Lab News

Selected Publications

Nou NO, Covington JK, Lai D, Mayali X, Seymour CO, Johnston J, Jiao JY, Buessecker S, Mosier D, Muok AR, Torosian N, Cook AM, Briegel A, Woyke T, Eloe-Fadrosh E, Shapiro N, Bryan SG, Sleezer S, Dimapilis J, Gonzalez C, Gonzalez L, Noriega M, Hess M, Carlson RP, Liu L, Li MM, Lian ZH, Zhu S, Liu F, Sun X, Gao B, Mewalal R, Harmon-Smith M, Blaby IK, Cheng JF, Weber PK, Grigorean G, Li WJ, Dekas AE, Pett-Ridge J, Dodsworth JA, Palmer M, Hedlund BP. 2024. Genome-guided isolation of Fervidibacter sacchari, an aerobic, hyperthermophilic polysaccharide-degrading specialist. Under review in Nature Communications. pdf

Luo ZH, Li Q, Xie YG, Lv AP, Qi YL, Li MM, Qu YN, Liu YX, Rao YZ, Jiao JY, Liu L, Rao MPN, Hedlund BP, Evans PN, Fang Y, Shu WS, Huang LN, Li WJ, Hua ZS. 2024. Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria. The ISME Journal. pdf

Lai D, Hedlund BP, Mau RL, Jiao JY, Li J, Hayer M, Dijkstra P, Schwartz E, Li WJ, Dong H, Palmer M, Dodsworth JA, Zhou EM, Hungate BA. 2023. Resource partitioning and amino acid assimilation in a terrestrial geothermal spring. The ISME Journal:1-11. pdf

Whitman WB, Hedlund BP, Palmer M, Sutcliffe I, Chuvochina M. 2023. Request for public discussion and ballot to amend SeqCode rules on priority of Candidatus names and correction of typographic and orthographic errors. ISME Communications 3:96-98 pdf

Seymour CO, Palmer M, Becraft ED, Stepanauskas R, Friel AD, Schulz F, Woyke T, Eloe-Fadrosh E, Lai D, Jiao JY, Hua ZS, Liu L, Lian ZH, Li WJ, Chuvochina M, Finley BK, Koch BJ, Schwartz E, Dijkstra P, Moser DP, Hungate BA, Hedlund BP. 2023. Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota. Nature Microbiology 8:727-744. pdf

Palmer M, Covington JK, Zhou EM, Thomas SC, Habib N, Seymour CO, Lai D, Johnston J, Hashimi A, Jiao JY, Muok AR, Liu L, Xian WD, Zhi XY, Li MM, Silva LP, Bowen BP, Louie K, Briegel A, Pett-Ridge J, Weber PK, Tocheva EI, Woyke T, Northen TR, Mayali X, Li WJ, Hedlund BP. 2023. Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. The ISME Journal 17:952-966. pdf

Doss RK, Palmer M, Mead DA, Hedlund BP. 2023. Functional biology and biotechnology of thermophilic viruses. Essays in Biochemistry 67:671-684. pdf

Snyder C, Centlivre JP, Bhute S, Shipman G, Friel AD, Viver T, Palmer M, Konstantinidis KT, Sun HJ, Rossello-Mora R, Nadeau J, Hedlund BP. 2023. Microbial Motility at the Bottom of North America: Digital Holographic Microscopy and Genomic Motility Signatures in Badwater Spring, Death Valley National Park. Astrobiology 23:295-307. pdf

Qu YN, Rao YZ, Qi YL, Li YX, Li A, Palmer M, Hedlund BP, Shu WS, Evans PN, Nie GX, Hua ZS, Li WJ. 2023. Panguiarchaeum symbiosum, a potential hyperthermophilic symbiont in the TACK superphylum. Cell reports 42:112158. pdf

Wang J, Qu YN, Evans PN, Guo Q, Zhou F, Nie M, Jin Q, Zhang Y, Zhai X, Zhou M, Yu Z, Fu QL, Xie YG, Hedlund BP, Li WJ, Hua ZS, Wang Z, Wang Y. 2023. Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs. Science Advances 9:eadg6004. pdf

Viver T, Conrad RE, Lucio M, Harir M, Urdiain M, Gago JF, Suarez-Suarez A, Bustos-Caparros E, Sanchez-Martinez R, Mayol E, Fassetta F, Pang J, Madalin Gridan I, Venter S, Santos F, Baxter B, Llames ME, Cristea A, Banciu HL, Hedlund BP, Stott MB, Kampfer P, Amann R, Schmitt-Kopplin P, Konstantinidis KT, Rossello-Mora R. 2023. Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov. Systematic and Applied Microbiology 46:126416. pdf

Buessecker S, Chadwick GL, Quan ME, Hedlund BP, Dodsworth JA, Dekas AE. 2023. Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring. The ISME Journal 14:1-11. pdf

Friel AD, Pordel K, Meyers Z, Seymour CO, Thomas NJ, Phillips FM, Knott JR, Sada DW, Rademacher L, Frisbee M, Hedlund BP. 2023. Synecological response of spring benthic prokaryotes and macroinvertebrates to Paleozoic roof pendant-derived calcium. Ecosphere 14:e4464. pdf

