Microbial persistence beneath temporal restructuring in university wastewater metagenomes
- 1San Francisco State University
Abstract
Temporal changes in wastewater microbiomes can reflect shifts in microbial abundance, detectable membership, and genome recovery. We paired genome-resolved and read-based metagenomics to distinguish these signals in 25 spatially pooled university wastewater samples collected during wet and dry periods. The workflow recovered 203 wet-period and 230 dry-period metagenome-assembled genomes (MAGs). Community composition differed between periods in both MAG-derived presence/absence profiles (Jaccard PERMANOVA, R2 = 0.548, p = 0.001) and read-based relative-abundance profiles (BrayCurtis PERMANOVA, R2 = 0.167, p = 0.001). Greater dry-period read-based richness persisted after rarefaction but disappeared under more stringent abundance thresholds, indicating a substantial contribution from low-abundance detections. Of 57 period-associated core species in the MAG-derived profiles, 14 had exact species-level matches in the read-based dataset. All 14 remained detectable at >=90% prevalence in the opposite period, and 13 had higher relative abundance in the period corresponding to their MAG-based association. Continued species detection therefore accompanied changes in community composition and MAG-based representation. Perfect/Strict CARD/RGI resistance-associated annotations occurred in 94.1% of wet-period and 92.2% of dry-period MAGs and were distributed across shared-core and period-associated taxa. These findings reveal repeated detection of a matched subset of microbial taxa beneath temporal community restructuring, together with widespread resistance-associated genetic potential among recovered genomes. Combining read-based and genome-resolved profiles helps distinguish changes in detectable membership from changes in the genomic characterization available for wastewater surveillance.
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BibTeX
@misc{franco2026microbial,
title = {{Microbial persistence beneath temporal restructuring in university wastewater metagenomes}},
author = {G. Franco and A. Anand},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.13.758942},
url = {https://www.biorxiv.org/content/10.64898/2026.10.13.758942v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Microbial persistence beneath temporal restructuring in university wastewater metagenomes
AU - G. Franco
AU - A. Anand
PY - 2026
DA - 2026/10/13
PB - bioRxiv
DO - 10.64898/2026.10.13.758942
UR - https://www.biorxiv.org/content/10.64898/2026.10.13.758942v1
AB - Temporal changes in wastewater microbiomes can reflect shifts in microbial abundance, detectable membership, and genome recovery. We paired genome-resolved and read-based metagenomics to distinguish these signals in 25 spatially pooled university wastewater samples collected during wet and dry periods. The workflow recovered 203 wet-period and 230 dry-period metagenome-assembled genomes (MAGs). Community composition differed between periods in both MAG-derived presence/absence profiles (Jaccard PERMANOVA, R2 = 0.548, p = 0.001) and read-based relative-abundance profiles (BrayCurtis PERMANOVA, R2 = 0.167, p = 0.001). Greater dry-period read-based richness persisted after rarefaction but disappeared under more stringent abundance thresholds, indicating a substantial contribution from low-abundance detections. Of 57 period-associated core species in the MAG-derived profiles, 14 had exact species-level matches in the read-based dataset. All 14 remained detectable at >=90% prevalence in the opposite period, and 13 had higher relative abundance in the period corresponding to their MAG-based association. Continued species detection therefore accompanied changes in community composition and MAG-based representation. Perfect/Strict CARD/RGI resistance-associated annotations occurred in 94.1% of wet-period and 92.2% of dry-period MAGs and were distributed across shared-core and period-associated taxa. These findings reveal repeated detection of a matched subset of microbial taxa beneath temporal community restructuring, together with widespread resistance-associated genetic potential among recovered genomes. Combining read-based and genome-resolved profiles helps distinguish changes in detectable membership from changes in the genomic characterization available for wastewater surveillance.
ER -