Hot Spring Environments Research Articles

Mineralogical and microbial characterization of alkali hot spring microbial mats and deposits in Pong Dueat Pa Pae hot spring, Northern Thailand.

Hot spring environments encompass broad physicochemical ranges, in which temperature and pH account for crucial factors shaping hot spring microbial community and diversity. However, the presence of photosynthetic microbial mats adjacent to boiling hot spring vents, where fluid temperatures extend beyond photosynthetic capability, questions the microbial profiles and the actual temperatures of such adjacent mats. Therefore, this study aims to characterize thermophilic microbial communities at Pong Dueat Pa Pae hot spring using next-generation sequencing, including investigating hot spring mineralogy. Results suggest that Pong Dueat Pa Pae hot spring precipitates comprise mainly silica which also acts as the main preservative medium for microbial permineralization. Molecular results revealed the presence of cyanobacterial and Chloroflexi species in the thick, orange and green subaerial mats surrounding the vents, suggesting the mats would be at least 30°C cooler than source vents despite constantly receiving geyser splashes. Bacterial abundance was considerably higher than archaeal (97.9% versus 2.1%). Cyanobacterial (mainly Synechococcus and Leptolygbya) and Chloroflexi species (mainly Roseiflexus) accounted for almost half (40.04%) of the bacterial community, while DHVEG-6 and Thaumarchaeota comprised dominant members (> 90%) of the archaeal fraction. This study updates and provides insights into thermophilic microbial community composition and mineralogy of hot springs in Thailand.

Opaline silica precipitations in the Permian Fengcheng Formation indicate hot spring environments in north Mahu Sag, NW China

The Permian Fengcheng Formation represents a series of deposits formed in an alkaline saline lake, characterized by high proportions of cherts, located in the Northwestern Junggar Basin in China. While discussions on silica-rich hot springs as sources of silica for brine and subsequent chert deposition have been extensively conducted for Quaternary and Mesozoic-Cenozoic alkaline saline lakes worldwide, investigations into Paleozoic alkaline saline lakes are scarce due to challenges associated with identifying evidences of hot spring environments. In this study, we present detailed SEM-EDS analyses and examine silica isotope compositions as well as oxygen isotope compositions to discuss hydrothermal-associated silica precipitation processes. Our findings suggest that migrating silica-rich hot springs along deep-rooted faults released silica into the brine, leading to chert deposition during cooling periods and induction of thermophilic microorganism degradation. Microorganism-associated siliceous precipitates primarily consist of opal-A spheres adhered by extracellular polymeric substances (EPS), while numerous microorganism spheres have undergone silicification. Opal-A spheres within these structures were partially transformed into well-crystallized quartz through multiple stages of dissolution-precipitation processes during prolonged burial history. Furthermore, our results indicate that deep-rooted fault-related hot springs can occur both in marginal and subaqueous areas within alkaline saline lakes, with chert formations observed in shallow-marginal saline lake settings as well as deeper regions. The findings of this study provide valuable insights into the paleoenvironmental conditions, which can be further explored in investigating the accumulation of organic matter in chert-rich successions formed within an alkaline saline lake.

Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining

Enzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes. Metagenome mining is a valuable and efficient way to discover novel enzymes with unique properties for biotechnological applications. Here, we report the discovery and biocatalytic characterization of six novel metagenomic opine dehydrogenases from a hot spring environment (mODHs) (EC 1.5.1.X). These enzymes catalyze the asymmetric reductive amination between an amino acid and a keto acid resulting in opines which have defined biochemical roles and represent promising building blocks for pharmaceutical applications. The newly identified enzymes exhibit unique substrate specificity and higher thermostability compared to known examples. The feature that they preferably utilize negatively charged polar amino acids is so far unprecedented for opine dehydrogenases. We have identified two spatially correlated positions in their active sites that govern this substrate specificity and demonstrated a switch of substrate preference by site-directed mutagenesis. While they still suffer from a relatively narrow substrate scope, their enhanced thermostability and the orthogonality of their substrate preference make them a valuable addition to the toolbox of enzymes for reductive aminations. Importantly, enzymatic reductive aminations with highly polar amines are very rare in the literature. Thus, the preparative-scale enzymatic production, purification, and characterization of three highly functionalized chiral secondary amines lend a special significance to our work in filling this gap.Key points• Six new opine dehydrogenases have been discovered from a hot spring metagenome• The newly identified enzymes display a unique substrate scope• Substrate specificity is governed by two correlated active-site residues

