A5047368212- Microbial Community Ecology and Physiology
- Wastewater Treatment and Nitrogen Removal
- Genomics and Phylogenetic Studies
- Anaerobic Digestion and Biogas Production
- Alzheimer's disease research and treatments
- Bacterial biofilms and quorum sensing
- Microbial Fuel Cells and Bioremediation
- Gut microbiota and health
- Oral microbiology and periodontitis research
- Bacterial Genetics and Biotechnology
- Environmental DNA in Biodiversity Studies
- Water Treatment and Disinfection
- Microbial Metabolic Engineering and Bioproduction
- Parkinson's Disease Mechanisms and Treatments
- Water Quality Monitoring Technologies
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Protein Structure and Dynamics
- Microbial bioremediation and biosurfactants
- Chromium effects and bioremediation
- Protist diversity and phylogeny
- Vibrio bacteria research studies
- Enzyme Production and Characterization
- Bacteriophages and microbial interactions
- Methane Hydrates and Related Phenomena
Aalborg University
2016-2025
Ecologie Microbienne Lyon
2018
Aarhus University
2009-2011
Summary Surface‐associated amyloid fibrils have been described by bacteria in the family Enterbacteriaceae , but it is unknown to what extent adhesins are present natural biofilms. In this study, were specifically stained with Thioflavin T and two conformationally specific antibodies targeting fibrils. These three independent detection methods each combined fluorescence situ hybridization using fluorescently labelled oligonucleotide probes order link phenotype identity. Escherichia coli...
Abstract Microorganisms play crucial roles in water recycling, pollution removal and resource recovery the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential absence high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read short-read recover 1083 MAGs, including 57 closed circular genomes, from 23 Danish...
Abstract Microbial communities are responsible for biological wastewater treatment, but our knowledge of their diversity and function is still poor. Here, we sequence more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 treatment plants (WWTPs) across the world use to construct ‘MiDAS 4’ database. MiDAS 4 an amplicon variant resolved, reference database with a comprehensive taxonomy domain species level all sequences. We independent dataset (269 WWTPs) show that 4,...
Amyloids are highly abundant in many microbial biofilms and may play an important role their architecture. Nevertheless, little is known of the amyloid proteins. We report discovery a novel functional expressed by Pseudomonas strain P. fluorescens group. The protein was purified amyloid-like structure verified. Partial sequencing MS/MS combined with full genomic identified gene coding for major subunit fibril, termed fapC. FapC contains thrice repeated motif that differs from those...
The function of the microbiomes in wastewater treatment systems and anaerobic digesters is dictated by physiological activity their members complex interactions between them. Since functional traits are often conserved at low taxonomic ranks (genus, species, strain), high resolution classification crucial to understand role microbes any ecosystem. Here we present MiDAS 3, a comprehensive 16S rRNA gene reference database based on full-length amplicon sequence variants (FL-ASVs) derived from...
Anaerobic digestion for biogas production is reliant on the tightly coupled synergistic activities of complex microbial consortia. Members uncultured A6 phylotype, within phylum Chloroflexi, are among most abundant genus-level-taxa mesophilic anaerobic digester systems treating primary and surplus sludge from wastewater treatment plants, yet known only by their 16S rRNA gene sequence. This study applied metagenomics to obtain a complete circular genome (2.57 Mbp) representative taxon....
Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands cells. They occur worldwide in surface aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In absence pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes 3 marine Candidatus Electrothrix 1 freshwater Ca. Electronema species. These contain >50% unknown genes but still share their core...
Abstract Short-chain fatty acid (SCFA) degradation is an important process in methanogenic ecosystems, and usually catalyzed by SCFA-oxidizing bacteria syntrophy with methanogens. Current knowledge of this functional guild mainly based on isolates or enrichment cultures, but these may not reflect the true diversity situ activities syntrophs predominating full-scale systems. Here we obtained 182 medium to high quality metagenome-assembled genomes (MAGs) from microbiome two anaerobic...
The bacterial genus Tetrasphaera encompasses abundant polyphosphate accumulating organisms (PAOs) that are responsible for enhanced biological phosphorus removal (EBPR) in wastewater treatment plants. Recent analyses of genomes from pure cultures revealed 16S rRNA genes cannot resolve the lineage, and spp. several different genera within Dermatophilaceae. Here, we examine 14 recently recovered high-quality metagenome-assembled plants containing full-length identified as Tetrasphaera, 11...
