Acidic Hot Springs Research Articles

Microbial Diversity of Acidic Hot Spring (Kawah Hujan B) in Geothermal Field of Kamojang Area, West Java-Indonesia

Microbial communities in an acidic hot spring, namely Kawah Hujan B, at Kamojang geothermal field, West Java-Indonesia was examined using culture dependent and culture independent strategies. Chemical analysis of the hot spring water showed a characteristic of acidic-sulfate geothermal activity that contained high sulfate concentrations and low pH values (pH 1.8 to 1.9). Microbial community present in the spring was characterized by 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) analysis. The majority of the sequences recovered from culture-independent method were closely related to Crenarchaeota and Proteobacteria phyla. However, detail comparison among the member of Crenarchaeota showing some sequences variation compared to that the published data especially on the hypervariable and variable regions. In addition, the sequences did not belong to certain genus. Meanwhile, the 16S Rdna sequences from culture-dependent samples revealed mostly close to Firmicute and gamma Proteobacteria.

Tetramitus thermacidophilus n. sp., an Amoeboflagellate from Acidic Hot Springs

Tetramitus thermacidophilus n. sp. is a novel thermophilic and acidophilic amoeboflagellate isolated from acidic hot springs in the Caldera Uzon (Kamchatka, Russia) and in Pisciarelli Solfatara (Naples, Italy). We describe it based on physiological, morphological, and sequence data. It was grown in monoxenic culture on the archaeon Acidianus brierleyi as food. Tetramitus thermacidophilus multiplies in a pH range from 1.2 to 5 and in a temperature range from 28 °C to 54 °C. The shortest doubling time was 4.5 h at pH 3 at 45 °C. Its spindle-shaped biflagellated stage was only rarely found in culture. The amoeboid stage shows the typical locomotive form of vahlkampfiid amoebae. Sequence comparisons of the internal transcribed spacer sequences and the small subunit rRNA genes confirm that T. thermacidophilus is a novel species within the genus Tetramitus and that both isolates belong to that species.

Tetramitus thermacidophilusn. sp., an Amoeboflagellate from Acidic Hot Springs

ABSTRACT. Tetramitus thermacidophilus n. sp. is a novel thermophilic and acidophilic amoeboflagellate isolated from acidic hot springs in the Caldera Uzon (Kamchatka, Russia) and in Pisciarelli Solfatara (Naples, Italy). We describe it based on physiological, morphological, and sequence data. It was grown in monoxenic culture on the archaeon Acidianus brierleyi as food. Tetramitus thermacidophilus multiplies in a pH range from 1.2 to 5 and in a temperature range from 28 °C to 54 °C. The shortest doubling time was 4.5 h at pH 3 at 45 °C. Its spindle-shaped biflagellated stage was only rarely found in culture. The amoeboid stage shows the typical locomotive form of vahlkampfiid amoebae. Sequence comparisons of the internal transcribed spacer sequences and the small subunit rRNA genes confirm that T. thermacidophilus is a novel species within the genus Tetramitus and that both isolates belong to that species.

Computational modeling analyses of RNA secondary structures and phylogenetic inference of evolutionary conserved 5S rRNA in the prokaryotes

Bacteria are unicellular, ubiquitous microorganisms which grow on soil, acidic hot springs, radioactive wastes, etc. The genome of bacteria constitutes species specific conserved region. The 5S rRNA is one of the most conserved region determined in each bacteria and the size ranges between 110 and 148 bp. On this basis phylogenetic study of 37 bacterial strains was done which results in formation of seven clades and furthermore RNA secondary structure from each clade was made. The lowest free energy ( δG) of the 5S rRNA may divulge the most primitive bacteria and slow changes occurs throughout the evolution whereas the higher free energy indicates less stability during the evolution. The RNA secondary structure may provide new insights to understand bacteria evolution and stability.

Designer labels for virus coats

Protein nanoparticles derived from viruses are commonly studied, but a new rod-shaped thermophilic virus isolated from acidic hot springs may yield another class of protein building blocks that are stable and can be selectively modified with diverse chemical groups.

