Hydrochemical and Hydroacoustic Investigation of the Yugama Acid Crater Lake, Kusatsu-Shirane, Japan

The gases dissolved in the waters of volcanic lakes can present a serious hazard if the physical-chemical conditions change due to variations in the supply of magmatic gases. The monitoring of gases such as CO2 and He help us understand the degassing process and their connection with magmatic/hydrothermal system. One of the most acidic volcanic lakes on the planet is the Yugama, on Kusatsu Shirane volcano (Japan). We report the results of an interdisciplinary study carried out in August 2013 at Yugama consisting of the first estimation of rate of diffuse CO2 emission, the chemical and isotopic analysis of water and dissolved gases in samples from vertical lake profiles, and an echo-sounding survey. The lake water has an average temperature of 24-25°C, pH 1.01, concentrations of SO42- between 1,227 and 1,654 mgL−1 and Cl− between 1,506 and 2,562 mgL−1, with gas bubbling at several locations and floating sulfur globules with sulfide inclusions. A total of 66 CO2 efflux measurements were taken at the lake surface by means of the floating accumulation chamber method to estimate the diffuse CO2 output from the studied area. CO2 efflux values ranged from 82 up to 25,800 g m−2 d−1. Estimation of the diffuse CO2 emission at Yaguma Crater Lake was 30 ± 12 t d−1. Normalized CO2 emission rate (assuming an area of 0.066 km2) was 454 t km−2 d−1, a value within the range of acid volcanic lakes. Vertical profiles of major ions and dissolved gases showed variations with increases in ion content and dissolved CO2 and He with depth. Acoustic imaging shows the presence of intense bubbling and provides important information on the bathymetry of the lake. The 50–200 kHz echograms exhibit frequent vertical plumes of rising gas bubbles. Within the crater-lake, three circular submarine vents have been identified showing flares due to a significant activity of sublacustrine emissions. This work shows the first data of diffuse CO2 degassing, dissolved gases in water and echosounding (ES) from Yugama Crater Lake. Periodic hydrogeochemical and hydroacoustic surveys at Yugama Crater Lakemay thus help to document changes in the state of activity of this high-risk volcanic area.

The pathway of sulfide oxidation to octasulfur globules in the cytoplasm of aerobic bacteria

Sulfur-oxidizing bacteria can oxidize hydrogen sulfide (H 2 S) to produce sulfur globules. Although the process is common, the pathway is unclear. In recombinant Escherichia coli and wild-type Corynebacterium vitaeruminis DSM20294 with SQR but no enzymes to oxidize zero valence sulfur, SQR oxidized H 2 S into short-chain inorganic polysulfide (H 2 S n , n≥2) and organic polysulfide (RS n H, n≥2), which reacted with each other to form long-chain GS n H (n≥2) and H 2 S n before producing octasulfur (S 8 ), the main component of elemental sulfur. GS n H also reacted with GSH to form GSnG (n≥2) and H 2 S; H 2 S was again oxidized by SQR. After GSH was depleted, SQR simply oxidized H 2 S to H 2 S n , which spontaneously generated S 8 . S 8 aggregated into sulfur globules in the cytoplasm. The results highlight the process of sulfide oxidation to S 8 globules in the bacterial cytoplasm and demonstrate the potential of using heterotrophic bacteria with SQR to convert toxic H 2 S into relatively benign S 8 globules. IMPORTANCE Our results support a process of H 2 S oxidation to produce octasulfur globules via SQR catalysis and spontaneous reactions in the bacterial cytoplasm. Since the process is an important event in geochemical cycling, a better understanding facilitates further studies and provides theoretical support for using heterotrophic bacteria with SQR to oxidize toxic H 2 S into sulfur globules for recovery.

