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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. ...

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. ...

Speleology in Kazakhstan

Shakalov on 11 Jul, 2012
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 water of dehydration is water freed from hydrous minerals by chemical changes [16].?

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Featured articles from Cave & Karst Science Journals
Chemistry and Karst, White, William B.
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Geochemical and mineralogical fingerprints to distinguish the exploited ferruginous mineralisations of Grotta della Monaca (Calabria, Italy), Dimuccio, L.A.; Rodrigues, N.; Larocca, F.; Pratas, J.; Amado, A.M.; Batista de Carvalho, L.A.
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
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Your search for rdna (Keyword) returned 13 results for the whole karstbase:
Fungal communities on speleothem surfaces in Kartchner Caverns, Arizona, USA, , Vaughan Michael J. , Maier Raina M. , Pryor Barry M.

Kartchner Caverns, located near Benson, Arizona, USA, is an active carbonate cave that serves as the major attraction for Kartchner Caverns State Park. Low-impact development and maintenance have preserved prediscovery macroscopic cavern features and minimized disturbances to biological communities within the cave.. The goal of this study was to examine fungal diversity in Kartchner Caverns on actively-forming speleothem surfaces. Fifteen formations were sampled from five sites across the cave. Richness was assessed using standard culture-based fungal isolation techniques. A culture-independent analysis using denaturing gradient gel electrophoresis (DGGE) was used to assay evidence of community homogeneity across the cave through the separation of 18S rDNA amplicons from speleothem community DNA. The culturing effort recovered 53 distinct morphological taxonomic units (MTUs), corresponding to 43 genetic taxonomic units (GTUs) that represented 21 genera. From the observed MTU accumulation curve and the projected total MTU richness curve, it is estimated that 51 percent of the actual MTU richness was recovered. The most commonly isolated fungi belonged to the genera Penicillium, Paecilomyces, Phialophora, and Aspergillus. This culturebased analysis did not reveal significant differences in fungal richness or number of fungi recovered across sites. Cluster analysis using DGGE band profiles did not reveal distinctive groupings of speleothems by sample site. However, canonical correspondence analysis (CCA) analysis of culture-independent DGGE profiles showed a significant effect of sampling site and formation type on fungal community structure. Taken together, these results reveal that diverse fungal communities exist on speleothem surfaces in Kartchner Caverns, and that these communities are not uniformly distributed spatially. Analysis of sample saturation indicated that more sampling depth is required to uncover the full scale of mycological richness across spelothem surfaces.


Subsidence caused by gypsum dissolution at Ripon, North Yorkshire, 1999, Cooper Ah, Waltham Ac,
In the afternoon of Wednesday 23 April 1997, a large subsidence crater opened up in front of a house on Ure Bank Terrace, on the northern outskirts of Ripon in North Yorkshire. Overnight its sides collapsed inwards, so that the hole had doubled in size by the next morning (Fig. 1). The subsidence crater was then 10 m in diam- eter, and 5.5 m deep to a choke of debris overlain by water 1 m deep. Its sudden appearance was the cause of considerable concern to the occupants of the adjacent house, and the event was widely reported in the national press and media. A subsidence hollow was mapped at this site by the 1856 Ordnance Survey and documented by Cooper (1986). More subsidence had occurred at the Ure Bank site in previous years, but this latest collapse had rather more impact. Creeping movement of the soil towards the new hole meant that the adjacent house was destined for demolition. The event was the latest of a series of ground collapses that have occurred, at an average rate of about one per year, in and around the city of Ripon. While they are little more than an inconvenience in farmland, they have the potential to cause serious damage when they occur in built-up areas. The immediate cause of the Ure Bank subsidence was the downward movement of soil, drift and recent fill into actively expanding voids within the ground. Ultimately, it was caused by the partial collapse of a cave ... This 250-word extract was created in the absence of an abstract

