Welcome to ArchaeaCast! In our ninth and final episode of this season, our hosts Dr. Priyanka Chatterjee and Dr. Connor Hines discuss archaea as model systems and how they are being used in biotechnology! In the second part of the episode, Theopi Rados interviews Dr. Kelly Zatopek from New England Biolabs Inc (NEB).

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For nomenclature changes, current nomenclature can be found here

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Sources

Cowan DA. 1992. Biotechnology of the Archaea. Trends Biotechnol 10:315–323.

Cabrera MaÁ, Blamey JM. 2018. Biotechnological applications of archaeal enzymes from extreme environments. Biol Res 51:37.

Eichler J. 2001. Biotechnological uses of archaeal extremozymes. Biotechnol Adv 19:261–278.

Schiraldi C, Giuliano M, De Rosa M. 2002. Perspectives on biotechnological applications of archaea. Archaea 1:436561.

Welcome to ArchaeaCast! In our 8th episode, our hosts Priyanka Chatterjee and Dr. Alex Phillips discuss archaeal viruses, the even littler guys that infect our friendly archaeal cells! In the second part of the episode, Theopi Rados interviews Prof. Rachel Whitaker, from the University of Illinois Urbana-Champaign.

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Virus diversity image 1

Virus diversity image 2

STIV structure

STIV pyramids 1

STIV pyramids 2

Project Microbe

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Sources

DeWerff SJ et al. 2020. Killer Archaea: Virus-Mediated Antagonism to CRISPR-Immune Populations Results in Emergent Virus-Host Mutualism. mBio.

Forterre P. 2006. The origin of viruses and their possible roles in major evolutionary transitions. Virus Research.

Häring M et al. 2005. Viral Diversity in Hot Springs of Pozzuoli, Italy, and Characterization of a Unique Archaeal Virus, Acidianus Bottle-Shaped Virus, from a New Family, the Ampullaviridae. J Virol.

Hendrix RW et al. 1999. Evolutionary relationships among diverse bacteriophages and prophages: All the world’s a phage. PNAS.

Koonin EV et al. 2017. Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states. Biology Direct.

Krupovic M et al. 2018. Viruses of archaea: Structural, functional, environmental and evolutionary genomics. Virus Res.

Krupovic M et al. 2019. Origin of viruses: primordial replicators recruiting capsids from hosts. Nat Rev Microbiol.

Leão P et al. 2024. Asgard archaea defense systems and their roles in the origin of eukaryotic immunity. Nat Commun.

Mushegian AR. 2020. Are There 1031 Virus Particles on Earth, or More, or Fewer? J Bacteriol.

Peng X et al. 2020. Anti-CRISPR Proteins in Archaea. Trends Microbiol.

Prangishvili D et al. 2017. The enigmatic archaeal virosphere. Nat Rev Microbiol.

Quemin ERJ et al. 2016. Eukaryotic-Like Virus Budding in Archaea. mBio.

Quemin ERJ & Quax TEF. 2015. Archaeal viruses at the cell envelope: entry and egress. Front. Microbiol.

Rice G et al. 2004. The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life. PNAS.

Rice G et al. 2001. Viruses from extreme thermal environments. PNAS.

Snyder JC et al. 2011. Sulfolobus Turreted Icosahedral Virus c92 Protein Responsible for the Formation of Pyramid-Like Cellular Lysis Structures. J Virol.

Wang F et al. 2022. Spindle-shaped archaeal viruses evolved from rod-shaped ancestors to package a larger genome. Cell.

Welcome to ArchaeaCast! In our seventh episode, our hosts Priyanka Chatterjee and Dr. Connor Hines discuss Methanogens, the dinosaur killing Archaea! In the second part of the episode, Connor interviews Prof. Nicole Buan, from the University of Nebraska - Lincoln.

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For nomenclature changes, current nomenclature can be found here

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Sources

Lloyd, David. "Methanogenesis: Ecology, physiology, biochemistry and genetics: Edited by JG Ferry. Chapman & Hall, New York, 1993. ISBN 0-412-03531-6, pp. x+ 536." (1996): 65.

