About

Cara Santelli is an associate professor in the Department of Earth and Environmental Sciences at the University of Minnesota. She is a geomicrobiologist and a member of the BioTechnology Institute at UMN. Her research examines the impact of microbial activity on geological and environmental processes, including mineral formation, mineral alteration and weathering, metal(loid) redox transformations, nutrient biogeochemical cycling, and the remediation of polluted environments. Her work aims to conduct fundamental scientific research on environmentally relevant biogeochemical processes and key elements in nature that are influenced by anthropogenic activities such as mining, agriculture, and climate change. Santelli's research is highly interdisciplinary, involving a multidisciplinary team of scientists and students with diverse expertise. She employs multiple approaches, including metagenomics, genomics, transcriptomics, mineralogical X-ray, and spectroscopic techniques to understand microbial communities, molecular mechanisms, and mineral biomineralization products. Her goal is to elucidate mechanisms, metabolic pathways, and geochemical impacts of mineral—metal-microbe interactions, and to inform strategies for remediating inorganic pollutants to improve water and soil quality.

Research topics

• Ecology
• Political Science
• Sociology
• Economy
• Environmental ethics
• Botany
• Chemistry
• Law
• Geography
• Public relations
• Environmental chemistry
• Biology

Selected publications

• Aviti Sequencing and Marker Gene Data Analysis

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-09

  articleOpen accessSenior author

  Abstract Accurate identification of microbial species in complex populations and communities relies on the isolation of representative marker 16S, ITS, and 18S sequences through the use of DNA extraction, PCR, and sequencing. Aviti sequencing has brought an improvement in the read quality and depth of marker gene sequencing technology. Quality scores exceeding Q40 representing highly accurate sequencing allows researchers to ask more questions of their marker gene data. However, this improvement in quality and throughput also brings with it a surprising increase in diversity of amplicon sequencing variants (ASVs) making further analysis and comparisons to previous studies on Illumina platforms challenging. This increased diversity causes downstream processing issues, including an over-reporting of chimeric ASVs. Here we identify this problem and put forward straightforward solutions to retain counts and reduce technically introduced diversity, as well as tying chimeric read identification to minimum parent distance. Through the use of synthetic mock samples, we discovered that erroneous ASVs are systematically substitution errors introduced by the upstream PCR methods. This error can be reduced significantly bioinformatically through clustering of ASVs within 99% similarity. Further we highlight technically introduced variation as a result of variable region length, sample misassignment, and sample biomass. Collectively, these results improve the similarity of Aviti and Illumina datasets for better comparisons of microbial studies from different platforms.

  PublisherOA PDFDOI

• Data for EMSL Project 49262 from October 2024

  OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) · 2026-05-04

  articleOpen access
  PublisherDOI

• Transition Metal Recovery Using Manganese-Oxidizing Microbes and Recycled Carpet Fiber

  Environmental Science & Technology · 2025-09-09 · 2 citations

  articleSenior authorCorresponding

  Mining metals for the advancement of society requires innovative and cost-effective remediation strategies that protect the environment and, ideally, allow for concentration and recovery of metals from waste streams. Microbially mediated strategies that remove metals from aqueous waste streams via sorption and/or oxidation–reduction reactions show promise as eco-friendly, cost-effective solutions. Our objective was to use Mn-oxidizing fungi, isolated from the Soudan Underground Mine State Park, MN, a high-salinity, mine-impacted environment, to sequester transition metals Mn, Co, Cu, and Ni. Additionally, we demonstrate the use of recycled carpet fibers to support dense biomass growth and promote rapid Mn(II) oxidation rates, resulting in the formation of Mn(III/IV) oxides. The addition of fibers promoted increases in metal uptake in the presence of 500 μM Mn(II) along with 20 μM Co(II), 20 μM Cu(II), or 20 μM Ni(II) as well as with all metals combined where sequestration increased by as much as 6-fold for Mn and 3-fold for Co, following 10 days of incubation. The system was most effective in removing Co from solution with carpet fibers and Co and Cu without fibers. Recycled carpet fibers enhance the effectiveness of this bioremediation strategy while providing a use for spent carpet fibers or similar waste manufactured fiber materials.

