Several aspects of the proposal, which aims to expand open access, require serious discussion and, in some cases, a rethink.
Image credit: Dave Cutler (artist).
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Contributed by Norman R. Pace, December 21, 2004
Article Figures & SI
Figures
- Fig. 1.
Site locations. A map of Yellowstone National Park shows locations of hydrogen measurements indicated by site number (Tables 1 and 2). Boxed numbers identify sites with associated phylogenetic analyses.
- Fig. 2.
Cumulative rRNA gene analyses. (A) Distribution of sequences by phylogenetic group as identified with arb. Universal PCR primers (515F and 1391R) were used with environmental DNA templates from five hot springs, and resultant sequences were compiled for the assemblage. Five percent of the sequences are from one potentially new candidate bacterial division encountered in this study. (B) Distribution of archaeal sequences in three hot springs with two archaeal-specific PCR primer pairs. The majority, 77% of the sequences, are identified as crenarchaeotes. Eighteen percent fall within Euryarchaeota, and 5% fall within Korarchaeota. OPA-2, OPA-4, and OPA-Like represent environmental DNA sequences from a previous study of Obsidian Pool (16); FCG-1 represents sequences from marine/hydrothermal vent benthic archaea; and SEGMEG-1 represents sequences from deep South African mines.
- Fig. 3.
Bacterial rRNA gene clone libraries. Bacterial sequences (arb phylogenetic assignment) for five previously unexamined hot springs are shown as pie charts. At least two PCR primer pairs and as many as eight (Obsidian Pool Prime) were used to determine the compositions for each hot spring.
- Fig. 4.
Low- and high-sulfide communities compilation. (A) The phylogenetic distribution of rRNA gene sequences obtained from the two low-sulfide springs of this study (West Thumb Pool and Obsidian Pool Prime) combined with the five low-sulfide springs studied by Blank et al. in ref. 18 (Octopus Spring, Queens Laundry, Eclipse Geyser, Spindle Spring, and Boulder Spring). (B) The phylogenetic distribution of rRNA gene sequences obtained from the three high-sulfide springs in this study (Cinder Pool, Washburn Spring 1, and Washburn Spring 3).
- Fig. 5.
Results of thermodynamic models. Shown are the amounts of energy available from O2-consuming metabolic reactions, expressed in terms of available energy per mole of limiting O2 for comparative purposes. The available energy is shown for a range of hypothetical O2 concentrations because accurate O2 concentrations in hot waters are difficult to assess.
Tables
Location Site Temp., °C pH Eh, V D.O., mg/liter SSU* source Sulfide, μM Sulfate, μM H2, nM CH4, μM CO2, mM CnHn, ng/liter 2X Distilled Water (Control)† - 23 - 0 0 2.1 ± 0.00 0.0 ± 0.00 0.0 ± 0.00 0 Dragon Pool, (Norris Basin) 1 72 3.1 21 5.8 ND 2.9 ± 0.17 1.1 ± 0.14 22.5 ± 2.0 164 Well Y-7, Biscuit Basin 2 55 7 27 ND ND 3.8 ± 0.15 8.6 ± 1.10 2.7 ± 0.36 673 Yellowstone Lake 3 9 7 Several 0 ND 4.3 ± 0.00 0.1 ± 0.00 0.1 ± 0.00 20 Canary Spring, Mammoth 5 68 8.5 ND ND 11.0 ± 3.80 0.0 ± 0.00 8.1 ± 0.39 19 Octopus Spring Fall 2000 6 92 8.5 0.018‡ 0.92‡ 44 <0.47‡ 0.22‡ 15.0 ± 0.28 1.9 ± 0.15 1.5 ± 0.08 175 Summer 2001 92 8.5 14.0 ± 0.25 1.7 ± 0.15 1.5 ± 0.08 183 West Thumb Pool 7 89 7.3 This study 0 0.25 15.5 ± 0.00 7.8 ± 0.41 7.9 ± 0.27 524 Washburn Spring #3 8 86 6.2 0.223§ ND§ This study 167§ 44§ 18.5 ± 0.60 5.8 ± 0.30 9.75 ± 0.54 436 Queen's Laundry Fall 2000 9 89 8 18 2.2¶ 0.042¶ 28.0 ± 0.59 0.73 ± 0.03 1.7 ± 0.21 604 Summer 2001 89 8 30.4 ± 0.40 0.95 ± 0.04 2.2 ± 0.27 525 Cinder Pool Fall 2000 11 88 4.2 0.022§ 0.5§ This study 47§ 1.0§ 77.6 ± 27.8 1.2 ± 0.21 16.6 ± 3.80 241 Summer 2001 88 4.3 13.7 ± 0.23 1.85 ± 0.18 24.5 ± 3.18 362 Washburn Spring 1 12 76 6.7 0.067§ 0.3§ This study 235§ 32.5§ 103.1 ± 1.10 8.3 ± 0.36 17.2 ± 0.40 436 Obsidian Pool 13 80 6.5 19 17.6 0.33 133.2 ± 5.80 0.1 ± 0.00 14.9 ± 0.66 63 Obsidian Pool Prime 14 74 5.7 This study 17.6 0.52 325.3 ± 40.0 0.1 ± 0.01 12.8 ± 0.13 21 -
D.O., dissolved oxygen; Temp., temperature; ND, not determined; CnHn, totaled ethane, ethene, propane, propene, n-butane, isobutene.
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↵ * Small subunit rRNA gene analysis
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↵ † We take these values as baseline for assays
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↵ ‡ All values are from ref. 13
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↵ § All values are from ref. 12
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↵ ¶ Data are from ref. 53
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Location Site Al, μg/liter As, μg/liter Cl, mg/liter Li, μg/liter Mn, μg/liter Fe(II), mg/liter Octopus Spring* 6 512 1,380 262 3,420 3.4 0.0014† West Thumb Pool 7 66 1,265 153 1,384 13.2 DL Washburn Spring 3‡ 8 68,000 <1 6.7 <70 340 65 Queen's Laundry 9 282 1,313 239 1,996 0.87 DL Cinder Pool‡ 11 1,130 2,400 601 4,700 <6 0.088 Washburn Spring 1‡ 12 34,000 <1 <10 50 510 23.6 Obsidian Pool 13 349 DL 25 199 427 0.11 Obsidian Pool Prime 14 206 526 305 1,171 50 0.26
Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem
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