Pseudodesulfovibrio sediminis sp. nov., a mesophilic and neutrophilic sulfate-reducing bacterium isolated from sediment of a brackish lake

Sulfate-Reducing Bacteria Isolated from an Oil Field in Kazakhstan and a Description of Pseudodesulfovibrio karagichevae sp. nov

Sulfidogenic bacteria cause numerous issues in the oil industry since they produce sulfide, corroding steel equipment, reducing oil quality, and worsening the environmental conditions in oil fields. The purpose of this work was to isolate and taxonomically identify the sulfidogenic bacteria responsible for the corrosion of steel equipment at the Karazhanbas oil field (Kazakhstan). In this study, we characterized five sulfidogenic strains of the genera Pseudodesulfovibrio, Oleidesulfovibrio, and Acetobacterium isolated from the formation water of the Karazhanbas oil field (Kazakhstan). Sulfate-reducing strain 9FUST revealed 98.9% similarity of the 16S rRNA gene sequence with the closely related strain 'Pseudodesulfovibrio methanolicus' 5S69T and was studied in detail to enhance the taxonomic resolution. Strain 9FUST grew optimally at 23-28 °C, pH 6.5, and 0-2% (w/v) NaCl. The strain used lactate, pyruvate, methanol, ethanol, fructose, ribose, and H2/CO2 (in the presence of acetate) as carbon and energy sources for sulfate reduction. Iso-C17:1 ω11, C15:0, iso-C15:0, and C16:0 were the predominant fatty acids. The genome is 4.20 Mbp with a G + C content of 64.0%. The average nucleotide identity and digital DNA-DNA hybridization values with Pseudodesulfovibrio spp. genomes were 72.5-91.6% (<95%) and 18.5-45.0% (<70%), respectively, and supported our conclusion that 9FUST (=VKM B-3654T = KCTC 25498T) belonged to a novel Pseudodesulfovibrio species, for which the name Pseudodesulfovibrio karagichevae sp. nov. is proposed. Pangenome analysis of sixteen Pseudodesulfovibrio species and functional annotation analysis of identified genes revealed complete modules of enzymes of the main metabolic pathways, characteristic of bacteria of this genus, and unique genes highlighting the adaptations of strain 9FUST in carbohydrate metabolism, nutrient uptake, and environmental stress response. Isolation of these strains expands our understanding of the diversity of sulfidogens in oil reservoirs and can be used to test the effectiveness of biocides used in an oil field.

Pseudodesulfovibrio thermohalotolerans sp. nov., a novel obligately anaerobic, halotolerant, thermotolerant, and sulfate-reducing bacterium isolated from a western offshore hydrocarbon reservoir in India

OBJECTIVE

Characterization and documentation of strain MCM B-1480T, a novel sulfate-reducing bacterium isolated from produced water of India's western offshore hydrocarbon reservoir.

METHOD

Strain MCM B-1480T was unequivocally identified using a polyphasic approach routinely followed in bacterial systematics. The morphological and biochemical characterization of strain MCM B-1480T was carried out using standard microbiological techniques.

RESULTS

MCM B-1480T was a Gram-stain-negative, motile, non-spore-forming, curved-rod-shaped bacterium. MCM B-1480T could grow at temperatures between 20 and 60 °C (optimum 37 °C), pH 6-8 (optimum 7), and required 1-6% NaCl (optimum 3%) for growth. Strain MCM B-1480T was reducing sulfate to produce hydrogen sulfide during growth. This strain used lactate and pyruvate as prominent electron donors, whereas sulfate, sulfite, thiosulfate, and nitrate served as electron acceptors. MCM B-1480T shared maximum 16S rRNA gene sequence homology of 98.65% with the members of the genus Pseudodesulfovibrio. The G + C content of the 3.87 Mb MCM B-1480T genome was 60.39%. Digital DDH (27.7%) and average nucleotide identity (ANI 84%) with the closest phylogenetic affiliate (less than 70% and 95%, respectively) reaffirmed its distinctiveness. The major cellular fatty acids components, namely iso-C15:0, anteiso-C15:0, C16:0, and anteiso-C17:0, differentiated strain MCM B-1480T from other species of Pseudodesulfovibrio. Genome annotation revealed the presence of genes encoding dissimilatory sulfate reduction and nitrate reduction in strain MCM B-1480T.