Xie Y-G, Luo Z-H, Fang B-Z, Jiao J-Y, Xie Q-J, Cao X-R, Qu Y-N, Qi Y-L, Rao Y-Z, Li Y-X, Liu Y-H, Li A, Seymour CO, Palmer M, Hedlund BP, Li W-J, Hua Z-S. 2022. Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota. Microbiome 10:172-184. pdf

Hedlund BP, Whitman WB. 2022. Towards a unifying system for the naming of cultured and uncultured prokaryotes. Nature Microbiology 7:1514-1515. pdf

Hedlund BP, Chuvochina M, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach A-L, Rodriguez-R LM, Rossello-Mora R, Sutcliffe IC, Venter SN, Whitman WB. 2022. SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nature Microbiology 7:1702-1708.pdf

De la Haba RR, Antunes A, Hedlund BP. 2022. Extremophiles: Microbial genomics and taxogenomics. Frontiers in Microbiology 13:984632. pdf

Rattanasriampaipong R, Zhang YG, Pearson A, Hedlund BP, Zhang S. 2022. Archaeal lipids trace ecology and evolution of marine ammonia-oxidizing archaea. PNAS 119:e2123193119. pdf

Mefferd CC, Zhou E, Seymour CO, Bernardo N, Srivastava S, Bengtson AJ, Jiao JY, Dong H, Li WJ, Hedlund BP. 2022. Incomplete denitrification phenotypes in diverse Thermus species from diverse geothermal spring sediments and adjacent soils in southwest China. Extremophiles 26:23. pdf

Whitman WB, Chuvochina M, Hedlund BP, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe I, Venter SN. 2022. Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Systematic and Applied Microbiology 45:126305. pdf

Sushenko NS, Singh NK, Vellone DL, Tighe SW, Hedlund BP, Venkateswaran K, Moser DP. 2022. Complete genome sequence of Klebsiella quasipneumoniae subsp. similipneumoniae strain IF3SW-P1, isolated from the International Space Station. Microbiology Resource Announcements 11:e00476-22. pdf

Fang Y, Liu J, Yang J, Wu G, Hua Z, Dong H, Hedlund BP, Baker BJ, Jiang H. 2022. Compositional and metabolic responses of autotrophic microbial community to salinity in lacustrine environments. mSystems 7:e00335-22. pdf

Palmer M, Sutcliffe I, Venter SN, Hedlund BP. 2022. It is time for a new type of type to facilitate naming the microbial world. New Microbes and New Infections 47:100991. pdf

Bhute SS, Mefferd CC, Phan JR, Ahmed M, Fox-King AE, Alarcia S, Villarama JV, Abel-Santos E, Hedlund BP. 2022. A high-carbohydrate diet prolongs dysbiosis and Clostridioides difficile carriage and increases delayed mortality in a hamster model of infection. Microbiology Spectrum 10:e01804-21. pdf

Buessecker S, Palmer M, Lai D, Dimapilis J, Mayali X, Mosier D, Jiao JY, Colman DR, Keller LM, St. John E, Miranda M, Gonzalez C, Gonzalez L, Sam C, Villa C, Zhuo M, Bodman N, Robles F, Boyd ES, Cox AD, St. Clair B, Hua ZS, Li WJ, Reysenbach AL, Stott MB, Weber PK, Pett-Ridge J, Dekas AE, Hedlund BP, Dodsworth JA. 2022. An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea. Nature Communications 13:3773. pdf

Phan JR, Do DM, Truong MC, Ngo C, Phan JH, Sharma SK, Schilke A, Mefferd CC, Villarama JV, Lai D, Consul A, Hedlund BO, Firestine SM, Abel-Santos E. 2021. An aniline-substituted bile salt analog protects both mice and hamsters from multiple Clostridioides difficile strains. Antimicrobial Agents and Chemotherapy 66:e01435-21. pdf

Jiao JY, Lian ZH, Li MM, Salam N, Zhou EM, Liu L, Ming H, Nie G, Shu W, Zhao G, Hedlund BP, Li WJ. 2022. Comparative genomic analysis of Thermus provides insights into the evolutionary history of an incomplete denitrification pathway. mLife 1:198-209. pdf

Hedlund BP, Zhang C, Wang F, Rinke C, Martin WF. 2021. Ecology, metabolism and evolution on Archaea - Perspectives from proceedings of the International Workshop on geo-omics of Archaea. Frontiers in Microbiology 12:827229. pdf

Jiao JY, Liu L, Hua ZS, Fang BZ, Zhou EM, Salam N, Hedlund BP, Li WJ. 2021 Microbial dark matter coming to light: challenges and opportunities. National Science Review 8:nwaa280. pdf

Sun J, Evans PN, Gagen EJ, Woodcroft BJ, Hedlund BP, Woyke T, Hugenholtz P, Rinke C. 2021. Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME Communications 1:30. pdf

