Novel thermophilic sulfate-reducing bacteria from a geothermally active underground mine in Japan

The low-temperature germinating spores of the thermophilic Desulfofundulus contribute to an extremely high sulfate reduction in burning coal seams

Burning coal seams, characterized by massive carbon monoxide (CO) emissions, the presence of secondary sulfates, and high temperatures, represent suitable environments for thermophilic sulfate reduction. The diversity and activity of dissimilatory sulfate reducers in these environments remain unexplored. In this study, using metagenomic approaches, in situ activity measurements with a radioactive tracer, and cultivation we have shown that members of the genus Desulfofundulus are responsible for the extremely high sulfate reduction rate (SRR) in burning lignite seams in the Altai Mountains. The maximum SRR reached 564 ± 21.9 nmol S cm-3 day-1 at 60°C and was of the same order of magnitude for both thermophilic (60°C) and mesophilic (23°C) incubations. The 16S rRNA profiles and the search for dsr gene sequences in the metagenome revealed members of the genus Desulfofundulus as the main sulfate reducers. The thermophilic Desulfofundulus sp. strain Al36 isolated in pure culture, did not grow at temperatures below 50°C, but produced spores that germinated into metabolically active cells at 20 and 15°C. Vegetative cells germinating from spores produced up to 0.738 ± 0.026 mM H2S at 20°C and up to 0.629 ± 0.007 mM H2S at 15°C when CO was used as the sole electron donor. The Al36 strain maintains significant production of H2S from sulfate over a wide temperature range from 15°C to 65°C, which is important in variable temperature biotopes such as lignite burning seams. Burning coal seams producing CO are ubiquitous throughout the world, and biogenic H2S may represent an overlooked significant flux to the atmosphere. The thermophilic spore outgrowth and their metabolic activity at temperatures below the growth minimum may be important for other spore-forming bacteria of environmental, industrial and clinical importance.

Hydrogen Production from Alteration of Chicxulub Crater Impact Breccias: Potential Energy Source for a Subsurface Microbial Ecosystem

A sulfate-reducing population of thermophiles grew in porous, permeable niches within glass-bearing impact breccias of the Chicxulub impact crater. The microbial community grew in an impact-generated hydrothermal system that vented on the seafloor several hundred meters beneath the sea surface. Potential electron donors for that metabolism are hydrocarbons, although a strong C-isotope signature of that source does not exist. Model calculations explored here suggest that alteration of glass within the impact breccias may have produced H₂ in sufficient quantities for population growth as the hydrothermal system cooled through thermophilic temperatures, although it is sensitive to the oxidation state of iron in the melt rock prior to hydrothermal alteration and the secondary mineral assemblage. At high water-to-rock ratios and temperatures below 45°C, H₂ yields are insufficient to maintain a population of hydrogenotrophic sulfate-reducing bacteria, but yields double with a higher proportion of ferrous iron between 45 and 65°C. The most reduced rocks (i.e., highest proportion of ferrous iron) that are allowed to form andradite, which is observed in core samples, produce copious amounts of H₂ in the temperature window for thermophiles and hyperthermophiles. Mixtures of melt rock and carbonate, which is observed in breccia matrices, produce somewhat less H₂, and the onset of massive H₂ production is shifted to higher temperatures (i.e., lower W/R).

Nitrosopumilus zosterae sp. nov., an autotrophic ammonia-oxidizing archaeon of phylum Thaumarchaeota isolated from coastal eelgrass sediments of Japan