Research on the engineering performance of concrete containing waste liquid crystal glass and volcanic ash in a hot spring environment

The research aims to use industrial by-products such as slag, fly ash, and waste liquid crystal glass as concrete additives to reduce emissions and promote a circular economy. These efforts can contribute significantly to the development of a sustainable spa environment infrastructure. In the study, 40% and 60% high-content waste liquid crystal glass replaced the coarse aggregates, slag replaced part cement, fly ash replaced part of the sand, and according to specific ratios to make the concrete, then to evaluate the workability, hardening, and durability of concrete in hot spring water.The test results show that the workability of the concrete increases with the increase in substitution amount and that the slump increases from 61.1% to 66.7%. The concrete laying time increased by 7.56% but reduced the density by 9.79%. The compressive strength of concrete increases by 11.6%-13.41% and the velocity of the ultrasonic pulse is 4556–4717 m/s. Regarding durability, the chloride ion content is within the specified range between 0.014–0.031 kg/m3, and the surface resistance increases by about 9.95–10.93 times. In summary, we determined the optimal replacement amount that can effectively use the mixing ratio of waste liquid crystal glass, slag powder, and fly ash in concrete in the hot spring environment. This will improve waste reuse to cope with aggregate shortages increase the environmental pollution caused by cement manufacturing and achieve maximum environmental benefits.

Phylogenetically and physiologically diverse methanogenic archaea inhabit the Indian hot spring environments.

Mesophilic and thermophilic methanogens belonging to the hydrogenotrophic, methylotrophic, and acetotrophic groups were isolated from Indian hot spring environments using BY and BCYT growth media. Following initial Hinf I-based PCR-RFLP screening, 70 methanogens were sequenced to ascertain their identity. These methanogens were phylogenetically and physiologically diverse and represented different taxa distributed across three physiological groups, i.e., hydrogenotrophs (53), methylotrophs (14) and acetotrophs (3). Overall, methanogens representing three families, five genera, and ten species, including two putative novel species, were recognized. The highest number and diversity of methanogens was observed at 40℃, dominated by Methanobacterium (10; 3 species), Methanosarcina (9; 3 species), Methanothermobacter (7; 2 species), Methanomethylovorans (5; 1 species) and Methanoculleus (3; 1 species). Both putative novel methanogen species were isolated at 40℃ and belonged to the genera Methanosarcina and Methanobacterium. At 55℃, limited diversity was observed, and resulted in the isolation of only two genera of methanogens, i.e., Methanothermobacter (28; 2 species) and Methanosarcina (4; 1 species). At 70℃, only members of the genus Methanothermobacter (5; 2 species) were isolated, whereas no methanogen could be cultured at 85℃. Ours is the first study that documents the extensive range of cultivable methanogenic archaea inhabiting hot springs across various geothermal provinces of India.

MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets

Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems, our knowledge of archaeal viruses outside of extreme environments is limited. This largely stems from the lack of a robust, high-throughput, and systematic way to distinguish between bacterial and archaeal viruses in datasets of curated viruses. Here we upgrade our prior text-based tool (MArVD) via training and testing a random forest machine learning algorithm against a newly curated dataset of archaeal viruses. After optimization, MArVD2 presented a significant improvement over its predecessor in terms of scalability, usability, and flexibility, and will allow user-defined custom training datasets as archaeal virus discovery progresses. Benchmarking showed that a model trained with viral sequences from the hypersaline, marine, and hot spring environments correctly classified 85% of the archaeal viruses with a false detection rate below 2% using a random forest prediction threshold of 80% in a separate benchmarking dataset from the same habitats.

