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 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 Characterizing and Evaluating the Diverse Microbial Communities and Their Mercury Resistance Potential from Hot Spring Sites Representing Gradients in Temperature and pH in Yellowstone National Park

2020 ◽  
Vol 1 (1) ◽  
Author(s):  
Yelizaveta Rassadkina ◽  
Spencer Roth ◽  
Tamar Barkay
Keyword(s):  
Microbial Communities ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Hot Spring ◽  
Thermophilic Bacteria ◽  
Sequence Data ◽  
Mercury Resistance ◽  
Sample Site ◽  
Microorganism Community

Yellowstone National Park is home to many different hot springs, lakes, geysers, pools, and basins that range in pH, chemical composition, and temperature. These different environmental variations provide a broad range of conditions that select and grow diverse communities of microorganisms. In this study, we collected samples from geochemically diverse lakes and springs to characterize the microbial communities present through 16S rRNA metagenomic analysis. This information was then used to observe how various microorganisms survive in high mercury environments. The results show the presence of microorganisms that have been studied in previous literature. The results also depict gradients of microorganisms including thermophilic bacteria and archaea that exist in these extreme environments. In addition, beta diversity analyses of the sequence data showed site clustering based primarily on temperature instead of pH or sample site, suggesting that while pH, temperature, and sample site were all shown to be significant, temperature is the strongest factor driving microorganism community development. While it is important to characterize the microorganism community present, it is also important to understand how this community functions as a result of its selection. Along with looking at community composition, genomic material was tested to see if it contained mercury methylating (hgcA) or mercury reducing (merA) genes. Out of 22 samples, three of them were observed to have merA genes, while no samples had hgcA genes. These results indicate that microorganisms in Mustard and Nymph Springs may use mercury reduction. Understanding how microorganisms survive in environments with high concentrations of toxic pollutants is crucial because it can be used as a model to better understand mechanisms of resistance and the biogeochemical cycle, as well as for bioremediation and other solutions to anthropogenic problems.

scholarly journals Three Draft Single-Cell Genome Sequences of Novel SAR324 Strains Isolated from the Abyssopelagic Southern Ocean

2021 ◽  
Vol 10 (39) ◽  
Author(s):  
Diego J. Castillo ◽  
Marc W. Van Goethem ◽  
Thulani P. Makhalanyane
Keyword(s):  
Southern Ocean ◽  
Single Cell ◽  
Marine Environments ◽  
Genome Sequences ◽  
Content Type ◽  
Cell Genome ◽  
Indian Sector ◽  
Single Cell Genome

SAR324 is a ubiquitous and phylogenetically distinct clade of Deltaproteobacteria in marine environments. Here, we present three single-cell amplified genome sequences from the SAR324 lineage, obtained from the abyssopelagic zone of the Indian sector of the Southern Ocean.

scholarly journals Draft Genome Sequence of Methanothermobacter thermautotrophicus WHS, a Thermophilic Hydrogenotrophic Methanogen from Washburn Hot Springs in Yellowstone National Park, USA

2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Luke J. McKay ◽  
Korinne B. Klingelsmith ◽  
Adam M. Deutschbauer ◽  
William P. Inskeep ◽  
Matthew W. Fields
Keyword(s):  
Carbon Dioxide ◽  
Genome Sequence ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Hydrogenotrophic Methanogen ◽  
Methanothermobacter Thermautotrophicus

ABSTRACT A thermophilic methanogen was enriched in coculture from Washburn Hot Springs (Yellowstone National Park, USA), grown on carbon dioxide and hydrogen, and subsequently sequenced. The reconstructed 1.65-Mb genome sequence for Methanothermobacter thermautotrophicus WHS contributes to our understanding of hydrogenotrophic, CO2-reducing methanogenesis in geothermal ecosystems.

scholarly journals A Single-Cell Genome for Thiovulum sp.

