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Vermiculations from karst caves: The case of Pertosa-Auletta system (Italy)
Abstract
Unlike the spectacular speleothems that can often be found in numerous caves, vermiculations are rather un-assuming formations, whose origin and evolution still subject of several heated debates. In order to provide a quantitative basis for the understanding of the nature and evolution of vermiculations in karst environments, the geochemical properties of one of the most important karst systems of southern Italy, the Pertosa-Auletta Cave, were studied through a comprehensive approach which included elemental, mineralogical and microscopyanalyses. The chemical element abundances, mineral composition and microstructure of the vermiculations covering the entire range of morphologies and colours observed in the case-study cave were investigated, thus providing the first quantitative record of these traits.The vermiculations presented exceptional diversity in their morphology, colour, chemical and mineral composition,with it being due to exogenous determinants such as the deposition of stream sediments ororganic matter as well as the development of photoautotrophic communities. They were invariably composed of calcite, associated to quartz as well as clays and other secondary minerals, the formation of which may be biologically mediated. This occurrence, and the evidences of microbial activity observed through dissolution traces,support the possible involvement of biogenic processes in vermiculation development.
... These formations exhibit a network of "worm-like" tracks and splotches that are typically in positive relief compared to the surrounding substrate ( Figure 1). Biovermiculations are known from a variety of cave environments, where they were traditionally referred to as clay vermiculations (e.g., [7]). We use the term "biovermiculation" here in sensu Hose et al. [8], who found substantial microbial biomass and biofilm in biovermiculations from sulfide-rich Villa Luz cave. ...
... We use the term "biovermiculation" here in sensu Hose et al. [8], who found substantial microbial biomass and biofilm in biovermiculations from sulfide-rich Villa Luz cave. This term is now used more broadly, based on the recognition of a substantial microbial content in vermiculations in many cave systems (e.g., [6,7,9]). Similar formations have also been observed at the sub-millimeter scale in cyanobacterial hypoliths on the underside of a translucent rock in Strzelecki Desert, Australia [10] as well as in higher vegetation patterns in the Negev Desert, Israel that exhibit biovermiculation geometry on a multi-meter scale [11]. ...
... Cave biovermiculations are thought to be the result of physical and biological processes. Flocculation of sediments during wetting and drying of damp cave walls and properties of the underlying sediment likely play a role in pattern development [7,12], as do microbial growth characteristics [1,6]. However, the biological factors that contribute to their formation remain significantly less well understood. ...
Biovermiculations are uniquely patterned organic rich sediment formations found on the walls of caves and other subterranean environments. These distinctive worm-like features are the combined result of physical and biological processes. The diverse microbial communities that inhabit biovermiculations may corrode the host rock, form secondary minerals, and produce biofilms that stabilize the sediment matrix, thus altering cave surfaces and contributing to the formation of these wall deposits. In this study, we incubated basalt, limestone, and monzonite rock billets in biovermiculation mixed natural community enrichments for 468–604 days, and used scanning electron microscopy (SEM) to assess surface textures and biofilms that developed over the course of the experiment. We observed alteration of rock billet surfaces associated with biofilms and microbial filaments, particularly etch pits and other corrosion features in olivine and other silicates, calcite dissolution textures, and the formation of secondary minerals including phosphates, clays, and iron oxides. We identified twelve distinct biofilm morphotypes that varied based on rock type and the drying method used in sample preparation. These corrosion features and microbial structures inform potential biological mechanisms for the alteration of cave walls, and provide insight into possible small-scale macroscopically visible biosignatures that could augment the utility of biovermiculations and similarly patterned deposits for astrobiology and life detection applications.
... The aim of this work was to shed light on the ecohydrology of the Pertosa-Auletta show cave, in order to provide new insights (on both temporal and spatial scales) about compositional variations of the circulating water and to examine both the natural (physical and chemical) and anthropogenic (polluting) factors influencing the ecological processes as well as the potential anthropogenic alterations of the natural ecological equilibrium. In particular, we reported an extensive seasonal characterization of the chemistry of dripping and river waters collected from three branches of such model karst system, each characterized by distinct natural features and degree of anthropogenic disturbance, to verify their differences and analogies (Addesso et al., 2019;Addesso, De Waele, et al., 2022). ...
... Sampling of dripping waters was carried out along three main trails (namely tourist, fossil and paradise) of the cave, having different natural features and human fruition (Addesso et al., 2019), during the four seasons, from spring 2020 to winter 2021 ( Figure 1, Table 1). ...
Water and air flows connect underground systems to the surface, affecting the cave’s chemical and physical properties. The aim of this work was to investigate the chemical characteristics of waters in Pertosa-Auletta Cave (Italy), focusing on dripwater and on the underground Negro river, seasonally and in different areas of the cave. In particular, three trails with different environmental characteristics and tourism pressure, were investigated in order to highlight the processes affecting the ecological equilibrium of the hypogean ecosystem. Dripping and flowing river waters, both rich in Ca because of their interaction with carbonate rocks, show distinct chemical signatures regarding the other elements (especially K and Mg) due to lithological and hydrodynamical differences. Moreover, water chemistry is affected by the seasonality in the pluviometric regime and the related variability in the dilution effect. Bat colonies, dwelling mainly along the fossil trail, enrich dripping waters with P and N. Their concentrations have also been found at fairly high levels across the whole trail network , suggesting an additional potential role of leaching from agricultural and forested soils above the Pertosa-Auletta Cave in defining dripwater chemistry.
... Addesso et al., 2022a;Lang et al., 2015), and geochemical properties (e.g. Addesso et al., 2019), with cascade effects on the subterranean fauna (e.g. Nicolosi et al., 2021;Pacheco et al., 2021) and energy fluxes (e.g. ...
Anthropogenic disturbance on natural ecosystems is growing in frequency and magnitude affecting all ecosystems components. Understanding the response of different types of biocoenosis to human disturbance is urgently needed and it can be achieved by adopting a metacommunity framework. With the aid of advanced molecular techniques, we investigated sediment communities of Fungi, Bacteria and Archaea in four Italian show caves, aiming to disentangle the effects induced by tourism on their diversity and to highlight changes in the driving forces that shape their community composition. We modelled diversity measures against proxies of tourism pressure. With this approach we demonstrate that the cave tourism has a direct effect on the community of Bacteria and an indirect influence on Fungi and Archaea. By analysing the main driving forces influencing the community composition of the three microbial groups, we highlighted that stochastic factors override dispersal-related processes and environmental selection in show caves compared to undisturbed areas. Thanks to this approach, we provide new perspectives on the dynamics of microbial communities under human disturbance suggesting that a proper understanding of the underlying selective mechanisms requires a comprehensive and multi-taxonomic approach.
... Microbial communities in lava tubes grow forming extensive colored biofilms on speleothems and walls [3], similarly to what happens in karst caves [4,5]. Recent studies conducted in lava tubes revealed a highly diverse microbiome, dominated by new microbial life forms and interactions differing from those occurring on the surface [3,6]. ...