Bacterial and archaeal community distributions and cosmopolitanism across physicochemically diverse hot springs

Terrestrial hot springs harbor diverse microbial communities whose compositions are shaped by the wide-ranging physico-chemistries of individual springs. The effect of enormous physico-chemical differences on bacterial and archaeal distributions and population structures is little understood. We therefore analysed the prevalence and relative abundance of bacteria and archaea in the sediments (n = 76) of hot spring features, in the Taupō Volcanic Zone (New Zealand), spanning large differences in major anion water chemistry, pH (2.0–7.5), and temperature (17.5–92.9 °C). Community composition, based on 16S rRNA amplicon sequence variants (ASVs) was strongly influenced by both temperature and pH. However, certain lineages characterized diverse hot springs. At the domain level, bacteria and archaea shared broadly equivalent community abundances across physico-chemically diverse springs, despite slightly lower bacteria-to-archaea ratios and microbial 16S rRNA gene concentrations at higher temperatures. Communities were almost exclusively dominated by Proteobacteria, Euryarchaeota or Crenarchaeota. Eight archaeal and bacterial ASVs from Thermoplasmatales, Desulfurellaceae, Mesoaciditogaceae and Acidithiobacillaceae were unusually prevalent (present in 57.9–84.2% of samples) and abundant (1.7–12.0% sample relative abundance), and together comprised 44% of overall community abundance. Metagenomic analyses generated multiple populations associated with dominant ASVs, and showed characteristic traits of each lineage for sulfur, nitrogen and hydrogen metabolism. Differences in metabolic gene composition and genome-specific metabolism delineated populations from relatives. Genome coverage calculations showed that populations associated with each lineage were distributed across a physicochemically broad range of hot springs. Results imply that certain bacterial and archaeal lineages harbor different population structures and metabolic potentials for colonizing diverse hot spring environments.

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.

Methanogens-Driven Arsenic Methylation Preceding Formation of Methylated Thioarsenates in Sulfide-Rich Hot Springs

Hot springs represent a major source of arsenic release into the environment. Speciation is typically reported to be dominated by arsenite, arsenate, and inorganic thiolated arsenates. Much less is known about the relevance and formation of methylated thioarsenates, a group with species of high mobility and toxicity. In hot spring samples taken from the Tengchong volcanic region in China, methylated thioarsenates contributed up to 13% to total arsenic. Enrichment cultures were obtained from the corresponding sediment samples and incubated to assess their capability to convert arsenite into methylated thioarsenates over time and in the presence of different microbial inhibitors. In contrast to observations in other environmental systems (e.g., paddy soils), there was no solid evidence, supporting that the sulfate-reducing bacteria contributed to the arsenic methylation. Methanosarcina, the sole genus of methanogens detected in the enrichment cultures, as well as Methanosarcina thermophila TM-1, a pure strain within the genus, did methylate arsenic. We propose that methylated thioarsenates in a typical sulfide-rich hot spring environment like Tengchong form via a combination of biotic arsenic methylation driven by thermophilic methanogens and arsenic thiolation with either geogenic sulfide or sulfide produced by sulfate-reducing bacteria.

Use of modified ichip for the cultivation of thermo-tolerant microorganisms from the hot spring

BackgroundThermostable microorganisms are extremophiles. They have a special genetic background and metabolic pathway and can produce a variety of enzymes and other active substances with special functions. Most thermo-tolerant microorganisms from environmental samples have resisted cultivation on artificial growth media. Therefore, it is of great significance to isolate more thermo-tolerant microorganisms and study their characteristics to explore the origin of life and exploit more thermo-tolerant enzymes. Tengchong hot spring in Yunnan contains a lot of thermo-tolerant microbial resources because of its perennial high temperature. The ichip method was developed by D. Nichols in 2010 and can be used to isolate so-called “uncultivable” microorganisms from different environments. Here, we describe the first application of modified ichip to isolate thermo-tolerant bacteria from hot springs.ResultsIn this study, 133 strains of bacteria belonging to 19 genera were obtained. 107 strains of bacteria in 17 genera were isolated by modified ichip, and 26 strains of bacteria in 6 genera were isolated by direct plating methods. 25 strains are previously uncultured, 20 of which can only be cultivated after being domesticated by ichip. Two strains of previously unculturable Lysobacter sp., which can withstand 85 °C, were isolated for the first time. Alkalihalobacillus, Lysobacter and Agromyces genera were first found to have 85 °C tolerance.ConclusionOur results indicate that the modified ichip approach can be successfully applied in a hot spring environment.