A novel mesophilic and aerobic ammonia-oxidizing archaeon of the phylum Thaumarchaeota, strain NM25^T, was isolated from coastal eelgrass zone sediment sampled in Shimoda (Japan). The cells were rod-shaped with an S-layer cell wall. The temperature range for growth was 20-37 °C, with an optimum at 30 °C. The pH range for growth was pH 6.1-7.7, with an optimum at pH 7.1. The salinity range for growth was 5-40 %, with an optimum range of 15-32 %. Cells obtained energy from ammonia oxidation and used bicarbonate as a carbon source. Utilization of urea was not observed for energy generation and growth. Strain NM25^T required a hydrogen peroxide scavenger, such as α-ketoglutarate, pyruvate or catalase, for sustained growth on ammonia. Growth of strain NM25^T was inhibited by addition of low concentrations of some organic compounds and organic mixtures, including complete inhibition by glycerol, peptone and yeast extract. Phylogenetic analysis of four concatenated housekeeping genes (16S rRNA, rpoB, rpsI and atpD) and concatenated AmoA, AmoB, AmoC amino acid sequences indicated that the isolate is similar to members of the genus Nitrosopumilus. The closest relative is Nitrosopumilus ureiphilus PS0^T with sequence similarities of 99.5 % for the 16S rRNA gene and 97.2 % for the amoA gene. Genome relatedness between strain NM25^T and N. ureiphilus PS0^T was assessed by average nucleotide identity and digital DNA-DNA hybridization, giving results of 85.4 and 40.2 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NM25^T represents a novel species of the genus Nitrosopumilus, for which the name sp. nov, is proposed. The type strain is NM25^T (=NBRC 111181^T=ATCC TSD-147^T).

Molecular characterization of bacteria and archaea in a bioaugmented zero-water exchange shrimp pond

In the zero-water exchange shrimp culture pond maintained with the application of indigenous bioaugmentor, low levels of total ammonia–nitrogen were reported, indicating the relevance of indigenous microbial communities. Sediments (0–5 cm layer) were sampled from the pond (85th day) and the bacterial and archaeal communities; specifically, the ammonia oxidizers (ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and anaerobic ammonia-oxidizing bacteria) in the sediment metagenome of the pond were analysed using the 16S rRNA and functional genes. Bacterial and archaeal 16S rRNA genes showed the relative abundance of Delta-Proteobacteria and Bacteroidetes groups performing sulphur respiration and organic matter degradation, archaeal groups of anaerobic sulphur respiring Crenarchaeotae, and chemolithoautotrophic ammonia oxidizers belonging to Thaumarchaeota. The presence of these diverse bacterial and archaeal communities denotes their significant roles in the cycling the carbon, nitrogen, and sulphur thereby bringing out efficient bioremediation in the bioaugmented zero-water exchange shrimp culture pond. Similarly, the functional gene-specific study showed the predominance of Nitrosomonas sp. (ammonia-oxidizing bacteria), Nitrosopumilus maritimus (ammonia-oxidizing archaea), and Candidatus Kuenenia (anaerobic ammonia-oxidizing bacteria) in the system, which points to their importance in the removal of accumulated ammonia. Thus, this study paves the way for understanding the microbial communities, specifically the ammonia oxidizers responsible for maintaining healthy and optimal environmental conditions in the bioaugmented zero-water exchange shrimp culture pond.

Microbial Sulfur Isotope Fractionation in the Chicxulub Hydrothermal System

Target lithologies and post-impact hydrothermal mineral assemblages in a new 1.3 km deep core from the peak ring of the Chicxulub impact crater indicate sulfate reduction was a potential energy source for a microbial ecosystem (Kring et al., 2020). That sulfate was metabolized is confirmed here by microscopic pyrite framboids with δ³⁴S values of -5 to -35 ‰ and ΔS_{sulfate-sulfide} values between pyrite and source sulfate of 25 to 54 ‰, which are indicative of biologic fractionation rather than inorganic fractionation processes. These data indicate the Chicxulub impact crater and its hydrothermal system hosted a subsurface microbial community in porous permeable niches within the crater's peak ring.