Diatoms in Akita Prefecture, northern part of Japan, part 1—Diatoms in strongly acidic hot springs

Diatoms in Akita Prefecture, northern part of Japan, part 1—Diatoms in strongly acidic hot springs

Growth and surface properties of new thermoacidophilic Archaea strain Acidianus manzaensis YN-25 grown on different substrates

The growth and surface properties of new thermoacidophilic Archaea strain Acidianus manzaensis YN-25 isolated from an acid hot spring in Tengchong, Yunnan Province, China were investigated cultured on different substrates including soluble substrate ferrous sulfate and nonsoluble solid substrates S 0, pyrite and chalcopyrite. The growth characteristics of the cells in each substrate were characterized with the changes in cell number, pH, E h, and concentrations of Fe 2+ or SO 4 2−, or ratios of [Fe 2+] to [Fe 3+], and the surface properties were characterized and analyzed in terms of Zeta-potential, hydrophobicity, and surface FT-IR spectra of the cells. The results show that the cells grown on solid substrates have higher value of isoelectric points. They are more hydrophobic and express more surface proteins than ferrous sulfate grown cells.

Isolation and characterization of YNTC-1, a novel Alicyclobacillus sendaiensis strain

A heterotrophic acidothermophilic bacterial strain, YNTC-1, was isolated from an acidic hot spring in Tengchong, Yunan, China. YNTC-1 grows at pH value of 1.5–8.0 and temperature of 40–70 °C, with optimal pH and temperature at 3.0 and 55 °C, respectively. The cells of the strain are in shape of short rod, with 1.0–1.2 μm in length and 0.7–0.8 μm in diameter, and with distinct spores at both poles of each cell. The predominant fatty acids in cellular membrane of the strain are C18:1 θ7c. 16s rRNA gene analysis reveals that this strain is closely related to Alicyclobacillus sendaiensis, with over 99% sequence similarity. Based on phenotypic and genotypic analyses, YNTC-1 is identified as a member of A. sendaiensis. Considering some important morphological and biochemical differences between strain YNTC-1 and A. sendaiensis ATCC 27009T, YNTC-1 may be proposed to be a novel subspecies of A. sendaiensis. However, this viewpoint has to be confirmed by further studies. Co-bioleaching of pyrite and chalcopyrite with strain YN22, Sulfobacillus thermosulfidooxidans, shows that strain YNTC-1 has no evident influence on bioleaching rates of these two sulphide minerals.

Chemical evolution of thermal waters and changes in the hydrothermal system of Papandayan volcano (West Java, Indonesia) after the November 2002 eruption

Papandayan is a stratovolcano situated in West Java, Indonesia. Since the last magmatic eruption in 1772, only few hydrothermal explosions have occurred. An explosive eruption occurred in November 2002 and ejected ash and altered rocks. The altered rocks show that an advanced argillic alteration took place in the hydrothermal system by interaction between acid fluids and rocks. Four zones of alteration have been defined and are limited in extension and shape along faults or across permeable structures at different levels beneath the active crater of the volcano. At the present time, the activity is centered in the northeast crater with discharge of low temperature fumaroles and acid hot springs. Two types of acid fluids are emitted in the crater of Papandayan volcano: (1) acid sulfate-chloride waters with pH between 1.6 and 4.6 and (2) acid sulfate waters with pH between 1.2 and 2.5. The water samples collected after the eruption on January 2003 reveal an increase in the SO 4/Cl and Mg/Cl ratios. This evolution is likely explained by an increase in the neutralization of acid fluids and tends to show that water–rock interactions were more significant after the eruption. The evolution in the chemistry observed since 2003 is the consequence of the opening of new fractures at depth where unaltered (or less altered) volcanic rocks were in contact with the ascending acid waters. The high δ 34S values (9–17‰) observed in acid sulfate-chloride waters before the November 2002 eruption suggest that a significant fraction of dissolved sulfates was formed by the disproportionation of magmatic SO 2. On the other hand, the low δ 34S (− 0.3–7‰) observed in hot spring waters sampled after the eruption suggest that the hydrothermal contribution (i.e. the surficial oxidation of hydrogen sulfide) has increased.

