P. H. Nielsen

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants

The paper improves 16S rRNA gene primers to better detect Patescibacteria in wastewater treatment plants, revealing their global diversity and potential ecological roles.

MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters

The paper expands the MiDAS database with global anaerobic digester microbiome data, revealing environmental influences on microbial communities and identifying core taxa.

Amplicon-guided isolation and cultivation of previously uncultured microbial species from activated sludge

This paper introduces an experimental method to isolate previously uncultured microbial species from activated sludge using 16S rRNA gene amplicon sequencing, resulting in the cultivation of 102 strains from 200 colonies.

A comprehensive overview of the Chloroflexota community in wastewater treatment plants worldwide

This study characterizes Chloroflexota in wastewater treatment plants globally, identifying novel taxa and their ecological roles in carbon and nutrient cycling.

Production of extracellular polymeric substances in granular sludge under selection for Accumulibacter and Competibacter

This study investigates how microbial selection influences extracellular polymeric substance (EPS) production in granular sludge, showing that slow-growing organisms enhance granulation and EPS formation.

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

The paper sequenced closed genomes of cable bacteria, identifying a new species in brackish water and suggesting it bridges marine and freshwater lineages.

Signatures of Microbial Diversity at Multiple Scales of Resolution within Engineered Enrichment Communities

The paper examines microbial diversity signatures in lab-scale and full-scale phosphorus removal communities across multiple phylogenetic scales.

Re-evaluation of the phylogenetic diversity and global distribution of the genus Candidatus Accumulibacter

This paper re-evaluates the phylogeny and taxonomy of Candidatus Accumulibacter using genome, ppk1, and 16S rRNA gene data, identifying 15 new species and confirming PAO metabolism across all species.

MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

The paper constructs MiDAS 4, a comprehensive 16S rRNA gene reference database for wastewater treatment plants, improving classification accuracy and revealing microbial community patterns globally.

Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbiome structure and key drivers

This study characterizes the microbial communities in 46 anaerobic digesters over six years, identifying key drivers shaping microbiome structure and highlighting the role of immigration in bacterial diversity.

Connecting structure to function with the recovery of over 1000 high-quality activated sludge metagenome-assembled genomes encoding full-length rRNA genes using long-read sequencing

The paper uses long-read sequencing to recover over 1000 high-quality MAGs from wastewater treatment plants, enabling linkage of microbial community structure to function.

Global warming readiness: Feasibility of enhanced biological phosphorus removal from wastewater at 35oC

This study demonstrates that enhanced biological phosphorus removal (EBPR) can be stable at 35°C in lab-scale reactors, with nearly complete phosphorus removal and diverse PAO communities.

Quantification of biologically and chemically bound phosphorus in activated sludge from full-scale plants with biological P-removal

This study quantifies different phosphorus fractions in activated sludge from EBPR plants using multiple analytical techniques and finds that polyphosphate constitutes a significant portion of total phosphorus, primarily stored in known polyphosphate-accumulating organisms.

Candidatus Dechloromonas phosphatis and Candidatus Dechloromonas phosphovora, two novel polyphosphate accumulating organisms abundant in wastewater treatment systems

The paper identifies two novel polyphosphate accumulating organisms in wastewater treatment systems using metagenomics and FISH-Raman techniques, confirming their role in phosphorus removal.

A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria

The paper develops and evaluates new highly specific 16S rRNA-targeted oligonucleotide probes for accurate detection and differentiation of ammonia-oxidizing bacteria in environmental samples.

Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

This study identifies haloalkalitolerant Nitrospira species in extreme pH lakes, revealing their diversity and adaptive traits for nitrite oxidation at high pH.

Generation of comprehensive ecosystems-specific reference databases with species-level resolution by high-throughput full-length 16S rRNA gene sequencing and automated taxonomy assignment (AutoTax)

The paper generates ecosystem-specific 16S rRNA gene reference databases with high-identity sequences and introduces AutoTax for automated taxonomy assignment, improving classification accuracy for microbial communities.

Species-level microbiome composition of activated sludge - introducing the MiDAS 3 ecosystem-specific reference database and taxonomy

The paper introduces MiDAS 3, a 16S rRNA gene reference database for activated sludge and anaerobic digesters, and updates the MiDAS Field Guide with species-level taxonomy and functional information.

The proteome of Tetrasphaera elongata is adapted to changing conditions in wastewater treatment plants

This study investigates how Tetrasphaera elongata adapts to aerobic-anoxic shifts in wastewater treatment plants using proteomics and metabolomics, revealing efficient substrate utilization and pre-existing anaerobic pathways.

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta

This paper characterizes a thaumarchaeal symbiont in the sponge Ianthella basta, showing it is the sole ammonia-oxidizer and reveals adaptations for a mixotrophic lifestyle.

Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman-FISH

This study develops a single-cell approach to quantify microbial contributions to phosphorus removal in wastewater treatment plants and identifies Tetrasphaera as a key player in some systems.

The ecology of the Chloroflexi in full-scale activated sludge wastewater treatment plants

This study identifies key Chloroflexi genera in wastewater treatment plants and their ecological roles, showing some contribute to bulking while others are structurally important.

Novel prosthecate bacteria from the candidate phylum Acetothermia revealed by culture-independent genomics and advanced microscopy

The paper identifies a novel Acetothermia bacterium from anaerobic digesters, characterizes its genome and metabolism, and proposes a role for its unique prosthecae in nutrient uptake.

Peatland Acidobacteria with a dissimilatory sulfur metabolism

The paper identifies novel Acidobacteria in peatlands with sulfur metabolism capabilities, including both sulfate respiration and sulfur oxidation, and highlights their ecological roles in organic matter decomposition.

Identifying the abundant and active microorganisms common to full scale anaerobic digesters

The paper identifies abundant and active microorganisms in full-scale anaerobic digesters by analyzing microbial communities over six years using 16S rRNA sequencing.