Li YX, Rao YZ, Qi YL, Qu YN, Chen YT, Jiao JY, Shu WS, Jiang H, Hedlund BP, Hua ZS, Li WJ. 2021. Deciphering symbiotic interactions of Candidatus Aenigmarchaeota with inferred horizontal gene transfers and co-occurrence networks. mSystems 6:e00606-21. pdf

Qi YL, Evans PN, Li YX, Rao YZ, Qu YN, Tan S, Jiao JY, Chen YT, Hedlund BP, Shu WS, Hua ZS, Li WJ. 2021. Comparative genomics reveals thermal adaptation and a high metabolic diversity in Candidatus Bathyarchaeia. mSystems 6:e00252-21. pdf

Jiao JY, Fu Li, Hua ZS, Liu L, Salam N, Liu PF, Lv AP, Wu G, Xian WD, Zhu Q, Zhou EM, Fang BZ, Oren A, Hedlund BP, Jiang HC, Knight R, Cheng L, Li WJ. 2021. Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. ISME Journal. pdf

Thomas SC, Payne D, Tamadonfar KO, Seymour CO, Jiao J-Y, Murugapiran SK, Lai D, Lau R, Bowen BP, Silva LP, Louie KB, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, OMalley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Eloe-Fadrosh E, Hamilton TL, Dijkstra P, Dodsworth JA, Northen TR, Li WJ, Hedlund BP. 2021. Genomics, exometabolomics, and metabolic probing reveal conserved proteolytic metabolism of Thermoflexus hugenholtzii and three Candidate species from China and Japan. Frontiers in Microbiology 12:632731. pdf

Pang J, Palmer M, Sun HJ, Seymour CO, Zhang L, Hedlund BP, Zeng F. 2021. Diversity of root nodule-associated bacteria of diverse legumes along an elevation gradient in the Kunlun Mountains, China. Frontiers in Microbiology 12:633141. pdf

Luo ZH, Narsing RMP, Chen H, Hua ZS, Li Q, Hedlund BP, Dong ZY, Liu BB, Guo SX, Shu WS, Li WJ. 2021. Genomic insights of Candidatus Nitrosocaldaceae based on nine new metagenome-assembled genomes, including Candidatus Nitrosothermus gen nov. and two new species of Candidatus Nitrosocaldus. Frontiers in Microbiology 11:608832. pdf

Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, IMG/M Data Consortium*, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA. 2021. A genomic catalog of Earth's microbiomes. Nature Biotechnology 39:499-509.pdf

Palmer M, Hedlund BP, Roux S, Tsourkas PK, Doss RK, Stamereilers C, Mehta A, Dodsworth JA, Lodes M, Monsma S, Glavina del Rio T, Schoenfeld TW, Eloe-Fadrosh EA, Mead DA. 2020. Diversity and distribution of a novel genus of hyperthermophilic Aquificae viruses encoding a proof-reading family-A DNA polymerase. Frontiers in Microbiology 11:583361. pdf

Lai D, Hedlund BP, Xie W, Liu J, Phelps TJ, Zhang C, Wang P. 2020. Impact of terrestrial input on deep-sea benthic archaeal community structure in South China Sea sediments. Frontiers in Microbiology 11:572017. pdf

Beam JP, Becraft ED, Brown JM, Schulz F, Jarett JK, Bezuidt O, Poulton NJ, Clark K, Dunfield PF, Ravin NV, Spear JR, Hedlund BP, Kormas KA, Sievert SM, Elshahed MS, Barton HA, Stott MB, Eisen JA, Moser DP, Onstott TC, Woyke T, Stepanauskas R. 2020. Ancestral absence of electron transport chains in Patescibacteria and DPANN. Frontiers in Microbiology 11:1848. pdf

Friel AD, Neiswenter SA, Seymour CO, Bali LR, McNamara G, Leija F, Jewell J, Hedlund BP. 2020. Microbiome shifts associated with the introduction of wild Atlantic Horseshoe Crabs (Limulus polyphemus) into a touch-tank exhibit. Frontiers in Microbiology 11:1398. pdf

Gleason CL, Frisbee MD, Rademacher LK, Sada DW, Meyers ZP, Knott JR, Hedlund BP. 2020. Hydrogeology of desert springs in the Panamint Range, California, USA: Geologic controls on the geochemical kinetics, flowpaths, and mean residence times of springs. Hydrological Processes 34:2923-2948. pdf

Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kampfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Loffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedros-Alio C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Hedlund BP, Reysenbach AL. 2020. Roadmap for naming uncultivated archaea and bacteria. Nature Microbiology 5:987-994. pdf

Bhute SS, Escobedo B, Haider M, Mekonen Y, Ferrer D, Hillyard SD, Friel AD, van Breukelen F, Hedlund BP. 2020. The gut microbiome and its potential role in paradoxical anaerobism in pupfishes of the Mojave Desert. Animal Microbiome 2:20. pdf

Palmer M, Steenkamp ET, Blom J, Hedlund BP, Venter SN. 2020. All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy. International Journal of Systematic Evolutionary Microbiology 70(4). pdf

