Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems in Natural and in Vitro Biomineralization Conditions

The link between ancient microbial fluoride resistance mechanisms and bioengineering organofluorine degradation or synthesis

Fluorinated organic chemicals, such as per- and polyfluorinated alkyl substances (PFAS) and fluorinated pesticides, are both broadly useful and unusually long-lived. To combat problems related to the accumulation of these compounds, microbial PFAS and organofluorine degradation and biosynthesis of less-fluorinated replacement chemicals are under intense study. Both efforts are undermined by the substantial toxicity of fluoride, an anion that powerfully inhibits metabolism. Microorganisms have contended with environmental mineral fluoride over evolutionary time, evolving a suite of detoxification mechanisms. In this perspective, we synthesize emerging ideas on microbial defluorination/fluorination and fluoride resistance mechanisms and identify best approaches for bioengineering new approaches for degrading and making organofluorine compounds.

The microbiota characterizing huge carbonatic moonmilk structures and its correlation with preserved organic matter

BACKGROUND

Moonmilk represents complex secondary structures and model systems to investigate the interaction between microorganisms and carbonatic rocks. Grotta Nera is characterized by numerous moonmilk speleothems of exceptional size hanging from the ceiling, reaching over two meters in length. In this work we combined microbiological analyses with analytical pyrolysis and carbon stable isotope data to determine the molecular composition of these complex moonmilk structures as well as the composition of the associated microbiota.

RESULTS

Three moonmilk structures were dissected into the apical, lateral, and core parts, which shared similar values of microbial abundance, richness, and carbon isotopes but different water content, microbiota composition, and organic matter. Moonmilk parts/niches showed higher values of microbial biomass and biodiversity compared to the bedrock (not showing moonmilk development signs) and the waters (collected below dripping moonmilk), indicating the presence of more complex microbial communities linked to carbonate rock interactions and biomineralization processes. Although each moonmilk niche was characterized by a specific microbiota as well as a distinct organic carbon profile, statistical analyses clustered the samples in two main groups, one including the moonmilk lateral part and the bedrock and the other including the core and apical parts of the speleothem. The organic matter profile of both these groups showed two well-differentiated organic carbon groups, one from cave microbial activity and the other from the leaching of vascular plant litter above the cave. Correlation between organic matter composition and microbial taxa in the different moonmilk niches were found, linking the presence of condensed organic compounds in the apical part with the orders Nitrospirales and Nitrosopumilales, while different taxa were correlated with aromatic, lignin, and polysaccharides in the moonmilk core. These findings are in line with the metabolic potential of these microbial taxa suggesting how the molecular composition of the preserved organic matter drives the microbiota colonizing the different moonmilk niches. Furthermore, distinct bacterial and archaeal taxa known to be involved in the metabolism of inorganic nitrogen and C1 gases (CO2 and CH4) (Nitrospira, Nitrosopumilaceae, Nitrosomonadaceae, Nitrosococcaceae, and novel taxa of Methylomirabilota and Methanomassiliicoccales) were enriched in the core and apical parts of the moonmilk, probably in association with their contribution to biogeochemical cycles in Grotta Nera ecosystem and moonmilk development.

CONCLUSIONS

The moonmilk deposits can be divided into diverse niches following oxygen and water gradients, which are characterized by specific microbial taxa and organic matter composition originating from microbial activities or deriving from soil and vegetation above the cave. The metabolic capacities allowing the biodegradation of complex polymers from the vegetation above the cave and the use of inorganic nitrogen and atmospheric gases might have fueled the development of complex microbial communities that, by interacting with the carbonatic rock, led to the formation of these massive moonmilk speleothems in Grotta Nera.

The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives

Caves are ubiquitous subterranean voids, accounting for a still largely unexplored surface of the Earth underground. Due to the absence of sunlight and physical segregation, caves are naturally colonized by microorganisms that have developed distinctive capabilities to thrive under extreme conditions of darkness and oligotrophy. Here, the microbiomes colonizing three frequently studied cave types, i.e., limestone, sulfuric acid speleogenetic (SAS), and lava tubes among volcanic caves, have comparatively been reviewed. Geological configurations, nutrient availability, and energy flows in caves are key ecological drivers shaping cave microbiomes through photic, twilight, transient, and deep cave zones. Chemoheterotrophic microbial communities, whose sustenance depends on nutrients supplied from outside, are prevalent in limestone and volcanic caves, while elevated inorganic chemical energy is available in SAS caves, enabling primary production through chemolithoautotrophy. The 16S rRNA-based metataxonomic profiles of cave microbiomes were retrieved from previous studies employing the Illumina platform for sequencing the prokaryotic V3-V4 hypervariable region to compare the microbial community structures from different cave systems and environmental samples. Limestone caves and lava tubes are colonized by largely overlapping bacterial phyla, with the prevalence of Pseudomonadota and Actinomycetota, whereas the co-dominance of Pseudomonadota and Campylobacterota members characterizes SAS caves. Most of the metataxonomic profiling data have so far been collected from the twilight and transient zones, while deep cave zones remain elusive, deserving further exploration. Integrative approaches for future geomicrobiology studies are suggested to gain comprehensive insights into the different cave types and zones. This review also poses novel research questions for unveiling the metabolic and genomic capabilities of cave microorganisms, paving the way for their potential biotechnological applications.

