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Enviroscan Ukrainian Institute of Speleology and Karstology


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Community news

Speleology in Kazakhstan

Shakalov on 04 Jul, 2018
Hello everyone!   I pleased to invite you to the official site of Central Asian Karstic-Speleological commission ("Kaspeko")   There, we regularly publish reports about our expeditions, articles and reports on speleotopics, lecture course for instructors, photos etc. ...

New publications on hypogene speleogenesis

Klimchouk on 26 Mar, 2012
Dear Colleagues, This is to draw your attention to several recent publications added to KarstBase, relevant to hypogenic karst/speleogenesis: Corrosion of limestone tablets in sulfidic ground-water: measurements and speleogenetic implications Galdenzi,

The deepest terrestrial animal

Klimchouk on 23 Feb, 2012
A recent publication of Spanish researchers describes the biology of Krubera Cave, including the deepest terrestrial animal ever found: Jordana, Rafael; Baquero, Enrique; Reboleira, Sofía and Sendra, Alberto. ...

Caves - landscapes without light

akop on 05 Feb, 2012
Exhibition dedicated to caves is taking place in the Vienna Natural History Museum   The exhibition at the Natural History Museum presents the surprising variety of caves and cave formations such as stalactites and various crystals. ...

Did you know?

That floating pan is an evaporation pan floating in a water body with drum floats [16].?

Checkout all 2699 terms in the KarstBase Glossary of Karst and Cave Terms


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Featured articles from Cave & Karst Science Journals
Chemistry and Karst, White, William B.
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Featured articles from other Geoscience Journals
Karst environment, Culver D.C.
Mushroom Speleothems: Stromatolites That Formed in the Absence of Phototrophs, Bontognali, Tomaso R.R.; D’Angeli Ilenia M.; Tisato, Nicola; Vasconcelos, Crisogono; Bernasconi, Stefano M.; Gonzales, Esteban R. G.; De Waele, Jo
Calculating flux to predict future cave radon concentrations, Rowberry, Matt; Marti, Xavi; Frontera, Carlos; Van De Wiel, Marco; Briestensky, Milos
Microbial mediation of complex subterranean mineral structures, Tirato, Nicola; Torriano, Stefano F.F;, Monteux, Sylvain; Sauro, Francesco; De Waele, Jo; Lavagna, Maria Luisa; D’Angeli, Ilenia Maria; Chailloux, Daniel; Renda, Michel; Eglinton, Timothy I.; Bontognali, Tomaso Renzo Rezio
Evidence of a plate-wide tectonic pressure pulse provided by extensometric monitoring in the Balkan Mountains (Bulgaria), Briestensky, Milos; Rowberry, Matt; Stemberk, Josef; Stefanov, Petar; Vozar, Jozef; Sebela, Stanka; Petro, Lubomir; Bella, Pavel; Gaal, Ludovit; Ormukov, Cholponbek;
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Your search for geomicrobiology (Keyword) returned 38 results for the whole karstbase:
Showing 16 to 30 of 38
Iron oxide-rich filaments: Possible fossil bacteria in Lechuguilla Cave, New Mexico, 2001,
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Provencio P. P. , Polyak V. J. ,
Reddish filaments in two fragments of unusual iron oxide bearing stalactites, 'the Rusticles' from Lechuguilla Cave, New Mexico, are found only within the central canals of the Rusticles. The curved, helical, and/or vibrioidal filaments vary from 1 to 6 mum in outer diameter and 10 to >50 mum in length. SEM and TEM show the filaments have 0.5-mum diameter central tubes, with goethite crystals radiating outwardly along their lengths. The diameter of the central tubes is consistent with the diameter of many iron-oxidizing filamentous bacteria. Although most iron oxide depositing bacteria do not deposit well-crystallized radiating goethite, we propose thick hydrous iron oxide was slowly crystallized from amorphous material to goethite, in place, over a relatively long period of time. From the gross morphology and the particular setting, we suggest this represents an occurrence of fossilized, acidophilic iron-oxidizing bacteria

