Uzon Research Articles

A Novel Species of the Genus Thermanaerothrix Isolated from a Kamchatka Hot Spring Possesses Hydrolytic Capabilities.

Hot springs are inhabited by specific microbial communities which are reservoirs of novel taxa. In this work strain 4228-RoLT was isolated from the Solnechny hot spring, Uzon Caldera, Kamchatka. Cells of the strain 4228-RoLT were Gram-negative rods forming multicellular filaments. The strain grew optimally at 60°C and pH 7.0 and fermented various organic compounds including polysaccharides (microcrystalline cellulose, xylan, chitin, starch, dextrin, dextran, beta-glucan, galactomannan, glucomannan, mannan). Major fatty acids were iso-C17:0, C16:0, C18:0, C20:0, iso-C19:0, anteiso-C17:0 and C22:0. Genome of the strain was of 3.25 Mbp with GC content of 54.2%. Based on the whole genome comparisons and phylogenomic analysis the new isolate was affiliated to a novel species of Thermanaerothrix genus within Anaerolineae class of phylum Chloroflexota, for which the name T. solaris sp. nov. was proposed with 4228-RoLT (= VKM B-3776T = UQM 41594T = BIM B-2058T) as the type strain. 114 CAZymes including 43 glycoside hydrolases were found to be encoded in the genome of strain 4228-RoLT. Cell-bound and extracellular enzymes of strain 4228-RoLT were active against starch, dextran, mannan, xylan and various kinds of celluloses, with the highest activity against beta-glucan. Altogether, growth experiments, enzymatic activities determination and genomic analysis suggested that T. solaris strain 4228-RoLT could serve as a source of glycosidases suitable for plant biomass hydrolysis.

Electrotomography Studies in the Uzon Caldera at Shaman Geyser (Kamchatka Peninsula)

Electrotomography Studies in the Uzon Caldera at Shaman Geyser (Kamchatka Peninsula)

Ignisphaera cupida sp. nov., a hyperthermophilic hydrolytic archaeon from a hot spring of Uzon (Kamchatka), and emended description of the genus Ignisphaera

A novel strictly anaerobic hyperthermophilic archaeon, strain 4213-coT, was isolated from a terrestrial hot spring in the Uzon Caldera, Kamchatka (Russian Federation). Coccoid cells were present singly, in pairs, or aggregates, and occasionally were motile. The strain grew at 75–100 °C and within a pH range of 5.4–8.2 with the optimum at 92 °C and pH 6.4–6.7. Strain 4213-coT was a chemoorganoheterotroph, growing on proteinaceous substrates and mono-, di- and polysaccharides (starch, guar gum, xanthan gum). It did not require sodium chloride for growth. The complete genome of strain 4213-coT was 1.74 Mbp in size; its G+C content was 36.18 %. Genome analysis allowed to identify 25 genes encoding glycosidases involved in polysaccharide hydrolysis as well as genes of ADP-forming acetate-CoA ligase, lactate dehydrogenase and two [NiFe] hydrogenases responsible for acetate, lactate and hydrogen formation during fermentation. Moreover gene cluster encoding archaellum subunits was found. According to the phylogenomic analysis strain 4213-coT formed a species-level phylogenetic lineage within Ignisphaera genus. Our phylogenomic analysis also supports the delineation of the Ignisphaera genus into a separate family Ignisphaeraceae, as recently published. Here we propose a novel species Ignisphaera cupida, sp. nov. with type strain 4213-coT (=JCM 39446T=VKM B-3715T=UQM 41593T). Ecogenomic analysis showed that representatives of the Ignisphaera are thermophilic archaea, the majority of them were found in terrestrial hot springs and deep-sea hydrothermal vents. This study allowed a better understanding of physiology and ecology of Ignisphaeraceae – a rather understudied archaeal group.

Экспедиционные работы в центральной части восточного вулканического пояса и в долине р. Камчатка в 2023 г.

