Biology subjects

Stubbins, A.

Publications and source records attributed to Stubbins, A..

4 recordsLinked to original sources

bioRxiv2026

Accounting for DNA Recovery and Cell Culturability Enhances Quantitative Compatibility of Molecular and Legiolert Assays for Legionella pneumophila

Disagreement between molecular and culture-based assays for Legionella pneumophila detection is widely reported, yet comparisons have largely been based on direct assay-derived concentrations or binary positive/negative outcomes. However, it remains unclear whether molecular-culture disagreement reflects concentration-level incompatibility or unaccounted methodological and physiological differences related to DNA recovery and cell culturability. In this study, we also observed disagreement between molecular and Legiolert assays in source and finished drinking water samples collected from eight full-scale drinking water systems across the United States. Molecular thresholds adjusted for DNA recovery and cell culturability only partially resolved these discrepancies. We therefore developed a probabilistic Monte Carlo framework that incorporates sample-specific DNA recovery and cell culturability to evaluate the quantitative consistency of culturable L. pneumophila concentrations estimated by molecular and Legiolert assays. Quantitatively consistent and inconsistent samples occurred across both binary concordant and discordant classifications, demonstrating that positive/negative agreement poorly reflects concentration-level comparability. Overall, molecular and Legiolert assays showed strong quantitative consistency once sample-specific DNA recovery and cell culturability were considered. A small proportion of persistent inconsistencies at specific sampling sites, coupled with atypical microbial indicators, suggest that sample heterogeneity likely contributed to the remaining discrepancies. These findings demonstrate that integrating DNA recovery and cell culturability enhanced quantitative consistency between molecular and Legiolert assays and supports the use of molecular methods as rapid quantitative tools to complement culture-based L. pneumophila monitoring. SynopsisAccounting for DNA recovery and cell culturability revealed broad quantitative compatibility between molecular and Legiolert assays for Legionella pneumophila in drinking water. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/739452v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1e01cdcorg.highwire.dtl.DTLVardef@86bbc2org.highwire.dtl.DTLVardef@190fc66org.highwire.dtl.DTLVardef@1aa9ec8_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Legionella and Mycobacterium populations exhibit geographic structuring across and within drinking water systems

Opportunistic pathogens (OPs) within the Legionella and Mycobacterium can persist and sometimes proliferate in drinking water systems and pose a risk to public health. Most prior research has focused on isolated system components of the drinking water treatment and distribution system and has rarely examined spatiotemporal dynamics across the entire source water, treatment process, and distribution system continuum. This study addresses this critical knowledge gap by quantitative profiling of microbial communities with full length 16S rRNA gene sequencing and flow cytometry, and associated water chemistry parameters, including disinfection byproducts (DBPs), across five full-scale utilities. These utilities reflect varying source water types, geographic locations, treatment regimes, and climate zones. Microbial communities, including Legionella and Mycobacterium populations, in distribution system were shaped by source water type and exhibited significant community divergence across utilities. Within the same genus, strain-level analyses revealed highly distinct Legionella and Mycobacterium sequence variants unique to each utility. Interestingly, a substantial proportion of Legionella and Mycobacterium amplicon sequence variants were both utility specific and often specific to locations within the distribution system, indicating strong geographic structuring both across and within drinking water systems. Understanding the mechanistic underpinnings of this geographic structuring is critical to develop robust strategies for managing and monitoring Legionella and Mycobacterium populations in drinking water systems.

microbiology↗

bioRxiv2024

Building plumbing influences the microdiversity and community assembly of the drinking water microbiome.

Building plumbing microbial communities can significantly influence water quality at the point of use, particularly during periods of stagnation. Thus, a fine-scale understanding of factors governing community membership and structure, as well as environmental and ecological factors shaping building plumbing microbial communities is critical. In this study, we utilized full-length 16S ribosomal RNA (rRNA) gene sequencing to investigate the microdiversity and spatial-temporal dynamics of microbial communities in commercial and residential building plumbing systems. Bacterial operational taxonomic units (OTUs) within commercial buildings exhibited much lower microdiversity relative to the same OTUs in residential buildings. Microdiversity was associated with higher persistence and relative abundance of OTUs. Interestingly, amplicon sequencing variants within the same OTUs exhibited habitat preferences based on the building type while also demonstrating varying temporal turnover patterns. Dispersal limitation disproportionately governed community assembly in commercial buildings, whereas heterogeneous selection was the dominant ecological mechanism shaping the microbial community in residential buildings. Dispersal limitation in commercial buildings is consistent with larger building sizes and greater periods of water stagnation. Interestingly, the inability to explain the extent of heterogeneous selection-driven community assembly in residential locations using measured water chemistry may suggest a disproportionately large effect of fine-scale variation in plumbing characteristics on community assembly in residential locations.

microbiology↗

bioRxiv2023

Comammox bacterial preference for urea influences its interactions with aerobic nitrifiers.

While the co-existence of comammox bacteria with canonical nitrifiers is well documented in diverse ecosystems, there is still a dearth of knowledge about the mechanisms underpinning their interactions. Understanding these interaction mechanisms is important as they may play a critical role in governing nitrogen biotransformation in natural and engineered ecosystems. In this study, we tested the ability of two environmentally relevant factors (nitrogen source and availability) to shape interactions between strict ammonia and nitrite-oxidizing bacteria and comammox bacteria in continuous flow column reactors. The composition of inorganic nitrogen species in reactors fed either ammonia or urea was similar during the lowest nitrogen loading condition (1 mg-N/L), but higher loadings (2 and 4 mg-N/L) promoted significant differences in nitrogen species composition and nitrifier abundances. The abundance and diversity of comammox bacteria were dependent on both nitrogen source and loading conditions as multiple comammox bacterial populations were preferentially enriched in the urea-fed system. In contrast, their abundance was reduced in response to higher nitrogen loadings in the ammonia-fed system likely due to ammonia-based inhibition. The preferential enrichment of comammox bacteria in the urea-fed system could be associated with their ureolytic activity calibrated to their ammonia oxidation rates thus minimizing ammonia accumulation to inhibitory levels. However, an increased abundance of comammox bacteria was not associated with a reduced abundance of nitrite oxidizers in the urea-fed system while a negative correlation was found between them in the ammonia-fed system; the latter dynamic likely emerging from reduced availability of nitrite to strict nitrite oxidizers at low ammonia loading conditions. ImportanceNitrification is an essential biological process in drinking water and wastewater treatment systems for managing nitrogen and protecting downstream water quality. The discovery of comammox bacteria and their detection alongside canonical nitrifiers in these engineered ecosystems has made it necessary to understand the environmental conditions that regulate their abundance and activity relative to other better-studied nitrifiers. This study aimed to evaluate two important factors that could potentially influence the behavior of nitrifying bacteria, and therefore impact nitrification processes. Colum reactors fed with either ammonia or urea were systematically monitored to capture changes in nitrogen biotransformation and the nitrifying community as a function of influent nitrogen concentration, nitrogen source, and reactor depth. Our findings show that comammox bacterial abundance decreased and that of nitrite oxidizers increased with increased ammonia availability, while their abundance and diversity increased with increasing urea availability without driving a reduction in the abundance of canonical nitrifiers.

microbiology↗