While microbial communities in limestone caves across the world are relatively understood, knowledge of the microbial composition in lava tubes is lagging behind. These caves are found in volcanic regions worldwide and are typically lined with multicolored microbial mats on their walls and ceilings. The Mount Etna (Sicily, S-Italy) represents one of the most active volcanos in the world. Due to its outstanding biodiversity and geological features, it was declared Natural Heritage of Humanity by the UNESCO in 2013. Despite the presence of more than 200 basaltic lava tubes, the microbial diversity of these hypogean systems has never been investigated so far. Here, we investigated bacterial communities in four lava tubes of Mount Etna volcano. Field emission scanning electron microscopy (FESEM) was carried out for the morphological characterization and detection of microbial features. We documented an abundant presence of microbial cells with different morphotypes including rod-shaped, filamentous, and coccoidal cells with surface appendages, resembling actinobacteria reported in other lava tubes across the world. Based on 16S rRNA gene analysis, the colored microbial mats collected were mostly composed of bacteria belonging to the phyla Actinomycetota, Pseudomonadota, Acidobacteriota, Chloroflexota, and Cyanobacteria. At the genus level, the analysis revealed a dominance of the genus Crossiella, which is actively involved in biomineralization processes, followed by Pseudomonas, Bacillus, Chujaibacter, and Sphingomonas. The presence of these taxa is associated with the carbon, nitrogen, and ammonia cycles, and some are possibly related to the anthropic disturbance of these caves. This study provides the first insight into the microbial diversity of the Etna volcano lava tubes, and expands on previous research on microbiology of volcanic caves across the world.
... To simulate and model the airflow and the particle dispersions and depositions, the application Cylinder flow in COMSOL Multiphysics ® (v4.3, COMSOL, Inc., Burlington, MA, USA) software was employed, modeling tourism sections of the Pertosa-Auletta Cave (in total,~3 km long; Figure 1), located in the Alburni Massif, one of the most important limestone karst areas in Southern Italy [25]. This allowed the examination of the propagation of a variable and compressible flow within 2D geometry. ...
Underground ecosystems are often of interest for the tourism industry due to their important naturalistic and cultural heritage. Since these underground ecosystems are almost completely isolated, external agents (such as human presence) can easily disrupt their chemico-physical and biological processes, which can affect, sometimes irrevocably, their natural equilibrium, placing the preservation of such sites at risk. The most sensible managers of caves, catacombs, mines, and all the accessible cultural sites are searching for methods to control these dynamics and the modeling appears to be effective in preventing scenarios of the known impacts as well as suggesting strategies for their mitigation. In this study, by employing finite element analysis by the COMSOL Multiphysics software and reproducing, in a simplified way, a section of the tourist trail of the Pertosa-Auletta Cave (Italy), for the first time we provided a fact-finding survey of the airflow and the scattering and subsequent deposition of particles transported by tourists. Taking into account discontinuities in the pathway, the simulations rebuilt the possible natural airflow line, reproducing the particle movements induced by different tourist loads, whose high numbers increase the swirling movement of air masses, promoting a higher dispersion of particles, even in the remote cave areas. Performed simulations clearly indicated both the speed and direction followed by particles, as well as deposition sites, highlighting potential hotspots of damage, and demonstrating that the employed approach can be an excellent tool for planning the management of these extraordinary ecosystems, foretelling anthropogenic impacts, and supporting managers in decision-making processes.
... Addesso et al., 2022a;Lang et al., 2015), and geochemical properties (e.g. Addesso et al., 2019), with cascade effects on the subterranean fauna (e.g. Nicolosi et al., 2021;Pacheco et al., 2021) and energy fluxes (e.g. ...
The metacommunity framework has been rarely adopted to investigate the underlying ecological mechanisms shaping microbial communities. With the aid of advanced molecular techniques, we investigated sediment communities of Fungi, Bacteria and Archaea in four Italian show caves aiming to disentangle the effects induced by tourists on species richness and composition from environmental filtering and dispersal driven mechanisms. We modelled community changes against human disturbance —measured as the distance from the tourist path—demonstrating that the presence of visitors in caves decreases fungal species richness and causes species replacement in Bacteria and Archaea. Environmental filtering affects species richness and composition of Fungi and species richness of Archaea, while a minor role was played by dispersal, influencing only species richness in Fungi. We provide new perspectives on the dynamics of microbial communities under human disturbance suggesting that a proper understanding of the underlying selective mechanisms requires a comprehensive and multi-taxonomic approach.
... The two monitoring stations were located in two sections of the Pertosa-Auletta Cave ( Fig. 1), hereafter referred as "tourist trail" and "fossil trail" according to the official denomination of the managers, the description of which is extensively reported in Addesso et al. (2019Addesso et al. ( , 2021Addesso et al. ( , 2022. Station positioning aimed at evaluating the relative amplitude and scales of the tourist-induced contributions upon the natural fluctuations in atmospheric parameters, allegedly mainly driven by the cave coupling with the external environment. ...
In cave ecosystems tourists represent moving sources of discontinuous disturbances, able to induce transient system responses whose knowledge is crucial in defining appropriate conservation measures. Here we propose an approach to evaluate the amplitude and scales of cave alterations based on high-resolution air monitoring, through the use of purposely developed low-cost monitoring stations and a consistent analytical framework for information retrieval based on time series analysis. In particular, monitoring stations adopt a modular structure based on physical computing platforms acquiring data through several sensors, with means of preventing humidity damages and guaranteeing their continuous operation. Data are then analyzed using wavelet periodograms and cross-periodograms to extract the scales of tourism-induced alterations. The approach has been exemplified in the Pertosa-Auletta Cave, one of the most important underground environments in Southern Italy, highlighting the development of monitoring stations and the information obtainable with the proposed analytical workflow. Here, 2 monitoring stations acquiring data for 1 year at 1′ sampling time on temperature, relative humidity, CO2, VOCs, and particulate matter were deployed in trails subjected to different levels of tourism. In terms of Pertosa-Auletta Cave air dynamics, the approach allowed estimating the temporal and spatial scales of tourism-induced alterations in the order of minutes and meters, respectively, with parameter-dependent variations. On more general terms, the approach proved reliable and effective, with its modularity and low-cost fostering its straightforward adoption in other underground ecosystems, where it can support the development of tailored management strategies.
... Therefore, moonmilk is formed as a result of ongoing opposite processes as mineral dissolution occurs in one place, and then the same mineral is precipitated in others in the form of calcite [62,71,73]. Moonmilk composition and SEM images are presented in Figure 5. Vermiculations are deposits that form worm-like patterns on cave walls and they are represented by various morphologies, shapes, and colors and are generally composed of calcite, associated with quartz, and traces of clay minerals [74]. During studies carried out by various research groups it was discovered that, similarly to moonmilk, vermiculations are rich in microbial life forms [27,75]. ...
Caves have been an item of amateur and professional exploration for many years. Research on the karst caves has revealed great diversity of bacteria, algae, and fungi living on stone walls and speleothems, in mud puddles or sediments. They have become the source of interest for various research groups including geologists, chemists, ecologists, or microbiologists. The adaptations of cave-dwelling organisms applied to their survival are complex and some of their properties show potential to be used in various areas of human life. Secondary metabolites produced by cave’s bacteria show strong antimicrobial, anti-inflammatory, or anticancer properties. Furthermore, bacteria that can induce mineral precipitation could be used in the construction industry and for neutralization of radioisotopes. In this review we focus on bacteria and algae present in cave ecosystems, their role in shaping such specific environment, and their biotechnological and medical potential.
... The transition from Ca-smectite (always in the gel phase) to Na-smectite behavior (solid-to-liquid transition in low-mineralized water) takes place when Na + cations occupy a certain amount of the double-diffuse layer sites, typically 20% Birgersson et al., 2011). These smectite specific features were found to fit the experimental findings on cave sediment of vermiculations have been investigated by many authors, both in painted caves (Hoerlé et al., 2011;Konik et al., 2014) and non-painted ones (Bojar et al., 2015;Faucher & Lauriol, 2016;Addesso et al., 2019), using a wide range of analytical techniques (X-ray diffraction, scanning electron microscope (SEM), infrared spectroscopy, thermogravimetry, etc.). These analyses show that vermiculations contain a wide variety of materials, including minerals (calcite, quartz, and clay minerals, among others) and organic matter (fungi, algae, bacteria, and organic filaments). ...