Bacterial diversity and ecosystem function of filamentous microbial mats from aphotic (cave) sulfidic springs dominated by chemolithoautotrophic 'Epsilonproteobacteria', 2004, Engel As, Porter Ml, Stern La, Quinlan S, Bennett Pc,
Filamentous microbial mats from three aphotic sulfidic springs in Lower Kane Cave. Wyoming. were assessed with regard to bacterial diversity, community structure, and ecosystem function using a 16S rDNA-based phylogenetic approach combined with elemental content and stable carbon isotope ratio analyses. The most prevalent mat morphotype consisted of while filament bundles, with low C:N ratios (3.5-5.4) and high sulfur content (16.1-51.2%). White filament bundles and two other mat morphotypes organic carbon isotope values (mean delta(13)C = -34.7parts per thousand: 1sigma = 3.6) consistent with chemolithoautotrophic carbon fixation from a dissolved inorganic carbon reservoir (cave water, mean delta(13)C = -7.47parts per thousand for two springs, n = 8). Bacterial diversity was as low overall in the clone libraries, and the most abundant taxonomic group was affiliated with the 'Epsilonproteobacteria' (68%) with other bacterial sequences affiliated with Gammaproteobacteria (12.2%), Betaproteobacteria (11.7%), Deltaproteobacteria (0.8%), and the Acidobacterium (5.6%) and Bacteriodetes/Chlorobi (1.7%) divisions. Six distinct epsilonproteobacterial taxonomic groups were identified from the microbial mats. Epsilonproteobacterial and bacterial group abundances and community structure shifted front the spring orifices downstream. corresponding to changes in dissolved sulfide and oxygen concentrations and metabolic requirements of certain bacterial groups. Most of the clone sequences for epsilonproteobacterial groups were retrieved from areas with high sulfide and low oxygen concentrations, whereas Thiothrix spp. and Thiobacillus spp. had higher retrieved clone abundances where conditions of low sulfide and high oxygen concentrations were measured. Genetic and metabolic diversity among the 'Epsilonproteobacteria' maximizes overall cave ecosystem function, and these organisms play a significant role in providing chemolithoautotrophic energy to the otherwise nutrient-poor cave habitat. Our results demonstrate that sulfur cycling supports subsurface ecosystem through chemolithoautotrophy and expand the evolutionary and ecological views of 'Epsilonproteobacteria' in terrestrial habitats. (C) 2004 Federation of European Microbiological Societies. Published by Elsevier BY. All rights reserved

The distribution and life history of Arrhopalites caecus (Tullberg): Order: Collembola, in Wind Cave, South Dakota, USA., 2005, Moore J. C. , Saunders P. , Selby G. , Horton H. , Chelius M. K. , Chapman A. , Horrocks R. D.
Individuals of the collembolan species Arrhopalites caecus (Tullberg) were collected from drip pools within Wind Cave, South Dakota, at Methodist Church adjacent to the Natural Entrance Tour Route and Room Draculum near survey marker NP-39. Specimens were identified as A. caecus using direct interference and scanning electron microscopy. Molecular analysis of the D2 region of 28S rDNA was performed and the sequences were deposited in Genbank (accession number AY239037). We determined that our population of A. caecus reproduced parthenogenetically by successively isolating and rearing eggs through the F4 generation on 9:5 plaster:charcoal media maintained at 21C, and by the absence of males. Molecular analysis of 16S rDNA for bacterium within our specimens failed to detect the ?-pro-teobacterium (Rickettseales) Wolbachia. Generation times, fecundity, and molt frequency were consistent with other reports for Collembola.

