About

Rachel T. Noble is the Mary and Watts Hill Jr. Distinguished Professor of Marine Science at the University of North Carolina at Chapel Hill, within the Department of Earth, Marine and Environmental Sciences. She earned her Ph.D. in Biological Sciences from the University of Southern California in 1998. Her laboratory focuses on unraveling complex pathways of pathogen exposure in humans, aquaculture, food safety, built environments, and water quality. Using advanced molecular tools, her research tracks emerging pathogens to support public health initiatives, assist the shellfish aquaculture industry, and collaborate with municipal governments on coastal water quality issues. Her work aims to advance knowledge of viral, bacterial, and fungal mold pathogens with the goal of prioritizing resource allocation and improving public health. She is dedicated to serving rural coastal communities through collaboration and building trust.

Research topics

• Environmental science
• Medicine
• Environmental health
• Environmental engineering
• Business
• Environmental planning
• Virology
• Environmental protection
• Ecology
• Natural resource economics
• Pathology
• Engineering
• Intensive care medicine
• Waste management
• Biology

Selected publications

• Bio-Rad and QIAGEN digital PCR platforms provide equivalent quantification for wastewater-based SARS-CoV-2 surveillance

  Applied and Environmental Microbiology · 2026-04-22

  articleOpen accessSenior author

  ABSTRACT Digital PCR (dPCR) is increasingly used for wastewater surveillance due to its precision, absolute quantification, and reduced sensitivity to inhibition compared to quantitative PCR (qPCR). Although the Bio-Rad QX200 and QIAGEN QIAcuity dPCR platforms are widely adopted, their performance has not been directly compared for wastewater applications. We conducted a blinded comparison of these platforms using 93 archived wastewater influent samples from North Carolina collected in 2021–2022, spanning three orders of magnitude in SARS-CoV-2 concentration (1 × 10 3 –5 × 10 5 copies L −1 ). Samples were stratified into low, medium, and high concentration bins and analyzed in triplicate for N1 and N2 gene targets and a bovine coronavirus processing control. Both platforms demonstrated statistically equivalent quantification across all targets, with mean differences ≤0.12 log copies L −1 ( R 2 > 0.93). Coefficients of variation were similar (3.96%–7.61%), with no significant differences across concentration bins except for N2 in the low bin (difference: 0.87 percentage points). Measurement variability correlated strongly with wastewater treatment plant site ( R 2 = 0.89) rather than platform, indicating that sample matrix characteristics drive precision more than the analytical platform. Process limits of detection ranged from 2,160 to 2,680 copies L −1 for Bio-Rad QX200 and 5,650–9,700 copies L −1 for QIAGEN QIAcuity for N1 and N2, respectively. The Bio-Rad QX200 platform processed samples 32% faster (305 vs 435 minutes per 96 wells), while QIAGEN QIAcuity offered 29% lower consumables cost ($4.68 vs $6.11 per well). These findings support the interchangeable use of both platforms for wastewater surveillance, with platform selection based on laboratory-specific operational needs. IMPORTANCE As wastewater-based epidemiology transitions from emergency response to sustained public health infrastructure, standardized molecular methods are essential for reliable data integration across surveillance networks. This study provides the first blinded comparison of two dPCR platforms widely deployed for wastewater pathogen surveillance in the United States. We demonstrate quantitative equivalence between Bio-Rad QX200 and QIAGEN QIAcuity platforms across three orders of magnitude in viral concentration, establishing that data from both platforms can be interpreted interchangeably for public health decision-making. This platform equivalence is critical as national surveillance systems aggregate data from diverse laboratories and as monitoring expands beyond SARS-CoV-2 to encompass additional respiratory viruses, antimicrobial resistance genes, and emerging pathogens. Our findings provide a methodological foundation for multi-platform surveillance networks and demonstrate that measurement variability is driven primarily by sample matrix characteristics rather than analytical platform choice.