Identification and Genomic Characterization of Two Previously Unknown Magnetotactic Nitrospirae

Magnetotactic bacteria (MTB) are a group of microbes that biomineralize membrane-bound, nanosized magnetite (Fe3O4), and/or greigite (Fe3S4) crystals in intracellular magnetic organelle magnetosomes. MTB belonging to the Nitrospirae phylum can form up to several hundreds of Fe3O4 magnetosome crystals and dozens of sulfur globules in a single cell. These MTB are widespread in aquatic environments and sometimes account for a significant proportion of microbial biomass near the oxycline, linking these lineages to the key steps of global iron and sulfur cycling. Despite their ecological and biogeochemical importance, our understanding of the diversity and ecophysiology of magnetotactic Nitrospirae is still very limited because this group of MTB remains unculturable. Here, we identify and characterize two previously unknown MTB populations within the Nitrospirae phylum through a combination of 16S rRNA gene-based and genome-resolved metagenomic analyses. These two MTB populations represent distinct morphotypes (rod-shaped and coccoid, designated as XYR, and XYC, respectively), and both form more than 100 bullet-shaped magnetosomal crystals per cell. High-quality draft genomes of XYR and XYC have been reconstructed, and they represent a novel species and a novel genus, respectively, according to their average amino-acid identity values with respect to available genomes. Accordingly, the names Candidatus Magnetobacterium cryptolimnobacter and Candidatus Magnetomicrobium cryptolimnococcus for XYR and XYC, respectively, were proposed. Further comparative genomic analyses of XYR, XYC, and previously reported magnetotactic Nitrospirae reveal the general metabolic potential of this MTB group in distinct microenvironments, including CO2 fixation, dissimilatory sulfate reduction, sulfide oxidation, nitrogen fixation, or denitrification processes. A remarkably conserved magnetosome gene cluster has been identified across Nitrospirae MTB genomes, indicating its putative important adaptive roles in these bacteria. Taken together, the present study provides novel insights into the phylogenomic diversity and ecophysiology of this intriguing, yet poorly understood MTB group.

Genomic and morphologic characterization of a planktonic Thiovulum (Campylobacterota) dominating the surface waters of the sulfidic Movile Cave, Romania

ABSTRACTLife in Movile Cave (Romania) relies entirely on primary carbon fixation by bacteria oxidizing sulfide, methane and ammonia with oxygen, nitrate, sulfate, and ferric iron. There, large spherical-ovoid bacteria (12-16 μm diameter), rich in intracellular sulfur globules, dominate the stable microbial community in the surface water of a hypoxic Air Bell. These were identified as Thiovulum sp. (Campylobacterota). We obtained a closed genome of this Thiovulum and compared it to that of Thiovulum ES. The genes for oxidizing sulfide to sulfate are absent, therefore, Thiovulum likely avoids constant accumulation of elemental sulfur either by oxidizing sulfide to sulfite which is then excreted, or via dissimilatory nitrate reduction to ammonia using the formate-dependent nitrite reductase or hydroxylamine oxidoreductase. Thus, Thiovulum, found also in other caves, is likely important to both S and N cycles in subterranean aquatic ecosystems. Additionally, using electron microscopy, we suggest that in absence of motor-like structures along the membrane, the peritrichous flagella-like structures are type IV pili, for which genes were found in both Thiovulum genomes. These pili may play a role in veil formation, connecting adjacent cells. The force exerted by coordinated movement of such pili may partly explain the exceptionally fast swimming of these bacteria.

Comparative Genomics of Beggiatoa leptomitoformis Strains D-401 and D-402T with Contrasting Physiology But Extremely High Level of Genomic Identity

Representatives of filamentous colorless sulfur-oxidizing bacteria often dominate in sulfide biotopes, preventing the diffusion of toxic sulfide into the water column. One of the most intriguing groups is a recently described Beggiatoa leptomitoformis including strains D-401 and D-402T. Both strains have identical genes encoding enzymes which are involved in the oxidation of hydrogen sulfide and thiosulfate. Surprisingly, the B. leptomitoformis strain D-401 is not capable to grow lithotrophically in the presence of reduced sulfur compounds and to accumulate elemental sulfur inside the cells, in contrast to the D-402T strain. In general, genomes of D-401 and D-402T have an extremely high level of identity and only differ in 1 single-letter substitution, 4 single-letter indels, and 16 long inserts. Among long inserts, 14 are transposons. It was shown that in the D-401 strain, a gene coding for a sulfur globule protein was disrupted by one of the mentioned transposons. Based on comparative genomics, RT-qPCR, and HPLC-MS/MS, we can conclude that this gene plays a crucial role in the formation of the sulfur globules inside the cells, and the disruption of its function prevents lithotrophic growth of B. leptomitoformis in the presence of reduced sulfur compounds.