Physiological Capabilities of Cryoconite Hole Microorganisms

Cryoconite holes are miniature freshwater aquatic ecosystems that harbor a relatively diverse microbial community. This microbial community can withstand the extreme conditions of the supraglacial environment, including fluctuating temperatures, extreme and varying geochemical conditions and limited nutrients. We analyzed the physiological capabilities of microbial isolates from cryoconite holes from Antarctica, Greenland, and Svalbard in selected environmental conditions: extreme pH, salinity, freeze-thaw and limited carbon sources, to identify their physiological limits. The results suggest that heterotrophic microorganisms in cryoconite holes are well adapted to fast-changing environmental conditions, by surviving multiple freeze-thaw cycles, a wide range of salinity and pH conditions and scavenging a variety of organic substrates. Under oxic and anoxic conditions, the communities grew well in temperatures up to 30°C, although in anoxic conditions the community was more successful at colder temperatures (0.2°C). The most abundant cultivable microorganisms were facultative anaerobic bacteria and yeasts. They grew in salinities up to 10% and in pH ranging from 4 to 10.5 (Antarctica), 2.5 to 10 (Svalbard), and 3 to 10 (Greenland). Their growth was sustained on at least 58 single carbon sources and there was no decrease in viability for some isolates after up to 100 consecutive freeze-thaw cycles. The elevated viability of the anaerobic community in the lowest temperatures indicates they might be key players in winter conditions or in early melt seasons, when the oxygen is potentially depleted due to limited flow of meltwater. Consequently, facultative anaerobic heterotrophs are likely important players in the reactivation of the community after the polar night. This detailed physiological investigation shows that despite inhabiting a freshwater environment, cryoconite microorganisms are able to withstand conditions not typically encountered in freshwater environments (namely high salinities or extreme pH), making them physiologically more similar to arid soil communities. The results also point to a possible resilience of the most abundant microorganisms of cryoconite holes in the face of rapid change regardless of the location.

Nitrosomonas stercoris sp. nov., a Chemoautotrophic Ammonia-Oxidizing Bacterium Tolerant of High Ammonium Isolated from Composted Cattle Manure

Among ammonia-oxidizing bacteria, Nitrosomonas eutropha-like microbes are distributed in strongly eutrophic environments such as wastewater treatment plants and animal manure. In the present study, we isolated an ammonia-oxidizing bacterium tolerant of high ammonium levels, designated strain KYUHI-S^T, from composted cattle manure. Unlike the other known Nitrosomonas species, this isolate grew at 1,000 mM ammonium. Phylogenetic analyses based on 16S rRNA and amoA genes indicated that the isolate belonged to the genus Nitrosomonas and formed a unique cluster with the uncultured ammonia oxidizers found in wastewater systems and animal manure composts, suggesting that these ammonia oxidizers contributed to removing higher concentrations of ammonia in strongly eutrophic environments. Based on the physiological and phylogenetic data presented here, we propose and call for the validation of the provisional taxonomic assignment Nitrosomonas stercoris, with strain KYUHI-S as the type strain (type strain KYUHI-S^T = NBRC 110753^T = ATCC BAA-2718^T).

Phylogenetic evidence of noteworthy microflora from the subsurface of the former Homestake gold mine, Lead, South Dakota

Molecular characterization of subsurface microbial communities in the former Homestake gold mine, South Dakota, was carried out by 16S rDNA sequence analysis using a water sample and a weathered soil-like sample. Geochemical analyses indicated that both samples were high in sulphur, rich in nitrogen and salt, but with significantly different metal concentrations. Microbial diversity comparisons unexpectedly revealed three distinct operational taxonomic units (OTUs) belonging to the archaeal phylum Thaumarchaeota, typically identified from marine environments, and one OTU belonging to a potentially novel phylum that fell sister to Thaumarchaeota. To our knowledge this is only the second report of Thaumarchaeota in a terrestrial environment. The majority of the clones from Archaea sequence libraries fell into two closely related OTUs and were grouped most closely to an ammonia-oxidizing, carbon-fixing and halophilic thaumarchaeote genus, Nitrosopumilus. The two samples showed neither Euryarchaeota nor Crenarchaeota members that have often been identified from other subsurface terrestrial ecosystems. Bacteria OTUs containing the highest percentage of sequences were related to sulphur-oxidizing bacteria of the orders Chromatiales and Thiotrichales. Community members of Bacteria from individual Homestake ecosystems were heterogeneous and distinctive to each community, with unique phylotypes identified within each sample.