Vermiculations are aggregates of small particles commonly found on cave walls. They are a major concern for the conservation of painted caves, as they can potentially alter valuable prehistoric cave paintings. A previous rheological study of fine sediment deposits on cave walls revealed that this material can undergo a solid-to-liquid transition triggered by variations in the chemical composition of the water film on the wall. Such a transition could occur at the origin of vermiculations by allowing the sediment to flow under low mechanical stress. In this work, we provide quantitative information on the conditions leading to this transition and show the importance of the chemical composition of the water film on the cave walls. A complete understanding of the phenomenon will, however, require more field information. This includes monitoring of the evolution of vermiculations, for which we have developed a dedicated observation protocol. Based on the combination of photogrammetry and a geographic information system we were able to precisely map the walls of the Hall of Bulls in Lascaux cave from past and future photographs. To better understand the vermiculation process, pictures need to be taken regularly, and the chemical composition of the thin water film covering cave walls needs to be analyzed with a similar time step. The correlation between the evolution of vermiculations, the humidification phases of the walls, temperature changes and the chemical monitoring of the water film should shed new light on conditions triggering vermiculations.
... Other ecological niches, although still poorly known, are those constituted by microorganisms (Barton and Northup 2007). Their aggregation into colonies can create morphologies visible at naked eye, as for example vermiculations (Addesso et al. 2019). However, most of the time these microorganisms are invisible, and their identification is only possible by DNA studies (Sauro et al. 2018). ...
The concept of geoheritage is related to places of geological interest, generally of aesthetic, cultural, socioeconomic and/ or scientific value. Many geosites are of karstic nature, because of their intrinsic beauty, their singularity and high geodi-versity. Caves are among the most visited and economically exploited geological landforms. They constitute geosites as a whole, with their scenic landscapes, hydrogeological importance and the presence of bewildering natural rock and mineral formations including stalactites, stalagmites, flowstones and many other bizarre speleothem shapes. In some cases, a single speleothem, and the palaeoclimate record it contains, can be on its own of extraordinary importance to science. Once studied , these samples are often stored in research institution collections, rarely accessible to the wide public. In this paper, we report on the museumization of a stalagmite that has delivered a unique and exceptionally long glacial climate record from southern Italy, shedding light on the causes that led to the Neanderthal contraction and Modern Human expansion in this mild Mediterranean climate between 45 and 42 thousands years ago. The proposed museumization aims to demonstrate the potential of speleothems, after scientific application, in terms of educational and tourist resources. This approach allows to highlight the scientific importance of karst and cave geosites to the wide public, promoting their conservation and the valorisation of the studied cave-material.
... Fetida Cave hosts a peculiar type of vermiculation that has been previously named "biovermiculation" [12,16], because of their possible biological origin and the inclusion of highly diversified and active microbial populations [20]. The biovermiculations typically develop in sulfidic caves and present complex and highly diversified geometric forms resembling carbonic-acid caves vermiculations, although they lack significant clay content [17,20,73]. Instead, the mineralogy of vermiculations from FC showed the abundance of quartz, in addition to either Mg and Fe-rich minerals, in brown vermiculations, or K-and Al-rich minerals in grey vermiculations. ...
Fetida Cave is an active sulfuric acid cave influenced by seawater, showing abundant microbial communities that organize themselves under three main different morphologies: water filaments, vermiculations and moonmilk deposits. These biofilms/deposits have different cave distribution, pH, macro-and microelement and mineralogical composition, carbon and nitrogen content. In particular, water filaments and vermiculations had circumneutral and slightly acidic pH, respectively, both had abundant organic carbon and high microbial diversity. They were rich in macro-and microelements, deriving from mineral dissolution, and, in the case of water filaments, from seawater composition. Vermiculations had different color, partly associated with their mineralogy, and unusual minerals probably due to trapping capacities. Moonmilk was composed of gypsum, poor in organic matter, had an extremely low pH (0-1) and low microbial diversity. Based on 16S rRNA gene analysis, the microbial composition of the biofilms/deposits included autotrophic taxa associated with sulfur and nitrogen cycles and biomineralization processes. In particular, water filaments communities were characterized by bacterial taxa involved in sulfur oxidation and reduction in aquatic, aphotic, microaerophilic/anoxic environments (Campylobacterales, Thiotrichales, Arenicel-lales, Desulfobacterales, Desulforomonadales) and in chemolithotrophy in marine habitats (Oceanospirillales, Chromatiales). Their biodiversity was linked to the morphology of the water filaments and their collection site. Microbial communities within vermiculations were partly related to their color and showed high abundance of unclassified Betaproteobacteria and sulfur-oxidizing Hydrogenophilales (including Sulfuriferula), and Acidiferrobacterales (including Sulfurifustis), sulfur-reducing Desulfurellales, and ammonia-oxidizing Planctomy-cetes and Nitrospirae. The microbial community associated with gypsum moonmilk showed PLOS ONE | https://doi.org/10.1371/journal.
Removing lampenflora, phototrophic organisms developing on rock surfaces in tourist cavities due to the artificial lighting, is a challenge for sustainable and appropriate long-term management of caves. Photosynthetic-based biofilms usually cause rock biodeterioration and an ecological imbalance in cave ecosystems. In this work, a detailed investigation of the effects of the 3 most commonly used lampenflora cleaning operations (NaClO, H2O2 and UVC) was carried out in Pertosa-Auletta Cave (Italy). The application of NaClO showed good disinfection capability over extended periods of time without causing any appreciable rock deterioration. The H2O2 treatment showed to be corrosive for the rock surfaces covered with vermiculation deposits. The chemical alteration of organic and inorganic compounds by H2O2 did not remove biomass, favoring biofilm recovery after three months of treatment. Both NaClO and H2O2 treatments were effective at removing photoautotrophs, although the bacterial phyla Proteobacteria and Bacteroidetes as well as Apicomplexa and Cercozoa among the Eukaryotes, were found to be resistant to these treatments. The UVC treatments did not show any noticeable effect on the biofilms.
In this chapter, the authors deal with the physical, organic, and chemical deposits found in the dark or semi‐dark areas of caves, excluding those found in cave entrances or rock shelters. Clastic sediments in caves, excluding those found at entrances, have been the subject of numerous studies, mainly during the last 60 years. Phosphorite is a chemical deposit that can be deposited in caves. Speleothems are secondary mineral deposits that form in caves by flowing, dripping, ponded, or seeping water and take on a typical shape. They are mostly composed of minerals such as calcite, aragonite, or gypsum, but other minerals can also form entirely or partially speleothems. Speleothem texture and fabrics are increasingly used to support the interpretation of the geochemical signals (stable isotopes and trace elements) in the paleo‐environmental and paleoclimatic reconstructions based on speleothem archives.
We show through laboratory experiments that the self–patterning of a thin clayey layer can be triggered by condensation. The natural sediment used in the experiments was a highly polydisperse granular paste with smectite clay in the fine fraction. Under certain physicochemical conditions, condensation induces the solid–to–liquid transition of the sediment layer, resulting in sediment flow and the formation of band structures. These results suggest a physical mechanism for the formation of patterns commonly observed on the humid walls of underground cavities, referred to as vermiculations.
