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9 páginas.- 5 figuras.- 3 tablas.- referencias.-. The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb. 2022.982933/full#supplementary-material .- This article is part of the Research Topic Microbial Roles in Caves, The present study reports a sudden fungal outbreak that occurred in the corridor near the entrance of the Catacombs of SS. Marcellino and Pietro in Rome (Italy) observed after 1 year of a restoration treatment that interested the walls of the entrance of the Catacombs and some artifacts placed in situ. The colonization was observed on the vault at the entrance and in correspondence with the restored marble pieces displayed on the left side of the corridor. No growth was observed on the right side where similarly treated marble slabs were placed. Samples taken in correspondence with fungal biofilm were analyzed through the combined use of microscopical, cultural, and molecular tools and showed that the vault and the left side of the corridor entrance were colonized by a complex fungal biofilm consisting mainly of Coniophora sp. and other genera, such as Hypomyces, Purpureocillium, Acremonium, Penicillium, and Alternaria, many of which are well known as responsible of biodeterioration of stone surfaces. Regarding the brown-rot basidiomycete Coniophora, it was able to form very large colonies on the substrata with a diameter of up to 57 cm. Although the direct observation under a light microscope evidenced the presence of abundant brown fungal conidia, several attempts to cultivate the microorganism failed, therefore only through DNA sequencing analyses, it was possible to identify and characterize this fungus. There is very little literature on the genus Coniophora which is reported as one of the causes of wet-rot decay of wood in buildings. A connection with calcium-containing materials such as bricks and mortars was demonstrated, but no data were available about the possible role of this species in the biodeterioration of stones. This study features the first finding of a strain related to the basidiomycetous genus of Coniophora in the order Boletales in association with evident phenomena of biodeterioration., This project was supported thanks to the special funds provided by the University of Messina (approved on 21 February 2022 by the Academic Senatus) (Italy), the Spanish Ministry of Science and Innovation, and project PID2020-114978GB-I00 and project CIACCO DTC TE1 - FASE II - PROGETTI RSI8.

Bacteria isolated from the soils of three northern Spain caves were investigated for their growth at temperatures in the range 5-45°C, substrate utilization pattern, and cellular fatty acid components. All tested bacteria were able to grow comparatively well in a range of temperatures from 13° to 45°C. At 13°C the bacteria oxidized on average 87% of carbon sources provided while incubation at 28°C reduced to about 50% carbon source utilization. Changes in fatty acid profiles reflected an adaptative response to temperature. The results suggest the need of using low temperatures to detect maximum diversity of culturable bacteria (other than actinomycetes) and efficiency of carbon utilization by cave bacteria.

12 paginas.- 5 figuras.- referencias.- The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb.2022.869661/full#supplementary-material, Castañar Cave is a clear example of an oligotrophic ecosystem with high hygrothermal stability both seasonal and interannual and the particularity of registering extraordinary levels of environmental radiation. These environmental conditions make the cave an ideal laboratory to evaluate both the responses of the subterranean environment to sudden changes in the matter and energy fluxes with the exterior and also any impact derived from its use as a tourist resource under a very restrictive access regime. In 2008, a fungal outbreak provoked by a vomit contaminated the sediments which were removed and subsequently treated with hydrogen peroxide. Fungal surveys were carried out in 2008 and 2009. The visits were resumed in 2014. Here, 12 years after the outbreak, we present an exhaustive study on the cave sediments in order to know the distribution of the different fungal taxa, as well as the prevalence and spatio-temporal evolution of the fungi caused by the vomit over the years under the conditions of relative isolation and high radiation that characterize this cave., This research was supported by the Spanish Ministry of Science and Innovation through project PID2019-110603RB-I00 and the collaboration of PID2020-114978GB-I00 project, MCIN/AEI/FEDER, UE/10.13039/501100011033.

14 páginas.- 4 figuras.- 8 tablas.- 60 referencias, Background: Marine actinobacteria are a potential resource for natural products; their secondary bioactive metabolites have shown several biological activities. Most of the isolated and identified actinobacteria in Algeria were usually explored from caves, Saharan soil or palm groves. The marine ecosystem is poorly explored and documented. Methods: Five Streptomyces strains producing bioactive compounds were isolated from Rachgoun Island located in Western Algeria and characterised phenotypically and genotypically using microbiological and 16S rRNA sequencing methods, respectively. The crude extract of the most representative strain ¿Streptomyces sp. strain SM2.4¿ and its seven active fractions were characterised by GC/MS analysis. Results: Streptomyces sp. strain SM2.4 revealed the strongest activity against the Gram-positive bacteria Staphylococcus aureus and Bacillus subtilis, the fungus Aspergillus niger and was inactive against Gram-negative bacteria. GC/MS analysis of the methylated crude extract of Streptomyces sp. strain SM2.4 revealed the presence of 11 major compounds including fatty acids methyl ester (12-methyltridecanoic acid methyl ester, 9-hexadecenoic acid methyl ester, hexadecanoic acid methyl ester, 14-methylhexadecanoic acid methyl ester and 16-methylheptadecanoic acid methyl ester), 2,4-di-tert-butylphenol, (4S,4aS,8aR)-4,8a-dimethyloctahydro-4a(2H)-naphthalenol (geosmin), 2,4-dimethylbenzaldehyde, 3,4-difluorobenzaldehyde, dimethylfuran-2,4-dicarboxylate and pyrrolo(1,2-a)pyrazine-1,4-dione, hexahydro-3-(2-methylpropyl)-. Partial purification of the crude extract by Thin-layer chromatography provided seven active fractions which were tested by radial diffusion assay. GC/MS analysis of the active TLC-fractions revealed the presence of a mixture of active compounds from which 2-(bromomethyl)-2-(2-methylphenyl)-1,3-dioxolane was found to be a new 1,3 dioxolane derivative. Furthermore, 3,4-dimethylbenzamide and pyrido[2,3-d] pyridazine-1,4-dione, hexahydro-3-(2-methylpropyl)-, were extracted for the first time from a natural source. Conclusion: Our study reveals that marine Streptomyces sp. strain SM2.4 has an interesting antimicrobial potential due to its panel of bioactive compounds.

