scholarly journals Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park

2015 ◽  
Vol 81 (17) ◽  
pp. 5907-5916 ◽  
Author(s):  
Z. J. Jay ◽  
J. P. Beam ◽  
A. Dohnalkova ◽  
R. Lohmayer ◽  
B. Bodle ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Elemental Sulfur ◽  
De Novo ◽  
Hot Spring ◽  
Content Type ◽  
Physiological Attributes ◽  
And Function ◽  
Metagenome Sequence

ABSTRACTThermoproteales(phylumCrenarchaeota) populations are abundant in high-temperature (>70°C) environments of Yellowstone National Park (YNP) and are important in mediating the biogeochemical cycles of sulfur, arsenic, and carbon. The objectives of this study were to determine the specific physiological attributes of the isolatePyrobaculum yellowstonensisstrain WP30, which was obtained from an elemental sulfur sediment (Joseph's Coat Hot Spring [JCHS], 80°C, pH 6.1, 135 μM As) and relate this organism to geochemical processes occurringin situ. Strain WP30 is a chemoorganoheterotroph and requires elemental sulfur and/or arsenate as an electron acceptor. Growth in the presence of elemental sulfur and arsenate resulted in the formation of thioarsenates and polysulfides. The complete genome of this organism was sequenced (1.99 Mb, 58% G+C content), revealing numerous metabolic pathways for the degradation of carbohydrates, amino acids, and lipids. Multiple dimethyl sulfoxide-molybdopterin (DMSO-MPT) oxidoreductase genes, which are implicated in the reduction of sulfur and arsenic, were identified. Pathways for thede novosynthesis of nearly all required cofactors and metabolites were identified. The comparative genomics ofP. yellowstonensisand the assembled metagenome sequence from JCHS showed that this organism is highly related (∼95% average nucleotide sequence identity) toin situpopulations. The physiological attributes and metabolic capabilities ofP. yellowstonensisprovide an important foundation for developing an understanding of the distribution and function of these populations in YNP.

scholarly journals Stable Isotope Probing for Microbial Iron Reduction in Chocolate Pots Hot Spring, Yellowstone National Park

2018 ◽  
Vol 84 (11) ◽  
Author(s):  
Nathaniel W. Fortney ◽  
Shaomei He ◽  
Ajinkya Kulkarni ◽  
Michael W. Friedrich ◽  
Charlotte Holz ◽  
...  
Keyword(s):  
Microbial Community ◽  
Stable Isotope ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Spring ◽  
Redox Cycling ◽  
Stable Isotope Probing ◽  
Content Type ◽  
Insight Into

ABSTRACTChocolate Pots hot springs (CP) is a circumneutral-pH Fe-rich geothermal feature located in Yellowstone National Park. Previous Fe(III)-reducing enrichment culture studies with CP sediments identified close relatives of known dissimilatory Fe(III)-reducing bacterial (FeRB) taxa, includingGeobacterandMelioribacter. However, the abundances and activities of such organisms in the native microbial community are unknown. Here, we used stable isotope probing experiments combined with 16S rRNA gene amplicon and shotgun metagenomic sequencing to gain an understanding of thein situFe(III)-reducing microbial community at CP. Fe-Si oxide precipitates collected near the hot spring vent were incubated with unlabeled and13C-labeled acetate to target active FeRB. We searched reconstructed genomes for homologs of genes involved in known extracellular electron transfer (EET) systems to identify the taxa involved in Fe redox transformations. Known FeRB taxa containing putative EET systems (Geobacter,Ignavibacteria) increased in abundance under acetate-amended conditions, whereas genomes related toIgnavibacteriumandThermodesulfovibriothat contained putative EET systems were recovered from incubations without electron donor. Our results suggest that FeRB play an active role in Fe redox cycling within Fe-Si oxide-rich deposits located at the hot spring vent.IMPORTANCEThe identification of past near-surface hydrothermal environments on Mars emphasizes the importance of using modern Earth environments, such as CP, to gain insight into potential Fe-based microbial life on other rocky worlds, as well as ancient Fe-rich Earth ecosystems. By combining stable carbon isotope probing techniques and DNA sequencing technology, we gained insight into the pathways of microbial Fe redox cycling at CP. The results suggest that microbial Fe(III) oxide reduction is prominentin situ, with important implications for the generation of geochemical and stable Fe isotopic signatures of microbial Fe redox metabolism within Fe-rich circumneutral-pH thermal spring environments on Earth and Mars.