The microbiota associated with vermiculations from karst caves is largely unknown. Vermiculations are enigmatic deposits forming worm-like patterns on cave walls all over the world. They represent a precious focus for geomicrobiological studies aimed at exploring both the microbial life of these ecosystems and the vermiculation genesis. This study comprises the first approach on the microbial communities thriving in Pertosa-Auletta Cave (southern Italy) vermiculations by next-generation sequencing. The most abundant phylum in vermiculations was Proteobacteria, followed by Acidobacteria > Actinobacteria > Nitrospirae > Firmicutes > Planctomycetes > Chloroflexi > Gemmatimonadetes > Bacteroidetes > Latescibacteria. Numerous less-represented taxonomic groups (< 1%), as well as unclassified ones, were also detected. From an ecological point of view, all the groups co-participate in the biogeochemical cycles in these underground environments, mediating oxidation-reduction reactions, promoting host rock dissolution and secondary mineral precipitation, and enriching the matrix in organic matter. Confocal laser scanning microscopy and field emission scanning electron microscopy brought evidence of a strong interaction between the biotic community and the abiotic matrix, supporting the role of microbial communities in the formation process of vermiculations.
Sulfuric acid minerals are important clues to identify the speleogenetic phases of hypogene caves. Italy hosts ~25% of the known worldwide sulfuric acid speleogenetic (SAS) systems, including the famous well-studied Frasassi, Monte Cucco, and Acquasanta Terme caves. Nevertheless, other underground environments have been analyzed, and interesting mineralogical assemblages were found associated with peculiar geomorphological features such as cupolas, replacement pockets, feeders, sulfuric notches, and sub-horizontal levels. In this paper, we focused on 15 cave systems located along the Apennine Chain, in Apulia, in Sicily, and in Sardinia, where copious SAS minerals were observed. Some of the studied systems (e.g., Porretta Terme, Capo Palinuro, Cassano allo Ionio, Cerchiara di Calabria, Santa Cesarea Terme) are still active, and mainly used as spas for human treatments. The most interesting and diversified mineralogical associations have been documented in Monte Cucco (Umbria) and Cavallone-Bove (Abruzzo) caves, in which the common gypsum is associated with alunite-jarosite minerals, but also with baryte, celestine, fluorite, and authigenic rutile-ilmenite-titanite. In addition, the core of alunite and jarosite, from these two systems, results enriched in PO43-, clearly suggesting hypogene hydrothermal origin. Santa Cesarea Terme, Capo Palinuro, and Acqua Mintina caves show important native sulfur deposits, which abundantly cover walls, ceilings, and speleothems. Abundant copiapite, pickeringite, tamarugite, hexahydrate assemblages have been observed in the Calabrian systems; their association with pyrite and hematite would suggest they formed in very acidic conditions with pH ranging between 0 and 4.
Santa Cesarea Terme in Salento is the only area in which hypogenic caves have been recognized in the Apulia region. In this spa area, the rising of sulfidic thermal waters that mix with both recent fresh infiltration waters and coastal salt water has formed four active sulfuric acid speleogenesis (SAS) caves. These caves are characterized by the typical set of sulfuric acid meso- and micromorphologies, and also by the presence of both gypsum and native sulfur. In all caves, biofilms are visible in the sulfidic thermal waters and on the cave walls.
Interest in mineral-microbe interaction has grown enormously over recent decades, providing information in a puzzle-like manner which points towards an ever increasingly intimate relationship between the two; a relationship that can be truly termed co-evolution. Clay minerals play a very central role in this co-evolving system. Some 20 years ago, clay scientists looked at clay mineral- microbe studies as a peripheral interest only. Now, can clay scientists think that they understand the formation of clay minerals throughout geological history if they do not include life in their models? The answer is probably no, but we do not yet know the relative weight of biological and inorganic factors involved in driving clay-mineral formation and transformation. Similarly, microbiologists are missing out important information if they do not investigate the influence and modifications that minerals, particularly clay minerals, have on microbial activity and evolution. This review attempts to describe the several points relating clay minerals and microorganisms that have been discovered so far. The information obtained is still very incomplete and many opportunities exist for clay scientists to help to write the real history of the biosphere.
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.
Volcanic caves are filled with colorful microbial mats on the walls and ceilings. These volcanic caves are found worldwide, and studies are finding vast bacteria diversity within these caves. One group of bacteria that can be abundant in volcanic caves, as well as other caves, is Actinobacteria. As Actinobacteria are valued for their ability to produce a variety of secondary metabolites, rare and novel Actinobacteria are being sought in underexplored environments. The abundance of novel Actinobacteria in volcanic caves makes this environment an excellent location to study these bacteria. Scanning electron microscopy (SEM) from several volcanic caves worldwide revealed diversity in the morphologies present. Spores, coccoid, and filamentous cells, many with hair-like or knobby extensions, were some of the microbial structures observed within the microbial mat samples. In addition, the SEM study pointed out that these features figure prominently in both constructive and destructive mineral processes. To further investigate this diversity, we conducted both Sanger sequencing and 454 pyrosequencing of the Actinobacteria in volcanic caves from four locations, two islands in the Azores, Portugal, and Hawai'i and New Mexico, USA. This comparison represents one of the largest sequencing efforts of Actinobacteria in volcanic caves to date. The diversity was shown to be dominated by Actinomycetales, but also included several newly described orders, such as Euzebyales, and Gaiellales. Sixty-two percent of the clones from the four locations shared less than 97% similarity to known sequences, and nearly 71% of the clones were singletons, supporting the commonly held belief that volcanic caves are an untapped resource for novel and rare Actinobacteria. The amplicon libraries depicted a wider view of the microbial diversity in Azorean volcanic caves revealing three additional orders, Rubrobacterales, Solirubrobacterales, and Coriobacteriales. Studies of microbial ecology in volcanic caves are still very limited. To rectify this deficiency, the results from our study help fill in the gaps in our knowledge of actinobacterial diversity and their potential roles in the volcanic cave ecosystems.
Previous reports of reticulated filaments, an unknown microbe, document that they are ubiquitous in subsurface environments, including limestone caves, lava tubes, and even granite tunnels. Although initial reports of fossil reticulated filaments described preserved organic matter, additional instances involve replacement by calcite, Mn-oxides, silica, or copper silicates. We report on living reticulated filaments found in the limestone Herbstlabyrinth-Adventhöhle Cave System, Hesse, Germany. Samples from soft pool-fingers, pool-bottom clays, and clay-coated rocks along the flow path of incoming water all contain living reticulated filaments associated with abundant biofilm. Most of the reticulated filaments are approximately 0.5 mm in diameter, reach lengths between 150 and 200 mm, and have irregular chambers with spines, a newly identified morphological variant. EDX of these filaments confirms an organic composition not replaced by minerals. They are the dominant visible microbial form in these biofilms, providing hope that they can be isolated and identified.
it Profex is a graphical user interface for the Rietveld refinement program it BGMN. Its interface focuses on preserving it BGMN's powerful and flexible scripting features by giving direct access to it BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. it Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. it Profex and it BGMN are available under an open-source license for Windows, Linux and OS X operating systems.
