Dan Willard

College of Engineering

Works (17)

Updated: July 21st, 2025 14:37

2025 article

Metabolic engineering in Hot Acid: Strategies enabling chemolithotrophy in thermoacidophilic archaea

Willard, D. J., & Kelly, R. M. (2025, June 10). Metabolic Engineering, Vol. 91, pp. 366–378.

By: D. Willard n & R. Kelly n 

author keywords: extreme thermoacidophile; Archaea; Sulfur oxidation; Metabolic model
topics (OpenAlex): Microbial Metabolic Engineering and Bioproduction; Biofuel production and bioconversion; Anaerobic Digestion and Biogas Production
Sources: Web Of Science, NC State University Libraries
Added: June 23, 2025

2024 article

Beyond low lignin: Identifying the primary barrier to plant biomass conversion by fermentative bacteria

Bing, R. G., Sulis, D. B., Carey, M. J., Manesh, M. J. H., Ford, K. C., Straub, C. T., … Kelly, R. M. (2024, October 18). Science Advances, Vol. 10.

By: R. Bing n , D. Sulis  n, M. Carey n, M. Manesh  n, K. Ford n, C. Straub n, T. Laemthong n, B. Alexander  n ...

Contributors: R. Bing n , M. Carey n, M. Manesh  n, K. Ford n, C. Straub n, T. Laemthong n, B. Alexander  n, D. Willard n ...

MeSH headings : Lignin / metabolism; Biomass; Fermentation; Populus / metabolism; Populus / genetics; Bacteria / metabolism; Bacteria / genetics; Plants / metabolism
topics (OpenAlex): Biofuel production and bioconversion; Lignin and Wood Chemistry; Microbial Metabolic Engineering and Bioproduction
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: November 1, 2024

2024 article

Chalcopyrite bioleaching efficacy by extremely thermoacidophilic archaea leverages balanced iron and sulfur biooxidation

Manesh, M. J. H., Willard, D. J., John, K. M., & Kelly, R. M. (2024, August 6). Bioresource Technology, Vol. 408.

By: M. Manesh n, D. Willard n, K. John n & R. Kelly* 

author keywords: Bioleaching; Chalcopyrite extreme thermoacidophiles; Sulfolobales; Genomes; Biooxidation
MeSH headings : Sulfur / metabolism; Oxidation-Reduction; Copper / metabolism; Iron / metabolism; Archaea / metabolism; Hydrogen-Ion Concentration; Temperature; Sulfolobales / metabolism
topics (OpenAlex): Metal Extraction and Bioleaching; Minerals Flotation and Separation Techniques; Corrosion Behavior and Inhibition
Sources: Web Of Science, NC State University Libraries
Added: August 19, 2024

2024 article

Complete genome sequence for the extremely thermophilic bacterium Anaerocellum danielii (DSM:8977)

Manesh, M. J. H., Bing, R. G., Willard, D. J., Adams, M. W. W., & Kelly, R. M. (2024, January 24). (K. M. Stedman, Ed.). Microbiology Resource Announcements, Vol. 1.

By: M. Manesh  n, R. Bing n , D. Willard n, M. Adams * & R. Kelly n 

Ed(s): K. Stedman

author keywords: Anaerocellum danielii; extreme thermophile; cellulose
topics (OpenAlex): Biofuel production and bioconversion; Genomics and Phylogenetic Studies; Enzyme Production and Characterization
TL;DR: The complete genome sequence of the extremely thermophilic bacterium Anaerocellum Anaerocellum danielii (DSM:8977) is reported here and is capable of lignocellulose degradation with potential applications in biomass degradation and production of chemicals and fuels from renewable feedstocks. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: February 12, 2024

2024 article

Complete genome sequence for the thermoacidophilic archaeon Metallosphaera sedula (DSM:5348)

Manesh, M. J. H., Bing, R. G., Willard, D. J., & Kelly, R. M. (2024, February 8). Microbiology Resource Announcements, Vol. 2.