Abdelshafy Mohamad OA, Ma JB, Liu YH, Zhang D, Hua S, Bhute S, Hedlund BP, Li WJ, Li L. 2020. Beneficial endophytic bacterial populations associated with medicinal plant Thymus vulgaris alleviate salt stress and confer resistance to Fusarium oxysporum. Frontiers in Plant Science 11:47. pdf

Mefferd CC, Bhute SS, Phan JR, Villarama JV, Do DM, Alarcia S, Abel-Santos E, Hedlund BP. 2020. A high-fat/high-protein, Atkins-type diet exacerbates Clostridioides (Clostridium) difficile infection in mice, whereas a high-carbohydrate diet protects. mSystems 5(1). pdf

Doud DFR, Bowers RM, Schulz F, De Raad M, Deng K, Tarver A, Glasgow E, Vander Meulen K, Fox B, Deutsch S, Yoshikuni Y, Northen T, Hedlund BP, Singer SW, Ivanova N, Woyke T. 2020. Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere. ISME Journal 14:659-675. pdf

Hua ZS, Wang YL, Evans PN, Qu YN, Goh KM, Rao YZ, Qi YL, Li YX, Huang MJ, Jiao JY, Chen YT, Mao YP, Shu WS, Hozzein W, Hedlund BP, Tyson GW, Zhang T, Li WJ. 2019. Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring archaea. Nature Communications 10(1):4574. pdf

Zhou EM, Adegboruwa AL, Mefferd CC, Bhute SS, Murugapiran SK, Dodsworth JA, Thomas SC, Bengtson AJ, Liu L, Xian WD, Li WJ, Hedlund BP. 2020. Diverse respiratory capacity among Thermus strains from US Great Basin hot springs. Extremophiles 24(1):71-80. pdf

Thomas SC, Tamadonfar KO, Seymour CO, Lai D, Dodsworth JA, Murugapiran SK, Eloe-Fadrosh EA, Dijkstra P, Hedlund BP. 2019. Position-specific metabolic probing and metagenomics of microbial communities reveal conserved central carbon metabolic network activities at high temperatures. Frontiers in Microbiology 10:1427. pdf

Tan S, Liu J, Fang Y, Hedlund BP, Lian ZH, Huang LY, Li JT, Huang LN, Li WJ, Jiang HC, Dong HL. 2019. Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics. ISME Journal 1. pdf

Zhou E-M, Xian W-D, Mefferd CC, Thomas SC, Adegboruwa AL, Williams N, Murugapiran SK, Dodsworth JA, Ganji R, Li M-M, Ding Y-P, Liu L, Woyke T, Li W-J, Hedlund BP. 2018. Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California. Extremophiles 22:983-991. pdf

Li L, Mohamad OAA, Ma JB. Friel AD, Su Y, Wang Y, Musa Z, Liu Y, Hedlund BP, Li W. 2018. Synergistic plant-microbe interactions between endophytic bacterial communities and the medicinal plant Glycyrrhiza uralensis F. Antonie van Leeuwenhoek 10:1735-1748. pdf

Howerton A, Seymour CO, Murugapiran SK, Liao Z, Phan JR, Estrada A, Wagner AJ, Mefferd CC, Hedlund BP, Abel-Santos E. 2018. Effect of the synthetic bile salt analog CamSA on the hamster model of Clostridium difficile infection. Antimicrobial Agents and Chemotherapy 62:e02251-17. pdf

Hua ZS, Qu YN, Zhu Q, Zhou EM, Qi YL, Yin YR, Rao YZ, Tian Y, Li YX, Liu L, Castelle CJ, Hedlund BP, Shu WS, Knight R, Li WJ. 2018. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nature Communications 9:2832. pdf

Mohamad OAA, Li L, Ma JB, Hatab S, Xu L, Guo JW, Rasulov B, Liu Y, Hedlund BP, Li W. 2018. Evaluation of the antimicrobial activity of endophytic bacterial populations from Chinese traditional medicinal plant licorice and characterization of the bioactive secondary metabolites produced by Bacillus atrophaeus against Verticillium dahliae. Frontiers in Microbiology 9:924. pdf

Xie W, Luo H, Murugapiran SK, Dodsworth JA, Chen S, Sun Y, Hedlund BP, Wang P, Fang H, Deng M, Zhang CL. 2017. Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation. Environmental Microbiology 20(2):734-754. pdf

Becraft ED, Dodsworth JA, Murugapiran SK, Thomas SC, Ohlsson JI, Stepanauskas R, Hedlund BP, Swingley WD. 2017. Genomic comparison of two family-level groups of the uncultivated NAG1 archaeal lineage from chemically and geographically disparate hot springs. Frontiers in Microbiology 8:2082. pdf

Blunt SM, Sackett JD, Rosen MR, Benotti MJ, Trenholm RA, Vanderford BJ, Hedlund BP, Moser DP. 2017. Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead. Science of the Total Environment. 622-623:1640-1648. pdf

Hedlund BP, Sutcliffe IC, Trujillo ME. 2017. Special Issue: the 3rd meeting of the Bergey's International Society for Microbial Systematics (BISMIS). Antonie Van Leeuwenhoek. pdf

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glockner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. 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. pdf