Microbial contributions to cave formation: New insights into sulfuric acid speleogenesis, 2004,
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Engel As, Stern La, Bennett Pc,
The sulfuric acid speleogenesis (SAS) model was introduced in the early 1970s from observations of Lower Kane Cave, Wyoming, and was proposed as a cave-enlargement process due to primarily H2S autoxidation to sulfuric acid and subaerial replacement of carbonate by gypsum. Here we present a reexamination of the SAS type locality in which we make use of uniquely applied geochemical and microbiological methods. Little H2S escapes to the cave atmosphere, or is lost by abiotic autoxidation, and instead the primary H2S loss mechanism is by subaqueous sulfur-oxidizing bacterial communities that consume H2S. Filamentous 'Epsilonproteobacteria' and Gammaproteobacteria, characterized by fluorescence in situ hybridization, colonize carbonate surfaces and generate sulfuric acid as a metabolic byproduct. The bacteria focus carbonate dissolution by locally depressing pH, compared to bulk cave waters near equilibrium or slightly supersaturated with calcite. These findings show that SAS occurs in subaqueous environments and potentially at much greater phreatic depths in carbonate aquifers, thereby offering new insights into the microbial roles in subsurface karstification

Involvement of microorganisms in the formation of carbonate speleothems in the Cervo Cave (L'Aquila-Italy), 2004,
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Cacchio P, Contento R, Ercole C, Cappuccio G, Martinez Mp, Lepidi A,
Much is known about the bacterial precipitation of carbonate rocks, but comparatively little is known about the involvement of microbes in the formation of secondary mineral structures in caves. We hypothesized that bacteria isolated from calcareous stalactites, which are able to mediate CaCO3 precipitation in vitro, play a role in the formation of carbonate speleothems. We collected numerous cultivable calcifying bacteria from calcareous speleothems from Cervo cave, implying that their presence was not occasional. The relative abundance of calcifying bacteria among total cultivable microflora was found to be related to the calcifying activity in the stalactites. We also determined the delta(13)C and delta(18)O values of the Cervo cave speleothems from which bacteria were isolated and of the carbonates obtained in vitro to determine whether bacteria were indeed involved in the formation of secondary mineral structures. We identified three groups of biological carbonates produced in vitro at 11degreesC on the basis of their carbon isotopic composition: carbonates with delta(13)C values ( a) slightly more positive, (b) more negative, and (c) much more negative than those of the stalactite carbonates. The carbonates belonging to the first group, characterized by the most similar delta(13)C values to stalactites, were produced by the most abundant strains. Most of calcifying isolates belonged to the genus Kocuria. Scanning electron microscopy showed that dominant morphologies of the bioliths were sherulithic with fibrous radiated interiors. We suggest a mechanism of carbonate crystal formation by bacteria

The Geomicrobiology of Ore Deposits, 2005,
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Southam G. , Saunders James A. ,
Bacterial metabolism, involving redox reactions with carbon, sulfur, and metals, appears to have been important since the dawn of life on Earth. In the Archean, anaerobic bacteria thrived before the Proterozoic oxidation of the atmosphere and the oceans, and these organisms continue to prosper in niches removed from molecular oxygen. Both aerobes and anaerobes have profound effects on the geochemistry of dissolved metals and metal-bearing minerals. Aerobes can oxidize dissolved metals and reduced sulfur, as well as sulfur and metals in sulfide minerals can contribute to the supergene enrichment of sulfide ores, and can catalyze the formation of acid mine drainage. Heterotrophic anaerobes, which require organic carbon for their metabolism, catalyze a number of thermodynamically favorable reactions such as Fe-Mn oxyhydroxide reductive dissolution (and the release of sorbed metals to solution) and sulfate reduction. Bacterial sulfate reduction to H2S can be very rapid if reactive organic carbon is present and can lead to precipitation of metal sulfides and perhaps increase the solubility of elements such as silver, gold, and arsenic that form stable Me-H2S aqueous complexes. Similarly, the bacterial degradation of complex organic compounds such as cellulose and hemicellulose to simpler molecules, such as acetate, oxalate, and citrate, can enhance metal solubility by forming Me organic complexes and cause dissolution of silicate minerals. Bacterially induced mineralization is being used for the bioremediation of metal-contaminated environments. Through similar processes, bacteria may have been important contributors in some sedimentary ore-forming environments and could be important along the low-temperature edges of high-temperature systems such as those that form volcanogenic massive sulfides

Geomicrobiology of cave ferromanganese deposits: A field and laboratory investigation, 2005,
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Spilde M. N. , Northup D. E. , Boston P. J. , Schelble R. T. , Dano K. E. , Crossey L. J. , Dahm C. N. ,
Unusual ferromanganese deposits are found in several caves in New Mexico. The deposits are enriched in iron and manganese by as much as three orders of magnitude over the bedrock, differing significantly in mineralogy and chemistry from bedrock-derived insoluble residue. The deposits contain metabolically active microbial communities. Enrichment cultures inoculated from the ferromanganese deposits produced manganese oxides that were initially amorphous but developed into crystalline minerals over an 8-month period and beyond; no such progression occurred in killed controls. Phylogenetic analyses of sequences from clone libraries constructed from culture DNA identified two genera known to oxidize manganese, but most clones represent previously unknown manganese oxidizers. We suggest that this community is breaking down the bedrock and accumulating iron and manganese oxides in an oligotrophic environment

