Archaeal and bacterial diversity in five different hydrothermal ponds in the Copahue region in Argentina

Influence of Geothermal Fumaroles in Driving the Microbial Community Dynamics and Functions of Adjacent Ecosystems

Growing evidence suggests that the hydrochemical properties of geothermal fumaroles may play a crucial role in shaping the diversity and functions of microbial communities in various environments. In the present study, the impact of geothermal furaneols on the microbial communities and their metabolic functions across the rock-soil-plant continuum was explored considering varying distances from the fumarole source. The results revealed that bacterial phylum Proteobacteria was predominant in all sample types, except in the 10 m rock sample, irrespective of the sampling distance. Archaeal phyla, such as Euryarchaeota and Crenarchaeota, were more prevalent in rock and soil samples, whereas bacterial phyla were more prevalent in plant samples. Thermoacidophilic archaeons, including Picrophilus, Ferroplasma, and Thermogymnomonas were dominant in rocks and soil samples of 1 and 5 m distances; acidophilic mesophiles, including Ferrimicrobium and Granulicella were abundant in the rhizoplane samples, whereas rhizosphere-associated microbes including Pseudomonas, Pedobacter, Rhizobium, and Novosphingobium were found dominant in the rhizosphere samples. The functional analysis highlighted the higher expression of sulfur oxidative pathways in the rock and soil samples; dark iron oxidation and nitrate/nitrogen respiratory functions in the rhizosphere samples. The findings underscore microbial adaptations across the rock-soil-plant continuum, emphasizing the intricate relationship between geothermal fumaroles and microbial communities in adjacent ecosystems. These insights offer a crucial understanding of the evolution of microbial life and highlight their pivotal roles in shaping ecosystem dynamics and functions.

Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus 'Igneacidithiobacillus'

Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1T as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1TS), 'Igneacidithiobacillus siniensis' (S30A2T), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 TS), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 TS). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus 'Igneacidithiobacillus'.

An improved protocol for metagenomic DNA isolation from low microbial biomass alkaline hot-spring sediments and soil samples

High-quality, humic-acid-free pure DNA is a prerequisite for functional and sequence-based approaches of metagenomics. In the present investigation, an improved extraction buffer was developed by making a combination of powdered activated charcoal (2%; w/v), polyvinyl poly pyrrolidone (2%; w/v), and CaCl2 (2%; w/v). This trio significantly improved the purity and yield of the metagenomic DNA from the hot spring's hot and alkaline soil. The quality of extracted metagenomic DNA was successfully validated by PCR amplification and restriction enzymes. Besides, the thermophilic amylase encoding genes were also retrieved from these soil DNA samples. Extreme habitats I harbour low microbial biomass and, therefore, demand in-situ lysis of the microbial cells to access their genomes. The protocol can potentially extract DNA from geothermal spring habitats where the count of microbial cells is low.

Microbial community composition and hydrochemistry of underexplored geothermal waters in Croatia

In Croatia, a variety of geothermal springs with a wide temperature range and varied hydrochemical conditions exist, and they may harbor different niches for the distribution of microbial communities. In this study, 19 different sites, mainly located in central and eastern Croatia, were selected for primary characterization of spring hydrochemistry and microbial community composition. Using 16S rRNA gene amplicon sequencing, it was found that the bacterial communities that dominated most geothermal waters were related to Proteobacteria and Campylobacteria, while most archaeal sequences were related to Crenarchaeota. At the genus level, the prokaryotic community was highly site-specific and was often dominated by a single genus, including sites dominated by Hydrogenophilus, Sulfuricurvum, Sulfurovum, Thiofaba and Nitrospira, while the most abundant archaeal genera were affiliated to the ammonia-oxidizing archaea, Candidatus Nitrosotenuis and Candidatus Nitrososphaera. Whereas the microbial communities were overall highly location-specific, temperature, pH, ammonia, nitrate, total nitrogen, sulfate and hydrogen sulfide, as well as dissolved organic and inorganic carbon, were the abiotic factors that significantly affected microbial community composition. Furthermore, an aquifer-type effect was observed in the community composition, but there was no pronounced seasonal variability for geothermal spring communities (i.e. the community structure was mainly stable during the three seasons sampled). These results surprisingly pointed to stable and geographically unique microbial communities that were adapted to different geothermal water environments throughout Croatia. Knowing which microbial communities are present in these extreme habitats is essential for future research. They will allow us to explore further the microbial metabolisms prevailing at these geothermal sites that have high potential for biotechnological uses, as well as the establishment of the links between microbial community structure and the physicochemical environment of geothermal waters.

