scholarly journals Microbial Composition of Near-Boiling Silica-Depositing Thermal Springs throughout Yellowstone National Park

2002 ◽  
Vol 68 (10) ◽  
pp. 5123-5135 ◽  
Author(s):  
Carrine E. Blank ◽  
Sherry L. Cady ◽  
Norman R. Pace
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Hydrogen Oxidation ◽  
Large Subunit ◽  
Microbial Community Composition ◽  
Pcr Amplification ◽  
Small Subunit ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Microbial Composition

ABSTRACT The extent of hyperthermophilic microbial diversity associated with siliceous sinter (geyserite) was characterized in seven near-boiling silica-depositing springs throughout Yellowstone National Park using environmental PCR amplification of small-subunit rRNA genes (SSU rDNA), large-subunit rDNA, and the internal transcribed spacer (ITS). We found that Thermocrinis ruber, a member of the order Aquificales, is ubiquitous, an indication that primary production in these springs is driven by hydrogen oxidation. Several other lineages with no known close relatives were identified that branch among the hyperthermophilic bacteria. Although they all branch deep in the bacterial tree, the precise phylogenetic placement of many of these lineages is unresolved at this time. While some springs contained a fair amount of phylogenetic diversity, others did not. Within the same spring, communities in the subaqueous environment were not appreciably different than those in the splash zone at the edge of the pool, although a greater number of phylotypes was found along the pool's edge. Also, microbial community composition appeared to have little correlation with the type of sinter morphology. The number of cell morphotypes identified by fluorescence in situ hybridization and scanning electron microscopy was greater than the number of phylotypes in SSU clone libraries. Despite little variation in Thermocrinis ruber SSU sequences, abundant variation was found in the hypervariable ITS region. The distribution of ITS sequence types appeared to be correlated with distinct morphotypes of Thermocrinis ruber in different pools. Therefore, species- or subspecies-level divergences are present but not detectable in highly conserved SSU sequences.

scholarly journals Legionella Species Diversity in an Acidic Biofilm Community in Yellowstone National Park

2005 ◽  
Vol 71 (1) ◽  
pp. 507-511 ◽  
Author(s):  
Kathy B. Sheehan ◽  
Joan M. Henson ◽  
Michael J. Ferris
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Pcr Amplification ◽  
18S Rrna Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Thermal Gradients ◽  
Legionella Species ◽  
Legionella Micdadei

ABSTRACT Legionella species are frequently detected in aquatic environments, but their occurrence in extreme, acidic, geothermal habitats has not been explored with cultivation-independent methods. We investigated a predominately eukaryotic algal mat community in a pH 2.7 geothermal stream in Yellowstone National Park for the presence of Legionella and potential host amoebae. Our analyses, using PCR amplification with Legionella-specific primers targeting 16S rRNA genes, detected four known Legionella species, as well as Legionella sequences from species that are not represented in sequence databases, in mat samples and cultivated isolates. The nonrandom occurrence of sequences detected at lower (30�C) and higher (35 to 38�C) temperatures suggests that natural thermal gradients in the stream influence Legionella species distributions in this mat community. We detected only one sequence, Legionella micdadei, from cultivated isolates. We cultured and sequenced partial 18S rRNA gene regions from two potential hosts, Acanthamoeba and Euglena species.

scholarly journals Influence of Sulfide and Temperature on Species Composition and Community Structure of Hot Spring Microbial Mats

2000 ◽  
Vol 66 (7) ◽  
pp. 2835-2841 ◽  
Author(s):  
Sigurlaug Skirnisdottir ◽  
Gudmundur O. Hreggvidsson ◽  
Sigridur Hj�rleifsdottir ◽  
Viggo T. Marteinsson ◽  
Solveig K. Petursdottir ◽  
...  
Keyword(s):  
Microbial Mats ◽  
Hot Springs ◽  
Hot Spring ◽  
Pcr Amplification ◽  
Small Subunit ◽  
Rrna Genes ◽  
Published Data ◽  
Sulfide Concentration ◽  
Small Subunit Rrna ◽  
High Sulfide