3 páginas.- 1 tabla.- 14 referencis, Pseudomonas sp. strain L5B5 is an antimicrobial-producing bacterium isolated from an air sample collected in a pyrite mine in Lousal, Portugal. Genomic analyses predicted genes involved in virulence factors. Here, we report the complete genome sequence of this bacterium, which consists of a circular chromosome with a length of 6,811,662 bp. Copyright © 2021 Gonzalez-Pimentel et al., Financial support was obtained through project 0483_PROBIOMA_5_E, cofinanced by the European Regional Development Fund within the framework of the INTERREG VA Spain-Portugal program (POCTEP), 2014 to 2020.

10 páginas.- 1 figuras.- 3 tablas.- 41 referencias.- One supplementary table and four supplementary figures are available with the online version of this article., A novel facultatively anaerobic, non-motile, Gram-stain-negative, non-endospore-forming alphaproteobacterium, strain 1011MAR3C25T, was isolated from a white biofilm colonizing the walls of the Andalusian show cave Gruta de las Maravillas (Huelva, Spain). Strain 1011MAR3C25T grew at 8–42 °C (optimum, 20–30 °C), at pH 5.0–9.0 (optimum, pH 5.0–6.0) and in the presence of 0–12 % (w/v) NaCl (optimum 3–5 %). Cells were catalase- and oxidase-positive. The strain grew heterotrophically with various carbon sources and chemoautotrophically with thiosulfate under aerobic conditions. Results of phylogenetic analysis showed that strain 1011MAR3C25T was related to Paracoccus saliphilus DSM 18447T and Paracoccus alkanivorans LMG 30882T (97.90 % and 97.32 % 16S rRNA sequence identity values, respectively). The major respiratory quinone was ubiquinone Q-10 and the predominant fatty acid was C18 : 1 ω7c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid, an unidentified glycolipid and an unidentified polar lipid. The DNA G+C content was 60.3 mol%. Based on a polyphasic taxonomic study it is proposed that strain 1011MAR3C25T (=CECT 9092T=LMG 29414T) represents a novel species of the genus Paracoccus, for which the name Paracoccus onubensis sp. nov. is proposed., This study was supported by project 0483_PROBIOMA_5_E, co-financed by the European Regional Development Fund within the framework of the Interreg V A Spain–Portugal program (POCTEP) 2014–2020

16 páginas.- 4 figuras.- 2 tablas.- 81 referencias.- : The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/microorganisms10081575/s1 .- (This article belongs to the Section Environmental Microbiology), Antimicrobial resistance has become a global problem in recent decades. A gradual reduction in drug discoveries has led to the current antimicrobial resistance crisis. Caves and other subsurface environments are underexplored thus far, and they represent indispensable ecological niches that could offer new molecules of interest to medicine and biotechnology. We explored Spanish show caves to test the bioactivity of the bacteria dwelling in the walls and ceilings, as well as airborne bacteria. We reported the isolation of two strains of the genus Crossiella, likely representing a new species, isolated from Altamira Cave, Spain. In vitro and in silico analyses showed the inhibition of pathogenic Gram-positive and Gram-negative bacteria, and fungi, as well as the taxonomical distance of both strains from their closest relative, Crossiella cryophila. The presence of an exclusive combination of gene clusters involved in the synthesis of lanthipeptides, lasso peptides, nonribosomal peptides and polyketides indicates that species of this genus could represent a source of new compounds. Overall, there is promising evidence for antimicrobial discovery in subterranean environments, which increases the possibility of identifying new bioactive molecules. Crossiella; predicted gene clusters; Spanish show caves, Financial support for research in caves and mines was obtained through project 0483_PROBIOMA_5_E, co-financed by the European Regional Development Fund within the framework of the Interreg V-A Spain-Portugal program (POCTEP) 2014–2020