Speleothems and Biomineralization Processes in Hot Spring Environment: The Case of Aedipsos (Edipsos), Euboea (Evia) Island, Greece

Caves with hot springs and speleothem deposits are infrequent environments of high scientific interest due to their unique environmental conditions. The selected site is a small open cave with a hot spring and stalactites in the Aedipsos area (NW Euboea Island, Greece), which was studied through an interdisciplinary approach. The mineralogical composition of the speleothems was determined by optical microscopy, XRD, and SEM-EDS microanalysis, and identification of the Cyanobacteria species was made based on morphological characteristics. The main mineral phase in the studied samples is calcite, with several trace elements (i.e., up to 0.48 wt.% Na2O, up to 0.73 wt.% MgO, up to 4.19 wt.% SO3, up to 0.16 wt.% SrO and up to 2.21 wt.% Yb2O3) in the mineral-chemistry composition. The dominant facies are lamination and shrubs, which are the most common among the facies of the thermogenic travertines of the area. Based on the studied stalactites, twenty-nine different Cyanobacteria species were identified, belonging to the following orders: Synechococcales (28%), Oscillatoriales (27%), Chroococcales (21%) and Nostocales (21%), and Spirulinales (3%). Among them, thermophilic species (Spirulina subtilissima) and limestone substrate species (Chroococcus lithophilus, Leptolyngbya perforans, and Leptolyngbya ercegovicii) were identified. The identified Cyanobacteria were found to participate in biomineralization processes. The most characteristic biomineralization activity is made by the endolithic Cyanobacteria destroying calcite crystals in the outer layer. In a few cases, calcified cyanobacterial sheaths were detected. The presence of filamentous Cyanobacteria, along with extracellular polymeric substance (EPS), creates a dense net resulting in the retention of calcium carbonate crystals.

Microbial Mat Stratification in Travertine Depositions of Greek Hot Springs and Biomineralization Processes

The study of microbial mats in extreme environments is of high scientific interest from geological, ecological, and geomicrobiological aspects. These mats represent multilayer bio-structures where each taxonomic group dominates a specific vertical layering distribution resulting from its growth and metabolic activity. In the present study, microbial mats in a hot spring environment from Aedipsos (Euboea Island, Greece) resulting in the creation of thermogenic travertine, were studied through an interdisciplinary approach. The mineralogical composition was determined by optical microscopy, XRD, and SEM-EDS microanalysis, and the identification of Cyanobacteria was made primarily on morphological characteristics. The main mineral phase in the studied samples is calcite and, to a less extent, aragonite, with several trace elements in the mineral-chemistry composition, i.e., up to 1.93 wt. % MgO, up to 0.52 wt. % SrO, up to 0.44 wt. % Na2O, up to 0.17 wt. % K2O, and up to 3.99 wt. % SO3. The dominant facies are lamination and shrubs, which are the most common among the facies of thermogenic travertines of the area. Several layers were identified, (i) a top mainly abiotic layer consisting of calcium carbonate micritic crystals, (ii) a second biotic layer–the Cyanobacteria layer, dominated by the species Leptolyngbya perforans, (iii) a third biotic layer where Leptolyngbya perforans, Chloroflexus and other bacteria occur, and (iv) a deeper abiotic part with several layers where no photosynthetic microorganisms occur. In the upper layers, nineteen (19) species of Cyanobacteria were identified, classified in the orders Chroococcales (37%), Synechococcales (31%), Oscillatoriales (16%), and Spirulinales (6%). Among the identified Cyanobacteria, there are typical thermophilic and limestone substrate species. These Cyanobacteria are found to participate in the biomineralization and biologically-influenced processes, i.e., (i) filamentous Cyanobacteria are trapping calcium carbonate crystals, and diatoms, (ii) extracellular polymeric substances (EPS) create crystal retention lattice contributing to the biomineralization process, and (iii) filamentous sheaths of Cyanobacteria are calcified, resulting in the creation of calcium carbonate tubes.

Insights into ecological roles of uncultivated bacteria in Katase hot spring sediment from long-read metagenomics.

