A culture-independent survey of the bacterial community in a radon hot spring

Isolation and characterization of multiple-stress tolerant bacteria from radon springs

Radon springs, characterized by their high concentrations of radon gas (Rn222), are extreme environments with unique physicochemical conditions distinct from conventional aquatic ecosystems. Our research aimed to investigate microbial life in radon springs, focusing on isolating extremophilic bacteria and assessing their resistance to adverse conditions. Our study revealed the prevalence of Actinomycetia species in the radon spring environment. We conducted various tests to evaluate the resistance of these isolates to oxidative stress, irradiation, desiccation, and metal ion content. These extremophilic bacteria showed overall higher resistance to these stresses compared to control strains. Lipidomic analysis was also employed to provide insights into the adaptive mechanisms of these bacteria which were found mainly in the correlations among individual clusters and changes in content of fatty acids (FA) as well as differences between content and type of FAs of environmental isolates and type strains.

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.

Distribution and Activity of Sulfur-Metabolizing Bacteria along the Temperature Gradient in Phototrophic Mats of the Chilean Hot Spring Porcelana

In terrestrial hot springs, some members of the microbial mat community utilize sulfur chemical species for reduction and oxidization metabolism. In this study, the diversity and activity of sulfur-metabolizing bacteria were evaluated along a temperature gradient (48-69 °C) in non-acidic phototrophic mats of the Porcelana hot spring (Northern Patagonia, Chile) using complementary meta-omic methodologies and specific amplification of the aprA (APS reductase) and soxB (thiosulfohydrolase) genes. Overall, the key players in sulfur metabolism varied mostly in abundance along the temperature gradient, which is relevant for evaluating the possible implications of microorganisms associated with sulfur cycling under the current global climate change scenario. Our results strongly suggest that sulfate reduction occurs throughout the whole temperature gradient, being supported by different taxa depending on temperature. Assimilative sulfate reduction is the most relevant pathway in terms of taxonomic abundance and activity, whereas the sulfur-oxidizing system (Sox) is likely to be more diverse at low rather than at high temperatures. Members of the phylum Chloroflexota showed higher sulfur cycle-related transcriptional activity at 66 °C, with a potential contribution to sulfate reduction and oxidation to thiosulfate. In contrast, at the lowest temperature (48 °C), Burkholderiales and Acetobacterales (both Pseudomonadota, also known as Proteobacteria) showed a higher contribution to dissimilative sulfate reduction/oxidation as well as to thiosulfate metabolism. Cyanobacteriota and Planctomycetota were especially active in assimilatory sulfate reduction. Analysis of the aprA and soxB genes pointed to members of the order Burkholderiales (Gammaproteobacteria) as the most dominant and active along the temperature gradient for these genes. Changes in the diversity and activity of different sulfur-metabolizing bacteria in photoautotrophic microbial mats along a temperature gradient revealed their important role in hot spring environments, especially the main primary producers (Chloroflexota/Cyanobacteriota) and diazotrophs (Cyanobacteriota), showing that carbon, nitrogen, and sulfur cycles are highly linked in these extreme systems.

Culturomics of Bacteria from Radon-Saturated Water of the World's Oldest Radium Mine

Balneotherapeutic water springs, such as those with thermal, saline, sulfur, or any other characteristics, have recently been the subject of phylogenetic studies with a closer focus on the description and/or isolation of phylogenetically novel or biotechnologically interesting microorganisms. Generally, however, most such microorganisms are rarely obtained in pure culture or are even, for now, unculturable under laboratory conditions. In this culture-dependent study of radioactive water springs of Jáchymov (Joachimstahl), Czech Republic, we investigated a combination of classical cultivation approaches with those imitating sampling source conditions. Using these environmentally relevant cultivation approaches, over 1,000 pure cultures were successfully isolated from 4 radioactive springs. Subsequent dereplication yielded 121 unique taxonomic units spanning 44 genera and 9 taxonomic classes, ~10% of which were identified as hitherto undescribed taxa. Genomes of the latter were sequenced and analyzed, with a special focus on endogenous defense systems to withstand oxidative stress and aid in radiotolerance. Due to their origin from radioactive waters, we determined the resistance of the isolates to oxidative stress. Most of the isolates were more resistant to menadione than the model strain Deinococcus radiodurans DSM 20539T. Moreover, isolates of the Deinococcacecae, Micrococcaceae, Bacillaceae, Moraxellaceae, and Pseudomonadaceae families even exhibited higher resistance in the presence of hydrogen peroxide. In summary, our culturomic analysis shows that subsurface water springs contain diverse bacterial populations, including as-yet-undescribed taxa and strains with promising biotechnological potential. Furthermore, this study suggests that environmentally relevant cultivation techniques increase the efficiency of cultivation, thus enhancing the chance of isolating hitherto uncultured microorganisms. IMPORTANCE The mine Svornost in Jáchymov (Joachimstahl), Czech Republic is a former silver-uranium mine and the world's first and for a long time only radium mine, nowadays the deepest mine devoted to the extraction of water which is saturated with radon and has therapeutic benefits given its chemical properties. This healing water, which is approximately 13 thousand years old, is used under medical supervision for the treatment of patients with neurological and rheumatic disorders. Our culturomic approach using low concentrations of growth substrates or the environmental matrix itself (i.e., water filtrate) in culturing media combined with prolonged cultivation time resulted in the isolation of a broad spectrum of microorganisms from 4 radioactive springs of Jáchymov which are phylogenetically novel and/or bear various adaptive or coping mechanisms to thrive under selective pressure and can thus provide a wide spectrum of capabilities potentially exploitable in diverse scientific, biotechnological, or medical disciplines.

