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 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.

Lentilactobacillus fungorum sp. nov., isolated from spent mushroom substrates

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Masanori Tohno ◽  
Yasuhiro Tanizawa ◽  
Yoichiro Kojima ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
...  
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Protein Encoding ◽  
Polyphasic Characterization ◽  
Encoding Genes

In Japan, during a screening of lactic acid bacteria in spent mushroom substrates, an unknown bacterium was isolated and could not be assigned to any known species. Strain YK48GT is Gram-stain-positive, rod-shaped, non-motile, non-spore-forming and catalase-negative. The isolate grew in 0–4 % (w/v) NaCl, at 15–37 °C (optimum, 30 °C) and at pH 4.0–8.0 (optimum, pH 6.0). The genomic DNA G+C content of strain YK48GT was 42.5 mol%. Based on its 16S rRNA gene sequence, strain YK48GT represented a member of the genus Lentilactobacillus and showed the highest pairwise similarity to Lentilactobacillus rapi DSM 19907T (97.86 %). Phylogenetic analyses based on amino acid sequences of 466 shared protein-encoding genes also revealed that the strain was phylogenetically positioned in the genus Lentilactobacillus but did not suggest an affiliation with previously described species. The average nucleotide identity and digital DNA–DNA hybridization values between strain YK48GT and the type strains of phylogenetically related species were 72.2–76.6% and 19.0–21.2 %, respectively, indicating that strain YK48GT represents a novel species within the genus Lentilactobacillus . Phenotypic data further confirmed the differentiation of strain YK48GT from other members of the genus Lentilactobacillus . According to the results of the polyphasic characterization presented in this study, strain YK48GT represents a novel species of the genus Lentilactobacillus , for which the name Lentilactobacillus fungorum sp. nov. is proposed. The type strain is YK48GT (=JCM 32598T=DSM 107968T).

scholarly journals Comparative Genomic Analysis of Phylogenetically Closely Related Hydrogenobaculum sp. Isolates from Yellowstone National Park

2013 ◽  
Vol 79 (9) ◽  
pp. 2932-2943 ◽  
Author(s):  
Christine Romano ◽  
Seth D'Imperio ◽  
Tanja Woyke ◽  
Konstantinos Mavromatis ◽  
Roger Lasken ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Marker Gene ◽  
Genomic Analysis ◽  
Mercury Resistance ◽  
Nitrate Respiration ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Content Type ◽  
Outflow Channel

ABSTRACTWe describe the complete genome sequences of four closely relatedHydrogenobaculumsp. isolates (≥99.7% 16S rRNA gene identity) that were isolated from the outflow channel of Dragon Spring (DS), Norris Geyser Basin, in Yellowstone National Park (YNP), WY. The genomes range in size from 1,552,607 to 1,552,931 bp, contain 1,667 to 1,676 predicted genes, and are highly syntenic. There are subtle differences among the DS isolates, which as a group are different fromHydrogenobaculumsp. strain Y04AAS1 that was previously isolated from a geographically distinct YNP geothermal feature. Genes unique to the DS genomes encode arsenite [As(III)] oxidation, NADH-ubiquinone-plastoquinone (complex I), NADH-ubiquinone oxidoreductase chain, a DNA photolyase, and elements of a type II secretion system. Functions unique to strain Y04AAS1 include thiosulfate metabolism, nitrate respiration, and mercury resistance determinants. DS genomes contain seven CRISPR loci that are almost identical but are different from the single CRISPR locus in strain Y04AAS1. Other differences between the DS and Y04AAS1 genomes include average nucleotide identity (94.764%) and percentage conserved DNA (80.552%). Approximately half of the genes unique to Y04AAS1 are predicted to have been acquired via horizontal gene transfer. Fragment recruitment analysis and marker gene searches demonstrated that the DS metagenome was more similar to the DS genomes than to the Y04AAS1 genome, but that the DS community is likely comprised of a continuum ofHydrogenobaculumgenotypes that span from the DS genomes described here to an Y04AAS1-like organism, which appears to represent a distinct ecotype relative to the DS genomes characterized.

scholarly journals Whole-Genome De Novo Sequencing of the Lignin-Degrading Wood Rot Fungus Phanerochaete chrysosporium (ATCC 20696)

2017 ◽  
Vol 5 (32) ◽  
Author(s):  
Chang-Young Hong ◽  
Su-Yeon Lee ◽  
Sun-Hwa Ryu ◽  
Sung-Suk Lee ◽  
Myungkil Kim
Keyword(s):  
Phanerochaete Chrysosporium ◽  
De Novo ◽  
Gene Annotation ◽  
Draft Genome ◽  
Whole Genome ◽  
Content Type ◽  
Protein Encoding ◽  
Crucial Information ◽  
And Function ◽  
Encoding Genes

ABSTRACT Phanerochaete chrysosporium (ATCC 20696) has a catabolic ability to degrade lignin. Here, we report whole-genome sequencing used to identify genes related to lignin modification. We determined the 39-Mb draft genome sequence of this fungus, comprising 13,560 predicted gene models. Gene annotation provided crucial information about the location and function of protein-encoding genes.