CONCLUSION

The polyphasic studies, including SSU rRNA gene sequencing, average nucleotide identity, Digital DNA-DNA hybridization, cell wall fatty acids analysis, etc., identified strain MCM B-1480T as a novel taxon and Pseudodesulfovibrio thermohalotolerans sp. nov. was proposed (= JCM 39269T = MCC 4711T).

Pseudodesulfovibrio nedwellii sp. nov., a mesophilic sulphate-reducing bacterium isolated from a xenic culture of an anaerobic heterolobosean protist

A novel sulphate-reducing bacterium, strain SYK^T, was isolated from a xenic culture of an anaerobic protist obtained from a sulphidogenic sediment of the saline Lake Hiruga in Fukui, Japan. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that SYK^T clustered with the members of the genus Pseudodesulfovibrio. The closest relative of strain SYK^T was Pseudodesulfovibrio sediminis SF6^T, with 16S rRNA gene sequence identity of 97.43 %. Digital DNA-DNA hybridisation and average nucleotide identity values between SYK^T and species of the genus Pseudodesulfovibrio fell below the respective thresholds for species delineation, indicating that SYK^T represents a novel species of the genus Pseudodesulfovibrio. Cells measured 1.7-3.7×0.2-0.5 µm in size and were Gram-stain-negative, obligately anaerobic, motile by means of a single polar flagellum and had a curved rod or sigmoid shape. Cell growth was observed under saline conditions from pH 6.0 to 9.5 (optimum pH 8.0-9.0) and at a temperature of 10-30 °C (optimum 25 °C). SYK^T used lactate, pyruvate, fumarate, formate and H₂ as electron donors. It used sulphate, sulphite, thiosulphate and sulphur as terminal electron acceptors. Pyruvate and fumarate were fermented. Major cellular fatty acids were anteiso-C_15 : 0, C_16 : 0, anteiso-C_17 : 1ω9c, summed feature 3 (C_16 : 1ω6c and/or C_16 : 1ω7c) and summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c). The DNA G+C content of SYK^T was 49.4 mol%. On the basis of the the genetic and phenotypic features, SYK^T was determined to represent a novel species of the genus Pseudodesulfovibrio for which the name Pseudodesulfovibrio nedwellii sp. nov. is proposed with type strain SYK^T (=DSM 114958^T=JCM 35746^T).

Desulfoluna limicola sp. nov., a sulfate-reducing bacterium isolated from sediment of a brackish lake

A novel sulfate-reducing bacterium, strain ASN36^T, was isolated from sediment of a brackish lake in Japan. Cells of strain ASN36^T were not motile and rod-shaped, with length of 2.0-4.9 μm and width of 0.6-0.9 μm. Growth was observed at 5-35 °C with an optimum growth temperature of 25-30 °C. The pH range for growth was 6.6-8.8 with an optimum pH of 7.3. Major fatty acids were C_16:1 ω7c and C_16:0. Under sulfate-reducing conditions, strain ASN36^T utilized lactate, malate, pyruvate, butyrate, ethanol, butanol, glycerol, yeast extract and H₂/CO₂ as growth substrate. Fermentative growth occurred on malate and pyruvate. The novel isolate used sulfate, sulfite and thiosulfate as electron acceptors. The genome of strain ASN36^T is composed of a chromosome with length of 6.3 Mbp and G + C content of 55.1 mol%. Analyses of the 16S rRNA gene indicated that strain ASN36^T is related to Desulfoluna species. Overall genome relatedness indices indicated that strain ASN36^T does not belong to any existing species. In contrast to the closest relatives, strain ASN36^T lacks genes for reductive dehalogenase required for organohalide respiration and does not use halogenated aromatics as electron acceptors. On the basis of its genomic and phenotypic properties, strain ASN36^T (= DSM 111985 ^T = JCM 39257 ^T) is proposed as the type strain of a new species, Desulfoluna limicola sp. nov.