A systematic review on groundwater radon distribution with human health consequences and probable mitigation strategy

Groundwater radon contamination is a serious global concern for its eco-toxicological effects. The major health hazard occurs due to toxic indoor air inhalation and consumption of contaminated drinking water supplied from different distribution systems, especially groundwater. There are fragmented reports on the measurement of radon contamination and their health consequences with physical radon removal strategies as well as characterization of inhabitant microbial communities. As it concerned with human health, collective information is much essential on their groundwater distribution, their physicochemical properties and possible mitigation strategies, not done so far. In such prospect, this review summarizes the physicochemical properties of radon, their sources, global as well as Indian groundwater radon contamination scenario, health effects and inhabitant microbes along with their survival strategies. It also summarizes the physical radon removal techniques and especially emphasizes the microbes based bioremediation process as well as a combination of both as a future effective radon remediation process.

Diversity of Microfungi in a High Radon Cave Ecosystem

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.

Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity

The genus Nitrospira represents a dominant group of nitrite-oxidizing bacteria in natural and engineered ecosystems. This genus is phylogenetically divided into six lineages, for which vast phylogenetic and functional diversity has been revealed by recent molecular ecophysiological analyses. However, the genetic basis underlying these phenotypic differences remains largely unknown because of the lack of genome sequences representing their diversity. To gain a more comprehensive understanding of Nitrospira, we performed genomic comparisons between two Nitrospira strains (ND1 and NJ1 belonging to lineages I and II, respectively) previously isolated from activated sludge. In addition, the genomes of these strains were systematically compared with previously reported six Nitrospira genomes to reveal their similarity and presence/absence of several functional genes/operons. Comparisons of Nitrospira genomes indicated that their genomic diversity reflects phenotypic differences and versatile nitrogen metabolisms. Although most genes involved in key metabolic pathways were conserved between strains ND1 and NJ1, assimilatory nitrite reduction pathways of the two Nitrospira strains were different. In addition, the genomes of both strains contain a phylogenetically different urease locus and we confirmed their ureolytic activity. During gene annotation of strain NJ1, we found a gene cluster encoding a quorum-sensing system. From the enriched supernatant of strain NJ1, we successfully identified seven types of acyl-homoserine lactones with a range of C10–C14. In addition, the genome of strain NJ1 lacks genes relevant to flagella and the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated genes) systems, whereas most nitrifying bacteria including strain ND1 possess these genomic elements. These findings enhance our understanding of genomic plasticity and functional diversity among members of the genus Nitrospira.

The Microbial Community of a Radon Hot Spring

Paralana is an active, radon-containing hot spring situated in a region of South Australia's Flinders Ranges with a long history of hydrothermal activity. Gas bubbling into the pool is composed of radon (from the radioactive decay of radium), nitrogen, carbon dioxide, and trace helium and hydrogen. The microbial composition of mat and biofilm samples from Paralana was determined using culture-independent 16S rRNA techniques. We have previously demonstrated that the hot spring contains a diverse bacterial community. Here we summarise these findings and report on theArchaeaidentified in Paralana. Archaeal inhabitants include members of the Crenarchaeota and Euryarchaeota kingdoms.

Prokaryotic and eukaryotic airborne microorganisms as tracers of microclimatic changes in the underground (Postojna Cave, Slovenia)

Bioaerosols in cave air can serve as natural tracers and, together with physical parameters, give a detailed view of conditions in the cave atmosphere and responses to climatic changes. Airborne microbes in the Postojna Cave system indicated very dynamic atmospheric conditions, especially in the transitory seasonal periods between winter and summer. Physical parameters of cave atmosphere explained the highest variance in structure of microbial community in the winter and in the summer. The airborne microbial community is composed of different microbial groups with generally low abundances. At sites with elevated organic input, occasional high concentrations of bacteria and fungi can be expected of up to 1,000 colony-forming units/m(3) per individual group. The most abundant group of airborne amoebozoans were the mycetozoans. Along with movements of air masses, airborne algae also travel deep underground. In a cave passage with elevated radon concentration (up to 60 kBq/m(3)) airborne biota were less abundant; however, the concentration of DNA in the air was comparable to that in other parts of the cave. Due to seasonal natural air inflow, high concentrations of biological and inanimate particles are introduced underground. Sedimentation of airborne allochthonous material might represent an important and continuous source of organic material for cave fauna.