scholarly journals Genome Sequence of a Thermoacidophilic Methanotroph Belonging to the Verrucomicrobiota Phylum from Geothermal Hot Springs in Yellowstone National Park: A Metagenomic Assembly and Reconstruction

2022 ◽  
Vol 10 (1) ◽  
pp. 142
Author(s):  
Hye Won Kim ◽  
Na Kyung Kim ◽  
Alex P. R. Phillips ◽  
David A. Parker ◽  
Ping Liu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
De Novo ◽  
Marker Gene ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Sequencing Data

Verrucomicrobiotal methanotrophs are thermoacidophilic methane oxidizers that have been isolated from volcanic and geothermal regions of the world. We used a metagenomic approach that entailed obtaining the whole genome sequence of a verrucomicrobiotal methanotroph from a microbial consortium enriched from samples obtained from Nymph Lake (89.9 °C, pH 2.73) in Yellowstone National Park in the USA. To identify and reconstruct the verrucomicrobiotal genome from Illumina NovaSeq 6000 sequencing data, we constructed a bioinformatic pipeline with various combinations of de novo assembly, alignment, and binning algorithms. Based on the marker gene (pmoA), we identified and assembled the Candidatus Methylacidiphilum sp. YNP IV genome (2.47 Mbp, 2392 ORF, and 41.26% GC content). In a comparison of average nucleotide identity between Ca. Methylacidiphilum sp. YNP IV and Ca. Methylacidiphilum fumariolicum SolV, its closest 16S rRNA gene sequence relative, is lower than 95%, suggesting that Ca. Methylacidiphilum sp. YNP IV can be regarded as a different species. The Ca. Methylacidiphilum sp. YNP IV genome assembly showed most of the key genes for methane metabolism, the CBB pathway for CO2 fixation, nitrogen fixation and assimilation, hydrogenases, and rare earth elements transporter, as well as defense mechanisms. The assembly and reconstruction of a thermoacidophilic methanotroph belonging to the Verrucomicrobiota phylum from a geothermal environment adds further evidence and knowledge concerning the diversity of biological methane oxidation and on the adaptation of this geochemically relevant reaction in extreme environments.

scholarly journals Complete Genome Sequence of Salmonella enterica Bacteriophage PRF-SP1

2021 ◽  
Vol 10 (47) ◽  
Author(s):  
Prasanna Mutusamy ◽  
Sasireigga Jaya Jothi ◽  
Su Yin Lee ◽  
Bent Petersen ◽  
Thomas Sicheritz-Ponten ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Salmonella Enterica ◽  
Complete Genome ◽  
National Park ◽  
The Novel ◽  
Content Type ◽  
Double Stranded Dna ◽  
Protein Encoding ◽  
Encoding Genes

We characterized the complete genome sequence of the lytic Salmonella enterica bacteriophage PRF-SP1, isolated from Penang National Park, a conserved rainforest in northern Malaysia. The novel phage species from the Autographiviridae family has a 39,966-bp double-stranded DNA (dsDNA) genome containing 49 protein-encoding genes and shares 90.96% similarity with Escherichia phage DY1.

scholarly journals Identification of New Single Nucleotide Polymorphism-Based Markers for Inter- and Intraspecies Discrimination of Obligate Bacterial Parasites (Pasteuria spp.) of Invertebrates

2011 ◽  
Vol 77 (18) ◽  
pp. 6388-6394 ◽  
Author(s):  
Tim H. Mauchline ◽  
Rachel Knox ◽  
Sharad Mohan ◽  
Stephen J. Powers ◽  
Brian R. Kerry ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
The Other ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Single Nucleotide ◽  
Content Type ◽  
Protein Encoding ◽  
Encoding Genes ◽  
The 16S Rrna Gene

ABSTRACTProtein-encoding and 16S rRNA genes ofPasteuria penetranspopulations from a wide range of geographic locations were examined. Most interpopulation single nucleotide polymorphisms (SNPs) were detected in the 16S rRNA gene. However, in order to fully resolve all populations, these were supplemented with SNPs from protein-encoding genes in a multilocus SNP typing approach. Examination of individual 16S rRNA gene sequences revealed the occurrence of “cryptic” SNPs which were not present in the consensus sequences of anyP. penetranspopulation. Additionally, hierarchical cluster analysis separatedP. penetrans16S rRNA gene clones into four groups, and one of which contained sequences from the most highly passaged population, demonstrating that it is possible to manipulate the population structure of this fastidious bacterium. The other groups were made from representatives of the other populations in various proportions. Comparison of sequences among threePasteuriaspecies, namely,P. penetrans,P. hartismeri, andP. ramosa, showed that the protein-encoding genes provided greater discrimination than the 16S rRNA gene. From these findings, we have developed a toolbox for the discrimination ofPasteuriaat both the inter- and intraspecies levels. We also provide a model to monitor genetic variation in other obligate hyperparasites and difficult-to-culture microorganisms.