Lava caves differ from karstic caves in their genesis and mineral composition. Subsurface microbiology of lava tube caves in Canary Islands, a volcanic archipelago in the Atlantic Ocean, is largely unknown. We have focused the investigation in a representative lava tube cave, Fuente de la Canaria Cave, in La Palma Island, Spain, which presents different types of speleothems and colored microbial mats. Four samples collected in this cave were studied using DNA next-generation sequencing and field emission scanning electron microscopy for bacterial identification, functional profiling, and morphological characterization. The data showed an almost exclusive dominance of Bacteria over Archaea. The distribution in phyla revealed a majority abundance of Proteobacteria (37,89%), followed by Actinobacteria, Acidobacteria and Candidatus Rokubacteria. These four phyla comprised a total relative abundance of 72,96%. The main ecological functions in the microbial communities were chemoheterotrophy, methanotrophy, sulfur and nitrogen metabolisms, and CO2 fixation; although other ecological functions were outlined. Genome annotations of the especially representative taxon Ga0077536 (about 71% of abundance in moonmilk) predicted the presence of genes involved in CO2 fixation, formaldehyde consumption, sulfur and nitrogen metabolisms, and microbially-induced carbonate precipitation. The detection of several putative lineages associated with C, N, S, Fe and Mn indicates that Fuente de la Canaria Cave basalts are colonized by metabolically diverse prokaryotic communities involved in the biogeochemical cycling of major elements., This work was supported by the Spanish Ministry of Economy and Competitiveness through projects CGL2013-41674-P, CGL2016-75590-P, PID2019-110603RB-I00, AEI/FEDER, UE and CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).

19 páginas.- 9 figuras.- 2 tablas.- 91 referencias.- Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/s10123-021-00193-x, Airborne microorganisms can cause important conservation problems in caves with Paleolithic art and therefore the knowledge of cave aerodynamic is essential. La Garma Cave (Cantabria, Spain), an exceptional archaeological site with several levels of galleries interconnected and two entrances, presents a complex atmospheric dynamics. An approach including aerobiological sampling together with microclimate monitoring was applied to assess the factors controlling the origin of airborne fungi. Here we show that winter ventilation is critical for the increasing of Basidiomycota spores in the cave air and the highest concentrations were found in the most ventilated areas. On the contrary, Ascomycota spores prevailed in absence of ventilation. Besides, most Ascomycota were linked to insects and bats that visit or inhabit the cave. The combination of aerobiological and microclimate data constitutes a good approach to evaluate the influence of external climatic conditions and design the most suitable strategies for the conservation of cultural heritage in the cave environment., Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This research was supported by the Consejería de Universidades, Igualdad, Cultura y Deporte del Gobierno de Cantabria and the Spanish Ministry of Innovation and Science through projects CGL2016-75590-P with ERDF funds and PID2019-110603RB-I00/AEI/10.13039/501100011033.

33 páginas.- 14 figuras.- 3 tablas.- 97 referencias.- Supporting information, 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. © 2019 D’Angeli et al., C work was supported by UNIBO (Ricerca Fondamentale e Orientata—RFO) and the Rectorate of UNIBO. Funding for microbial analyses was provided by Europlanet 2020 15-EPN1-029 and 17-EPN3-021 grants. Europlanet 2020 RI has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 654208. Further funding was provided by the Spanish project MINECO CGL2016-75590-P with ERDF funds.

19 páginas.-- 2 figuras.-- 2 tablas.-- 43 referencias, Two Gram-positive, catalase-positive, oxidase-negative, motile, endospore-forming, rod-shaped bacteria, designated as 0911MAR22V3T and 0911TES10J4, were isolated from air samples collected in two show caves, located in Andalusia, Southern Spain. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both strains were indistinguishable and they were most closely related to Bacillus humi DSM 16318T (98%). DNA-DNA hybridization values of the strain 0911MAR22V3T with respect to strain 0911TES10J4 and B. humi DSM 16318T were 76.8% (73.9%, reciprocal) and 56.9% (63.3%, reciprocal analysis), respectively. Whole genome average nucleotide identity (ANI) values of both strains were in the threshold value for species delineation and less than 85% with B. humi. Strains 0911MAR22V3T and 0911TES10J4 grew at 10-47. °C (optimum 37. °C), at pH 6-9.5 and with 0-8% (w/v) NaCl (optimum 1%). In both strains the dominant isoprenoid quinone was MK-7, the major cellular polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and two more phospholipids, the predominant fatty acids were iso-C15:0 and anteiso-C15:0 and the DNA G + C content was 38. mol%. On the basis of their phylogenetic relatedness and their phenotypic and genotypic features, the strains 0911MAR22V3T and 0911TES10J4 should be attributed to a novel species within the genus Bacillus, for which the name Bacillus onubensis sp. nov. is proposed. The type strain is 0911MAR22V3T (=LMG 27963T = CECT 8479T); and strain 0911TES10J4 (CECT 8478) is a reference strain., This study was supported by the project RNM 5137, Consejería de Innovación, Ciencia y Empresa, Junta de Andalucía, co-financed by 2007-2013 FEDER programme