About

Jake Bailey is a Professor in the Department of Earth & Environmental Sciences at the University of Minnesota Twin Cities. His primary scientific interest is to better understand interactions between the biosphere and geosphere in both modern and ancient settings. His research focuses on the Earth's lithosphere, hydrosphere, and atmosphere, particularly how microorganisms influence geobiological processes that underpin modern biogeochemical cycles and have shaped ancient environments. Bailey's lab studies microbes and their metabolisms to understand their biology, evolution, and biogeochemical significance, employing both isolated organisms and culture-independent approaches such as metagenomics, metatranscriptomics, and community characterization techniques. His active research explores the ecophysiology and genomics of sulfide-oxidizing bacteria like Thiomargarita, the role of sulfur-oxidizing bacteria in mineral precipitation and dissolution, and the metabolic and ecological diversity of chemolithoautotrophic microbes. Bailey also develops methods such as immunodetection for studying microbial activity in modern and ancient environments. His work contributes to understanding microbial roles in geochemical processes, mineral formation, and environmental change.

Research topics

• Biology
• Computer Science
• Genetics
• Computational biology
• Evolutionary biology
• Ecology
• Astronomy
• Chemistry
• World Wide Web
• Library science
• Biochemistry
• Environmental chemistry
• Data science

Selected publications

• ExOW_4_CarbDissolution

  Astrobiology Habitable Environments Database · 2026-01-19

  datasetOpen access1st authorCorresponding

  Research paper and associated data showing dissolution of methane seep authigenic carbonates by sulfur metabolizing microbes.

  PublisherDOI

• Diverse <i>Sulfuriferula</i> spp. from sulfide mineral weathering environments oxidize ferrous iron and reduced inorganic sulfur compounds

  Applied and Environmental Microbiology · 2025-06-05 · 1 citations

  articleOpen access

  ABSTRACT Microorganisms are important catalysts for the oxidation of reduced inorganic sulfur compounds. One environmentally important source of reduced sulfur is metal sulfide minerals that occur in economic mineral deposits and mine waste. Previous research found that Sulfuriferula spp. were abundant and active in long-term weathering experiments with simulated waste rock and tailings from the Duluth Complex, Northern Minnesota. We, therefore, isolated several strains of Sulfuriferula spp. from these long-term experiments and characterized their metabolic and genomic properties to provide insight into microbe-mineral interactions and the microbial biogeochemistry in these and other moderately acidic to circumneutral environments. The Sulfuriferula strains are all obligate chemolithoautotrophs capable of oxidizing inorganic sulfur compounds and ferrous iron. The strains grew over different pH ranges, but all grew between pH 4.5 and 7, matching the weathering conditions of the Duluth Complex rocks. All strains grew on the iron-sulfide mineral pyrrhotite (Fe 1 − x S, 0 &lt; x &lt; 0.125) as the sole energy source, as well as hydrogen sulfide and thiosulfate, which are products of sulfide mineral breakdown. Despite their metabolic similarities, each strain encodes a distinct pathway for the oxidation of reduced inorganic sulfur compounds as well as differences in nitrogen metabolism that reveal diverse genomic capabilities among the group. Our results show that Sulfuriferula spp. are primary producers that likely play a role in sulfide mineral breakdown in moderately acidic to circumneutral mine waste, and the metabolic diversity within the genus may explain their success in sulfide mineral-rich and other sulfidic environments. IMPORTANCE Metal sulfide minerals, such as pyrite and pyrrhotite, are one of the main sources of reduced sulfur in the global sulfur cycle. The chemolithotrophic microorganisms that break down these minerals in natural and engineered settings are catalysts for biogeochemical sulfur cycling and have important applications in biotechnological processes such as biomining and bioremediation. Sulfuriferula is a recently described genus of sulfur-oxidizing bacteria that are abundant primary producers in diverse terrestrial environments, including waste rock and tailings from metal mining operations. In this study, we explored the genomic and metabolic properties of new isolates from this genus, and the implications for their ecophysiology and biotechnological potential in ore and waste from economic mineral deposits.