scholarly journals Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

2015 ◽  
Vol 81 (22) ◽  
pp. 7860-7868 ◽  
Author(s):  
Jacob H. Munson-McGee ◽  
Erin K. Field ◽  
Mary Bateson ◽  
Colleen Rooney ◽  
Ramunas Stepanauskas ◽  
...  
Keyword(s):  
Single Cell ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Hot Spring ◽  
Genome Comparison ◽  
Fish Analysis ◽  
Content Type ◽  
Cell Genome ◽  
Single Cell Genome

ABSTRACTNanoarchaeotaare obligate symbionts with reduced genomes first described from marine thermal vent environments. Here, both community metagenomics and single-cell analysis revealed the presence ofNanoarchaeotain high-temperature (∼90°C), acidic (pH ≈ 2.5 to 3.0) hot springs in Yellowstone National Park (YNP) (United States). Single-cell genome analysis of two cells resulted in two nearly identical genomes, with an estimated full length of 650 kbp. Genome comparison showed that these two cells are more closely related to the recently proposedNanobsidianus stetterifrom a more neutral YNP hot spring than to the marineNanoarchaeum equitans. Single-cell and catalyzed reporter deposition-fluorescencein situhybridization (CARD-FISH) analysis of environmental hot spring samples identified the host of the YNPNanoarchaeotaas aSulfolobalesspecies known to inhabit the hot springs. Furthermore, we demonstrate thatNanoarchaeotaare widespread in acidic to near neutral hot springs in YNP. An integrated viral sequence was also found within oneNanoarchaeotasingle-cell genome and further analysis of the purified viral fraction from environmental samples indicates that this is likely a virus replicating within the YNPNanoarchaeota.

scholarly journals Thermosinus carboxydivorans gen. nov., sp. nov., a new anaerobic, thermophilic, carbon-monoxide-oxidizing, hydrogenogenic bacterium from a hot pool of Yellowstone National Park

2004 ◽  
Vol 54 (6) ◽  
pp. 2353-2359 ◽  
Author(s):  
Tatyana G. Sokolova ◽  
Juan M. González ◽  
Nadezhda A. Kostrikina ◽  
Nikolai A. Chernyh ◽  
Tatiana V. Slepova ◽  
...  
Keyword(s):  
Yeast Extract ◽  
Yellowstone National Park ◽  
Type Strain ◽  
National Park ◽  
Elemental Sulfur ◽  
Ferric Iron ◽  
Hot Spring ◽  
Wall Structure ◽  
Elemental Selenium ◽  
Rrna Gene