Buan, Nicole R. "Methanogens: pushing the boundaries of biology." Emerging Topics in Life Sciences 2.4 (2018): 629-646.

Thauer, Rudolf K., et al. "Methanogenic archaea: ecologically relevant differences in energy conservation." Nature Reviews Microbiology 6.8 (2008): 579-591.

https://www.eesi.org/papers/view/fact-sheet-landfill-methane

https://www.epa.gov/lmop/landfill-gas-energy-project-development-handbook

https://www.fao.org/news/story/en/item/197623/icode/

Rothman, Daniel H., et al. "Methanogenic burst in the end-Permian carbon cycle." Proceedings of the National Academy of Sciences 111.15 (2014): 5462-5467.

Fournier, Gregory P., and J. Peter Gogarten. "Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia." Journal of bacteriology 190.3 (2008): 1124-1127.

Ogden, Darcy E., and Norman H. Sleep. "Explosive eruption of coal and basalt and the end-Permian mass extinction." Proceedings of the National Academy of Sciences 109.1 (2012): 59-62.

Mah, R. A., et al. "Biogenesis of methane." Annual Reviews in Microbiology 31.1 (1977): 309-341.

Leigh, John A. "Nitrogen fixation in methanogens: the archaeal perspective." Current issues in molecular biology 2.4 (2000): 125-131.

Bae, Hee-Sung, et al. "Methanogens are major contributors to nitrogen fixation in soils of the Florida Everglades." Applied and environmental microbiology 84.7 (2018): e02222-17.

Boyd, E. S., et al. "A late methanogen origin for molybdenum‐dependent nitrogenase." Geobiology 9.3 (2011): 221-232.

Webster, Christopher R., et al. "Background levels of methane in Mars’ atmosphere show strong seasonal variations." Science 360.6393 (2018): 1093-1096.

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We’d love to hear from you! Contact us at [email protected]

Welcome to ArchaeaCast! In our sixth episode, our hosts Priyanka Chatterjee and Dr. Connor Hines discuss the archaea that are very close to home–the ones that can live in and on us! In the second part of the episode, Priyanka interviews Dr. Christine Moissl-Eichinger, from the Medical University of Graz in Austria.

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For nomenclature changes, current nomenclature can be found here

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Sources

Triantafyllou K, Chang C, Pimentel M. 2014. Methanogens, Methane and Gastrointestinal Motility. J Neurogastroenterol Motil 20:31–40.

Probst AJ, Auerbach AK, Moissl-Eichinger C. 2013. Archaea on Human Skin. PLOS ONE 8:e65388.

Matarazzo F, Ribeiro AC, Faveri M, Taddei C, Martinez MB, Mayer MPA. 2012. The domain Archaea in human mucosal surfaces. Clin Microbiol Infect Off Publ Eur Soc Clin Microbiol Infect Dis 18:834–840.

Dridi B, Henry M, Khéchine AE, Raoult D, Drancourt M. 2009. High Prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae Detected in the Human Gut Using an Improved DNA Detection Protocol. PLOS ONE 4:e7063.

Takakura W, Pimentel M. 2020. Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome – An Update. Front Psychiatry 11:664.

Hook SE, Wright A-DG, McBride BW. 2010. Methanogens: Methane Producers of the Rumen and Mitigation Strategies. Archaea 2010:945785.

Probiotics: Usefulness and Safety. NCCIH. https://www.nccih.nih.gov/health/probiotics-usefulness-and-safety.

Archaebiotics: Archaea as Pharmabiotics for Treating Chronic Disease in Humans? | IntechOpen. https://www.intechopen.com/chapters/56434.

Kim JY, Whon TW, Lim MY, Kim YB, Kim N, Kwon M-S, Kim J, Lee SH, Choi H-J, Nam I-H, Chung W-H, Kim J-H, Bae J-W, Roh SW, Nam Y-D. 2020. The human gut archaeome: identification of diverse haloarchaea in Korean subjects. Microbiome 8:114.

