Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park

Bowen De León, Kara; Gerlach, Robin; Peyton, Brent M.; Fields, Matthew W.

doi:10.3389/fmicb.2013.00330

Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park

Journal Article · Mon Dec 31 23:00:00 EST 2012 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2013.00330· OSTI ID:1628099

Bowen De León, Kara ^[1]; Gerlach, Robin ^[2]; Peyton, Brent M. ^[2]; Fields, Matthew W. ^[3]

Montana State Univ., Bozeman, MT (United States). Dept. of Microbiology; Montana State Univ., Bozeman, MT (United States). Center for Biofilm Engineering; DOE/OSTI
Montana State Univ., Bozeman, MT (United States). Center for Biofilm Engineering; Montana State Univ., Bozeman, MT (United States). Thermal Biology Inst.; Montana State Univ., Bozeman, MT (United States). Dept. of Chemical and Biological Engineering
Montana State Univ., Bozeman, MT (United States). Dept. of Microbiology; Montana State Univ., Bozeman, MT (United States). Center for Biofilm Engineering; Montana State Univ., Bozeman, MT (United States). Thermal Biology Inst.; Montana State Univ., Bozeman, MT (United States). Dept. of Chemical and Biological Engineering; National Center for Genome Resources, Santa Fe, NM (United States)

The Heart Lake Geyser Basin (HLGB) is remotely located at the base of Mount Sheridan in southern Yellowstone National Park (YNP), Wyoming, USA and is situated along Witch Creek and the northwestern shore of Heart Lake. Likely because of its location, little is known about the microbial community structure of springs in the HLGB. Bacterial and archaeal populations were monitored via small subunit (SSU) rRNA gene pyrosequencing over 3 years in 3 alkaline (pH 8.5) hot springs with varying temperatures (44°C, 63°C, 75°C). The bacterial populations were generally stable over time, but varied by temperature. The dominant bacterial community changed from moderately thermophilic and photosynthetic members (Cyanobacteria and Chloroflexi) at 44°C to a mixed photosynthetic and thermophilic community (Deinococcus-Thermus) at 63°C and a non-photosynthetic thermophilic community at 75°C. The archaeal community was more variable across time and was predominantly a methanogenic community in the 44 and 63°C springs and a thermophilic community in the 75°C spring. The 75°C spring demonstrated large shifts in the archaeal populations and was predominantly Candidatus Nitrosocaldus, an ammonia-oxidizing crenarchaeote, in the 2007 sample, and almost exclusively Thermofilum or Candidatus Caldiarchaeum in the 2009 sample, depending on SSU rRNA gene region examined. The majority of sequences were dissimilar (≥10% different) to any known organisms suggesting that HLGB possesses numerous new phylogenetic groups that warrant cultivation efforts.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1628099

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 4; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

References (34)