ABSTRACT In solfataric fields in southwestern Iceland, neutral and sulfide-rich hot springs are characterized by thick bacterial mats at 60 to 80�C that are white or yellow from precipitated sulfur (sulfur mats). In low-sulfide hot springs in the same area, grey or pink streamers are formed at 80 to 90�C, and a Chloroflexusmat is formed at 65 to 70�C. We have studied the microbial diversity of one sulfur mat (high-sulfide) hot spring and oneChloroflexus mat (low-sulfide) hot spring by cloning and sequencing of small-subunit rRNA genes obtained by PCR amplification from mat DNA. Using 98% sequence identity as a cutoff value, a total of 14 bacterial operational taxonomic units (OTUs) and 5 archaeal OTUs were detected in the sulfur mat; 18 bacterial OTUs were detected in theChloroflexus mat. Although representatives of novel divisions were found, the majority of the sequences were >95% related to currently known sequences. The molecular diversity analysis showed that Chloroflexus was the dominant mat organism in the low-sulfide spring (1 mg liter−1) below 70�C, whereasAquificales were dominant in the high-sulfide spring (12 mg liter−1) at the same temperature. Comparison of the present data to published data indicated that there is a relationship between mat type and composition of Aquificales on the one hand and temperature and sulfide concentration on the other hand.

Analysis of the ITS region and partial ssu and lsu rRNA genes ofBlastocystisandProteromonas lacertae

Parasitology ◽  
2005 ◽  
Vol 131 (2) ◽  
pp. 187-196 ◽  
Author(s):  
J. D. HOEVERS ◽  
K. F. SNOWDEN
Keyword(s):  
Large Subunit ◽  
Geographic Origin ◽  
Its Region ◽  
Small Subunit ◽  
Rdna Sequence ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Chattonella Marina ◽  
Internal Transcribed Spacer Region ◽  
Cylindrotheca Closterium

Blastocystisis a common single-celled enteric parasite found in a large variety of hosts. Recent molecular analysis supports the concept that this eukaryotic organism is a stramenopile most closely related toProteromonas lacertae, a parasite of reptiles. In this study, the internal transcribed spacer region, partial small subunit rRNA and large subunit rRNA genes from 7Blastocystisisolates (5 human, 1 pig and 1 sheep), and aProteromonas lacertaeisolate were amplified by PCR, cloned and sequenced.Blastocystiswas found to be a typical eukaryote with both ITS1 and ITS2 regions present. Phylogenetic analysis based on the entire PCR amplicon revealed that theBlastocystisisolates did not segregate according to host or geographic origin. The highest sequence identities with the conservedBlastocystis5·8S rDNA sequence were with the stramenopilesFibrocapsa japonica,Chattonella marina,Cylindrotheca closteriumandHyphochytrium catenoides. The most parsimonious tree based on the 5·8S rDNA sequence fromP. lacertae, 11 other stramenopiles, 2 fungi, 3 algae and 3 alveolates showedBlastocystispositioned within the stramenopiles, withP. lacertaeas its closest relative. This work therefore supports the hypothesis thatBlastocystisis most closely related toP. lacertae, and that it should be regarded as an unusual stramenopile.

scholarly journals Caldicellulosiruptor obsidiansis sp. nov., an Anaerobic, Extremely Thermophilic, Cellulolytic Bacterium Isolated from Obsidian Pool, Yellowstone National Park

2009 ◽  
Vol 76 (4) ◽  
pp. 1014-1020 ◽  
Author(s):  
Scott D. Hamilton-Brehm ◽  
Jennifer J. Mosher ◽  
Tatiana Vishnivetskaya ◽  
Mircea Podar ◽  
Sue Carroll ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Optimal Growth ◽  
Small Subunit ◽  
Rrna Gene ◽  
Cellulolytic Bacterium ◽  
Small Subunit Rrna ◽  
Phenotypic Properties ◽  
Fermentative Growth ◽  
Ph Range