Bacterial dynamics in spring water of alpine karst aquifers indicates the presence of stable autochthonous microbial endokarst communities, 2005, Farnleitner Ah, Wilhartitz I, Ryzinska G, Kirschner Akt, Stadler H, Burtscher Mm, Hornek R, Szewzyk U, Herndl G, Mach Rl,
Spring water of two alpine karst aquifers differing in hydrogeology but of nearby catchments were investigated for their bacterial population dynamics. Dolomite karst aquifer spring 1 (DKAS 1) represents a dolomitic-limestone karst aquifer spring showing high average water residence time and relative constant flow. Limestone karst aquifer spring 2 (LKAS 2) constitutes a typical limestone karst aquifer spring with a dynamic hydrological regime and discharge. Dolomite karst aquifer spring 1 yielded constantly lower cell counts and biomasses (median of 15 x 10(6) cells l(-1) and 0.22 mu g C l(-1)) as the LKAS 2 (median of 63 x 10(6) cells l(-1) and 1.1 mu g C l(-1)) and distribution of morphotypes and mean cell volumes was also different between the considered systems, indicating the influence of hydrogeology on microbial spring water quality. Molecular bacterial V3 16S-rDNA profiles revealed remarkable constancy within each spring water throughout the investigation period. Time course analysis of a flood event in LKAS 2 further supported the trend of the temporal constancy of the microbial community. Except for one case, retrieval of partial and full length 16S rDNA gene sequences from the relative constant DKAS 1 revealed similarities to presently known sequences between 80% to 96%, supporting the discreteness of the microbial populations. The gathered results provide first evidence for the presence of autochthonous microbial endokarst communities (AMEC). Recovery of AMEC may be considered of relevance for the understanding of alpine karst aquifer biogeochemistry and ecology, which is of interest as many alpine and mountainous karst springs are important water resources throughout the world

Dominant Microbial Populations in Limestone-Corroding Stream Biofilms, Frasassi Cave System, Italy, 2006, Macalady Jennifer L. , Lyon Ezra H. , Koffman Bess, Albertson Lindsey K. , Meyer Katja, Galdenzi Sandro, Mariani Sandro,
Waters from an extensive sulfide-rich aquifer emerge in the Frasassi cave system, where they mix with oxygen-rich percolating water and cave air over a large surface area. The actively forming cave complex hosts a microbial community, including conspicuous white biofilms coating surfaces in cave streams, that is isolated from surface sources of C and N. Two distinct biofilm morphologies were observed in the streams over a 4-year period. Bacterial 16S rDNA libraries were constructed from samples of each biofilm type collected from Grotta Sulfurea in 2002. {beta}-, {gamma}-, {delta}-, and {varepsilon}-proteobacteria in sulfur-cycling clades accounted for [≥]75% of clones in both biofilms. Sulfate-reducing and sulfur-disproportionating {delta}-proteobacterial sequences in the clone libraries were abundant and diverse (34% of phylotypes). Biofilm samples of both types were later collected at the same location and at an additional sample site in Ramo Sulfureo and examined, using fluorescence in situ hybridization (FISH). The biomass of all six stream biofilms was dominated by filamentous {gamma}-proteobacteria with Beggiatoa-like and/or Thiothrix-like cells containing abundant sulfur inclusions. The biomass of {varepsilon}-proteobacteria detected using FISH was consistently small, ranging from 0 to less than 15% of the total biomass. Our results suggest that S cycling within the stream biofilms is an important feature of the cave biogeochemistry. Such cycling represents positive biological feedback to sulfuric acid speleogenesis and related processes that create subsurface porosity in carbonate rocks

How long does evolution of the troglomorphic form take? Estimating divergence times in Astyanax mexicanus, 2007, Porter M. L. , Dittmar K. , Pé, Rezlosada M.

Features including colonization routes (stream capture) and the existence of both epigean and cave-adapted hypogean popula­tions make Astyanax mexicanus an attractive system for investi­gating the subterranean evolutionary time necessary for acqui­sition of the troglomorphic form. Using published sequences, we have estimated divergence times for A. mexicanus using: 1) two different population-level mitochondrial datasets (cyto­chrome b and NADH dehydrogenase 2) with both strict and relaxed molecular clock methods, and 2) broad phylogenetic approaches combining fossil calibrations and with four nuclear (recombination activating gene, seven in absentia, forkhead, and α-tropomyosin) and two mitochondrial (16S rDNA and cytochrome b) genes. Using these datasets, we have estimated divergence times for three events in the evolutionary history of troglomorphic A. mexicanus populations. First, divergence among cave haplotypes occurred in the Pleistocene, possibly correlating with fluctuating water levels allowing the coloni­zation and subsequent isolation of new subterranean habitats. Second, in one lineage, A. mexicanus cave populations expe­rienced introgressive hybridization events with recent surface populations (0.26-2.0 Ma), possibly also correlated with Pleis­tocene events. Finally, using divergence times from surface populations in the lineage without evidence of introgression as an estimate, the acquisition of the troglomorphic form in A. mexicanus is younger than 2.2 (fossil calibration estimates) – 5.2 (cytb estimate) Ma (Pliocene).