This article provides a brief description of the expedition work conducted by the staff of the Institute of Volcanology and Seismology, FEBRAS, in the central part of the Eastern Volcanic belt of Kamchatka, and in the Kamchatka River valley in the Summer-Autumn of 2023. In order to study the conditions for the formation and discharge of thermal waters of large volcanic centers, to estimate the hydrothermal discharge of magmatic volatiles (primarily CO2), hydrochemical and gas testing was carried out on the thermal fields of the Kikhpinych and Bolshoi Semyachik volcanic massifs, and in the Uzon caldera. In parallel with geochemical sampling, aerial and infrared photography of thermal sites was carried out. To determine the degree of influence of volcanic and hydrothermal activity on the ion runoff into the Pacific Ocean, hydrochemical and hydrological works were carried out in the Kamchatka Riverv alley. A comprehensive study of unique alkaline cold springs was carried out in the Belaya River valley (Kamchatsky Peninsula). A large number of water and gas samples, sediments and mineral salts were collected for further analytical studies during the expedition works.

Water and Sediments of an Acidic Hot Spring—Distinct Differentiation with Regard to the Microbial Community Composition and Functions

Over the last half-century, microbial communities of the Kamchatka hot springs have been largely studied using molecular, radioisotopic, and cultural approaches. Generally, these results were obtained for mixed samples of water with sediments, for only hydrothermal water, or for only sediment samples. Simultaneous comparative analysis of the microbial communities of water and sediments was performed for only one Kamchatka hot spring with circumneutral pH. Here, the microbial communities of both sediments and water (separately) of hot spring #4229 (the Uzon Caldera, Kamchatka) with a temperature of 50–56 °C and pH of 3.2 were analyzed by 16S rRNA gene V4 fragment amplicon sequencing. It was revealed that the microbial community of sediments was represented by uncultured phylogenetically deep-branching lineages of archaea, such as ARK-15 within Thermoplasmatota and ‘Ca. Marsarchaeales’ from the Thermoproteota phyla. Metagenome analysis showed that these archaea most probably carried out the degradation of organic matter. The microbial community of the hot water is represented by thermoacidophilic, (micro)aerobic, chemolithoautotrophic, hydrogen- and sulfur-oxidizing bacteria of the genera Hydrogenobaculum (phylum Aquificota) and Acidithiobacillus (phylum Pseudomonadota). Radioisotopic tracing and DNA-stable-isotope probing techniques proved their role as primary producers in the hot spring. The experiment revealed significant differences in the composition and functions of the microbial communities of sediments and water through the example of a typical acidic hot spring in Kamchatka.

Geochemical Significance of Bicyclic Sesquiterpanes in Hydrothermal Oil of the Uzon Volcano Caldera (Kamchatka)

The composition and relative content of C14-C16 bicyclic sesquiterpanes in oil seeps from thermal springs of the Uzon Caldera have been studied by GC-MS technique. It is shown that C16 homodrimanes prevail in oil composition, C15 drimane content is insignificant, and C14 nordrimanes are present in trace amounts. Homodrimane with biological configuration 8α(H) was detected. Bicyclic sesquiterpanes of Uzon oil are probably its derivatives. It has been revealed that the relative content of C15 drimanes increases with the oil maturity. A sesquiterpane maturity index, which has not been used previously in organic geochemistry, is proposed.

Genetic Potential of Dissulfurimicrobium hydrothermale, an Obligate Sulfur-Disproportionating Thermophilic Microorganism