Production and characterization of a new detergent-stable keratinase expressed by Pedobacter sp. 3.14.7, a novel Antarctic psychrotolerant keratin-degrading bacterium

BACKGROUND

Antarctica is one of the harshest environments in the world. Despite this fact, it has been colonized by microorganisms, which had to develop different adaptations in order to survive. By studying their enzymes, we can harness these adaptations in order to use them in various industrial processes. Keratinases (E.C. 3.4.99.11) are characterized by their robustness in withstanding extreme conditions and, along with other enzymes, are commonly added to laundry detergents, which makes their study of industrial interest.

RESULTS

In this work, a novel keratinase producer, Pedobacter sp. 3.14.7 (MF 347939.1), isolated from Antarctic birds' nests, was identified. This psychrotolerant isolate displays a typical psychrotolerant growth pattern, with an optimal temperature of 20 °C (μmax=0.23 h^-1). After 238 h, maximum proteolytic (22.00 ± 1.17 U ml^-1) and keratinolytic (33.04 ± 1.09 U ml^-1) activities were achieved with a feather sample conversion of approximately 85%. The keratinase present in crude extract was characterized as a metalloprotease with a molecular weight of 25 kDa, stable in a wide range of pH, with an optimum pH of 7.5. Optimum temperature was 55 °C. Wash performance at 20 °C using this crude extract could remove completely blood stain from cotton cloth.

CONCLUSION

We report a new keratinolytic bacteria from maritime Antarctica. Among its biochemical characteristics, its stability in the presence of different detergents and bleaching agents and its wash performance showed promising results regarding its potential use as a laundry detergent additive.

Cyanobacterial Community Structure and Isolates From Representative Hot Springs of Yunnan Province, China Using an Integrative Approach

Cyanobacteria from the representative hot springs of Yunnan Province, China are explored for their diversity and community composition following an integrative approach of cultivation-independent and -dependent studies and further isolation of potential taxa for future biotechnological perspective. 16S rRNA amplicon sequencing of microbial mats in these hot springs with temperature ranging from 38 to 90°C revealed Cyanobacteria and Proteobacteria constituting a bounteous portion of the bacterial community. The combined approach of 16S rRNA amplicon sequencing and phenotypic analysis revealed the diversity of cyanobacteria (a total of 45 genera). Out of these, a total of 19 cyanobacterial taxa belonging to 6 genera and 10 species were isolated as individuals with the possibility of biotechnological utilization. These isolates were subjected to a thorough morphological study and molecular characterization using 16S rRNA gene sequencing for identification and understanding their phylogeny. The identity and phenotypic and genotypic characteristics of 7 cyanobacterial isolates are not identical to any known cyanobacterial species, generating scope for future taxonomic novelties. Preliminary experiments based on high-temperature (50°C) cultivation showed that most of the isolates were thermotolerant and suggested for their high biotechnological usage potential.

A Preliminary Study of SARS-CoV-2's Permanence and Potential Infective Capacity in Mineromedicinal Waters of Copahue, Neuquén, Argentina

Copahue Thermal Center is characterized by the presence of mineromedicinal acidic waters with high temperatures, therapeutic peloids, and relevant consortia of extremophiles species, distributed in small natural pools which cannot be disinfected. The objective of this research was to investigate the survival of SARS-CoV-2 in Copahue's waters and its remaining infective capacity. In a first assay, a decrease of more than 50% of the initially viral load compared to the initially inoculated positive sample was detected for all the water samples analyzed. After that, two of the Copahue springs, which are used as an immersion bath in closed environments without going through any disinfection treatment, was selected to determine the viral viability. VERO cell infections were performed, with no cytopathic effect detected, but a strikingly high resistance of the virus, detecting its genome by real time PCR, during the seven days of study under laboratory conditions. SARS-CoV-2 survival in acid media was reaffirmed, which is a peculiarity for a covered virus. A decrease in the detectable viral load of the positive sample was found as the infection time passed, becoming completely negative in the subsequent blind passages. More research is needed to further study the feasibility of SARS-CoV-2 in mineromedicinal waters, especially natural acidic waters that cannot disinfected, in order to expand information about the risk to populations that are exposed to them.

