Franco, G. | bioRxiv Science

bioRxiv2026

Microbial persistence beneath temporal restructuring in university wastewater metagenomes

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.

microbiology↗

bioRxiv2024

Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster reefs

Oyster reefs are invaluable ecosystems that provide a wide array of critical ecosystem services, including water filtration, coastal protection, and habitat provision for various marine species. However, these essential habitats face escalating threats from climate change and anthropogenic stressors. To combat these challenges, numerous oyster restoration initiatives have been undertaken, representing a global effort to preserve and restore these vital ecosystems. A significant, yet poorly understood, component of oyster reefs is the microbial communities. These communities account for a substantial proportion of marine reefs and are pivotal in driving key biogeochemical processes. Particularly, the environmental microbiome plays a crucial role in supporting the health and resilience of oyster populations. In our study, we sought to shed light on the microbiome within oyster reef ecosystems by characterizing the abundance, and diversity of microorganisms in the soil, biofilm, and oysters in 4 sites using a combinatorial approach to identify differentially abundant microbes by sample type and by sampling location. Our investigation revealed distinct microbial taxa in oysters, sediment and biofilm. The maximum Shannon Index indicated a slightly increased diversity in Herons Head (5.47), followed by Brickyard park (5.35), Dunphy Park (5.17) and Point Pinole (4.85). This is likely to be driven by significantly higher oyster mortality observed at Point Pinole during routine monitoring and restoration efforts. Interestingly Ruminococcus, Streptococcus, Staphylococcus, Prevotella, Porphyromonas, Parvimonas, Neisseria, Lactococcus, Haemophilus, Fusobacterium, Dorea, Clostridium, Campylobacter, Bacteroides, and Akkermansia were positively associated with the biofilm. Yet we have limited understanding of their beneficial and/or detrimental implications to oyster growth and survival. By unraveling the intricate relationships in microbial composition across an oyster reef, our study contributes to advancing the knowledge needed to support effective oyster reef conservation and restoration efforts.

microbiology↗