The Saprospiraceae family within the phylum Bacteroidota is commonly present and highly abundant in wastewater treatment plants (WWTPs) worldwide, but little known about its role. In this study, we used MiDAS 4 global survey with samples from 30 countries to analyze abundance distribution of members Saprospiraceae. Phylogenomics were delineate five new genera a set 31 high-quality metagenome-assembled genomes Danish WWTPs. Newly designed probes for fluorescence situ hybridization (FISH)...
Abstract Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity function the bacteria archaea in ADs worldwide. The sequences are processed amplicon sequence variants (FL-ASVs) used MiDAS 4 database for wastewater treatment systems, creating 5. expansion increases coverage worldwide, leading...
Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance of Patescibacteria due to low coverage commonly used PCR primers highly divergent bacterial phylum. Therefore, our current understanding global diversity, distribution, ecological role WWTPs very incomplete. This particularly relevant as considered be...
The success of Pseudomonas species as opportunistic pathogens derives in great part from their ability to form stable biofilms that offer protection against chemical and mechanical attack. extracellular matrix contains numerous biomolecules, it has recently been discovered one the components includes β-sheet rich amyloid fibrils (functional amyloid) produced by fap operon. However, role functional within biofilm not yet investigated detail. Here we investigate how fap-based affects...
The fap operon, encoding functional amyloids in Pseudomonas (Fap), is present most pseudomonads, but so far the expression and importance for biofilm formation has only been investigated P. fluorescens strain UK4. In this study, we demonstrate capacity of aeruginosa PAO1, Pf-5, putida F1 to express Fap fibrils, effect on aggregation formation. operon all three species conferred ability fibrils as shown using a recombinant approach. This overexpression consistently resulted highly aggregative...
Anaerobic digestion is widely applied to treat organic waste at wastewater treatment plants. Characterisation of the underlying microbiology represents a source information develop strategies for improved operation. Hence, we investigated microbial communities thirty-two full-scale anaerobic digesters over six-year period using 16S rRNA gene amplicon sequencing. Sampling sludge fed into these systems revealed that several most abundant populations were likely inactive and immigrating with...
Escherichia coli and a few other members of the Enterobacteriales can produce functional amyloids known as curli. These extracellular fibrils are involved in biofilm formation studies have shown that they may act virulence factors during infections. It is not whether curli restricted to or if phylogenetically widespread. The growing number genome-sequenced bacteria spanning many phylogenetic groups allows reliable bioinformatic investigation diversity system. Here we show system much more...
High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this presently hampered by lack high-identity reference sequences many environmental microbes in public databases absence a systematic comprehensive taxonomy uncultured majority. Here, we demonstrate how high-throughput synthetic long-read can be applied to create ecosystem-specific full-length sequence variant (FL-ASV) resolved that include...
Anaerobic digestion (AD) is a key technology at many wastewater treatment plants (WWTPs) for converting primary and surplus activated sludge to methane-rich biogas. However, the limited number of surveys lack comprehensive datasets have hindered deeper understanding characteristics associations between variables microbial community composition. Here, we present six-year survey 46 anaerobic digesters, located 22 WWTPs in Denmark, which first largest known study ecology AD regional scale. For...
Abstract Microbial communities in activated sludge (AS) are the core of sanitation wastewater treatment plants (WWTPs). AS have shown seasonal changes, however, long-term experiments (>2 years) rarely conducted, limiting our understanding true dynamics WWTPs. In this study, we resolved microbial at species level four municipal full-scale WWTPs, sampled every 7–10 days, during 3–5 consecutive years. By applying a new time-series analysis approach, revealed that pattern was...
"Candidatus Accumulibacter" was the first microorganism identified as a polyphosphate-accumulating organism (PAO) important for phosphorus removal from wastewater. Members of this genus are diverse, and current phylogeny taxonomic framework appear complicated, with most publicly available genomes classified Accumulibacter phosphatis," despite notable phylogenetic divergence. The ppk1 marker gene allows finer-scale differentiation into different "types" "clades"; nevertheless, assignments...
Abstract Anaerobic digestion represents a key biotechnology for the transformation of organic waste into renewable energy (biogas) and relies on complex microbial communities that work in concert to degrade substrates methane carbon dioxide. Here, we sequenced more than half million high-quality, full-length 16S rRNA gene sequences from 285 full-scale anaerobic digesters (ADs) across world expand our knowledge about diversity function bacteria archaea ADs. The were processed amplicon...