Connecting molecular biomarkers, mineralogical composition, and microbial diversity from Mars analog lava tubes

Lanzarote (Canary Islands, Spain) is one of the best terrestrial analogs to Martian volcanology. Particularly, Lanzarote lava tubes may offer access to recognizably preserved chemical and morphological biosignatures valuable for astrobiology. By combining microbiological, mineralogical, and organic geochemistry tools, an in-depth characterization of speleothems and associated microbial communities in lava tubes of Lanzarote is provided. The aim is to untangle the underlying factors influencing microbial colonization in Earth's subsurface to gain insight into the possibility of similar subsurface microbial habitats on Mars and to identify biosignatures preserved in lava tubes unequivocally. The microbial communities with relevant representativeness comprise chemoorganotrophic, halophiles, and/or halotolerant bacteria that have evolved as a result of the surrounding oceanic environmental conditions. Many of these bacteria have a fundamental role in reshaping cave deposits due to their carbonatogenic ability, leaving behind an organic record that can provide evidence of past or present life. Based on functional profiling, we infer that Crossiella is involved in fluorapatite precipitation via urea hydrolysis and propose its Ca-rich precipitates as compelling biosignatures valuable for astrobiology. In this sense, analytical pyrolysis, stable isotope analysis, and chemometrics were conducted to characterize the complex organic fraction preserved in the speleothems and find relationships among organic families, microbial taxa, and precipitated minerals. We relate organic compounds with subsurface microbial taxa, showing that organic families drive the microbiota of Lanzarote lava tubes. Our data indicate that bacterial communities are important contributors to biomarker records in volcanic-hosted speleothems. Within them, the lipid fraction primarily consists of low molecular weight n-alkanes, α-alkenes, and branched-alkenes, providing further evidence that microorganisms serve as the origin of organic matter in these formations. The ongoing research in Lanzarote's lava tubes will help develop protocols, routines, and predictive models that could provide guidance on choosing locations and methodologies for searching potential biosignatures on Mars.

Biomineral deposits and coatings on stone monuments as biodeterioration fingerprints

Biominerals deposition processes, also called biomineralisation, are intimately related to biodeterioration on stone surfaces. They include complex processes not always completely well understood. The study of biominerals implies the identification of organisms, their molecular mechanisms, and organism/rock/atmosphere interactions. Sampling restrictions of monument stones difficult the biominerals study and the in situ demonstrating of biodeterioration processes. Multidisciplinary works are required to understand the whole process. Thus, studies in heritage buildings have taken advantage of previous knowledge acquired thanks to laboratory experiments, investigations carried out on rock outcrops and within caves from some years ago. With the extrapolation of such knowledge to heritage buildings and the advances in laboratory techniques, there has been a huge increase of knowledge regarding biomineralisation and biodeterioration processes in stone monuments during the last 20 years. These advances have opened new debates about the implications on conservation interventions, and the organism's role in stone conservation and decay. This is a review of the existing studies of biominerals formation, biodeterioration on laboratory experiments, rocks, caves, and their application to building stones of monuments.

Prokaryotic communities inhabiting a high-radon subterranean ecosystem (Castañar Cave, Spain): Environmental and substrate-driven controls

Castañar Cave (Caceres, Spain) is a unique show cave known for its high natural radiation levels. This study presents a comprehensive analysis of its prokaryotic diversity, specifically focusing on investigating the influence of environmental conditions and substrate characteristics on the prokaryotic community structure in the cave sediments. Additionally, the research aims to evaluate the potential impact of human activities on the cave ecosystem. The identification of distinct bioclimatic zones within the cave was made possible through a combination of environmental and microbial monitoring (ATP assays). The results reveal sediment texture as a significant factor, notably affecting the structure, diversity, and phylogenetic variability of the microbial community, including both Bacteria and Archaea. The proportion of clay minerals in sediments plays a crucial role in regulating moisture levels and nutrient availability. These substrate properties collectively exert a significant selective pressure on the structure of prokaryotic communities within cave sediments. The molecular approach shows that heterotrophic bacteria, including those with chitinolytic enzymes, primarily inhabit the cave. Furthermore, chemoautotrophic nitrifiers such as the archaea Nitrososphaeria and the genus Nitrospira, as well as methanotrophic bacteria from the phyla Methylomirabilota, Pseudomonadota, and Verrucomicrobiota, are also present. Remarkably, despite being a show cave, the cave microbiota displays minimal impacts from human activities and the surface ecosystem. Prokaryotic populations exhibit stability in the innermost areas, while the tourist trail area experiences slightly higher biomass increases due to visitor traffic. This suggests that conservation efforts have successfully limited the entry of external nutrients into the innermost cave areas. Additionally, the results suggest that integrating biomarkers like ATP into environmental monitoring can significantly enhance the methods used to study the negative impacts of tourism on cave ecosystems.