En The clay-slime vermiculations, termed "foval" (from italian "Formazioni Vermicolari Argillo-Limose), are speleothemes of still obscure origin. In the Zinzulusa cave (Pu 107, SE-Italy) foval are very abundant, scattered on all vertical and horizontal rock surfaces, including those of calcitic speleothemes (stalactites and stalagmites). Foval with different texture complexity (c1-c4, according to the classification proposed in this paper), with or without halo, were found. The foval study took into consideration both morphological (inclination, perimeter, area, length, thickness, diameters, and colour) and microbiological characteristics. Microbiological analysis revealed the fungus Geotrichum sp. as dominant organism, besides several bacteria of clinical interest (Shigella sp., Campylobacter concisus, Enterobacter aerogenes, E. hafniae, Pseudomonas sutzeri, P. aeruginosa, Ancalomicrobium adetum, Klebsiella pneumoniae, Moraxella lacunata, M. osloensis).Geotrichum-cultures suggest that this organism is responsible for the vermicular effect: infact, Geotrichum produces a thick mucus aggregating clay particles; in addition, the colonies show a tendency to develop lineally according to a dendritic pattern, thus being considered as precursors of the most common foval morphology. These data support the hypothesis of biologic origin for the Zinzulusa foval complex.
Coralloid-type speleothems were recorded on the ceiling of the Ana Heva lava tube in Easter Island (Chile). These speleothems were morphologically, geochemically and mineralogically characterized using a wide variety of microscopy and analytical techniques. They consist dominantly of amorphous Mg silicate and opal-A. Field emission scanning electron microscopy revealed a variety of filamentous and bacillary bacteria on the surface of the Ana Heva coralloid speleothems, including silicified filamentous microorganisms. Among them, intriguing reticulated filaments resemble those filaments documented earlier in limestone caves and lava tubes. The identification of silicified microorganisms on the coralloid speleothems from the Ana Heva lava tube suggests a possible role of these microorganisms in silica deposition.
Microorganisms inhabit all possible biosphere ecosystems including subsurface rock environments, such as caves, mines, tunnels, etc. These environments are nutrient-limited and contain a wide variety of redox interfaces and microorganisms able to promote biomineralization processes. By interacting with minerals, microorganisms play an important role in reshaping the mineral environment, and may help to form features such as mineral deposits and some types of speleothems in cave environments.
Biomineralization, the processes by which organisms form minerals, is a fascinating topic that is receiving renewed attention by various fields of science. This chapter presents an overview of the microbial mineralization in caves and briefly describes which minerals are most commonly precipitated in the subsurface environments.
Bauxite deposits are studied because of their economic value and because they play an important role in the study of paleoclimate and paleogeography of continents. They provide a rare record of the weathering and evolution of continental surfaces. Geomicrobiological analysis makes it possible to verify that microorganisms have played a critical role during the formation of bauxite with the possibility already intimated in previous studies. Ambient temperature, abundance of water, organic carbon and bioavailable iron and other metal substrates provide a suitable environment for microbes to inhabit. Thiobacillus, Leptospirilum, Thermophilic bacteria and Heterotrophs have been shown to be able to oxidize ferrous iron and to reduce sulfate-generating sulfuric acid, which can accelerate the weathering of aluminosilicates and precipitation of iron oxyhydroxides. Microorganisms referred to the genus Bacillus can mediate the release of alkaline metals. Although the dissimilatory iron-reducing and sulfate-reducing bacteria in bauxites have not yet been identified, some recorded authigenic carbonates and “bacteriopyrites” that appear to be unique in morphology and grain size might record microbial activity. Typical bauxite minerals such as gibbsite, kaolinite, covellite, galena, pyrite, zircon, calcium plagioclase, orthoclase, and albite have been investigated as part of an analysis of microbial mediation. The paleoecology of such bauxitic microorganisms inhabiting continental (sub) surfaces, revealed through geomicrobiological analysis, will add a further dimension to paleoclimatic and paleoenvironmental studies.
Nontronite and microbes were detected in the surface layers of deep-sea sediments from Iheya Basin, Okinawa Trough, Japan. Nontronite, an Fe-rich smectite mineral, was embedded in acidic polysaccharides that were exuded by microbial cells and electron microscopy showed that the nontronite layers were apparently oriented in the polysaccharide materials. We propose that the formation of nontronite was induced by the accumulation of Si and Fe ions from the ambient seawater and that extracellular polymeric substances (EPS) served as a template for layer-silicate synthesis. Experimental evidence for this hypothesis was obtained by mixing a solution of polysaccharides (dextrin and pectin) with ferrosiliceous groundwater. After stirring the mixture in a sealed vessel for two days, and centrifuging, Fe-rich layer silicates were identified within the precipitate of both the dextrin and pectin aggregates, whereas rod-shaped or spheroidal Si-bearing iron hydroxides were found in the external solution. Microbial polysaccharides would appear to have affected layer-silicate formation.
2 Abstract: We report on a reticulated filament found in modern and fossil cave samples that cannot be correlated to any known microorganism or organism part. These filaments were found in moist environments in five limestone caves (four in New Mexico, U.S.A., one in Tabasco, Mexico), and a basalt lava tube in the Cape Verde Islands. Most of the filaments are fossils revealed by etching into calcitic speleothems but two are on the surface of samples. One hundred eighty individual reticulated filaments were imaged from 16 different samples using scanning electron microscopy. The filaments are up to 75 mm (average 12 mm) long, but all filaments appear broken. These reticulated filaments are elongate, commonly hollow, tubes with an open mesh reminiscent of a fish net or honeycomb. Two different cross-hatched patterns occur; 77% of filaments have hexagonal chambers aligned parallel to the filament and 23% of filaments have diamond-shaped chambers that spiral along the filament. The filaments range from 300 nm to 1000 nm in diameter, but there are two somewhat overlapping populations; one 200-400 nm in size and the other 500-700 nm. Individual chambers range from 40 to 100 nm with 30-40 nm thick walls. Similar morphologies to the cave reticulated filaments do exist in the microbial world, but all can be ruled out due to the absence of silica (diatoms), different size (diatoms, S-layers), or the presence of iron (Leptothrix sp.). Given the wide range of locations that contain reticulated filaments, we speculate that they are a significant cave microorganism albeit with unknown living habits.
Show caves represent an important tourist attraction, especially when located in rural territories where not many sites of interest, except those naturalistic, are present. For people working on karst and cave science, they are the main way to allow great number of people to visit a cave, experience safely the underground world, transfer information to raise public awareness about karst environments, and understand the need to protect and develop them in a sustainable way. Some consid-erations about management of show caves in peninsular Southern Italy are pre-sented through description of lessons learned from direct and indirect experience in show caves in Campania and Apulia. Overall, many problems have to be faced, starting from the lighting system (often quite old and promoting the lampenflora growth), the quality in the guides' explanations as well as updating safety measures. In addition, the high number of tourists allowed, regardless of the visitor capacity of each cave, has also to be mentioned, since it determines degradation in the cave atmosphere and the overall underground environment.
Certain caves formed by dissolution of bedrock have maze patterns composed of closed loops in which many intersecting fractures or pores have enlarged simultaneously. Their origin can be epigenic (by shallow circulation of meteoric groundwater) or hypogenic (by rising groundwater or production of deep-seated solutional aggressiveness). Epigenic mazes form by diffuse infiltration through a permeable insoluble caprock or by floodwater supplied by sinking streams. Most hypogenic caves involve deep sources of aggressiveness. Transverse hypogenic cave origin is a recently proposed concept in which groundwater of mainly meteoric origin rises across strata in the distal portions of large flow systems, to form mazes in soluble rock sandwiched between permeable but insoluble strata. The distinction between maze types is debated and is usually based on examination of diagnostic cave features and relation of caves to their regional setting. In this paper, the principles of mass transfer are applied to clarify the limits of each model, to show how cave origin is related to groundwater discharge, dissolution rate, and time. The results show that diffuse infiltration and floodwater can each form maze caves at geologically feasible rates (typically within 500 ka). Transverse hypogenic mazes in limestone, to enlarge significantly within 1 Ma, require an unusually high permeability of the non-carbonate beds (generally ≥ 10−4 cm/s), large discharge, and calcite saturation no greater than 90%, which is rare in deep diffuse flow in sedimentary rocks. Deep sources of aggressiveness are usually required. The origin of caves by transverse hypogenic flow is much more favorable in evaporite rocks than in carbonate rocks.