Blunt SM, Benotti MJ, Rosen MR, Hedlund BP, Moser DP. 2017. Reversible reduction of estrone to 17β-Estradiol by Rhizobium, Sphingopyxis, and Pseudomonas isolates from the Las Vegas Wash. Journal of Environmental Quality. 46(2):281-287. pdf

Hedlund BP, Thomas SC, Dodsworth JA, and CL Zhang. 2016. Life in high-temperature environments. In MV Yates, CH Nakatsu, RV Miller, and SD Pillai (eds.) Manual of Environmental Microbiology, 4th Edition. ASM Press, Washington, DC. pp. 863-877. pdf

Ganji R, Murugapiran SK, Ong JC, Manoharan N, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TB, Ngan CY, Daum C, Duffy K, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Dodsworth JA, Hedlund BP. 2016. High-quality draft genome sequence of Thermocrinis jamiesonii GBS1T isolated from Great Boiling Spring, Nevada. Genome Announcements. 4:e01112-16. pdf

Mefferd CC, Zhou E-M, Yu T-T, Ming H, Murugapiran SK, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Ngan CY, Daum C, Duffy K, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Williams AJ, Woyke T, Li W-J, Hedlund BP. 2016. High-quality draft genomes from Thermus caliditerrae YIM 77777 and T. tengchongensis YIM 77401, isolates from Tengchong, China. Genome Announcements. 4:e00312-16. pdf

Zhou E-M, Murugapiran SK, Mefferd CC, Liu L, Xian W-D, Yin Y-R, Ming H, Yu T-T, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Ngan CY, Daum C, Shapiro N, Markowitz V, Ivanova N, Spunde A, Kyrpides N, Woyke T, Li W-J, Hedlund BP. 2016. High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409T with an incomplete denitrification pathway. Standards in Genomic Sciences 11:20. pdf

Eloe-Fadrosh EA, Paez-Espino D, Jarett J, Dunfield PF, Hedlund BP, Dekas AE, Grasby SE, Brady AL, Dong H, Briggs BR, Li WJ, Goudeau D, Malmstrom R, Pati A, Pett-Ridge J, Rubin EM, Woyke T, Kyrpides NC, Ivanova NN. 2016. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nature Communications. 7:10476. pdf

Becraft ED, Dodsworth, JA, Murugapiran SK, Ohlsson JI, Briggs BR, Kanbar J, De Vlaminck I, Quake SR, Dong H, Hedlund BP, Swingley WD. 2015. Single-cell genomics facilitate read-first binning of candidate phylum EM19 populations in geothermal springs. Applied and Environmental Microbiology. 82:992-1003. pdf

Hedlund BP, Murugapiran SK, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TB, Ngan CY, Daum C, Duffy K, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Williams AJ, Cole JK, Dodsworth JA, Woyke T. 2015. High-quality draft genome sequence of Kallotenue papyrolyticum JKG1T reveals broad heterotrophic capacity focused on carbohydrate and amino acid metabolism. Genome Announcements. 3:e01410-15. pdf

Dodsworth JA, Ong JC, Williams AJ, Dohnalkova AC, Hedlund BP. 2015. Thermocrinis jamiesonii sp. nov., a thiosulfate-oxidizing, autotropic thermophile isolated from Great Boiling Spring, NV, USA. International Journal of Systematic and Evolutionary Microbiology. 65:4769-4775. pdf

Saw J, Spang A, Zaremba-Niedzwiedzka K, Juzokaite L, Dodsworth J, Murugapiran S, Colman D, Takacs-Vesbach C, Hedlund BP, Guy L, Ettema T. 2015. Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes. Phil. Trans. R. Soc. B. 370:20140328. pdf

Hedlund BP, Murugapiran S, Alba T, Levy A, Dodsworth J, Goertz G, Ivanova N, Woyke T. 2015. Uncultivated thermophiles: current status and spotlight on 'Aigarchaeota'. Current Opinion in Microbiology. 25:136-145. pdf

Nobu M, Dodsworth J, Murugapiran S, Rinke C, Gies E, Webster G, Schwientek P, Kille P, Parkes J, Sass H, Jorgensen B, Weightman A, Liu W, Hallam S, Tsiamis G, Woyke T, Hedlund BP. 2015. Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics. ISME Journal. 10:273-286. pdf

Yang J, Zhou E, Jiang H, Li W, Wu G, Huang L, Hedlund BP, Dong H. 2015. Distribution and diversity of aerobic carbon monoxideoxidizing bacteria in geothermal springs of China, the Philippines, and the United States. Geomicrobiology Journal. 32:903-913. pdf

Hedlund BP, Dodsworth JA, Staley JT. 2015. The changing landscape of microbial biodiversity exploration and its implications for systematics. Systematic and Applied Microbiology. 38(4):231-236. pdf

Hedlund BP, Reysenbach A-L, Huang L, Ong J, Liu Z, Dodsworth JA, Ahmed R, Williams AJ, Briggs BR, Liu Y, Hou W, Dong H. 2015. Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China. Frontiers in Microbiology. 6:157. pdf