Genesis and preservation of a uranium-rich paleozoic epithermal system with a surface expression (Northern Flinders Ranges, South Australia): radiogenic heat driving regional hydrothermal circulation over geological timescales

The surface expressions of hydrothermal systems are prime targets for astrobiological exploration, and fossil systems on Earth provide an analogue to guide this endeavor. The Paleozoic Mt. Gee-Mt. Painter system (MGPS) in the Northern Flinders Ranges of South Australia is exceptionally well preserved and displays both a subsurface quartz sinter (boiling horizon) and remnants of aerial sinter pools that lie in near-original position. The energy source for the MGPS is not related to volcanism but to radiogenic heat produced by U-Th-K-rich host rocks. This radiogenic heat source drove hydrothermal circulation over a long period of time (hundreds of millions of years, from Permian to present), with peaks in hydrothermal activity during periods of uplift and high water supply. This process is reflected by ongoing hot spring activity along a nearby fault. The exceptional preservation of the MGPS resulted from the lack of proximal volcanism, coupled with tectonics driven by an oscillating far-field stress that resulted in episodic basement uplift. Hydrothermal activity caused the remobilization of U and rare earth elements (REE) in host rocks into (sub)economic concentrations. Radiogenic-heat-driven systems are attractive analogues for environments that can sustain life over geological times; the MGPS preserves evidence of episodic fluid flow for the past ∼300 million years. During periods of reduced hydrothermal activity (e.g., limited water supply, quiet tectonics), radiolytic H(2) production has the potential to support an ecosystem indefinitely. Remote exploration for deposits similar to those at the MGPS systems can be achieved by combining hyperspectral and gamma-ray spectroscopy.

Isolation and characterization of a moderately thermophilic nitrite-oxidizing bacterium from a geothermal spring

Geothermal environments are a suitable habitat for nitrifying microorganisms. Conventional and molecular techniques indicated that chemolithoautotrophic nitrite-oxidizing bacteria affiliated with the genus Nitrospira are widespread in environments with elevated temperatures up to 55 °C in Asia, Europe, and Australia. However, until now, no thermophilic pure cultures of Nitrospira were available, and the physiology of these bacteria was mostly uncharacterized. Here, we report on the isolation and characterization of a novel thermophilic Nitrospira strain from a microbial mat of the terrestrial geothermal spring Gorjachinsk (pH 8.6; temperature 48 °C) from the Baikal rift zone (Russia). Based on phenotypic properties, chemotaxonomic data, and 16S rRNA gene phylogeny, the isolate was assigned to the genus Nitrospira as a representative of a novel species, for which the name Nitrospira calida is proposed. A highly similar 16S rRNA gene sequence (99.6% similarity) was detected in a Garga spring enrichment grown at 46 °C, whereas three further thermophilic Nitrospira enrichments from the Garga spring and from a Kamchatka Peninsula (Russia) terrestrial hot spring could be clearly distinguished from N. calida (93.6-96.1% 16S rRNA gene sequence similarity). The findings confirmed that Nitrospira drive nitrite oxidation in moderate thermophilic habitats and also indicated an unexpected diversity of heat-adapted Nitrospira in geothermal hot springs.

Moderately thermophilic nitrifying bacteria from a hot spring of the Baikal rift zone

Samples from three hot springs (Alla, Seya and Garga) located in the northeastern part of Baikal rift zone (Buryat Republic, Russia) were screened for the presence of thermophilic nitrifying bacteria. Enrichment cultures were obtained solely from the Garga spring characterized by slightly alkaline water (pH 7.9) and an outlet temperature of 75 degrees C. The enrichment cultures of the ammonia- and nitrite oxidizers grew at temperature ranges of 27-55 and 40-60 degrees C, respectively. The temperature optimum was approximately 50 degrees C for both groups and thus they can be designated as moderate thermophiles. Ammonia oxidizers were identified with classical and immunological techniques. Representatives of the genus Nitrosomonas and Nitrosospira-like bacteria with characteristic vibroid morphology were detected. The latter were characterized by an enlarged periplasmic space, which has not been previously observed in ammonia oxidizers. Electron microscopy, denaturing gradient gel electrophoresis analyses and partial 16S rRNA gene sequencing provided evidence that the nitrite oxidizers were members of the genus Nitrospira.