Hazel A. Barton and Diana E. Northup, 2007,
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Barton Hazel A. And Northup Diana E.
The Karst Waters Institute Breakthroughs in Karst Geomicrobiology and Redox Geochemistry conference in 1994 was a watershed event in the history of cave geomicrobiology studies within the US. Since that time, studies of cave geomicrobiology have accelerated in number, complexity of techniques used, and depth of the results obtained. The field has moved from being sparse and largely descriptive in nature, to rich in experimental studies yielding fresh insights into the nature of microbe-mineral interactions in caves. To provide insight into the changing nature of cave geomicrobiology we have divided our review into research occurring before and after the Breakthroughs conference, and concentrated on secondary cave deposits: sulfur (sulfidic systems), iron and manganese (ferromanganese, a.k.a. corrosion residue deposits), nitrate (a.k.a. saltpeter), and carbonate compounds (speleothems and moonmilk deposits). The debate concerning the origin of saltpeter remains unresolved; progress has been made on identifying the roles of bacteria in sulfur cave ecosystems, including cavern enlargement through biogenic sulfuric acid; new evidence provides a model for the action of bacteria in forming some moonmilk deposits; combined geochemical and molecular phylogenetic studies suggest that some ferromanganese deposits are biogenic, the result of redox reactions; and evidence is accumulating that points to an active role for microorganisms in carbonate precipitation in speleothems.

The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments, 2007,
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Barton Hazel A. , Taylor Nicholas M. , Kreate Michael P. , Springer Austin C. , Oehrle Stuart A. And Bertog Janet L.
Despite extremely starved conditions, caves contain surprisingly diverse microbial communities. Our research is geared toward understanding what ecosystems drivers are responsible for this high diversity. To asses the effect of rock fabric and mineralogy, we carried out a comparative geomicrobiology study within Carlsbad Cavern, New Mexico, USA. Samples were collected from two different geologic locations within the cave: WF1 in the Massive Member of the Capitan Formation and sF88 in the calcareous siltstones of the Yates Formation. We examined the organic content at each location using liquid chromatography mass spectroscopy and analyzed microbial community structure using molecular phylogenetic analyses. In order to assess whether microbial activity was leading to changes in the bedrock at each location, the samples were also examined by petrology, X-ray diffraction (XRD) and scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX). Our results suggest that on the chemically complex Yates Formation (sF88), the microbial community was significantly more diverse than on the limestone surfaces of the Capitan (WF1), despite a higher total number of cells on the latter. Further, the broader diversity of bacterial species at sF88 reflected a larger range of potential metabolic capabilities, presumably due to opportunities to use ions within the rock as nutrients and for chemolithotrophic energy production. The use of these ions at sF88 is supported by the formation of a corrosion residue, presumably through microbial scavenging activities. Our results suggest that rock fabric and mineralogy may be an important driver of ecosystem function and should be carefully reviewed when carrying out microbial community analysis in cave environments.

The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments., 2007,
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Barton Hazel A. , Taylor Nicholas M. , Kreate Michael P. , Springer Austin C. , Oehrle Stuart A, Bertog Janet L.
Despite extremely starved conditions, caves contain surprisingly diverse microbial communities. Our research is geared toward understanding what ecosystems drivers are responsible for this high diversity. To asses the effect of rock fabric and mineralogy, we carried out a comparative geomicrobiology study within Carlsbad Cavern, New Mexico, USA. Samples were collected from two different geologic locations within the cave: WF1 in the Massive Member of the Capitan Formation and sF88 in the calcareous siltstones of the Yates Formation. We examined the organic content at each location using liquid chromatography mass spectroscopy and analyzed microbial community structure using molecular phylogenetic analyses. In order to assess whether microbial activity was leading to changes in the bedrock at each location, the samples were also examined by petrology, X-ray diffraction (XRD) and scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX). Our results suggest that on the chemically complex Yates Formation (sF88), the microbial community was significantly more diverse than on the limestone surfaces of the Capitan (WF1), despite a higher total number of cells on the latter. Further, the broader diversity of bacterial species at sF88 reflected a larger range of potential metabolic capabilities, presumably due to opportunities to use ions within the rock as nutrients and for chemolithotrophic energy production. The use of these ions at sF88 is supported by the formation of a corrosion residue, presumably through microbial scavenging activities. Our results suggest that rock fabric and mineralogy may be an important driver of ecosystem function and should be carefully reviewed when carrying out microbial community analysis in cave environments.

