Biology subjects

Spröer, C.

Publications and source records attributed to Spröer, C..

4 recordsLinked to original sources

bioRxiv2026

Old Compound, New Context: Naphthocyclinones Mediate Microbial Competition in Wild Bee Nests

Although thousands of microbial specialized metabolites have been identified, the ecological functions of most remain unknown. Naphthocyclinones are aromatic polyketide antibiotics discovered more than five decades ago, yet their biological role has remained elusive. Investigating the microbial community of the oligolectic ivy bee (Colletes hederae), a bacterial community that included several Streptomyces species and members of the class Bacilli was recovered from fermented nest provisions. One Streptomyces isolate, B-004T (DSM 121525T = LMG 34598T), was identified as representing a novel species based on polyphasic taxonomic studies, for which the name Streptomyces hederae sp. nov. is proposed. This strain showed potent antibacterial activity against co-isolated Gram-positive bacteria as well as Paenibacillus larvae, the causative agent of American foulbrood. Bioassay-guided fractionation coupled with liquid chromatography-mass spectrometry analysis led to the identification of naphthocyclinone congeners as the active metabolites. Whole-genome sequencing and genome mining revealed a type II polyketide synthase biosynthetic gene cluster closely related to that of the characterized naphthocyclinone pathway. Targeted deletion of the cluster-encoded ketosynthase gene (B-004_07360) abolished naphthocyclinone production and resulted in the complete loss of antibacterial activity, whereas heterologous overexpression of the Streptomyces antibiotic regulatory protein gene papR2 significantly increased antibiotic production, confirming the function of the naphthocyclinone biosynthetic gene cluster. Furthermore, naphthocyclinone biosynthesis was found to be induced by sympatric bacterial isolates from bee nests. Together, our findings provide the first evidence for an ecological function of naphthocyclinones as mediators of bacterial competition in wild bee nests and highlight their potential as antimicrobial substances against P. larvae.

microbiology↗

bioRxiv2019

Comparative genomics unravels mechanisms of genetic adaptation for the catabolism of the phenylurea herbicide linuron in Variovorax

Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full genome sequences of six linuron degrading Variovorax strains isolated from geographically distant locations were analyzed to acquire insight in the mechanisms of genetic adaptation towards linuron metabolism in Variovorax. Whole genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade within Variovorax and indicated their unlikely origin from a common ancestral linuron degrader. The linuron degraders differentiated from non-degraders by the presence of multiple plasmids of 20 to 839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed (i) high conservation and synteny and (ii) strain-dependent distribution among the different plasmids. All were bordered by IS1071 elements forming composite transposon structures appointing IS1071 as key for catabolic gene recruitment. Most of the strain carried at least one broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire to acquire linuron biodegradation.\n\nImportanceThe genus Variovorax and especially a clade of strains that phylogenetically separates from the majority of Variovorax species, appears to be a specialist in the biodegradation of the phenyl urea herbicide linuron. Horizontal gene transfer (HGT) likely played an essential role in the genetic adaptation of those strain to acquire the linuron catabolic genotype. However, we do not know the genetic repertoire involved in this adaptation both regarding catabolic gene functions as well as gene functions that promote HGT neither do we know how this varies between the different strains. These questions are addressed in this paper by analyzing the full genome sequences of six linuron degrading Variovorax strains. This knowledge is important for understanding the mechanisms that steer world-wide genetic adaptation in a particular species and this for a particular phenotypic trait as linuron biodegradation.

microbiology↗

bioRxiv2018

Genomic inversion drives small colony variant formation and increased virulence in P. aeruginosa

Phenotypic change is a hallmark of bacterial adaptation during chronic infection. In the case of chronic Pseudomonas aeruginosa lung infection in patients with cystic fibrosis, well-characterised phenotypic variants include mucoid and small colony variants (SCVs). It has previously been shown that SCVs can be reproducibly isolated from the murine lung following the establishment of chronic infection with mucoid P. aeruginosa strain NH57388A. Here we show, using a combination of singlemolecule real-time (PacBio) and Illumina sequencing that the genetic switch for conversion to the SCV phenotype is a large genomic inversion through recombination between homologous regions of two rRNA operons. This phenotypic conversion is associated with large-scale transcriptional changes distributed throughout the genome. This global rewiring of the cellular transcriptomic output results in changes to normally differentially regulated genes that modulate resistance to oxidative stress, central metabolism and virulence. These changes are of clinical relevance since the appearance of SCVs during chronic infection is associated with declining lung function.

microbiology↗

bioRxiv2018

Long-read DNA metabarcoding of ribosomal rRNA in the analysis of fungi from aquatic environments

DNA metabarcoding is now widely used to study prokaryotic and eukaryotic microbial diversity. Technological constraints have limited most studies to marker lengths of ca. 300-600 bp. Longer sequencing reads of several 5 thousand bp are now possible with third-generation sequencing. The increased marker lengths provide greater taxonomic resolution and enable the use of phylogenetic methods of classifcation, but longer reads may be subject to higher rates of sequencing error and chimera formation. In addition, most well-established bioinformatics tools for DNA metabarcoding were originally 10 designed for short reads and are therefore not suitable. Here we used Pacifc Biosciences circular consensus sequencing (CCS) to DNA-metabarcode environmental samples using a ca. 4,500 bp marker that included most of the eukaryote ribosomal SSU and LSU rRNA genes and the ITS spacer region. We developed a long-read analysis pipeline that reduced error rates to levels 15 comparable to short-read platforms. Validation using fungal isolates and a mock community indicated that our pipeline detected 98% of chimeras de novo i.e., even in the absence of reference sequences. We recovered 947 OTUs from water and sediment samples in a natural lake, 848 of which could be classifed to phylum, 486 to family, 397 to genus and 330 to species. By 20 allowing for the simultaneous use of three global databases (Unite, SILVA, RDP LSU), long-read DNA metabarcoding provided better taxonomic resolution than any single marker. We foresee the use of long reads enabling the cross-validation of reference sequences and the synthesis of ribosomal rRNA gene databases. The universal nature of the rRNA operon and our recovery of >100 25 non-fungal OTUs indicate that long-read DNA metabarcoding holds promise for the study of eukaryotic diversity more broadly.

ecology↗