PIRE News

Publications

2015

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. doi: 10.1038/ismej.2015.97. 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. doi: 10.1080/01490451.2015.1008605. pdf

Hedllund BP, Dodsworth JA, Staley JT. 2015. The changing landscape of microbial biodiversity exploration and its implications for systematics. Systematic and Applied Microbiology. doi:10.1016/j.syapm.2015.03.003. pdf

Urschel MR, Kubo MD, Hoehler TM, Peters JW, Boyd ES. 2015. Carbon source preference in chemosynthetic hot spring communities. Applied and Environmental Microbiology. doi:10.1128/AEM.00511-15. pdf

2014

Hamilton, T. L., E. Koonce, A. Howells, J.R. Havig, T. Jewell, J.R. de al Torre, J.W. Peters and E.S. Boyd. 2014. Competition for Ammonia influences the structure of chemotrophic communities in geothermal springs. Applied and Environmental Microbiology 80: 653-661. pdf

2013

Briggs, B.R., E.L. Brodie, L.M. Tom, H. Dong, H. Jiang, Q. Huang, S. Wang, W. Hou, G. Wu, L. Huang, B.P. Hedlund, C.L. Zhang, P. Dijkstra and B.A. Hungate. 2013. Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China. Environmental microbiology, DOI:10.1111/1462-2920.12311. pdf

Cole, J.K., B.A. Gieler, D.L. Heisler, M.M. Palisoc, A.J. Williams, A.C. Dohnalkova, H. Ming, T.T. Yu, J.A. Dodsworth, W.J. Li and B.P. Hedlund. 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

McGlynn, S.E., E.S. Boyd, J.W. Peters, and V.J. Orphan. 2013. Classifying the metal dependence of uncharacterized nitrogenases. Frontiers in Microbiology 3:419. pdf

Boyd, E.S., T.L. Hamilton, J. Wang, L. He, C.L. Zhang. 2013. The role of tetraether lipid composition in the adaptation of thermophilic archaea to acidity. Frontiers in Terrestrial Microbiology 4:62. pdf

Boyd, E.S. and G.K. Druschel. 2013. Involvement of intermediate sulfur species in biological reduction of elemental sulfur under acidic, hydrothermal conditions. Applied and Environmental Microbiology 79:2061-2068. pdf

Cole, J. K., J.P. Peacock, J.A. Dodsworth, A.J. Williams, D.B. Thompson, H. Dong, G. Wu, and B.P. Hedlund. 2013. Sediment microbial communities in Great Boiling Spring, Nevada, are controlled by temperature and distinct from water communities. ISME Journal 7:718-729. pdf

Dodsworth, J. A., P.C. Blainey, S.K. Murugapiran, W.D. Swingley, C.A. Ross, S.G. Tringe, P.S.G. Chain, J. Raymond, S.R. Quake, and B. P. Hedlund. 2013. Single-cell and metagenomic analyses indicate a fermentative, saccharolytic lifestyle for members of the OP9 lineage. Nature Communications 4:1854. 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. doi: 10.1111/1574-6941.12117. pdf

Hedlund, B. P., J.A. Dodsworth, J.K. Cole, and H. H. Panosyan. 2013. An integrated study reveals diverse methanogens, Thaumarchaeota, and yet-uncultivated archaeal lineages in Armenian hot springs. Antonie van Leeuwenhoek. DOI 10.1007/s10482-013-9927-z. pdf

Hou, W., S. Wang, S., H. Jiang, B.R. Briggs, H. Dong, J.P. Peacock, Q. Huang, G. Wu, X. Zhi, W. Li, J.A. Dodsworth, B. P. Hedlund, C. Zhang, H. Hartnett, P. Dijkstra, and B. Hungate. 2013. A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province, China using 16S rRNA gene pyrosequencing. PLoS One 8:e53350. doi:10.1371/journal.pone.0053350. pdf

Huang, Q., Jiang, H., Briggs, B., Wang, S., Hou, W., Li, G., Wu, G., Solis, B., Arcilla, C.A., and Dong, H. (2013) Archaeal and bacterial diversity in acidic hot springs in the Philippines. FEMS Microbiology Ecology. DOI: 10.1111/1574-6941.12134.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

