Archaeal and bacterial communities in three alkaline hot springs in heart lake geyser basin, yellowstone national park

Frontiers in Microbiology

Volumn 4, Issue NOV, 2013, Pages

  De León, Kara Bowen ^a,b   Gerlach, Robin ^a,b   Peyton, Brent M ^a,b   Fields, Matthew W ^a,b,c  

^a MONTANA STATE UNIVERSITY   (United States)

^b Montana State University   (United States)

^c NATIONAL CENTER FOR GENOME RESOURCES   (United States)

Author keywords

16S rRNA pyrosequencing; Alkaline hot spring; Heart lake geyser basin; Methanogenic community; Phylogeny; Thermoalkaline; Thermus; Yellowstone national park

Indexed keywords

BARIUM; CALCIUM; MAGNESIUM; SMALL SUBUNIT RIBOSOMAL RNA; SODIUM; SULFIDE;

ALKALINITY; ARTICLE; CHLOROFLEXI; CHLOROFLEXUS; CONTROLLED STUDY; CYANOBACTERIUM; DEINOCOCCUS; DNA SEQUENCE; GEOCHEMISTRY; LAKE; MASS SPECTROMETER; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; PH; POLYMERASE CHAIN REACTION; PYROSEQUENCING; RIVER BASIN; SEQUENCE ANALYSIS; TEMPERATURE; THERMAL SPRING; THERMOFILUM; THERMUS; VERRUCOMICROBIUM;

EID: 84890293078     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2013.00330     Document Type: Article

References (40)