The Genus Thermus and Relatives Da Costa, Milton S.; Rainey, Fred A.; Nobre, M. Fernanda The Prokaryotes https://doi.org/10.1007/0-387-30747-8_32	book	January 2006
Quality-Score Refinement of SSU rRNA Gene Pyrosequencing Differs Across Gene Region for Environmental Samples Bowen De León, Kara; Ramsay, Bradley D.; Fields, Matthew W. Microbial Ecology, Vol. 64, Issue 2 https://doi.org/10.1007/s00248-012-0043-9	journal	April 2012
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 Mühl, Helge; Kochem, Anna-Julia; Disqué, Claudia Diagnostic Microbiology and Infectious Disease, Vol. 66, Issue 1 https://doi.org/10.1016/j.diagmicrobio.2008.07.011	journal	January 2010
The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology Pester, Michael; Schleper, Christa; Wagner, Michael Current Opinion in Microbiology, Vol. 14, Issue 3 https://doi.org/10.1016/j.mib.2011.04.007	journal	June 2011
Phylogeny and evolution of the Archaea: one hundred genomes later Brochier-Armanet, Celine; Forterre, Patrick; Gribaldo, Simonetta Current Opinion in Microbiology, Vol. 14, Issue 3 https://doi.org/10.1016/j.mib.2011.04.015	journal	June 2011
Review and re-analysis of domain-specific 16S primers Baker, G. C.; Smith, J. J.; Cowan, D. A. Journal of Microbiological Methods, Vol. 55, Issue 3 https://doi.org/10.1016/j.mimet.2003.08.009	journal	December 2003
Species richness in soil bacterial communities: A proposed approach to overcome sample size bias Youssef, Noha H.; Elshahed, Mostafa S. Journal of Microbiological Methods, Vol. 75, Issue 1 https://doi.org/10.1016/j.mimet.2008.05.009	journal	September 2008
Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths Hwang, Chiachi; Wu, Weimin; Gentry, Terry J. The ISME Journal, Vol. 3, Issue 1 https://doi.org/10.1038/ismej.2008.77	journal	September 2008
Archaea in Yellowstone Lake Kan, Jinjun; Clingenpeel, Scott; Macur, Richard E. The ISME Journal, Vol. 5, Issue 11 https://doi.org/10.1038/ismej.2011.56	journal	May 2011
The Population Frequencies of Species and the Estimation of Population Parameters Good, I. J. Biometrika, Vol. 40, Issue 3-4 https://doi.org/10.1093/biomet/40.3-4.237	journal	January 1953
Short pyrosequencing reads suffice for accurate microbial community analysis Liu, Z.; Lozupone, C.; Hamady, M. Nucleic Acids Research, Vol. 35, Issue 18 https://doi.org/10.1093/nar/gkm541	journal	August 2007
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis Cole, J. R.; Wang, Q.; Cardenas, E. Nucleic Acids Research, Vol. 37, Issue Database https://doi.org/10.1093/nar/gkn879	journal	January 2009
Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group Nunoura, Takuro; Takaki, Yoshihiro; Kakuta, Jungo Nucleic Acids Research, Vol. 39, Issue 8 https://doi.org/10.1093/nar/gkq1228	journal	December 2010
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons Haas, B. J.; Gevers, D.; Earl, A. M. Genome Research, Vol. 21, Issue 3 https://doi.org/10.1101/gr.112730.110	journal	January 2011
Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol de la Torre, José R.; Walker, Christopher B.; Ingalls, Anitra E. Environmental Microbiology, Vol. 10, Issue 3 https://doi.org/10.1111/j.1462-2920.2007.01506.x	journal	March 2008
Insidious effects of sequencing errors on perceived diversity in molecular surveys: Letters Dickie, Ian A. New Phytologist, Vol. 188, Issue 4 https://doi.org/10.1111/j.1469-8137.2010.03473.x	journal	September 2010
On the energetics of chemolithotrophy in nonequilibrium systems: case studies of geothermal springs in Yellowstone National Park Inskeep, W. P.; Ackerman, G. G.; Taylor, W. P. Geobiology, Vol. 3, Issue 4 https://doi.org/10.1111/j.1472-4669.2006.00059.x	journal	October 2005
Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis: PCR parameters influencing quantitative bias Sipos, Rita; SzÃ©kely, Anna J.; Palatinszky, MÃ¡rton FEMS Microbiology Ecology, Vol. 60, Issue 2 https://doi.org/10.1111/j.1574-6941.2007.00283.x	journal	May 2007