The biochemical pathways of anaerobic sulfur disproportionation are only partially deciphered, and the mechanisms involved in the first step of S0-disproportionation remain unknown. Here, we present the results of sequencing and analysis of the complete genome of Dissulfurimicrobium hydrothermale strain Sh68T, one of two strains isolated to date known to grow exclusively by anaerobic disproportionation of inorganic sulfur compounds. Dissulfurimicrobium hydrothermale Sh68T is a motile, thermophilic, anaerobic, chemolithoautotrophic microorganism isolated from a hydrothermal pond at Uzon caldera, Kamchatka, Russia. It is able to produce energy and grow by disproportionation of elemental sulfur, sulfite and thiosulfate. Its genome consists of a circular chromosome of 2,025,450 base pairs, has a G + C content of 49.66% and a completion of 97.6%. Genomic data suggest that CO2 assimilation is carried out by the Wood–Ljungdhal pathway and that central anabolism involves the gluconeogenesis pathway. The genome of strain Sh68T encodes the complete gene set of the dissimilatory sulfate reduction pathway, some of which are likely to be involved in sulfur disproportionation. A short sequence protein of unknown function present in the genome of strain Sh68T is conserved in the genomes of a large panel of other S0-disproportionating bacteria and was absent from the genomes of microorganisms incapable of elemental sulfur disproportionation. We propose that this protein may be involved in the first step of elemental sulfur disproportionation, as S0 is poorly soluble and unable to cross the cytoplasmic membrane in this form.

Specific of Stable Carbon Isotopes Determination in Organic-Bearing Sediments

The study of the carbon isotopic composition in organic-bearing bottom sediments of the thermal lake Fumarolnoye (Uzon caldera, Kamchatka) has been carried out. The results of studying δ13C changes in the bottom sediments of a thermal lake during the sequential extraction of H3PO4 for 2 hours, 24 hours and 7 days are presented. The change in δ13С with time and after treatment with HCl and H2O2 is shown using two samples as an example. After treatment with HCl, the δ13С values change relative to the initial ones from 1 to 3 ‰, which can be taken into account when interpreting the data. The standard procedure for removing carbonate with hydrogen peroxide reveals a significant transformation of the residual C‑containing substance in the case of a prolonged reaction with H3PO4 at elevated temperatures

Young \xaboil site\xbb of the Uzon Caldera as a habitat for unique microbial life

BackgroundThe Uzon Caldera is one of the places on our planet with unique geological, ecological, and microbiological characteristics. Uzon oil is the youngest on Earth. Uzon oil has unique composition, with low proportion of heavy fractions and relatively high content of saturated hydrocarbons. Microbial communities of the «oil site» have a diverse composition and live at high temperatures (up to 97 °C), significant oscillations of Eh and pH, and high content of sulfur, sulfides, arsenic, antimony, and mercury in water and rocks.ResultsThe study analyzed the composition, structure and unique genetics characteristics of the microbial communities of the oil site, analyzed the metabolic pathways in the communities. Metabolic pathways of hydrocarbon degradation by microorganisms have been found. The study found statistically significant relationships between geochemical parameters, taxonomic composition and the completeness of metabolic pathways. It was demonstrated that geochemical parameters determine the structure and metabolic potential of microbial communities.ConclusionsThere were statistically significant relationships between geochemical parameters, taxonomic composition, and the completeness of metabolic pathways. It was demonstrated that geochemical parameters define the structure and metabolic potential of microbial communities. Metabolic pathways of hydrocarbon oxidation was found to prevail in the studied communities, which corroborates the hypothesis on abiogenic synthesis of Uzon hydrothermal petroleum.

A CO2-Driven Gas Lift Mechanism in Geyser Cycling (Uzon Caldera, Kamchatka)

Here, we report on a new geyser (named Shaman) formed in the Uzon caldera (Kronotsky Federal Nature Biosphere Reserve, Russia) in autumn 2008 from a cycling hot Na-Cl spring. The geyser is a pool-type CO2-gas lift driven. From 2012 to 2018, the geyser has shown a rather stable interval between eruptions (IBE) from 129 to 144 min with a fountain height up to 4 m, and the geyser conduit has gradually enlarged. In 2019, the Shaman geyser eruption mode significantly changed: cold water inflow from the adjacent stream was re-directed into the geyser conduit and the average IBE decreased to 80 min. We observed two eruptive modes: a cycling hot spring (June 2019) and a cycling geyser (after June 2019). Bottom-hole temperature recording was performed in the geyser conduit to understand its activity. The TOUGH2-EOS2 model was used to reproduce the obtained temperature records and estimate geyser recharge/discharge parameters in both modes. Modeling shows that a larger cold inflow into the conduit causes a switch from cycling geyser to hot cycling spring mode. It was also found that the switch to cycling geyser mode corresponds to a larger mass of CO2 release during the time of the eruption.