By: M. Manesh  n, R. Bing n , D. Willard n & R. Kelly n 

author keywords: Metallosphaera sedula; thermoacidophile; archeaon
topics (OpenAlex): Genomics and Phylogenetic Studies; Microbial Community Ecology and Physiology; Building materials and conservation
TL;DR: The complete genome sequence of the thermoacidophilic archaeon Metallosphaera sedula, originally isolated from a volcanic field in Italy, is reported here, and has applications in bioleaching of sulfide minerals. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: February 19, 2024

2024 article

Engineering ethanologenicity into the extremely thermophilic bacterium Anaerocellum (f. Caldicellulosiriuptor) bescii

Bing, R. G., Ford, K. C., Willard, D. J., Manesh, M. J. H., Straub, C. T., Laemthong, T., … Kelly, R. M. (2024, September 19). Metabolic Engineering, Vol. 86, pp. 99–114.

By: R. Bing n , K. Ford n, D. Willard n, M. Manesh  n, C. Straub n, T. Laemthong n, B. Alexander  n, T. Tanwee * ...

author keywords: Anaerocellum bescii; Ethanol; Extreme thermophile; Cellulose
MeSH headings : Metabolic Engineering; Ethanol / metabolism; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Firmicutes / genetics; Firmicutes / metabolism; Caldicellulosiruptor
topics (OpenAlex): Biofuel production and bioconversion; Anaerobic Digestion and Biogas Production; Microbial Metabolic Engineering and Bioproduction
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: October 14, 2024

2024 article

Phenotype-driven assessment of the ancestral trajectory of sulfur biooxidation in the thermoacidophilic archaea Sulfolobaceae

Willard, D. J., Manesh, M. J. H., Bing, R. G., Alexander, B. H., & Kelly, R. M. (2024, July 2). MBio, Vol. 7.

By: D. Willard n, M. Manesh  n, R. Bing n , B. Alexander  n & R. Kelly n 

author keywords: archaea; sulfur; thermoacidophile; genomes; chemolithotrophy
MeSH headings : Sulfur / metabolism; Oxidation-Reduction; Sulfolobaceae / metabolism; Sulfolobaceae / genetics; Phenotype; Phylogeny; Gene Expression Profiling; Genome, Archaeal
topics (OpenAlex): Metal Extraction and Bioleaching; Genomics and Phylogenetic Studies; Microbial Community Ecology and Physiology
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: July 17, 2024

2023 article

Complete Genome Sequences of Caldicellulosiruptor acetigenus DSM 7040, Caldicellulosiruptor morganii DSM 8990 (RT8.B8), and Caldicellulosiruptor naganoensis DSM 8991 (NA10)

Bing, R. G., Willard, D. J., Manesh, M. J. H., Laemthong, T., Crosby, J. R., Adams, M. W. W., & Kelly, R. M. (2023, February 1). Microbiology Resource Announcements, Vol. 2.

By: R. Bing n , D. Willard n, M. Manesh  n, T. Laemthong n, J. Crosby n, M. Adams *, R. Kelly n 

topics (OpenAlex): Genomics and Phylogenetic Studies; Insect symbiosis and bacterial influences; Protist diversity and phylogeny
TL;DR: The genome sequences of three extremely thermophilic, lignocellulolytic Caldicellulosiruptor species were closed, improving previously reported multiple-contig assemblies and enhancing bioinformatic analysis of the species. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: February 20, 2023

2023 article

Complete Genome Sequences of Two Thermophilic Indigenous Bacteria Isolated from Wheat Straw, Thermoclostridium stercorarium subsp. Strain RKWS1 and Thermoanaerobacter sp. Strain RKWS2

Bing, R. G., Willard, D. J., Manesh, M. J. H., Laemthong, T., Crosby, J. R., Adams, M. W. W., & Kelly, R. M. (2023, February 7). Microbiology Resource Announcements, Vol. 12.

