Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential.

Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential.

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.

A multidisciplinary approach to the comparison of three contrasting treatments on both lampenflora community and underlying rock surface.

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.

Fundamental Science and Engineering Questions in Planetary Cave Exploration.

Nearly half a century ago, two papers postulated the likelihood of lunar lava tube caves using mathematical models. Today, armed with an array of orbiting and fly-by satellites and survey instrumentation, we have now acquired cave data across our solar system-including the identification of potential cave entrances on the Moon, Mars, and at least nine other planetary bodies. These discoveries gave rise to the study of planetary caves. To help advance this field, we leveraged the expertise of an interdisciplinary group to identify a strategy to explore caves beyond Earth. Focusing primarily on astrobiology, the cave environment, geology, robotics, instrumentation, and human exploration, our goal was to produce a framework to guide this subdiscipline through at least the next decade. To do this, we first assembled a list of 198 science and engineering questions. Then, through a series of social surveys, 114 scientists and engineers winnowed down the list to the top 53 highest priority questions. This exercise resulted in identifying emerging and crucial research areas that require robust development to ultimately support a robotic mission to a planetary cave-principally the Moon and/or Mars. With the necessary financial investment and institutional support, the research and technological development required to achieve these necessary advancements over the next decade are attainable. Subsequently, we will be positioned to robotically examine lunar caves and search for evidence of life within Martian caves; in turn, this will set the stage for human exploration and potential habitation of both the lunar and Martian subsurface.

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.

Dominance of Arcobacter in the white filaments from the thermal sulfidic spring of Fetida Cave (Apulia, southern Italy).

The thermal spring of Fetida Cave, a still active sulfuric acid cave opening at sea level and located in Santa Cesarea Terme, southeastern Salento (Apulia region, Southern Italy) hosts abundant floating white filaments. The white filaments were mainly composed of sulfur crystals surrounded by microbial mass of the phyla Epsilonbacteraeota, Proteobacteria, Bacteroidetes, and Patescibacteria. The most abundant genus in the white filaments collected from the waters in the innermost part of the cave dominated by sulfidic exhalations was Arcobacter. This abundance can be related to the higher concentration of sulfide dissolved in water, and low oxygen and pH values. Conversely, lower Arcobacter abundances were obtained in the filaments collected in the entrance and middle part of the cave, where sulfidic water mixes with seawater, as the cave is subjected to tides and the mixing of fresh (continental) with marine water. The geochemical analysis of water and atmospheric gases confirmed these environmental constraints. In fact, the highest concentrations of H2S in the air and water were recorded closest to the spring upwelling in the innermost part of the cave, and the lowest ones near the cave entrance. The metabolic versatility of Arcobacter might provide a competitive advantage in the colonization of water bodies characterized by high sulfide, low oxygen, and dynamic fluid movement.

Unveiling an odd fate after death: The isolated Eneolithic cranium discovered in the Marcel Loubens Cave (Bologna, Northern Italy).

An isolated human cranium, dated to the early Eneolithic period, was discovered in 2015 at the top of a vertical shaft in the natural Marcel Loubens gypsum Cave (Bologna area, northern Italy). No other anthropological or archaeological remains were found inside the cave. In other caves of the same area anthropic and funerary use are attested from prehistory to more recent periods. We focused on investigating the circumstances surrounding the death of this individual, since the cranium shows signs of some lesions that appear to be the results of a perimortem manipulation probably carried out to remove soft tissues. Anthropological analyses revealed that the cranium belonged to a young woman. We analysed the taphonomic features and geological context to understand how and why the cranium ended up (accidentally or intentionally) in the cave. The analyses of both the sediments accumulated inside the cranium and the incrustations and pigmentation covering its outer surface suggested that it fell into the cave, drawn by a flow of water and mud, likely from the edges of a doline. The accidental nature of the event is also seemingly confirmed by some post-mortem lesions on the cranium. The comparison with other Eneolithic archaeological sites in northern Italy made it possible to interpret the find as likely being from a funerary or ritual context, in which corpse dismemberment (in particular the displacement of crania) was practiced.

