Microbial composition and ecological features of phototrophic biofilms proliferating in the Moidons Caves (France): investigation at the single-cell level

16S and 18S rDNA Amplicon Sequencing Analysis of Aesthetically Problematic Microbial Mats on the Walls of the Petralona Cave: The Use of Essential Oils as a Cleaning Method

The presence of microbial communities on cave walls and speleothems is an issue that requires attention. Traditional cleaning methods using water, brushes, and steam can spread the infection and cause damage to the cave structures, while chemical agents can lead to the formation of toxic compounds and damage the cave walls. Essential oils (EOs) have shown promising results in disrupting the cell membrane of bacteria and affecting their membrane permeability. In this study, we identified the microorganisms forming unwanted microbial communities on the walls and speleothems of Petralona Cave using 16S and 18S rDNA amplicon sequencing approaches and evaluated the efficacy of EOs in reducing the ATP levels of these ecosystems. The samples exhibited a variety of both prokaryotic and eukaryotic microorganisms, including Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, the SAR supergroup, Opisthokonta, Excavata, Archaeplastida, and Amoebozoa. These phyla are often found in various habitats, including caves, and contribute to the ecological intricacy of cave ecosystems. In terms of the order and genus taxonomy, the identified biota showed abundances that varied significantly among the samples. Functional predictions were also conducted to estimate the differences in expressed genes among the samples. Oregano EO was found to reduce ATP levels by 87% and 46% for black and green spots, respectively. Consecutive spraying with cinnamon EO further reduced ATP levels, with reductions of 89% for black and 88% for green spots. The application of a mixture solution caused a significant reduction up to 96% in ATP levels of both areas. Our results indicate that EOs could be a promising solution for the treatment of microbial communities on cave walls and speleothems.

Effects of Anthropogenic Disturbance and Seasonal Variation on Aerobiota in Highly Visited Show Caves in Slovenia

Aerosols in caves are natural tracers and, together with climatic parameters, provide a detailed insight into atmospheric conditions, responses to climatic changes and anthropogenic influences in caves. Microbiological air monitoring in show caves is becoming increasingly useful to understand changes in cave ecosystems and to implement and review measures for sustainable cave use and tourism development. In 2017 and 2018, air along tourist trails in caves Postojnska jama and Škocjanske jame (Slovenia) was sampled before and after tourist visits. Samples were analysed using culture-dependent methods, flow cytometry, detection of β-D-glucan and lipopolysaccharide and compared with CO2 and temperature data to measure anthropogenic influences and seasonality on aerobiota. While the presence of tourists significantly increased concentrations of airborne microorganisms (p < 0.05), β-D-glucan and CO2 did not show such a trend and were more dependent on seasonal changes. Locally, concentrations of cultivable microorganisms above 1000 CFU/m3 were detected, which could have negative effects on the autochthonous microbiota and possibly on human health. A mixture of bacteria typically associated with humans was found in the air and identified with MALDI-TOF MS. Using MALDI-TOF MS, we achieved a 69.6% success rate in identification. Micrococcus luteus, Streptococcus mitis, Staphylococcus epidermidis and Moraxella spp. were recognized as good indicators of cave anthropisation.

When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment

In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.

Into the Unknown: Microbial Communities in Caves, Their Role, and Potential Use

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.

Analysis of Biodeteriogens on Architectural Heritage. An Approach of Applied Botany on a Gothic Building in Southern Italy

The degradation of stone materials depends on several interlinked factors. The effects caused by biodeteriogens on mineral-based substrates are now increasingly considered in the field of cultural heritage conservation from different experimental approaches. In this study, biodeteriogenic micro- and macroflora within the gothic building of Santa Maria della Pietà, Squillace, Calabria, have been analyzed using multiple approaches, such as optical microscopy and molecular techniques. All 17 plant species detected are usually widespread in Mediterranean regions and some of these, such as Ailanthus altissima and Ficus carica, showed a very high hazard index, which is potentially dangerous for masonry stability. Fungi, cyanobacteria, and green algae were identified within biofilm compositions in a total of 23 different taxa, showing many similarities with microbial associations commonly found in cave and hypogean environments. All of the 11 fungal taxa detected belong to Ascomycota phylum, with Penicillium as the most represented genus. Photoautotrophic organisms are mostly represented by filamentous genera, with widespread presence of Leptolyngbya as the most abundant genus. The results highlighted how the singular environmental conditions of the study site, combined with the architectural features and the building materials, determined all the degradation phenomena affecting the building’s internal surfaces, compromising over time the structural integrity.