  PublisherDOI

• Survey of pathogens and human fecal markers in stormwater across a highly populated urban region

  Environmental Science Processes & Impacts · 2025-01-01 · 1 citations

  article

  . We reported PCR inhibition in 83-90% of the samples but found that separating sediment and adding proteinase K during lysis improved DNA/RNA extraction efficiency and reduced inhibition.

  PublisherDOI

• Broodstock Genetics, More than Ploidy Alone, Explains Oyster Resilience at Farm Sites Impacted by Sudden Unusual Mortality Syndrome (Sums)

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• Broodstock genetics, more than ploidy alone, explains oyster resilience at farm sites impacted by sudden unusual mortality syndrome

  Aquaculture · 2025-05-11 · 2 citations

  article
  PublisherDOI

• Advancing Wastewater-Based Epidemiology through Curricular Innovation

  ACS ES&T Water · 2025-07-30

  article
  PublisherDOI

• Bacterial community analysis of recreational beach waters reveals human fecal contamination and pathogenicity across varying field conditions

  Water Research · 2025-04-22 · 1 citations

  articleOpen access

  Assessing human fecal contamination of recreational beach waters is a public health challenge owing to multiple sources and environmental conditions affecting indicator, pathogen, and source marker relationships. Human fecal-associated markers, such as HF183, accurately indicate human waste, but reliance on individual markers risks false negative diagnoses, owing to marker source loading variations and attenuation. Bacterial community analysis is a data-dense approach that could improve the accuracy of human waste detection, but relatedness to actual human health hazards under complex coastal water conditions is unproven. Here, two Malibu and one Pacific Palisades, CA recreational beaches differing in urbanization and sewerage were studied over two years across varying seasonal rainfall, and beach berm, conditions. Fecal indicator bacteria (FIB), HF183, and human norovirus concentrations were quantified and related to bacterial community 16S rRNA gene sequences which were further analyzed for putative human pathogens and sewage proportions. All lower watersheds harbored human fecal sources, and surf zone contamination was enhanced by rainfall runoff with berm breaching, which intensified with urbanization. Notably, for sequenced surf zone waters sampled across all weather conditions (n = 36), sequence-based putative pathogen proportions correlated with qPCR HF183 concentrations (w/ and w/o PMA treatment; p = 0.0) and with human norovirus G1concentrations (p = 0.04) which also correlated with HF183 sequence abundance in bacterial communities (p = 0.02). Although human fecal sources appeared to vary seasonally and a range of physical conditions influenced surf zone fecal contamination, human fecal contamination and associated health hazard were reliably evidenced by bacterial community analysis in this study.

  PublisherDOI

• Farmed oyster mortality follows consistent Vibrio community reorganization

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-24 · 1 citations

  preprintOpen accessSenior author

  Abstract Mortality events in marine bivalves cause substantial economic losses in aquaculture, yet the microbial dynamics underlying these events remain poorly characterized. Here, we investigated succession patterns in oyster-associated Vibrio communities during mortality events by sampling eastern oysters ( Crassostrea virginica ) at a North Carolina commercial farm that has experienced repeated, unexplained mortality events. Through whole-genome sequencing of 110 Vibrio isolates from 26 oysters sampled across mortality events in two consecutive years, we identified six conserved phylogenetic clades with distinct temporal associations. Vibrio mediterranei and a clade of resident Vibrios consistently dominated the initial cultured community at the onset of mortality. However, V. mediterranei was absent as mortality progressed, coinciding with increased abundance of V. harveyi, V. alginolyticus, V. diabolicus , and V. astriarenae . Comparative genomic analysis revealed that initial isolates were enriched in pathways associated with host colonization and complex carbon metabolism, while isolates from elevated mortality showed enrichment in virulence mechanisms and adaptation to degraded host tissues. Temporal separation between genetically distinct clades suggests microbial competition shapes community assembly during mortality events that ultimately reached >85% in both years. This predictable succession from commensal to potentially pathogenic Vibrio species provides genome-level insight into microbial community dynamics during oyster mortality. The consistent absence of V. mediterranei prior to severe mortality suggests this species could serve as a bioindicator for early warning systems to mitigate economic losses in shellfish aquaculture. Importance Mortality events in aquaculture systems represent complex host-microbe-environment interactions that challenge our ability to predict and prevent disease. By characterizing succession patterns in oyster-associated Vibrio communities at whole-genome resolution, we reveal a consistent transition from metabolically versatile species associated with healthy oysters to functionally distinct Vibrio taxa enriched in virulence factors and tissue degradation pathways as mortality progresses. This genome-level evidence for predictable community reorganization suggests that monitoring commensal Vibrio populations, particularly the presence or absence of V. mediterranei , could provide earlier warning of impending disease compared to tracking only known pathogens. This shift in monitoring approach could advance aquaculture disease management while expanding our fundamental understanding of how microbial community transitions contribute to host health and disease progression.