Viruses in acidic geothermal environments of the Kamchatka Peninsula

Screening for viruses in samples taken from acidic hot springs of Kamchatka (Russia) revealed a collection of morphotypes, including linear, spherical and complex fusiform shapes, which show partial similarity to those found in acidic geothermal environments in other geographical locations. One of the viruses, Acidianus filamentous virus 9, AFV9, was isolated and its structure and genome were studied in detail.

Cysteine usage in Sulfolobus spindle-shaped virus 1 and extension to hyperthermophilic viruses in general

Fuselloviridae are ubiquitous crenarchaeal viruses found in high-temperature acidic hot springs worldwide. The type virus, Sulfolobus spindle-shaped virus 1 (SSV1), has a double-stranded DNA genome that contains 34 open reading frames (ORFs). Fuselloviral genomes show little similarity to other organisms, generally precluding functional predictions. However, tertiary protein structure can provide insight into protein function. We have thus undertaken a systematic investigation of the SSV1 proteome and report here on the F112 gene product. Biochemical, proteomic and structural studies reveal a monomeric intracellular protein that adopts a winged helix DNA binding fold. Notably, the structure contains an intrachain disulfide bond, prompting analysis of cysteine usage in this and other hyperthermophilic viral genomes. The analysis supports a general abundance of disulfide bonds in the intracellular proteins of hyperthermophilic viruses, and reveals decreased cysteine content in the membrane proteins of hyperthermophilic viruses infecting Sulfolobales. The evolutionary implications of the SSV1 distribution are discussed.

Airborne Viruses Migrate on Vapors among Yellowstone Hot Springs

Viruses in acidic hot springs at Yellowstone National Park appear to migrate on steam droplets, sometimes traveling up to 20 miles between pools. The unexpected finding helps to explain how such viruses spread far and wide, according to molecular microbiologist Frank Roberto of the Idaho National Laboratory (INL), Idaho Falls, virologist Mark Young at Montana State University (MSU), Bozeman, and their collaborators. These findings emerged during a two-year survey of microbial diversity in those hot springs, part of the National Science Foundation Microbial Observatories Program.

Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum

Methanotrophic bacteria constitute a ubiquitous group of microorganisms playing an important role in the biogeochemical carbon cycle and in control of global warming through natural reduction of methane emission. These bacteria share the unique ability of using methane as a sole carbon and energy source and have been found in a great variety of habitats. Phylogenetically, known methanotrophs constitute a rather limited group and have so far only been affiliated with the Proteobacteria. Here, we report the isolation and initial characterization of a nonproteobacterial obligately methanotrophic bacterium. The isolate, designated Kam1, was recovered from an acidic hot spring in Kamchatka, Russia, and is more thermoacidophilic than any other known methanotroph, with optimal growth at approximately 55 degrees C and pH 3.5. Kam1 is only distantly related to all previously known methanotrophs and belongs to the Verrucomicrobia lineage of evolution. Genes for methane monooxygenases, essential for initiation of methane oxidation, could not be detected by using standard primers in PCR amplification and Southern blot analysis, suggesting the presence of a different methane oxidation enzyme. Kam1 also lacks the well developed intracellular membrane systems typical for other methanotrophs. The isolate represents a previously unrecognized biological methane sink, and, due to its unusual phylogenetic affiliation, it will shed important light on the origin, evolution, and diversity of biological methane oxidation and on the adaptation of this process to extreme habitats. Furthermore, Kam1 will add to our knowledge of the metabolic traits and biogeochemical roles of the widespread but poorly understood Verrucomicrobia phylum.

Thermoanaerobacterium aciditolerans sp. nov., a moderate thermoacidophile from a Kamchatka hot spring