Moissl-Eichinger C, Probst AJ, Birarda G, Auerbach A, Koskinen K, Wolf P, Holman H-YN. 2017. Human age and skin physiology shape diversity and abundance of Archaea on skin. Sci Rep 7:4039.

Bovaer®. @anh. https://www.dsm-firmenich.com/anh/products-and-services/products/methane-inhibitors/bovaer.html.

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We’d love to hear from you! Contact us at [email protected]

Welcome to ArchaeaCast! In our fifth episode, our hosts Priyanka Chatterjee and Dr. Connor Hines talk about Acidophiles, the heavy metal rockin’ Archaea! In the second part of the episode, Connor Hines interviews Prof. Paul Blum, from the University of Nebraska Lincoln.

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Article link for: “Yellowstone National Park Death: Oregon Man Died In Acidic Hot Spring Trying To ‘Hot Pot’”

Video showing Cans dissolving in Acid

Sacki Dog Meme

Picture of “Ferroplasma acidiphilum”

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For nomenclature changes, current nomenclature can be found here

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Sources

Howland, J. L. (2000). The surprising archaea: discovering another domain of life. Oxford University Press. ISBN: 9780195111835

Chen, Lanming, et al. "The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota."

Ferrer, Manuel, et al. "The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated."

McCarthy, Samuel, et al. "Expanding the limits of thermoacidophily in the archaeon Sulfolobus solfataricus by adaptive evolution."

Krzmarzick, Mark James, et al. "Diversity and niche of archaea in bioremediation."

Rastädter, Kerstin, et al. "The cell membrane of Sulfolobus spp.-homeoviscous adaption and biotechnological applications."

Baker-Austin, Craig, and Mark Dopson. "Life in acid: pH homeostasis in acidophiles."

Mikael Sehlin, H. B. L. E., and E. Börje Lindström. "Oxidation and reduction of arsenic by Sulfolobus acidocaldarius strain BC."

“Abandoned Mine Drainage”

“Where do acid-sulfate hot springs come from and why are they important?”

Nordstrom, D. Kirk, James W. Ball, and R. Blaine McCleskey. "Ground water to surface water: chemistry of thermal outflows in Yellowstone National Park." Geothermal biology and geochemistry in Yellowstone National Park (2005): 73-94.

Welcome to ArchaeaCast! In our fourth episode, our hosts Dr. Connor Hines and Dr. Alex Philips talk about Thermophiles, the Archaea which are almost too hot to handle! In the second part of the episode, Theopi Rados interviews Prof. Rachel Whitaker, from the University of Illinois at Urbana-Champaign.

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Picture of Pyrococcus furiosus

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For nomenclature changes, current nomenclature can be found here

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Sources

Atomi, Haruyuki, et al. 2004. https://doi.org/10.1128/jb.186.14.4829-4833.2004

Boyd, Eric S., et al. 2013. https://doi.org/10.3389/fmicb.2013.00062

Brochier-Armanet, et al. 2006. https://doi.org/10.1155/2006/582916

Charles-Orszag, et al. 2021. https://doi.org/10.3389/fmicb.2021.707124

Charles-Orszag, Arthur, et al. 2023. https://doi.org/10.1016/j.bpj.2022.11.1527

Erauso, Gaël, et al. 1993. https://doi.org/10.1007/BF00252219

Fiala, Gerhard, and Karl O. Stetter. 1986. https://doi.org/10.1007/BF00413027

Forterre, Patrick. 2002. https://doi.org/10.1016/S0168-9525(02)02650-1

Fröls, Sabrina, et al. 2007. https://doi.org/10.1128/jb.01016-07

Grogan, Dennis W., Geraldine T. Carver, and John W. Drake. 2001. https://doi.org/10.1073/pnas.141113098

Han, Wenyuan, et al. 2017. https://doi.org/10.3390/ijms18071340

Hsieh, Tao-shih, and Jody L. Plank. 2006. https://doi.org/10.1074/jbc.M513252200

Mackwan, Reena R, et al. 2008. https://doi.org/10.1534/genetics.108.089086.