ABSTRACT A novel, obligately anaerobic, extremely thermophilic, cellulolytic bacterium, designated OB47T, was isolated from Obsidian Pool, Yellowstone National Park, WY. The isolate was a nonmotile, non-spore-forming, Gram-positive rod approximately 2 μm long by 0.2 μm wide and grew at temperatures between 55 and 85°C, with the optimum at 78°C. The pH range for growth was 6.0 to 8.0, with values of near 7.0 being optimal. Growth on cellobiose produced the fastest specific growth rate at 0.75 h−1. The organism also displayed fermentative growth on glucose, maltose, arabinose, fructose, starch, lactose, mannose, sucrose, galactose, xylose, arabinogalactan, Avicel, xylan, filter paper, processed cardboard, pectin, dilute acid-pretreated switchgrass, and Populus. OB47T was unable to grow on mannitol, fucose, lignin, Gelrite, acetate, glycerol, ribose, sorbitol, carboxymethylcellulose, and casein. Yeast extract stimulated growth, and thiosulfate, sulfate, nitrate, and sulfur were not reduced. Fermentation end products were mainly acetate, H2, and CO2, although lactate and ethanol were produced in 5-liter batch fermentations. The G+C content of the DNA was 35 mol%, and sequence analysis of the small subunit rRNA gene placed OB47T within the genus Caldicellulosiruptor. Based on its phylogenetic and phenotypic properties, the isolate is proposed to be designated Caldicellulosiruptor obsidiansis sp. nov. and OB47 is the type strain (ATCC BAA-2073).

scholarly journals Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring

1998 ◽  
Vol 180 (2) ◽  
pp. 366-376 ◽  
Author(s):  
Philip Hugenholtz ◽  
Christian Pitulle ◽  
Karen L. Hershberger ◽  
Norman R. Pace
Keyword(s):  
Bacterial Diversity ◽  
Hot Spring ◽  
Hydrogen Oxidation ◽  
Small Subunit ◽  
Rrna Genes ◽  
Universal Primers ◽  
Small Subunit Rrna ◽  
Rdna Sequences ◽  
Culture Independent ◽  
Sequence Types

ABSTRACT A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OP), a Yellowstone National Park hot spring previously shown to contain remarkable archaeal diversity (S. M. Barns, R. E. Fundyga, M. W. Jeffries, and N. R. Page, Proc. Natl. Acad. Sci. USA 91:1609–1613, 1994). Small-subunit rRNA genes (rDNA) were amplified directly from OP sediment DNA by PCR with universally conserved orBacteria-specific rDNA primers and cloned. Unique rDNA types among >300 clones were identified by restriction fragment length polymorphism, and 122 representative rDNA sequences were determined. These were found to represent 54 distinct bacterial sequence types or clusters (≥98% identity) of sequences. A majority (70%) of the sequence types were affiliated with 14 previously recognized bacterial divisions (main phyla; kingdoms); 30% were unaffiliated with recognized bacterial divisions. The unaffiliated sequence types (represented by 38 sequences) nominally comprise 12 novel, division level lineages termed candidate divisions. Several OP sequences were nearly identical to those of cultivated chemolithotrophic thermophiles, including the hydrogen-oxidizing Calderobacterium and the sulfate reducers Thermodesulfovibrio andThermodesulfobacterium, or belonged to monophyletic assemblages recognized for a particular type of metabolism, such as the hydrogen-oxidizing Aquificales and the sulfate-reducing δ-Proteobacteria. The occurrence of such organisms is consistent with the chemical composition of OP (high in reduced iron and sulfur) and suggests a lithotrophic base for primary productivity in this hot spring, through hydrogen oxidation and sulfate reduction. Unexpectedly, no archaeal sequences were encountered in OP clone libraries made with universal primers. Hybridization analysis of amplified OP DNA with domain-specific probes confirmed that the analyzed community rDNA from OP sediment was predominantly bacterial. These results expand substantially our knowledge of the extent of bacterial diversity and call into question the commonly held notion that Archaea dominate hydrothermal environments. Finally, the currently known extent of division level bacterial phylogenetic diversity is collated and summarized.

scholarly journals Endophytic microbial diversity in coffee cherries ofCoffea arabicafrom southeastern Brazil

2013 ◽  
Vol 59 (4) ◽  
pp. 221-230 ◽  
Author(s):  
Marcelo N.V. Oliveira ◽  
Thiago M.A. Santos ◽  
Helson M.M. Vale ◽  
Júlio C. Delvaux ◽  
Alexander P. Cordero ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phylogenetic Analyses ◽  
Critical Role ◽  
Geographic Location ◽  
Small Subunit ◽  
Rrna Genes ◽  
Southeastern Brazil ◽  
Small Subunit Rrna ◽  
Microbial Composition