Habitat-related variability in the morphological and taxonomic diversity of microbial communities in two Hungarian epigenic karst caves

The physical and chemical characteristics of the bedrock, along with the geological and hydrological conditions of karst caves may influence the taxonomic and functional diversity of prokaryotes. Most studies so far have focused on microbial communities of caves including only a few samples and have ignored the chemical heterogeneity of different habitat types such as sampling sites, dripping water, carbonate precipitates, cave walls, cave sediment and surface soils connected to the caves. The aim of the present study was to compare the morphology, the composition and physiology of the microbiota in caves with similar environmental parameters (temperature, host rock, elemental and mineral composition of speleothems) but located in different epigenic karst systems. Csodabogyós Cave and Baradla Cave (Hungary) were selected for the analysis of bacterial and archaeal communities using electron microscopy, amplicon sequencing, X-ray diffraction, and mass spectroscopic techniques. The microbial communities belonged to the phyla Pseudomonadota, Acidobacteriota, Nitrospirota and Nitrososphaerota, and they showed site-specific variation in composition and diversity. The results indicate that morphological and physiological adaptations provide survival for microorganisms according to the environment. In epigenic karst caves, prokaryotes are prone to increase their adsorption surface, cooperate in biofilms, and implement chemolithoautotrophic growth with different electron-donors and acceptors available in the microhabitats.

Environmental Drivers of the Moonmilk Microbiome Diversity in Some Temperate and Tropical Caves

Moonmilk is a cave deposit that was used for medical and cosmetic purposes and has lately raised interest for its antimicrobial potential. We studied five moonmilk samples from four caves with different microclimatic conditions, two temperate in north-western and northern Romania (Ferice, Fața Apei, and Izvorul Tăușoarelor caves) and one tropical in Minas Gerais, Brazil (Nestor Cave). The physicochemical and mineralogical analyses confirmed the presence of calcite and dolomite as the main phase in the moonmilk. A 16S rRNA gene-based metabarcoding approach showed the most abundant bacteria phyla Proteobacteria, GAL15, Actinobacteriota, and Acidobacteriota. The investigated caves differed in the dominant orders of bacteria, with the highest distance between the Romanian and Nestor Cave samples. Climate and, implicitly, the soil microbiome can be responsible for some differences we found between all the samples. However, other factors can be involved in shaping the moonmilk microbiome, as differences were found between samples in the same cave (Ferice). In our five moonmilk samples, 1 phylum, 70 orders (~ 36%), and 252 genera (~ 47%) were unclassified, which hints at the great potential of cave microorganisms for future uses.

Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity

The Borra caves, the second largest subterranean karst cave ecosystem in the Indian sub-continent, are located at the Ananthagiri hills of Araku Valley in the Alluri district of Andhra Pradesh, India. The present investigation applied a shotgun metagenomic approach to gain insights into the microbial community structure, metabolic potential, and biosynthetic gene cluster (BGC) diversity of the microbes colonizing the surface of the speleothems from the aphotic zone of Borra caves. The taxonomic analysis of the metagenome data illustrated that the speleothem-colonizing core microbial community was dominated mainly by Alpha-, Beta-, and Gamma-Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key energy metabolic pathways analysis provides strong evidence of chemolithoautotrophic and chemoheterotrophic modes of nutrition in the speleothem-colonizing microbial community. Metagenome data suggests that sulfur reducers and sulfur-disproportionating microbes might play a vital role in energy generation in this ecosystem. Our metagenome data also suggest that the dissimilatory nitrifiers and nitrifying denitrifiers might play an essential role in conserving nitrogen pools in the ecosystem. Furthermore, metagenome-wide BGCs mining retrieved 451 putative BGCs; NRPS was the most abundant (24%). Phylogenetic analysis of the C domain of NRPS showed that sequences were distributed across all six function categories of the known C domain, including several novel subclades. For example, a novel subclade had been recovered within the LCL domain clade as a sister subclade of immunosuppressant cyclosporin encoding C domain sequences. Our result suggested that subterranean cave microbiomes might be a potential reservoir of novel microbial metabolites.

Dark-zone alterations expand throughout Paleolithic Lascaux Cave despite spatial heterogeneity of the cave microbiome

BACKGROUND

Cave anthropization related to rock art tourism can lead to cave microbiota imbalance and microbial alterations threatening Paleolithic artwork, but the underpinning microbial changes are poorly understood. Caves can be microbiologically heterogeneous and certain rock wall alterations may develop in different rooms despite probable spatial heterogeneity of the cave microbiome, suggesting that a same surface alteration might involve a subset of cosmopolitan taxa widespread in each cave room. We tested this hypothesis in Lascaux, by comparing recent alterations (dark zones) and nearby unmarked surfaces in nine locations within the cave.

