Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Авг. 30, 2024

Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity known genomes cause database bias reference-based metagenomics. To improve surveillance, we seek recover sewage develop a quantification correlation workflow for these AMR over time. We use longitudinal sampling seven treatment plants from five major European cities explore the utility catch-all sequencing population-level samples. Using metagenomic assembly methods, 2332 metagenome-assembled (MAGs) prokaryotic species, 1334 which were previously undescribed. These account ~69% sequenced DNA provide insight into microbial dynamics. Rotterdam (Netherlands) Copenhagen (Denmark) show strong seasonal community shifts, while Bologna, Rome, (Italy) Budapest (Hungary) have occasional blooms Pseudomonas-dominated communities, accounting up ~95% sample DNA. Seasonal shifts present challenges effective surveillance. find that bacteria shared origin, like human gut microbiota, form suggesting potential source-attributing novel their ARGs through network analysis. This could significantly tracking environments.

Язык: Английский

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Metagenome‐Assembled Genomes for Oligotrophic Nitrifiers From a Mountainous Gravelbed Floodplain

Environmental Microbiology, Год журнала: 2025, Номер 27(3)

Опубликована: Март 1, 2025

ABSTRACT Riparian floodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, ammonia‐oxidising archaea (AOA) and comammox bacteria Slate River (SR) floodplain sediments (Crested Butte, CO, US). Additionally, explore potential nitrite‐oxidising (NOB) the Nitrospirales . AOA diversity in SR is lower than observed other western US Nitrosotalea ‐like lineages such as genus TA‐20 dominant AOA. No (AOB) were recovered. Microorganisms Palsa‐1315 (clade B comammox) most abundant ammonia‐oxidizers sediments. Established NOB conspicuously absent; however, recovered uncultured of NS‐4 family ( ) Nitrospiraceae that propose putative NOB. Nitrite oxidation may be carried out by organisms sister to established Nitrospira based on genomic content clades. Nitrifier harbour genes using alternative sources ammonia, urea, cyanate, biuret, triuret nitriles. The therefore appears a low ammonia flux environment selects oligotrophic nitrifiers.

Язык: Английский

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Revisiting the interplay between Comammox and Anammox: cooperative or competitive?

Journal of Water Process Engineering, Год журнала: 2025, Номер 75, С. 107918 - 107918

Опубликована: Май 10, 2025

Язык: Английский

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Exploring the ecological niche of comammox Nitrospira by in-situ enrichment within mainstream nitrification systems

Water Research, Год журнала: 2025, Номер unknown, С. 123810 - 123810

Опубликована: Май 1, 2025

Язык: Английский

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Time-series sewage metagenomics can separate the seasonal, human-derived and environmental microbial communities, holding promise for source-attributed surveillance

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 31, 2024

Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity known genomes cause database bias reference-based metagenomics. To improve surveillance, we designed this study recover sewage develop a quantification correlation workflow for these AMR over time. We used longitudinal sampling seven treatment plants from five major European cities explore the utility catch-all sequencing population-level samples. Using metagenomic assembly methods, recovered 2,332 metagenome-assembled (MAGs) prokaryotic species, 1,334 which were previously undescribed. These account ~69% sequenced DNA provide insight into microbial dynamics. Rotterdam (Netherlands) Copenhagen (Denmark) showed strong seasonal community shifts, while Bologna, Rome, (Italy) Budapest (Hungary) had occasional blooms Pseudomonas-dominated communities, accounting up ~95% sample DNA. Seasonal shifts present challenges effective surveillance. find that bacteria shared origin, like human gut microbiota, form suggesting potential source-attributing novel their ARGs through network analysis. This could significantly tracking environments.

Язык: Английский

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Deciphering the roles of nitrogen source in sharping synchronous metabolic pathways of linear alkylbenzene sulfonate and nitrogen in a membrane biofilm for treating greywater

Environmental Research, Год журнала: 2024, Номер 260, С. 119650 - 119650

Опубликована: Июль 20, 2024

Язык: Английский

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