Microorganisms of Two Thermal Pools on Kunashir Island, Russia

The Kuril Archipelago is a part of the Circum-Pacific Belt (Ring of Fire). These islands have numerous thermal springs. There are very few studies on these microbial communities, and none of them have been conducted by modern molecular biological methods. Here we performed the first metagenomic study on two thermophilic microbial communities of Kunashir Island. Faust Lake is hot (48 °C) and highly acidic (pH 2.0). We constructed 28 metagenome-assembled genomes as well as 17 16S ribosomal RNA sequences. We found that bottom sediments of Faust Lake are dominated by a single species of red algae belonging to the Cyanidiaceae family. Archaeans in Faust Lake are more diverse than bacteria but less abundant. The Tretyakovsky Thermal Spring is also hot (52 °C) but only weakly acidic (pH 6.0). It has much higher microbial diversity (233 metagenome-assembled genomes; 93 16S ribosomal RNAs) and is dominated by bacteria, with only several archaeans and one fungus. Despite their geographic proximity, these two thermal springs were found to not share any species. A comparison of these two lakes with other thermal springs of the Circum-Pacific Belt revealed that only a few members of the communities are shared among different locations.

The keratinolytic bacteria Bacillus cytotoxicus as a source of novel proteases and feather protein hydrolysates with antioxidant activities

BACKGROUND

Argentina's geothermal areas are niches of a rich microbial diversity. In 2020, species of Bacillus cytotoxicus were isolated for the first time from these types of pristine natural areas. Bacillus cytotoxicus strains demonstrated the capability to grow and degrade chicken feathers with the concomitant production of proteases with keratinolytic activity, enzymes that have multitude of industrial applications. The aim of this research was to study the production of the proteolytic enzymes and its characterization. Also, feather protein hydrolysates produced during fermentation were characterized.

RESULTS

Among the thermotolerant strains isolated from the Domuyo geothermal area (Neuquén province, Argentina), Bacillus cytotoxicus LT-1 and Oll-15 were selected and put through submerged cultures using feather wastes as sole carbon, nitrogen, and energy source in order to obtain proteolytic enzymes and protein hydrolysates. Complete degradation of feathers was achieved after 48 h. Zymograms demonstrated the presence of several proteolytic enzymes with an estimated molecular weight between 50 and > 120 kDa. Optimum pH and temperatures of Bacillus cytotoxicus LT-1 crude extract were 7.0 and 40 °C, meanwhile for Oll-15 were 7.0 and 50 °C. Crude extracts were inhibited by EDTA and 1,10 phenanthroline indicating the presence of metalloproteases. Feather protein hydrolysates showed an interesting antioxidant potential measured through radical-scavenging and Fe³⁺-reducing activities.

CONCLUSION

This work represents an initial approach on the study of the biotechnological potential of proteases produced by Bacillus cytotoxicus. The results demonstrated the importance of continuous search for new biocatalysts with new characteristics and enzymes to be able to cope with the demands in the market.

Effect of heavy metal-induced stress on two extremophilic microbial communities from Caviahue-Copahue, Argentina