Xie W, Zhang CL, Wang J, Chen Y, Zhu Y, de la Torre JR, Dong H, Hartnett HE, Hedlund BP, Klotz MG. 2014. Distribution of ether lipids and composition of the archaeal community in terrestrial geothermal springs: impact of environmental variables. Environmental Microbiology. 17:1600-1614. pdf

Li F, Zhang CL, Wang S, Chen Y, Sun C, Dong H, Li WJ, Klotz MG, Hedlund BP. 2014. Production of branched tetraether lipids in Tibetan hot springs: A possible linkage to nitrite reduction by thermotolerant or thermophilic bacteria? Chemical Geology. 386:209-217. pdf

Hedlund BP, Dodsworth JA, Murugapiran SK, Rinke C, Woyke T. 2014. Impact of single-cell genomics and metagenomics on the emerging view of extremophile "microbial dark matter". Extremophiles. 18:865-875. pdf

Dodsworth JA, Gevorkian J, Despujos F, Cole JK, Murugapiran SK, Ming H, Li WJ, Zhang G, Dohnalkova A, Hedlund BP. 2014. Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov. International Journal of Systematic and Evolutionary Microbiology. 64:2119-2127. pdf

Briggs BR, Brodie EL, Tom LM, Dong H, Jiang H, Huang Q, Wang S, Hou W, Wu G, Huang L, Hedlund BP, Zhang C, Dijkstra P, Hungate BA. 2013. Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China. Environmental Microbiology. 16:1579-1591. pdf

Cole JK, Gieler BA, Heisler DL, Palisoc MM, Williams AJ, Dohnalkova AC, Ming H, Yu TT, Dodsworth JA, Li WJ, Hedlund BP. 2013. Kallotenue papyrolyticum gen. nov., sp. nov., a cellulolytic and filamentous thermophile that represents a novel lineage (Kallotenuales ord. nov., Kallotenuaceae fam. nov.) within the class Chloroflexia. International Journal of Systematic and Evolutionary Microbiology 63:4675-4682. pdf

Hedlund BP, Li WJ, Zhang CL. 2013. Addressing questions on life in terrestrial geothermal systems. Eos. 94:325. pdf

Paraiso JJ, Williams AJ, Huang Q, Wei Y, Dijkstra P, Hungate BA, Dong H, Hedlund BP, Zhang CL. 2013. The distribution and abundance of archaeal tetraether lipids in U.S. Great Basin hot springs. Frontiers in Microbiology. 4:247. pdf

Hedlund BP, Paraiso JJ, Williams MJ, Huang Q, Wei Y, Dijkstra P, Hungate BA, Dong H, Zhang CL. 2013. Wide distribution of autochthonous branched glycerol dialkyl glycerol tetraethers (bGDGTs) in U.S. Great Basin hot springs. Frontiers in Microbiology. 4:222. pdf

Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 499:431-437. pdf

Zhang CL, Wang J, Dodsworth JA, Williams AJ, Zhu C, Hinrichs KU, Zheng F, Hedlund BP. 2013. In situ production of branched glycerol dialkyl glycerol tetraethers in a great basin hot spring (USA). Frontiers in Microbiology. 4:181. pdf

Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, Tringe SG, Chain PS, Scholz MB, Lo CC, Raymond J, Quake SR, Hedlund BP. 2013. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nature Communications. 4:1854. pdf

Schoenfeld, TA, Murugapiran S, Dodsworth JA, Hermersmann N, Floyd S, Lodes M, Mead D, Hedlund BP. 2013. A group of Family A DNA polymerases in thermophilic viruses is an evolutionary progenitor of Aquificae and Apicomplexa plastid DNA polymerases. Molecular Biology and Evolution. 30:1653-1664. pdf

Hedlund BP, Dodsworth JA, Cole JK, Panosyan HH. 2013. An integrated study reveals diverse methanogens, Thaumarchaeota, and yet-uncultivated archaeal lineages in Armenian hot springs. Antonie van Leeuwenhoek. 104:71-82. pdf

Edwards TA, Calica NA, Huang DA, Manoharan N, Hou W, Huang L, Panosyan H, Dong H, Hedlund BP. 2013. Cultivation and characterization of thermophilic Nitrospira species from geothermal springs in the U.S. Great Basin, China, and Armenia. FEMS Microbiology Ecology. 85:283-292. pdf

Murphy CN, Dodsworth JA, Babbitt AB, Hedlund BP. 2013. Community microrespirometry and molecular analyses reveal a diverse energy economy in Great Boiling Spring and Sandy's Spring West in the U.S. Great Basin. Applied and Environmental Microbiology 79:3306-3310. pdf

Murugapiran SK, Huntemann M, Wei CL, Han J, Detter JC, Han CS, Erkkila TH, Teshima H, Chen A, Kyrpides N, Mavrommatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Lam J, McDonald AI, Dodsworth JA, Pati A, Goodwin L, Peters L, Pitluck S, Woyke T, Hedlund BP. 2013. Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling. Standards in Genomic Sciences 7:449-468. pdf

Peacock JP, Cole JK, Murugapiran SK, Dodsworth JA, Fisher JC, Moser DP, Hedlund BP. 2013. Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment. PLoS One 8:1-12. pdf