  PublisherDOI

• <i>Sulfuriferula</i> spp. from sulfide mineral weathering environments have diverse sulfur- and iron-cycling capabilities

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-30

  preprintOpen access

  Microorganisms are important catalysts for the oxidation of reduced inorganic sulfur compounds. One environmentally important source of reduced sulfur is metal sulfide minerals that occur in economic mineral deposits and mine waste. Previous research found that Sulfuriferula spp. were abundant and active in long-term weathering experiments with simulated waste rock and tailings from the Duluth Complex, Northern Minnesota. We therefore isolated several strains of Sulfuriferula spp. from these long-term experiments and characterized their metabolic and genomic properties to provide insight into microbe-mineral interactions and the microbial biogeochemistry in these and other moderately acidic to circumneutral environments. The Sulfuriferula strains are all obligate chemolithoautotrophs capable of oxidizing inorganic sulfur compounds and ferrous iron. The strains grew over different pH ranges, but all grew between pH 4.5-7, matching the weathering conditions of the Duluth Complex rocks. All strains grew on the iron-sulfide mineral pyrrhotite (Fe 1-x S, 0 &lt; x &lt; 0.125) as the sole energy source, as well as hydrogen sulfide and thiosulfate, which are products of sulfide mineral breakdown. Despite their metabolic similarities, each strain encodes a distinct pathway for the oxidation of reduced inorganic sulfur compounds as well as differences in nitrogen metabolism that reveal diverse genomic capabilities among the group. Our results show that Sulfuriferula spp. are primary producers that likely play a role in sulfide mineral breakdown in moderately acidic to circumneutral mine waste, and the metabolic diversity within the genus likely explains their success in sulfide mineral-rich and other sulfidic environments.

  PublisherOA PDFDOI

• First report of <i>Tamarillo fruit ring virus</i> in <i>Solanum</i> spp. in Uganda, Tanzania and Rwanda

  New Disease Reports · 2024-01-01

  articleOpen access

  Between July and November 2021, diseased fruit of Solanum melongena from Rwanda, S. aethiopicum from Tanzania, and S. macrocarpon and S. aethiopicum from Uganda were intercepted by the Animal and Plant Health Agency at Heathrow Airport and submitted to Fera Science Ltd. for diagnosis The fruit exhibited putative symptoms of virus infection including distortion, arcs and pale mottling. The S. melongena sample was tested by ELISA for Cucumber mosaic virus (Agdia, USA) Pepino mosaic virus (Bioreba, Switzerland), Tomato spotted wilt virus (DSMZ, Germany), and potyvirus (DSMZ, Germany). It was positive only for potyviruses. RNA was extracted from the sample and tested by RT-PCR using universal potyvirus primers (van der Vlugt et al., 1999). The PCR product was sent to Eurofins (Germany) for Sanger sequencing. Sequence comparison by BLASTn confirmed the presence of a potyvirus, with 99% nucleic acid identity to Tamarillo fruit ring virus (TaFRV; GenBank Accession No. MZ031983) detected in S. betacum in Rwanda. The sequence was deposited in GenBank (OR963261). Solanum aethiopicum fruits from Tanzania and Uganda were tested as above by ELISA with the addition of Chilli veinal mottle virus (DSMZ, Germany). They were positive only for potyvirus. Extracted RNA was tested by RT-PCR and the products were sent for Sanger sequencing as described previously. BLASTn comparison identified them to be TaFRV (Tanzania, OR963263; Uganda, OR963262) with 95–96% nucleic acid identity to GenBank Accession No. MZ031983. Solanum macrocarpon was tested as above, with additional ELISA tests for Eggplant mosaic virus (Nano Diagnostics, USA), Eggplant mottled dwarf virus (Loewe, Germany). Tomato mosaic virus (DSMZ, Germany), Tomato ringspot virus (Agdia, USA) and tospovirus (Bioreba, Switzerland), Again only potyvirus was detected. The result was confirmed using RT-PCR as before, and the amplicon sequence was identified using BLASTn as TaFRV (OR963262) with 96% nucleic acid identity to GenBank Accession No. MZ031983. For confirmation, a specific real-time RT-PCR test for TaFRV was developed using Primer Express v.2 (Life Technologies Co., USA) (Table 1). All four samples tested positive. To obtain the genome of the virus, both S. macrocarpon and S. aethiopicum from Uganda were tested by high throughput sequencing on a MiSeq Sequencer (Illumina, UK) (Fowkes et al., 2021). The complete coding sequence was obtained for each sample and the sequences were deposited in GenBank (S. aethiopicum-Uganda, OR963259; S macrocarpon-Uganda, OR963260). A phylogenetic analysis for both sequences with other potyviruses was inferred by using the maximum-likelihood method (Jukes & Cantor, 1969) (Figure 1). This showed that the sequence isolates obtained in this study are closely related to MZ031983 and align alongside other solanaceous potyviruses. Information on TaFRV is limited with a single unpublished Genbank accession from 2021 in S. betacum in Rwanda. The additional reports here from S. melongena (Rwanda), S. aethiopicum (Uganda and Tanzania), and S. macrocarpon (Uganda) indicate that this virus has a wider host range and is more widely distributed than reported previously. In 2022, Rwanda produced 89,265 t of aubergine (FAOSTAT, 2024), and although production figures are not available for Uganda and Tanzania, the produce from crops in these three countries represent major export commodities. It is difficult to gauge the potential impact on production on the region and this should be monitored. The real-time RT- PCR primers used in this study can be used for easier and reliable virus detection. This work was funded under the Defra-Fera Long Term Service Agreement

