About

Nathan Yee is a Professor at Rutgers University in the Department of Earth and Planetary Sciences. His research interests focus on environmental geochemistry and geomicrobiology, with the goal of understanding the impact of microorganisms on the geochemical cycling of inorganic elements. He employs microscopic, spectroscopic, and genetic techniques to investigate microbe-mineral interactions, biotransformation of contaminants, and anaerobic redox reactions. His work involves developing models based on experimental data to predict microbial behavior, including activity mechanisms and conditions under which these mechanisms operate. The principal area of his current research is centered on elucidating the molecular pathways of microbial-catalyzed redox reactions involving mercury and metalloid elements such as selenium, tellurium, and arsenic.

Research topics

• Chemistry
• Environmental chemistry
• Ecology
• Inorganic chemistry
• Geology
• Biology
• Geochemistry
• Oceanography
• Astrobiology

Selected publications

• Low bandgap conjugated polymers based on thiadiazoloquinoxaline for high performance shortwave infrared photodetection

  Journal of Materials Chemistry C · 2025-01-01 · 1 citations

  articleOpen access1st author

  The photodiode device based on P5 exhibited the highest specific detectivity of 2.0 × 10 10 Jones at 1200 nm under −1 V bias, making it a promising material for applications including bioimaging, environmental sensing, and optical communications.

  PublisherOA PDFDOI

• Air-Stable Short-Wave Infrared Tin Telluride and Tin Telluride/Zinc Telluride Core–Shell Colloidal Quantum Dots

  Chemistry of Materials · 2025-09-30 · 1 citations

  articleOpen access

  To date, colloidal quantum dots (CQDs) with absorption in the short-wave infrared region (SWIR, 1–2.6 μm) typically consist of hazardous cadmium, lead, or mercury chalcogenides, which limit commercial acceptance. Environmentally friendly alternatives are therefore required to ensure minimal damage to ecosystems during fabrication, use, and disposal. A promising hazardous-element-free SWIR absorbing nanomaterial candidate is tin chalcogenide. We have developed tin telluride (SnTe) CQDs, with a size ranging from ∼17 to 26 nm and corresponding absorption peak from ∼2.3 to 2.5 μm, indicative of size-dependent quantum confinement. Air-stable tin salts (tin chloride or tin acetate) were employed instead of the typical air-sensitive bis(bis(trimethylsilyl)amino tin(II). The synthesis was systematically investigated by optimizing the ligand type (1-dodecanethiol was used to replace oleic acid to prevent oxidation), injection method, growth temperature, reaction time, and feed molar ratio between tin and tellurium precursors. To improve stability in air, a ZnTe shell was successfully synthesized via cation exchange reaction at 70 °C with zinc acetate. The SnTe/ZnTe core–shell nanocrystals were fully characterized, revealing the formation of a protective ZnTe shell with a thickness of two to three monolayers, resulting in long-term stability in air (up to 1 month). These air-stable CQDs may offer a low-toxicity alternative nanomaterial for low-cost solution-processable fabrication of SWIR optoelectronics.

  PublisherDOI

• Genetic identification of the selenate reductase in <i>Enterobacter cloacae</i> SLD1a-1

  Applied and Environmental Microbiology · 2025-11-26

  articleOpen accessSenior author

  ABSTRACT Bacterial selenate reduction is a key microbial process that affects the speciation and mobility of selenium in the environment. In this study, we identified the selenate reductase gene in the facultative anaerobe Enterobacter cloacae SLD1a-1. Genome sequencing revealed a membrane-bound, twin-arginine translocation (TAT) exported molybdoenzyme operon designated as srnABCD , under the regulation of the fumarate and nitrate reductase regulator (FNR) transcription factor. The srnA gene encodes a molybdenum-containing subunit; srnB and srnC encode iron-sulfur and membrane anchor subunits, respectively; and srnD encodes a TAT chaperone. Targeted mutagenesis of the srnA gene resulted in a mutant defective in selenate reduction. Complementation with the wild-type srnA sequence restored the abolished phenotype. Heterologous expression of srnA in an Escherichia coli Δ ynfEF mutant conferred selenate reduction activity, demonstrating cross-species functionality. Protein structure modeling of the selenate reductase using Boltz-1 showed a funnel-shaped active site involved in selenate binding and reduction. These findings provide new molecular insights into the genetics and mechanism of bacterial selenate reduction. IMPORTANCE Selenium pollution poses risks to ecosystems and human health, largely due to the mobility and toxicity of selenate, a common form found in soil and water. Diverse bacterial species are able to convert soluble selenate into insoluble elemental selenium, but the genes and enzymes that underpin this process are not fully understood. In this study, we identified a gene in Enterobacter cloacae SLD1a-1 that enables the bacterium to catalyze selenate reduction. We showed that this gene produces a functional enzyme even when it is transferred into a different species, Escherichia coli . Protein structure modeling revealed features of the enzyme that help it recognize and reduce selenate. This information advances our understanding of how selenium is enzymatically cycled in the environment.