1. Acinas, S. G., Sarma-Rupavtarm, R., Klepac-Ceraj, V., and Polz, M. F. (2005). PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl. Environ. Microbiol. 71, 8966-8969. doi: 10.1128/AEM.71.12.8966-8969.2005.
2. APHA. (1998). Standard Methods for the Examination of Water and Wastewater. Washington, DC: American Public Health Association.
3. Baker, G. C., Smith, J. J., and Cowan, D. A. (2003). Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods 55, 541-555. doi: 10.1016/j.mimet.2003.08.009.
4. Boomer, S. M., Lodge, D. P., Dutton, B. E., and Pierson, B. (2002). Molecular characterization of novel red green nonsulfur bacteria from five distinct hot spring communities in Yellowstone National Park. Appl. Environ. Microbiol. 68, 346-355. doi: 10.1128/AEM.68.1.346-355.2002.
5. Bowen De León, K., Ramsay, B. D., and Fields, M. W. (2012). Quality-score refinement of SSU rRNA gene pyrosequencing differs across gene region for environmental samples. Microb. Ecol. 64, 499-508. doi: 10.1007/s00248-012-0043-9.
6. Brochier-Armanet, C., Forterre, P., and Gribaldo, S. (2011). Phylogeny and evolution of the Archaea: one hundred genomes later. Curr. Opin. Microbiol. 14, 274-281. doi: 10.1016/j.mib.2011.04.015.
7. Brock, T. D. (1967). Life at high temperatures. Science 158, 1012-1019. doi: 10.1126/science.158.3804.1012.
8. Claesson, M. J., O'Sullivan, O., Wang, Q., Nikkilä, J., Marchesi, J. R., Smidt, H., et al. (2009). Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 4:e6669. doi: 10.1371/journal.pone.0006669.
9. Claesson, M. J., and O'Toole, P. W. (2010). Evaluating the latest high-throughput molecular techniques for the exploration of microbial gut communities. Gut Microbes 1, 277-278. doi: 10.4161/gmic.1.4.12306.
10. Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., et al. (2009). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37, D141-D145. doi: 10.1093/nar/gkn879.
11. da Costa, M. S., Rainey, F. A., and Nobre, M. F. (2006). The genus Thermus and relatives. Prokaryotes 7, 797-812. doi: 10.1007/0-387-30747-8_32.
12. de la Torre, J. R., Walker, C. B., Ingalls, A. E., Könneke, M., and Stahl, D. A. (2008). Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ. Microbiol. 10:810-818. doi: 10.1111/j.1462-2920.2007.01506.x.
13. Dickie, I. A. (2010). Insidious effects of sequencing errors on perceived diversity in molecular surveys. New Phytol. 188, 916-918. doi: 10.1111/j.1469-8137.2010.03473.x.
14. Gihring, T. M., Green, S. J., and Schadt, C. W. (2012). Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ. Microbiol. 14, 285-290. doi: 10.1111/j.1462-2920.2011.02550.x.
15. Good, I. J. (1953). The population frequencies of species and the estimation of population parameters. Biometrika 40:237-264. doi: 10.1093/biomet/40.3-4.237.
16. Haas, B. J., Gevers, D., Earl, A. M., Feldgarden, M., Ward, D. V., Giannoukos, G., et al. (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21, 494-504. doi: 10.1101/gr.112730.110.
17. Hamilton, T. L., Vogl, K., Bryant, D. A., Boyd, E. S., and Peters, J. W. (2012). Environmental constraints defining the distribution, composition, and evolution of chlorophototrophs in thermal features of Yellowstone National Park. Geobiology 10, 236-249. doi: 10.1111/j.1472-4669.2011.00296.x.
18. Huber, H., Huber, R., and Stetter, K. O. (2006). Thermoproteales. Prokaryotes 3, 10-22. doi: 10.1007/0-387-30743-5_2.
19. Hugenholtz, P., Pitulle, C., Hershberger, K. L., and Pace, N. R. (1998). Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180, 366-376.
20. Huse, S. M., Huber, J. A., Morrison, H. G., Sogin, M. L., and Welch, D. M. (2007). Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8:R143. doi: 10.1186/gb-2007-8-7-r143.
21. Huse, S. M., Welch, D. M., Morrison, H. G., and Sogin, M. L. (2010). Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12, 1889-1898. doi: 10.1111/j.1462-2920.2010.02193.x.
22. Hwang, C., Wu, W., Gentry, T. J., Carley, J., Corbin, G. A., Carroll, S. L., et al. (2009). Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths. ISME J. 3, 47-64. doi: 10.1038/ismej.2008.77.
23. Inskeep, W. P., Ackerman, G. G., Taylor, W. P., Kozubal, M., Korf, S., and Macur, R. E. (2005). On the energetics of chemolithotrophy in nonequilibrium systems: case studies of geothermal springs in Yellowstone National Park. Geobiology 3, 297-317. doi: 10.1111/j.1472-4669.2006.00059.x.
24. Inskeep, W. P., Rusch, D. B., Jay, Z. J., Herrgard, M. J., Kozubal, M. A., Richardson, T. H., et al. (2010). Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS ONE 5:e9773. doi: 10.1371/journal.pone.0009773.
25. Kan, J., Clingenpeel, S., Macur, R. E., Inskeep, W. P., Lovalvo, D., Varley, J., et al. (2011). Archaea in Yellowstone Lake. ISME J. 5, 1784-1795. doi: 10.1038/ismej.2011.56.
26. Liu, Z., Lozupone, C., Hamady, M., Bushman, F. D., and Knight, R. (2007). Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 35, e120. doi: 10.1093/nar/gkm541.
27. Lowenstern, J. B., Bergfeld, D., Evans, W. C., and Hurwitz, S. (2012). Generation and evolution of hydrothermal fluids at Yellowstone: insights from the Heart Lake Geyser Basin. Geochem. Geophy. Geosy. 13, Q01017. doi: 10.1029/2011GC003835.
28. Mühl, H., Kochem, A.-J., Disqué, C., and Sakka, S. G. (2010). Activity and DNA contamination of commercial polymerase chain reaction reagents for the universal 16S rDNA real-time polymerase chain reaction detection of bacterial pathogens in blood. Diagn. Microbiol. Infect. Dis. 66, 41-49. doi: 10.1016/j.diagmicrobio.2008.07.011.
29. Nunoura, T., Takaki, Y., Kakuta, J., Nishi, S., Sugahara, J., Kazama, H., et al. (2011). Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 39, 3204-3223. doi: 10.1093/nar/gkq1228.
30. Pester, M., Schleper, C., and Wagner, M. (2011). The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr. Opin. Microbiol. 14, 300-306. doi: 10.1016/j.mib.2011.04.007.
31. Philipp, S., Huemer, H. P., Irschick, E. U., and Gassner, C. (2010). Obstacles of multiplex real-time PCR for bacterial 16S rDNA: primer specifity and DNA decontamination of Taq polymerase. Transfus. Med. Hemoth. 37, 21-28. doi: 10.1159/000265571.
32. Reysenbach, A.-L., Wickham, G. S., and Pace, N. R. (1994). Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Appl. Environ. Microbiol. 60, 2113-2119.
33. Schouten, S., van der Meer, M. T. J., Hopmans, E. C., Rijpstra, W. I. C., Reysenbach, A.-L., Ward, D. M., et al. (2007). Archaeal and bacterial glycerol dialkyl glycerol tetraether lipids in hot springs of Yellowstone National Park. Appl. Environ. Microbiol. 73, 6181-6191. doi: 10.1128/AEM.00630-07.
34. Sipos, R., Székely, A. J., Palatinszky, M., Révész, S., Márialigeti, K., and Nikolausz, M. (2007). Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiol. Ecol. 60, 341-350. doi: 10.1111/j.1574-6941.2007.00283.x.
35. Ward, D. M. (1978). Thermophilic methanogenesis in a hot-spring algal-bacterial mat (71 to 30°C). Appl. Environ. Microbiol. 35, 1019-1026.
36. Ward, D. M., Ferris, M. J., Nold, S. C., and Bateson, M. M. (1998). A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiol. Mol. Biol. Rev. 62, 1353-1370.
37. Wu, J.-Y., Jiang, X.-T., Jiang, Y.-X., Lu, S.-Y., Zou, F., and Zhou, H.-W. (2010). Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method. BMC Microbiol. 10:255. doi: 10.1186/1471-2180-10-255.
38. Youssef, N. H., and Elshahed, M. S. (2008). Species richness in soil bacterial communities: a proposed approach to overcome sample size bias. J. Microbiol. Methods 75, 86-91. doi: 10.1016/j.mimet.2008.05.009.
39. Zeikus, J. G., Ben-Bassat, A., and Hegge, P. W. (1980). Microbiology of methanogenesis in thermal, volcanic environments. J. Bacteriol. 143, 432-440.
40. Zhou, J., Bruns, M. A., and Tiedje, J. M. (1996). DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62, 316-322.