  PublisherOA PDFDOI

• Fluoride and gallein regulate polyphosphate accumulation in dental caries-associated Lacticaseibacillus

  Microbiology · 2024-11-28 · 3 citations

  articleOpen accessSenior author

  Inorganic polyphosphates (polyPs) are energy-storing biopolymers synthesized by all three domains of life. PolyP accumulation has been well studied with respect to its role in stress response, but its role in dental disease has received less attention. Dental decay can be promoted by changes in pH as well as the chemical activity of ions such as phosphate in oral fluids at the enamel interface. Previous work has shown that the drawdown of phosphate from biofilm fluids can alter the saturation state of oral fluids to thermodynamically favour mineral dissolution. The members of the Lactobacillaceae are known to accumulate polyP and play a role in early-stage and late-stage dental caries. In this study, we examined the effects of potential metabolic inhibitors on polyP accumulation in Lacticaseibacillus rhamnosus . We observed that two inhibitors of the enzyme responsible for polyP synthesis, gallein and fluoride, inhibited polyP accumulation in a balanced medium. However, fluoride and gallein treatments amended with either glucose or lactate were found to enhance polyP accumulation. These results illustrate the potential complexity of polyP metabolism in the oral environment.

  PublisherDOI

• Microbial communities from weathered outcrops of a sulfide‐rich ultramafic intrusion, and implications for mine waste management

  Environmental Microbiology · 2023-09-05 · 3 citations

  articleOpen access

  The Duluth Complex (DC) contains sulfide-rich magmatic intrusions that represent one of the largest known economic deposits of copper, nickel, and platinum group elements. Previous work showed that microbial communities associated with experimentally-weathered DC waste rock and tailings were dominated by uncultivated taxa and organisms not typically associated with mine waste. However, those experiments were designed for kinetic testing and do not necessarily represent the conditions expected for long-term environmental weathering. We used 16S rRNA gene methods to characterize the microbial communities present on the surfaces of naturally-weathered and historically disturbed outcrops of DC material. Rock surfaces were dominated by diverse uncultured Ktedonobacteria, Acetobacteria, and Actinobacteria, with abundant algae and other phototrophs. These communities were distinct from microbial assemblages from experimentally-weathered DC rocks, suggesting different energy and nutrient resources in environmental samples. Sulfide mineral incubations performed with and without algae showed that photosynthetic microorganisms could have an inhibitory effect on autotrophic populations, resulting in slightly lower sulfate release and differences in dominant microorganisms. The microbial assemblages from these weathered outcrops show how communities develop during weathering of sulfide-rich DC rocks and represent baseline data that could evaluate the effectiveness of future reclamation of waste produced by large-scale mining operations.

