A5048814675- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Environmental DNA in Biodiversity Studies
- Protist diversity and phylogeny
- Wastewater Treatment and Nitrogen Removal
- Viral Infectious Diseases and Gene Expression in Insects
- CRISPR and Genetic Engineering
University of Duisburg-Essen
2023-2024
University Alliance
2024
Ruhr University Bochum
2023
Abstract Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes enrichment cultures, no single technique render simultaneous data on both metabolic capacities and mobile genetic elements. Here, we apply long-read sequencing to monitor incorporation non-canonical bases genome-resolved metagenomic datasets elucidate replication patterns bacteria phages. This...
Abstract Microbial communities in freshwater streams play an essential role ecosystem functioning via biogeochemical cycling. Yet, the impacts of treated wastewater influx into stream ecosystems on microbial strain diversity remain mostly unexplored. Here, we coupled full‐length 16S ribosomal RNA gene Nanopore sequencing and strain‐resolved metagenomics to investigate impact a mesocosm system (AquaFlow) run with restored river water. Over 10 days, community Bray–Curtis dissimilarities...
Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap knowledge by studying viral infections Altivir_1_MSI biofilms dominated the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from anoxic over a period four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual particles was 15%, show significant steady increase virus 2019 to 2022. Based on fluorescence micrographs...
While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies short-reads often result incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing increasingly been used as long reads greatly improve the assembly quality MAGs, recommended DNA quantity usually exceeds recoverable amount samples. Here, we evaluated lower-than-recommended...
Abstract Background While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies short-reads often result incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing increasingly been used as long reads greatly improve the assembly quality MAGs, recommended DNA quantity usually exceeds recoverable amount samples. Here, we evaluated...
Aquatic ecosystems house a significant fraction of Earth’s biosphere, yet most prokaryotes inhabiting these environments remain uncultivated. While recently developed genome-resolved metagenomics and single-cell genomics techniques have underscored the immense genetic breadth metabolic potential residing in uncultivated Bacteria Archaea, cultivation microorganisms is required to study their physiology via systems, confirm predicted biochemical pathways, exploit biotechnological potential,...
Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes enrichment cultures, no single technique render simultaneous data on both metabolic capacities and mobile genetic elements. Here, we apply long-read sequencing to monitor incorporation non-canonical bases genome-resolved metagenomic datasets elucidate replication patterns bacteria phages. This...
ABSTRACT Lytic viruses can be prevalent in deep groundwater, yet their spatial and temporal distribution such an ecosystem remains unexplored. Here, we tackle this gap of knowledge by studying viral infections individual, archaea-dominated biofilm flocks sampled from anoxic groundwater over a period three years. Using virusFISH whose detection efficiency for individual particles was 15%, show significant steady increase virus between the years 2019 2022. Based on various fluorescence...