Pulschen, Andre Arashiro, et al. 2020. https://doi.org/10.1016/j.bpj.2022.11.1527

Russell, M. J., A. J. Hall, and W. Martin. 2010. https://doi.org/10.1111/j.1472-4669.2010.00249.x

Wolferen, Marleen van, et al. 2020. https://doi.org/10.1128/mbio.03014-19

Yang, Xi, et al. 2020. https://doi.org/10.1073/pnas.1921848117

Welcome to ArchaeaCast! In our third episode, our hosts Priyanka Chatterjee and Connor Hines talk about Asgardarcheota, Norse mythology named Archaea! In the second part of the episode, Dr. Alex Phillips interviews Prof. Brett Baker, from the University of Texas at Austin.

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For nomenclature changes, current nomenclature can be found here

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Sources

Scientists Break Record By Finding Northernmost Hydrothermal Vent Field

Complex archaea that bridge the gap between prokaryotes and eukaryotes

Cultured Asgard Archaea Shed Light on Eukaryogenesis

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

Asgard archaea illuminate the origin of eukaryotic cellular complexity

Isolation of an archaeon at the prokaryote–eukaryote interface

Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche

Fantastic article on the history of Metagenomics

Press release which includes the E3 image from JAMSTEC, and a great video on E3 from JAMSTEC.

Other work cited:

Booth A, Doolittle WF. Eukaryogenesis, how special really? Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10278-85. doi: 10.1073/pnas.1421376112. Epub 2015 Apr 16. PMID: 25883267; PMCID: PMC4547297.

Jørgensen, Steffen Leth, et al. "Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean spreading ridge." Frontiers in microbiology (2013)

Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, Maiden MCJ, Nesme X, Rosselló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol. 2002 May;52(Pt 3):1043-1047. doi: 10.1099/00207713-52-3-1043. PMID: 12054223.

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ArchaeaCast episodes drop every other Tuesday on your favorite audio platform!

We’d love to hear from you! Contact us at [email protected]

Welcome to ArchaeaCast! In our second episode, our hosts Priyanka Chatterjee and Connor Hines talk about Halophiles, the salt-loving Archaea! In the second part of the episode, Dr. Alex Phillips interviews Prof. Amy Schimd, from Duke University.

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Some species and genera names have changed since this episode was recorded. Current nomenclature can be found here.

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Bibliography:

Cited in the episode:

Pietrangelo, A. "Pink Himalayan Salt: Benefits, Risks, and Alternatives." Healthline, 2 Sept. 2023

Papp, ZJ. "Morphological and Microchemical Characterization of Himalayan Salt Samples." Revue Roumaine de Chimie, vol. 61, no. 3, Mar. 2016

Duarte CM et al D. Discovery of Afifi, the shallowest and southernmost brine pool reported in the Red Sea. Sci Rep. 2020

Wilkanski, B. Life in the Dead Sea. Nature 138, 467 (1936).

Yim, K.,et al et al. Occurrence of viable, red-pigmented haloarchaea in the plumage of captive flamingoes. Sci Rep 5, 16425 (2015).

Giani M et al Haloarchaeal Carotenoids: Healthy Novel Compounds from Extreme Environments. Mar Drugs. 2019 Sep 6;17(9):524.

Aharon Oren, John E. Hallsworth, Microbial weeds in hypersaline habitats: the enigma of the weed-like Haloferax mediterranei, FEMS Microbiology Letters, 2014.

DasSarma S, et al Extremophilic models for astrobiology: haloarchaeal survival strategies and pigments for remote sensing. Extremophiles. 2020 Jan;24(1):31-41. doi: 10.1007/s00792-019-01126-3.

Cited in the interview:

Biotechnological applications of haloarchaea: Mitra, R., Xu, T., Xiang, H. et al. Current developments on polyhydroxyalkanoates synthesis by using halophiles as a promising cell factory. Microb Cell Fact 19, 86 (2020).