  PublisherOA PDFDOI

• Exploring the origins of vagrant Yellow-browed Warblers in Western Europe

  2023-03-08

  preprintOpen access

  Vagrancy, where individuals occur outside of known population distributions, is a poorly understood ecological phenomenon. It can however be a key driver of site colonisation and range expansion. Evidence is emerging that presumed vagrant Siberian passerines in Western Europe, e.g. Richard’s Pipits Anthus ricardii, are colonists, with geolocator-tracked individuals returning to breed in Siberia after wintering in Western Europe. As such, ‘vagrancy’ patterns in these taxa could provide a model system to understand large-scale range shifts. For example, determining the origins of vagrant individuals and linking these to morphology and arrival date could help to identify the potential drivers of range dynamics. Here, we investigate the origins of vagrant Yellow-browed Warblers Phylloscopus inornatus (a migratory Siberian breeding passerine) in Western Europe by analysing stable hydrogen isotopes, morphology and phenology. We measure the isotopic patterns of feathers grown on the breeding grounds and their relation to those from two sub-species of Common Chiffchaff Phylloscopus collybita. We found that Yellow-browed Warblers have similar hydrogen isotopic signatures (δ2H) to the Siberian sub-species of Common Chiffchaff Phylloscopus collybita tristis and δ2H values did not overlap with those from the European nominate race of Common Chiffchaff Phylloscopus collybita collybita. There was weak evidence that variation in δ2H values was linked to differences in migratory distances in sampled Yellow-browed Warblers. The variation in δ2H values for Yellow-browed Warblers was similar to Chiffchaffs of the collybita and tristis sub-species. This suggests that Yellow-browed Warblers in Western Europe may originate from a relatively broad-front and not exclusively from an expanding western breeding range margin. It is unclear if vagrant Yellow-browed Warblers in Western Europe make viable return migrations to Siberia. If they are, the subset of individuals that become colonists could help us understand how vagrancy drives biogeographic processes, such as the establishment of novel migration routes.

  PublisherOA PDFDOI

• Fluoride and gallein inhibit polyphosphate accumulation by oral pathogen <i>Rothia dentocariosa</i>

  Letters in Applied Microbiology · 2023-01-28 · 8 citations

  articleOpen access

  The uptake and storage of extracellular orthophosphate (Pi) by polyphosphate (polyP) accumulating bacteria may contribute to mineral dissolution in the oral cavity. To test the effect of potential inhibitors of polyP kinases on Rothia dentocariosa, gallein (0, 25, 50, and 100 μM) and fluoride (0, 50, and 100 ppm) were added to R. dentocariosa cultures grown in brain-heart infusion broth. At a late log growth phase (8 h), extracellular Pi was measured using an ascorbic acid assay, and polyP was isolated from bacterial cells treated with RNA/DNAases using a neutral phenol/chloroform extraction. Extracts were hydrolyzed and quantified as above. Gallein and fluoride had minor effects on bacterial growth with NaF having a direct effect on media pH. Gallein (≥25 μM) and fluoride (≥50 ppm) attenuated the bacterial drawdown of extracellular Pi by 56.7% (P < 0.05) and 37.3% (P < 0.01). There was a corresponding polyP synthesis decrease of 73.2% (P < 0.0001) from gallein and 83.1% (P < 0.0001) from fluoride. Attenuated total reflectance-Fourier-transform infrared spectroscopy validated the presence of polyP and its reduced concentration in R. dentocariosa bacterial cells following gallein and fluoride treatment. Rothia dentocariosa can directly change extracellular Pi and accumulate intracellular polyP, but the mechanism is attenuated by gallein and NaF.

