Microbial communities in carbonate precipitates from drip waters in Nerja Cave, Spain

Carbonate mineral precipitation induced by microorganisms enriched from the cave water and biofilm in a lime-decorated lava tube

Cave microorganisms associated with calcareous speleothems have been reported to facilitate calcium carbonate precipitation through crystal nucleation and mineral growth. In this study, we used carbonate-forming microorganisms enriched from cave water droplets and stalactite biofilm samples to induce precipitation of Mg2+ or Sr2+-coprecipitated carbonate minerals and explored their mineralogical properties. The samples for these analyses were collected from Yongcheon Cave, a lime-decorated lava tube located on Jeju Island in South Korea. They included five soil and sediment samples from outside the cave, seven drip water samples from inside the cave, and nine biofilm samples swiped using sterilized cotton swabs from inside the cave. The microorganisms enriched from the drip water samples comprised bacterial genera, including Pseudomonas, Bacillus, Stenotrophomonas, Acinetobacter, and Morganella. which are known to contribute to carbonate formation. In contrast, the microorganisms enriched from the biofilms were dominated by Pseudomonas. When only Ca2+ was present in the growth medium (Ca:Sr = 3:0), these microorganisms precipitated calcite and vaterite. Conversely, when Ca2+ and Sr2+ were present at varying ratios (Ca:Sr = 2:1, 1:1, and 1:2), calcian-strontianite was precipitated. Furthermore, when only Sr2+ was present (Ca:Sr = 0:3), strontianite was formed. Adding Ca2+ and Mg2+ at varying ratios (Ca:Mg = 2:1, 1:1, and 1:2) led to the precipitation of magnesian-calcite and monohydrocalcite. When only Mg2+ was added to the medium (Ca:Mg = 0:3), nesquehonite and struvite precipitated. These findings suggest that microorganisms enriched from the lava tube cave induce calcium carbonate precipitation through ureolysis and that Sr/Cr and Mg/Ca ratios influence the type of precipitated carbonate or phosphate minerals.

Bacterial communities forming yellow biofilms in different cave types share a common core

The walls of different types of caves under diverse geological settings (limestone, gypsum and volcanic) are colonized by biofilms of different colors: white, yellow, pink, grey, green to dark brown, but only a few colored biofilms such as the white, yellow and grey ones have been extensively studied. However, an assessment among the microbial communities originating these biofilms in different lithologies is lacking. Here we compare the yellow biofilms from two caves, Covadura and C3, in the Gypsum Karst of Sorbas in Spain, with those from two Spanish limestone caves (Pindal and Santian), and four volcanic caves in Spain and Italy (Viento, Honda del Bejenado, Grotta del Santo, Grotta di Monte Corruccio). The structure of yellow biofilms in gypsum caves closely resembles that found in other Spanish and European limestone caves. However, volcanic cave biofilms exhibit greater variability in their microbial community structure and morphologies. Biofilms from gypsum, limestone and volcanic caves were characterized by the abundance of the genera Crossiella and the gammaproteobacterial wb1-P19. The uncultured Euzebyaceae were abundant in gypsum and Spanish volcanic caves, while in the limestone and Italian volcanic caves, they were rare or absent. Nitrospira was also abundant in limestone and volcanic caves, but not in gypsum caves. Due to the abundances of Crossiella, gammaproteobacterial wb1-P19, and uncultured Euzebyaceae, in many different ecosystems, not only in caves, as recently reported, understanding the functional diversity in which these lineages are involved seems critical. Although we have studied a limited number of yellow biofilms from caves in Spain and Italy, data from other caves in USA and Russia also point out the existence of a similarity among the most abundant members composing the structure of yellow biofilms, suggesting that they share a common core.

Diversity pattern and antibiotic activity of microbial communities inhabiting a karst cave from Costa Rica

The studies of cave bacterial communities worldwide have revealed their potential to produce antibiotic molecules. In Costa Rica, ~400 caves have been identified; however, their microbial diversity and biotechnological potential remain unexplored. In this work, we studied the chemical composition and microbial diversity of a Costa Rican cave (known as the Amblipigida cave) located in Puntarenas, Costa Rica. Additionally, through culture-dependent methods, we evaluated the potential of its microbiota to produce antibiotic molecules. Mineralogical and elemental analyses revealed that the Amblipigida cave is primarily composed of calcite. However, small variations in chemical composition were observed as a result of specific conditions, such as light flashes or the input of organic matter. The 16S rRNA gene metabarcoding revealed an extraordinarily high microbial diversity (with an average Shannon index of ~6.5), primarily comprising bacteria from the phyla Pseudomonadota, Actinomycetota, Firmicutes and Acidobacteriota, with the family Pseudomonadaceae being the most abundant. A total of 93 bacteria were isolated, of which 15% exhibited antibiotic activity against at least one Gram-positive or yeast strain and were classified within the genera Lysobacter, Streptomyces, Pseudomonas, Brevundimonas and Bacillus. These findings underscore the highly diverse nature of cave microbiota and their significant biotechnological potential, particularly in the production of antibiotic compounds.