1] Highly altered, glassy tephras within the active steam vents at Kilauea Volcano, Hawaii, contain subsurface bacteria characterized by small (<500 nm in diameter), epicellular grains attached directly to the cell walls. Compositionally, the grains were dominated by Si, Al, Fe, and K, in a stoichiometry similar to a dioctahedral smectite. The initial dissolution of glass, which may in part have been microbiologically mediated, served as the source for many of the elements sequestered into the biomineralized clays. Overlying the tephras are white crusts (silica and calcite) and green-colored biofilms. The biofilms comprise a filamentous, likely cyanobacterial, community coated with spherical (<100 nm in diameter) grains of amorphous silica directly attached to the sheaths. Individual precipitates can easily be resolved, but quite often they coalesce, forming a dense mineral matrix of amorphous silica. For both the clays and silica, the microbial surfaces are clearly sites for mineral nucleation and growth. These observations imply that microbial biomineralization may be a significant process in the overall alteration of primary basaltic glass in active steam vent systems. Components: 6149 words, 4 figures, 3 tables.
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 (d 13 C 5 235 to 243%, and d 15 N 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.
Samples collected in low-temperature (2-50 degrees C) waters near hydrothermal vents of the Southern Explorer Ridge, in the
northeast Pacific Ocean, contained fine (<500 nm) Fe -and Mn-oxide and Fe-silicate particles coating bacterial surfaces. Partially
to totally mineralized bacteria, along with bacterial exopolymers, were covered with a mixture of poorly ordered Si-rich Fe-oxides
(possibly ferrihydrite), Mn-oxides, and Fe-silicates (possibly nontronite). Minerals occur as very fine (2-20 nm) granular
material, fine (20-100 nm) needles and sheets, small (200-500 nm) nodules and filaments (i.e., mineralized exopolymers). Under
saturation conditions, we infer that bacterial surfaces provided nucleation sites for poorly ordered oxides and silicates.
The formation of Fe- and Mn-oxides was likely initiated by the direct binding of soluble Fe and Mn species to reactive sites
(like carboxyl, phosphate, and hydroxyl groups) present within the bacterial cell wall and the exopolymers. Fe-silicate formation
involved a more complex binding mechanism, whereas metal ions, such as Fe, possibly bridged reactive sites within the cell
walls to silicate anions to initiate silicate nucleation.
Karstic caves represent one of the most important subterranean carbon storages on Earth and provide windows into the subsurface.
The recent discovery of the Herrenberg Cave, Germany, gave us the opportunity to investigate the diversity and potential role
of bacteria in carbonate mineral formation. Calcite was the only mineral observed by Raman spectroscopy to precipitate as
stalactites from seepage water. Bacterial cells were found on the surface and interior of stalactites by confocal laser scanning
microscopy. Proteobacteria dominated the microbial communities inhabiting stalactites, representing more than 70% of total
16S rRNA gene clones. Proteobacteria formed 22 to 34% of the detected communities in fluvial sediments, and a large fraction
of these bacteria were also metabolically active. A total of 9 isolates, belonging to the genera Arthrobacter, Flavobacterium, Pseudomonas, Rhodococcus, Serratia, and Stenotrophomonas, grew on alkaline carbonate-precipitating medium. Two cultures with the most intense precipitate formation, Arthrobacter sulfonivorans and Rhodococcus globerulus, grew as aggregates, produced extracellular polymeric substances (EPS), and formed mixtures of calcite, vaterite, and monohydrocalcite.
R. globerulus formed idiomorphous crystals with rhombohedral morphology, whereas A. sulfonivorans formed xenomorphous globular crystals, evidence for taxon-specific crystal morphologies. The results of this study highlighted
the importance of combining various techniques in order to understand the geomicrobiology of karstic caves, but further studies
are needed to determine whether the mineralogical biosignatures found in nutrient-rich media can also be found in oligotrophic
caves.
With more than 250 caves, the Alburni Mts represent one of the most important karst areas of southern Italy. The backbone of this ridge is constituted of Mesozoic-Cenozoic limestone with limited outcrops of Miocene siliciclastic formations and internal shale units, often trapped in elongated downthrown structures. NW-SE- and NE-SW-trending faults with a clear morphological expression are responsible for the genesis of a squared framework of flat-topped ridges and flat-bottomed valleys at the top of the massif. In an approximate way, the Alburni Mts can be described as a roughly NW-SE-trending monocline, dipping toward the SW, covering an area of about 350 km2. The fault system has partially disrupted an ancient flat landscape, as testified by the widespread fragments of the southern Apennines late Pliocene - early Pleistocene summit palaeosurface. This work aims at understanding the role played by tectonic structures on karst development based upon a morphometric analysis. We also try to constrain the age of the karst phenomena using the relationships among morpholineaments, land surfaces, and other morphotectonic markers. New data, besides confirming the role of the map-scale faults as a controlling factor of the surface and hypogean karst development, also highlight the strong influence of the small-scale faults and pervasive jointing. Further, the presence of different levels of hypogean karst seems to trace the arrangement in several orders of land surfaces, thus suggesting a discontinuous lowering of the (relative) erosion base level due to a multi-phase tectonic uplift.
The Circular Mausoleum tomb (Roman Necropolis of Carmona, Spain) dates back from the first century AD and is characterized by a dense microbial (phototrophic) colonization on the walls and ceiling. However, some walls exhibited an important number of violet stains of unknown origin. The microbial communities of these violet stains are mainly composed of cyanobacteria, streptomycetes and fungi. A strain of Streptomyces parvus, isolated from the walls, produces a violet pigment in culture media. High performance liquid chromatography-mass spectrometry of the culture extracts obtained from this Streptomyces revealed the presence of a few granaticins, pigments with a benzoisochromanequinone structure. When metabolically active in the tomb, S. parvus synthesizes the pigments that diffuse into the mortar. During rain and/or wetting periods, the pigments are solubilized by alkaline waters and elute from the starting position to the surrounding mortar, enlarging the pigmented area and thus contributing to this exceptional biodeterioration phenomenon.
The aim of this article is to examine the distribution and characteristics of vermiculations found in a cave located in the easternmost region of the Canadian Shield. This is the first study undertaken on this particular topic, on Canadian soil, and more specifically in the Laurentian mixed forest region. Our results indicate that the texture of the material which constitutes the vermiculations found on the Wilson cave walls does not differ from the texture of the inter-vermicular material and the loose soil found on the ground. On the other hand, the size of the vermiculations varies throughout the cave and their longest axis tends to be parallel or perpendicular to the ground. We suggest that these vermiculations are composed of loose material found on the ground of the cave that has been lifted up by animals. The airborne material then accumulates on the walls of the cave and forms these particular patterns. This accumulation depends on the air and water circulation inside the cave. The presence of vermiculations and their water content partially explains the local marble dissolution of walls and ceilings of the Wilson cave.