Lighting Effects on the Development and Diversity of Photosynthetic Biofilm Communities in Carlsbad Cavern, New Mexico

Photosynthetic cave communities ("lampenflora") proliferate in Carlsbad Cavern and other show caves worldwide due to artificial lighting. These biofilms mar the esthetics and can degrade underlying cave surfaces. The National Park Service recently modernized the lighting in Carlsbad Cavern to a light-emitting diode (LED) system that allows adjustment of the color temperature and intensity. We hypothesized that lowering the color temperature would reduce photopigment development. We therefore assessed lampenflora responses to changes in lighting by monitoring photosynthetic communities over the course of a year. We measured photopigments using reflected-light spectrophotometric observations and analyzed microbial community composition with 16S and 18S rRNA gene amplicon sequencing. Reflected-light spectrophotometry revealed that photosynthetic biofilm development is affected by lighting intensity, color temperature, substrate type, and cleaning of the substrate. Gene sequencing showed that the most abundant phototrophs were Cyanobacteria and members of the algal phyla Chlorophyta and Ochrophyta At the end of the study, visible growth of lampenflora was seen at all sites. At sites that had no established biofilm at the start of the study period, Cyanobacteria became abundant and outpaced an increase in eukaryotic algae. Microbial diversity also increased over time at these sites, suggesting a possible pattern of early colonization and succession. Bacterial community structure showed significant effects of all variables: color temperature, light intensity, substrate type, site, and previous cleaning of the substrate. These findings provide fundamental information that can inform management practices; they suggest that altering lighting conditions alone may be insufficient to prevent lampenflora growth.IMPORTANCE Artificial lighting in caves visited by tourists ("show caves") can stimulate photosynthetic algae and cyanobacteria, called "lampenflora," which are unsightly and damage speleothems and other cave surfaces. The most common mitigation strategy employs bleach, but altering intensities and wavelengths of light might be effective and less harsh. Carlsbad Cavern in New Mexico, a U.S. National Park and UNESCO World Heritage Site, has visible lampenflora despite adjustment of LED lamps to decrease the energetic blue light. This study characterized the lampenflora communities and tested the effects of color temperature, light intensity, rock or sediment texture, and time on lampenflora development. DNA amplicon sequence data show a variety of algae and cyanobacteria and also heterotrophic bacteria. This study reveals microbial dynamics during colonization of artificially lit surfaces and indicates that while lowering the color temperature may have an effect, management of lampenflora will likely require additional chemical or UV treatment.

Natural limestone discolouration triggered by microbial activity-a contribution

Colour is a major argument that drives the decision of an architect in a specific architecture project and one of the most important characteristics and perceptible aspects of natural building stones. “Blue” limestones are building rocks, with different geological ages, typically used in several countries, and are known for their vulnerability to alteration, which causes colour change and the occurrence of unaesthetic patterns. Owing to this vulnerability, the conservation-restoration works in monuments, or new buildings constructed with “blue” limestone is extremely costly. Considering that the main limitation of this lithological variation is the chromatic change, a multidisciplinary approach was envisaged in this study to allow a closer insight into the chemical and mineralogical alterations and the microbial communities. Results obtained suggest that the inorganic alteration in the “blue” limestone may create favourable conditions for microbial growth and could lead to an increment in deterioration process.

Biofilm biodiversity in French and Swiss show caves using the metabarcoding approach: First data

In recent decades, show caves have begun to suffer from microorganism proliferation due to artificial lighting installations for touristic activity. In addition to the aesthetic problem, light encourages microorganisms that are responsible for physical and chemical degradation of limestone walls, speleothems and prehistoric paintings of cultural value. Microorganisms have previously been described by microscopy or culture-dependent methods, but data provided by new generation sequencing are rare. The authors identified, for the first time, microorganisms proliferating in one Swiss and in four French show caves using three different primers. The results showed that both photosynthetic and non-photosynthetic bacteria were the dominant taxa present in biofilms. Microalgae were heavily represented by the Trebouxiophyceae, Eustigmatophyceae and Chlorophyceae groups. Twelve diatoms were also recorded, with dominance of Syntrichia sp. (96.1%). Fungi were predominantly represented by Ascomycota, Zygomycota and Basidiomycota, fully half of the sampled biofilms where Fungi were detected. Comparing microbial communities from bleach-treated caves to those in untreated caves showed no significant difference except for a low-level change in the abundance of certain taxa. These findings provided by Illumina sequencing reveal a complex community structure in the 5 caves based on the assembly of bacteria, cyanobacteria, algae, diatoms, fungi and mosses.