Modern Mineral Formation in the Thermal Lake Fumarolnoe (Uzon Caldera, Kamchatka) as a Key to Paleoreconstruction

Paleoreconstruction of events involved in the bottom sedimentation has been carried out on the basis of mineral composition of the section of the minor lake IV (Lake Fumarolnoe, Kamchatka) bottom sediments. The lower sediments are composed mainly of smectite in association with gypsum and jarosite; they are overlain by smectite–kaolinite with a large amount of framboidal pyrite and diatom shells. There is also a layer of sinter opal–pyrite units and calcite. It is concluded that initially the minor lake IV was a mud pit with sulfide-bearing solutions. Then, after the lowering of the water level and the partial exposure of the bottom sediments on the surface, the latter were oxidized. The subsequent phreatic explosion provided the covering of oxidized sediments with the reduced substance from the lower horizons of the pit. Further setting of sediment accumulation corresponded to a source with cyanobacterial community developing around the gryphon, and then it changed to that of a shallow-water lake similar to a contemporary one. Sediments also include two layers of pyroclastic material originated from eruptions of neighboring volcanoes.

Comparison of the contribution of differently depth geological processes in the formation of a trace elements characteristic of caustobiolites

The article analyzes the correlation dependences between the logarithms of the concentrations of trace elements (TE) in various geochemical environments (oil, coal, fuel and black shales, as well as in clays, organic matter (OM) of various types and biota) in comparison with the average chemical composition of the upper, middle and lower continental crust. At the same time, along with the TE content of oils of the main oil and gas basins (OGB) – the Volga-Ural and West Siberian ones, the data on the TE content in the so-called young oils were summarized; as such, data on the oil fields of the West Kamchatka oil and gas field and oil manifestations in the area of ​​the caldera of the Uzon volcano were used. Particular attention was also paid to the results of the analysis of the TE composition of the oils of the Romashkino group of fields, as it is possible that they are subject to the influence of deep-seated processes. The correlation coefficients between the studied parameters for the various studied oil- and gas-generating basins, including for the Romashkino group of fields, turned out to be close. For all oils, except for the young oils of Kamchatka and the caldera of the Uzon volcano, a closer connection of their TE composition with the TE composition of the lower crust was revealed. For young oils of the Uzon caldera in Kamchatka, this trend is absent, and a slightly closer relationship is revealed with the average composition of the upper but not lower crust, while for statistically more reliable data on the TE composition of the hydrothermal waters of the caldera of the Uzon volcano, a significantly closer relationship is observed with the average chemical composition of the middle and upper crust. Based on the identified correlations between the TE compositions of oil, caustobioliths and the crust of different levels, conclusions are made about the likely relationship between biogenic and deep processes in the formation of oil and gas fields. According to the authors, the obtained results support the crucially important role in the processes of naphthidogenesis of the upward flows of the low crustal fluids with the dominant source of hydrocarbons from the initial OM of sedimentary basins.

Influence of hydrous pyrolysis on distribution of carbon and hydrogen isotopes by organic matter fractions. The nature of oil generation in the calder of Uzone Volcano in Kamchatka

The process of oil seeps transformation from the Uzon volcano caldera under the influence of hydrous pyrolysis at a temperature of 350 °C in argon and oxygen was investigated. It is shown that carbon and hydrogen isotope type curves (ITC) reflect the processes occurring in organic matter during hydrous pyrolysis in oxidizing and neutral media. The similarity in forms between carbon ITC of the Uzon oil seeps, the Bogachevka oil and biota of hydrothermal sources is revealed. Hydrogen ITCs have a more complex form, apparently associated with exchange processes occurring in hydrothermal water. Based on the conducted studies, it was assumed that on the one hand oil seeps in the Uzon caldera can serve as a source for the formation of Bogachevka oil, and on the other hand, it is possible that the circulating hydrothermal water in the caldera of the Uzon volcano brings to the surface the organic matter of the Bogachevka oil formation.