Metal pollution is a great concern worldwide and the development of new technologies for more sustainable extraction methods as well as for the remediation of polluted sites is essential. Extremophilic microorganisms are attractive for this purpose since they have poly-resistance mechanisms which make them versatile. In this work, we sampled an acidic river and a hot spring of Caviahue-Copahue volcanic environment. The indigenous microbial communities were exposed to five heavy metals (Cd, Co, Cu, Ni and Zn) in batch-cultures favouring different metabolisms of biotechnological interest. Remarkably, high tolerance values were reached in all the cultures, even though most of the metals studied were not present in the environmental sample. Particularly, outstanding tolerances were exhibited by acidophiles, which grew at concentrations as high as 400 mM of Zn and Ni. High-throughput amplicon sequencing of 16S rRNA gene was used to study the indigenous communities and the resistant consortia. We took three approaches for the analysis: phylotypes, OTUs and amplicon sequence variants (ASVs). Interestingly, similar conclusions were drawn in all three cases. Analysing the phylogenetic structure and functional potential of the adapted consortia, we found that the strongest selection was exerted by the culture media. Notably, there was a poor correlation between alpha diversity and metal stress; furthermore, metal stress did not seem to harm the functional potential of the consortia. All these results reveal a great adaptability and versatility. At the end, 25 metal-resistant extremophilic consortia with potential uses in bioremediation, bioleaching or biomonitoring processes were obtained.

Characterization of Thermophilic Microorganisms in the Geothermal Water Flow of El Chichón Volcano Crater Lake

This study reports for the first time the isolation, identification and characterization of lipase-producing thermophilic strain from the geothermal water of the El Chichón volcano crater lake. Two strains were identified by 16S rRNA sequencing as Geobacillus jurassicus CHI2 and Geobacillus stearothermophilus CHI1. Results showed that G. jurassicus CHI2 is Gram-positive, able to ferment maltose, fructose and sucrose and to hydrolyze starch and casein; while G. stearothermophilus CHI1 showed to be Gram-variable, able to ferment maltose and fructose and to hydrolyze starch. Colonies of both strains presented irregular shape, umbilicated elevation of gummy texture and cells presented flagellar movement to survive in fluids with high temperature and mass gradients due to complex phenomena of heat and mass transfer present in the geothermal fluids. Lipase production for G. stearothermophilus CHI1 was also evaluated. It was found that this strain possesses a growth associated with extracellular lipase production with a high activity of 143 U/mL at 8.3 h of incubation time, superior to the activities reported for other microorganisms of genus Geobacillus; for this reason, it can be said that the thermal flow of the El Chichón volcano crater lake can be a useful source of lipase-producing thermophilic bacteria.

Defining Culture Conditions for the Hidden Nitrite-Oxidizing Bacterium Nitrolancea

Nitrification is a key process for N-removal in engineered and natural environments, but recent findings of novel nitrifying microorganisms with surprising features revealed that our knowledge of this functional guild is still incomplete. Especially nitrite oxidation - the second step of nitrification - is catalyzed by a phylogenetically diverse bacterial group, and only recently bacteria of the phylum Chloroflexi have been identified as thermophilic nitrite-oxidizing bacteria (NOB). Among these, Nitrolancea hollandica was isolated from a laboratory-scale nitrifying bioreactor operated at 35°C with a high load of ammonium bicarbonate. However, its distribution remains cryptic as very few closely related environmental 16S rRNA gene sequences have been retrieved so far. In this study, we demonstrate how such thermophilic NOB can be enriched using modified mineral media inoculated with samples from a wastewater side-stream reactor operated at 39.5°C. Distinct cultivation conditions resulted in quick and reproducible high enrichment of two different strains of Nitrolancea, closely related to Nl. hollandica. The same cultivation approach was applied to a complex nitrite-oxidizing pre-enrichment at 42°C inoculated with biomass from a geothermal spring in the Copahue volcano area in Neuquen, Argentina. Here, an additional distinct representative of the genus Nitrolancea was obtained. This novel species had 16S rRNA and nitrite oxidoreductase alpha subunit (nxrA) gene sequence identities to Nl. hollandica of 98.5% and 97.2%, respectively. A genomic average nucleotide identity between the Argentinian strain and Nl. hollandica of 91.9% indicates that it indeed represents a distinct species. All Nitrolancea cultures formed lancet-shaped cells identical to Nl. hollandica and revealed similar physiological features, including the capability to grow at high nitrite concentrations. Growth was optimal at temperatures of 35-37°C and was strongly enhanced by ammonium supplementation. Genomic comparisons revealed that the four Nitrolancea strains share 2399 out of 3387 orthologous gene clusters and encode similar key functions. Our results define general growth conditions that enable the selective enrichment of Nitrolancea from artificial and natural environments. In most natural habitats these NOB apparently are of low abundance and their proliferation depends on the balanced presence of nitrite and ammonium, with an optimal incubation temperature of 37°C.

Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature

The study of microbial communities from extreme environments is a fascinating topic. With every study, biologists and ecologists reveal interesting facts and questions that dispel the old belief that these are inhospitable environments. In this work, we assess the microbial diversity of three hot springs from Neuquén, Argentina, using high-throughput amplicon sequencing. We predicted a distinct metabolic profile in the acidic and the circumneutral samples, with the first ones being dominated by chemolithotrophs and the second ones by chemoheterotrophs. Then, we collected data of the microbial communities of hot springs around the world in an effort to comprehend the roles of pH and temperature as shaping factors. Interestingly, there was a covariation between both parameters and the phylogenetic distance between communities; however, neither of them could explain much of the microbial profile in an ordination model. Moreover, there was no correlation between alpha diversity and these parameters. Therefore, the microbial communities' profile seemed to have complex shaping factors beyond pH and temperature. Lastly, we looked for taxa associated with different environmental conditions. Several such taxa were found. For example, Hydrogenobaculum was frequently present in acidic springs, as was the Sulfolobaceae family; on the other hand, Candidatus Hydrothermae phylum was strongly associated with circumneutral conditions. Interestingly, some singularities related to sites featuring certain taxa were also observed.

Enrichment and isolation of acid-tolerant sulfate-reducing microorganisms in the anoxic, acidic hot spring sediments from Copahue volcano, Argentina

The geothermal Copahue-Caviahue (GCC) system (Argentina) is an extreme acidic environment, dominated by the activity of Copahue volcano. Environments characterised by low pH values, such as volcanic areas, are of particular interest for the search of acidophilic microorganisms with application in biotechnological processes. In this work, sulfate-reducing microorganisms were investigated in geothermal acidic, anaerobic zones from GCC system. Sediment samples from Agua del Limón (AL1), Las Máquinas (LMa2), Las Maquinitas (LMi) and Baño 9 (B9-2, B9-3) were found to be acidic (pH values 2.1-3.0) to moderate acidic (5.1-5.2), containing small total organic carbon values, and ferric iron precipitates. The organic electron donor added to the enrichment was completely oxidised to CO2. Bacteria related to 'Desulfobacillus acidavidus' strain CL4 were found to be dominant (67-83% of the total number of clones) in the enrichment cultures, and their presence was confirmed by their isolation on overlay plates. Other bacteria were also detected with lower abundance (6-20% of the total number of clones), with representatives of the genera Acidithiobacillus, Sulfobacillus, Alicyclobacillus and Athalassotoga/Mesoaciditoga. These enrichment and isolates found at low pH confirm the presence of anaerobic activities in the acidic sediments from the geothermal Copahue-Caviahue system.

Bacillus cytotoxicus Isolated from a Pristine Natural Geothermal Area Reveals High Keratinolytic Activity

Geothermal areas are the niches of a rich microbial diversity that is not only part of the intangible patrimony of a country but also the source of many microbial species with potential biotechnological applications. Particularly, microbial species in geothermal areas in Argentina have been scarcely explored regarding their possible biotechnological uses. The purpose of this work was to explore the proteolytic and keratinolytic enzymatic potential of microorganisms that inhabit in the Domuyo geothermal area in the Neuquén Province. To this end, we did enrichment cultures from two high-temperature natural samples in mineral media only supplemented with whole chicken feathers. After the isolation and the phylogenetic and morphologic characterization of different colonies, we obtained a collection of Bacillus cytotoxicus isolates, a species with no previous report of keratinolytic activity and only reported in rehydrated meals connected with food poisoning outbreaks. Its natural habitat has been unknown up to now. We characterized the proteolytic and keratinolytic capacities of the B. cytotoxicus isolates in different conditions, which proved to be remarkably high compared with those of other similar species. Thus, our work represents the first report of the isolation as well as the keratinolytic capacity characterization of strains of B. cytotixicus obtained from a natural environment.

