Six benzoic acid-degrading bacteria of the genus Dietzia were isolated from the saline ecotopes of the Verkhnekamskoe and Yakshinskoe salt deposits (Perm region, Komi Republic, Russia). Benzoic acid (BA) may accumulate in ecosystems through technogenic processes, as well as during the microbiological decomposition of complex organic compounds containing an aromatic ring. The strains studied here were found to be closely related to D. psychralcaliphila, D. kunjamensis subsp. kunjamensis, D. cercidiphylli, and D. maris. It was shown that they are halotolerant and able to thrive on BA as their sole carbon and energy source in the absence of salt or in the presence of 50–70 g/L NaCl. They also contain benA genes encoding the α-subunit of benzoate 1,2-dioxygenase, the key enzyme of BA degradation. The highest level of similarity (79.32–91.38%) was observed between the nucleotide sequences of the benA genes of the strains considered and the homologous sequences of Actinomycetes representatives from genera such as Dietzia, Mycolicibacterium, Geodermatophilus, Pseudonocardia, Corynebacterium, and Raineyella. The described active BA degraders belonging to the genus Dietzia have the potential to aid in the development of bioremediation techniques for environmental objects contaminated with mono(poly)aromatic pollutants and subject to salting.
The taxonomic composition of soil (Technosol and Retisol) bacterial communities near the salt dump of a potassium enterprise (Solikamsk, Perm krai) was analyzed by the method of high-throughput sequencing of the 16S rRNA gene. Soil samples without plants and of the rhizosphere of plants of the species Calamagrostis epigeios (L.) Roth from plots located 1–1.5, 8, and 780 m and 11 km from the salt dump were studied. It was found that bacteria of the phyla Pseudomonadota, Bacteroidota, Actinomycetota, Acidobacteriota, Verrucomicrobiota, and Gemmatimonadota predominated in all soil samples. The impact of halite waste on the taxonomic composition of bacterial communities in soils was the greatest on plots in the salinization zone in the immediate vicinity of the salt dump (1–1.5 m). In soil samples without plants taken in these areas, bacteria of the order “Candidatus Actinomarinales“ predominated, the proportion of representatives of the phyla Acidobacteriota and Verrucomicrobiota, the class Actinobacteria, and the family Chitinophagaceae decreased, and the proportion of bacteria of the family Xanthomonadaceae in bacterial communities increased in comparison with nonsaline soils (at a distance of 8 and 780 m and 11 km from the salt dump). In the rhizosphere bacterial communities of plants, growing in the salinization zone, the proportion of representatives of the phylum Acidobacteriota and of the families Chitinophagaceae and Enterobacteriaceae decreased, while the proportion of the families Xanthomonadaceae and Flavobacteriaceae became greater. The influence of the salt dump on soil bacterial communities from plots located 8 m and 730 m from the salt dump was revealed: it was manifested in the presence of representatives of the order “Candidatus Actinomarinales“ (1.4–1.6
Using the method of high-throughput sequencing of the 16S rRNA gene, the taxonomic composition of soil bacterial communities (Technosol and Retisol) near the salt dump of a potassium enterprise (Solikamsk, Perm region) was analyzed. Soil samples without plants and the rhizosphere of plants of the species Calamagrostis epigeios (L.) Roth) from areas located 1–1.5, 8, 780 m and 11 km from the salt dump were studied. It was found that bacteria from the phyla Pseudomonadota, Bacteroidota, Actinomycetota, Acidobacteriota, Verrucomicrobiota and Gemmatimonadota predominated in all soil samples. Halite waste had the greatest impact on the taxonomic composition of bacterial communities on the soils of areas (in the salinity zone) located in the immediate vicinity of the salt dump (1–1.5 m). In soil samples without plants collected in these areas, relative to soils samples without salinity (at a distance of 8, 780 m, 11 km from the salt dump), bacteria of the order “Candidatus Actinomarinales” predominated; the proportion in the bacterial communities of representatives of the phyla Acidobacteriota, Verrucomicrobiota, class Actinobacteria and the Chitinophagaceae family, the proportion of bacteria of the family Xanthomonadaceae increased. In rhizosphere bacterial communities of the plants growing in the salinity zone, the proportion of representatives of the phylum Acidobacteriota and the families Chitinophagaceae, Enterobacteriaceae decreased, and the proportion of the families Xanthomonadaceae and Flavobacteriaceae increased. The influence of the salt dump on the soil bacterial communities from areas located 8 m and 730 m from the salt dump was revealed, manifested in the presence of representatives of the order “Candidatus Actinomarinales” (1.4–1.6%), families Nitrosomonadaceae (3.0–6.1%), Saprospiraceae (1.0–1.9%), the genus Ilumatobacter (1.6–2.8%) and unculturable bacteria of the family Rhodanobacteraceae (1.3–1.5%).
Proton magnetic resonance spectroscopy was used for investigation of the pool of compatible solutes accumulated in the cells of Glutamicibacter sp. strain SMB32 in response to abiotic environmental factors. The original habitat of the strain was anthropogenically salinated soil at the Verkhnekamsk deposit of potassium and magnesium salts (Perm krai, Russia). The strain grew within the temperature range from 5 to 35°C. At 5 and 32°C, the intracellular content of trehalose in the cells of Glutamicibacter sp. SMB32 was significantly higher than at 25°C. Glutamicibacter sp. SMB32 was able to grow both in the absence of NaCl and at its concentrations up to 11
Screening of ability to utilize benzoate as the sole carbon and energy source was carried out for 124 strains of the family Halomonadaceae (genera Halomonas, Chromohalobacter, Salinicola, and Kushneria) isolated from mining sites of the Upper Kama deposit of potassium and magnesium salts. Active growth on benzoate (in the presence of 30‒70 g/L NaCl) was shown for 28 Halomonas strains closely related to the species H. taeanensis, H. olivaria, H. ventosae, H. titanicae, H. alkaliantarctica, H. neptunia, H. radicis, and H. sulfidaeris. Strains of the genera Chromohalobacter, Salinicola, and Kushneria either did not grow on benzoate or carried out its transformation (two Chromohalobacter strains). PCR screening for the benA gene encoding the α-subunit of benzoate 1,2-dioxygenase (1,2-DO), the key enzyme for benzoate degradation, within the family Halomonadaceae revealed its presence in all benzoate-degrading Halomonas strains. The sequences of the amplified fragments had the highest similarity (not exceeding 95.50%) with the genes encoding the α-subunits of benzoate 1,2-DO, 2-chlorobenzoate 1,2-DO, and other dioxygenases of Halomonas strains containing Rieske-type [2Fe-2S] clusters. New data on the genetic systems regulating benzoate degradation in Halomonas isolates are of interest for better understanding of molecular mechanisms of aromatics degradation under salinization conditions. The isolated active benzoate degraders may be used to develop the technologies for bioremediation and monitoring of polluted soils.
Bacterial communities producing ectoine were studied in the rhizosphere of red goosefoot (Chenopodium rubrum L.) and weeping alkaligrass (Puccinellia distans (Jacq.) Parl.) growing on technogenic soil (Technosol) near the salt dump of the Solikamsk Potash Industrial Ore Administration 2 (SPIOA 2) of Uralkali PJSC (Solikamsk, Perm region) in order to assess the effect of this osmoprotective compound on plants under the conditions of technogenic salinization. It was found that most of bacteria in the studied soil are capable of synthesizing ectoine. The content of ectoine in the soil, as well as the number of producing bacteria, was higher in the rhizosphere than in the soil without plants. The concentration of ectoine was 167.4 ± 9.8 µmol/kg in the rhizosphere of red goosefoot, 92.9 ± 14.1 µmol/kg in the rhizosphere of weeping alkaligrass, and 23.9 ± 8.4 µmol/kg in the soil without plants. Bacteria belonging to the Pseudomonas genus predominated in the bacterial community of the rhizosphere of red goosefoot, and representatives of the Halomonas genus predominated in the rhizosphere of weeping alkaligrass. A stimulating effect on the growth of seedling roots under the conditions of salt stress was found for the following ectoine-producing strains: Halomonas sp. MK 2-1, Pseudomonas sp. BR 19-12, and Dietzia sp. PMK 9. The data obtained indicate the existence of positive effect of rhizosphere bacterial communities on plants under salinization due to the production of ectoine and may be used to develop biotechnologies that increase the productivity of plants growing on saline soils.
This article provides the first description of the bacterial diversity in the Permian rock of the Upper Pechora salt basin. Halophilic and halotolerant bacteria of the classes Gammaproteobacteria (from the genera Halomonas , Marinobacter , and Idiomarina) and Actinomycetia (from the genus Dietzia) were isolated from the brines extracted during the underground dissolution of carnallite rocks in the pilot well of the Yakshinskoe deposit (Komi Republic, Russia) of potassium-magnesium salts. The analysis of 16S rRNA gene sequences cloned from the total DNA of the floatable part of the insoluble brine resi-dues revealed the following bacterial classes: Gammaproteobacteria (closely related to the genera Idio-marina , Marinimicrobium , Marinobacter , Methylophaga , and Pseudidiomarina), Betaproteobacteria (phenologically similar to the genera Achromobacter and Methylotenera), as well as Alphaproteobacteria and Flavobacteriia (related to the genera Sulfitobacter and Salegentibacter , respectively). Several identified phy-lotypes (clones 113YS, 8YS, 150YS, and 157YS) had a low level of similarity with the closest type strains of the genera Methylophaga (M. nitratireducenticrescens JAM1T , 96.86%), Salegentibacter (S. salarius ISL-6T , 98.58%), and Methylotenera (M. versatilis 301T , 98.05% and 98.19%). This indicates that the brine samples contained new, previously undescribed, bacterial taxa. The results obtained define and shape the future prospects for studying the phylogenetic and functional diversity of microorganisms in the salt strata of the Yakshinskoe deposit.
Из глинистых отложений рассолоотводящих выработок и рассолосборников рудника Верхнекамского месторождения солей (Пермский край) было выделено 29 штаммов галофильных/галотолерантных бактерий. В результате филогенетического анализа, проведенного на основе сравнения последовательностей гена 16S рРНК, было установлено, что выделенные культуры являются представителями классов Gammaproteobacteria (семейств Halomonadaceae и Salinisphaeraceae) и Bacilli (семейства Bacillaceae). Три галофильных штамма SHV2, RV14 и SWV1 имели сходство с ближайшим типовым штаммом вида Salinisphaera hydrothermalis на уровне 95.94‒96.62% (ген 16S рРНК), что указывает на принадлежность этих штаммов к новому таксону. Большинство выделенных бактерий семейств Halomonadaceae и Bacillaceae являются экстремофилами: растут при рН 9‒10 и высокой солености среды (до 250‒270 г/л NaCl). У двух галофильных штаммов рода Halomonas обнаружена способность к деструкции салициловой и бензойной кислот (продуктов разложения полиароматических соединений), что делает их перспективными для использования в биотехнологиях восстановления загрязненных территорий с высоким уровнем минерализации.
29 strains of halophilic/halotolerant bacteria were isolated from clay deposits of brine-diverting workings and brine pits of the mine of the Verkhnekamsky salt deposit (Perm krai). As a result of phylogenetic analysis based on a comparison of the 16S rRNA gene sequences, it was found that the isolated cultures are representatives of the classes Gammaproteobacteria (Halomonadaceae and Salinisphaeraceae fami-lies) and Bacilli (family Bacillaceae). Three halophilic strains SHV2, RV14, and SWV1 were similar to the closest type strain of the Salinisphaera hydrothermalis species at the level of 95.94-96.62% (16S rRNA gene), which indicates that these strains belong to a new taxon. Most of the isolated bacteria of the families Halomonadaceae and Bacillaceae are extremophiles: they grow at pH 9-10 and high sa-linity (up to 250-270 g/L NaCl). Two halophilic strains of the genus Halomonas have been found to de-grade salicylic and benzoic acids (decomposition products of polyaromatic compounds), which makes them promising for use in biotechnologies for the restoration of contaminated areas with a high level of mineralization.
We have identified 25 halotolerant strains of ortho-phthalic acid (OPC) decomposer bacteria from samples of soil, sludge, and bottom sediments taken in the area of salt mining enterprises of Uralkalij (Berezniki, Russia). Based on an analysis of the 16S rRNA gene, the isolates were assigned to the genera Rhodococcus, Dietzia, Bacillus, Halomonas, Pseudomonas, Idiomarina, Stappia, Martelella, Erythrobacter, Alcanivorax, Marinobacter, Oceanisphaera, Nitratireductor, and Breoghania. Eight OPC decomposer strains are capable of using the phthalic acid esters Dibutyl phthalate (DBP) and Diethyl phthalate (DEP) as the sole source of carbon and energy. The strains utilized 90–98% of DBP and 49–80% of DEP (the phthalate concentration is 500 mg/L), both in the absence of NaCl in the cultivation medium and with a concentration in the medium of 50 g/L. An increase in the NaCl concentration in the medium to 70 and 90 g/L did not significantly affect the utilization of phthalates. The ability of bacteria of the genera Halomonas, Martelella, and Oceanisphaera to decompose DEF and DBP has been shown for the first time. Isolated phthalate (OPC, DEP and DBP) decomposer strains are promising for the development of new methods for the bioremediation of saline soils contaminated with phthalates.