Journal Article: Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea
Hua, Zheng-Shuang, Wang, Yu-Lin, Evans, Paul N., Qu, Yan-Ni, Goh, Kian Mau, Rao, Yang-Zhi, Qi, Yan-Ling, Li, Yu-Xian, Huang, Min-Jun, Jiao, Jian-Yu, Chen, Ya-Ting, Mao, Yan-Ping, Shu, Wen-Sheng, Hozzein, Wael, Hedlund, Brian P., Tyson, Gene W., Zhang, Tong and Li, Wen-Jun (2019) Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea. Nature Communications, 10 1: 4574. doi:10.1038/s41467-019-12574-y
Journal Article: A genomic view of the reef-building coral Porites lutea and its microbial symbionts
Robbins, Steven J., , , Singleton, Caitlin M., Chan, Cheong Xin, Messer, Lauren F., Geers, Aileen U., Ying, Hua, Baker, Alexander, Bell, Sara C., Morrow, Kathleen M., Ragan, Mark A., Miller, David J., Forêt, Sylvain, Voolstra, Christian R., Tyson, Gene W. and Bourne, David G. (2019) A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nature Microbiology, . doi:10.1038/s41564-019-0532-4
Journal Article: Acetate production from anaerobic oxidation of methane via intracellular storage compounds
Cai, Chen, Shi, Ying, Guo, Jianhua, Tyson, Gene W., Hu, Shihu and Yuan, Zhiguo (2019) Acetate production from anaerobic oxidation of methane via intracellular storage compounds. Environmental Science & Technology, 53 13: 7371-7379. doi:10.1021/acs.est.9b00077
Uncovering new microbial players and processes in the global methane cycle
(2018–2022) ARC Future Fellowships
(2018) UQ Major Equipment and Infrastructure
(2018) University of Western Australia
Characterisation of novel archaea evolved to oxidise methane and short chain alkanes
(2019) Doctor Philosophy
Functional omics investigation and isolation of microorganisms involved in anaerobic methane oxidation
Doctor Philosophy
Development of meta omic tools to explore microbial carbon cycling
Doctor Philosophy
Hugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2018). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. In Marilena Aquino de Muro and Ralph Rapley (Ed.), Gene probes: principles and protocols (pp. 029-042) New Jersey, United States: Humana Press. doi:10.1385/1-59259-238-4:029
Metagenomics using next-generation sequencing
Bragg,Lauren and Tyson, Gene W. (2014). Metagenomics using next-generation sequencing. In Ian T. Paulsen and Andrew J. Holmes (Ed.), Environmental Microbiology: Methods and Protocols (pp. 183-201) New York, NY United States: Humana Press Inc.. doi:10.1007/978-1-62703-712-9_15
Rhizosphere Metatranscriptomics: Challenges and Opportunities
Carvalhais, Lilia C., Dennis, Paul G., Tyson, Gene W. and Schenk, Peer M. (2013). Rhizosphere Metatranscriptomics: Challenges and Opportunities. In Frans J. de Bruijn (Ed.), Molecular Microbial Ecology of the Rhizosphere (pp. 1137-1144) Hoboken, NJ United States: Wiley-Blackwell. doi:10.1002/9781118297674.ch109
Environmental shotgun sequencing
Tyson, Gene W. and Hugenholtz, Philip (2005). Environmental shotgun sequencing. In Lynn B. Jorde (Ed.), Encyclopedia of genetics, genomics, proteomics, and bioinformatics (pp. 1386-1391) West Sussex, U.K.: John Wiley & Sons. doi:10.1002/047001153X.g205313
Banfield, Jillian, F., Tyson, Gene W., Allen, E. E. and Whitaker, B. J. (2005). The search for a molecular-level understanding of the processes that underpin the Earth's biogeochemical cycles. In Banfield, Jillian F., Cervini-Silva, Javiera and Nealson, Kenneth M. (Ed.), Molecular geomicrobiology (pp. 1-7) Chantilly, U.S.: Mineralogical Society of America, Geochemical Society.
Hugenholtz, P., Tyson, G. and Blackall, L. L. (2002). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridisation (FISH). In Aquino de Muro. M and Rapley. R (Ed.), Gene Probes - Principles and Protocols (pp. 1-17) London: Humana Press.
Hua, Zheng-Shuang, Wang, Yu-Lin, Evans, Paul N., Qu, Yan-Ni, Goh, Kian Mau, Rao, Yang-Zhi, Qi, Yan-Ling, Li, Yu-Xian, Huang, Min-Jun, Jiao, Jian-Yu, Chen, Ya-Ting, Mao, Yan-Ping, Shu, Wen-Sheng, Hozzein, Wael, Hedlund, Brian P., Tyson, Gene W., Zhang, Tong and Li, Wen-Jun (2019) Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea. Nature Communications, 10 1: 4574. doi:10.1038/s41467-019-12574-y
A genomic view of the reef-building coral Porites lutea and its microbial symbionts
Robbins, Steven J., , , Singleton, Caitlin M., Chan, Cheong Xin, Messer, Lauren F., Geers, Aileen U., Ying, Hua, Baker, Alexander, Bell, Sara C., Morrow, Kathleen M., Ragan, Mark A., Miller, David J., Forêt, Sylvain, Voolstra, Christian R., Tyson, Gene W. and Bourne, David G. (2019) A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nature Microbiology, . doi:10.1038/s41564-019-0532-4
Acetate production from anaerobic oxidation of methane via intracellular storage compounds
Cai, Chen, Shi, Ying, Guo, Jianhua, Tyson, Gene W., Hu, Shihu and Yuan, Zhiguo (2019) Acetate production from anaerobic oxidation of methane via intracellular storage compounds. Environmental Science & Technology, 53 13: 7371-7379. doi:10.1021/acs.est.9b00077
Biochar-mediated anaerobic oxidation of methane
Zhang, Xueqin, Xia, Jun, Pu, Jiaoyang, Cai, Chen, Tyson, Gene W., Yuan, Zhiguo and Hu, Shihu (2019) Biochar-mediated anaerobic oxidation of methane. Environmental Science and Technology, 53 12: 6660-6668. doi:10.1021/acs.est.9b01345
Wilson, Rachel M., Neumann, Rebecca B., Crossen, Kelsey B., Raab, Nicole M., Hodgkins, Suzanne B., Saleska, Scott R., Bolduc, Ben, Woodcroft, Ben J., Tyson, Gene W., Chanton, Jeffrey P. and Rich, Virginia (2019) Microbial community analyses inform geochemical reaction network models for predicting pathways of greenhouse gas production. Frontiers in Earth Science, 7 . doi:10.3389/feart.2019.00059
Nguyen, Marcus, Long, S. Wesley, McDermott, Patrick F., Olsen, Randall J., Olson, Robert, Stevens, Rick L., Tyson, Gregory H., Zhao, Shaohua and Davis, James J. (2019) Using machine learning to predict antimicrobial MICs and associated genomic features for nontyphoidal Salmonella. Journal of Clinical Microbiology, 57 2: . doi:10.1128/JCM.01260-18
Toward unrestricted use of public genomic data
Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A. N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Munoz, Alejandro Reyes, Roberts, Richard J., Rossello-Mora, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, Jogo C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B. and Xenarios, Ioannis (2019) Toward unrestricted use of public genomic data. Science, 363 6425: 350-352. doi:10.1126/science.aaw1280
An evolving view of methane metabolism in the Archaea
Evans, Paul N., Boyd, Joel A., Leu, Andy O., Woodcroft, Ben J., Parks, Donovan H., Hugenholtz, Philip and Tyson, Gene W. (2019) An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology, . doi:10.1038/s41579-018-0136-7
Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi
Boyd, Joel A., Jungbluth, Sean P., Leu, Andy O., Evans, Paul N., Woodcroft, Ben J., Chadwick, Grayson L., Orphan, Victoria J., Amend, Jan P., Rappé, Michael S. and Tyson, Gene W. (2019) Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. The ISME Journal, 13 5: 1269-1279. doi:10.1038/s41396-018-0343-2
Martinez, Miguel A., Woodcroft, Ben J., Ignacio Espinoza, Julio C., Zayed, Ahmed A., Singleton, Caitlin M., Boyd, Joel A., Li, Yueh-Fen, Purvine, Samuel, Maughan, Heather, Hodgkins, Suzanne B., Anderson, Darya, Sederholm, Maya, Temperton, Ben, Bolduc, Benjamin, Saleska, Scott R., Tyson, Gene W. and Rich, Virginia I. (2019) Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov. Systematic and Applied Microbiology, . doi:10.1016/j.syapm.2018.12.003
Rinke, Christian, Rubino, Francesco, Messer, Lauren F., Youssef, Noha, Parks, Donovan H., Chuvochina, Maria, Brown, Mark, Jeffries, Thomas, Tyson, Gene W., Seymour, Justin R. and Hugenholtz, Philip (2018) A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). The ISME Journal, . doi:10.1038/s41396-018-0282-y
Soil viruses are underexplored players in ecosystem carbon processing
Trubl, Gareth, Jang, Ho Bin, Roux, Simon, Emerson, Joanne B., Solonenko, Natalie, Vik, Dean R., Solden, Lindsey, Ellenbogen, Jared, Runyon, Alexander T., Bolduc, Benjamin, Woodcroft, Ben J., Saleska, Scott R., Tyson, Gene W., Wrighton, Kelly C., Sullivan, Matthew B. and Rich, Virginia I. (2018) Soil viruses are underexplored players in ecosystem carbon processing. mSystems, 3 5: . doi:10.1128/mSystems.00076-18
Hoedt, Emily C., Parks, Donovan H., Volmer, James G., Rosewarne, Carly P., Denman, Stuart E., McSweeney, Christopher S., Muir, Jane G., Gibson, Peter R., Cuív, Páraic Ó, Hugenholtz, Philip, Tyson, Gene W. and Morrison, Mark (2018) Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME Journal, . doi:10.1038/s41396-018-0225-7
Genome-centric view of carbon processing in thawing permafrost
Woodcroft, Ben J., Singleton, Caitlin M., Boyd, Joel A., Evans, Paul N., Emerson, Joanne B., Zayed, Ahmed A. F., Hoelzle, Robert D., Lamberton, Timothy O., McCalley, Carmody K., Hodgkins, Suzanne B., Wilson, Rachel M., Purvine, Samuel O., Nicora, Carrie D., Li, Changsheng, Frolking, Steve, Chanton, Jeffrey P., Crill, Patrick M., Saleska, Scott R., Rich, Virginia I. and Tyson, Gene W. (2018) Genome-centric view of carbon processing in thawing permafrost. Nature, 560 7716: 49-54. doi:10.1038/s41586-018-0338-1
Host-linked soil viral ecology along a permafrost thaw gradient
Emerson, Joanne B., Roux, Simon, Brum, Jennifer R., Bolduc, Benjamin, Woodcroft, Ben J., Jang, Ho Bin, Singleton, Caitlin M., Solden, Lindsey M., Naas, Adrian E., Boyd, Joel A., Hodgkins, Suzanne B., Wilson, Rachel M., Trubl, Gareth, Li, Changsheng, Frolking, Steve, Pope, Phillip B., Wrighton, Kelly C., Crill, Patrick M., Chanton, Jeffrey P., Saleska, Scott R., Tyson, Gene W., Rich, Virginia I. and Sullivan, Matthew B. (2018) Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology, 3 8: 870-880. doi:10.1038/s41564-018-0190-y
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B.K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O., Gilbert, Jack A, Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J.G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, Mcmahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip and Woyke, Tanja (2018) Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893). Nature Biotechnology, 36 7: 660-660. doi:10.1038/nbt0718-660a
Biogenic methane cycling in a laboratory model of an abandoned bituminous coal mine
Raudsepp, Maija J., Fluggen, Markus, Shypanski, Adam H., Tyson, Gene W., Golding, Suzanne D. and Southam, Gordon (2018) Biogenic methane cycling in a laboratory model of an abandoned bituminous coal mine. Geomicrobiology Journal, 35 6: 491-502. doi:10.1080/01490451.2017.1392652
The importance of designating type material for uncultured taxa
Chuvochina, Maria, Rinke, Christian, Parks, Donovan H., Rappé, Michael S., Tyson, Gene W., Yilmaz, Pelin, Whitman, William B. and Hugenholtz, Philip (2018) The importance of designating type material for uncultured taxa. Systematic and Applied Microbiology, . doi:10.1016/j.syapm.2018.07.003
Methanotrophy across a natural permafrost thaw environment
Singleton, Caitlin M., McCalley, Carmody K., Woodcroft, Ben J., Boyd, Joel A., Evans, Paul N., Hodgkins, Suzanne B., Chanton, Jeffrey P., Frolking, Steve, Crill, Patrick M., Saleska, Scott R., Rich, Virginia I. and Tyson, Gene W. (2018) Methanotrophy across a natural permafrost thaw environment. The ISME journal, 12 10: 2544-2558. doi:10.1038/s41396-018-0065-5
A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction
Cai, Chen, Leu, Andy O., Xie, Guo-Jun, Guo, Jianhua, Feng, Yuexing, Zhao, Jian-Xin, Tyson, Gene W., Yuan, Zhiguo and Hu, Shihu (2018) A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. The ISME Journal, 12 8: 1929-1939. doi:10.1038/s41396-018-0109-x
GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes
Boyd, Joel A., Woodcroft, Ben J. and Tyson, Gene W. (2018) GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. Nucleic Acids Research, 46 10: e59-e59. doi:10.1093/nar/gky174
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glockner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. Murat, Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip and Woyke, Tanja (2018) Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (vol 35, pg 725, 2017). Nature Biotechnology, 36 2: 196-196. doi:10.1038/nbt0218-196a
Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip and Tyson, Gene W. (2017) Author correction: recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 3 253: 253-253. doi:10.1038/s41564-017-0083-5
Shiffman, Miriam E, Soo, Rochelle M, Dennis, Paul G, Morrison, Mark, Tyson, Gene W and Hugenholtz, Philip (2017) Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ, 5 1-32. doi:10.7717/peerj.4075
Tout, Jessica, Astudillo-García, Carmen, Taylor, Michael W., Tyson, Gene W., Stocker, Roman, Ralph, Peter J., Seymour, Justin R. and Webster, Nicole S. (2017) Redefining the sponge-symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host-derived compounds. Environmental Microbiology Reports, 9 6: 750-755. doi:10.1111/1758-2229.12591
Skennerton, Connor T., Chourey, Karuna, Iyer, Ramsunder, Hettich, Robert L., Tyson, Gene W. and Orphan, Victoria J. (2017) Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea (vol 8, e00530-17, 2017). Mbio, 8 5: 1-2. doi:10.1128/mBio.01561-17
Raudsepp, Maija J., Gagen, Emma J., Golding, Suzanne D., Tyson, Gene W. and Southam, Gordon (2017) The effect of bituminous coal on methanogenic mixed cultures and pure cultures of Methanococcus and Methanosarcina. Fuel, 205 60-70. doi:10.1016/j.fuel.2017.05.059