  PublisherDOI

• On the emergence of metabolism: the evolution of proteins that powered life

  Philosophical Transactions of the Royal Society B Biological Sciences · 2025-08-07 · 2 citations

  reviewOpen access

  Life is far from thermodynamic equilibrium. Hence, life must extract energy from the environment. On Earth, that energy is driven by networks of metabolic reactions in all cells which ultimately move electrons and protons (i.e. hydrogen atoms) across the planet. The origin of metabolism required the emergence and evolution of proteins. Proteins are nanometre-scale chemical machines-i.e. literal nanomachines which physically move. These nanomachines enable living systems to perform essential biochemical tasks from replication to metabolism; the latter being the engines of life. In all extant life on Earth, a small set of these nanomachines, called oxidoreductases, couple chemical energy from the environment with core redox reactions including photosynthesis, respiration and nitrogen fixation. The origins and emergence of complex life have been intimately tied with evolution of oxidoreductases. Here, using structure-based analyses, we describe the evolution of the protein catalysts in three biological epochs. First, thermodynamically driven polymerization reactions generated simple metal-binding peptides with specific sequences that catalysed core metabolic reactions. Second, these catalysts were incorporated in small structural 'folds'. In the third epoch, these folds served as building blocks for extant, complex nanomachines.This article is part of the discussion meeting issue 'Chance and purpose in the evolution of biospheres'.

  PublisherDOI

• Amino Acid Complexation Fractionates Nickel Isotopes: Implications for Tracing Nickel Cycling in the Environment

  Environmental Science & Technology Letters · 2025-02-27 · 4 citations

  articleOpen accessSenior author

  Nickel (Ni) is an essential cofactor in many proteins. Ni stable isotopes have been shown to undergo isotope fractionation in microorganisms and plants. However, the mechanisms driving this fractionation are poorly understood. Here, we present experimental data on Ni isotope fractionation during binding by common Ni-binding amino acids: glutamate (carboxylate side chain), histidine (imidazole side chain), and cysteine (sulfhydryl side chain). We used an equilibrium Donnan dialysis approach to separate free versus bound Ni and measured the isotopic composition of both pools via multicollector inductively coupled plasma mass spectrometry (MC-ICP-MS). Our results reveal that the glutamate and cysteine favor heavy 60Ni (Δ60/58Niglutamate = +0.80 ± 0.08; Δ60/58Nicysteine = +1.27 ± 0.08‰), while histidine causes little isotope shift (−0.12 ± 0.16‰). We then conducted experiments using a short peptide that is a structural analogue for acetyl-CoA synthetase and Ni-iron hydrogenase metal-binding sites. The peptide preferentially bound the heavy 60Ni with a Δ60/58Nipeptide value of +0.74 ± 0.04‰. The Ni isotope effect associated with peptide binding corresponded directly to the fractionation expected based on the coordinating ligands. This work represents an important first step in understanding the mechanistic controls on Ni isotope fractionation and the drivers of Ni isotope fractionation in biological and environmental systems.

  PublisherOA PDFDOI

• Copper isotopic evidence of microbial gold fixation in the Mesoarchean Witwatersrand Basin

