Thermodesulfitimonas autotrophica gen. nov., sp. nov., a thermophilic, obligate sulfite-reducing bacterium isolated from a terrestrial hot spring

Culture-Independent Survey of Thermophilic Microbial Communities of the North Caucasus

Simple Summary

The Republic of North Ossetia-Alania, located in the southern part of the North Caucasus, possess a number of hydrothermal habitats, including both subterranean thermal reservoirs and terrestrial hot springs. At the same time, reports on microbiology of numerous geothermal sites are rather scarce for the whole North Caucasus region. In this paper, we report on the first culture-independent metabarcoding study of thermal habitats in the North Caucasus, coupled with a chemical analysis of the elemental composition of water. The results of this work include the conclusions regarding key metabolic characteristics of these habitats as well as detection of few but abundant deep lineages of uncultivated microorganisms which could be regarded as endemic. This study may represent a first step in closing the knowledge gap in extremophilic microbial communities of the North Caucasus.

Abstract

The Greater Caucasus is a part of seismically active Alpine–Himalayan orogenic belt and has been a center of significant volcanic activity during the Quaternary period. That led to the formation of the number of hydrothermal habitats, including subterranean thermal aquifers and surface hot springs. However, there are only a limited number of scientific works reporting on the microbial communities of these habitats. Moreover, all these reports concern only studies of specific microbial taxa, carried out using classical cultivation approaches. In this work, we present first culture-independent study of hydrotherms in the Republic of North Ossetia-Alania, located in the southern part of the North Caucasus. Using 16S metabarcoding, we analyzed the composition of the microbial communities of two subterranean thermal aquifers and terrestrial hot springs of the Karmadon valley. Analysis of correlations between the chemical composition of water and the representation of key taxa allowed us to identify the key factors determining the formation of microbial communities. In addition, we were able to identify a significant number of highly abundant deep phylogenetic lineages. Our study represents a first glance on the thermophilic microbial communities of the North Caucasus and may serve as a basis for further microbiological studies of the extreme habitats of this region.

Performance and mechanism of carbon dioxide fixation by a newly isolated chemoautotrophic strain Paracoccus denitrificans PJ-1

CO₂ is regarded as a major contributor to the global warming. CO₂ utilization is promising to reduce the CO₂ emissions. Currently, the biofixation of CO₂ using chemoautotrophs has markedly gain interest in CO₂ utilization. In this study, a newly isolated chemoautotroph, Paracoccus denitrificans PJ-1, was used for the biofixation of CO₂ under anaerobic condition. Experimental results revealed that Paracoccus denitrificans PJ-1 achieved a high carbon fixation rate (13.25 mg·L^-1·h^-1) which was ∼10 times faster than the previous reported chemotrophic bacteria using thiosulfate as electron donor. The best CO₂ fixation activity of Paracoccus denitrificans PJ-1 was achieved at the pH value of 9.0 and CO₂ concentration of 20 vol%. Meanwhile, a high CO₂ fixation yield of 106.03 mg·L^-1 was reached. The presence of oxygen was adverse to the biofixation, indicating that strain PJ-1 was more suitable for CO₂ fixation in anaerobic environments. Carbon mass balance analysis revealed that the carbon from CO₂ was mainly fixed into the extracellular organic carbon rather than the biomass. GC-MS analysis and cbbL gene test revealed that Paracoccus denitrificans PJ-1 fixed CO₂ through the Calvin-Benson-Bassham cycle and mainly converted CO₂ to oxalic acid and succinic acid. Overall, the excellent CO₂ fixation capacity of Paracoccus denitrificans PJ-1 suggests that it had potential for CO₂ utilization.

From an extremophilic community to an electroautotrophic production strain: identifying a novel Knallgas bacterium as cathodic biofilm biocatalyst

Coupling microbial electrosynthesis to renewable energy sources can provide a promising future technology for carbon dioxide conversion. However, this technology suffers from a limited number of suitable biocatalysts, resulting in a narrow product range. Here, we present the characterization of the first thermoacidophilic electroautotrophic community using chronoamperometric, metagenomic, and ¹³C-labeling analyses. The cathodic biofilm showed current consumption of up to -80 µA cm^-2 over a period of 90 days (-350 mV vs. SHE). Metagenomic analyses identified members of the genera Moorella, Desulfofundulus, Thermodesulfitimonas, Sulfolobus, and Acidianus as potential primary producers of the biofilm, potentially thriving via an interspecies sulfur cycle. Hydrogenases seem to be key for cathodic electron uptake. An isolation campaign led to a pure culture of a Knallgas bacterium from this community. Growth of this organism on cathodes led to increasing reductive currents over time. Transcriptomic analyses revealed a distinct gene expression profile of cells grown at a cathode. Moreover, pressurizable flow cells combined with optical coherence tomography allowed an in situ observation of cathodic biofilm growth. Autotrophic growth was confirmed via isotope analysis. As a natural polyhydroxybutyrate (PHB) producer, this novel species, Kyrpidia spormannii, coupled the production of PHB to CO₂ fixation on cathode surfaces.

Form III RubisCO-mediated transaldolase variant of the Calvin cycle in a chemolithoautotrophic bacterium

The Calvin-Benson-Bassham (CBB) cycle assimilates CO₂ for the primary production of organic matter in all plants and algae, as well as in some autotrophic bacteria. The key enzyme of the CBB cycle, ribulose-bisphosphate carboxylase/oxygenase (RubisCO), is a main determinant of de novo organic matter production on Earth. Of the three carboxylating forms of RubisCO, forms I and II participate in autotrophy, and form III so far has been associated only with nucleotide and nucleoside metabolism. Here, we report that form III RubisCO functions in the CBB cycle in the thermophilic chemolithoautotrophic bacterium Thermodesulfobium acidiphilum, a phylum-level lineage representative. We further show that autotrophic CO₂ fixation in T. acidiphilum is accomplished via the transaldolase variant of the CBB cycle, which has not been previously demonstrated experimentally and has been considered unlikely to occur. Thus, this work reveals a distinct form of the key pathway of CO₂ fixation.