RESULTS

Illumina MiSeq metabarcoding of unmarked surfaces confirmed microbiome heterogeneity of the cave. Against this background, the microbial communities of unmarked and altered surfaces differed at each location. The use of a decision matrix showed that microbiota changes in relation to dark zone formation could differ according to location, but dark zones from different locations displayed microbial similarities. Thus, dark zones harbor bacterial and fungal taxa that are cosmopolitan at the scale of Lascaux, as well as dark zone-specific taxa present (i) at all locations in the cave (i.e. the six bacterial genera Microbacterium, Actinophytocola, Lactobacillus, Bosea, Neochlamydia and Tsukamurella) or (ii) only at particular locations within Lascaux. Scanning electron microscopy observations and most qPCR data evidenced microbial proliferation in dark zones.

CONCLUSION

Findings point to the proliferation of different types of taxa in dark zones, i.e. Lascaux-cosmopolitan bacteria and fungi, dark zone-specific bacteria present at all locations, and dark zone-specific bacteria and fungi present at certain locations only. This probably explains why dark zones could form in various areas of the cave and suggests that the spread of these alterations might continue according to the area of distribution of key widespread taxa.

Insights into the microbial life in silica-rich subterranean environments: microbial communities and ecological interactions in an orthoquartzite cave (Imawarì Yeuta, Auyan Tepui, Venezuela)

Microbial communities inhabiting caves in quartz-rich rocks are still underexplored, despite their possible role in the silica cycle. The world’s longest orthoquartzite cave, Imawarì Yeuta, represents a perfect arena for the investigation of the interactions between microorganisms and silica in non-thermal environments due to the presence of extraordinary amounts of amorphous silica speleothems of different kinds. In this work, the microbial diversity of Imawarì Yeuta was dissected by analyzing nineteen samples collected from different locations representative of different silica amorphization phases and types of samples. Specifically, we investigated the major ecological patterns in cave biodiversity, specific taxa enrichment, and the main ecological clusters through co-occurrence network analysis. Water content greatly contributed to the microbial communities’ composition and structures in the cave leading to the sample clustering into three groups DRY, WET, and WATER. Each of these groups was enriched in members of Actinobacteriota, Acidobacteriota, and Gammaproteobacteria, respectively. Alpha diversity analysis showed the highest value of diversity and richness for the WET samples, while the DRY group had the lowest. This was accompanied by the presence of correlation patterns including either orders belonging to various phyla from WET samples or orders belonging to the Actinobacteriota and Firmicutes phyla from DRY group samples. The phylogenetic analysis of the dominant species in WET and DRY samples showed that Acidobacteriota and Actinobacteriota strains were affiliated with uncultured bacteria retrieved from various oligotrophic and silica/quartz-rich environments, not only associated with subterranean sites. Our results suggest that the water content greatly contributes to shaping the microbial diversity within a subterranean quartzite environment. Further, the phylogenetic affiliation between Imawarì Yeuta dominant microbes and reference strains retrieved from both surface and subsurface silica- and/or CO₂/CO-rich environments, underlines the selective pressure applied by quartz as rock substrate. Oligotrophy probably in association with the geochemistry of silica/quartz low pH buffering activity and alternative energy sources led to the colonization of specific silica-associated microorganisms. This study provides clues for a better comprehension of the poorly known microbial life in subsurface and surface quartz-dominated environments.

Biomineralization in Cave Bacteria—Popcorn and Soda Straw Crystal Formations, Morphologies, and Potential Metabolic Pathways

Caves are extreme, often oligotrophic, environments that house diverse groups of microorganisms. Many of these microbes can perform microbiologically induced carbonate precipitation (MICP) to form crystalline secondary cave deposits known as speleothems. The urease family is a group of enzymes involved in MICP that catalyze the breakdown of urea, which is a source of energy, into ammonia and carbonate. Carbonate anions are effluxed to the extracellular surface of the bacterium where it then binds to environmental calcium to form calcium carbonate which then continues to grow in crystal form. Here, we studied bacterial communities from speleothems collected from the Iron Curtain Cave (ICC) in Chilliwack, B.C., Canada, to characterize these organisms and determine whether urease-positive (U+) bacteria were present in the cave and their potential impact on speleothem formation. The ICC is a carbonate cave located on the northside of Chipmunk Ridge, presenting a unique environment with high iron content sediment and limestone structures throughout. With six pools of water throughout the cave, the environment is highly humid, with temperatures ranging between 4 and 12°C depending on the time of year. Ninety-nine bacterial strains were isolated from popcorn (PCS) and soda straw (SSS) speleothems. These isolates were screened for urease enzymatic activity, with 11 candidates found to be urease-positive. After incubation, species-specific crystal morphologies were observed. Popcorn speleothem provided more bacterial diversity overall when compared to soda straw speleothem when examined under a culture-based method. Nearly twice as many U+ isolates were isolated from popcorn speleothems compared to soda straw speleothems. The U+ candidates were identified to the genus level by 16S rRNA analysis, and two isolates underwent whole-genome sequencing. Two novel species were identified as Sphingobacterium sp. PCS056 and Pseudarthrobacter sp. SSS035. Both isolates demonstrated the most crystal production as well as the most morphologically dissimilar crystal shapes in broth culture and were found to produce crystals as previously observed in both agar and broth media. The results from this study are consistent with the involvement of urease-positive bacteria isolated from the ICC in the formation of cave speleothems. 16S rRNA sequencing revealed a diverse set of microbes inhabiting the speleothems that have urease activity. Whole-genome sequencing of the two chosen isolates confirmed the presence of urease pathways, while revealing differences in urease pathway structure and number. This research contributes to understanding microbial-associated cave formation and degradation, with applications to cave conservation, microbiota composition, and their role in shaping the cave environment.