Hou W, Wang S, Dong H, Jiang H, Briggs BR, Peacock JP, Huang Q, Huang L, Wu G, Zhi X, Li W, Dodsworth JA, Hedlund BP, Zhang C, Hartnett HE, Dijkstra P, Hungate BA. 2013. A comprehensive census of microbial diversity in hot spring of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing. PLoS One. 8:1-15 pdf

Murugapiran SK, Huntemann M, Wei CL, Han J, Detter JC, Han CS, Erkkila TH, Teshima H, Chen A, Kyrpides N, Mavrommatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Lam J, McDonald AI, Dodsworth JA, Pati A, Goodwin L, Peters L, Pitluck S, Woyke T, Hedlund BP. 2013. Whole genome sequencing of Thermus oshimai JL-2 and T. thermophilus JL-18, incomplete denitrifiers from the U.S. Great Basin. Genome Announcements 1: e00106-12. pdf

Cole JK, Peacock JP, Dodsworth JA, Williams AJ, Thompson DB, Dong H, Wu G, Hedlund BP. 2013. Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities. ISME Journal 7:718-729. pdf

Dodsworth JA, McDonald AI, Hedlund BP. 2012. Calculation of total free energy yield as an alternative approach for predicting the importance of potential chemolithotrophic reactions in geothermal springs. FEMS Microbiology Ecology 81(2):446-454. pdf

Miller-Coleman RL, Dodsworth JA, Ross CA, Shock EL, Williams AJ, Hartnett HE, McDonald AI, Havig JR, Hedlund BP. 2012. Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning. PLoS One 7: e35964. pdf

Hedlund BP, Cole JK, Williams AJ, Hou W, Zhou E, Li W, Dong H. 2012. A review of the microbiology of the Rehai geothermal field in Tengchong, Yunnan Province, China. Geoscience Frontiers 3(2):273-288. pdf

Dodsworth JA, Hungate B, de la Torre JR, Jiang H, Hedlund BP. 2011. Measuring nitrification, denitrification, and related biomarkers in continental geothermal ecosystems. Methods in Enzymology 486:171-203. pdf

Dodsworth JA, Hungate BA, Hedlund BP. 2011. Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea. Environmental Microbiology 8:2371-2386. pdf

Hedlund BP, McDonald AI, Lam J, Dodsworth JA, Brown JR, Hungate BA. 2011. Potential role of Thermus thermophilus and T. oshimai in high rates of nitrous oxide (N2O) production in ~80°C hot springs in the US Great Basin. Geobiology 9:471-480. pdf

Zhang CL, Hedlund BP, Meng J. 2011. Diversity of archaea in terrestrial hot springs and role in ammonia oxidation. In De Bruijn FJ, (ed) Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. John Wiley & Sons, Hoboken, New Jersey. pp. 381-394. pdf

Lefevre CT, Abreu F, Schmidt ML, Lins U, Frankel RB, Hedlund BP, Bazylinski DA. 2010. Moderately thermophilic magnetotactic bacteria from hot springs in Nevada USA. Applied and Environmental Microbiology 76:3740-3743. pdf

Vick TJ, Dodsworth JA, Costa KC, Shock EL, Hedlund BP. 2010. Microbiology and geochemistry of Little Hot Creek, a hot spring environment in the Long Valley Caldera. Geobiology 8:140-154. pdf

Dodsworth JA and Hedlund BP. 2010. Microbiology and geochemistry of Smith Creek and Grass Valley hot springs: Emerging evidence for wide distribution of novel thermophilic lineages in the US Great Basin. Journal of Earth Science 21: 315-318. pdf

Dodsworth JA, Li L, Wei S, Hedlund BP, Leigh JA, de Figueiredo P. 2010. Interdomain conjugal transfer of DNA from bacteria to archaea. Applied and Environmental Microbiology 76:5644-5647. pdf

Costa KC, Navarro JB, Shock EL, Zhang CL, Soukup D, Hedlund BP. 2009. Microbiology and geochemistry of Great Boiling and Mud Hot Springs in the United States Great Basin. Extremophiles 13:447-459. pdf

Sun HJ, V. Saccomanno, Hedlund B, McKay CP. 2009. Stereo-Specific Glucose Consumption May Be Used to Distinguish Between Chemical and Biological Reactivity on Mars: A Preliminary Test on Earth. Astrobiology 9:443-446. pdf

Navarro JB, Moser DP, Flores A, Ross C, Rosen MR, Dong H, Zhang G, Hedlund BP. 2009. Bacterial succession within an ephemeral hypereutrophic Mojave Desert playa lake. Microbial Ecology 57:307-320. pdf

Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M, Stetter KO. 2008. A korarchaeal genome reveals insights into the evolution of archaea. Proceedings of the National Academy of Sciences 105: 8102-8107. pdf

Zhang CL, Ye Q, Huang Z, Li W, Chen J, Song Z, Zhao W, Bagwell C, Inskeep WP, Ross C, Gao L, Wiegel J, Romanek CS, Shock EL, Hedlund BP. 2008. Global occurrence and biogeography of putative archaeal amoA genes in terrestrial hot springs. Applied and Environmental Microbiology 74: 6417-26. pdf

