogenase gene clusters (rdhABC) and corrinoid biosynthesis genes in their genomes. Brominated but not chlorinated aromatic compounds were dehalogenated by all three strains. The Desulfoluna strains maintained OHR in the presence of 20 mM sulfate or 20 mM sulfide, which often negatively affect OHR. Strain DBB sustained OHR with 2% oxygen in the gas phase, in line with its genetic potential for reactive oxygen species detoxification. Reverse transcription-quantitative PCR (RT-qPCR) revealed differential induction of rdhA genes in strain DBB in response to 1,4-dibromobenzene or 2,6-dibromophenol. Proteomic analysis confirmed differential expression of rdhA1 with 1,4-dibromobenzene, and revealed a possible electron transport chain from lactate dehydrogenases and pyruvate oxidoreductase to RdhA1 via menaquinones and either RdhC, or Fix complex (electron transfer flavoproteins), or Qrc complex (Type-1 cytochrome c3:menaquinone oxidoreductase).

microbiology↗