  PublisherOA PDFDOI

• Farmed oyster mortality follows consistent Vibrio community reorganization

  mSystems · 2025-10-02 · 4 citations

  articleOpen accessSenior author

  ABSTRACT Mortality events in marine bivalves cause substantial economic losses in aquaculture, yet the microbial dynamics underlying these events remain poorly characterized. Here, we investigated succession patterns in oyster-associated Vibrio communities during mortality events by sampling eastern oysters ( Crassostrea virginica ) at a North Carolina commercial farm that has experienced repeated, unexplained mortality events. Through whole-genome sequencing of 110 Vibrio isolates from 26 oysters sampled across mortality events in two consecutive years, we identified six conserved phylogenetic clades with distinct temporal associations. Vibrio mediterranei and a clade of resident vibrios consistently dominated the initial cultured community at the onset of mortality. However, V. mediterranei was absent as mortality progressed, coinciding with increased abundance of V. harveyi , V. alginolyticus , V. diabolicus , and V. agarivorans . Comparative genomic analysis revealed that initial isolates were enriched in pathways associated with host colonization and complex carbon metabolism, while isolates from elevated mortality showed enrichment in virulence mechanisms and adaptation to degraded host tissues. Temporal separation between genetically distinct clades suggests microbial competition shapes community assembly during mortality events that ultimately reached >85% mortality in both years. This predictable succession from commensal to potentially pathogenic Vibrio species provides genome-level insight into microbial community dynamics during oyster mortality. The consistent loss of V. mediterranei prior to severe mortality suggests this species could serve as a bioindicator for early warning systems to mitigate economic losses in shellfish aquaculture. IMPORTANCE Mortality events in aquaculture systems represent complex host–microbe-environment interactions that challenge our ability to predict and prevent disease. By characterizing succession patterns in oyster-associated Vibrio communities at whole-genome resolution, we reveal a consistent transition from metabolically versatile species associated with healthy oysters to functionally distinct Vibrio taxa enriched in virulence factors and tissue degradation pathways as mortality progresses. This genome-level evidence for predictable community reorganization suggests that monitoring commensal Vibrio populations, particularly the presence or absence of Vibrio mediterranei , could provide earlier warning of impending disease compared to tracking only known pathogens. This shift in monitoring approach could advance aquaculture disease management while expanding our fundamental understanding of how microbial community transitions contribute to host health and disease progression.

  PublisherDOI

• What is eDNA method standardisation and why do we need it?

  Metabarcoding and Metagenomics · 2025-02-13 · 13 citations

  articleOpen access

  The rapid advancement of environmental DNA (eDNA) science in the past two decades has inspired a concomitant growth in the development of eDNA sampling and analytical methods. However, these methods are often developed by individual laboratories or institutions, which can isolate protocols within programmes, agencies or regions and prevent the beneficial exchange of data and ideas. Recent efforts to advance national and international coordination have resulted in a groundswell of standardisation efforts, but there is still considerable confusion around the role of formal standards for regulatory or research applications. With this commentary, we hope to provide clarity on the terminology used in standardisation discussions, including the differences between formal standards and best practice guidelines. Additionally, we discuss how eDNA method choice may be informed by environmental management scenarios and review examples of formal eDNA method standards being used to inform management action. The eDNA community now has an opportunity to develop a roadmap for method development to help close standardisation gaps, advance eDNA method adoption and accelerate our ability to monitor biological life at the scales our current environmental challenges demand.