This book is written for researchers and students interested in the function and role of chemical elements in biological or environmental systems. Experts have long known that the Periodic System of Elements (PSE) provides only an inadequate chemical description of elements of biological, environmental or medicinal importance. This book explores the notion of a Biological System of the Elements (BSE) established on accurate and precise multi-element data, including evolutionary aspects, representative sampling procedures, inter-element relationships, the physiological function of elements and uptake mechanisms. The book further explores the concept Stoichiometric Network Analysis (SNA) to analyze the biological roles of chemical species. Also discussed is the idea of ecotoxicological identity cards which give a first-hand description of properties relevant for biological and toxicological features of a certain chemical element and its geo biochemically plausible speciation form. The focus of this book goes beyond both classical bioinorganic chemistry and toxicology.
Cet article présente les premiers résultats des analyses physico-chimiques de vermiculations observées dans la grotte de Lascaux. Ce travail a été mené suite à l'observation à l'automne 2009, de «nouvelles » vermiculations à certains emplacements sur des parois de la Salle des Taureaux. Un protocole d'étude, dont l'objectif est de comprendre les mécanismes de formation des vermiculations susceptibles de s'exercer dans la grotte de Lascaux, a été mis en place afin de prévenir tout impact de ce phénomène sur les œuvres pariétales. Rappelons que les vermiculations, très courantes en milieu souterrain, sont des agrégats de particules fines (ici < 10 µm) liées par une matrice.
La caractérisation physico-chimique des agrégats prélevés dans la grotte de Lascaux met en évidence que ceux-ci sont essentiellement des grains de calcite, de quartz, mais aussi d'aluminosilicates variés, d'oxydes (de fer, de manganèse et parfois de titane) et des fibres (naturelles ou synthétiques). Cette composition apparaît directement en relation avec le support et les sources de matériaux proches. Les vermiculations comportent, en outre, une fraction de matière organique importante (environ 5-10 % en masse de matière sèche), dont une partie peut être attribuée à des fibres incorporées et à une activité microbienne. En effet, de nombreux indices d'une telle activité (grains de calcite à faciès caractéristique d'une origine microbienne, filaments, carbone «amorphe ») sont observables dans les agrégats prélevés.
Mud and clay vermiculations are irregular and discontinuous deposits of incoherent materials, almost ubiquitous. Found both inside and outside of caves, overlying limestone or other materials, they are formed from many substances (clay, mud, candle-black, colloidal silica, etc.). Also their shape dimensions vary greatly. The following genetical hypotheses have been proposed: fossil fillings; chemico-genetical deposition; biological formation; mechanical deposition from moving water or air; clay-layer drying process (Montoriol-Pous hypothesis); physicochemical deposition from drying liquid films. The last is proposed by the authors who, having discussed the various hypotheses, give many examples and the results of some experiments. They distinguish two types of vermiculations: Type 1 or negative vermiculations and Type II or normal vermiculations. The genesis of type I is explained by the Montoriol-Pous hypothesis; these vermiculations are large and made of clay or other colloidal material, and are due to the gradual drying of a layer of clay or other substance. The last stage of this drying process causes the vermiculations to form in a more or less dried state. The vermiculations of the second type are small and thin, much ramified and always with a clear "halo" around them. Vermiculations consisting of many materials have been observed, usually as macroscopic aggregates. They are caused by the drying of a liquid film containing suspended colloidal particles. The proposed mechanism provides a good explanation of all the observed characteristics of vermiculations.
Bacterial textures are present on clay minerals in Oligocene Frio Formation sandstones from the subsurface of the Corpus Christi area, Texas. In shallower samples, beads 0.05--0.1 μm in diameter rim the clay flakes; at greater depth these beads become more abundant and eventually are perched on the ends of clay filaments of the same diameter. The authors believe that the beads are nannobacteria (dwarf forms) that have precipitated or transformed the clay minerals during burial of the sediments. Rosettes of chlorite also contain, after HCl etching, rows of 0.1 μm bodies. In contrast, kaolinite shows no evidence of bacterial precipitation. The authors review other examples of bacterially precipitated clay minerals. A danger present in interpretation of earlier work (and much work of others) is the development of nannobacteria-looking artifacts caused by gold coating times in excess of one minute; the authors strongly recommend a 30-second coating time. Bacterial growth of clay minerals may be a very important process both in the surface and subsurface.
Microorganisms can mediate the formation of minerals by a process called biomineralization. This process offers an efficient way to sequester inorganic pollutants within relatively stable solid phases. Here we review some of the main mechanisms involved in the mediation of mineral precipitation by microorganisms. This includes supersaturation caused by metabolic activity, the triggering of nucleation by production of more or less specific organic molecules, and the impact of mineral growth. While these processes have been widely studied in the laboratory, assessment of their importance in the environment is more difficult. We illustrate this difficulty using a case study on an As-contaminated acid mine drainage located in the South of France (Carnoulès, Gard). In particular, we explore the potential relationships that might exist between microbial diversity and mineral precipitation. The present review, far from being exhaustive, highlights some recent advances in the field of biomineralogy and provides non-specialists an introduction to some of the main approaches and some questions that remain unanswered.
Clays and clay minerals are common components in soils, sediments, and sedimentary rocks, and they play an important role in many environmental processes. Iron is ubiquitous in clays and clay minerals and its oxidation state, in part, controls the physical and chemical properties of these fine-grained minerals. The structural ferric iron in clay minerals can be reduced either chemically or biologically. Biological reductants include mesophilic and thermophilic microorganisms from diverse environments such as soils, sediments, sedimentary rocks, and hydrothermal hot springs. Multiple clay minerals have been used for microbial reduction studies, including dioctahedral smectite-illite series, palygorskite, chlorite, and their various mixtures in natural soils and sediments. All of these clay minerals are reducible by microorganisms under various conditions with smectite (nontronite) being the most reducible and illite the least. The rate and extent of bioreduction depends on many experimental factors, such as the type of microorganisms and clay minerals, solution chemistry, and temperature. Despite significant efforts, current understanding of the mechanisms of microbial reduction of ferric iron in clay minerals is still limited. Whereas some studies have presented evidence for a solid-state reduction mechanism, others argue that the clay mineral structure partially dissolves when the extent of reduction is high. This inconsistency may be related to several experimental conditions, and their specific effects are discussed in this paper. Whereas past experiments have been largely conducted in well-controlled laboratory systems, recent efforts have attempted to transfer knowledge to the field to improve our understanding of more complex soil systems for better agricultural practices. Biologically reduced clay minerals are also important agents in remediating inorganic and organic contaminants in soil and groundwater systems. This paper reviews the most recent developments and suggests some directions for future research.
In the last few years, geomicrobiologists have focused their researches on the nature and origin of enigmatic reticulated filaments reported in modern and fossil samples from limestone caves and basalt lava tubes. Researchers have posed questions on these filaments concerning their nature, origin, chemistry, morphology, mode of formation and growth. A tentative microbial origin has been elusive since these filaments are found as hollow tubular sheaths and could not be affiliated to any known microorganism. We describe the presence of similar structures in a 16th century granite tunnel in Porto, Northwest Portugal. The reticulated filaments we identify exhibit fine geometry surface ornamentation formed by cross-linked Mn-rich nanofibres, surrounded by a large amount of extracellular polymeric substances. Within these Mn-rich filaments we report for the first time the occurrence of microbial cells.
The results obtained by the author in the study of clay‐minerals diagenesis are compared critically with the principal publications in this field, giving a general picture of the transformation of sheet silicates.