A new anaerobic, thermophilic, facultatively carboxydotrophic bacterium, strain Nor1T, was isolated from a hot spring at Norris Basin, Yellowstone National Park. Cells of strain Nor1T were curved motile rods with a length of 2·6–3 μm, a width of about 0·5 μm and lateral flagellation. The cell wall structure was of the Gram-negative type. Strain Nor1T was thermophilic (temperature range for growth was 40–68 °C, with an optimum at 60 °C) and neutrophilic (pH range for growth was 6·5–7·6, with an optimum at 6·8–7·0). It grew chemolithotrophically on CO (generation time, 1·15 h), producing equimolar quantities of H2 and CO2 according to the equation CO+H2O→CO2+H2. During growth on CO in the presence of ferric citrate or amorphous ferric iron oxide, strain Nor1T reduced ferric iron but produced H2 and CO2 at a ratio close to 1 : 1, and growth stimulation was slight. Growth on CO in the presence of sodium selenite was accompanied by precipitation of elemental selenium. Elemental sulfur, thiosulfate, sulfate and nitrate did not stimulate growth of strain Nor1T on CO and none of these chemicals was reduced. Strain Nor1T was able to grow on glucose, sucrose, lactose, arabinose, maltose, fructose, xylose and pyruvate, but not on cellobiose, galactose, peptone, yeast extract, lactate, acetate, formate, ethanol, methanol or sodium citrate. During glucose fermentation, acetate, H2 and CO2 were produced. Thiosulfate was found to enhance the growth rate and cell yield of strain Nor1T when it was grown on glucose, sucrose or lactose; in this case, acetate, H2S and CO2 were produced. In the presence of thiosulfate or ferric iron, strain Nor1T was also able to grow on yeast extract. Lactate, acetate, formate and H2 were not utilized either in the absence or in the presence of ferric iron, thiosulfate, sulfate, sulfite, elemental sulfur or nitrate. Growth was completely inhibited by penicillin, ampicillin, streptomycin, kanamycin and neomycin. The DNA G+C content of the strain was 51·7±1 mol%. Analysis of the 16S rRNA gene sequence revealed that strain Nor1T belongs to the Bacillus–Clostridium phylum of the Gram-positive bacteria. On the basis of the studied phenotypic and phylogenetic features, we propose that strain Nor1T be assigned to a new genus, Thermosinus gen. nov. The type species is Thermosinus carboxydivorans sp. nov. (type strain, Nor1T=DSM 14886T=VKM B-2281T).

Evidence for high-temperature in situ nifH transcription in an alkaline hot spring of Lower Geyser Basin, Yellowstone National Park

2012 ◽  
Vol 14 (5) ◽  
pp. 1272-1283 ◽  
Author(s):  
Sara T. Loiacono ◽  
D'Arcy R. Meyer-Dombard ◽  
Jeff R. Havig ◽  
Amisha T. Poret-Peterson ◽  
Hilairy E. Hartnett ◽  
...  
Keyword(s):  
High Temperature ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Spring

scholarly journals Predominant Acidilobus-Like Populations from Geothermal Environments in Yellowstone National Park Exhibit Similar Metabolic Potential in Different Hypoxic Microbial Communities

2013 ◽  
Vol 80 (1) ◽  
pp. 294-305 ◽  
Author(s):  
Z. J. Jay ◽  
D. B. Rusch ◽  
S. G. Tringe ◽  
C. Bailey ◽  
R. M. Jennings ◽  
...  
Keyword(s):  
High Temperature ◽  
Yellowstone National Park ◽  
National Park ◽  
De Novo ◽  
Rrna Gene ◽  
Acid Fermentation ◽  
Metabolic Potential ◽  
Content Type ◽  
Protein Encoding ◽  
Encoding Genes

ABSTRACTHigh-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions.Acidilobusspp. (orderDesulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of theThermoprotealesandSulfolobales. Consequently, the primary goals of the current study were to analyze and compare replicatede novosequence assemblies ofAcidilobus-like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populationsin situ. De novoassemblies of the highly similarAcidilobus-like populations (>99% 16S rRNA gene identity) represent near-complete consensus genomes based on an inventory of single-copy genes, deduced metabolic potential, and assembly statistics generated across sites. Functional analysis of coding sequences and confirmation of gene transcription byAcidilobus-like populations provide evidence that they are primarily chemoorganoheterotrophs, generating acetyl coenzyme A (acetyl-CoA) via the degradation of carbohydrates, lipids, and proteins, and auxotrophic with respect to several external vitamins, cofactors, and metabolites. No obvious pathways or protein-encoding genes responsible for the dissimilatory reduction of sulfur were identified. The presence of a formate dehydrogenase (Fdh) and other protein-encoding genes involved in mixed-acid fermentation supports the hypothesis thatAcidilobusspp. function as degraders of complex organic constituents in high-temperature, mildly acidic, hypoxic geothermal systems.

scholarly journals Complete Genome Sequence of Caloramator sp. Strain E03, a Novel Ethanologenic, Thermophilic, Obligately Anaerobic Bacterium

2019 ◽  
Vol 8 (32) ◽  
Author(s):  
E. Anne Hatmaker ◽  
Dawn M. Klingeman ◽  
Roman K. Martin ◽  
Adam M. Guss ◽  
James G. Elkins
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Yellowstone National Park ◽  
Complete Genome ◽  
National Park ◽  
Anaerobic Bacterium ◽  
Hot Spring ◽  
Content Type ◽  
Obligately Anaerobic