Sulfur globule oxidation in green sulfur bacteria is dependent on the dissimilatory sulfite reductase system

Green sulfur bacteria (GSB) oxidize sulfide and thiosulfate to sulfate, with extracellular globules of elemental sulfur as an intermediate. Here we investigated which genes are involved in the formation and consumption of these sulfur globules in the green sulfur bacterium Chlorobaculum tepidum. We show that sulfur globule oxidation is strictly dependent on the dissimilatory sulfite reductase (DSR) system. Deletion of dsrM/CT2244 or dsrT/CT2245, or the two dsrCABL clusters (CT0851–CT0854, CT2247–2250), abolished sulfur globule oxidation and prevented formation of sulfate from sulfide, whereas deletion of dsrU/CT2246 had no effect. The DSR system also seems to be involved in the formation of thiosulfate, because thiosulfate was released from wild-type cells during sulfide oxidation, but not from the dsr mutants. The dsr mutants incapable of complete substrate oxidation oxidized sulfide and thiosulfate about twice as fast as the wild-type, while having only slightly lower growth rates (70–80 % of wild-type). The increased oxidation rates seem to compensate for the incomplete substrate oxidation to satisfy the requirement for reducing equivalents during growth. A mutant in which two sulfide : quinone oxidoreductases (sqrD/CT0117 and sqrF/CT1087) were deleted exhibited a decreased sulfide oxidation rate (∼50 % of wild-type), yet formation and consumption of sulfur globules were not affected. The observation that mutants lacking the DSR system maintain efficient growth suggests that the DSR system is dispensable in environments with sufficiently high sulfide concentrations. Thus, the DSR system in GSB may have been acquired by horizontal gene transfer as a response to a need for enhanced substrate utilization in sulfide-limiting habitats.

Azospirillum thiophilum sp. nov., a diazotrophic bacterium isolated from a sulfide spring

A novel nitrogen-fixing strain, designated BV-ST, was isolated from a sulfur bacterial mat collected from a sulfide spring of the Stavropol Krai, North Caucasus, Russia. Strain BV-ST grew optimally at pH 7.5 and 37 °C. According to the results of phylogenetic analysis, strain BV-ST belonged to the genus Azospirillum within the family Rhodospirillaceae of the class Alphaproteobacteria. Within the genus Azospirillum, strain BV-ST was most closely related to Azospirillum doebereinerae GSF71T, A. picis IMMIB TAR-3T and A. lipoferum ATCC 29707T (97.7, 97.7 and 97.4 % 16S rRNA gene sequence similarity, respectively). DNA–DNA relatedness between strain BV-ST and A. doebereinerae DSM 13131T, A. picis DSM 19922T and A. lipoferum ATCC 29707T was 38, 55 and 42 %, respectively. Similarities between nifH sequences of strain BV-ST and members of the genus Azospirillum ranged from 94.5 to 96.8 %. Chemotaxonomic characteristics (quinone Q-10, major fatty acid C18 : 1 ω7c and G+C content 67 mol%) were similar to those of members of the genus Azospirillum. In contrast to known Azospirillum species, strain BV-ST was capable of mixotrophic growth under microaerobic conditions with simultaneous utilization of organic substrates and thiosulfate as electron donors for energy conservation. Oxidation of sulfide was accompanied by deposits of sulfur globules within the cells. Based on these observations, strain BV-ST is considered as a representative of a novel species of the genus Azospirillum, for which the name Azospirillum thiophilum sp. nov. is proposed. The type strain is BV-ST (=DSM 21654T =VKM B-2513T).