Complete genome sequence of the Sulfodiicoccus acidiphilus strain HS-1T, the first crenarchaeon that lacks polB3, isolated from an acidic hot spring in Ohwaku-dani, Hakone, Japan

OBJECTIVE

Sulfodiicoccus acidiphilus HS-1^T is the type species of the genus Sulfodiicoccus, a thermoacidophilic archaeon belonging to the order Sulfolobales (class Thermoprotei; phylum Crenarchaeota). While S. acidiphilus HS-1^T shares many common physiological and phenotypic features with other Sulfolobales species, the similarities in their 16S rRNA gene sequences are less than 89%. In order to know the genomic features of S. acidiphilus HS-1^T in the order Sulfolobales, we determined and characterized the genome of this strain.

RESULTS

The circular genome of S. acidiphilus HS-1^T is comprised of 2353,189 bp with a G+C content of 51.15 mol%. A total of 2459 genes were predicted, including 2411 protein coding and 48 RNA genes. The notable genomic features of S. acidiphilus HS-1^T in Sulfolobales species are the absence of genes for polB3 and the autotrophic carbon fixation pathway, and the distribution pattern of essential genes and sequences related to genomic replication initiation. These insights contribute to an understanding of archaeal genomic diversity and evolution.

Metal biorecovery and bioremediation: Whether or not thermophilic are better than mesophilic microorganisms

Metal mobilization and immobilization catalyzed by microbial action are key processes in environmental biotechnology. Metal mobilization from ores, mining wastes, or solid residues can be used for recovering metals and/or remediating polluted environments; furthermore, immobilization reduces the migration of metals; cleans up effluents plus ground- and surface water; and, moreover, can help to concentrate and recover metals. Usually these processes provide certain advantages over traditional technologies such as more efficient economical and environmentally sustainable results. Since elevated temperatures typically increase chemical kinetics, it could be expected that bioprocesses should also be enhanced by replacing mesophiles with thermophiles or hyperthermophiles. Nevertheless, other issues like process stability, flexibility, and thermophile-versus-mesophile resistance to acidity and/or metal toxicity should be carefully considered. This review critically analyzes and compares thermophilic and mesophilic microbial performances in recent and selected representative examples of metal bioremediation and biorecovery.

Global Microbiome Diversity Scaling in Hot Springs With DAR (Diversity-Area Relationship) Profiles

The spatial distribution of biodiversity (i.e., the biogeography) of the hot-spring microbiome is critical for understanding the microbial ecosystems in hot springs. We investigated the microbiome diversity scaling (changes) over space by analyzing the diversity-area relationship (DAR), which is an extension to classic SAR (species-area relationship) law in biogeography. We built DAR models for archaea and bacteria with 16S-rRNA sequencing datasets from 165 hot springs globally. From the DAR models, we sketch out the biogeographic maps of hot-spring microbiomes by constructing: (i) DAR profile-measuring the archaea or bacteria diversity scaling over space (areas); (ii) PDO (pair-wise diversity overlap or similarity) profile-estimating the PDO between two hot springs; (iii) MAD (maximal accrual diversity) profile-predicting the global MAD; (iv) LRD/LGD (ratio of local diversity to regional or global diversity) profile. We further investigated the differences between archaea and bacteria in their biogeographic maps. For example, the comparison of DAR-profile maps revealed that the archaea diversity is more heterogeneous (i.e., more diverse) or scaling faster than the bacterial diversity does in terms of species numbers (species richness), but is less heterogeneous (i.e., less diverse) or scaling slower than bacteria when the diversity (Hill numbers) were weighted in favor of more abundant dominant species. When the diversity is weighted equally in terms of species abundances, archaea, and bacteria are equally heterogeneous over space or scaling at the same rate. Finally, unified DAR models (maps) were built with the combined datasets of archaea and bacteria.