Diverse yet-uncultivated bacteria and archaea, i.e., microbial dark matter, are present in terrestrial hot spring environments. Numerous metagenome-assembled genomes (MAGs) of these uncultivated prokaryotes by short-read metagenomics have been reported so far, suggesting their metabolic potential. However, more reliable MAGs, i.e., circularized complete MAGs (cMAGs), have been rarely reported from hot spring environments. Here, we report 61 high-quality (HQ)-MAGs, including 14 cMAGs, of diverse uncultivated bacteria and archaea retrieved from hot spring sediment (52°C, pH 7.2) by highly accurate long-read sequencing using PacBio Sequel II. The HQ MAGs were affiliated with one archaeal and 13 bacterial phyla. Notably, nine of the 14 cMAGs were the first reported cMAGs for the family- to class-level clades that these cMAGs belonged to. The genome information suggests that the bacteria represented by MAGs play a significant role in the biogeochemical cycling of carbon, nitrogen, iron, and sulfur at this site. In particular, the genome analysis of six HQ MAGs including two cMAGs of Armatimonadota, of which members are frequently abundant in hot spring environments, predicts that they are aerobic, moderate thermophilic chemoorganoheterotrophs, and potentially oxidize and/or reduce iron. This prediction is consistent with the environmental conditions where they were detected. Our results expand the knowledge regarding the ecological potential of uncultivated bacteria in moderately-high-temperature environments.

Determination of extracellular hydrolytic enzyme capabilities of some Anoxybacillus isolated from hot spring environments

The development of microbial enzymes was a crucial event in the industrial sectors as a result of the tremendous growth of biotechnology in recent years. Popularity of waste management and bioremediation processes have both made extensive use of microorganisms’ whole cells and their enzymes. The pharmaceutical, textile, food, cosmetics, leather, paper, energy, biomaterials, fine chemicals, cellulose, and detergent sectors are some of the uses area of microbial enzymes. Depending on different uses, researchers can search for novel bacterial strains that might exhibit previously unrecognized enzymatic activity. Also for searching for plasmids that could be used as cloning vectors to tackle medication resistance in thermophilic microorganisms. The Anoxybacillus flavithermus bacteria, which were isolated from a hot spring in the Turkish city of Afyon, was employed in this investigation. The ability of the identified bacteria to produce extracellular hydrolytic enzymes was tested. For this, the activities of catalase, urease, and lipase as well as the hydrolysis of starch, casein, xylan, and asparagine were researched. Additionally, tests for antibiotic resistance were studied on the isolated bacteria using four different antibiotics (erythromycin, chloramphenicol, rifamycin, and ampicillin). All identified strains fermented starch as carbon and energy sources, and after 24 hours of incubation, amylase activity was detected at 50°C and pH 7.0. All strains were determined to be catalase-positive, and with a few exceptions, the majority of A. flavithermus strains were also found to be urease and caseinase positive. Industrial products that can be obtained from bacteria found in extreme environments will be effective in the development of future technology.

Isolation and Characterization of Thermophilic Bacillus subtilis subsp. inaquosorum CGR-1 from Cangar Hot Springs

Bioindustries often involve biochemical processes that occur at higher temperatures. However, most proteins, including enzymes, lose their structural integrity and functionality at higher temperatures. Thus, thermostable enzymes from thermophilic microorganisms are best suited candidates for successful bioprocessing under such conditions. Indonesia is one of the best study sites for performing bioprospecting of thermostable enzyme-producing thermophilic microorganisms due to the numerous hot springs. To explore the biodiversity of thermophilic microorganisms with potential industrial applications, we isolated and characterized thermophilic bacteria from the Cangar hot spring, Batu, East Java, Indonesia. One isolate (CGR-1) showed growth at 60°C and was identified as Bacillus subtilis subsp. inaquosorum based on 16s rRNA gene sequencing followed by bioinformatic analysis. This is the first report on the isolation of Bacillus subtilis subsp. inaquosorum CGR-1 from Indonesia, especially from a hot spring environment. This isolate showed cellulolytic and amylolytic activity at 50°C, which would encourage further exploration on the industrial and environmental applications.

Mineralogical and Genomic Constraints on the Origin of Microbial Mn Oxide Formation in Complexed Microbial Community at the Terrestrial Hot Spring.