  PublisherDOI

• The potential for coupled organic and inorganic sulfur cycles across the terrestrial deep subsurface biosphere

  Nature Communications · 2025-04-23 · 6 citations

  articleOpen access

  Organosulfur compounds (OrgS) are fundamental components of life’s biomass, yet the cycling of these compounds in the terrestrial deep subsurface, one of Earth’s largest ecosystems, has gone relatively unexplored. Here, we show that all subsurface microbial genomes reconstructed from Soudan Underground Mine State Park have the capacity to cycle organic sulfur species. Our findings suggest that OrgS degradation may be an integral link between the organic and inorganic sulfur cycle via the production of sulfite and sulfide. Furthermore, despite isolation from surface ecosystems, most Soudan microorganisms retained genes for dimethylsulfoniopropionate and taurine biosynthesis. Metagenomic analyses of an additional 54 deep subsurface sites spanning diverse lithologies revealed the capacity for OrgS cycling to be widespread, occurring in 89% of assembled metagenomes. Our results indicate that consideration of OrgS cycling may be necessary to accurately constrain sulfur fluxes, discern the energetic limits of deep life, and determine the impact of deep subsurface biogeochemical sulfur cycling on greater Earth system processes. Organic sulfur compounds are vital to life but often overlooked in the sulfur cycle, especially in the subsurface. Subsurface microbes can metabolize diverse organosulfur compounds, hinting at a more complex sulfur cycle than previously thought.

  PublisherOA PDFDOI

• Perfluorooctanesulfonates (PFOS) Bioremediation Coupled to Fungal Manganese Oxidation

  Abstracts with programs - Geological Society of America · 2025-01-01

  article
  PublisherDOI

• Combined Impacts of Land Use and Climate Change on Manoomin in the Otter Tail River Watershed, Minnesota

  Abstracts with programs - Geological Society of America · 2025-01-01

  articleSenior author
  PublisherDOI

• Distinct Fracture Mineralogy That is Out of Equilibrium With Modern Groundwaters Provides Important Context for Subsurface Life

  Journal of Geophysical Research Biogeosciences · 2025-10-01

  articleOpen access

  Abstract Rock fracture surfaces in the crust are essential habitat for microorganisms. Fracture‐groundwater interfaces provide physical substrates for biofilm growth and are sources of carbon, nutrients, and electron donors and acceptors. To better understand geochemical processes impacting fracture surfaces and the subsurface microbiome, we identified fractures in archived rock cores from the Soudan formation, which is known to host saline groundwaters and isolated microbial communities dependent on rock‐water interactions. Cores with open fractures were thin sectioned and studied via electron microprobe and synchrotron X‐ray fluorescence microprobe. Most fracture surfaces had mineralogy distinct from that of the bulk rock. Chlorite minerals were abundant on fracture surfaces and had elemental compositions suggesting deposition during late‐stage hydrothermal alteration. Fracture‐lining chlorites likely limit access to iron oxide and sulfide minerals that are active in subsurface biogeochemical cycles. Calcium‐rich rinds were also observed along fracture edges. These rinds were too thin and poorly ordered to be identified via light microscopy or X‐ray diffraction; however, Ca K‐edge micro‐X‐ray absorption near‐edge structure spectroscopy identified them as carbonates, minerals not observed in the bulk rock. Thermodynamic modeling shows that carbonate precipitation is largely unfavorable in Soudan groundwaters, indicating that fracture edge conditions differed from those in modern water samples. Because of the low carbon concentrations in Soudan groundwaters, carbonate rinds likely play an important role in subsurface carbon cycling and may mark fracture surfaces that once hosted biofilms. Overall, this study suggests that fracture alteration can both play an active role in and suppress rock‐water interactions essential to subsurface life.

