Biology subjects

Schnurer, A.

Publications and source records attributed to Schnurer, A..

4 recordsLinked to original sources

bioRxiv2026

Stage-resolved dynamics of antibiotic resistance genes and mobile genetic elements in full-scale anaerobic digestion systems

Anaerobic digestion (AD) has the potential to reduce antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) during waste treatment, yet evidence from full-scale plants remains limited and the relative importance of operational and physicochemical drivers is poorly resolved. Here, we profiled stage-resolved resistome and mobilome dynamics across substrates, digestates, and post-digestion storages from ten Swedish farm-scale AD plants (42 samples). High-throughput qPCR (ResistoMap) was combined with absolute 16S rRNA gene quantification and 16S rRNA gene amplicon sequencing to quantify ARG/MGE abundances and characterise bacterial community structure. ARGs and MGEs showed heterogeneous changes during digestion and subsequent storage, with both increases and decreases across plants. Non-metric multidimensional scaling (NMDS) suggested that higher pH and free ammonia were associated with decreasing trends in ARG and MGE relative abundance. Stage-resolved correlation networks revealed a dominant ARG-MGE association backbone that remained largely conserved from substrates to digestates and storage, whereas host-ARG and host-MGE associations were extensively restructured across processing stages. Collectively, these results show that stage-resolved, network-informed analyses offer a more informative framework than pooled, static approaches for evaluating resistance persistence and potential environmental risks associated with digestate application.

microbiology↗

bioRxiv2021

Acetobase: database update and reanalysis offormyltetrahydrofolate synthetase amplicon sequencing data from the anaerobic digesters

AcetoBase is a public repository and database published in 2019, for the formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial formyltetrahydrofolate nucleotide and protein sequences from the genomes and metagenome assembled genomes (MAGs), as well as sequences generated by clone library sequencing. In addition, AcetoBase was first to establish connection between FTHFS gene with the Wood-Ljungdahl pathway and 16S rRNA genes. Since the publication of AcetoBase, significant improvements were seen in the taxonomy of many bacterial lineages and accessibility/availability of public genomics and metagenomics data. Thus, an update to the AcetoBase database with new sequence data and taxonomy has been made along with improvements in web-functionality and user interface. The update in AcetoBase reference database version 2 was furthermore evaluated by reanalysis of publicly accessible FTHFS amplicon sequencing data previously analysed with AcetoBase version 1. The latest database update showed significant improvements in the taxonomic assignments of FTHFS sequences. AcetoBase with its enhancements in functionality and content is publicly accessible at https://acetobase.molbio.slu.se.

bioinformatics↗

bioRxiv2021

Profiling acetogenic community dynamics in anaerobic digesters - comparative analyses using next-generation sequencing and T-RFLP

Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional T-RFLP of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/427894v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@14ac78org.highwire.dtl.DTLVardef@1472ea3org.highwire.dtl.DTLVardef@46fc19org.highwire.dtl.DTLVardef@50ce7a_HPS_FORMAT_FIGEXP M_FIG C_FIG ONE SENTENCE SUMMARYOur high-throughput FTHFS gene AmpSeq method for barcoded samples and unsupervised analysis with AcetoScan accurately reveals temporal dynamics of acetogenic community structure in anaerobic digesters.

microbiology↗

bioRxiv2019

The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation in Methanosarcina mazei.

Inorganic polyphosphate (polyP) is ubiquitous across all forms of life, but the study of its metabolism has been mainly confined to bacteria and yeasts. Few reports detail the presence and accumulation of polyP in Archaea, and little information is available on its functions and regulation. Here, we report that homologs of bacterial polyP metabolism proteins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a greater contribution to global phosphorus cycling than has previously been recognised. We also demonstrate that polyP accumulation can be induced under strictly anaerobic conditions, in response to changes in phosphate (Pi) availability, i.e. Pi starvation, followed by incubation in Pi replete media (overplus), in cells of the methanogenic archaeon Methanosarcina mazei. Pi-starved M. mazei cells increased transcript abundance of the PHO-regulated alkaline phosphatase (phoA) gene and of the high-affinity phosphate transport (pstSCAB-phoU) operon: no increase in polyphosphate kinase 1 (ppk1) transcript abundance was observed. Subsequent incubation of Pi-starved M. mazei cells under Pi replete conditions, led to a 237% increase in intracellular polyphosphate content and a >5.7-fold increase in ppk1 gene transcripts. Ppk1 expression in M. mazei thus appears not to be under classical PHO regulon control.

microbiology↗