UV-C as an efficient means to combat biofilm formation in show caves: evidence from the La Glacière Cave (France) and laboratory experiments

Ultra-violet C (UV-C) treatment is commonly used in sterilization processes in industry, laboratories, and hospitals, showing its efficacy against microorganisms such as bacteria, algae, or fungi. In this study, we have eradicated for the first time all proliferating biofilms present in a show cave (the La Glacière Cave, Chaux-lès-Passavant, France). Colorimetric measurements of irradiated biofilms were then monitored for 21 months. To understand the importance of exposition of algae to light just after UV radiation, similar tests were carried out in laboratory conditions. Since UV-C can be deleterious for biofilm support, especially parietal painting, we investigated their effects on prehistoric pigment. Results showed complete eradication of cave biofilms with no algae proliferation observed after 21 months. Moreover, quantum yield results showed a decrease directly after UV-C treatment, indicating inhibition of algae photosynthesis. Furthermore, no changes in pigment color nor in chemical and crystalline properties has been demonstrated. The present findings demonstrate that the UV-C method can be considered environmentally friendly and the best alternative to chemicals. This inexpensive and easily implemented method is advantageous for cave owners and managers.

UV-C as a means to combat biofilm proliferation on prehistoric paintings: evidence from laboratory experiments

A laboratory investigation of UV-C effects was conducted over a 62-h period: a much higher dose than in classic UV-C treatment was applied to five pigments and two painting binders used by prehistoric humans. Colorimetric parameters were compared to a control to see if UV-C can change pigment and binder color. Infrared spectroscopy, scanning electron microscopy, inductively coupled plasma and X-ray crystallography were also carried out to confirm colorimetric measurement. In order to understand how microorganism may physically deteriorate paintings, limestone blocks were painted and monitored until their complete colonization by algae, cyanobacteria, fungi and/or mosses. The results show that UV-C has no effect on mineral compounds. Conversely, it is noteworthy that binder color changed under both UV-C light conditions as well as in visible light. Concerning painted blocks, a fast proliferation has been observed with deterioration of the paintings. These results show the high importance of treating biofilm as soon as possible. Moreover, these findings may be a promising avenue inducing cave managers to use friendly UV-C light to treat contaminated cave paintings and also in the prevention of biodeterioration by lampenflora.

Assessing ultraphytoplankton and heterotrophic prokaryote composition by flow cytometry in a Mediterranean lagoon

In the eutrophic Ghar El Melh Lagoon (GML, Tunisia), the distribution of heterotrophic prokaryotes, pico- and nanophytoplankton was studied at five stations in November 2012 at the single cell level, along with environmental factors. Flow cytometry analysis of ultraplankton (<10 μm) resolved (i) two heterotrophic prokaryote groups, low and high nucleic acid contents (LNA and HNA, respectively), and (ii) eight to nine ultraphytoplankton groups (cryptophyte-like cells, two nanoeukaryote subgroups, two picoeukaryote subgroups and three Synechococcus-like cells subgroups). Prochlorococcus was not detected. According to redundancy analysis (RDA), a significant difference was found in the distribution of the ultraplankton between stations (F = 2.61, p < 0.05); maximum proliferations of heterotrophic prokaryotes were observed in the inner parts of the lagoon at stations 3, 4 and 5 affected by urban, agricultural and industrial discharges. Ultraphytoplankton concentrations were the highest near the outlet of the lagoon at stations 1 and 2 influenced by freshwater outflow and oligotrophic Mediterranean water inflow, respectively. At station 1, the large ultraphytoplankton concentration derives from the high abundance of cryptophyte-like cells favoured by the freshwater outflow whereas at station 2, the input of oligotrophic Mediterranean water enhanced the abundance of Synechococcus and picoeukaryotes at the expense of nanoeukaryotes. Two trophic regimes were thus differentiated in GML.