Haloarchaea can survive months of desiccation: Kottemann M, Kish A, Iloanusi C, Bjork S, DiRuggiero J. Physiological responses of the halophilic archaeon Halobacterium sp. strain NRC1 to desiccation and gamma irradiation. Extremophiles. 2005 Jun;9(3):219-27. doi: 10.1007/s00792-005-0437-4. Epub 2005 Apr 21. PMID: 15844015.

Halite deposits on Mars:M. M. Osterloo et al. Chloride-Bearing Materials in the Southern Highlands of Mars.Science 319,1651-1654(2008), among others

Haloarchaea can survive for millennia in salt inclusions: Fendrihan S, Dornmayr-Pfaffenhuemer M, Gerbl FW, Holzinger A, Grösbacher M, Briza P, Erler A, Gruber C, Plätzer K, Stan-Lotter H. Spherical particles of halophilic archaea correlate with exposure to low water activity--implications for microbial survival in fluid inclusions of ancient halite. Geobiology. 2012 Sep;10(5):424-33. doi: 10.1111/j.1472-4669.2012.00337.x. Epub 2012 Jul 15. PMID: 22804926; PMCID: PMC3495301, among others

Halo handbook (protocols) by Mike Dyall-Smith

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Cool videos and pictures:

Hot tub of despair, Pink Lakes

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ArchaeaCast episodes drop every other Tuesday on your favorite audio platform!

We’d love to hear from you! Contact us at [email protected]

Welcome to ArchaeaCast! In our first episode, our hosts Priyanka Chatterjee and Connor Hines talk about the history of Archaea, how we discovered that they were different from bacteria, and discuss their unique classification.

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For nomenclature changes, current nomenclature can be found at: https://gtdb.ecogenomic.org/genome?gid=GCA_003086455.1

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Bibliography:

Singer, Charles J. (1931). A short history of biology, a general introduction to the study of living things. Oxford: Clarendon Press.

Woese, Carl R., Otto Kandler, and Mark L. Wheelis. "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya." Proceedings of the National Academy of Sciences 87.12 (1990): 4576-4579.

Cavalier-Smith, Thomas. "A revised six-kingdom system of life." Biological Reviews 73.3 (1998): 203-266.

Cavalier-Smith, Thomas. "Only six kingdoms of life." Proceedings of the Royal Society of London. Series B: Biological Sciences 271.1545 (2004): 1251-1262.

Ruggiero, Michael A., et al. "A higher level classification of all living organisms." PloS one 10.4 (2015): e0119248.

Koonin, Eugene V. "Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1678 (2015): 20140333.

Noller, H. Carl Woese (1928–2012). Nature 493, 610 (2013). https://doi.org/10.1038/493610a

Pauling, L., & Zuckerkandl, E. (1963). Chemical paleogenetics. Acta Chem. Scand, 17, S9–S16.

Woese, C. R., & Fox, G. E. (1977). Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proceedings of the National Academy of Sciences, 74(11), 5088–5090.\

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ArchaeaCast episodes drop every other Tuesday on your favorite audio platform!

We’d love to hear from you! Contact us at [email protected]

Welcome to ArchaeaCast! In this primer episode, our hosts Priyanka Chatterjee and Connor Hines introduce our podcast and subject of study - Archaea!

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Bibliography:

Cavicchioli R, Curmi PM, Saunders N, Thomas T. Pathogenic archaea: do they exist? Bioessays. 2003 Nov;25(11):1119-28. doi: 10.1002/bies.10354. PMID: 14579252.

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Pictures of Haloquadratum walsbyi, misnomered as a bacterium, can be found here: https://www.nature.com/articles/news041011-3

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Current, more up-to-date nomenclature can be found at: https://gtdb.ecogenomic.org/genome?gid=GCA_003086455.1

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ArchaeaCast episodes drop every other Tuesday on your favorite audio platform!

We’d love to hear from you! Contact us at [email protected]