Diversity and ecophysiological features of thermophilic carboxydotrophic anaerobes

Both natural and anthropogenic hot environments contain appreciable levels of carbon monoxide (CO). Anaerobic microbial communities play an important role in CO conversion in such environments. CO is involved in a number of redox reactions. It is biotransformed by thermophilic methanogens, acetogens, hydrogenogens, sulfate reducers, and ferric iron reducers. Most thermophilic CO-oxidizing anaerobes have diverse metabolic capacities, but two hydrogenogenic species are obligate carboxydotrophs. Among known thermophilic carboxydotrophic anaerobes, hydrogenogens are most numerous, and based on available data they are most important in CO biotransformation in hot environments.

Thermovorax subterraneus, gen. nov., sp. nov., a thermophilic hydrogen-producing bacterium isolated from geothermally active underground mine

A thermophilic, rod-shaped, motile, Gram-positive, spore-forming bacterium strain 70B(T) was isolated from a geothermally active underground mine in Japan. The temperature and pH range for growth was 50-81 degrees C (optimum 71 degrees C) and 6.2-9.8 (optimum pH 7-7.5), respectively. Growth occurred in the presence 0-2% NaCl (optimum 1% NaCl). Strain 70B(T) could utilize glucose, fructose, mannose, mannitol, pyruvate, cellobiose and tryptone as substrates. Thiosulfate was used as electron acceptor. Major whole-cell fatty acids were iso-C(15:0), C(16:0) DMA (dimethyl acetal), C(16:0) and anteiso-C(15:0). The G+C mol% of the DNA was 44.2%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the closest relatives of strain 70B(T) were Thermosediminibacter oceani DSM 16646(T) (94% similarity) and Thermosediminibacter litoriperuensis DSM 16647 (93% similarity). The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain 70B(T) represents a novel species in a new genus, for which the name Thermovorax subterraneus gen. nov., sp. nov. is proposed. The type strain of Thermovorax subterraneus is 70B(T) (=DSM 21563 = JCM 15541).

Sulfidogenic fluidized-bed treatment of metal-containing wastewater at 8 and 65 degrees C temperatures is limited by acetate oxidation

Acetate utilization in sulfidogenic fluidized-bed reactors (FBRs) was investigated for the treatment of iron containing wastewater at low (8 degrees C) and high (65 degrees C) temperatures. The FBRs operated at low and high temperatures were inoculated with cultures of sulfate-reducing bacteria (SRB) originally enriched from arctic and hot mining environments, respectively. Acetate was not utilized as a carbon and electron source for SRB at 8 degrees C. With ethanol, hydrogen sulfide was produced from ethanol to acetate oxidation, which precipitated the iron. Then, several attempts were made to obtain acetate oxidation at 8 degrees C. Inoculation of two different low temperature enrichments and operating the FBR for a long period of time (321 days) did not result in enrichment of acetate oxidizing SRB. Due to the absence of acetate oxidation at 8 degrees C, external alkalinity addition was required to keep the pH neutral. At 65 degrees C, average acetate and sulfate removals were 52+/-12% and 24+/-8% at 670 mg/Ld acetate and 1500 mg/Ld sulfate loadings, respectively. The produced alkalinity from acetate oxidation increased the pH from 6.4 to around 7.5 and electron flow to sulfate reduction averaged 65%. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes showed quite stable SRB community at 8 degrees C, whereas, at 65 degrees C SRB community was dynamic. In the FBRs, Desulfomicrobium apsheronum and Desulfosporosinus sp. at 8 degrees C and Desulfotomaculum sp. at 65 degrees C were detected.