Microbial Community Characterizing Vermiculations from Karst Caves and Its Role in Their Formation.

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.

Author Correction: Speleothem record attests to stable environmental conditions during Neanderthal-modern human turnover in southern Italy.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Speleothem record attests to stable environmental conditions during Neanderthal-modern human turnover in southern Italy.

The causes of Neanderthal-modern human (MH) turnover are ambiguous. While potential biocultural interactions between the two groups are still little known, it is clear that Neanderthals in southern Europe disappeared about 42 thousand years ago (ka) after cohabitation for ~3,000 years with MH. Among a plethora of hypotheses on Neanderthal extinction, rapid climate changes during the Middle to Upper Palaeolithic transition (MUPT) are regarded as a primary factor. Here we show evidence for stable climatic and environmental conditions during the MUPT in a region (Apulia) where Neanderthals and MH coexisted. We base our findings on a rare glacial stalagmite deposited between ~106 and ~27 ka, providing the first continuous western Mediterranean speleothem palaeoclimate archive for this period. The uninterrupted growth of the stalagmite attests to the constant availability of rainfall and vegetated soils, while its δ13C-δ18O palaeoclimate proxies demonstrate that Apulia was not affected by dramatic climate oscillations during the MUPT. Our results imply that, because climate did not play a key role in the disappearance of Neanderthals in this area, Neanderthal-MH turnover must be approached from a perspective that takes into account climatic and environmental conditions favourable for both species.

Geomicrobiology of a seawater-influenced active sulfuric acid cave.

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, Arenicellales, 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 Planctomycetes and Nitrospirae. The microbial community associated with gypsum moonmilk showed the strong dominance (>60%) of the archaeal genus Thermoplasma and lower abundance of chemolithotrophic Acidithiobacillus, metal-oxidizing Metallibacterium, Sulfobacillus, and Acidibacillus. This study describes the geomicrobiology of water filaments, vermiculations and gypsum moonmilk from Fetida Cave, providing insights into the microbial taxa that characterize each morphology and contribute to biogeochemical cycles and speleogenesis of this peculiar seawater-influenced sulfuric acid cave.

Microbial diversity and biosignatures of amorphous silica deposits in orthoquartzite caves.

Chemical mobility of crystalline and amorphous SiO2 plays a fundamental role in several geochemical and biological processes, with silicate minerals being the most abundant components of the Earth's crust. Although the oldest evidences of life on Earth are fossilized in microcrystalline silica deposits, little is known about the functional role that bacteria can exert on silica mobility at non-thermal and neutral pH conditions. Here, a microbial influence on silica mobilization event occurring in the Earth's largest orthoquartzite cave is described. Transition from the pristine orthoquartzite to amorphous silica opaline precipitates in the form of stromatolite-like structures is documented through mineralogical, microscopic and geochemical analyses showing an increase of metals and other bioessential elements accompanied by permineralized bacterial cells and ultrastructures. Illumina sequencing of the 16S rRNA gene describes the bacterial diversity characterizing the consecutive amorphization steps to provide clues on the biogeochemical factors playing a role in the silica solubilization and precipitation processes. These results show that both quartz weathering and silica mobility are affected by chemotrophic bacterial communities, providing insights for the understanding of the silica cycle in the subsurface.

The influence of human exploration on the microbial community structure and ammonia oxidizing potential of the Su Bentu limestone cave in Sardinia, Italy.