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

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:e59927 pdf

Rinke, C., P. Schwientek, A. Sczyrba, N. N. Ivanova, I. J. Anderson, J.-F. Cheng, S. Malfatti, A. Darling, B. K. Swan, B. P. Hedlund, G. Tsiamis, S. M. Sievert, W.-T. Liu, S. Hallam, J. A. Eisen, N. Kyrpides, R. Stepanauskas, E. Rubin, P. Hugenholtz, and T. Woyke. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature. doi:10.1038/nature12352. pdf

Schoenfeld, T.A., S. Murugapiran, J.A. Dodsworth, S. Floyd, M. Lodes, D. Mead, and B. P. Hedlund. 2013. Lateral Gene Transfer of Family A DNA Polymerases between Thermophilic Viruses, Aquificae, and Apicomplexa. Molecular Biology and Evolution. doi:10.1093/molbev/mst078. pdf

Wang, S., Hou, W., Dong, H., Jiang, H., Huang, L., Wu, G., Zhang, C., Song, Z., Zhang, Y., and Ren, H., Zhang, J., and Zhang, L. (2013) Control of temperature on microbial community structure in hot springs of the Tibetan Plateau. PLoS ONE. 8(5):e62901. doi:10.1371/journal.pone.0062901.pdf

Zhang, C.L., J. Wang, J.A. Dodsworth, A.J. Williams, C. Zhu, K. Hinrichs, and B.P. Hedlund. 2013. In Situ Production of Branched Glycerol Dialkyl Glycerol Tetraethers in a Great Basin Hot Spring (USA). Frontiers in Terrestrial Microbiology. doi:10.3389/fmicb.2013.00181.pdf

2012

Boyd, E.S. and T. Barkay. 2012. The mercury resistance operon: From an origin in a geothermal environment to an efficient detoxification machine. Frontiers in Terrestrial Microbiology 3:349.pdf

Dodsworth, J.A., A.I. McDonald, and B.P. Hedlund. 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

Hamilton, T.L., Vogl, K., Boyd, E.S., Peters, J.W. 2012. Environmental contstraints defining the distribution, composition, and evolution of chlorophototrophs in thermal features of Yellowstone National Park. Geobiology doi:10.1111/j.1472-4669.2011.00296.x. pdf

He L., Zhang C.L., Dong H., Fang B., Wang G. 2012. Distribution of glycerol dialkyl glycerol tetraethers in Tibetan hot springs. Geoscience Frontiers. 3: 289-300. pdf

Hedlund, B. P., Cole, J. K., Williams, A.J., Hou, W., Zhou, E., Li, W.J., Dong, H. 2012. A review of the microbiology of the Rehai geothermal field in Tengchong, Yunnan Province, China. Geoscience Frontiers doi:10.1111/j.1472-4669.2011.00296.x. pdf

2011

Dodsworth, J. A., B. Hungate, J.R. de la Torre, H. Jiang, and B. P. Hedlund. 2011. Measuring nitrification, denitrification, and related biomarkers in continental geothermal ecosystems. Meth. Enzymol. 486: 171-203. pdf

Dodsworth, J. A., B. Hungate, and B. P. Hedlund. 2011. Ammonia oxidation, denitrification, and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea. Env. Microbiol. 13: 2371-2386. pdf

Hamilton, T.L., Boyd, E.S., Peters, J.W. 2011. Environmental Constraints Underpin the Distribution and Phylogenetic Diversity of nifH in the Yellowstone Geothermal Complex. Microbial Ecology. 61:860-870. doi: 10.1007/s00248-011-9824-9. pdf

Hamilton, T.L., Lange, R.K., Boyd, E.S., Peters, J.W. 2011. Biological nitrogen fixation in acidic high-temperature geothermal springs in Yellowstone National Park, Wyoming. Env. Microbiol. 13:2204-2215. doi:10.1111/j.1462-2920.2011.02475.x. pdf

Hedlund, B. P., McDonald, A. I., Lam, J., Dodsworth, J. A., Brown, J., Hungate, B.A. 2011. Potential role of Thermus thermophilus and T. oshimai in high nitrous oxide flux in Great Basin hot springs. Geobiology 9:471-480.pdf

Huang, Q., Dong, C.Z., Dong, R.M., Jiang, H., Wang, S., Wang, G., Fang, B., Ding, X., Niu, L., Li, X., Zhang, C.L., and Dong, H. 2011. Archaeal and Bacterial Diversity in Hot Springs on the Tibetan Plateau, China. Extremophiles 15:549-563.pdf