Here, we report the complete genome sequence of Caloramator sp. strain E03, an anaerobic thermophile that was isolated from a hot spring within the Rabbit Creek area of Yellowstone National Park. The assembly contains a single 2,984,770-bp contig with a G+C content of 31.3% and is predicted to encode 2,678 proteins.

scholarly journals Archaeal and Bacterial Glycerol Dialkyl Glycerol Tetraether Lipids in Hot Springs of Yellowstone National Park

2007 ◽  
Vol 73 (19) ◽  
pp. 6181-6191 ◽  
Author(s):  
Stefan Schouten ◽  
Marcel T. J. van der Meer ◽  
Ellen C. Hopmans ◽  
W. Irene C. Rijpstra ◽  
Anna-Louise Reysenbach ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Membrane Lipids ◽  
Hot Spring ◽  
Ph Values ◽  
Group I ◽  
Low Concentrations ◽  
Tetraether Lipids

ABSTRACTGlycerol dialkyl glycerol tetraethers (GDGTs) are core membrane lipids originally thought to be produced mainly by (hyper)thermophilic archaea. Environmental screening of low-temperature environments showed, however, the abundant presence of structurally diverse GDGTs from both bacterial and archaeal sources. In this study, we examined the occurrences and distribution of GDGTs in hot spring environments in Yellowstone National Park with high temperatures (47 to 83°C) and mostly neutral to alkaline pHs. GDGTs with 0 to 4 cyclopentane moieties were dominant in all samples and are likely derived from both (hyper)thermophilicCrenarchaeotaandEuryarchaeota. GDGTs with 4 to 8 cyclopentane moieties, likely derived from the crenarchaeotal orderSulfolobalesand the euryarchaeotal orderThermoplasmatales, are usually present in much lower abundance, consistent with the relatively high pH values of the hot springs. The relative abundances of cyclopentane-containing GDGTs did not correlate with in situ temperature and pH, suggesting that other environmental and possibly genetic factors play a role as well. Crenarchaeol, a biomarker thought to be specific for nonthermophilic group ICrenarchaeota, was also found in most hot springs, though in relatively low concentrations, i.e., <5% of total GDGTs. Its abundance did not correlate with temperature, as has been reported previously. Instead, the cooccurrence of relatively abundant nonisoprenoid GDGTs thought to be derived from soil bacteria suggests a predominantly allochthonous source for crenarchaeol in these hot spring environments. Finally, the distribution of bacterial branched GDGTs suggests that they may be derived from the geothermally heated soils surrounding the hot springs.

scholarly journals Temporal and Seasonal Variations of the Hot Spring Basin Hydrothermal System, Yellowstone National Park, USA

2013 ◽  
Vol 5 (12) ◽  
pp. 6587-6610 ◽  
Author(s):  
Cheryl Jaworowski ◽  
Henry Heasler ◽  
Christopher Neale ◽  
Sivarajan Saravanan ◽  
Ashish Masih
Keyword(s):  
Seasonal Variations ◽  
Hydrothermal System ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Spring

scholarly journals Whole-Genome Sequence of a Unique Elioraea Species Strain Isolated from a Yellowstone National Park Hot Spring

2019 ◽  
Vol 8 (44) ◽  
Author(s):  
Sydney Robertson ◽  
Robert F. Ramaley ◽  
Terry Meyer ◽  
John A. Kyndt
Keyword(s):  
New Species ◽  
Genome Sequence ◽  
Yellowstone National Park ◽  
National Park ◽  
Photosynthetic Bacteria ◽  
Hot Spring ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Anoxygenic Photosynthetic Bacteria

The genus Elioraea has only one species characterized microbiologically and two genomes sequenced. We have sequenced the genome of a unique Elioraea strain isolated from Yellowstone National Park and found it to be a distinct new species. Elioraea is suggested to be a member of the aerobic anoxygenic photosynthetic bacteria.

Sign in / Sign up

Export Citation Format

Share Document