Desulfurispora thermophila gen. nov., sp. nov., a thermophilic, spore-forming sulfate-reducer isolated from a sulfidogenic fluidized-bed reactor

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterium was isolated from a sulfidogenic fluidized-bed reactor treating acidic metal- and sulfate-containing water. The strain, designated RA50E1T, was rod-shaped and motile. The strain grew at 40–67 °C (optimum growth at 59–61 °C) and pH 6.4–7.9 (optimum growth at pH 7.0–7.3). The strain tolerated up to 1 % NaCl. Sulfate, sulfite, thiosulfate and elemental sulfur were used as electron acceptors, but not nitrate, nitrite or iron(III). Electron donors utilized were H2/CO2 (80 : 20, v/v), alcohols, various carboxylic acids and some sugars. Fermentative growth occurred on lactate and pyruvate. The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone MK-7. Major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 0. Strain RA50E1T was distantly related to representatives of the genera Desulfotomaculum, Pelotomaculum, Sporotomaculum and Cryptanaerobacter. On the basis of 16S rRNA gene sequence data, the strain cannot be assigned to any known genus. Based on the phenotypic and phylogenetic features of strain RA50E1T, it is proposed that the strain represents a novel species in a new genus, for which the name Desulfurispora thermophila gen. nov., sp. nov. is proposed. The type strain of Desulfurispora thermophila is RA50E1T (=DSM 16022T=JCM 14018T).

Sulfidogenic fluidized-bed treatment of metal-containing wastewater at low and high temperatures

The applicability of a fluidized-bed reactor (FBR)-based sulfate reducing bioprocess was investigated for the treatment of iron-containing (40-90 mg/L) acidic wastewater at low (8 degrees C) and high (65 degrees C) temperatures. The FBRs operated at low and high temperatures were inoculated with cultures of sulfate-reducing bacteria (SRB) originally enriched from arctic and hot mining environments, respectively. Ethanol was supplemented as carbon and electron source for SRB. At 8 degrees C, ethanol oxidation and sulfate reduction rates increased steadily and reached 320 and 265 mg/L.day, respectively, after 1 month of operation. After this point, the rates did not change significantly during 130 days of operation. Despite the complete ethanol oxidation and iron precipitation, the average sulfate reduction efficiency was 35 +/- 4% between days 30 and 130 due to the accumulation of acetate. At 65 degrees C, a rapid startup was observed as 99.9, 46, and 29% ethanol, sulfate, acetate removals, in respective order, were observed after 6 days. The feed pH was decreased gradually from its initial value of 6 to around 3.7 during 100 days of operation. The wastewater pH of 4.3-4.4 was neutralized by the alkalinity produced in acetate oxidation and the average effluent pH was 7.8 +/- 0.8. As in the low temperature FBR, acetate accumulated. Hence, the oxidation of acetate is the rate-limiting step in the sulfidogenic ethanol oxidation by thermophilic and psychrotrophic SRB. The sulfate reduction rate is three times and acetate oxidation rate is four times higher at 65 degrees C than at 8 degrees C.

Desulfovirgula thermocuniculi gen. nov., sp. nov., a thermophilic sulfate-reducer isolated from a geothermal underground mine in Japan