The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments, 2007,
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Barton H. A. , Taylor N. M. , Kreate M. P. , Springer A. C. , Oehrle S. A. , Bertog J. L.

Despite extremely starved conditions, caves contain surprisingly diverse microbial communities. Our research is geared toward understanding what ecosystems drivers are responsible for this high diversity. To asses the effect of rock fabric and mineralogy, we carried out a comparative geomicrobiology study within Carlsbad Cavern, New Mexico, USA. Samples were collected from two different geologic locations within the cave: WF1 in the Massive Member of the Capitan Formation and sF88 in the calcareous siltstones of the Yates Formation. We examined the organic content at each location using liquid chromatography mass spectroscopy and analyzed microbial community structure using molecular phylogenetic analyses. In order to assess whether microbial activity was leading to changes in the bedrock at each location, the samples were also examined by petrology, X-ray diffraction (XRD) and scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX). Our results suggest that on the chemically complex Yates Formation (sF88), the microbial community was significantly more diverse than on the limestone surfaces of the Capitan (WF1), despite a higher total number of cells on the latter. Further, the broader diversity of bacterial species at sF88
reflected a larger range of potential metabolic capabilities, presumably due to opportunities to use ions within the rock as nutrients and for chemolithotrophic energy production. The use of these ions at sF88 is supported by the formation of a corrosion residue, presumably through microbial scavenging activities. Our results suggest that rock fabric and mineralogy may be an important driver of ecosystem function and should be carefully reviewed when carrying out microbial community analysis in cave environments.


, 2008,
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Jones O. S. , Lyon E. H. , And Macalady J. L.
Su lfid ic cave walls host abundant, rapid ly-growing micro bia l communities that display a variety o f mo rphologies previously described for verrn iculations. Here we present molecular, microscopic, isotopic, and geochemical data describing the geomicrobiology o f these biovennic ulations from the Frasassi cave system, Italy. The biove rm iculations are compo sed of densely packed prokaryo tic and funga l cells in a mineral-organ ic matrix co ntaining 5 to 25% o rganic carbon. The carbon and nitrogen isoto pe compositions o f the biovermiculations (ti 13e = - 35 to - 43%0, and til 5N = 4 to - 270/00. respectively) indicate that with in sulfidic zo nes, the o rga nic matter o rigina tes from chemolithotrophic bacterial primary productivity. Based on 165 rRNA gene cloning (n=67). the bioverrn ... iculation communitv is extrernelv diverse, incl uding 48 . ~ . ... representative phylotypes (>98% identity) from at least 15 major bacterial lineages. Important lineages include the Betaproteobacteria (1 9.5% of clones). Gammaproteobacteria (1 8%). Acidobacteria (1 0.5%). Nitrospirae (7.5%). and Planctomyces (7.5%). The most abundant phylotype, comprising over 100/0 of the 16S rRNA gene sequences. groups in an unnamed clade within the Gammaproteobacteria. Based on phylogenetic analysis, we have identified potential sulfur- and nitrite-oxidizing bacte ria. as well as both auto- and heterotrophic members of the biovermiculation community. Additionally. many of the clones a re representatives of deeply branching bacterial lineages with no cultivated representatives. The geochemistry and microbial composition of the biovermicula tions suggest that they play a role in acid production and carbonate disso lution. thereby contributing to cave formation.

Geomicrobiology of biovermiculations from the Frasassi Cave System, Italy, 2008,
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D. S. Jones, E. H. Lyon, And J. L. Macalady

Sulfidic cave walls host abundant, rapidly-growing microbial communities that display a variety of morphologies previously described for vermiculations. Here we present molecular, microscopic, isotopic, and geochemical data describing the geomicrobiology of these biovermiculations from the Frasassi cave system, Italy. The biovermiculations are composed of densely packed prokaryotic and fungal cells in a mineral-organic matrix containing 5 to 25% organic carbon. The carbon and nitrogen isotope compositions of the biovermiculations (d13C 5 235 to 243%, and d15N 5 4 to 227%, respectively) indicate that within sulfidic zones, the organic matter originates from chemolithotrophic bacterial primary productivity. Based on 16S rRNA gene cloning (n567), the biovermiculation community is extremely diverse, including 48 representative phylotypes (.98% identity) from at least 15 major bacterial lineages. Important lineages include the Betaproteobacteria (19.5% of clones), Gammaproteobacteria (18%), Acidobacteria (10.5%), Nitrospirae (7.5%), and Planctomyces (7.5%). The most abundant phylotype, comprising over 10% of the 16S rRNA gene sequences, groups in an unnamed clade within the Gammaproteobacteria. Based on phylogenetic analysis, we have identified potential sulfur- and nitrite-oxidizing bacteria, as well as both auto- and heterotrophic members of the biovermiculation community. Additionally, many of the clones are representatives of deeply branching bacterial lineages with no cultivated representatives. The geochemistry and microbial composition of the biovermiculations suggest that they play a role in acid production and carbonate dissolution, thereby contributing to cave formation.