By: R. Bing n , D. Willard n, M. Manesh  n, T. Laemthong n, J. Crosby n, M. Adams *, R. Kelly n 

topics (OpenAlex): Genomics and Phylogenetic Studies; Microbial Community Ecology and Physiology; Bacteriophages and microbial interactions
TL;DR: Discovery of indigenous thermophiles in plant biomass suggests that high-temperature microorganisms are more ubiquitous than previously thought. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: April 17, 2023

2023 article

Complete genome sequence for the thermoacidophilic archaeon Sulfuracidifex (f . Sulfolobus ) metallicus DSM 6482

Willard, D. J., Manesh, M. J. H., Bing, R. G., & Kelly, R. M. (2023, December 6). Microbiology Resource Announcements, Vol. 12.

By: D. Willard n, M. Manesh  n, R. Bing n  & R. Kelly n 

author keywords: thermoacidophile; archaea; crenarchaea; genome
topics (OpenAlex): Metal Extraction and Bioleaching; Corrosion Behavior and Inhibition; Electrocatalysts for Energy Conversion
TL;DR: The complete genome sequence for the thermoacidophilic archaeon Sulfuracidifex (f. Sulfolobus) metallicus DSM 6482 is reported, which is a prolific metal and sulfur oxidizer and has application in metal bioleaching operations. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: December 18, 2023

2023 article

Extremely thermoacidophilic archaea for metal bioleaching: What do their genomes tell Us?

Manesh, M. J. H., Willard, D. J., Lewis, A. M., & Kelly, R. M. (2023, November 9). Bioresource Technology, Vol. 391.

By: M. Manesh  n, D. Willard n, A. Lewis n & R. Kelly n 

author keywords: Archaea; Sulfolobales; Metal biooxidation; Sulfur biooxidation; Chalcopyrite; High temperatures
MeSH headings : Archaea / genetics; Archaea / metabolism; Oxidation-Reduction; Metals / metabolism; Copper / metabolism; Minerals
topics (OpenAlex): Metal Extraction and Bioleaching; Corrosion Behavior and Inhibition; Extraction and Separation Processes
TL;DR: The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: December 18, 2023

2023 article

Interplay between transcriptional regulators and VapBC toxin–antitoxin loci during thermal stress response in extremely thermoacidophilic archaea

Cooper, C. R., Lewis, A. M., Notey, J. S., Mukherjee, A., Willard, D. J., Blum, P. H., & Kelly, R. M. (2023, February 8). Environmental Microbiology, Vol. 2.

By: C. Cooper  n, A. Lewis n, J. Notey n, A. Mukherjee n, D. Willard n, P. Blum *, R. Kelly n 

MeSH headings : Antitoxins / genetics; Toxins, Biological / genetics; Toxins, Biological / metabolism; Heat-Shock Response / genetics; Sulfolobus solfataricus / genetics; Sulfolobus solfataricus / metabolism; Escherichia coli / genetics
topics (OpenAlex): Enzyme Structure and Function; Genomics and Phylogenetic Studies; Protein Structure and Dynamics
TL;DR: The interplay between VapBC TA loci and heat shock regulators in Sa. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: March 13, 2023

2023 article

Stay or Go: Sulfolobales Biofilm Dispersal Is Dependent on a Bifunctional VapB Antitoxin

Lewis, A. M., Willard, D. J., Manesh, M. J. H., Sivabalasarma, S., Albers, S.-V., & Kelly, R. M. (2023, April 10). MBio, Vol. 4.

By: A. Lewis n, D. Willard n, M. Manesh  n, S. Sivabalasarma *, S. Albers * & R. Kelly n 

author keywords: toxin-antitoxin loci; biofilms; Sulfolobales; thermoacidophiles; Sulfolobus acidocaldarius
MeSH headings : Antitoxins / metabolism; Bacterial Proteins / metabolism; Bacterial Toxins / metabolism; Sulfolobales; Biofilms
topics (OpenAlex): Bacterial biofilms and quorum sensing; Vibrio bacteria research studies; Antibiotic Resistance in Bacteria
TL;DR: The findings here suggest that a stand-alone VapB-type antitoxin was the product of selective evolutionary pressure to influence biofilm formation in these archaea, a vital microbial community behavior. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: May 9, 2023

2023 article

Whither the genus Caldicellulosiruptor and the order Thermoanaerobacterales: phylogeny, taxonomy, ecology, and phenotype

Bing, R. G., Willard, D. J., Crosby, J. R., Adams, M. W. W., & Kelly, R. M. (2023, August 3). Frontiers in Microbiology, Vol. 14.