The microbiota associated with coffee plants may play a critical role in the final expression of coffee quality. However, the microbial diversity in coffee cherries is still poorly characterized. Here, we investigated the endophytic diversity in cherries of Coffea arabica by using culture-independent approaches to identify the associated microbes, ultimately to better understand their ecology and potential role in determining coffee quality. Group-specific 16S rRNA and 26S rRNA genes polymerase chain reaction – denaturing gradient gel electrophoresis and clone library sequencing showed that the endophytic community is composed of members of the 3 domains of life. Bacterial sequences showing high similarity with cultured and uncultured bacteria belonged to the Betaproteobacteria, Gammaproteobacteria, and Firmicutes phyla. Phylogenetic analyses of cloned sequences from Firmicutes revealed that most sequences fell into 3 major genera: Bacillus, Staphylococcus, and Paenibacillus. Archaeal sequences revealed the presence of operational taxonomic units belonging to Euryarchaeota and Crenarchaeota phyla. Sequences from endophytic yeast were not recovered, but various distinct sequences showing high identity with filamentous fungi were found. There was no obvious correlation between the microbial composition and cultivar or geographic location of the coffee plant. To the best of our knowledge, this is the first report demonstrating internal tissue colonization of plant fruits by members of the Archaea domain. The finding of archaeal small-subunit rRNA in coffee cherries, although not sufficient to indicate their role as active endophytes, certainly expands our perspectives toward considering members of this domain as potential endophytic microbes.

scholarly journals Bar-Coded Pyrosequencing Reveals Shared Bacterial Community Properties along the Temperature Gradients of Two Alkaline Hot Springs in Yellowstone National Park

2009 ◽  
Vol 75 (13) ◽  
pp. 4565-4572 ◽  
Author(s):  
Scott R. Miller ◽  
Aaron L. Strong ◽  
Kenneth L. Jones ◽  
Mark C. Ungerer
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Small Subunit ◽  
Physical Distance ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Data Set ◽  
Outflow Channels ◽  
Strong Negative Association

ABSTRACT An understanding of how communities are organized is a fundamental goal of ecology but one which has historically been elusive for microbial systems. We used a bar-coded pyrosequencing approach targeting the V3 region of the bacterial small-subunit rRNA gene to address the factors that structure communities along the thermal gradients of two alkaline hot springs in the Lower Geyser Basin of Yellowstone National Park. The filtered data set included a total of nearly 34,000 sequences from 39 environmental samples. Each was assigned to one of 391 operational taxonomic units (OTUs) identified by their unique V3 sequence signatures. Although the two hot springs differed in their OTU compositions, community resemblance and diversity changed with strikingly similar dynamics along the two outflow channels. Two lines of evidence suggest that these community properties are controlled primarily by environmental temperature. First, community resemblance decayed exponentially with increasing differences in temperature between samples but was only weakly correlated with physical distance. Second, diversity decreased with increasing temperature at the same rate along both gradients but was uncorrelated with other measured environmental variables. This study also provides novel insights into the nature of the ecological interactions among important taxa in these communities. A strong negative association was observed between cyanobacteria and the Chloroflexi, which together accounted for ∼70% of the sequences sampled. This pattern contradicts the longstanding hypothesis that coadapted lineages of these bacteria maintain tightly cooccurring distributions along these gradients as a result of a producer-consumer relationship. We propose that they instead compete for some limiting resource(s).

Theileria parva ribosomal internal transcribed spacer sequences exhibit extensive polymorphism and mosaic evolution: application to the characterization of parasites from cattle and buffalo

Parasitology ◽  
1999 ◽  
Vol 118 (6) ◽  
pp. 541-551 ◽  
Author(s):  
N. E. COLLINS ◽  
B. A. ALLSOPP
Keyword(s):  
Genetic Recombination ◽  
Large Subunit ◽  
Small Subunit ◽  
Internal Transcribed Spacers ◽  
Rrna Genes ◽  
Gene Pools ◽  
Theileria Parva ◽  
Causative Agents ◽  
Internal Transcribed Spacer Sequences