  PublisherOA PDFDOI

• A suite of ddPCR assays targeting microbial pathogens for improved management of shellfish aquaculture

  Applied and Environmental Microbiology · 2025-04-04 · 5 citations

  articleOpen accessSenior author

  ABSTRACT The shellfish aquaculture industry is one of the fastest-growing sectors of global food production, but it is currently facing major challenges stemming from microbial pathogens. This study presents an optimized and validated suite of droplet digital PCR (ddPCR) assays using water samples proximal to oyster farms in North Carolina to quantify pathogens relevant to the aquaculture industry. Two of the molecular assays enable the quantification of the pathogens, Vibrio parahaemolyticus and Perkinsus marinus , that threaten human health and oyster performance, respectively. This work also introduces two ddPCR assays that enable the simultaneous quantification of at least nine ecologically relevant Vibrio spp . using only two sets of primers and probes targeting the glycosyl hydrolase family 18 (GH18) domain of the chiA gene in Vibrio bacteria. The entire suite of assays was applied to single assessments at 12 sites, revealing heterogeneity in microbial pathogen concentrations across the coastal landscape and variability of abundances within individual estuarine river systems. Additionally, a longitudinal study conducted at a demonstration lease elucidated unique temporal trends for all microbial targets. Notably, when concentrations of Vibrio spp . quantified using the two assays targeting the chiA gene reached their maximum, the daily probability of mortality increased, suggesting a role for other ecologically pertinent Vibrio spp . in the progression of mortality that would otherwise be missed. This study highlights the utility of ddPCR for the advancement of shellfish management by offering insights into the spaciotemporal dynamics of microbial pathogens. IMPORTANCE Climate change is drastically altering the environment and changing the abundance and geographical distribution of marine pathogens. These microbial species put additional pressure on the aquaculture industry by acting as sources of disease for animals important to the food industry as well as for humans upon consumption of contaminated food. To address growing concerns, high-resolution monitoring of pathogens can offer insights for effective management in a critical industry. Validated in the field, the suite of molecular droplet digital PCR assays presented here improves upon current methods, enabling the simultaneous quantification of several targets. This technology makes it possible to track pathogens as they move through the environment and reveals changes in abundance that may inform adjustments to farming practices aimed at mitigating negative outcomes. Additionally, this work presents a unique approach to molecular assay design that unveils potential drivers of ecological shifts and emerging etiologies of disease more efficiently.

  PublisherDOI

Recent grants

• Collaborative Research: Linkage of Bacterial Pathogens to Human infectious Disease in an Estuary Subjected to Extreme Climatic Events

  NSF · $1.5M · 2008–2014

• PFI:AIR - TT: Rapid, quantitative, molecular diagnostics for virulent Vibrio pathogens in water and shellfish

  NSF · $350k · 2016–2021

• RAPID: Identifying Geographic and Demographic Drivers of Rural Disease Transmission for Improved Modeling and Decision Making

  NSF · $136k · 2020–2023

Frequent coauthors

• A. Denene Blackwood

  University of North Carolina at Chapel Hill

  44 shared

• Jed A. Fuhrman

  University of Southern California

  24 shared

• Brett Froelich

  George Mason University

  24 shared

• John F. Griffith

  Southern California Coastal Water Research Project

  23 shared

• Stephen B. Weisberg

  Southern California Coastal Water Research Project

  23 shared

• Marc L. Serre

  University of North Carolina at Chapel Hill

  17 shared

• Denene Blackwood

  University of North Carolina at Chapel Hill

  16 shared

• Raúl González

  16 shared

Labs

• Earth, Marine and Environmental SciencesPI