Costa KC, Moser DP, Hallmark J, Navarro JB, Soukup D, LaBahn S, Hedlund BP. 2008. Diversity of heterotrophic microorganisms and geochemistry in two ephemeral desert playa lakes. Geomicrobiology Journal 25:250-259. pdf

Huang Z, Hedlund BP, Wiegel J, Zhou J, Zhang CL. 2007. Molecular phylogeny of uncultivated Crenarchaeota in Great Basin hot springs of moderately elevated temperature. Geomicrobiology Journal 24:535-542. pdf

Hedlund BP, Staley JT. 2006. Isolation and characterization of Pseudoalteromonas strains with divergen polycyclic aromatic hydrocarbon catabolic properties. Environmental Microbiology 8:178-182. pdf

Stetter KO, Hohn MJ, Huber H, Rachel R, Mathur E, Hedlund BP, Jahn U. 2005. A novel kingdom of parasitic archaea. In W.P. Inskeep and T.R. McDermott (eds.) Geothermal Biology and Geochemistry in Yellowstone National Park, Montana State University Publications, Bozeman, MT, USA. pp. 249-259. pdf

Oakley B, North M, Franklin JF, Hedlund BP, Staley JT. 2004. Diversity and distribution of Frankia strains symbiotic with Ceanothus in California. Applied and Environmental Microbiology 70:6444-6452. pdf

Gu AZ, Hedlund BP, Staley JT, Strand SE, Stensel HD. 2004. Analysis and comparison of the microbial community structures of two enrichment cultures capable of reductively dechlorinating TCE and cis-DCE. Environmental Microbiology 6:45-54. pdf

Hedlund BP, Staley JT. 2003. Microbial Endemism and Biogeography. In A.T. Bull (ed.) Microbial Diversity and Bioprospecting, ASM Press, Washington DC , USA . pp. 225-231. pdf

Hedlund BP, Staley JT. 2002. Phylogeny of the genus Simonsiella and other members of the Neisseriaceae. International Journal of Systematic and Evolutionary Microbiology 52:1377-1382. pdf

Rachel R, Bettstetter M, Hedlund BP, Haring M, Kessler A, Stetter KO, Prangishvili D. 2002. Remarkable morphological diversity of viruses and virus-like particles in hot terrestrial environments. Archives of Virology 147:2419-2429. pdf

Hohn MJ, Hedlund BP, Huber H. 2002. Detection of 16S rDNA sequences representing the novel phylum Nanoarchaeota: indication for a world-wide distribution in high temperature biotopes. Systematic and Applied Microbiology 25:551-554. pdf

Jenkins C, Samudrala R, Anderson I, Hedlund BP, Petroni G, Michailova N, Pinel N, Overbeek R, Rosati G, Staley JT. 2002. Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter. Proceedings of the National Academy of Sciences 99:17049-17054. pdf

Hedlund BP, Staley JT. 2001. Vibrio cyclotrophicus sp. nov., a polycyclic hydrocarbon (PAH)-degrading marine bacterium. Internantional Journal of Systematic and Evolutionary Microbiology 51:61-66. pdf

Hedlund BP, Geiselbrecht AD, Staley JT. 2001. Marinobacter strain NCE312 has a Pseudomonas-like naphthalene dioxygenase. FEMS Microbiology Letters 20:47-51. pdf

Rockne KJ, Chee-Sanford JC, Sanford RA, Hedlund BP, Staley JT, Strand SE. 2000. Anaerobic naphthalene degradation by microbial pure cultures under nitrate-reducing conditions. Applied and Environmental Microbiology 66:1595-1601. pdf

Ward NL, Rainey FA, Hedlund BP, Staley JT, Ludwig W, Stackebrandt E. 2000. Comparative phylogenetic analyses of members of the order Planctomycetales and the division Verrucomicrobia: 23S rRNA gene sequence analysis supports the 16S rRNA gene sequence-derived phylogeny. Internantional Journal of Systematic and Evolutionary Microbiology 50:1965-1972. pdf

Hedlund BP, Geiselbrecht AD, Bair TJ, Staley JT. 1999. Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. nov. Applied and Environmental Microbiology 65:251-259. pdf

Geiselbrecht AD, Hedlund BP, Tichi MA, Staley JT. 1998. Isolation of marine polycyclic aromatic hydrocarbon (PAH)-degrading Cycloclasticus strains from the Gulf of Mexico and comparison of their PAH degradation ability with that of Puget Sound Cycloclasticus strains. Applied and Environmental Microbiology 64:4703-4710. pdf

Hedlund BP, Gosink JJ, Staley JT. 1997. Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter. Antonie van Leeuwenhoek 72: 29-38. pdf

Hedlund BP, Gosink JJ, Staley JT. 1996. Phylogeny of Prosthecobacter, the fusiform caulobacters: Members of a recently discovered division of the Bacteria. Internantional Journal of Systematic Bacteriolology 46:960-966. pdf