  Geochimica et Cosmochimica Acta · 2024-11-26 · 3 citations

  article
  PublisherDOI

• On the mechanisms underpinning biological nickel isotope fractionation

  2024-01-01

  articleOpen access

  Background: Microbes use nickel (Ni) as a cofactor in several vital proteins, including key enzymes in methanogenesis and anaerobic carbon cycling.Ni proteins are also used to manage oxidative stress, metabolize hydogen, and access urea as a nitrogen source.Recent work suggests that marine microbes bind and preferentially take up isotopically-light Ni ( 58 Ni), with the expression of this effect dependent on community composition and/or function 1 .In contrast, laboratory cultures show preference for isotopically-heavy Ni ( 60 Ni) 2 .This presentation will consider whether such discrepancies can be explained, in part, by Ni 2+ binding to different amino acid ligands and differential expression of Ni proteins. Materials and Methods:We employed a machine learning model to predict metal binding sites (e.g.coordination number and amino acid ligand identity) in proteomes of marine phototrophs, including the diatom Thalassiosira and the cyanobacterium Synechococcus.Protein sequences were retrieved from the UniProt database and analyzed using the machine learning program M-Ionic 3 .Benchtop experiments were then conducted to assess Ni isotope fractionation during complexation by different amino acid ligands including histidine, cysteine, glutamate and a Ni-binding peptide.Free and complexed Ni was separated via equilibrium Donnan dialysis following Selden et al. (2024) 4 and measured via multicollector inductively coupled plasma mass spectrometry (MC-ICP-MS).Results and Discussion: The machine learning analysis of the Thalassiosira and Synechococcus proteomes revealed that Ni binding to proteins is dominated by complexation to the nitrogen ligands of histidine and sulfhydryl ligands of cysteine.Laboratory experiments showed Ni 2+ binding to histidine favored light 58 Ni ( 60/58 D complex-free = -0.120.08) while ligation to cysteine favored the heavy 60 Ni ( 60/58 D complex-free = +1.270.19).Glutamate (oxygen ligands) preferentially bound 60 Ni as observed for copper 3 ( 60/58 D complex-free = +0.14).These results can explain the Ni isotope effects observed in a more complex peptide (3 S and 1 N; 60/58 D complex-free = +0.740.04).In the context of the varied Ni-binding structures observed across multiple clades, these results suggest that binding by structurally distinct proteins may explain variability in Ni isotopes observed across multiple environments.

  PublisherOA PDFDOI

• Extracellular organic disulfide reduction by <i>Shewanella oneidensis</i> MR-1

  Microbiology Spectrum · 2024-02-28 · 4 citations

  articleOpen accessSenior author

  ABSTRACT Microbial reduction of organic disulfides affects the macromolecular structure and chemical reactivity of natural organic matter. Currently, the enzymatic pathways that mediate disulfide bond reduction in soil and sedimentary organic matter are poorly understood. In this study, we examined the extracellular reduction of 5,5′-dithiobis(2-nitrobenzoic acid) (DTNB) by Shewanella oneidensis strain MR-1. A transposon mutagenesis screen performed with S. oneidensis resulted in the isolation of a mutant that lost ~90% of its DTNB reduction activity. Genome sequencing of the mutant strain revealed that the transposon was inserted into the dsbD gene, which encodes for an oxidoreductase involved in cytochrome c maturation. Complementation of the mutant strain with the wild-type dsbD partially restored DTNB reduction activity. Because DsbD catalyzes a critical step in the assembly of multi-heme c -type cytochromes, we further investigated the role of extracellular electron transfer cytochromes in organic disulfide reduction. The results indicated that mutants lacking proteins in the Mtr system were severely impaired in their ability to reduce DTNB. These findings provide new insights into extracellular organic disulfide reduction and the enzymatic pathways of organic sulfur redox cycling. IMPORTANCE Organic sulfur compounds in soils and sediments are held together by disulfide bonds. This study investigates how Shewanella oneidensis breaks apart extracellular organic sulfur compounds. The results show that an enzyme involved in the assembly of c -type cytochromes as well as proteins in the Mtr respiratory pathway is needed for S. oneidensis to transfer electrons from the cell surface to extracellular organic disulfides. These findings have important implications for understanding how organic sulfur decomposes in terrestrial ecosystems.

  PublisherDOI

• Deeply branching <i>Bacillota</i> species exhibit atypical Gram-negative staining