Cayford, Barry I., Jiang, Guangming, Keller, Jurg, Tyson, Gene and Bond, Philip L. (2017) Comparison of microbial communities across sections of a corroding sewer pipe and the effects of wastewater flooding. Biofouling, 33 9: 780-792. doi:10.1080/08927014.2017.1369050
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip and Tyson, Gene W. (2017) Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 2 11: 1533-1542. doi:10.1038/s41564-017-0012-7
Lambert, Bennett S., Raina, Jean-Baptiste, Fernandez, Vicente I., Rinke, Christian, Siboni, Nachshon, Rubino, Francesco, Hugenholtz, Philip, Tyson, Gene W., Seymour, Justin R. and Stocker, Roman (2017) A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities. Nature Microbiology, 2 10: 1344-1349. doi:10.1038/s41564-017-0010-9
Pedroso, Marcelo Monteiro, Selleck, Christopher, Enculescu, Charmaine, Harmer, Jeffrey R., Mitic, Natasa, Craig, Whitney R., Helweh, Waleed, Hugenholtz, Philip, Tyson, Gene W., Tierney, David L., Larrabee, James A. and Schenk, Gerhard (2017) Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community. Metallomics, 9 8: 1157-1168. doi:10.1039/c7mt00195a
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip and Woyke, Tanja (2017) Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology, 35 8: 725-731. doi:10.1038/nbt.3893
Bohorquez, H., Seal, J.B., Cohen, A.J., Kressel, A., Bugeaud, E., Bruce, D.S., Carmody, I.C., Reichman, T.W., Battula, N., Alsaggaf, M., Therapondos, G., Bzowej, N., Tyson, G., Joshi, S., Nicolau-Raducu, R., Girgrah, N. and Loss, G.E. (2017) Safety and outcomes in 100 consecutive donation after circulatory death liver transplants using a protocol that includes thrombolytic therapy. American Journal of Transplantation, 17 8: 2155-2164. doi:10.1111/ajt.14261
Skennerton, Connor T., Chourey, Karuna, Iyer, Ramsunder, Hettich, Robert L., Tyson, Gene W. and Orphan, Victoria J. (2017) Methane-fueled syntrophy through extracellular electron transfer: uncovering the genomic traits conserved within diverse bacterial partners of anaerobic methanotrophic archaea. MBio, 8 4: e00530-17. doi:10.1128/mBio.00530-17
Deng, Jia, McCalley, Carmody K., Frolking, Steve, Chanton, Jeff, Crill, Patrick, Varner, Ruth, Tyson, Gene, Rich, Virginia, Hines, Mark, Saleska, Scott R. and Li, Changsheng (2017) Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling. Journal of Advances in Modeling Earth Systems, 9 2: 1412-1430. doi:10.1002/2016MS000817
Dennis, Paul G., Virdis, Bernardino, Vanwonterghem, Inka, Hassan, Alif, Hugenholtz, Phil, Tyson, Gene W. and Rabaey, Korneel (2016) Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes. Scientific Reports, 6 39114. doi:10.1038/srep39114
Santini, Talitha C., Malcolm, Laura I., Tyson, Gene W. and Warren, Lesley A. (2016) PH and organic carbon dose rates control microbially driven bioremediation efficacy in alkaline bauxite residue. Environmental Science and Technology, 50 20: 11164-11173. doi:10.1021/acs.est.6b01973
Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota
Vanwonterghem, Inka, Evans, Paul N., Parks, Donovan H., Jensen, Paul D., Woodcroft, Ben J., Hugenholtz, Philip and Tyson, Gene W. (2016) Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology, 1 16170: 16170. doi:10.1038/nmicrobiol.2016.170
Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
Rinke, Christian, Low, Serene, Woodcroft, Ben J., Raina, Jean-Baptista, Skarshewski, Adam, Le, Xuyen H., Butler, Margaret K., Stocker, Roman, Seymour, Justin, Tyson, Gene W. and Hugenholtz, Philip (2016) Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ, 4 9: 1-28. doi:10.7717/peerj.2486
Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion
Vanwonterghem, Inka, Jensen, Paul D., Rabaey, Korneel and Tyson, Gene W. (2016) Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion. Environmental Microbiology, 18 9: 3144-3158. doi:10.1111/1462-2920.13382
Robbins, Steven J., Evans, Paul N., Parks, Donovan H., Golding, Suzanne D. and Tyson, Gene W. (2016) Genome-centric analysis of microbial populations enriched by hydraulic fracture fluid additives in a coal bed methane production well. Frontiers in Microbiology, 7 731: 1-15. doi:10.3389/fmicb.2016.00731
Skennerton, Connor T., Haroon, Mohamed F., Briegel, Ariane, Shi, Jian, Jensen, Grant J., Tyson, Gene W. and Orphan, Victoria J. (2016) Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps. ISME Journal, 10 11: 2679-2692. doi:10.1038/ismej.2016.55
Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon
Angly, Florent E., Pantos, Olga, Morgan, Thomas C., Rich, Virginia, Tonin, Hemerson, Bourne, David G., Mercurio, Philip, Negri, Andrew P. and Tyson, Gene W. (2016) Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon. PeerJ, 4 3: e1758. doi:10.7717/peerj.1758
The influence of hydrogeological disturbance and mining on coal seam microbial communities
Raudsepp, M. J., Gagen, E. J., Evans, P., Tyson, G. W., Golding, S. D. and Southam, G. (2016) The influence of hydrogeological disturbance and mining on coal seam microbial communities. Geobiology, 14 2: 163-175. doi:10.1111/gbi.12166
The opportunity for high-performance biomaterials from methane
Strong, Peter James, Laycock, Bronwyn, Syed Mahamud, Syarifah, Jensen, Paul, Lant, Paul A., Gene Tyson and Pratt, Steven (2016) The opportunity for high-performance biomaterials from methane. Microorganisms, 4 1: 11. doi:10.3390/microorganisms4010011
The effect of coal rank on biogenic methane potential and microbial composition
Robbins, Steven J., Evans, Paul N., Esterle, Joan S., Golding, Suzanne D. and Tyson, Gene W. (2016) The effect of coal rank on biogenic methane potential and microbial composition. International Journal of Coal Geology, 154 205-212. doi:10.1016/j.coal.2016.01.001
A phylogenomic analysis of the bacterial phylum fibrobacteres
Abdul Rahman, Nurdyana, Parks, Donovan H., Vanwonterghem, Inka, Morrison, Mark, Tyson, Gene W. and Hugenholtz, Philip (2016) A phylogenomic analysis of the bacterial phylum fibrobacteres. Frontiers in Microbiology, 6 JAN: 1469.1-1469.15. doi:10.3389/fmicb.2015.01469
Angly, Florent E., Heath, Candice, Morgan, Thomas C., Tonin, Hemerson, Rich, Virginia, Schaffelke, Britta, Bourne, David G. and Tyson, Gene W. (2016) Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events. PeerJ, 4 1: 1-24. doi:10.7717/peerj.1511
Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic Alaska
Kao-Kniffin, J., Woodcroft, B.J., Carver, S.M., Bockheim J.G., Handelsman, J., Tyson, G.W., Hinkel, K.M. and Mueller, C.W. (2015) Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic Alaska. Scientific Reports, 5 . doi:10.1038/srep18165
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.