Kaolinite minerals are related to the surficial zones of the earth's crust where they are formed. They are characterized by the hexacoordination of aluminium. They furnish paleogeographic indications in ancient sediments. During diagenesis they are very sensitive to the geochemical environment, stable in acid conditions, unstable in alkaline conditions. However, the increase in temperature by burial causes their destruction sooner or later. In the transitional zone to metamorphism (anchizone), kaolinite is not present. Only dickite and nacrite can be observed, provided that the environment is acid.
Montmorillonites are hydrated minerals. The rise in temperature and above all in pressure during burial expels water from the interlayers. Concentrated interstitial solutions of diagenesis provide cations which replace molecules of water between the layers. It is an irreversible reaction which produces 14‐Å minerals (chlorites) or 10‐Å minerals (illites), passing generally through mixed‐layer structures. The lack of montmorillonite is normal in formations which have undergone a marked burial.
Mixed‐layers are intermediate stages which occur during degradation by weathering and during aggradation by deep diagenesis. This aggradation is the result of an incorporation of certain cations taken up from interstitial solutions, and of a rearrangement within the lattice. There are two major pathways: a potassium and sodium pathway, which produces the illites, then the micas, passing possibly by regular mixed‐layering of the allevardite‐rectorite type; and a magnesium pathway, which produces the chlorites, passing possibly by a regular mixed‐layering of the corrensite type. These mixed‐layers can remain stable until the border of meta‐morphism (anchizone).
Micaceous clay minerals or illites form a very heterogenous group in the sediments which have been hardly diagenetized. Particles of diverse origin are found. They become more regular during burial. In deep diagenesis and the anchizone, crystallo‐graphic parameters of the illite are sufficiently well defined to serve as a scale of recrystallization, a zoneographic index. The morphology of the particles changes. Polymorphic types 1Md and 1M are replaced by the 2M‐type. The sharpness of the 10‐Å peak, conventionally called “crystallinity”, is an interesting quantitative criterium, together with the intensity ratio of the 5‐Å and 10‐Å peaks, which is related to the chemical composition of the octahedral layer.
Micas in low‐grade metamorphism, called sericites by petrographers, replace the illites discussed above. They are different from the true micas by a weaker layer charge, less than 0.9 by half‐cell. They often contain sodium (paragonitic muscovites and paragonites). The octahedral charge (zero for the muscovite) is generally high, due to the replacement of Al by Fe ²⁺ and Mg (phengites). These transformations should not obscure the fact that metamorphism is also accompanied by crystalline growth and massive neoformation.
Chlorites are the least well‐known clay minerals in diagenesis. Detrital particles can be aggraded to chlorite during early diagenesis by passing through the mixed‐layer stage of corrensite. A massive growth of chlorite is observed in late diagenesis and the anchizone. Illite and chlorite slates give place to sericite and chlorite schists. At present, general data are not available on the crystal chemistry of chlorites in the anchizone and the greenschist facies.
The stages in the diagenetic evolution of clay minerals are too little understood to be able to give them precise limits. However, the following provisional scheme can be proposed:
( 1 ) Early diagenesis (= “diagenesis” of Russian authors; = the “shallow‐burial stage” of M üller , 1967a). In this stage all the clay minerals are stable; some undergo aggradation by adsorption of Mg, K and Na (various mixed‐layers); some are neoformed (montmorillonites).
( 2 ) Middle diagenesis (= “early catagenesis or epigenesis” of Russian authors; the “deep‐burial stage” of M üller , 1967a, includes this stage and all the following until metamorphism). In this stage the sediment becomes compact. It has lost at least 50% of its connate water. Porosity is high and circulation still plays an essential part. Some detrital minerals, such as biotite, are unstable. All the clay minerals are still stable, but many types of replacement take place, due to interstitial circulation. Dickitization of kaolinite and illitization of montmorillonite can already be observed.
( 3 ) Deep or late diagenesis (= “late catagenesis or epigenesis” of Russian authors). In this stage the temperature is greater than 100 °C, pressure increases and porosity becomes very weak. Montmorillonites and irregular mixed‐layers disappear. Kaolinite recrystallizes as dickite in acid environment. These changes are irreversible.
( 4 ) Anchizone (= “metagenesis” of Russian authors; = “zone anchimétamorphique” of K ubler , 1964). This is the transitional zone to metamorphism. It agrees with temperatures around 200 °C. Illite and chlorite are almost the only sheet silicates. However, dickite can be observed as well as pyrophyllite generally associated with allevardite. The crystallographic parameters of illite define the limit of the following zone, the metamorphic epizone or greenschist facies.
The crystallochemical processes that take place during the diagenetic evolution of clay minerals are schematically the following:
( 1 ) Gradual tetracoordination of aluminium.
( 2 ) Filling of octahedral sites either by interlayer cations, either by cations derived from outside the lattice, without the distinction dioctahedral‐trioctahedral becoming very clear.
( 3 ) Interlayer exchange between crystal lattice and interstitial solution. Gradual closing of the layers by alkaline cations or octahedral brucite‐like sheets.
( 4 ) Massive crystalline growth in the anchizone and the epizone.
These processes are roughly symmetrical with those which occur during weathering.
This review is a summary of the conclusions drawn in a Docteur‐ès‐Sciences thesis (G. D unoyer de S egonzac , 1969: Les Minéraux argileux dans la Diagenèse. Passage au Métamorphisme , 339 p., 45 tables, 110 illus.) to be published as part of the series Mémoires du Service de la Carte Géologique d'Alsace et de Lorraine . Most of the evidence on which these conclusions have been based is not cited directly in this article, but can be found in the thesis mentioned above, to which the reader is referred.
Transmission electron microscopic (TEM) analyses of freshwater biofilms and bacterial cells, grown in experimental culture, have shown that these microorganisms are commonly associated with fine-grained (Fe, Al)-silicates of variable composition. The inorganic phases develop in a predictable manner, beginning with the adsorption of cationic iron to anionic cellular surfaces, supersaturation of the proximal fluid with Fe3+, nucleation and precipitation of a precursor ferric hydroxide phase on the cell surface, followed by reaction with dissolved silica and aluminum and eventually the growth of an amorphous clay-like phase. Alternatively, colloidal species of (Fe, Al)-silicate composition may react directly with either the anionic cellular polymers or adsorbed iron, depending on their net charge. Over time, these hydrous precursors may dehydrate and convert to more stable crystalline phases. Because microbial biofilms are expansive and highly reactive surfaces at the sediment–water interface, coupled with their ability to bind soluble components and form solid inorganic phases, they should influence the chemical composition of the overlying aqueous microenvironment, and ultimately contribute to the makeup of river bottom sediment.
Lava caves contain a wealth of yellow, white, pink, tan, and gold-colored microbial mats; but in addition to these clearly biological mats, there are many secondary mineral deposits that are nonbiological in appearance. Secondary mineral deposits examined include an amorphous copper-silicate deposit (Hawai'i) that is blue-green in color and contains reticulated and fuzzy filament morphologies. In the Azores, lava tubes contain iron-oxide formations, a soft ooze-like coating, and pink hexagons on basaltic glass, while gold-colored deposits are found in lava caves in New Mexico and Hawai'i. A combination of scanning electron microscopy (SEM) and molecular techniques was used to analyze these communities. Molecular analyses of the microbial mats and secondary mineral deposits revealed a community that contains 14 phyla of bacteria across three locations: the Azores, New Mexico, and Hawai'i. Similarities exist between bacterial phyla found in microbial mats and secondary minerals, but marked differences also occur, such as the lack of Actinobacteria in two-thirds of the secondary mineral deposits. The discovery that such deposits contain abundant life can help guide our detection of life on extraterrestrial bodies.
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