  Microbiology Spectrum · 2024-08-20 · 8 citations

  articleOpen access

  ABSTRACT The Gram staining method differentiates bacteria based on their cell envelope structure, with the monoderm and diderm cell envelope types traditionally being synonymous with Gram-positive and Gram-negative stain results, respectively. Monoderms have a single phospholipid membrane surrounded by a thick layer of peptidoglycan, while diderms have a lipopolysaccharide outer membrane exterior to a thin peptidoglycan layer. The Bacillota (formerly Firmicutes ) phylum has members with both cell wall types, and recent phylogenetic analyses have shown that monoderm Bacillota evolved from diderm ancestors on multiple occasions. Here, we compiled Gram staining and ultrastructural data for Bacillota species with complete genomes to further investigate the evolution of Gram-positive and Gram-negative cell wall types. The results indicate that many deeply branching lineages at the root of Bacillota phylum stain Gram-negative but do not harbor genes for outer membrane protein or lipopolysaccharide biosynthesis. Phylogenetic reconstructions suggest that several deeply branching Bacillota species have retained a thin peptidoglycan layer in their cell walls, which was inherited from a diderm ancestor. Taxa with this atypical Gram-negative-staining cell wall structure include the thermophilic anaerobe Symbiobacterium thermophilum and members of the Desulfotomaculia, Syntrophamonadia, Desulfitobacteriia, Thermosediminibacteria, and Thermoanaerobacteria . Using Gram-staining results as a proxy for cell wall thickness, our analysis indicates that several independent peptidoglycan thickening events may have occurred in the evolution of the Gram-positive cell envelope. IMPORTANCE In this study, we examined the evolution of bacterial cell envelopes, specifically focusing on Gram-positive and Gram-negative cell wall types in the Bacillota phylum. Our results indicate that certain bacteria can stain Gram-negative despite having a monoderm cell wall structure, thus challenging the conventional interpretation of Gram-staining results. Our observations also question the assumption that Gram-negative staining is always indicative of a diderm structure. These findings have broader implications for understanding how and when cell walls thicken during the evolution of bacterial cell envelopes.

  PublisherDOI

• Metal-binding amino acid ligands commonly found in metalloproteins differentially fractionate copper isotopes

  Scientific Reports · 2024-01-22 · 15 citations

  articleOpen accessSenior author

  Abstract Copper (Cu) is a cofactor in numerous key proteins and, thus, an essential element for life. In biological systems, Cu isotope abundances shift with metabolic and homeostatic state. However, the mechanisms underpinning these isotopic shifts remain poorly understood, hampering use of Cu isotopes as biomarkers. Computational predictions suggest that isotope fractionation occurs when proteins bind Cu, with the magnitude of this effect dependent on the identity and arrangement of the coordinating amino acids. This study sought to constrain equilibrium isotope fractionation values for Cu bound by common amino acids at protein metal-binding sites. Free and bound metal ions were separated via Donnan dialysis using a cation-permeable membrane. Isotope ratios of pre- and post-dialysis solutions were measured by MC-ICP-MS following purification. Sulfur ligands (cysteine) preferentially bound the light isotope ( 63 Cu) relative to water (Δ 65 Cu complex-free = − 0.48 ± 0.18‰) while oxygen ligands favored the heavy isotope ( 65 Cu; + 0.26 ± 0.04‰ for glutamate and + 0.16 ± 0.10‰ for aspartate). Binding by nitrogen ligands (histidine) imparted no isotope effect (− 0.01 ± 0.04‰). This experimental work unequivocally demonstrates that amino acids differentially fractionate Cu isotopes and supports the hypothesis that metalloprotein biosynthesis affects the distribution of transition metal isotopes in biological systems.

  PublisherOA PDFDOI

Recent grants

• Collaborative Research: Selenium redox reactions and isotope ratios: The role of microbial and abiotic Selenium oxidation

  NSF · $78k · 2015–2019

• RAPID: Transformation of Elemental Mercury Dispersed by Flooding During Hurricane Harvey

  NSF · $50k · 2017–2018

• Molecular studies of dissimilatory selenium reduction by subsurface microorganisms

  NSF · $400k · 2009–2013

Frequent coauthors

• Jihua Hao

  22 shared

• Jennifer L. Goff

  Purchase College

  16 shared

• Paul G. Falkowski

  Rutgers, The State University of New Jersey

  15 shared

• David A. Fowle

  University of Kansas

  15 shared

• Dimitrios Ntarlagiannis

  14 shared

• Jeremy B. Fein

  University of Notre Dame

  14 shared

• Tamar Barkay

  Rutgers, The State University of New Jersey

  14 shared

• Lee Slater

  Rutgers, The State University of New Jersey

  13 shared

Labs

• Earth and Planetary Science Isotope Laboratory (EPSIL)PI

Education

• Ph.D., Earth and Planetary Sciences

  Rutgers University

  2005

• M.S., Earth and Planetary Sciences

  Rutgers University

  2002

• B.S., Earth and Planetary Sciences

  Rutgers University

  2000

Awards & honors

• 2009 Houtermans Medal, European Society for Geochemistry
• 2010 Academic Excellence Award for Excellence in Teaching, R…
• 2010 Rutgers Board of Trustees Research Fellowship for Schol…