Evans, Paul N., Parks, Donovan H., Chadwick, Grayson L., Robbins, Steven J., Orphan, Victoria J., Golding, Suzanne D. and Tyson, Gene W. (2015) Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.. Science, 350 6259: 434-438. doi:10.1126/science.aac7745
ReFuGe 2020 Consortium, Voolstra, Christian R, Miller, David J., Ragan, Mark A., Hoffmann, Ary A., Hoegh-Guldberg, Ove, Bourne, David G., Ball, Eldon E., Ying, Hua, Forêt, Sylvain, Takahashi, Shunichi, Weynberg, Karen D., van Oppen, Madeleine J. H., Morrow, Kathleen, Chan, Cheong Xin, Rosic, Nedeljka, Leggat, William, Sprungala, Susanne, Imelfort, Michael, Tyson, Gene W., Kassahn, Karin S., Lundgren, Petra B., Beeden, Roger J., Ravasi, Timothy, Berumen, Michael L., Abal, Eva and Fyffe, Theresa (2015) The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change. Frontiers in Marine Science, 2 Art No.: 68: . doi:10.3389/fmars.2015.00068
Patil, Sunil A., Arends, Jan B. A., Vanwonterghem, Inka, Van Meerbergen, Jarne, Guo, Kun, Tyson, Gene W. and Rabaey, Korneel (2015) Selective enrichment establishes a stable performing community for microbial electrosynthesis of acetate from CO2. Environmental Science and Technology, 49 14: 8833-8843. doi:10.1021/es506149d
Parks, Donovan H., Imelfort, Michael, Skennerton, Connor T., Hugenholtz, Philip and Tyson, Gene W. (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25 7: 1043-1055. doi:10.1101/gr.186072.114
Wang, Jack T.H., Daly, Joshua N., Willner, Dana L., Patil, Jayee, Hall, Roy A., Schembri, Mark A., Tyson, Gene W. and Hugenholtz, Philip (2015) Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome. Journal of Microbiology and Biology Education, 16 1: 50-60. doi:10.1128/jmbe.v16i1.816
Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.
Soo, Rochelle M., Woodcroft, Ben J., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2015) Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.. PeerJ, 2015 5: Art. No.: e968-Art. No.: e968. doi:10.7717/peerj.968
Effects of nitrate dosing on sulfidogenic and methanogenic activities in sewer sediment
Liu, Yiwen, Sharma, Keshab R., Ni, Bing-Jie, Fan, Lu, Murthy, Sudhir, Tyson, Gene Q. and Yuan, Zhiguo (2015) Effects of nitrate dosing on sulfidogenic and methanogenic activities in sewer sediment. Water Research, 74 155-165. doi:10.1016/j.watres.2015.02.017
Hu, Shihu, Zeng, Raymond J., Haroon, Mohamed F., Keller, Jurg, Lant, Paul A., Tyson, Gene W. and Yuan, Zhiguo (2015) A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments. Scientific Reports, 5 8706: 1-9. doi:10.1038/srep08706
Vanwonterghem, Inka, Jensen, Paul D., Rabaey, Korneel and Tyson, Gene W. (2015) Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters.. Scientific Reports, 5 . doi:10.1038/srep08496
Pantos, Olga, Bongaerts, Pim, Dennis, Paul G., Tyson, Gene W. and Hoegh-Guldberg, OVe (2015) Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix. The ISME Journal, 9 9: 1916-1927. doi:10.1038/ismej.2015.3
Sekiguchi, Yuji, Ohashi, Akiko, Parks, Donovan H., Yamauchi, Toshihiro, Tyson, Gene W. and Hugenholtz, Philip (2015) First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ, 3 e740: 1-24. doi:10.7717/peerj.740
Where next for microbiome research?
Waldor, Matthew K., Tyson, Gene, Borenstein, Elhanan, Ochman, Howard, Moeller, Andrew, Finlay, Brett B., Kong, Hedi H., Gordon, Jeffrey I., Nelson, Karen E., Dabbagh, Karim and Smith, Hamilton (2015) Where next for microbiome research?. PLoS Biology, 13 1: 1-9. doi:10.1371/journal.pbio.1002050
Chemotaxis by natural populations of coral reef bacteria.
Tout, Jessica, Jeffries, Thomas C., Petrou, Katherina, Tyson, Gene W., Webster, Nicole S., Garren, Melissa, Stocker, Roman, Ralph, Peter J. and Seymour, Justin R. (2015) Chemotaxis by natural populations of coral reef bacteria.. ISME Journal, 9 8: 1764-1777. doi:10.1038/ismej.2014.261
Barr, Jeremy J., Dutilh, Bas E., Skennerton, Connor T., Fukushima, Toshikazu, Hastie, Marcus L., Gorman, Jeffrey J., Tyson, Gene W. and Bond, Philip L. (2015) Metagenomic and metaproteomic analyses of Accumulibacter phosphatis enriched floccular and granular biofilm. Environmental Microbiology, 18 1: 273-287. doi:10.1111/1462-2920.13019
Susilawati, Rita, Evans, Paul N., Esterle, Joan S., Robbins, Steven J., Tyson, Gene W., Golding, Suzanne D. and Mares, Tennille E. (2015) Temporal changes in microbial community composition during culture enrichment experiments with Indonesian coals. International Journal of Coal Geology, 137 66-76. doi:10.1016/j.coal.2014.10.015
Methane dynamics regulated by microbial community response to permafrost thaw
McCalley, Carmody K., Woodcroft, Ben J., Hodgkins, Suzanne B., Wehr, Richard A., Kim, Eun-Hae, Mondav, Rhiannon, Crill, Patrick M., Chanton, Jeffrey P., Rich, Virginia I., Tyson, Gene W. and Saleska, Scott R. (2014) Methane dynamics regulated by microbial community response to permafrost thaw. Nature, 514 7523: 478-481. doi:10.1038/nature13798
GroopM: an automated tool for the recovery of population genomes from related metagenomes
Imelfort, Michael, Parks, Donovan, Woodcroft, Ben J., Dennis, Paul, Hugenholtz, Philip and Tyson, Gene W. (2014) GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ, 2014 1: 1-16. doi:10.7717/peerj.603
Expanding our view of genomic diversity in Candidatus Accumulibacter clades
Skennerton, Connor T., Barr, Jeremy J., Slater, Frances R., Bond, Philip L. and Tyson, Gene W. (2014) Expanding our view of genomic diversity in Candidatus Accumulibacter clades. Environmental Microbiology, 17 5: 1574-1585. doi:10.1111/1462-2920.12582
STAMP: Statistical analysis of taxonomic and functional profiles.
Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip and Beiko, Robert G. (2014) STAMP: Statistical analysis of taxonomic and functional profiles.. Bioinformatics., 30 21: 3123-3124. doi:10.1093/bioinformatics/btu494
The Bio-Community Perl toolkit for microbial ecology
Angly, Florent E., Fields, Christopher J. and Tyson, Gene W. (2014) The Bio-Community Perl toolkit for microbial ecology. Bioinformatics, 30 13: 1926-1927. doi:10.1093/bioinformatics/btu130
Vanwonterghem, Inka, Jensen, Paul D., Ho, Dang P., Batstone Damien J. and Tyson, Gene W. (2014) Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Current Opinion in Biotechnology, 27 55-64. doi:10.1016/j.copbio.2013.11.004
De Vrieze, Jo, Gildemyn, Sylvia, Arends, Jan B. A., Vanwonterghem, Inka, Verbeken, Kim, Boon, Nico, Verstraete, Willy, Tyson, Gene W., Hennebel, Tom and Rabaey, Korneel (2014) Biomass retention on electrodes rather than electrical current enhances stability in anaerobic digestion. Water Research, 54 211-221. doi:10.1016/j.watres.2014.01.044
Vanwonterghem, Inka, Jensen, Paul D., Dennis, Paul G., Hugenholtz, Philip, Rabaey, Korneel and Tyson, Gene W. (2014) Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. ISME Journal, Advance Online 10: 1-14. doi:10.1038/ismej.2014.50
An expanded genomic representation of the phylum Cyanobacteria
Soo, Rochelle M., Skennerton, Connor T., Sekiguchi, Yuji, Imelfort, Michael, Paech, Samuel J., Dennis, Paul G., Steen, Jason A., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2014) An expanded genomic representation of the phylum Cyanobacteria. Genome Biology and Evolution, Advance Access 5: 1-42. doi:10.1093/gbe/evu073
Angly, Florent E., Dennis, Paul G., Skarshewski, Adam, Vanwonterghem, Inka, Hugenholtz, Philip and Tyson, Gene W. (2014) CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. Microbiome, 2 11: 11. doi:10.1186/2049-2618-2-11
Discovery of a novel methanogen prevalent in thawing permafrost
Mondav, Rhiannon, Woodcroft, Ben J., Kim, Eun-Hae, McCalley, Carmody K., Hodgkins, Suzanne B., Crill, Patrick M., Chanton, Jeffrey, Hurst, Gregory B., VerBerkmoes, Nathan C., Saleska, Scott R., Hugenholtz, Philip, Rich, Virginia I. and Tyson, Gene W. (2014) Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications, 5 1: 3212.1-3212.7. doi:10.1038/ncomms4212
Pervin, Hasina M., Dennis, Paul G., Lim, Hui J., Tyson, Gene W., Batstone, Damien J. and Bond, Philip L. (2013) Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors. Water Research, 47 19: 7098-7108. doi:10.1016/j.watres.2013.07.053
Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage
Haroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo and Tyson, Gene W. (2013) Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 501 7468: 578-578. doi:10.1038/nature12619
Future reef decalcification under a business-as-usual CO2 emission scenario
Dove, Sophie G., Kline, David I., Pantos, Olga, Angly, Florent E., Tyson, Gene W. and Hoegh-Guldberg, Ove (2013) Future reef decalcification under a business-as-usual CO2 emission scenario. Proceedings of the National Academy of Sciences of the United States of America, 110 38: 15342-15347. doi:10.1073/pnas.1302701110
Coral reef invertebrate microbiomes correlate with the presence of photosymbionts
Bourne, David G., Dennis, Paul G., Uthicke, Sven, Soo, Rochelle M., Tyson, Gene W. and Webster, Nicole (2013) Coral reef invertebrate microbiomes correlate with the presence of photosymbionts. Isme Journal, 7 7: 1452-1458. doi:10.1038/ismej.2012.172
Coral reef invertebrate microbiomes correlate with the presence of photosymbionts
Bourne, David G, Dennis, Paul G., Uthicke, Sven, Soo, Rochelle M., Tyson, Gene W. and Webster, Nicole (2013) Coral reef invertebrate microbiomes correlate with the presence of photosymbionts. Isme Journal, 7 7: 1459-1459. doi:10.1038/ismej.2013.71
Dennis, Paul G., Harnisch, Falk, Yeoh, Yun Kit, Tyson, Gene W. and Rabaey, Korneel (2013) Dynamics of cathode-associated microbial communities and metabolite profiles in a glycerol-fed bioelectrochemical system. Applied and Environmental Microbiology, 79 13: 4008-4014. doi:10.1128/AEM.00569-13
Albertsen, Mads, Hugenholtz, Philip, Skarshewski, Adam, Nielsen, Kare L., Tyson, Gene W. and Nielsen, Per H. (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 31 6: 533-538+. doi:10.1038/nbt.2579
Sequencing platform and library preparation choices impact viral metagenomes
Solonenko, Sergei A., Ignacio-Espinoza, J. Cesar, Alberti, Adriana, Cruaud, Corinne, Hallam, Steven, Konstantinidis, Kostas, Tyson, Gene, Wincker, Patrick and Sullivan, Matthew B. (2013) Sequencing platform and library preparation choices impact viral metagenomes. Bmc Genomics, 14 1: 320.1-320.12. doi:10.1186/1471-2164-14-320
Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data
Bragg, Lauren M., Stone, Glenn, Butler, Margaret K., Hugenholtz, Philip and Tyson, Gene W. (2013) Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. Plos Computational Biology, 9 4: e1003031.1-e1003031.18. doi:10.1371/journal.pcbi.1003031
Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients
Dennis, Paul G., Seymour, Justin, Kumbun, Kimber and Tyson, Gene W. (2013) Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients. ISME Journal, 7 8: 1661-1664. doi:10.1038/ismej.2013.47
Crass: identification and reconstruction of CRISPR from unassembled metagenomic data
Skennerton, Connor T., Imelfort, Michael and Tyson, Gene W. (2013) Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Research, 41 10: e105.1-e105.10. doi:10.1093/nar/gkt183
Carvalhais, Lilia C., Dennis, Paul G., Badri, Dayakar V., Tyson, Gene W., Vivanco, Jorge M. and Schenk, Peer M. (2013) Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities. PLoS ONE, 8 2: e56457. doi:10.1371/journal.pone.0056457
Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage
Haroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo and Tyson, Gene W. (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 500 7464: 567-570. doi:10.1038/nature12375
Haroon, Mohamed F., Skennerton, Connor T., Steen, Jason A., Lachner, Nancy, Hugenholtz, Philip and Tyson, Gene W. (2013) In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery. Methods in Enzymology, 531 3-19. doi:10.1016/B978-0-12-407863-5.00001-0
Spatial uniformity of microbial diversity in a continuous bioelectrochemical system
Dennis, Paul G., Guo, Kun, Imelfort, Michael, Jensen, Paul, Tyson, Gene W. and Rabaey, Korneel (2012) Spatial uniformity of microbial diversity in a continuous bioelectrochemical system. Bioresource Technology, 129 10: 599-605. doi:10.1016/j.biortech.2012.11.098
Application of metatranscriptomics to soil environments
Carvalhais, Lilia C., Dennis, Paul G., Tyson, Gene W. and Schenk, Peer M. (2012) Application of metatranscriptomics to soil environments. Journal of Microbiological Methods, 91 2: 246-251. doi:10.1016/j.mimet.2012.08.011
Cayford, Barry I., Dennis, Paul G., Keller, Jurg, Tyson, Gene W. and Bond, Philip L. (2012) High-throughput amplicon sequencing reveals distinct communities within a corroding concrete sewer system. Applied and Environmental Microbiology, 78 19: 7160-7162. doi:10.1128/AEM.01582-12
Grinder: a versatile amplicon and shotgun sequence simulator
Angly, Florent E., Willner, Dana, Rohwer, Forest, Hugenholtz, Philip and Tyson, Gene W. (2012) Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Research, 40 12: e94.1-e94.8. doi:10.1093/nar/gks251
Fast, accurate error-correction of amplicon pyrosequences using Acacia
Bragg, Lauren, Stone, Glenn, Imelfort, Michael, Hugenholtz, Philip and Tyson, Gene W. (2012) Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nature Methods, 9 5: 245-246. doi:10.1038/nmeth.1990
Shi, Yanmei, Tyson, Gene, Eppley, John M. and DeLong, Edward F. (2011) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. The ISME Journal, 5 6: 999-1013. doi:10.1038/ismej.2010.189
Phage encoded H-NS: A potential Achilles heel in the bacterial defence system
Skennerton, Connor T., Angly, Florent E., Breitbart, Mya, Bragg, Lauren, He, Shaomei, McMahon, Katherine D., Hugenholtz, Philip and Tyson, Gene W. (2011) Phage encoded H-NS: A potential Achilles heel in the bacterial defence system. Plos One, 6 5: e20095-1-e20095-7. doi:10.1371/journal.pone.0020095
Are divergent viral communities controlling individual gut microbiota?