Manganese (Mn) oxides are widespread on the surface environments of the modern Earth. The role of microbial activities in the formation of Mn oxides has been discussed for several decades. However, the mechanisms of microbial Mn oxidation, and its role in complex microbial communities in natural environments, remain uncertain. Here, we report the geochemical, mineralogical, and metagenomic evidence for biogenic Mn oxides, found in Japanese hot spring sinters. The low crystallinity of Mn oxides, and their spatial associations with organic matter, support the biogenic origin of Mn oxides. Specific multicopper oxidases (MCOs), which are considered Mn-oxidizing enzymes, were identified using metagenomic analyses. Nanoscale nuggets of copper sulfides were, also, discovered in the organic matter in Mn-rich sinters. A part of these copper sulfides most likely represents traces of MCOs, and this is the first report of traces of Mn-oxidizing enzyme in geological samples. Metagenomic analyses, surprisingly, indicated a close association of Mn oxides, not only in aerobic but also in anaerobic microbial communities. These new findings offer the unique and unified positions of Mn oxides, with roles that have not been ignored, to sustain anaerobic microbial communities in hot spring environments.

Silicification of feathers in a modern hot spring in New Zealand

ABSTRACT Fossil feathers have greatly improved our understanding of the evolutionary transition from non-avian dinosaurs to birds and the evolution of feathers, and may be the only evidence for their source animals in the fossil record. Hot spring environments have been demonstrated to be conducive to the preservation of fossils, but internal silicification of feathers was not observed in the only avian carcass so far discovered in ancient hot spring deposits. To determine whether feathers can be internally silicified, here we analyse feathers sampled from a modern hot spring vent pool – Champagne Pool – in New Zealand. Our results of scanning electron microscopy (SEM)-energy dispersive X-ray spectrometry elemental mapping show that the sampled feathers are silicified to different degrees, and one of them is pervasively silicified. SEM observations show that feathers can be silicified at the cellular level. Degradation is involved in the silicification of feathers, as indicated by the reduction of the abundance of carbon and the loss of keratin fibrils. Our findings suggest that ancient deposits of hot spring vent pools are promising targets in search for fossil feathers.

Polyphasic Identification and Genomic Insights of Leptothermofonsia sichuanensis gen. sp. nov., a Novel Thermophilic Cyanobacteria Within Leptolyngbyaceae

Thermal environments are an important reservoir of thermophiles with significant ecological and biotechnological potentials. However, thermophilic isolates remain largely unrecovered from their habitats and are rarely systematically identified. In this study, we characterized using polyphasic approaches a thermophilic strain, PKUAC-SCTAE412 (E412 hereafter), recovered from Lotus Lake hot spring based in Ganzi prefecture, China. The results of 16S rRNA/16S-23S ITS phylogenies, secondary structure, and morphology comparison strongly supported that strain E412 represent a novel genus within Leptolyngbyaceae. This delineation was further confirmed by genome-based analyses [phylogenomic inference, average nucleotide/amino-acid identity, and the percentages of conserved proteins (POCP)]. Based on the botanical code, the isolate is herein delineated as Leptothermofonsia sichuanensis gen. sp. nov, a genus adjacent to recently delineated Kovacikia and Stenomitos. In addition, we successfully obtained the first complete genome of this new genus. Genomic analysis revealed its adaptations to the adverse hot spring environment and extensive molecular components related to mobile genetic elements, photosynthesis, and nitrogen metabolism. Moreover, the strain was capable of modifying the composition of its light-harvesting apparatus depending on the wavelength and photoperiod, showing chromatic adaptation capacity characteristic for T1 and T2 pigmentation types. Other physiological studies showed the strain’s ability to utilize sodium bicarbonate and various sulfur compounds. The strain was also shown to be diazotrophic. Interestingly, 24.6% of annotated protein-coding genes in the E412 genome were identified as putatively acquired, hypothesizing that a large number of genes acquired through HGT might contribute to the genome expansion and habitat adaptation of those thermophilic strains. Most the HGT candidates (69.4%) were categorized as metabolic functions as suggested by the KEGG analysis. Overall, the complete genome of strain E412 provides the first insight into the genomic feature of the genus Leptothermofonsia and lays the foundation for future global ecogenomic and geogenomic studies.