Environmental parameters, and not phylogeny, determine the composition of extracellular polymeric substances in microbial mats from extreme environments

The ability to establish biofilms is a key trait for microorganisms growing in extreme environments. The extracellular polymeric substances (EPS) present in biofilms provide not only surface attachment, but also protection against all kinds of environmental stressors, including desiccation, salinity, temperature or heavy metal pollution. The acquisition of suitable biofilm characteristics might thus be an important process mediating the adaptation of microorganisms to novel environmental conditions. In this work we have characterized the EPS of 20 phylogenetically diverse biofilms collected in situ from five contrasting extreme environments, including two geothermal areas (Copahue, Argentina; Seltun, Iceland), two cold areas (Pastoruri glacier, Peru; Byers Peninsula, Antarctica) and one extremely acidic river (Río Tinto, Spain). Biofilms were subjected to biochemical characterization, glycan profiling and immunoprofiling with an antibody microarray. Our results showed that environmental conditions strongly influence biofilm characteristics, with microorganisms from the same environment achieving similar EPS compositions regardless of the phylogeny of their main species. The concentration of some monosaccharides in the EPS could be related to environmental conditions such as temperature or heavy metal toxicity, suggesting that in some cases stress resistance can be mediated by specific sugars. Overall, our results highlight the existence of conserved EPS compositional patterns for each extreme environment, which could in turn be exploited to engineer ecological adaptations in genetically modified microorganisms.

Saccharolobus caldissimus gen. nov., sp. nov., a facultatively anaerobic iron-reducing hyperthermophilic archaeon isolated from an acidic terrestrial hot spring, and reclassification of Sulfolobus solfataricus as Saccharolobus solfataricus comb. nov. and Sulfolobus shibatae as Saccharolobus shibatae comb. nov

A novel hyperthermophilic archaeon of strain HS-3^T, belonging to the family Sulfolobaceae, was isolated from an acidic terrestrial hot spring in Hakone Ohwaku-dani, Japan. Based on 16S rRNA gene sequence analysis, the closest phylogenetic relatives of strain HS-3^T were, first, Sulfolobus solfataricus (96.4 %) and, second, Sulfolobus shibatae (96.2 %), indicating that the strain belongs to the genus Sulfolobus. However, the sequence similarity to the type species of the genus Sulfolobus (Sulfolobus acidocaldarius) was remarkably low (91.8 %). In order to determine whether strain HS-3^T belongs to the genus Sulfolobus, its morphological, biochemical and physiological characteristics were examined in parallel with those of S. solfataricus and S. shibatae. Although there were some differences in chemolithotrophic growth between strain HS-3^T, S. solfataricus and S. shibatae, their temperature, pH and facultatively anaerobic characteristics of growth, and their utilization of various sugars were almost identical. In contrast, the utilization of various sugars by S. acidocaldarius was quite different from that of HS-3^T, S. solfataricus and S. shibatae. Phylogenetic evidence based on the 16S and the 23S rRNA gene sequences also clearly distinguished the monophyletic clade composed of strain HS-3^T, S. solfataricus, and S. shibatae from S. acidocaldarius. Based on these results, we propose a new genus and species, Saccharolobus caldissimus gen. nov., sp. nov., for strain HS-3^T, as well as two reclassifications, Saccharolobus solfataricus comb. nov. and Saccharolobus shibatae comb. nov. The type strain of Saccharolobus caldissimus is HS-3^T (=JCM 32116^T and InaCC Ar80^T). The type species of the genus is Saccharolobus solfataricus.

Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs

Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3–V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334–26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity.

Geochemical behavior of an acid drainage system: the case of the Amarillo River, Famatina (La Rioja, Argentina)

The Amarillo River (Famatina range, Argentina, ~29° S and ~67° W) is unusual because acid mine drainage (AMD) is superimposed on the previously existing acid rock drainage (ARD) scenario, as a Holocene paleolake sedimentary sequence shows. In a markedly oxidizing environment, its water is currently ferrous and of the sulfate-magnesium type with high electrical conductivity (>10 mS cm^-1 in uppermost catchments). At the time of sampling, the interaction of the mineralized zone with the remnants of mining labors determined an increase in some elements (e.g., Cu ~3 to ~45 mg L^-1; As ~0.2 to ~0.5 mg L^-1). Dissolved concentrations were controlled by pH, decreasing significantly by precipitation of neoformed minerals (jarosite and schwertmannite) and subsequent metal sorption (~700 mg kg^-1 As, 320 mg kg^-1 Zn). Dilution also played a significant role (i.e., by the mixing with circumneutral waters which reduces the dissolved concentration and also enhances mineral precipitation). Downstream, most metals exhibited a significant attenuation (As 100 %, Fe 100 %, Zn 99 %). PHREEQC-calculated saturation indices (SI) indicated that Fe-bearing minerals, especially schwertmannite, were supersaturated throughout the basin. All positive SI increased through the input of circumneutral water. PHREEQC inverse geochemical models showed throughout the upper and middle basin, that about 1.5 mmol L^-1 of Fe-bearing minerals were precipitated. The modeling exercise of mixing different waters yielded results with a >99 % of correlation between observed and modeled data.