  PublisherOA PDFDOI

• Outside-in: intracellular vesicles in giant sulfur bacteria contain peptidoglycan

  bioRxiv (Cold Spring Harbor Laboratory) · 2022-04-12 · 2 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Until recently, the cellular envelopes of bacteria were regarded as static and rigid relative to those of eukaryotes. While investigating peptidoglycan synthesis in populations of giant sulfur bacteria, Candidatus Thiomargarita spp., we observed internal vesicle-like features (VLFs). VLFs, as imaged following the active incorporation of D-amino acids, appear to begin as invaginations and delaminations of the cellular envelope. Staining with wheat germ agglutinin confirmed the presence of peptidoglycan in VLFs, while polymyxin B revealed that the outer membrane is present in some VLFs. Transmission electron microscopy revealed a complex network of interconnected VLFs. Genomes of Ca . Thiomargarita nelsonii lack a canonical divisome, while possessing homologs to genes such as actin, membrane scaffolding proteins, and dynamins that are associated with phagocytosis in eukaryotes. The physiological role of VLFs remains unclear, but the presence of sulfur globules in some suggests compartmentalization of metabolism and energy production. This is the first report of peptidoglycan and outer membrane bound intracellular vesicles within prokaryotic cells. These findings transform the canonical view of the inflexible bacterial cell envelope and further narrow the divide between prokaryotes and eukaryotes.

  PublisherOA PDFDOI

• Microbial communities from weathered outcrops of a sulfide-rich ultramafic intrusion, and implications for mine waste management

  bioRxiv (Cold Spring Harbor Laboratory) · 2022-10-03

  preprintOpen access

  ABSTRACT The Duluth Complex, Northeastern Minnesota, contains sulfide-rich magmatic intrusions that, collectively, represent one of the world’s largest known economic deposits of copper, nickel, and platinum group elements (Cu-Ni-PGEs). Previous work showed that microbial communities associated with experimentally-weathered Duluth Complex waste rock and tailings were dominated by uncultivated taxa and other populations not typically associated with mine waste. However, those experiments were designed for kinetic testing and do not necessarily represent the conditions expected for reclaimed mine waste or long-term weathering in the environment. We therefore used 16S rRNA gene methods to characterize the microbial communities present on the surfaces of naturally-weathered and historically disturbed outcrops of Duluth Complex material, as well as a circumneutral seep draining a reclaimed blast pit. Rock surfaces were dominated by diverse uncultured Ktedonobacteria, Acetobacteria , and Actinobacteria while seeps were dominated by Proteobacteria , including Leptothrix spp. and Methylovulum spp. All samples had abundant algae and other phototrophs. These communities were distinct from previously-described microbial assemblages from experimentally-weathered Duluth Complex rocks, suggested different energy and nutrient resources in the reclaimed rocks, outcrops, and seeps. Sulfide mineral incubations performed with and without algae showed that photosynthetic microorganisms could have an inhibitory effect on some of the autotrophic populations from the site, resulting in slightly lower sulfate release and differences in the dominant microorganisms. The microbial assemblages from these weathered outcrops show how communities are expected to develop during natural weathering of sulfide-rich Duluth Complex rocks, and represent baseline data that could be used to evaluate the effectiveness of future reclamation of tailings and waste rock produced by large scale mining operations.

  PublisherOA PDFDOI

Recent grants

• In the belly of the whale: endobionts inhabit the world's largest bacteria

  NSF · $892k · 2020–2025

• CAREER: Investigating the relationship between giant sulfur bacteria and microfossil-bearing phosphorites.

  NSF · $460k · 2011–2017

• The Unrecognized Role of Phosphate-accumulating Bacteria in Oral Health

  NIH · $2.8M · 2018–2024

Frequent coauthors

• Beverly E. Flood

  University of Minnesota

  39 shared

• Daniel S. Jones

  New Mexico Institute of Mining and Technology

  26 shared

• Frank A. Corsetti

  18 shared

• Aivo Lepland

  13 shared

• Chris H. Crosby

  University of Minnesota

  12 shared

• Fernando Medina

  University of Minnesota

  8 shared

• B. K. Harrison

  University of Minnesota

  8 shared

• Kathryn Hobart

  7 shared

Labs

• Geobiology LabPI

Awards & honors

• Simons Foundation Early Career Investigator in Marine Microb…
• National Academy of Sciences Kavli Frontiers of Science Fell…
• Alfred P. Sloan Foundation Research Fellow (2014)
• UMN Graduate and Professional Student Assembly Outstanding A…
• UMN McKnight Land Grant Professorship (2013)