Structural evolution of the ancient enzyme, dissimilatory sulfite reductase.

Dissimilatory sulfite reductase is an ancient enzyme that has linked the global sulfur and carbon biogeochemical cycles since at least 3.47 Gya. While much has been learned about the phylogenetic distribution and diversity of DsrAB across environmental gradients, far less is known about the structural changes that occurred to maintain DsrAB function as the enzyme accompanied diversification of sulfate/sulfite reducing organisms (SRO) into new environments. Analyses of available crystal structures of DsrAB from Archaeoglobus fulgidus and Desulfovibrio vulgaris, representing early and late evolving lineages, respectively, show that certain features of DsrAB are structurally conserved, including active siro-heme binding motifs. Whether such structural features are conserved among DsrAB recovered from varied environments, including hot spring environments that host representatives of the earliest evolving SRO lineage (e.g., MV2-Eury), is not known. To begin to overcome these gaps in our understanding of the evolution of DsrAB, structural models from MV2.Eury were generated and evolutionary sequence co-variance analyses were conducted on a curated DsrAB database. Phylogenetically diverse DsrAB harbor many conserved functional residues including those that ligate active siro-heme(s). However, evolutionary co-variance analysis of monomeric DsrAB subunits revealed several False Positive Evolutionary Couplings (FPEC) that correspond to residues that have co-evolved despite being too spatially distant in the monomeric structure to allow for direct contact. One set of FPECs corresponds to residues that form a structural path between the two active siro-heme moieties across the interface between heterodimers, suggesting the potential for allostery or electron transfer within the enzyme complex. Other FPECs correspond to structural loops and gaps that may have been selected to stabilize enzyme function in different environments. These structural bioinformatics results suggest that DsrAB has maintained allosteric communication pathways between subunits as SRO diversified into new environments. The observations outlined here provide a framework for future biochemical and structural analyses of DsrAB to examine potential allosteric control of this enzyme.

Insect and Plant Diversity in Hot-Spring Ecosystems during the Jurassic-Cretaceous Boundary from Spain (Aguilar Fm., Palencia).

Simple SummaryIn this study, we show and identify new plant and insect remains found in travertine deposits from the Jurassic-Cretaceous boundary of the Aguilar Formation (Palencia, North Spain). From this hot-spring palaeoenvironment, we have identified the presence of dragonflies of the families Cymatophlebiidae and Aktassiidae, representing the first report of these families for the Iberian Peninsula. In addition, we find a flora dominated by Bennettitales and the presence of ferns that differ from other floras of the same age and geographical area. The unusual environmental and palaeoecological conditions of this hot-spring environment are also discussed, suggesting that this niche was an “ecological oasis” for some plants and insects.Hydrothermal palaeoenvironments are very uncommon in Upper Jurassic and Lower Cretaceous deposits worldwide. We present new plant and insect remains from travertines formed during the Jurassic-Cretaceous boundary in northern Spain (Aguilar Fm., Palencia province). A total of 136 plant specimens and three insect wings were collected and studied. This entomofauna consists of dragonfly (Odonata) wings including Cymatophlebiidae and an undetermined new genus and species of Aktassiidae, representing the first report of these families for the Iberian Peninsula. The fossil flora shows different morphotypes of plants, which have been tentatively assigned to three different genera. The taphocoenosis of the flora was dominated by Bennettitales (98.5%) including cf. Pterophyllum sp., Ptilophyllum cf. acutifolium, Ptilophyllum cf. pecten, Ptilophyllum cf. pectiniformis and cf. Ptilophyllum sp., and the occasional presence of ferns (1.5%) represented by the taxon Cladophlebis cf. denticulata. The presence of the Anisoptera Cymatophlebia cf. longialata suggests a higher affinity for a Tithonian age of the studied site, and the anatomy and palaeogeographical distribution of this species suggest capacity to migrate for rather long distances. The floristic composition of the site differs remarkably from other Tithonian-Berriasian floras of the Iberian Peninsula. The presence of Odonata and the distinctive flora in (semi)arid conditions could be due to the hot-spring providing an environmental niche with constant conditions of warmth and humidity forming an ‘ecological oasis’.