A 16S rRNA Gene-Based Metabarcoding of Phosphate-Rich Deposits in Muierilor Cave, South-Western Carpathians

Muierilor Cave is one of Romania's most important show caves, with paleontological and archeological deposits. Recently, a new chamber was discovered in the cave, with unique yellow calcite crystals, fine-grained crusts, and black sediments. The deposits in this chamber were related to a leaking process from the upper level that contains fossil bones and a large pile of guano. Samples were taken from the new chamber and another passage to investigate the relationship between the substrate and microbial community. Chemical, mineralogical, and whole community 16S rRNA gene-based metabarcoding analyses were undertaken, and the base of the guano deposit was radiocarbon dated. Our study indicated bacteria linked to the presence of high phosphate concentration, most likely due to the nature of the substrate (hydroxyapatite). Bacteria involved in Fe, Mn, or N cycles were also found, as these elements are commonly identified in high concentrations in guano. Since no bat colonies or fossil bones were present in the new chamber, a high concentration of these elements could be sourced by organic deposits inside the cave (guano and fossil bones) even after hundreds of years of their deposition and in areas far from both deposits. Metabarcoding of the analyzed samples found that ∼0.7% of the identified bacteria are unknown to science, and ∼47% were not previously reported in caves or guano. Moreover, most of the identified human-related bacteria were not reported in caves or guano before, and some are known for their pathogenic potential. Therefore, continuous monitoring of air and floor microbiology should be considered in show caves with organic deposits containing bacteria that can threaten human health. The high number of unidentified taxa in a small sector of Muierilor Cave indicates the limited knowledge of the bacterial diversity in caves that can have potential applications in human health and biotechnology.

Microbial ecology of tourist Paleolithic caves

Microorganisms colonize caves extensively, and in caves open for tourism they may cause alterations on wall surfaces. This is a major concern in caves displaying Paleolithic art, which is usually fragile and may be irremediably damaged by microbial alterations. Therefore, many caves were closed for preservation purposes, e.g. Lascaux (France), Altamira (Spain), while others were never opened to the public to avoid microbial contamination, e.g. Chauvet Cave (France), etc. The recent development of high-throughput sequencing technologies allowed several descriptions of cave microbial diversity and prompted the writing of this review, which focuses on the cave microbiome for the three domains of life (Bacteria, Archaea, microeukaryotes), the impact of tourism-related anthropization on microorganisms in Paleolithic caves, and the development of microbial alterations on the walls of these caves. This review shows that the microbial phyla prevalent in pristine caves are similar to those evidenced in water, soil, plant and metazoan microbiomes, but specificities at lower taxonomic levels remain to be clarified. Most of the data relates to Bacteria and Fungi, while other microeukaryotes and Archaea are poorly documented. Tourism may cause shifts in the microbiota of Paleolithic caves, but larger-scale investigation are required as these shifts may differ from one cave to the next. Finally, different types of alterations can occur in caves, especially in Paleolithic caves. Many microorganisms potentially involved have been identified, but diversity analyses of these alterations have not always included a comparison with neighboring unaltered zones as controls, making such associations uncertain. It is expected that omics technologies will also allow a better understanding of the functional diversities of the cave microbiome. This will be needed to decipher microbiome dynamics in response to touristic frequentation, to guide cave management, and to identify the most appropriate reclamation approaches to mitigate microbial alterations in tourist Paleolithic caves.

Recent Progress and Prospects in Catalytic Water Treatment

Presently, conventional technologies in water treatment are not efficient enough to completely mineralize refractory water contaminants. In this context, the implementation of catalytic processes could be an alternative. Despite the advantages provided in terms of kinetics of transformation, selectivity, and energy saving, numerous attempts have not yet led to implementation at an industrial scale. This review examines investigations at different scales for which controversies and limitations must be solved to bridge the gap between fundamentals and practical developments. Particular attention has been paid to the development of solar-driven catalytic technologies and some other emerging processes, such as microwave assisted catalysis, plasma-catalytic processes, or biocatalytic remediation, taking into account their specific advantages and the drawbacks. Challenges for which a better understanding related to the complexity of the systems and the coexistence of various solid-liquid-gas interfaces have been identified.