The bacterial diversity in the Su Bentu Cave in Sardinia was investigated by means of 16S rRNA gene-based analysis. This 15 km long cave, carved in Jurassic limestone, hosts a variety of calcite speleothems, and a long succession of subterranean lakes with mixed granite and carbonate sands. The lower level is occasionally flooded by a rising groundwater level, but with only scarce input of organic remains (leaves and charcoal fragments). On the quiet cave pools there are visible calcite rafts, whereas walls are locally coated with manganese deposits. In the drier upper levels, where organic input is much more subdued, moonmilk-a hydrated calcium-magnesium carbonate speleothem-can be found. Relative humidity approaches 100% and the measured mean annual cave air temperature is 14.8°C. Samples were obtained in 2014 from calcite rafts, moonmilk, manganese oxide deposits and soil (limestone and granite grains). Microclimatic conditions in the cave near the sampling sites, sample properties, physico-chemical parameters of water, and sediment composition were determined. The microbial community of this system is predominately composed of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Nitrospirae, and Firmicutes. Sampling sites near the entrance of the cave and in close proximity of the underground campsite-located 500 meters deep into the cave-revealed the highest diversity as well as the highest number of human associated microorganisms. Two samples obtained in very close proximity of each other near the campsite, indicate that the human impact is localized and is not distributed freely within the system. Analysis of the abundance of bacterial and archaeal amoA genes revealed a far greater abundance of archaeal amoA genes compared to bacterial representatives. The results of this study highlight that human impact is confined to locations that are utilized as campsites and that exploration leaves little microbial trails. Furthermore, we uncovered a highly specialized microbiome, which is perfectly adapted to survive and thrive in an environment with low nutrient availability.

Geochemistry and microbial diversity of cave waters in the gypsum karst aquifers of Emilia Romagna region, Italy.

Fifty-seven control points of waters (sinking streams, rivers in caves, and resurgences) hosted in gypsum karst areas in Emilia Romagna region (N-Italy) were sampled in the framework of a Project LIFE+08NAT/IT/000369 "Gypsum" in the period 2010-2014. The microbiology and chemistry of these waters have been analyzed to evaluate the impact of human activities or natural factors, in the gypsum karst systems. Waters have been analyzed for major chemistry (Ca, Mg, Na, K, SO4, HCO3, Cl, NO3) and some minor constituents (F, Br, NH4 and PO4), measuring pH, electric conductivity (EC), total dissolved solids (TDS) and temperature (T) in situ. The same samples have been analyzed with traditional microbiology techniques focused on total microbial count and on fecal microbiota, as index of human and/or animal contamination, and molecular biology techniques (sequencing of 16S rRNA segment and PCR-DGGE), focused on the characterization of microbial populations in the different sampling sites and determination of their variations and/or changes during the five years of the project. As expected, waters tend to be increasingly mineralized from sinking streams to resurgences, with only local and temporarily high contents in nitrates and ammonium, often related to the presence of bat colonies. PCR-DGGE revealed ecological changes, in terms of microbial populations present in the bulk water samples, in different sampling sites within the same cave. Although the impact of fecal microorganisms only rarely exceeded 2 log UFC/ml, the results evidenced fluctuations of these microorganisms mainly correlated to the season and to the biological activity of bats.

Microbial mediation of complex subterranean mineral structures.

Helictites--an enigmatic type of mineral structure occurring in some caves--differ from classical speleothems as they develop with orientations that defy gravity. While theories for helictite formation have been forwarded, their genesis remains equivocal. Here, we show that a remarkable suite of helictites occurring in Asperge Cave (France) are formed by biologically-mediated processes, rather than abiotic processes as had hitherto been proposed. Morphological and petro-physical properties are inconsistent with mineral precipitation under purely physico-chemical control. Instead, microanalysis and molecular-biological investigation reveals the presence of a prokaryotic biofilm intimately associated with the mineral structures. We propose that microbially-influenced mineralization proceeds within a gliding biofilm which serves as a nucleation site for CaCO3, and where chemotaxis influences the trajectory of mineral growth, determining the macroscopic morphology of the speleothems. The influence of biofilms may explain the occurrence of similar speleothems in other caves worldwide, and sheds light on novel biomineralization processes.