Angly, Florent and Tyson, Gene (2011) Are divergent viral communities controlling individual gut microbiota?. Medecine Sciences, 27 3: 229-231. doi:10.1051/medsci/2011273229
Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations
Yilmaz, S, Haroon, MF, Rabkin, BA, Tyson, GW and Hugenholtz, P (2010) Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. The ISME Journal, 4 10: 1352-1356. doi:10.1038/ismej.2010.73
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column
Shi, Yanmei, Tyson, Gene W. and DeLong, Edward F. (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature, 459 7244: 266-269. doi:10.1038/nature08055
Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities
Baker, Brett J., Tyson, Gene W., Goosherst, Lindsey and Banfield, Jillian F. (2009) Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities. Applied and Environmental Microbiology, 75 7: 2192-2199. doi:10.1128/AEM.02500-08
Martinex, Asuncion, Tyson, Gene W. and DeLong, Edward F. (2009) Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses. Environmental Microbiology, 12 1: 222-238. doi:10.1111/j.1462-2920.2009.02062.x
Hugenhotz, Philip and Tyson, Gene W. (2008) Microbiology: Metagenomics. Nature, 455 7212: 481-483. doi:10.1038/455481a
Microbial community gene expression in ocean surface waters
Frias-Lopez, Jorge, Shi,Yanmei, Tyson, Gene, Coleman, Maureen, Schuster, Stephan, Chisholm, Sallie and DeLong, Edward (2008) Microbial community gene expression in ocean surface waters. Proceedings of the National Academy of Sciences of the United States of America, 105 10: 3805-3810. doi:10.1073/pnas.0708897105
Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses
Tyson, Gene W. and Banfield, Jillian F. (2008) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environmental Microbiology, 10 1: 200-207. doi:10.1111/j.1462-2920.2007.01444.x
Strainer: Software for analysis of population variation in community genomic datasets
Eppley John M., Tyson Gene W., Getz Wayne M. and Banfield Jillian F. (2007) Strainer: Software for analysis of population variation in community genomic datasets. BMC Bioinformatics, 8 398: 1-11. doi:10.1186/1471-2105-8-398
Genetic exchange across a species boundary in the Archaeal genus Ferroplasma
Eppley, John M., Tyson, Gene W., Getz, Wayne M. and Banfield, Jillian F. (2007) Genetic exchange across a species boundary in the Archaeal genus Ferroplasma. Genetics, 177 1: 407-416. doi:10.1534/genetics.107.072892
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
Lo, Ian, Denef, Vincent J., VerBerkmoes, Nathan C., Shah, Manesh B., Goltsman, Daniela, DiBartolo, Genevieve, Tyson, Gene W., Allen, Eric E., Ram, Rachna J., Detter, J. Chris, Richardson, Paul, Thelen, Michael P., Hettich, Robert L. and Banfield, Jillian F. (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 446 7135: 537-541. doi:10.1038/nature05624
Genome dynamics in a natural archaeal population
Allen, Eric E., Tyson, Gene W., Whitaker, Rachel J., Detter, John C., Richardson, Paul M. and Banfield, Jillian F. (2007) Genome dynamics in a natural archaeal population. Proceedings of the National Academy of Sciences of the United States of America, 104 6: 1883-1888. doi:10.1073/pnas.0604851104
Lineages of acidophilic archaea revealed by community genomic analysis
Baker, Brett J., Tyson, Gene W., Webb, Richard I., Flanagan, Judith, Hugenholtz, Philip, Allen, Eric E. and Banfield, Jillian F. (2006) Lineages of acidophilic archaea revealed by community genomic analysis. Science, 314 5807: 1933-1935. doi:10.1126/science.1132690
Tyson, Gene W., Lo, Ian, Baker, Brett J., Allen, Eric E., Hugenholtz, Philip and Banfield, Jillian F. (2005) Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community. Applied and Environmental Microbiology, 71 10: 6319-6324. doi:10.1128/AEM.71.10.6319-6324.2005
Cultivating the uncultivated: A community genomics perspective
Tyson, Gene W. and Banfield, Jillian F. (2005) Cultivating the uncultivated: A community genomics perspective. Trends in Microbiology, 13 9: 411-415. doi:10.1016/j.tim.2005.07.003
Community proteomics of a natural microbial biofilm
Ram, Rachna J., VerBerkmoes, Nathan C., Thelen, Michael P., Tyson, Gene W., Baker, Brett J., Blake, Robert C., Shah, Manesh, Hettich, Robert L. and Banfield, Jillian F. (2005) Community proteomics of a natural microbial biofilm. Science, 308 5730: 1915-1920. doi:10.1126/science.1109070
Banfield, , Tyson, GW, Allen, EE and Whitaker, RJ (2005) The search for a molecular-level understanding of the processes that underpin the earth's biogeochemical cycles. Molecular Geomicrobiology, 59 1: 1-7. doi:10.2138/rmg.2005.59.1
Community structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, Gene W., Chapman, Jarrod, Hugenholtz, Philip, Allen, Eric E., Ram, Rachna J., Richardson, Paul M., Solovyev, Victor V., Rubin, Edward M., Rokhsar, Daniel S. and Banfield, Jillian F. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428 6978: 37-43. doi:10.1038/nature02340
Bjornsson, Lovisa, Hugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2002) Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology, 148 8: 2309-2318.