Effect of Hydrous Pyrolysis on the Distribution of Carbon and Hydrogen Isotopes between Fractions of Organic Matter. The Nature of Oil Seeps in the Uzon Caldera, Kamchatka, Russia

The paper presents data on the transformations of oil from seeps in the caldera of Uzon volcano under the effect of hydrous pyrolysis at a temperature of 350°C in an argon and oxygen atmosphere. The carbon and hydrogen isotopic-fractionation characteristics (IFC) are proved to reflect processes occurring in the organic matter at its hydrous pyrolysis in oxidizing and neutral environments. Similarities in configuration are detected between the carbon IFC of Uzon oil seeps, Bogachevskoe field, and the biota of hydrothermal springs. The hydrogen IFC are of more complicated form, perhaps, because of exchange processes in the hydrothermal water. It is hypothesized that oil seeps in the interiors of the Uzon caldera can provide material for the origin of oil at the Bogachevskoe field. At the same time, it cannot be ruled out that hydrothermal water circulating in the caldera of Uzon volcano brings the material of the Bogachevskoe oil to the surface.

Composition and distribution of saturated hydrocarbons in the thermal waters and vapor–water mixture of the Mutnovskii geothermal field and Uzon caldera, Kamchatka

The paper presents data on the composition and molecular-mass distribution of saturated hydrocarbons in sterile vapor–water mixture from wells and in high-temperature springs in the Mutnovskii hydrothermal area and Uzon caldera. The condensate of the vapor–water mixture and thermal waters from the Mutnovskii area contain low-molecule n-alkanes, which were generated by thermogenic processes. The boiling mud pot of the Donnoe fumarole field typically contains hydrocarbons whose origin is likely related to thermocatalytic transformations of the biomass of thermophilic microorganisms. A separate type of the molecular-mass distribution is typical of the geyser in the caldera of Uzon volcano: this material contains n-alkanes, which were generated by two processes: chemical re-synthesis of floral organic remnants and biogenic synthesis with the probable involvement of bacteria and algae.

Composition and Distribution of Saturated Hydrocarbons in the Thermal Waters and Vapor–Water Mixture of the Mutnovskii Geothermal Field and Uzon Caldera, Kamchatka

The paper presents data on the composition and molecular-mass distribution of saturated hydrocarbons in sterile vapor–water mixture from wells and in high-temperature springs in the Mutnovskii hydrothermal area and Uzon caldera. The condensate of the vapor–water mixture and thermal waters from the Mutnovskii area contain low-molecule n-alkanes, which were generated by thermogenic processes. The boiling mud pot of the Donnoe fumarole field typically contains hydrocarbons whose origin is likely related to thermocatalytic transformations of the biomass of thermophilic microorganisms. A separate type of the molecular-mass distribution is typical of the geyser in the caldera of Uzon volcano: this material contains n-alkanes, which were generated by two processes: chemical re-synthesis of floral organic remnants and biogenic synthesis with the probable involvement of bacteria and algae.

Paternal transmission of vulnerability to high fat diet-induced metabolic and neurobehavioural impairments

The draft genome sequence of Caldanaerobacter sp. strain 1523vc, a thermophilic bacterium, isolated from a hot spring of Uzon Caldera, (Kamchatka, Russia) is presented. The complete genome assembly was of 2 713 207 bp with predicted completeness of 99.38%. Genome structural annotation revealed 2674 protein-coding genes, 127 pseudogenes and 77 RNA genes. Pangenome analysis of 7 currently available high quality Caldanaerobacter spp. genomes including 1523vc revealed 4673 gene clusters. Of them, 1130 clusters formed a core genome of genus Caldanaerobacter. Of the rest 3543 Caldanaerobacter pangenome genes, 385 were exclusively represented in 1523vc genome. 101 of 2801 Caldanaerobacter CDS were found to be encoding carbohydrate-active enzymes (CAZymes). The majority of CAZymes were predicted to be involved in degradation of beta-linked polysaccharides as chitin, cellulose and hemicelluloses, reflecting the metabolism of strain 1523vc, isolated on cellulose. 5 of 101 CAZyme genes were found to be unique for the strain 1523vc and belonged to GH23, GT56, GH15 and two CE9 family proteins.The draft genome of strain 1523vc was deposited at DBJ/EMBL/GenBank under the accessions JABEQB000000000, PRJNA629090 and SAMN14766777 for Genome, Bioproject and Biosample, respectively.