Lactobacillus corticis sp. nov., isolated from hardwood bark

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Masanori Tohno ◽  
Yasuhiro Tanizawa ◽  
Yoichiro Kojima ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Lactobacillus Jensenii ◽  
Protein Encoding ◽  
Strain Type ◽  
Encoding Genes

During a study on the biodiversity of bacteria that inhabit woody biomass, we isolated a strain coded B40T from hardwood bark used as a compost ingredient in Japan. The strain, characterized as B40T, is a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming and catalase-negative bacterium. This novel isolate showed growth at 30–50 °C, at pH 3.5–7.5 and in the presence of up to 4 % (w/v) NaCl. Its major fatty acids include C16:0, C18:1 ω9c and summed feature 8. The genomic DNA G+C content of strain B40T is 42.2 mol%. Results of 16S rRNA gene sequence-based phylogenetic analysis indicated that strain B40T belongs to the genus Lactobacillus and the closest neighbours of strain B40T are Lactobacillus gigeriorum 202T (95.7 %), Lactobacillus pasteurii CRBIP 24.76T (95.6 %), Lactobacillus psittaci DSM 15354T (95.4 %), Lactobacillus fornicalis TV1018T (95.4 %) and Lactobacillus jensenii ATCC 25258T (95.2 %). The amino acid sequence-based phylogenetic analyses of 489 shared protein-encoding genes showed that the strain forms a phylogenetically independent lineage in the genus Lactobacillus but could not be assigned to any known species. Strain B40T has an average nucleotide identify of <70.2 % and a digital DNA–DNA hybridization value of 19.2 % compared with the strains of other closely related Lactobacillus species. Differential genomic, phenotypic and chemotaxonomic properties, in addition to phylogenetic analyses, indicated that strain B40T represents a novel species of the genus Lactobacillus , for which the name Lactobacillus corticis sp. nov. is proposed. The strain type is B40T (=JCM 32597T=DSM 107967T).

Microstructure of high-temperature (>73 °C) siliceous sinter deposited around hot springs and geysers, Yellowstone National Park: the role of biological and abiological processes in sedimentation

2003 ◽  
Vol 40 (11) ◽  
pp. 1611-1642 ◽  
Author(s):  
Donald R Lowe ◽  
Deena Braunstein
Keyword(s):  
High Temperature ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Strain Effect ◽  
Temperature Sinter ◽  
Architectural Features ◽  
Siliceous Sinter ◽  
High Temperature Sinter

Slightly alkaline hot springs and geysers in Yellowstone National Park exhibit distinctive assemblages of high-temperature (>73 °C) siliceous sinter reflecting local hydrodynamic conditions. The main depositional zones include subaqueous pool and channel bottoms and intermittently wetted subaerial splash, surge, and overflow areas. Subaqueous deposits include particulate siliceous sediment and dendritic and microbial silica framework. Silica framework forms thin, porous, microbe-rich films coating subaqueous surfaces. Spicules with intervening narrow crevices dominate in splash zones. Surge and overflow deposits include pool and channel rims, columns, and knobs. In thin section, subaerial sinter is composed of (i) dark brown, nearly opaque laminated sinter deposited on surfaces that evaporate to dryness; (ii) clear translucent silica deposited subaqueously through precipitation driven by supersaturation; (iii) heterogeneous silica representing silica-encrusted microbial filaments and detritus; and (iv) sinter debris. Brownish laminations form the framework of most sinter deposited in surge and overflow zones. Pits and cavities are common architectural features of subaerial sinter and show concave-upward pseudo-cross-laminations and micro-unconformities developed through migration. Marked birefringence of silica deposited on surfaces that evaporate to dryness is probably a strain effect. Repeated wetting and evaporation, often to dryness, and capillary effects control the deposition, morphology, and microstructure of most high-temperature sinter outside of the fully subaqueous zone. Microbial filaments are abundant on and within high-temperature sinter but do not provide the main controls on morphology or structuring except in biofilms developed on subaqueous surfaces. Millimetre-scale lamination cyclicity in much high-temperature sinter represents annual layering and regular seasonal fluctuations in silica sedimentation.

scholarly journals Autotransporter Protein-Encoding Genes of Diarrheagenic Escherichia coli Are Found in both Typical and Atypical Enteropathogenic E. coli Strains

2012 ◽  
Vol 79 (1) ◽  
pp. 411-414 ◽  
Author(s):  
Afonso G. Abreu ◽  
Vanessa Bueris ◽  
Tatiane M. Porangaba ◽  
Marcelo P. Sircili ◽  
Fernando Navarro-Garcia ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Content Type ◽  
E Coli ◽  
Diarrheagenic Escherichia Coli ◽  
Virulence Markers ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Specific Virulence

ABSTRACTAutotransporter (AT) protein-encoding genes of diarrheagenicEscherichia coli(DEC) pathotypes (cah,eatA,ehaABCDJ,espC,espI,espP,pet,pic,sat, andtibA) were detected in typical and atypical enteropathogenicE. coli(EPEC) in frequencies between 0.8% and 39.3%. Although these ATs have been described in particular DEC pathotypes, their presence in EPEC indicates that they should not be considered specific virulence markers.

Sign in / Sign up

Export Citation Format

Share Document