Life at High Temperatures: Evolutionary, ecological, and biochemical significance of organisms living in hot springs is discussed Brock, T. D. Science, Vol. 158, Issue 3804 https://doi.org/10.1126/science.158.3804.1012	journal	November 1967
Archaeal and Bacterial Glycerol Dialkyl Glycerol Tetraether Lipids in Hot Springs of Yellowstone National Park Schouten, Stefan; van der Meer, Marcel T. J.; Hopmans, Ellen C. Applied and Environmental Microbiology, Vol. 73, Issue 19 https://doi.org/10.1128/aem.00630-07	journal	August 2007
Thermophilic methanogenesis in a hot-spring algal-bacterial mat (71 to 30 degrees C). Ward, D. M. Applied and Environmental Microbiology, Vol. 35, Issue 6 https://doi.org/10.1128/aem.35.6.1019-1026.1978	journal	January 1978
Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park. Reysenbach, A. L.; Wickham, G. S.; Pace, N. R. Applied and Environmental Microbiology, Vol. 60, Issue 6 https://doi.org/10.1128/aem.60.6.2113-2119.1994	journal	January 1994
DNA recovery from soils of diverse composition. Zhou, J.; Bruns, M. A.; Tiedje, J. M. Applied and environmental microbiology, Vol. 62, Issue 2 https://doi.org/10.1128/aem.62.2.316-322.1996	journal	January 1996
Molecular Characterization of Novel Red Green Nonsulfur Bacteria from Five Distinct Hot Spring Communities in Yellowstone National Park Boomer, S. M.; Lodge, D. P.; Dutton, B. E. Applied and Environmental Microbiology, Vol. 68, Issue 1 https://doi.org/10.1128/aem.68.1.346-355.2002	journal	January 2002
PCR-Induced Sequence Artifacts and Bias: Insights from Comparison of Two 16S rRNA Clone Libraries Constructed from the Same Sample Acinas, S. G.; Sarma-Rupavtarm, R.; Klepac-Ceraj, V. Applied and Environmental Microbiology, Vol. 71, Issue 12 https://doi.org/10.1128/aem.71.12.8966-8969.2005	journal	December 2005
Microbiology of Methanogenesis in Thermal, Volcanic Environments Zeikus, J. G.; Ben-Bassat, Arie; Hegge, P. W. Journal of Bacteriology, Vol. 143, Issue 1 https://doi.org/10.1128/jb.143.1.432-440.1980	journal	January 1980
Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring Hugenholtz, Philip; Pitulle, Christian; Hershberger, Karen L. Journal of Bacteriology, Vol. 180, Issue 2 https://doi.org/10.1128/jb.180.2.366-376.1998	journal	January 1998
A Natural View of Microbial Biodiversity within Hot Spring Cyanobacterial Mat Communities Ward, David M.; Ferris, Michael J.; Nold, Stephen C. Microbiology and Molecular Biology Reviews, Vol. 62, Issue 4 https://doi.org/10.1128/mmbr.62.4.1353-1370.1998	journal	December 1998
Obstacles of Multiplex Real-Time PCR for Bacterial 16S rDNA: Primer Specifity and DNA Decontamination ofTaqPolymerase Philipp, Sebastian; Huemer, Hartwig P.; Irschick, Eveline U. Transfusion Medicine and Hemotherapy, Vol. 37, Issue 1 https://doi.org/10.1159/000265571	journal	January 2010
Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method Wu, Jin-Ya; Jiang, Xiao-Tao; Jiang, Yun-Xia BMC Microbiology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2180-10-255	journal	January 2010
Accuracy and quality of massively parallel DNA pyrosequencing Huse, Susan M.; Huber, Julie A.; Morrison, Hilary G. Genome Biology, Vol. 8, Issue 7 https://doi.org/10.1186/gb-2007-8-7-r143	journal	January 2007
Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine Claesson, Marcus J.; O'Sullivan, Orla; Wang, Qiong PLoS ONE, Vol. 4, Issue 8 https://doi.org/10.1371/journal.pone.0006669	journal	August 2009
Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function Inskeep, William P.; Rusch, Douglas B.; Jay, Zackary J. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009773	journal	March 2010
Evaluating the latest high-throughput molecular techniques for the exploration of microbial gut communities Claesson, Marcus J.; O'Toole, Paul W. Gut Microbes, Vol. 1, Issue 4 https://doi.org/10.4161/gmic.1.4.12306	journal	July 2010