  PublisherDOI

• Transition Metal Recovery using Manganese-oxidizing Microbes and Recycled Carpet Fiber

  2025-01-01

  articleSenior author
  PublisherDOI

• Predicting lead hotspots in urban stormwater ponds across the Twin Cities Metro

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-19

  preprintOpen access

  Abstract Stormwater ponds play an important role in urban food webs. Critically these same ponds could also serve as pollution hotspots since stormwater ponds can act as local concentrators of urban runoff. One such contaminant of concern is lead, which remains a significant issue for human and ecosystem health in the United States despite regulatory bans on its use in paint and gasoline imposed in the 1970s. Despite high levels of lead in some urban stormwater, little is known about the distribution of lead in urban aquatic ecosystems. Therefore, we characterized lead within the sediment, water column, and surrounding soil of stormwater ponds across the Minneapolis-Saint Paul Metro Area. We hypothesized that lead would be highest in ponds that receive runoff from landscapes with older construction (i.e., legacy leaded paint and gasoline), have high traffic volume (i.e., legacy leaded gasoline), and areas with low impervious surface cover (i.e., increased mobilization of contaminated soil). Moreover, we hypothesized that stormwater ponds capture lead within sediments, with more dissolved lead at the bottom of the water column, where it would interact with lead containing sediments. Across ponds, we found that age of parcel development where the pond was located was the strongest predictor of surface sediment lead content. Within pond sediments, we found that lead concentrations increased with depth below the sediment surface, which is unsurprising since depth is likely correlated with time. The strongest predictor of surface water lead concentration was the strength of pond stratification, while the strongest predictor of bottom water lead concentration was pond duckweed cover and water conductivity. Water column oxygen concentrations varied across ponds yet were not important in determining dissolved lead within the water column. Importantly, lead within pond water remained quite low despite elevated sediment lead levels. These findings confirm that stormwater ponds can act as one source of environmental lead remediation by capturing lead within sediments under a wide range of environmental conditions. Our results suggest relatively low lead release from ponds to downstream areas, indicating that ponds generally serve as sinks, not sources within the urban lead cycle.

  PublisherOA PDFDOI

• Genetic factors driving multi-host infection in a core member of the root mycobiota

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-01 · 1 citations

  preprint

  Abstract Core members of the fungal root microbiota include pathogens capable of colonizing multiple hosts, yet the underlying genetic determinants remain unknown. We report that Plectosphaerella cucumerina is a core member of the Arabidopsis thaliana root microbiota displaying high pathogenic potential and multi-host colonization capabilities. Establishment of a Plectosphaerella reference culture collection, followed by whole-genome sequencing of 72 strains reveals subtle phenotypic and genotypic variation that associate with fungal phylogeny, but not host plant identity. Transcriptome profiling of a model P. cucumerina isolate in roots of multiple hosts identifies core and host-specific fungal processes linked to carbon catabolism and root cell wall deconstruction of the hosts. A fungal gene encoding a candidate β-1,3-glucanase (GH64) was identified as a key genetic factor driving infection and disease in plants that diverged 110 million years ago. The gene is enriched in plant-colonizing fungi and consistently functions as a disease determinant in the root pathogen Colletotrichum incanum . We conclude that diverse and tunable fungal repertoires of carbohydrate-active enzymes act as disease determinants and drive multi-host compatibility belowground.

  PublisherDOI

Recent grants

• Collaborative Research: Optimization of metal attenuation in biologically-active remediation systems

  NSF · $188k · 2013–2017

• Collaborative Research: Optimization of metal attenuation in biologically-active remediation systems

  NSF · $111k · 2017–2017

• CAREER: Genome-enabled investigations into the mechanisms and ecological controls on selenium transformations by fungi

  NSF · $856k · 2018–2026

Frequent coauthors

• Colleen M. Hansel

  Woods Hole Oceanographic Institution

  99 shared

• Carolyn Zeiner

  University of St. Thomas - Minnesota

  46 shared

• Carla E. Rosenfeld

  44 shared

• Brandy M. Toner

  University of Minnesota

  40 shared

• Si Wu

  Zunyi Medical University

  40 shared

• Scott Lea

  Environmental Molecular Sciences Laboratory

  36 shared

• Christopher Anderton

  Environmental Molecular Sciences Laboratory

  36 shared

• David Hoyt

  36 shared

Labs

• Santelli Geomicrobiology LabPI

Education

• B.S., Department of Geoscience

  University of Wisconsin

  2000

Awards & honors

• NSF CAREER Award (2018 – 2023)
• Environmental Initiative Organization, Local Sustainability…
• NSF CNH2-L “First We Must Consider Manoomin” (Wild Rice): A…
• DOE SBR “Interactions between molecular-scale biogeochemical…
• NSF IES “Collaborative research: Banded together: modern wat…