An anaerobic, moderately thermoacidophilic bacterium, strain 761-119T, was isolated from an acidic hot spring in the Orange Field of the Uzon Caldera (Kamchatka, far-eastern Russia). Cells were spore-forming, Gram-positive rods, possessing one polar flagellum. Growth of strain 761-119T was observed between 37 and 68 degrees C and in the pH(20 degrees C) range 3.2-7.1. No growth was observed within 5 days of incubation at or below 35 degrees C and at or above 70 degrees C, as well as at or below pH(20 degrees C) 2.8 and at or above pH(20 degrees C) 7.5. The optimal temperature and pH(20 degrees C) for growth were 55 degrees C and pH(20 degrees C) 5.7, respectively. A wide range of carbohydrates and polysaccharides were fermented, as well as peptides and proteinaceous substrates. The main products of glucose fermentation were acetate, ethanol, lactate, H2 and CO2. The DNA G+C content was 34 (+/-0.5) mol%. 16S rRNA gene sequence analysis indicated that strain 761-119T belonged to the genus Thermoanaerobacterium. The level of 16S rRNA gene sequence similarity with other Thermoanaerobacterium species was 86.5-97.8 %, with the only moderately acidophilic member of this genus, Thermoanaerobacterium aotearoense, being one of its closest relatives. DNA-DNA hybridization with T. aotearoense showed 33 % relatedness. Thus, morphological (one polar flagellum) and physiological characteristics (lower pH limit of growth at pH(20 degrees C) 3.2 compared with T. aotearoense) and 16S rRNA gene sequence analyses revealed that strain 761-119T represents a novel species in the genus Thermoanaerobacterium, for which the name Thermoanaerobacterium aciditolerans sp. nov. is proposed, with the type strain 761-119T (=DSM 16487T=VKM B-2363T).

Structure of A197 from Sulfolobus Turreted Icosahedral Virus: a Crenarchaeal Viral Glycosyltransferase Exhibiting the GT-A Fold

Sulfolobus turreted icosahedral virus (STIV) was the first icosahedral virus characterized from an archaeal host. It infects Sulfolobus species that thrive in the acidic hot springs (pH 2.9 to 3.9 and 72 to 92 degrees C) of Yellowstone National Park. The overall capsid architecture and the structure of its major capsid protein are very similar to those of the bacteriophage PRD1 and eukaryotic viruses Paramecium bursaria Chlorella virus 1 and adenovirus, suggesting a viral lineage that predates the three domains of life. The 17,663-base-pair, circular, double-stranded DNA genome contains 36 potential open reading frames, whose sequences generally show little similarity to other genes in the sequence databases. However, functional and evolutionary information may be suggested by a protein's three-dimensional structure. To this end, we have undertaken structural studies of the STIV proteome. Here we report our work on A197, the product of an STIV open reading frame. The structure of A197 reveals a GT-A fold that is common to many members of the glycosyltransferase superfamily. A197 possesses a canonical DXD motif and a putative catalytic base that are hallmarks of this family of enzymes, strongly suggesting a glycosyltransferase activity for A197. Potential roles for the putative glycosyltransferase activity of A197 and their evolutionary implications are discussed.

Selective mineralization of microbes in Fe-rich precipitates (jarosite, hydrous ferric oxides) from acid hot springs in the Waiotapu geothermal area, North Island, New Zealand

A group of small springs that are informally called “Orange Spring”, located near Hakereteke Stream in the northern part of the Waiotapu geothermal area, feed hot (∼ 80 °C), acidic (pH: 2.1 – 2.4), As-rich sulfate waters into a discharge channel that is up to 25 cm deep. Submerged reddish-brown precipitates on the channel floor are formed largely of noncrystalline As-rich hydrous ferric oxide (HFO: mainly goethite), poorly crystalline lepidocrocite, and crystalline jarosite. Well-preserved coccoid and rod-shaped microbes are found in the As-rich HFO, but not in the lepidocrocite or jarosite. The jarosite was probably precipitated when the water had a low pH (< 3) and high SO 4 content, whereas the goethite and lepidocrocite were probably precipitated when the water had a slightly higher pH (> 4) and lower SO 4 content. The fluctuations in the pH and SO 4 content, which led to precipitation of the different mineral phases, may reflect mixing of the spring water with stream water that flowed through the channel when Hakereteke Stream was in flood stage. The goethite probably formed when coccoid and rod-shaped bacteria ( Acidithiobacillus ferrooxidans?) mediated rapid oxidization of the Fe 2+ to Fe 3+ that was then immediately coprecipitated with the As. Such rapid precipitation promoted mineralization of the microbes. The lack of mineralized microbes and the lower As in the lepidocrocite and jarosite may reflect precipitation rates that were slower than the decay rates of the microbes, or ecological factors that limited their growth.