Hugenholtz, P., Tyson, G. W. and Blackall, L. L. (2002) Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Methods in molecular biology (Clifton, N.J.), 179 29-42.
Hugenholtz, Philip, Tyson, Gene W., Webb, Richard I., Wagner, Ankia M. and Blackall, Linda L. (2001) Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Applied And Environmental Microbiology, 67 1: 411-419. doi:10.1128/AEM.67.1.411-419.2001
Accelerating bauxite residue remediation with microbial biotechnology
Santini, T. C., Warren, K., Raudsepp, M., Carter, N., Hamley, D., McCosker, C., Couperthwaite, S., Southam, G., Tyson, G. W. and Warren, L. A. (2019). Accelerating bauxite residue remediation with microbial biotechnology. In: Light Metals 2019. Light Metals Symposium held at the TMS Annual Meeting and Exhibition, 2019, San Antonio, TX United States, (69-77). 10-14 March 2019. doi:10.1007/978-3-030-05864-7_10
OrfM: a fast open reading frame predictor for metagenomic data
Woodcroft, Ben J., Boyd, Joel A. and Tyson, Gene W. (2016) OrfM: a fast open reading frame predictor for metagenomic data. Bioinformatics, 32 17: 2702-2703. doi:10.1093/bioinformatics/btw241
Future gas through bioconversion of waster coal
Golding, S. D., Hamilton, S. K., Baublys, K. A., Esterle, J. S., Tyson, G., Robbins, S., Rudolph, V., Zheng, H., Gilcrease, P. C. and Papendick, S. L. (2013). Future gas through bioconversion of waster coal. In: Goldschmidt Conference Abstracts 2013. Goldschmidt Conference 2013, Florence, Italy, (1187-1187). 25-30 August 2013. doi:10.1180/minmag.2013.077.5.7
Pervin, H.P., Hastie, M., Dennis, P.G., Jensen, P., Gorman, J., Tyson, G.W., Batstone, D. and Bond, P.L. (2013). Microbial community composition and function associated with enhanced anaerobic digestion of organic biosolids.. In: 2nd Water Research Conference, Singapore EXPO, Singapore, (). 20-23 January, 2013.
Pervin, H.P., Dennis, P.G., Lim, H.J., Tyson, G.W., Batstone, D. and Bond, P.L. (2013). Microbial community dynamics correlate to reactor parameters and performance in a pre-treatment stage of temperature–phased anaerobic digestion.. In: 2nd Water Research Conference, Singapore International Convention and Exhibition Centre, (). 20-23 January 2013.
Pervin, H. P., Hastie, M., Dennis, P. G., Gorman, J., Tyson, G. W., Batstone, D. and Bond, P. L. (2012). Determining ecosystem community and function important for enhanced anaerobic digestion of organic biosolids. In: Australian Society for Microbiology Annual Scientific Meeting (ASM2012), Brisbane, Australia, (). 1-4 July 2012.
Metaproteomic and metagenomic characterisation of floccular and granular phosphorus removal biofilms
Barr, Jeremy, Dutilh, Bas, Cook, Andrew, Fukushima, Toshikazu, Hastie, Marcus, Gorman, Jeffery, Pan, Chongle, Hettich, Rorbert, Tyson, Gene and Bond, Philip (2012). Metaproteomic and metagenomic characterisation of floccular and granular phosphorus removal biofilms. In: 14th International Symposium on Microbial Ecology (ISME14), Copenhagan, Denmark, (). 19-24 August 2012.
Microbial communities involved in the corrosion of concrete sewer infrastructure
Cayford, Barry I., Dennis, Paul G., Tyson, Gene W. and Bond, Philip L. (2012). Microbial communities involved in the corrosion of concrete sewer infrastructure. In: 14th International Symposium on Microbial Ecology (ISME14), Copenhagan, Denmark, (). 19-24 August 2012.
Microbial corrosion of concrete sewer pipes
Cayford, B. I., Tyson, G. W., Dennis, P. G., Keller, J. and Bond, P .L. (2012). Microbial corrosion of concrete sewer pipes. In: Australian Society for Microbiology Annual Scientific Meeting (ASM2012), Brisbane, Australia, (). 1-4 July 2012.
Coal-to-biomethane potential of microbial consortia native to coal seam formation waters
Papendick, Samuel, Tyson, Gene, Esterle, Joan, Golding, Suzanne D., Rudolph, Victor and Gilcrease, Patrick C. (2011). Coal-to-biomethane potential of microbial consortia native to coal seam formation waters. In: Sustainable Engineering Forum: Core Programming Topic at the 2011 AIChE Annual Meeting. Sustainable Engineering Forum: Core Programming Topic at the 2011 AIChE Annual Meeting, Minneapolis, MN, (1302-1303). October 16, 2011-October 21, 2011.
Coal-to-biomethane potential of microbial consortia native to coal seam formation waters
Papendick, Samuel, Tyson, Gene, Esterle, Joan, Golding, Suzanne D., Rudolph, Victor and Gilcrease, Patrick C. (2011). Coal-to-biomethane potential of microbial consortia native to coal seam formation waters. In: Catalysis and Reaction Engineering Division - Core Programming Topic at the 2011 AIChE Annual Meeting. Catalysis and Reaction Engineering Division - Core Programming Topic at the 2011 AIChE Annual Meeting, Minneapolis, MN, (1110-1110). October 16, 2011-October 21, 2011.
Microbial community composition associated with sewer corrosion
Cayford, B. I., Tyson, G. W., Keller, J and Bond, P. L. (2011). Microbial community composition associated with sewer corrosion. In: Engineers Australia Queensland Water Panel's Post-Graduate Presentation Evening, Engineers Australia Queensland Branch, (). 18 May 2011.
Bridges cnd Chasms: Summary of the IMAGE 2 meeting in Montreal, Canada, 30 April to 3 May 2007
Bender, Robert A., Downs, Diana, Kiley, Patricia, LaRossa, Robert A., Sonenshein, Abraham L., Storz, Gisela, Bender, Robert, Roth, John, Schilling, Christoff, Rine's, Jasper, Merrick, Mike, Tyson, Gene, Skovran, Elizabeth, Liao, J., Stephanopolous', Greg, Anesiades, Nikolas, San, Kai-Yu, Durot, Maxim, Reich, Claudia, De Crecy-Legard, Valerie, Dean's, Dennis, Barras, Frederic, Dwyer, Daniel, De Reuse, Hilde, Massé, Eric, Hwa, Terrance, Vanderpool, Carin, Henkin's, Tina, Warner, Digby, Ron, Eliora, Gourse, Rick, Wang, Jade, Nicholson, Wayne, Burkholder, Bill, Gon, Stephanie, Ellison, Michael, Savchenko, Alexei, Pichersky, Eran, Wanner, Barry, Mori, Hirotada, LaRossa, Bob and Straight, Paul (2008). Bridges cnd Chasms: Summary of the IMAGE 2 meeting in Montreal, Canada, 30 April to 3 May 2007. In: , , (792-797). . doi:10.1128/JB.01097-07
Whitaker, R, Allen, E, Tyson, G and Banfield, J (2005). Population dynamics in acid mine drainage biofilms from the Richmond Mine at Iron Mountain, California. In: 15th Annual V M Goldschmidt Conference, Moscow Id, (A222-A222). May, 2005.