Metataxonomic Analysis of Bacteria Entrapped in a Stalactite's Core and Their Possible Environmental Origins

Much is known about microbes originally identified in caves, but little is known about the entrapment of microbes (bacteria) in stalactites and their possible environmental origins. This study presents data regarding the significant environmental distribution of prokaryotic bacterial taxa of a Greek stalactite core. We investigated the involvement of those bacteria communities in stalactites using a metataxonomic analysis approach of partial 16S rRNA genes. The metataxonomic analysis of stalactite core material revealed an exceptionally broad ecological spectrum of bacteria classified as members of Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and other unclassified bacteria. We concluded that (i) the bacterial transport process is possible through water movement from the upper ground cave environment, forming cave speleothems such as stalactites, (ii) bacterial genera such as Polaromonas, Thioprofundum, and phylum Verrucomicrobia trapped inside the stalactite support the paleoecology, paleomicrobiology, and paleoclimate variations, (iii) the entrapment of certain bacteria taxa associated with water, soil, animals, and plants such as Micrococcales, Propionibacteriales, Acidimicrobiales, Pseudonocardiales, and α-, β-, and γ-Proteobacteria.

Human kidney stones: a natural record of universal biomineralization

GeoBioMed - a new transdisciplinary approach that integrates the fields of geology, biology and medicine - reveals that kidney stones composed of calcium-rich minerals precipitate from a continuum of repeated events of crystallization, dissolution and recrystallization that result from the same fundamental natural processes that have governed billions of years of biomineralization on Earth. This contextual change in our understanding of renal stone formation opens fundamentally new avenues of human kidney stone investigation that include analyses of crystalline structure and stratigraphy, diagenetic phase transitions, and paragenetic sequences across broad length scales from hundreds of nanometres to centimetres (five Powers of 10). This paradigm shift has also enabled the development of a new kidney stone classification scheme according to thermodynamic energetics and crystalline architecture. Evidence suggests that ≥50% of the total volume of individual stones have undergone repeated in vivo dissolution and recrystallization. Amorphous calcium phosphate and hydroxyapatite spherules coalesce to form planar concentric zoning and sector zones that indicate disequilibrium precipitation. In addition, calcium oxalate dihydrate and calcium oxalate monohydrate crystal aggregates exhibit high-frequency organic-matter-rich and mineral-rich nanolayering that is orders of magnitude higher than layering observed in analogous coral reef, Roman aqueduct, cave, deep subsurface and hot-spring deposits. This higher frequency nanolayering represents the unique microenvironment of the kidney in which potent crystallization promoters and inhibitors are working in opposition. These GeoBioMed insights identify previously unexplored strategies for development and testing of new clinical therapies for the prevention and treatment of kidney stones.

Bioconservation of Historic Stone Buildings—An Updated Review

Cultural heritage buildings of stone construction require careful restorative actions to maintain them as close to the original condition as possible. This includes consolidation and cleaning of the structure. Traditional consolidants may have poor performance due to structural drawbacks such as low adhesion, poor penetration and flexibility. The requirement for organic consolidants to be dissolved in volatile organic compounds may pose environmental and human health risks. Traditional conservation treatments can be replaced by more environmentally acceptable, biologically-based, measures, including bioconsolidation using whole bacterial cells or cell biomolecules; the latter include plant or microbial biopolymers and bacterial cell walls. Biocleaning can employ microorganisms or their extracted enzymes to remove inorganic and organic surface deposits such as sulfate crusts, animal glues, biofilms and felt tip marker graffiti. This review seeks to provide updated information on the innovative bioconservation treatments that have been or are being developed.

Biodeteriogens Characterization and Molecular Analyses of Diverse Funeral Accessories from XVII Century

A historical crypt offers us a particular view of the conditions of some buried materials (in this case textiles) and the various biogenic phenomena to which they were subjected over the centuries. In addition, significant knowledge can come by studying the DNA of buried objects which allows the recognition of materials, but also to reveal some practice of the funeral ceremony. In this study, the deteriorating microbial communities colonizing various funeral textile items were identified and characterized using microscopic observation, cultivation, polymerase chain reaction (PCR) and sequencing, hydrolytic tests; and culture-independent analysis (high-throughput sequencing, MinION platform). Different PCR assays and consequent sequencing of amplicons were employed to recognize the animal origin of bodice reinforcements and the type of plant used to embellish the young girl. The analysis of ancient DNA (aDNA from animal and plant) was also completed by the application of high-throughput sequencing through Illumina platform. The combination of all these techniques permitted the identification of a complex microbiota composed by dangerous degradative microorganisms able to hydrolyze various organic substrates such as fibroin, keratin, and cellulose. Bacteria responsible for metal corrosion and bio-mineralization, and entomopathogenic and phytopathogenic fungi. The analysis of aDNA identified the animal component used in bodice manufacturing, the plant utilized as ornament and probably the season of this fatal event.