DISTRIBUTION AND CHARACTER OF KARST IN THE LAO PDR, 2009, Kiernan Kevin
The extensive karst areas of the Lao PDR are poorly documented but are known to include extensive limestone mountain plateaus; isolated ridges including towerkarst; hillslopes that are locally underlain by limestone; and alluvium-covered limestone plains. Palaeokarst phenomena attest to a very long history of karstification while sediments in some caves offer insight into environmental change during the Quaternary. Limited financial and technical resources, political factors and the dangers posed by massive volumes of unexploded ordnance that remain after decades of war are major impediments to karst area documentation, analysis, planning and management. Assessment of karst extent based on aerial photographs and other remote sensing techniques is complicated by very extensive pseudokarst formed due to bombardment during past military con*icts, including hundreds of thousands of closed depressions formed in both carbonate and non-carbonate rocks. Notwithstanding such practical di+culties, the extent and importance of the karst is such that improved inventory at the national, provincial and local levels is required if satisfactory environmental management and sustainable social and economic development are to be achieved.

A recently evolved symbiosis between chemoautotrophic bacteria and a cave-dwelling amphipod, 2009, Dattagupta, S. , Schaperdoth, I. , Montanari, A. , Mariani, S. , Kita, N. , Valley, J. W. And Macalady, J. L.
Symbioses involving animals and chemoautotrophic bacteria form the foundation of entire ecosystems at deep-sea hydrothermal vents and cold seeps, but have so far not been reported in terrestrial or freshwater environments. A rare example of a terrestrial ecosystem sustained by chemoautotrophy is found within the sulfide-rich Frasassi limestone cave complex of central Italy. In this study, we report the discovery of abundant filamentous bacteria on the exoskeleton of Niphargus ictus, a macroinvertebrate endemic to Frasassi. Using 16S rDNA sequencing and fluorescence in situ hybridization (FISH), we show that N. ictus throughout the large cave complex are colonized by a single phylotype of bacteria in the sulfur-oxidizing clade Thiothrix. The epibiont phylotype is distinct from Thiothrix phylotypes that form conspicuous biofilms in the cave streams and pools inhabited by N. ictus. Using a combination of 13C labeling, FISH, and secondary ion mass spectrometry (SIMS), we show that the epibiotic Thiothrix are autotrophic, establishing the first known example of a non-marine chemoautotroph-animal symbiosis. Conditions supporting chemoautotrophy, and the N. ictus-Thiothrix association, likely commenced in the Frasassi cave complex between 350 000 and 1 million years ago. Therefore, the N. ictus-Thiothrix symbiosis is probably significantly younger than marine chemoautotrophic symbioses, many of which have been evolving for tens to hundreds of million years.

Fungal communities on speleothem surfaces in Kartchner Caverns, Arizona, USA, 2011, Vaughan M. J. , Maier R. M. , Pryor B. M.

