About

Kara Nelson is a Professor of Civil and Environmental Engineering and holds the Blum Chancellor’s Chair in Development Engineering. She is associated with the Department of Civil and Environmental Engineering at UC Berkeley and is part of the Center for Computational Biology. Her contact email is karanelson@berkeley.edu, and she is involved in research related to computational biology, with a focus on areas such as computational epidemiology, infectious disease modeling, and systems biology. She is also an affiliated faculty member within the Center for Computational Biology, contributing to interdisciplinary research efforts that integrate computational methods with biological and environmental engineering.

Research topics

• Political Science
• Nursing
• Engineering
• Geography
• Medicine
• Public relations
• Business
• Environmental engineering
• Environmental planning

Selected publications

• Making waves: One Water quality standardization concept – A leap for sustainable water management

  Water Research X · 2026-02-20 · 1 citations

  articleOpen access

  • A paradigm shift to downstream use-based regulations reduces system inefficiencies • Multidimensional, risk-based standards support water cycle sustainability • Advanced technologies enable manufactured water tailored to specific uses • Standards for specific water use categories maximize beneficial water use Current water management frameworks are often disjointed, failing to consider the full range of potential water uses. This fragmentation leads to inconsistent regulations; for example, potable water production from wastewater often faces stricter quality standards than water sourced from even wastewater-impacted surface waters. This article proposes a use-based approach to water management, developing water quality standards that account for the economic, public health, and ecological needs of downstream users. We advocate for expanding the concept of water quality from simple pollutant removal to “building water” to match the needs of users so desired constituents are either left in the source water or added to treated water to meet specific user needs. This strategy requires a multidimensional, risk-based regulatory framework, supported by advances in data science and affordable measurement tools for effective enforcement. Such advancement enables a move beyond binary standards to foster sustainable global water resource management and mitigate scarcity.

  PublisherDOI

• AEESP President’s Letter: Spreading Light

  Environmental Engineering Science · 2026-03-28

  article1st authorCorresponding
  PublisherDOI

• Using wastewater surveillance to improve infectious disease control in correctional facilities and congregate living settings: A modeling perspective

  Epidemics · 2026-02-14 · 1 citations

  articleOpen access

  Wastewater surveillance is a valuable tool for monitoring infectious disease dynamics. However, its integration into outbreak control strategies in congregate settings requires further exploration. As observed during the SARS-CoV-2 pandemic, these high-risk environments can facilitate large outbreaks, further exacerbated by residents' heightened vulnerability. Congregate settings exhibit distinct epidemiological dynamics that influence wastewater surveillance. For instance, their semi-closed populations and reduced mobility can lower environmental noise in wastewater signals, but small population sizes also increase stochastic fluctuations, complicating the interpretation of disease trends. In this context, mathematical modeling helps translate wastewater signals into actionable insights for outbreak response. This work synthesizes key benefits and challenges in applying wastewater surveillance in congregate settings and identifies modeling approaches that have potential to improve outbreak detection, enhance monitoring of transmission dynamics, and optimize infection control strategies. This provides a conceptual framework for expanding wastewater surveillance to strengthen infectious disease control in these high-risk populations.

  PublisherDOI

• Solid evidence and liquid gold: trade-offs of processing settled solids, whole influent, or centrifuged influent for co-detecting viral, bacterial, and eukaryotic pathogens in wastewater

  medRxiv · 2025-03-05 · 3 citations

  preprintOpen access

  Abstract Effective methods for simultaneously measuring viral, bacterial, protozoan, and fungal pathogens in wastewater are needed. Here, we investigate how sample type and nucleic acid extraction protocols affect broad-range pathogen detection. We compared methods for analyzing wastewater solids and whole influent by dPCR detection of spiked and endogenous targets including DNA and RNA viruses (mpox, norovirus, SARS-CoV-2), bacteria ( Clostridium difficile, Campylobacter jejuni ), protozoa ( Cryptosporidium spp .), fungi ( Candida auris ), and antibiotic resistance genes. Using selected methods, we then analyzed date-matched 1) solid, 2) centrifuged influent, and 3) whole influent samples collected from eleven facilities at three time points. We demonstrate that one workflow can be used to simultaneously detect all targets and that all sample types yielded similar detection levels and nucleic acid concentrations. Comparing normalization of targets by concentration of PMMoV, carjivirus, and 16S, we show that using different controls together can complicate interpretation of concentrations across targets. Centrifuged influent produced comparable or higher target concentrations overall, suggesting that centrifuged influent is a viable option when settled solids are not available and can circumvent the limitation of varying residence times for primary settled solids. Abstract Figure Synopsis We report successful simultaneous detection of viral, bacterial, and eukaryotic pathogens in both solid and liquid wastewater samples and explore multiple ways to compare sample concentrations measured in different matrices.

