D. R. Noguera

Refinement of the "Candidatus Accumulibacter" Genus Based on a Metagenomic Analysis of Biological Nutrient Removal (BNR) Pilot-Scale Plants Operated with Reduced Aeration

This paper refines the 'Candidatus Accumulibacter' genus classification using genome-resolved metagenomics from low-aeration BNR plants, identifying a new species and improving phylogenetic understanding.

Tools for Genetic Engineering and Gene Expression Control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides

This paper develops genetic tools for Novosphingobium aromaticivorans and Rhodobacter sphaeroides to enable efficient gene insertion and expression control using Tn7 transposition and synthetic promoters.

Investigating the chemolithoautotrophic and formate metabolism of Nitrospira moscoviensis by constraint-based metabolic modeling and 13C-tracer analysis

This study reconstructs a genome-scale metabolic model of Nitrospira moscoviensis and validates it using proteomics, 13C-tracer, and metabolomic analysis to elucidate its autotrophic and formate metabolism.

Functional pathway redundancy in the metabolism of plant-derived phenolics by Novosphingobium aromaticivorans

This study identifies a new metabolic pathway in Novosphingobium aromaticivorans for converting phenolic compounds into 2-pyrone-4,6-dicarboxylic acid, improving strain engineering for lignin valorization.

Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mapping

This study uses isotope tracing and metabolomics to resolve the central carbon metabolism of an anammox bacterium, revealing discrepancies between genomic predictions and in vivo metabolic fluxes.

Diagnosing and predicting mixed culture fermentations with unicellular and guild-based metabolic models

The paper constructs two metabolic models to predict and improve medium-chain fatty acid production in microbial communities using genomic, transcriptomic, and metabolomic data.

Anaerobic degradation of syringic acid by an adapted strain of Rhodopseudomonas palustris

This paper isolates and characterizes a Rhodopseudomonas palustris strain capable of anaerobically degrading syringic acid, revealing a novel metabolic pathway distinct from the benzoyl-CoA degradation pathway.

Multi-omic analysis of medium-chain fatty acid synthesis by Candidatus Weimerbacter bifidus, gen. nov., sp. nov., and Candidatus Pseudoramibacter fermentans, sp. nov.

The paper characterizes two MCFA-producing bacteria using multi-omic analysis of an anaerobic microbiome involved in chain elongation from organic waste.

Integrated ‘omic’ analyses provide evidence that a Ca. Accumulibacter phosphatis strain performs denitrification under micro-aerobic conditions

This study uses integrated omics analysis to show that an Accumulibacter strain can simultaneously respire oxygen and nitrate under micro-aerobic conditions, supporting denitrification.

Design and assessment of species-level qPCR primers targeting comammox

The paper designs and tests new qPCR primers for species-level detection of comammox in low DO activated sludge systems, finding Ca. N. nitrosa is abundant while others are rare.

Genome-Enabled Insights Into The Ecophysiology Of The Comammox Bacterium Candidatus Nitrospira nitrosa

This study identifies and compares genomic traits of comammox and nitrite-oxidizing Nitrospira strains to understand their ecological and physiological adaptations.