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterial strain, designated RL80JIVT, was isolated from a geothermally active underground mine in Japan. Cells were rod-shaped and motile. The temperature and pH ranges for growth were 61–80 °C (optimum at 69–72 °C) and pH 6.4–7.9 (optimum at pH 6.8–7.3), and the strain tolerated up to 0.5 % NaCl. Strain RL80JIVT utilized sulfate, sulfite, thiosulfate and elemental sulfur as electron acceptors. Electron donors utilized were H2 in the presence of CO2, and carboxylic acids. Fermentative growth occurred on lactate and pyruvate. The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone MK-7. Major whole-cell fatty acids were iso-C15 : 0, iso-C17 : 0 and C16 : 0. Strain RL80JIVT was found to be affiliated with the thiosulfate-reducer Thermanaeromonas toyohensis DSM 14490T (90.9 % 16S rRNA gene sequence similarity) and with the sulfate-reducer Desulfotomaculum thermocisternum DSM 10259T (90.0 % similarity). Strain RL80JIVT is therefore considered to represent a novel species of a new genus, for which the name Desulfovirgula thermocuniculi gen. nov., sp. nov. is proposed. The type strain of Desulfovirgula thermocuniculi is RL80JIVT (=DSM 16036T=JCM 13928T).

Neural network prediction of thermophilic (65°C) sulfidogenic fluidized-bed reactor performance for the treatment of metal-containing wastewater

The performance of a fluidized-bed reactor (FBR) based sulfate reducing bioprocess was predicted using artificial neural network (ANN). The FBR was operated at high (65 degrees C) temperature and it was fed with iron (40-90 mg/L) and sulfate (1,000-1,500 mg/L) containing acidic (pH = 3.5-6) synthetic wastewater. Ethanol was supplemented as carbon and electron source for sulfate reducing bacteria (SRB). The wastewater pH of 4.3-4.4 was neutralized by the alkalinity produced in acetate oxidation and the average effluent pH was 7.8 +/- 0.8. The oxidation of acetate is the rate-limiting step in the sulfidogenic ethanol oxidation by thermophilic SRB, which resulted in acetate accumulation. Sulfate reduction and acetate oxidation rates showed variation depending on the operational conditions with the maximum rates of 1 g/L/d (0.2 g/g volatile solids (VS)/d) and 0.3 g/L/d (0.06 g/g VS/d), respectively. This study presents an ANN model predicting the performance of the reactor and determining the optimal architecture of this model; such as best back-propagation (BP) algorithm and neuron numbers. The Levenberg-Marquardt algorithm was selected as the best of 12 BP algorithms and optimal neuron number was determined as 20. The developed ANN model predicted acetate (R=0.91), sulfate (R=0.95), sulfide (R=0.97), and alkalinity (R=0.94) in the FBR effluent. Hence, the ANN based model can be used to predict the FBR performance, to control the operational conditions for improved process performance.

Desulfotomaculum thermosubterraneum sp. nov., a thermophilic sulfate-reducer isolated from an underground mine located in a geothermally active area

A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterium was isolated from an underground mine in a geothermally active area in Japan. Cells of this strain, designated RL50JIIIT, were rod-shaped and motile. The temperature range for growth was 50–72 °C (optimum growth at 61–66 °C) and the pH range was 6.4–7.8 (optimum at pH 7.2–7.4). Strain RL50JIIITtolerated up to 1.5 % NaCl, but optimum growth occurred in the presence of 0–1 % NaCl. Electron acceptors utilized were sulfate, sulfite, thiosulfate and elemental sulfur. Electron donors utilized were H2in the presence of CO2, alanine, various carboxylic acids and alcohols. Fermentative growth occurred on lactate and pyruvate. The cell wall contained mesodiaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone 7 (MK-7). Major whole-cell fatty acids were iso-C15 : 0, iso-C17 : 0DMA (dimethyl acetal), iso-C15 : 0DMA and iso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed 98.7 % similarity withDesulfotomaculum solfataricumDSM 14956T. However, DNA–DNA hybridization experiments withDesulfotomaculum kuznetsovii,Desulfotomaculum luciaeandD. solfataricumand the G+C content of the DNA (54.4 mol%) allowed the differentiation of strain RL50JIIITfrom the recognized species of the genusDesulfotomaculum. Strain RL50JIIITtherefore represents a novel species, for which the nameDesulfotomaculum thermosubterraneumsp. nov. is proposed. The type strain is RL50JIIIT(=DSM 16057T=JCM 13837T).