Bacterial Calcium Carbonate Mineralization in situ Strategies for Conservation of Stone Artworks: From Cell Components to Microbial Community

Calcareous stones have been widely used in artworks and buildings by almost all human cultures. Now, more than ever, the increased environmental pollution and global warming are threatening the stone cultural heritage. Weathering due to physical, chemical and biological factors results in monumental calcareous stone deterioration. These agents induce a progressive dissolution of the mineral matrix, increase porosity, and lead to structural weakening. Bacterial Calcium Carbonate Mineralization is a widespread naturally occurring process which in the last decades was proposed as an environmentally friendly tool to protect monumental and ornamental calcareous stones. The advantage of this treatment is that it mimics the natural process responsible for stone formation, producing a mineral product similar to the stone substrate. This mini review highlights the milestones of the biomineralization approaches with focus on in situ stone artworks protection. The strategies explored to date are based on three main approaches: (i) the use of allochthonous and (ii) autochthonous alive cells that, due to the bacterial metabolism, foster biomineralization; (iii) the cell-free approach which uses fractionated cellular components inducing biomineralization. We discuss the challenging aspects of all these techniques, focusing on in situ applications and suggesting perspectives based on recent advances.

Microbe-Mediated Extracellular and Intracellular Mineralization: Environmental, Industrial, and Biotechnological Applications

Microbe-mediated mineralization is ubiquitous in nature, involving bacteria, fungi, viruses, and algae. These mineralization processes comprise calcification, silicification, and iron mineralization. The mechanisms for mineral formation include extracellular and intracellular biomineralization. The mineral precipitating capability of microbes is often harnessed for green synthesis of metal nanoparticles, which are relatively less toxic compared with those synthesized through physical or chemical methods. Microbe-mediated mineralization has important applications ranging from pollutant removal and nonreactive carriers, to other industrial and biomedical applications. Herein, the different types of microbe-mediated biomineralization that occur in nature, their mechanisms, as well as their applications are elucidated to create a backdrop for future research.

Geomicrobial Investigations of Colored Outer Coatings from an Ethiopian Rock Art Gallery

The open rock shelter of Yabelo in Ethiopia hosts diverse Holocene paintings of great cultural importance. The paintings are characterized by the presence of different mineral coatings, whose features have not been studied yet. Our goal was to understand whether different rock samples from the Yabelo paintings collected in close proximity may reveal coatings with different minerology and biology. Thus, elemental analyses combined with microscopic and molecular investigations were performed on two coatings, one whitish (sample 1) and one reddish (sample 2). Although both samples were dominated by heterotrophic bacteria, the two coatings showed distinct mineralogical and microbiological characteristics. Sample 1 contained higher amounts of Ca and P than sample 2, which was likely related to the presence of organic matter. Sample 1 hosted bacterial genera that are potentially involved in biomineralization processes, metal redox cycles and metal resistance. In contrast, sample 2 showed mainly pathogenic and commensal bacteria that are characteristic of animal and human microbiota, and other microorganisms that are involved in nitrogen and metal biogeochemical cycles. Overall, our results indicated that the bacterial communities were particular to the coating mineralogy, suggesting a potential role of the biological components in the crust genesis.

Understanding and creating biocementing beachrocks via biostimulation of indigenous microbial communities

Bacterially induced precipitation of minerals leading to cementation of natural geological formations has been well recorded in a variety of environments. A range of microbial pathways and geochemical processes have been found to influence the cementation processes; but detailed formation mechanisms and biogeochemical relationships are still not very clear. There has been a growing demand for the application of bacterially driven biocementation in a number of geotechnical engineering applications recently. Here, we aimed to unpin the mechanisms behind the formation of actively mineralising beachrock sediments at Lucky Bay in Western Australia to understand the natural accretionary processes and potential of indigenous bacterial communities in biocementation. We observed ferruginous, aluminosilicate and carbonate cements along with extensive extra polymeric substances, borings with possible microbial activities in certain sections of native beachrock sediments. Cement precipitation under calcium- and iron-rich microenvironments sourced from seawater and iron creek seems to be driven by both biogenic and abiogenic processes in nature. Native microbial communities with a dominance of the genera Halococcus and Marinobacter were recorded. Enrichment of native bacterial communities under seawater media conditions was conducted which lead to successful biomineralisation of calcitic and ferruginous cements under in vitro conditions although the community composition changed significantly. Nanomechanical properties of natural and laboratory synthesised cement crystals showed that engineered biocement is highly promising. The results of this study clearly demonstrate biological influence in the formation of natural cements and hint significant potential of biostimulation which can be harnessed for different engineering applications including coastal erosion.

