Biology subjects

Vollmers, J.

Publications and source records attributed to Vollmers, J..

4 recordsLinked to original sources

bioRxiv2026

Temporal emergence of functional dark matter in microbial responses to PFAS revealed by materials-based cultivation

Microbial responses to xenobiotic compounds are difficult to resolve due to environmental complexity and limited functional annotation. Here, we establish a materials-based cultivation framework using macroporous elastomeric silicone foams (MESIF) to capture microbial adaptation across environmental contexts and timescales. Using glyphosate as a model compound and per- and polyfluoroalkyl substances (PFAS) as a poorly understood class, we show that responses differ depending on the availability of established metabolic pathways. Glyphosate exposure induced rapid, pathway-specific functional enrichment with minimal taxonomic change. In contrast, PFAS exposure did not yield consistent taxonomic or annotation-based signals but instead produced responses that emerged over time and were primarily detectable at protein and genome-resolved levels. LC-MS analyses revealed transformation dynamics, including formation of shorter-chain products. These responses were not explained by known degrader taxa but involved uncharacterized proteins and microbial populations, highlighting the extent of functional "dark matter" in microbial responses to persistent contaminants.

microbiology↗

bioRxiv2025

Structural and regulatory determinants of flagellar motility in Rhodobacterales - The archetypal flagellum of Phaeobacter inhibens DSM 17395

Flagellar motility is crucial for the swim-and-stick lifestyle of Rhodobacterales and plays an important role for bacterial-algal interactions. This alphaproteobacterial order contains three distinct types of flagellar gene clusters (FGCs) for the formation of a functional flagellum. Our phylogenetically broad taxon sampling of more than 300 genomes revealed that the most common FGC, the fla1-type, was probably already present in the common ancestor of Rhodobacterales and was strictly vertically inherited, while the other two FGC types, fla2 and fla3, were spread via horizontal operon transfers. Swimming of the marine model organism Phaeobacter inhibens DSM 17395 (Roseobacteraceae) is mediated by the archetypal fla1-type flagellum. Screening of 13,000 transposon mutants of P. inhibens on soft agar plates revealed that 40 genes, including four genes encoding conserved but not yet characterized proteins (CP1-4) within the FGC, are essential for motility. Exoproteome analyses indicated that CP1-4 are required at different stages of flagellar assembly. Only eight genes outside the FGC were identified as essential for swimming motility, including all three genes of the CtrA phosphorelay. Using comparative transcriptomics of {Delta}cckA, {Delta}chpT and {Delta}ctrA mutants of the distantly related model organisms P. inhibens and Dinoroseobacter shibae DFL 12, we identified genes for the flagellum and cyclic di-GMP turnover as core targets of the CtrA phosphorelay and a conserved connection with quorum sensing across members of the Rhodobacterales. ImportanceThe bacterial flagellum is a sophisticated nanomachine for swimming motility and rapid chemotactic response to gradients of attractants or repellents in the environment. It is structurally highly conserved and has been intensively studied in gammaproteobacterial standard bacteria such as Escherichia coli and Salmonella enterica. However, the flagellar gene clusters of different alphaproteobacterial orders have distinct structures and compositions, as demonstrated by the three flagellar systems of Rhodobacterales investigated in the current study. The archetypal fla1-type flagellum originated in its common ancestor and evolved synchronously with the host. The universal presence of four as yet uncharacterized essential genes in fla1-type FGCs (CP1-4) reflects the order-specific adaptation of the flagellar system during bacterial evolution. Comparative transcriptome analyses of {Delta}cckA, {Delta}chpT and {Delta}ctrA mutants showed that the core function of the CtrA phosphorelay in Rhodobacterales is the expression of flagellar genes.

microbiology↗

bioRxiv2023

Midi-metagenomics: A novel approach for cultivation independent microbial genome reconstruction from environmental samples

Since the majority of microbial organisms still evade cultivation attempts, genomic insights into many taxa are limited to cultivation-independent approaches. However, current methods of metagenomics and single cell genome sequencing have individual drawbacks, which can limit the quality as well as completeness of the reconstructed genomes. Current attempts to combine both approaches still use amplification techniques which are prone to bias. Here, we propose a novel approach for the purpose of genome reconstructions, that utilizes the potential of cell sorting for targeted enrichment and depletion of different cell types to create distinct cell fractions of sufficient size, circumventing amplification. By distributing sequencing efforts over these fractions as well as the original sample, co-assemblies become highly optimized for co-abundance variation based binning approaches. "Midi-metagenomics" enables accurate metagenome assembled genome (MAG) reconstruction from individual sorted samples with higher quality than co-assembly of multiple distinct samples and has potential for the targeted enrichment and sequencing of microbial dark matter.

genomics↗

bioRxiv2016

No evidence for a bovine mastitis Escherichia coli pathotype

BackgroundEscherichia coli bovine mastitis is a disease of significant economic importance in the dairy industry. Molecular characterization of mastitis-associated E. coli (MAEC) did not result in the identification of common traits. Nevertheless, a mammary pathogenic E. coli (MPEC) pathotype has been proposed suggesting virulence traits that differentiate MAEC from commensal E. coli. The present study was designed to investigate the MPEC pathotype hypothesis by comparing the genomes of MAEC and commensal bovine E. coli.\n\nResultsWe sequenced the genomes of eight E. coli isolated from bovine mastitis cases and six fecal commensal isolates from udder-healthy cows. We analyzed the phylogenetic history of bovine E. coli genomes by supplementing this strain panel with eleven bovine-associated E. coli from public databases. The majority of the isolates originate from phylogroups A and B1, but neither MAEC nor commensal strains could be unambiguously distinguished by phylogenetic lineage. The gene content of both MAEC and commensal strains is highly diverse and dominated by their phylogenetic background. Although individual strains carry some typical E. coli virulence-associated genes, no traits important for pathogenicity could be specifically attributed to MAEC. Instead, both commensal strains and MAEC have very few gene families enriched in either pathotype. Only the aerobactin siderophore gene cluster was enriched in commensal E. coli within our strain panel.\n\nConclusionsThis is the first characterization of a phylogenetically diverse strain panel including several MAEC and commensal isolates. With our comparative genomics approach we could not confirm previous studies that argue for a positive selection of specific traits enabling MAEC to elicit bovine mastitis. Instead, MAEC are facultative and opportunistic pathogens recruited from the highly diverse bovine gastrointestinal microbiota. Virulence-associated genes implicated in mastitis are a by-product of commensalism with the primary function to enhance fitness in the bovine gastrointestinal tract. Therefore, we put the definition of the MPEC pathotype into question and suggest to designate corresponding isolates as MAEC.

genomics↗