Kartchner Caverns, located near Benson, Arizona, USA, is an active carbonate cave that serves as the major attraction for Kartchner
Caverns State Park. Low-impact development and maintenance have preserved prediscovery macroscopic cavern features and
minimized disturbances to biological communities within the cave.. The goal of this study was to examine fungal diversity in Kartchner
Caverns on actively-forming speleothem surfaces. Fifteen formations were sampled from five sites across the cave. Richness
was assessed using standard culture-based fungal isolation techniques. A culture-independent analysis using denaturing gradient
gel electrophoresis (DGGE) was used to assay evidence of community homogeneity across the cave through the separation of
18S rDNA amplicons from speleothem community DNA. The culturing effort recovered 53 distinct morphological taxonomic units
(MTUs), corresponding to 43 genetic taxonomic units (GTUs) that represented 21 genera. From the observed MTU accumulation
curve and the projected total MTU richness curve, it is estimated that 51 percent of the actual MTU richness was recovered. The
most commonly isolated fungi belonged to the genera Penicillium, Paecilomyces, Phialophora, and Aspergillus. This culturebased
analysis did not reveal significant differences in fungal richness or number of fungi recovered across sites. Cluster analysis
using DGGE band profiles did not reveal distinctive groupings of speleothems by sample site. However, canonical correspondence
analysis (CCA) analysis of culture-independent DGGE profiles showed a significant effect of sampling site and formation type on
fungal community structure. Taken together, these results reveal that diverse fungal communities exist on speleothem surfaces in
Kartchner Caverns, and that these communities are not uniformly distributed spatially. Analysis of sample saturation indicated that
more sampling depth is required to uncover the full scale of mycological richness across spelothem surfaces.


Chemoorganotrophic bacteria isolated from biodeteriorated surfaces in cave and catacombs, 2012, De Leo F. , Iero A. , Zammit G. , Urz C.

The main objective of this work was the comparative analysis of a large number of bacterial strains isolated from biodeteriorated surfaces in three different sites, namely the catacombs of St. Callistus in Rome, Italy, the catacombs dedicated to St. Agatha in Rabat, Malta and the Cave of Bats in Zuheros, Spain. Our results showed that even considering only culturable chemoorganotrophic bacteria the variability is very high, reflecting the great variety of microhabitats present. Hence any strategies to prevent, control or eliminate the biofilm-embedded microbiota from an archeological surface should take into account a number of considerations as stipulated in our study.


Bacterial community survey of sediments at Naracoorte Caves, Australia, 2012, Adetutu E. M. , Thorpe K. , Shahsavari E. , Bourne S. , Cao X. , Fard R. M. N, Kirby G. , Ball A. S.

Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial communities in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits) and Strawhaven Cave was used as control (no tourist access). Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey of tourist accessible and inaccessible areas of show (tourist accessible) and control caves. Other detected sediment bacterial groups were assigned to the Firmicutes, Actinobacteria and Proteobacteria. The survey also showed differences in bacterial diversity in caves with human access compared to the control cave with the control cave having unique microbial sequences (Acinetobacter, Agromyces, Micrococcus and Streptomyces). The show caves had higher bacterial counts, different 16S rDNA based DGGE cluster patterns and principal component groupings compared to Strawhaven. Different factors such as human access, cave use and configurations could have been responsible for the differences observed in the bacterial community cluster patterns (tourist accessible and inaccessible areas) of these caves. Cave sediments can therefore act as reservoirs of microorganisms. This might have some implications on cave conservation activities especially if these sediments harbor rock art degrading microorganisms in caves with rock art.


Bacterial migration through low-permeability fault zones in compartmentalised aquifer systems: a case study in Southern Italy., 2014, Bucci Antonio, Petrella Emma, Naclerio Gino, Gambatese Sabrina, Celico Fulvio

The aim of this study was to experimentally verify the significance of microbial transport through low-permeability fault zones in a compartmentalised carbonate aquifer system in Southern Italy.

The temporal variability of microbial communities in two springs fed by the same aquifer system, but discharging up- and down-gradient of two low-permeability fault zones, was analysed using a 16S rDNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)-based approach. At both springs, a remarkable temporal variation in PCR-DGGE profiles was detected throughout the observation period. When comparing the PCR-DGGE profiles of the two springs, a synchronous evolution over time was observed. Moreover, the per cent of PCR-DGGE bands common to both springs progressively increased from early (23%) to late recharge (70%), only to decrease once more in late recession (33%). Considering the results of the hydrogeological and isotopic investigations and EC measurements, the results of biomolecular analyses demonstrate that, at the study site, compartments straddling the analysed fault zones have microbial interconnections, despite the existence of low-permeability fault cores.


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