Analysis and optimization of process parameters for in vitro biomineralization of CaCO3 by Klebsiella pneumoniae, isolated from a stalactite from the Sahastradhara cave

Stalactite is a speleothem which is usually made up of calcium carbonate crystals. In the present study the bacterial isolates, recovered from a stalactite from the Sahastradhara cave, were screened for their ability to precipitate calcium carbonate in order to understand whether mineralization in caves is a biogenic process or not. Five bacterial isolates were found to precipitate calcium carbonate via urease. The most potent bacterial isolate was identified as Klebsiella pneumoniae (accession number MG946801) based on 16S rDNA sequencing. The optimized conditions, for calcium carbonate precipitation, determined by response surface methodology using CCD were found to be: 1.5625% urea, 19.98% inoculum level, 6.98 pH and 38 h 24 min. The morphology and crystalline structure of the precipitated mineral were revealed by SEM. EDX analysis confirmed the presence of carbon, oxygen and calcium in a precipitated crystal. XRD analysis confirmed the crystalline structure of a mineral with rhombohedral shape and 166 Å crystal size. This bacterium can serve as a promising candidate for producing bioconcrete.

Stalactite is a speleothem which is usually made up of calcium carbonate crystals.

Engineered Ureolytic Microorganisms Can Tailor the Morphology and Nanomechanical Properties of Microbial-Precipitated Calcium Carbonate

We demonstrate for the first time that the morphology and nanomechanical properties of calcium carbonate (CaCO₃) can be tailored by modulating the precipitation kinetics of ureolytic microorganisms through genetic engineering. Many engineering applications employ microorganisms to produce CaCO₃. However, control over bacterial calcite morphology and material properties has not been demonstrated. We hypothesized that microorganisms genetically engineered for low urease activity would achieve larger calcite crystals with higher moduli. We compared precipitation kinetics, morphology, and nanomechanical properties for biogenic CaCO₃ produced by two Escherichia coli (E. coli) strains that were engineered to display either high or low urease activity and the native producer Sporosarcina pasteurii. While all three microorganisms produced calcite, lower urease activity was associated with both slower initial calcium depletion rate and increased average calcite crystal size. Both calcite crystal size and nanoindentation moduli were also significantly higher for the low-urease activity E. coli compared with the high-urease activity E. coli. The relative resistance to inelastic deformation, measured via the ratio of nanoindentation hardness to modulus, was similar across microorganisms. These findings may enable design of novel advanced engineering materials where modulus is tailored to the application while resistance to irreversible deformation is not compromised.

Isolation, Characterization, and Antibacterial Activity of Hard-to-Culture Actinobacteria from Cave Moonmilk Deposits

Cave moonmilk deposits host an abundant and diverse actinobacterial population that has a great potential for producing novel natural bioactive compounds. In our previous attempt to isolate culturable moonmilk-dwelling Actinobacteria, only Streptomyces species were recovered, whereas a metagenetic study of the same deposits revealed a complex actinobacterial community including 46 actinobacterial genera in addition to streptomycetes. In this work, we applied the rehydration-centrifugation method to lessen the occurrence of filamentous species and tested a series of strategies to achieve the isolation of hard-to-culture and rare Actinobacteria from the moonmilk deposits of the cave “Grotte des Collemboles”. From the “tips and tricks” that were tested, separate autoclaving of the components of the International Streptomyces Project (ISP) medium number 5 (ISP5) medium, prolonged incubation time, and dilution of the moonmilk suspension were found to most effectively improve colony forming units. Taxonomic analyses of the 40 isolates revealed new representatives of the Agromyces, Amycolatopsis, Kocuria, Micrococcus, Micromonospora, Nocardia, and Rhodococcus species, as well as additional new streptomycetes. The applied methodologies allowed the isolation of strains associated with both the least and most abundant moonmilk-dwelling actinobacterial operational taxonomic units. Finally, bioactivity screenings revealed that some isolates displayed high antibacterial activities, and genome mining uncovered a strong potential for the production of natural compounds.

High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits

Moonmilk are cave carbonate deposits that host a rich microbiome, including antibiotic-producing Actinobacteria, making these speleothems appealing for bioprospecting. Here, we investigated the taxonomic profile of the actinobacterial community of three moonmilk deposits of the cave "Grotte des Collemboles" via high-throughput sequencing of 16S rRNA amplicons. Actinobacteria was the most common phylum after Proteobacteria, ranging from 9% to 23% of the total bacterial population. Next to actinobacterial operational taxonomic units (OTUs) attributed to uncultured organisms at the genus level (~44%), we identified 47 actinobacterial genera with Rhodoccocus (4 OTUs, 17%) and Pseudonocardia (9 OTUs, ~16%) as the most abundant in terms of the absolute number of sequences. Streptomycetes presented the highest diversity (19 OTUs, 3%), with most of the OTUs unlinked to the culturable Streptomyces strains that were previously isolated from the same deposits. Furthermore, 43% of the OTUs were shared between the three studied collection points, while 34% were exclusive to one deposit, indicating that distinct speleothems host their own population, despite their nearby localization. This important spatial diversity suggests that prospecting within different moonmilk deposits should result in the isolation of unique and novel Actinobacteria. These speleothems also host a wide range of non-streptomycetes antibiotic-producing genera, and should therefore be subjected to methodologies for isolating rare Actinobacteria.