Focus Group on Caves and Karst as Model Systems in Geomicrobiology, 2008,
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Engel A. S. , Northup D. , Gary M. , Gonzalez B. , Gonzalez J. , Hutchens E. , Jones D. , Macalady J. , Spear J. , Spilde M.

Impacts of Alterations of Organic Inputs on the Bacterial Community within the sediments of Wind Cave, South Dakota, USA., 2009,
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Chelius M. K. , Beresford G. , Horton H. , Quirk M. , Selby G. , Simpson R. T. , Horrocks R. , Moore J. C.
Wind Cave (WICA) in the Black Hills of South Dakota, like many mostly dry caves in temperate regions is an energy-starved system. The biotic communities that reside in these systems are low in diversity and simple in structure, and sensitive to changes in external inputs of organic matter. Caves open to tourist traffic offer an opportunity to study the impacts of organic matter amendments in the form of human and rodent hair and dander, clothing lint, material from rodent activity (nesting materials and feces), and algal growth in and around artificial lighting. This study reports on the impacts of carbon amendments from humans and rodents on the bacterial and archaeal communities within the sediments of WICA from annual surveys and from a manipulative study that added lint (L; cellulose plus rodent dander and rodent hair), rodent feces (F), and a combination of both (LF). The survey confirmed that bacterial biomass was higher in regions of the cave with the highest rates of lint (hair and natural clothing fibers) input. The manipulative study found that organic amendments in the forms of lint (L) and rodent feces (F) altered the WICA bacterial community structure in both abundance and diversity, with the combined lint and feces (LF) amendment having the most significant response. The high similarity of the LF and L communities suggests that the cave bacterial community is more carbon than nitrogen limited. The implication of cave development to management practices is immediate and practical. Even small amounts of lint and organic matter foreign to cave bacteria significantly compromise the integrity of the endemic community resulting in the replacement of undescribed species by assemblages with at best, unknown impacts to natural cave features.

Microbial Communities and Associated Mineral Fabrics in Altamira Cave, Spain., 2009,
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Cuezva S. , Sanchezmoral S. , Saizjimenez C. And Caaveras J. C.
Evidences of microbial colonizations were observed in Altamira Cave, Spain. These consisted of distinct small coloured colonies, both on walls and ceiling, mainly located in the area near the cave entrance, which progressed until reaching the Polychromes Hall. The colonizations were characterized by a high morphological and microstructural variability and related to biomineralization processes. Two main types of CaCO3 deposits were related to the colonies: rosette- or nest-like aggregates of rhombohedral calcite crystals, and spheroid to hemispheroid CaCO3 elements. Colonies distribution seems to be controlled by microenvironmental conditions inside the cavity. The areas of the cave showing higher temperature, relative humidity, and CO2 concentration fluctuations presented a minor biomineralization capability.

Unique iron-manganese colonies of microorganisms in Zoloushka Cave (Ukraine-Moldova), 2009,
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Andreychouk V. N. , Klimchouk A. , Boston P. , Galuskin E.

During open-pit quarrying and related lowering of groundwater level in the gypsum karst aquifer (since 1950), large cave Zoloushka became accessible for direct exploration, in which considerable geochemical transformations of environment occurred, accompanied by the formation of specific deposits, as well as by burst of microbial activity. Among microorganisms, some of the most active were various iron bacteria. Microbial activity has resulted in precipitation of black and red biochemical formations – microbialites (coatings, crusts, films, stalactites, stalagmites, etc.), which cover walls and floors of cave passages. Most interesting among the microbialites are iron-rich colonial formations of various shapes (stalagmite-like, tube-like, coral-like, etc.) formed by yet unidentified fungi-like microorganisms which likely are new to science. In this paper, we characterize occurrence and morphology of the colonial aggregates, morphology and chemical composition of microorganisms  and develop working hypotheses of their identification.


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