Geochemical interpretation of long-term variations in rare earth element concentrations in acidic hot spring waters from the Tamagawa geothermal area, Japan

The rare earth elements (REE) concentrations in the waters of Obuki hot spring, Tamagawa geothermal system, Akita Prefecture, Japan, have been determined in order to investigate their long-term variations over a 30-year period. The temporal patterns of REE and SO 4 2− concentrations are synchronous. Leaching experiments using source rock demonstrated that the relatively high REE concentrations in the waters were likely the result of dissolution of near-surface rocks by the acidic waters. The non-magnetic mineral group, enriched in light rare earth elements (LREE) and Eu(II), is easily attacked by the acid solution. The LREE will be selectively dissolved from the non-magnetic mineral group when the SO 4 2− concentration is increased by SO 2 derived from magmatic gases.

Geochemical and Biological Diversity of Acidic, Hot Springs in Lassen Volcanic National Park

We used phylogenetic approaches and chemical/physical analyses to investigate the diversity of microorganisms in geochemically distinct acidic hot springs of Lassen Volcanic National Park (LVNP) in northern California. Geochemical composition was analyzed for twelve sites within LVNP, and 16S rRNA clone libraries were prepared and analyzed for three sites (DK12 -93.5°C, pH 1.2; USW5 -86.2°C, pH 2.2; and SW3 -82°C, pH 1.2) using universal and Archaeal-specific primers. Phylogenetic relationships of sequences were estimated using parsimony, maximum likelihood, and Bayesian methods. The geochemical composition of the features varied widely even among proximate sites having similar temperature and pH values. Acridine Orange Direct Counts indicated cell concentrations of 106 to 108 cells/ml in the sites analyzed, which is comparable to neutral pH, mesophilic environments. In contrast to similar studies of less-acidic hot springs in which members of the Bacterial order Aquificales have been shown to dominate, no Bacterial sequences were detected in any of the libraries. Using 97% sequence identity as a cutoff value, approximately 65 phylotypes were detected, many with low similarity (<85%) to the closest database sequences. The most prevalent clones exhibited ∼92% identity with the Crenarchaeotes Stygioglobus azoricus and Sulfolobus solfataricus, while others exhibited high similarity (∼97%) to Vulcanisaeta distributa. These descriptive studies will help direct cultivation efforts and aid in modeling relationships among geochemistry, temperature, pH, and microbial diversity, to investigate the role of biotic processses (and population dynamics) in the geochemistry of these systems.

Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses.

Archaea and their viruses are poorly understood when compared with the Eukarya and Bacteria domains of life. We report here the crystal structure of the major capsid protein (MCP) of the Sulfolobus turreted icosahedral virus, an archaeal virus isolated from an acidic hot spring (pH 2-4, 72-92 degrees C) in Yellowstone National Park. The structure is nearly identical to the MCP structures of the eukaryotic Paramecium bursaria Chlorella virus, and the bacteriophage PRD1, and shows a common fold with the mammalian adenovirus. Structural analysis of the capsid architecture, determined by fitting the subunit into the electron cryomicroscopy reconstruction of the virus, identified a number of key interactions that are akin to those observed in adenovirus and PRD1. The similar capsid proteins and capsid architectures strongly suggest that these viral capsids originated and evolved from a common ancestor. Hence, this work provides a previously undescribed example of a viral relationship spanning the three domains of life (Eukarya, Bacteria, and Archaea). The MCP structure also provides insights into the stabilizing forces required for extracellular hyperthermophilic proteins to tolerate high-temperature hot springs.

Independent virus development outside a host

Viruses are thought to be functionally inactive once they are outside and independent of their host cell. Here we describe an exceptional property of a newly discovered virus that infects a hyperthermophilic archaeon growing in acidic hot springs: the lemon-shaped viral particle develops a very long tail at each of its pointed ends after being released from its host cell. The process occurs only at the temperature of the host's habitat (75-90 degrees C) and it does not require the presence of the host cell, an exogenous energy source or any cofactors. This host-independent morphological development may be a strategy for viral survival in an environment that is unusually harsh and has limited host availability.