By: R. Bing n , D. Willard n, J. Crosby n, M. Adams * & R. Kelly n 

author keywords: Caldicellulosiruptor; Thermoanaerobacterales; bacteria; thermophiles; phylogeny; ecology; fermentative anaerobes
topics (OpenAlex): Microbial Community Ecology and Physiology; Genomics and Phylogenetic Studies; Enzyme Production and Characterization
TL;DR: A main outcome of ANI/AAI analysis indicates the need to reclassify several previously designated species in the Thermoanaerobacterales and Caldicellulosiruptorales by condensing them into strains of single species. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 28, 2023

2022 article

Fermentative conversion of unpretreated plant biomass: A thermophilic threshold for indigenous microbial growth

Bing, R. G., Carey, M. J., Laemthong, T., Willard, D. J., Crosby, J. R., Sulis, D. B., … Kelly, R. M. (2022, November 5). Bioresource Technology, Vol. 367.

By: R. Bing n , M. Carey n, T. Laemthong n, D. Willard n, J. Crosby n, D. Sulis  n, J. Wang n , M. Adams *, R. Kelly n 

Contributors: R. Bing n , M. Carey n, T. Laemthong n, D. Willard n, J. Crosby n, R. Kelly n , D. Sulis  n, J. Wang n , M. Adams *

author keywords: Thermophiles; Lignocellulose; Consolidated bioprocessing; Caldicellulosiruptor bescii; Acetivibrio thermocellus
MeSH headings : Biomass; Fermentation; Lignin / chemistry; Clostridium thermocellum / metabolism; Plants / metabolism
topics (OpenAlex): Biofuel production and bioconversion; Microbial Metabolic Engineering and Bioproduction; Anaerobic Digestion and Biogas Production
TL;DR: Thermophiles that naturally grow at and above 75°C offer specific advantages as platform microorganisms for biomass conversion into fuels and chemicals that prevents native microbes from competing with engineered microbes and forming undesirable by-products. (via Semantic Scholar)
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries, ORCID
Added: January 17, 2023

2021 article

Intersection of Biotic and Abiotic Sulfur Chemistry Supporting Extreme Microbial Life in Hot Acid

Willard, D. J., & Kelly, R. M. (2021, May 12). The Journal of Physical Chemistry B, Vol. 5.

By: D. Willard n & R. Kelly n 

MeSH headings : Metals; Oxidation-Reduction; Oxidoreductases / metabolism; Sulfolobus acidocaldarius; Sulfur
topics (OpenAlex): Metal Extraction and Bioleaching; Hydrocarbon exploration and reservoir analysis; Radioactive element chemistry and processing
TL;DR: Extreme thermoacidophily, a characteristic of species in the archaeal order Sulfolobales, is considered from the perspective of sulfur chemistry, both biotic and abiotic, as it relates to microbial bioenergetics. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: June 14, 2021

2020 journal article

The biology of thermoacidophilic archaea from the order Sulfolobales

FEMS Microbiology Reviews, 1.

By: A. Lewis n, A. Recalde *, C. Bräsen *, J. Counts n, P. Nussbaum*, J. Bost*, L. Schocke*, L. Shen * ...

author keywords: Archaea; Thermoacidophiles; Sulfolobales
MeSH headings : Archaea / genetics; Biology; Iron; Sulfolobales
topics (OpenAlex): Genomics and Phylogenetic Studies; Microbial Community Ecology and Physiology; Enzyme Production and Characterization
TL;DR: The nuances of the thermoacidophilic lifestyle of the Sulfolobales are discussed, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes, and physiological attributes together with how these characteristics make thermo Acidophiles ideal platforms for specialized industrial processes. (via Semantic Scholar)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: July 14, 2021

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