  PublisherOA PDFDOI

• Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater

  Research Square · 2025-10-13

  preprintOpen access
  PublisherOA PDFDOI

• Leadership in Environmental Engineering and Science: Celebrating Dr. Domenico Grasso’s Editorial Legacy and Presidential Appointment

  Environmental Engineering Science · 2025-06-25 · 1 citations

  articleCorresponding
  PublisherDOI

• Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-20

  preprintOpen access

  Influenza A viruses (IAV) remain a persistent One Health threat, and whole-genome sequencing from wastewater offers a promising surveillance tool. However, IAV is at low abundance in wastewater, making it difficult to sequence. We benchmarked four targeted enrichment methods suited for whole-genome sequencing including custom and off-the-shelf amplicon and probe-based methods. Our custom HA tiled-amplicon panel was sensitive, fast, and cost-effective, making it suitable for monitoring low-abundance seasonal variants of known subtypes. However, its reliance on conserved and intact primer-binding sites limited primer design to fewer subtypes. A previously published universal amplicon method targeted all IAV subtypes, but it performed poorly in wastewater due to its reliance on intact genome segments. Probe-capture methods were resilient to RNA degradation and mismatches, potentially enabling broader surveillance and detection of emerging strains. However, probes were costly, labor-intensive, and less sensitive than tiled-amplicon. When testing compatibility of sequencing methods with upstream virus concentration and extraction methods, ultrafiltration-based virus concentration outperformed large-volume direct extraction with all four sequencing methods. This set of benchmarking comparisons and custom panels provides needed information for the translation of IAV genomic sequencing into a routine component of wastewater surveillance.

  PublisherOA PDFDOI

• Reverse Osmosis in an Advanced Water Treatment Train Produces a Simple, Consistent Microbial Community

  ACS ES&T Engineering · 2025-02-04 · 2 citations

  articleOpen accessSenior authorCorresponding

  Potable water reuse has become a key component of water sustainability planning in arid regions. Many advanced water purification facilities use reverse osmosis (RO) as part of treatment, including as a barrier for microorganisms; however, regrowth after RO treatment has been observed. Questions remain about the identity, source, and survival mechanisms of microorganisms in RO permeate, but the extremely low biomass of this water is a limitation for common microbiological methods. Here, we performed high-throughput sequencing on samples collected throughout a potable reuse train, including samples collected by filtering large volumes of RO permeate and biomass collected from RO membranes during an autopsy. We observed a stable, consistent microbial community across three months and in two parallel RO trains. RO permeate samples contained Burkholderiaceae at high relative abundance, including one Aquabacterium sp. that accounted for 29% of the community, on average. Like most other RO permeate microorganisms, this sequence was not seen in upstream samples and we suggest that biofilm growing on unit process infrastructure, rather than active treatment breakthrough, was the primary source. A metagenome-assembled genome corresponding to Aquabacterium sp. from RO permeate was found to lack most sugar-utilization pathways and to be able to consume low molecular weight organic molecules, potentially those that pass through RO.

  PublisherDOI

• Mandated on-site wastewater treatment and reuse in San Francisco: The role of distributive fairness perceptions for policy acceptance

  Research Square · 2025-09-18

  preprintOpen access
  PublisherOA PDFDOI

• Solid Evidence and Liquid Gold: Trade-Offs of Processing Settled Solids, Whole Influent, or Centrifuged Influent for Codetecting Viral, Bacterial, and Eukaryotic Pathogens in Wastewater

  Environmental Science & Technology · 2025-07-29 · 6 citations

  articleOpen access

  Effective methods for simultaneously measuring viral, bacterial, protozoan, and fungal pathogens in wastewater are needed. Here, we investigate how the sample type and nucleic acid extraction protocols affect broad-range pathogen detection. We compared methods for analyzing wastewater solids and whole influent by dPCR detection of spiked and endogenous targets including DNA and RNA viruses (mpox, norovirus, SARS-CoV-2), bacteria (Clostridium difficile, Campylobacter jejuni), protozoa (Cryptosporidium spp.), fungi (Candida auris), and antibiotic resistance genes. Using selected methods, we then analyzed date-matched (1) solid, (2) centrifuged influent, and (3) whole influent samples collected from 11 facilities at three time points. We demonstrate that one workflow can be used to simultaneously detect all of the targets. Comparing normalization of targets by concentration of PMMoV, carjivirus, and 16S rRNA, we show that using different controls together can complicate the interpretation of concentrations across targets. We observed similar detection rates and nucleic acid concentrations for the targets examined in this study across all three sample types with slightly higher concentrations in centrifuged influent. These results suggest that centrifuged influent is a viable option and can circumvent the limitation of varying residence times for primary settled solids.

  PublisherDOI

Recent grants

• PECASE: Understanding Sunlight-mediated Inactivation of Pathogens in Water - An Integrated Resarch and Education Career Development Plan

  NSF · $400k · 2003–2008

• Engineering a stable water microbiome in direct potable reuse distribution systems

  NSF · $392k · 2018–2024

• Collaborative Research: The role of sunlight in controlling fecal indicator bacteria and human virus concentrations in recreational waters

  NSF · $150k · 2009–2013

• IRES: U.S.-India Collborative Research on the Impact of Conversion from Intermittent to Continuous Water Supply in Hubli-Dharwad, India

  NSF · $150k · 2010–2014

• Collaborative Research: Sunlight Inactivation Mechanisms of Pathogenic Bacteria in Natural Waters

  NSF · $189k · 2013–2016

Frequent coauthors

• Rose S. Kantor

  University of California, Berkeley

  106 shared

• Lauren C. Kennedy

  Stanford University

  95 shared

• Hannah Greenwald

  University of California, Berkeley

  72 shared

• Basem Al-Shayeb

  Innovative Genomics Institute

  60 shared

• Adrian Hinkle

  University of California, Berkeley

  54 shared

• Vinson B. Fan

  University of California, Berkeley

  52 shared

• Oscar N. Whitney

  University of California, Berkeley

  50 shared

• Robert Tjian

  California Institute for Regenerative Medicine

  46 shared

Labs

• Center for Computational BiologyPI