We sequenced the rRNA genes and internal transcribed spacers (ITS) of several Theileria parva isolates in an attempt to distinguish between the causative agents of East coast fever and Corridor disease. The small subunit (SSU) and large subunit (LSU) rRNA genes from a cloned T. p. lawrencei parasite were sequenced; the former was identical to that of T. p. parva Muguga, and there were minor heterogeneities in the latter. The 5·8S gene sequences of 11 T. parva isolates were identical, but major differences were found in the ITS. Six characterization oligonucleotides were designed to hybridize within the variable ITS1 region; 93·5% of T. p. parva isolates examined were detected by probe TPP1 and 81·8% of T. p. lawrencei isolates were detected by TPL2 and/or TPL3a. There was no absolute distinction between T. p. parva and T. p. lawrencei and the former hybridized with fewer of the probes than did the latter. It therefore seems that a relatively homogenous subpopulation of T. parva has been selected in cattle from a more diverse gene pool in buffalo. The ITSs of both T. p. parva and T. p. lawrencei contained different combinations of identifiable sequence segments, resulting in a mosaic of segments in any one isolate, suggesting that the two populations undergo genetic recombination and that their gene pools are not completely separate.

scholarly journals Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park

2007 ◽  
Vol 73 (20) ◽  
pp. 6669-6677 ◽  
Author(s):  
Eric S. Boyd ◽  
Robert A. Jackson ◽  
Gem Encarnacion ◽  
James A. Zahn ◽  
Trevor Beard ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Lipid Fraction ◽  
Carbon Sources ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Pcr Analysis ◽  
Geothermal Springs ◽  
Physiological Characterization

ABSTRACT Elemental sulfur (S0) is associated with many geochemically diverse hot springs, yet little is known about the phylogeny, physiology, and ecology of the organisms involved in its cycling. Here we report the isolation, characterization, and ecology of two novel, S0-reducing Crenarchaea from an acid geothermal spring referred to as Dragon Spring. Isolate 18U65 grows optimally at 70 to 72°C and at pH 2.5 to 3.0, while isolate 18D70 grows optimally at 81°C and pH 3.0. Both isolates are chemoorganotrophs, dependent on complex peptide-containing carbon sources, S0, and anaerobic conditions for respiration-dependent growth. Glycerol dialkyl glycerol tetraethers (GDGTs) containing four to six cyclopentyl rings were present in the lipid fraction of isolates 18U65 and 18D70. Physiological characterization suggests that the isolates are adapted to the physicochemical conditions of Dragon Spring and can utilize the natural organic matter in the spring as a carbon and energy source. Quantitative PCR analysis of 16S rRNA genes associated with the S0 flocs recovered from several acid geothermal springs using isolate-specific primers indicates that these two populations together represent 17 to 37% of the floc-associated DNA. The physiological characteristics of isolates 18U65 and 18D70 are consistent with their potential widespread distribution and putative role in the cycling of sulfur in acid geothermal springs throughout the Yellowstone National Park geothermal complex. Based on phenotypic and genetic characterization, the designations Caldisphaera draconis sp. nov. and Acidilobus sulfurireducens sp. nov. are proposed for isolates 18U65 and 18D70, respectively.

scholarly journals Culture-Independent Analysis of Indomethacin-Induced Alterations in the Rat Gastrointestinal Microbiota

2006 ◽  
Vol 72 (10) ◽  
pp. 6707-6715 ◽  
Author(s):  
Andrew B. Dalby ◽  
Daniel N. Frank ◽  
Allison L. St. Amand ◽  
Alison M. Bendele ◽  
Norman R. Pace
Keyword(s):  
Small Intestine ◽  
Lymph Nodes ◽  
Small Subunit ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Mesenteric Lymph Nodes ◽  
Gastrointestinal Microbiota ◽  
Mesenteric Lymph ◽  
Independent Analysis ◽  
Culture Independent

ABSTRACT Nonsteroidal anti-inflammatory drugs (NSAIDs) are commonly prescribed for a variety of inflammatory conditions; however, the benefits of this class of drugs are accompanied by deleterious side effects, most commonly gastric irritation and ulceration. NSAID-induced ulceration is thought to be exacerbated by intestinal microbiota, but previous studies have not identified specific microbes that contribute to these adverse effects. In this study, we conducted a culture-independent analysis of ∼1,400 bacterial small-subunit rRNA genes associated with the small intestines and mesenteric lymph nodes of rats treated with the NSAID indomethacin. This is the first molecular analysis of the microbiota of the rat small intestine. A comparison of clone libraries and species-specific quantitative PCR results from rats treated with indomethacin and untreated rats revealed that organisms closely related to Enterococcus faecalis were heavily enriched in the small intestine and mesenteric lymph nodes of the treated rats. These data suggest that treatment of NSAID-induced ulceration may be facilitated by addressing the microbiological imbalances.

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