Discriminating organic carbon from endokarstic moonmilk-type deposits by LIBS. The case of a natural carbonated Martian analogue

Moonmilk-type deposits exemplify carbonated Martian analogues existing in the subsurface of Earth, an endokarstic speleothem with a possible biochemical origin composed principally by carbonates, mainly huntite and dolomite. In this work, samples of moonmilk located in Nerja Cave (southern Spain) have been studied by LIBS with the aim of identifying carbon of biogenic origin by establishing a relationship between a molecular emission indicator, CN signal, and the organic carbon content. The characterization of this kind of carbonate deposit with a multiple mineralogical composition has been completed using scanning electron microscopy (SEM), energy dispersive X-ray (EDX) and X-ray diffraction techniques for qualitative and semi-quantitative analysis. The information attained from LIBS regarding energy thresholds and time-resolved kinetics of CN emissions provides useful insight into the identification of different molecular emitters, namely organic and inorganic CN, depending on the laser irradiance and time settings conditions. These promising results are of application in the search and identification of biosignatures in upcoming planetary missions with astrobiological purposes.

Microclimate, airborne particles, and microbiological monitoring protocol for conservation of rock-art caves: The case of the world-heritage site La Garma cave (Spain)

Cave heritage is often threatened by tourism or even scientific activities, which can lead to irreversible deterioration. We present a preventive conservation monitoring protocol to protect caves with rock art, focusing on La Garma Cave (Spain), a World Heritage Site with valuable archaeological materials and Palaeolithic paintings. This study assessed the suitability of the cave for tourist use through continuous microclimate and airborne particles monitoring, biofilm analysis, aerobiological monitoring and experimental visits. Our findings indicate several factors that make it inadvisable to adapt the cave for tourist use. Human presence and transit within the cave cause cumulative effects on the temperature of environmentally very stable and fragile sectors and significant resuspension of particles from the cave sediments. These environmental perturbations represent severe impacts as they affect the natural aerodynamic control of airborne particles and determine bacterial dispersal throughout the cave. This monitoring protocol provides part of the evidence to design strategies for sustainable cave management.

Baseline investigation on soil solidification through biocementation using airborne bacteria

Microbial induced carbonate precipitation (MICP) through the ureolysis metabolic pathway is one of the most studied topics in biocementation due to its high efficiency. Although excellent outcomes have proved the potential of this technique, microorganisms face some obstacles when considering complicated situations in the real field, such as bacterial adaptability and survivability issues. This study made the first attempt to seek solutions to this issue from the air, exploring ureolytic airborne bacteria with resilient features to find a solution to survivability issues. Samples were collected using an air sampler in Sapporo, Hokkaido, a cold region where sampling sites were mostly covered with dense vegetation. After two rounds of screening, 12 out of 57 urease-positive isolates were identified through 16S rRNA gene analysis. Four potentially selected strains were then evaluated in terms of growth pattern and activity changes within a range of temperatures (15°C-35°C). The results from sand solidification tests using two Lederbergia strains with the best performance among the isolates showed an improvement in unconfined compressive strength up to 4-8 MPa after treatment, indicating a high MICP efficiency. Overall, this baseline study demonstrated that the air could be an ideal isolation source for ureolytic bacteria and laid a new pathway for MICP applications. More investigations on the performance of airborne bacteria under changeable environments may be required to further examine their survivability and adaptability.

Coronavirus pandemic: An opportunity to study the anthropogenic impact on micro-climate conditions and CaCO3 crystal morphology in the Nerja Cave (SE Spain)

Following the declaration of the COVID-19 pandemic, the Spanish Government restricted non-essential movements of all citizens and closed all public spaces, such as the Nerja Cave, until May 31, 2020. This particular condition of the closure of the cave provided a unique opportunity to study the micro-climate conditions and carbonate precipitation in this tourist cave without the presence of visitors. Our results show the significant effect of visitors on the air isotopic signature of the cave and on the genesis of the extensive dissolution features affecting the carbonate crystals formed in the tourist sector of the cave, alerting us to the possible corrosion of the speleothems located there. The movement of visitors within the cave also favours the mobilisation of aerial fungi and bacterial spores and their subsequent sedimentation simultaneously with the abiotic precipitation of carbonates from the drip water. The traces of these biotic elements could be the origin of the micro-perforations previously described in the carbonate crystals formed in the tourist galleries of the cave, but they are subsequently enlarged due to abiotic dissolution of the carbonates through these weaker zones.