Genomic Insights Into Energy Metabolism of Carboxydocella thermautotrophica Coupling Hydrogenogenic CO Oxidation With the Reduction of Fe(III) Minerals.

The genus Carboxydocella forms a deeply branching family in the class Clostridia and is currently represented by three physiologically diverse species of thermophilic prokaryotes. The type strain of the type species, Carboxydocella thermautotrophica 41T, is an obligate chemolithoautotroph growing exclusively by hydrogenogenic CO oxidation. Another strain, isolated from a hot spring at Uzon caldera, Kamchatka in the course of this work, is capable of coupling carboxydotrophy and dissimilatory reduction of Fe(III) from oxic and phyllosilicate minerals. The processes of carboxydotrophy and Fe(III) reduction appeared to be interdependent in this strain. The genomes of both isolates were sequenced, assembled into single chromosome sequences (for strain 41T a plasmid sequence was also assembled) and analyzed. Genome analysis revealed that each of the two strains possessed six genes encoding diverse Ni,Fe-containing CO dehydrogenases (maximum reported in complete prokaryotic genomes), indicating crucial role of carbon monoxide in C. thermautotrophica metabolism. Both strains possessed a set of 30 multiheme c-type cytochromes, but only the newly isolated Fe-reducing strain 019 had one extra gene of a 17-heme cytochrome, which is proposed to represent a novel determinant of dissimilatory iron reduction in prokaryotes. Mössbauer studies revealed that strain 019 induced reductive transformation of the abundant ferric/ferrous-mica mineral glauconite to siderite during carboxydotrophic growth. Reconstruction of the C. thermautotrophica strains energy metabolism is the first comprehensive genome analysis of a representative of the deep phylogenetic branch Clostridia Incertae Sedis, family V. Our data provide insights into energy metabolism of C. thermautotrophica with an emphasis on its ecological implications.

Tepidibaculum saccharolyticum gen. nov., sp. nov. a moderately thermophilic, anaerobic, spore-forming bacterium isolated from a terrestrial hot spring.

A novel moderately thermophilic, anaerobic bacterium, strain STR9T was isolated from terrestrial hot spring at Uzon Caldera, Kamchatka peninsula, Russia. Cells of strain STR9T were spore-forming motile straight or slightly curved rods 0.3μm in diameter and 1.0-2.0μm in length having a Gram-positive cell-wall structure. The temperature range for growth was 30-58°C, with an optimum at 50°C. The pH range for growth was 5.0-10.5, with an optimum at pH 8.0-9.0. NaCl inhibited growth of the strain STR9T and no growth was evident above 0.5% NaCl (w/v). Several mono-, di-, and polysaccharides as well as beef extract and yeast extract supported growth. The main end products of glucose fermentation were ethanol, acetate, hydrogen, and carbon dioxide. The G + C content of DNA of strain STR9T was 40.0mol% (Tm). Analysis of the 16S rRNA gene sequences revealed that strain STR9T belongs to the family Ruminococcaceae, class Clostridia, with less than 93% 16S rRNA gene sequence similarity to any species with validly published name. We propose to assign strain STR9T to a new species of a novel genus Tepidibaculum saccharolyticum gen. nov., sp. nov. The type strain is STR9T (= DSM 28577T = VKM B-2882T = UNIQEM STR9T).

Production of organic matter and diversity of the ribulose bisphosphate carboxylase genes in sediments of the Solnechny Spring, Uzon Caldera, Kamchatka

Production of organic matter and diversity of the ribulose bisphosphate carboxylase genes in sediments of the Solnechny Spring, Uzon Caldera, Kamchatka