Thermophilic microorganisms in biomining

Biomining is an applied biotechnology for mineral processing and metal extraction from ores and concentrates. This alternative technology for recovering metals involves the hydrometallurgical processes known as bioleaching and biooxidation where the metal is directly solubilized or released from the matrix for further solubilization, respectively. Several commercial applications of biomining can be found around the world to recover mainly copper and gold but also other metals; most of them are operating at temperatures below 40-50 °C using mesophilic and moderate thermophilic microorganisms. Although biomining offers an economically viable and cleaner option, its share of the world´s production of metals has not grown as much as it was expected, mainly considering that due to environmental restrictions in many countries smelting and roasting technologies are being eliminated. The slow rate of biomining processes is for sure the main reason of their poor implementation. In this scenario the use of thermophiles could be advantageous because higher operational temperature would increase the rate of the process and in addition it would eliminate the energy input for cooling the system (bioleaching reactions are exothermic causing a serious temperature increase in bioreactors and inside heaps that adversely affects most of the mesophilic microorganisms) and it would decrease the passivation of mineral surfaces. In the last few years many thermophilic bacteria and archaea have been isolated, characterized, and even used for extracting metals. This paper reviews the current status of biomining using thermophiles, describes the main characteristics of thermophilic biominers and discusses the future for this biotechnology.

Copahue Geothermal System: A Volcanic Environment with Rich Extreme Prokaryotic Biodiversity

The Copahue geothermal system is a natural extreme environment located at the northern end of the Cordillera de los Andes in Neuquén province in Argentina. The geochemistry and consequently the biodiversity of the area are dominated by the activity of the Copahue volcano. The main characteristic of Copahue is the extreme acidity of its aquatic environments; ponds and hot springs of moderate and high temperature as well as Río Agrio. In spite of being an apparently hostile location, the prokaryotic biodiversity detected by molecular ecology techniques as well as cultivation shows a rich and diverse environment dominated by acidophilic, sulphur oxidising bacteria or archaea, depending on the conditions of the particular niche studied. In microbial biofilms, found in the borders of the ponds where thermal activity is less intense, the species found are completely different, with a high presence of cyanobacteria and other photosynthetic species. Our results, collected during more than 10 years of work in Copahue, have enabled us to outline geomicrobiological models for the different environments found in the ponds and Río Agrio. Besides, Copahue seems to be the habitat of novel, not yet characterised autochthonous species, especially in the domain Archaea.

Thermophiles in the genomic era: Biodiversity, science, and applications

Thermophiles and hyperthermophiles are present in various regions of the Earth, including volcanic environments, hot springs, mud pots, fumaroles, geysers, coastal thermal springs, and even deep-sea hydrothermal vents. They are also found in man-made environments, such as heated compost facilities, reactors, and spray dryers. Thermophiles, hyperthermophiles, and their bioproducts facilitate various industrial, agricultural, and medicinal applications and offer potential solutions to environmental damages and the demand for biofuels. Intensified efforts to sequence the entire genome of hyperthermophiles and thermophiles are increasing rapidly, as evidenced by the fact that over 120 complete genome sequences of the hyperthermophiles Aquificae, Thermotogae, Crenarchaeota, and Euryarchaeota are now available. In this review, we summarise the major current applications of thermophiles and thermozymes. In addition, emphasis is placed on recent progress in understanding the biodiversity, genomes, transcriptomes, metagenomes, and single-cell sequencing of thermophiles in the genomic era.

Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing

The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0–9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community.