Challenges of life in an extremely acidic environment
Ram, RJ, VerBerkmoes, N, Tyson, GW, Baker, BJ, Thelen, MP, Hettich, RL and Banfield, JF (2005). Challenges of life in an extremely acidic environment. In: 229th National Meeting of the American-Chemical-Society, San Diego Ca, (U889-U889). Mar 13-17, 2005.
Parks, Donovan H., Imelfort, Michael, Skennerton, Connor T., Hugenholtz, Philip and Tyson, Gene W. (2015): CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes: supplemental material. Cold Spring Harbor Laboratory Press. Dataset. doi:10.14264/uql.2016.841
Microscale Experiments to Understand a Microscale World
Tyson, Gene and Rinke, Christian (2015): Microscale Experiments to Understand a Microscale World. The University of Queensland. Collection. doi:10.14264/uql.2017.105
Uncovering new microbial players and processes in the global methane cycle
(2018–2022) ARC Future Fellowships
(2018) UQ Major Equipment and Infrastructure
(2018) University of Western Australia
(2016–2020) California Institute of Technology
(2016–2020) Ohio State University
Genome-level insight into the dynamics of a model coral microbiome
(2016–2019) ARC Discovery Projects
From tailings to soil: in situ remediation in mine site rehabilitation
(2016–2018) ARC Linkage Projects
Instrumentation for the analysis of cellular and metabolic phenotypes
(2016) UQ Major Equipment and Infrastructure
The Australian human microbiota project-microbe isolation facility
(2016) UQ Major Equipment and Infrastructure
Biogeochemistry of ferruginous duricrusts
(2015–2019) ARC Linkage Projects
(2015–2016) QGC Pty Limited
Coral genomes along environmental gradients
(2014–2017) Queensland Government Accelerate Partnerships
(2014) UQ Major Equipment and Infrastructure
(2014) UQ Foundation Research Excellence Awards - DVC(R) Funding
(2013–2018) University of Technology Sydney
(2013–2018) University of Arizona
Sea-quence Bioinformatics Fellowships
(2013–2017) Great Barrier Reef Foundation
(2013–2017) California Institute of Technology
Future gas through bioconversion of stranded and waste coal
(2012–2015) Queensland Government Smart Futures Research Partnerships Program
Methane and Nitrous Oxide Emissions from Sewers - Understanding, Modelling and Mitigation
(2012–2015) ARC Linkage Projects
A high-throughput screening and sequencing facility for single cell genomics
(2012–2013) ARC Linkage Infrastructure, Equipment and Facilities
The Geomicrobiology Laboratory
(2012) UQ Major Equipment and Infrastructure
(2011–2014) ARC Linkage Projects
(2011–2013) University of Technology Sydney
Anaerobic workstations for experimental and pure culture research.
(2011) UQ Major Equipment and Infrastructure
GC-IRMS for stable isotope ratio analysis of complex gas and liquid mixtures
(2011) UQ Major Equipment and Infrastructure
(2010–2014) University of Arizona
The only constant is change: ecology and evolution of phage-host interactions in a model ecosystem
(2010–2014) ARC Discovery Projects
Functional screens for novel cellulases A (CSIRO Energy Transformed Flagship Cluster led by ANU)
(2010–2013) Australian National University
(2010) Queensland Bulk Water Supply Authority trading as Seqwater
ResTeach 2009 0.1 FTE School of Chemistry and Molecular Biosciences
(2009–2011)
Functional omics investigation and isolation of microorganisms involved in anaerobic methane oxidation
Doctor Philosophy — Principal Advisor
Other advisors:
Development of meta omic tools to explore microbial carbon cycling
Doctor Philosophy — Principal Advisor
Other advisors:
Seasonal changes in the structure and function of the microbiome of Acropora tenius
Doctor Philosophy — Principal Advisor
Other advisors:
Uncovering new microbial players and processes in the global methane cycle
Doctor Philosophy — Principal Advisor
Other advisors:
Exploring the structure and function of coral microbial communities
Doctor Philosophy — Principal Advisor
Other advisors:
Characterisation of Novel Enzymes from Metagenomic Datasets related to Iron, Polysaccharide, and Methane metabolism
Doctor Philosophy — Principal Advisor
Other advisors:
From the cradle to the grave: Unraveling symbiotic interactions across life stages of the reef sponge Ianthella basta
Doctor Philosophy — Associate Advisor
Other advisors:
Functional annotation in microbial communities with metabolomics
Doctor Philosophy — Associate Advisor
Other advisors:
Understanding the dissemination of antibiotic resistance in water systems through metagenomic sequencing
Doctor Philosophy — Associate Advisor
Other advisors:
Human gut archaebacteria and their involvement with chronic digestive diseases.
Doctor Philosophy — Associate Advisor
Other advisors:
Metagenomic sequencing to investigate the effects of probiotics on the gut microbiome composition in pregnancy
Doctor Philosophy — Associate Advisor
Other advisors:
Tracking recent lateral gene transfers in human gut and oral microbiome
Doctor Philosophy — Associate Advisor
Other advisors:
Characterisation of novel archaea evolved to oxidise methane and short chain alkanes
(2019) Doctor Philosophy — Principal Advisor
Other advisors:
Microbial community structural and metabolic dynamics in thawing permafrost
(2018) Doctor Philosophy — Principal Advisor
Other advisors:
Microbial community dynamics, function and interactions in anaerobic digestion
(2015) Doctor Philosophy — Principal Advisor
Other advisors:
Molecular characterisation of microbial communities involved in coal bed methane production
(2015) Doctor Philosophy — Principal Advisor
Other advisors:
(2015) Doctor Philosophy — Principal Advisor
Other advisors:
Phage-host Evolution in Model Ecosystem
(2014) Doctor Philosophy — Principal Advisor
Other advisors:
(2013) Doctor Philosophy — Principal Advisor
Other advisors:
Trophic ecology of shallow and deep reef-building corals
(2019) Doctor Philosophy — Associate Advisor
Other advisors:
(2017) Doctor Philosophy — Associate Advisor
Other advisors:
(2017) Doctor Philosophy — Associate Advisor
Other advisors:
Coal mine microbial communities and biogenic methane cycling
(2016) Doctor Philosophy — Associate Advisor
Other advisors:
Molecular Investigation of Australian Termites and their Gut Symbionts
(2016) Doctor Philosophy — Associate Advisor
Other advisors:
In search of non-photosynthetic Cyanobacteria
(2015) Doctor Philosophy — Associate Advisor
Other advisors:
(2013) Doctor Philosophy — Associate Advisor
Other advisors:
(2013) Doctor Philosophy — Associate Advisor
Other advisors:
Marine sponge-associated planctomycetes and actinobacteria
(2012) Doctor Philosophy — Associate Advisor
Other advisors:
The Microbial Ecology of Granular Sludge in Enhanced Biological Phosphorus Removal
(2011) Doctor Philosophy — Associate Advisor
Other advisors: