The presence and diversity of the cbb genes encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) (a key enzyme of the Calvin–Benson cycle of autotrophic CO₂ assimilation) were investigated in pure cultures of seven genera of halophilic chemolithoautotrophic sulfur-oxidizing bacteria (SOB) and in sediments from a hypersaline lake in which such bacteria have been recently discovered. All of the halophilic SOB strains (with the exception of Thiohalomonas nitratireducens) possessed the cbbL gene encoding RuBisCO form I, while the cbbM gene encoding RuBisCO form II was detected only in some of the pure cultures. The general topologies of the CbbL/CbbM trees and the 16S rRNA gene tree were different, but both markers showed that the halophilic SOB genera formed independent lineages in the Gammaproteobacteria. In some cases, such as with several strains of the genus Thiohalospira and with Thioalkalibacter halophilus, the cbbL clustering was incongruent with the positions of these strains on the ribosomal tree. In the cbbM tree, the clustering of Thiohalospira and Thiohalorhabdus strains was incongruent with their branching in both cbbL and 16S rRNA gene trees. cbbL and cbbM genes related to those found in the analysed halophilic SOB were also detected in a sediment from a hypersaline lake in Kulunda Steppe (Russia). Most of the cbbL and cbbM genes belonged to members of the genus Thiohalorhabdus. In the cbbL clone library, sequences related to those of Halothiobacillus and Thiohalospira were detected as minor components. Some of the environmental cbbM sequences belonged to as yet unknown phylotypes, representing deep lineages of halophilic autotrophs.

The diversity of soxB gene encoding a key enzyme of the Sox pathway sulfate thiohydrolase has been investigated in pure cultures of various halophili

Anaerobic, fermentative, halotolerant bacteria, strains 4-11^Tand 585, were isolated from production water of two low-temperature petroleum reservoirs (Russia) and were characterized by using a polyphasic approach. Cells of the strains were spherical, non-motile and 0.30–2.5 µm in diameter. Strain 4-11^Tgrew optimally at 35 °C, pH 6.0 and 1.0–2.0% (w/v) NaCl. Both strains grew chemoorganotrophically with mono-, di- and trisaccharides. The major cellular fatty acids of both strains were C_14:0, C_16:0, C_16:1ω9 and C_18:03-OH. Major polar lipids were glycolipids and phospholipids. The 16S rRNA gene sequences of the strains 4-11^Tand 585 had 99.9% similarity and were most closely related to the sequence ofSphaerochaeta associataGLS2^T(96.9, and 97.0% similarity, respectively). The G+C content of the genomic DNA of strains 4-11^Tand 585 were 46.8 and 46.9%, respectively. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of strain 4-11^TandS. associataGLS2^Twere 73.0 and 16.9%, respectively. Results of phylogenomic metrics analysis of the genomes and 120 core proteins of strains 4-11^Tand 585 and their physiological and biochemical characteristics confirmed that the strains represented a novel species of the genusSphaerochaeta, for which the nameSphaerochaeta halotoleranssp. nov. is proposed, with the type strain 4-11^T(=VKM B-3269^T=KCTC 15833^T). Based on the results of phylogenetic analysis,Sphaerochaeta coccoideswas reclassified as member of a new genusParasphaerochaetagen. nov.,Parasphaerochaeta coccoidescomb. nov. The generaSphaerochaetaandParasphaerochaetaform a separate clade, for which a novel family,Sphaerochaetaceaefam. nov., is proposed.

The contamination of marine and freshwater ecosystems with the items from thermoplastics, including polystyrene (PS), necessitates the search for efficient microbial degraders of these polymers. In the present study, the composition of prokaryotes in biofilms formed on PS samples incubated in seawater and the industrial water of a petrochemical plant were investigated. Using a high-throughput sequencing of the V3–V4 region of the 16S rRNA gene, the predominance of Alphaproteobacteria (Blastomonas), Bacteroidetes (Chryseolinea), and Gammaproteobacteria (Arenimonas and Pseudomonas) in the biofilms on PS samples exposed to industrial water was revealed. Alphaproteobacteria (Erythrobacter) predominated on seawater-incubated PS samples. The local degradation of the PS samples was confirmed by scanning microscopy. The PS-colonizing microbial communities in industrial water differed significantly from the PS communities in seawater. Both communities have a high potential ability to carry out the carbohydrates and amino acids metabolism, but the potential for xenobiotic degradation, including styrene degradation, was relatively higher in the biofilms in industrial water. Bacteria of the genera Erythrobacter, Maribacter, and Mycobacterium were potential styrene-degraders in seawater, and Pseudomonas and Arenimonas in industrial water. Our results suggest that marine and industrial waters contain microbial populations potentially capable of degrading PS, and these populations may be used for the isolation of efficient PS degraders.

A methanogenic enrichment growing on a medium with methanol was obtained from a petroleum reservoir (Republic of Azerbaijan) and stored for 33 years without transfers to fresh medium. High-throughput sequencing of the V4 region of the 16S rRNA gene revealed members of the genera Desulfovibrio, Soehngenia, Thermovirga, Petrimonas, Methanosarcina, and Methanomethylovorans. A novel gram-positive, rod-shaped, anaerobic fermentative bacterium, strain 1933P^T, was isolated from this enrichment and characterized. The strain grew at 13–55 °C (optimum 35 °C), with 0–3.0% (w/v) NaCl (optimum 0–2.0%) and in the pH range of 6.7–8.0 (optimum pH 7.0). The 16S rRNA gene sequence similarity, the average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) values between strain 1933P^T and the type strain of the most closely related species Soehngenia saccharolytica DSM 12858^T were 98.5%, 70.5%, and 22.6%, respectively, and were below the threshold accepted for species demarcation. Genome-based phylogenomic analysis and physiological and biochemical characterization of the strain 1933P^T (VKM B-3382^T = KCTC 15984^T) confirmed its affiliation to a novel species of the genus Soehngenia, for which the name Soehngenia longivitae sp. nov. is proposed. Genome analysis suggests that the new strain has potential in the degradation of proteinaceous components.

Intensive human activity in the Arctic region leads to hydrocarbon pollution of reservoirs and soils. Isolation of bacteria capable of growing at low temperatures and degrading oil and petroleum products is of scientific and practical value. The aim of this work was to study the physiology and growth in oil at temperatures below 0 °C of four strains of bacteria of the genera Pseudomonas, Rhodococcus, Arthrobacter, and Sphingomonas—previously isolated from diesel-contaminated soils of the Franz Josef Land archipelago—as well as genomic analysis of the Sphingomonas sp. AR_OL41 strain. The studied strains grew on hydrocarbons at temperatures from −1.5 °C to 35 °C in the presence of 0–8% NaCl (w/v). Growth at a negative temperature was accompanied by visual changes in the size of cells as well as a narrowing of the spectrum of utilized n-alkanes. The studied strains were psychrotolerant, degraded natural biopolymers (xylan, chitin) and n-alkanes of petroleum, and converted phosphates into a soluble form. The ability to degrade n-alkanes is rare in members of the genus Sphingomonas. To understand how the Sphingomonas sp. AR_OL41 strain has adapted to a cold, diesel-contaminated environment, its genome was sequenced and analyzed. The Illumina HiSeq 2500 platform was used for AR_OL41 genome strain sequencing. The genome analysis of the AR_OL41 strain showed the presence of genes encoding enzymes of n-alkane oxidation, pyruvate metabolism, desaturation of membrane lipids, and the formation of exopolysaccharides, confirming the adaptation of the strain to hydrocarbon pollution and low habitat temperature. Average nucleotide identity and digital DNA–DNA hybridization values for genomes of the AR_OL41 strain with that of the phylogenetically relative Sphingomonas alpine DSM 22537^T strain were 81.9% and 20.9%, respectively, which allows the AR_OL41 strain to be assigned to a new species of the genus Sphingomonas. Phenomenological observations and genomic analysis indicate the possible participation of the studied strains in the self-purification of Arctic soils from hydrocarbons and their potential for biotechnological application in bioremediation of low-temperature environments.