Cited By (14)

Metagenomic analysis of microbial community of an Amazonian geothermal spring in Peru Paul, Sujay; Cortez, Yolanda; Vera, Nadia Genomics Data, Vol. 9 https://doi.org/10.1016/j.gdata.2016.06.013	journal	September 2016
Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous ‘streamer’ community Beam, Jacob P.; Jay, Zackary J.; Schmid, Markus C. The ISME Journal, Vol. 10, Issue 1 https://doi.org/10.1038/ismej.2015.83	journal	July 2015
Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota Hua, Zheng-Shuang; Qu, Yan-Ni; Zhu, Qiyun Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05284-4	journal	July 2018
Evaluation of prokaryotic diversity of five hot springs in Eritrea Ghilamicael, Amanuel M.; Budambula, Nancy L. M.; Anami, Sylvester E. BMC Microbiology, Vol. 17, Issue 1 https://doi.org/10.1186/s12866-017-1113-4	journal	September 2017
Temperature-controlled thermophilic bacterial communities in hot springs of western Sichuan, China Tang, Jie; Liang, Yuanmei; Jiang, Dong BMC Microbiology, Vol. 18, Issue 1 https://doi.org/10.1186/s12866-018-1271-z	journal	October 2018
Metagenomics of an Alkaline Hot Spring in Galicia (Spain): Microbial Diversity Analysis and Screening for Novel Lipolytic Enzymes López-López, Olalla; Knapik, Kamila; Cerdán, Maria-Esperanza Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.01291	journal	November 2015
Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments Saxena, Rituja; Dhakan, Darshan B.; Mittal, Parul Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.02123	journal	January 2017
Abundant and Rare Microbial Biospheres Respond Differently to Environmental and Spatial Factors in Tibetan Hot Springs Zhang, Yanmin; Wu, Geng; Jiang, Hongchen Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02096	journal	September 2018
Global Microbiome Diversity Scaling in Hot Springs With DAR (Diversity-Area Relationship) Profiles Li, Lianwei; Ma, Zhanshan (Sam) Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00118	journal	February 2019
An introduction to the analysis of shotgun metagenomic data Sharpton, Thomas J. Frontiers in Plant Science, Vol. 5 https://doi.org/10.3389/fpls.2014.00209	journal	June 2014
Bacterial diversity analysis of Yumthang hot spring, North Sikkim, India by Illumina sequencing Panda, Amrita Kumari; Bisht, Satpal Singh; Kaushal, Bodh Raj Big Data Analytics, Vol. 2, Issue 1 https://doi.org/10.1186/s41044-017-0022-8	journal	August 2017
Seasonal variations in culturable archaea and their plant growth promoting attributes to predict their role in establishment of vegetation in Rann of Kutch Yadav, Ajar Nath; Gulati, Sneha; Sharma, Divya Biologia, Vol. 74, Issue 8 https://doi.org/10.2478/s11756-019-00259-2	journal	May 2019
Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing Chan, Chia Sing; Chan, Kok-Gan; Tay, Yea-Ling Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00177	journal	March 2015
Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community Szafranek-Nakonieczna, Anna; Pytlak, Anna; Grządziel, Jarosław International Journal of Molecular Sciences, Vol. 20, Issue 18 https://doi.org/10.3390/ijms20184415	journal	September 2019

Similar Records

Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

Journal Article · Wed Aug 06 00:00:00 EDT 2014 · PLoS ONE · OSTI ID:1627721

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

Journal Article · Thu Feb 28 23:00:00 EST 2013 · The ISME Journal, 7(3):622-634 · OSTI ID:1064570

A new symbiotic nanoarchaeote (Candidatus Nanoclepta minutus) and its host (Zestosphaera tikiterensis gen. nov., sp. nov.) from a New Zealand hot spring

Journal Article · Thu Aug 16 00:00:00 EDT 2018 · Systematic and Applied Microbiology · OSTI ID:1470848

Related Subjects

16S rRNA pyrosequencing
54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
Heart Lake Geyser Basin
Microbiology
Yellowstone National Park
alkaline hot spring
methanogenic community
phylogeny Thermus
thermoalkaline

Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park

Citation Formats

References (34)

Cited By (14)

Similar Records

Related Subjects