2012 ◽  
Vol 78 (24) ◽  
pp. 8555-8563 ◽  
Author(s):  
Ian P. G. Marshall ◽  
Paul C. Blainey ◽  
Alfred M. Spormann ◽  
Stephen R. Quake
Keyword(s):  
Single Cell ◽  
Multiple Displacement Amplification ◽  
Bacterial Cells ◽  
Content Type ◽  
Swimming Motility ◽  
Elkhorn Slough ◽  
Naturally Occurring ◽  
Wide Range ◽  
Cell Genome ◽  
Single Cell Genome

ABSTRACTWe determined a significant fraction of the genome sequence of a representative ofThiovulum, the uncultivated genus of colorless sulfurEpsilonproteobacteria, by analyzing the genome sequences of four individual cells collected from phototrophic mats from Elkhorn Slough, California. These cells were isolated utilizing a microfluidic laser-tweezing system, and their genomes were amplified by multiple-displacement amplification prior to sequencing.Thiovulumis a gradient bacterium found at oxic-anoxic marine interfaces and noted for its distinctive morphology and rapid swimming motility. The genomic sequences of the four individual cells were assembled into a composite genome consisting of 221 contigs covering 2.083 Mb including 2,162 genes. This single-cell genome represents a genomic view of the physiological capabilities of isolatedThiovulumcells.Thiovulumis the second-fastest bacterium ever observed, swimming at 615 μm/s, and this genome shows that this rapid swimming motility is a result of a standard flagellar machinery that has been extensively characterized in other bacteria. This suggests that standard flagella are capable of propelling bacterial cells at speeds much faster than typically thought. Analysis of the genome suggests that naturally occurringThiovulumpopulations are more diverse than previously recognized and that studies performed in the past probably address a wide range of unrecognized genotypic and phenotypic diversities ofThiovulum. The genome presented in this article provides a basis for future isolation-independent studies ofThiovulum, where single-cell and metagenomic tools can be used to differentiate between differentThiovulumgenotypes.

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 Draft Genome Sequence of Bacillus altitudinis YNP4-TSU, Isolated from Yellowstone National Park

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Joshua A. OHair ◽  
Hui Li ◽  
Santosh Thapa ◽  
Matthew Scholz ◽  
Suping Zhou
Keyword(s):  
Genome Sequence ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Bacillus Altitudinis

ABSTRACT Undisturbed hot springs inside Yellowstone National Park remain a dynamic biome for novel cellulolytic thermophiles. We report here the draft genome sequence of one of these isolates, Bacillus altitudinis YNP4-TSU.

scholarly journals Molecular Characterization of Novel Red Green Nonsulfur Bacteria from Five Distinct Hot Spring Communities in Yellowstone National Park

2002 ◽  
Vol 68 (1) ◽  
pp. 346-355 ◽  
Author(s):  
Sarah M. Boomer ◽  
Daniel P. Lodge ◽  
Bryan E. Dutton ◽  
Beverly Pierson
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Hot Spring ◽  
Site Specificity ◽  
Absorption Bands ◽  
Specific Primers ◽  
In Vivo Absorption

ABSTRACT We characterized and compared five geographically isolated hot springs with distinct red-layer communities in Yellowstone National Park. Individual red-layer communities were observed to thrive in temperatures ranging from 35 to 60°C and at pH 7 to 9. All communities were dominated by red filamentous bacteria and contained bacteriochlorophyll a (Bchl a), suggesting that they represented novel green nonsulfur (GNS) bacteria. The in vivo absorption spectra of individual sites were different, with two sites showing unusual Bchl a protein absorption bands beyond 900 nm. We prepared and analyzed 16S rRNA libraries from all of these sites by using a combination of general bacterial primers and new GNS-specific primers described here. These studies confirmed the presence of novel GNS-like bacteria in all five communities. All GNS-like clones were most similar to Roseiflexus castenholzii, a red filamentous bacterium from Japan that also contains only Bchl a. Phylogenies constructed by using GNS-like clones from Yellowstone red-layer communities suggest the presence of a moderately diverse new “red” cluster within the GNS lineage. Within this cluster, at least two well-supported subclusters emerged: YRL-A was most similar to Roseiflexus and YRL-B appeared to be novel, containing no known isolates. While these patterns showed some site specificity, they did not correlate with observed Bchl a spectrum differences or obvious features of the habitat.

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.

Sign in / Sign up

Export Citation Format

Share Document