Highly Diverse Aquatic Microbial Communities Separated by Permafrost in Greenland Show Distinct Features According to Environmental Niches

The Greenland Analog Project (GAP) study area in the vicinity of Kangarlussuaq, Western Greenland, was sampled for surface water and deep groundwater in order to determine the composition and estimate the metabolic features of the microbial communities in water bodies separated by permafrost. The sampling sites comprised a freshwater pond, talik lake, deep anoxic groundwater, glacier ice and supraglacial river, meltwater river and melting permafrost active layer. The microbial communities were characterized by amplicon sequencing of the bacterial and archaeal 16S rRNA genes and fungal ITS1 spacer. In addition, bacterial, archaeal and fungal numbers were determined by qPCR and plate counts, and the utilization pattern of carbon and nitrogen substrates was determined with Biolog AN plates and metabolic functions were predicted with FAPROTAX. Different sample types were clearly distinguishable from each other based on community composition, microbial numbers, and substrate utilization patterns, forming four groups, (1) pond/lake, (2) deep groundwater, (3) glacial ice, and (4) meltwater. Bacteria were the most abundant microbial domain, ranging from 0.2–1.4 × 10⁷ 16S rRNA gene copies mL^-1 in pond/lake and meltwater, 0.1-7.8 × 10⁶ copies mL^-1 in groundwater and less than 10⁴ copies mL^-1 in ice. The number of archaeal 16S and fungal 5.8S rRNA genes was generally less than 6.0 × 10³ and 1.5 × 10³, respectively. N₂-fixing and methane-oxidizing Actinomycetes, Bacteroidetes and Verrucomicrobia were the dominant microorganisms in the pond/lake samples, whereas iron reducing Desulfosporosinus sp. dominated the deep anaerobic groundwater. The glacial ice was inhabited by Cyanobacteria, which were mostly Chloroplast-like. The meltwater contained methano- and methylotrophic Proteobacteria, but had also high relative abundances of the nano-sized Parcubacteria. The archaea composed approximately 1% of the 16S rRNA gene pool in the pond/lake samples with nano-sized Woesearchaeota as the dominating taxon, while in the other sample types archaea were almost negligent. Fungi were also most common in the pond/lake communities, were zoospore-forming Chytridiomycetes dominated. Our results show highly diverse microbial communities inhabiting the different cold Greenlandic aqueous environments and show clear segregation of the microbial communities according to habitat, with distinctive dominating metabolic features specifically inhabiting defined environmental niches and a high relative abundance of putatively parasitic or symbiotic nano-sized taxa.

Deep-Sourced Fluids From a Convergent Margin Host Distinct Subseafloor Microbial Communities That Change Upon Mud Flow Expulsion

Submarine mud volcanoes (MVs) along continental margins emit mud breccia and globally significant amounts of hydrocarbon-rich fluids from the subsurface, and host distinct chemosynthetic communities of microbes and macrofauna. Venere MV lies at 1,600 m water depth in the Ionian Sea offshore Italy and is located in a forearc basin of the Calabrian accretionary prism. Porewaters of recently extruded mud breccia flowing from its west summit are considerably fresher than seawater (10 PSU), high in Li⁺ and B (up to 300 and 8,000 μM, respectively), and strongly depleted in K⁺ (<1 mM) at depths as shallow as 20 cm below seafloor. These properties document upward transport of fluids sourced from >3 km below seafloor. 16S rRNA gene and metagenomic sequencing were used to characterize microbial community composition and gene content within deep-sourced mud breccia flow deposits as they become exposed to seawater along a downslope transect of Venere MV. Summit samples showed consistency in microbial community composition. However, beta-diversity increased markedly in communities from downslope cores, which were dominated by methyl- and methanotrophic genera of Gammaproteobacteria. Methane, sulfate, and chloride concentrations were minor but significant contributors to variation in community composition. Metagenomic analyses revealed differences in relative abundances of predicted protein categories between Venere MV and other subsurface microbial communities, characterizing MVs as windows into distinct deep biosphere habitats.

Multidisciplinary involvement and potential of thermophiles

The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.

Desulfothermobacter acidiphilus gen. nov., sp. nov., a thermoacidophilic sulfate-reducing bacterium isolated from a terrestrial hot spring

An anaerobic sulfate-reducing micro-organism, strain 3408-1^T, was isolated from a terrestrial hot spring in Kamchatka peninsula (Russia). The cells were spore-forming rods with a Gram-positive type of cell wall. The new isolate was a moderately thermoacidophilic anaerobe able to grow either by sulfate or thiosulfate respiration with H2 or formate as substrates, or by fermenting yeast extract, maltose, sucrose, glucose and pyruvate. The fermentation products were acetate, CO2 and H2. The pH range for growth was 2.9-6.5, with an optimum at 4.5. The temperature range for growth was 42-70 °C, with an optimum at 55 °C. The G+C content of DNA was 58 mol%. Phylogenetic analysis of the 16S rRNA gene showed that strain 3408-1^T belongs to the family Thermoanaerobacteraceae, order Thermoanaerobacterales and was distantly related to the species of the genus Ammonifex(93-94 % sequence similarity). On the basis of physiological properties and results of phylogenetic analysis, strain 3408-1^T is considered to represent a novel species of a new genus, for which the name Desulfothermobacter acidiphilus gen. nov., sp. nov. is proposed. The type strain is 3408-1^T (=DSM 105356^T=VKM B-3183^T).