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To date, the largest Russian rivers discharging to the Arctic Ocean remain a “blank spot” on the world map of data on the distribution of microplastics in freshwater systems. This study characterizes the abundance and morphology of microplastics in surface water of the Ob River and its large tributary, the Tom River, in western Siberia. The average number of particles for the two rivers ranged from 44.2 to 51.2 items per m3 or from 79.4 to 87.5 μg per m3 in the Tom River and in the Ob River, respectively. Of the recovered microplastics, 93.5% were less than 1 mm in their largest dimension, the largest group (45.5% of total counts) consisted of particles with sizes range 0.30–1.00 mm. Generally, microfragments of irregular shape were the most abundant among the Ob and Tom samples (47.4%) and exceeded microfibers (22.1%), microfilms (20.8%), and microspheres (9.74%) by average counts. Results from this study provide a baseline for understanding the scale of the transport of microplastics by the Ob River system into the Arctic Ocean and add to currently available data on microplastics abundance and diversity in freshwater systems of differing global geographic locations.
Yulia Frank; Egor Vorobiev; Danil Vorobiev; Andrey Trifonov; Dmitry Antsiferov; Tina Soliman Hunter; Scott Wilson; Vladimir Strezov. Preliminary Screening for Microplastic Concentrations in the Surface Water of the Ob and Tom Rivers in Siberia, Russia. Sustainability 2020, 13, 80 .
AMA StyleYulia Frank, Egor Vorobiev, Danil Vorobiev, Andrey Trifonov, Dmitry Antsiferov, Tina Soliman Hunter, Scott Wilson, Vladimir Strezov. Preliminary Screening for Microplastic Concentrations in the Surface Water of the Ob and Tom Rivers in Siberia, Russia. Sustainability. 2020; 13 (1):80.
Chicago/Turabian StyleYulia Frank; Egor Vorobiev; Danil Vorobiev; Andrey Trifonov; Dmitry Antsiferov; Tina Soliman Hunter; Scott Wilson; Vladimir Strezov. 2020. "Preliminary Screening for Microplastic Concentrations in the Surface Water of the Ob and Tom Rivers in Siberia, Russia." Sustainability 13, no. 1: 80.
Small lakes in areas of intensive crude oil production may be susceptible to oil pollution arising from accidental spills and leaks, eventually leading to the pollution of bottom sediments. Effective cleaning of aquatic bottom sediments remains a challenge. Flotation is a potentially simple and reliable approach for the cleanup of bottom sediments without their excavation from the water body. Full-scale testing of flotation-based technology using the specially designed airlift plant allowed the cleaning of bottom sediments of an unnamed boreal lake (‘the lake’) within the Samotlor oil field, North Russia, heavily polluted with crude oil several decades ago. The lake bottom sediments are dominated by peat and unevenly polluted with oil. The average oil content in the lake bottom sediments was 111 g kg−1. During the 1.5 months' field test in July–August 2018, the average total oil concentration in the bottom sediments of the lake was reduced to 1.99 g kg−1. Secondary water contamination was minimal; the content of oil hydrocarbons in the water after completion of work did not exceed 0.09 ± 0.04 mg L−1. This study demonstrates that flotation-based technology can be applied for in situ cleaning of oil-contaminated lake bottom sediments including those in boreal climates.
Yulia A. Frank; Danil S. Vorobiev; Oleg E. Merzlyakov; Farid R. Sataev; Andrey A. Trifonov; Evgeny O. Kopylov; Konstantin V. Stryuk; Ekaterina A. Kalinovskaya; Sergey V. Gronskiy; Oleg V. Chibrikov; Vladislava V. Perminova; Yaroslav V. Branevskiy; Sergey P. Kulizhskiy; Tina Soliman Hunter. Cleaning of oil-polluted bottom sediments of the boreal lake, Samotlor oil field, North Russia: case report. Water Science and Technology 2020, 82, 3062 -3073.
AMA StyleYulia A. Frank, Danil S. Vorobiev, Oleg E. Merzlyakov, Farid R. Sataev, Andrey A. Trifonov, Evgeny O. Kopylov, Konstantin V. Stryuk, Ekaterina A. Kalinovskaya, Sergey V. Gronskiy, Oleg V. Chibrikov, Vladislava V. Perminova, Yaroslav V. Branevskiy, Sergey P. Kulizhskiy, Tina Soliman Hunter. Cleaning of oil-polluted bottom sediments of the boreal lake, Samotlor oil field, North Russia: case report. Water Science and Technology. 2020; 82 (12):3062-3073.
Chicago/Turabian StyleYulia A. Frank; Danil S. Vorobiev; Oleg E. Merzlyakov; Farid R. Sataev; Andrey A. Trifonov; Evgeny O. Kopylov; Konstantin V. Stryuk; Ekaterina A. Kalinovskaya; Sergey V. Gronskiy; Oleg V. Chibrikov; Vladislava V. Perminova; Yaroslav V. Branevskiy; Sergey P. Kulizhskiy; Tina Soliman Hunter. 2020. "Cleaning of oil-polluted bottom sediments of the boreal lake, Samotlor oil field, North Russia: case report." Water Science and Technology 82, no. 12: 3062-3073.
This preliminary study investigated the abundance of microplastic particles in gastrointestinal tracts of the dace (Leuciscus leuciscus L.) from the Tom River, a large tributary of the Ob River in West Siberia. A total of 13 dace specimens of 2+ to 4+ years of age were studied. Microplastic particles extracted from fish guts were counted and classified by shapes and sizes. In average 204 ± 28.7 items of microplastics were detected for one dace specimen. Microplastic particles were categorized as fragments of irregular shape (70%), spheres (16%), films (7%) and fibers (7%), with size ranging from
Yulia A. Frank; Egor D. Vorobiev; Irina B. Babkina; Dmitry V. Antsiferov; Danil S. Vorobiev; Tomsk Darwin Llc; Russian Federation) Darwin Llc (Tomsk. Microplastics in fish gut, first records from the Tom River in West Siberia, Russia. Vestnik Tomskogo gosudarstvennogo universiteta. Biologiya 2020, 130 -139.
AMA StyleYulia A. Frank, Egor D. Vorobiev, Irina B. Babkina, Dmitry V. Antsiferov, Danil S. Vorobiev, Tomsk Darwin Llc, Russian Federation) Darwin Llc (Tomsk. Microplastics in fish gut, first records from the Tom River in West Siberia, Russia. Vestnik Tomskogo gosudarstvennogo universiteta. Biologiya. 2020; (52):130-139.
Chicago/Turabian StyleYulia A. Frank; Egor D. Vorobiev; Irina B. Babkina; Dmitry V. Antsiferov; Danil S. Vorobiev; Tomsk Darwin Llc; Russian Federation) Darwin Llc (Tomsk. 2020. "Microplastics in fish gut, first records from the Tom River in West Siberia, Russia." Vestnik Tomskogo gosudarstvennogo universiteta. Biologiya , no. 52: 130-139.
A. P. Lukina; Yu. A. Frank; Denis Ivasenko; L. B. Glukhova; E. V. Danilova; Marat Avakyan; O. V. Karnachuk. Isolation of New Thermophilic Sulfidogens from Microbial Mat Associated with Groundwater Discharge in the Tunkin Valley. Microbiology 2019, 88, 642 -645.
AMA StyleA. P. Lukina, Yu. A. Frank, Denis Ivasenko, L. B. Glukhova, E. V. Danilova, Marat Avakyan, O. V. Karnachuk. Isolation of New Thermophilic Sulfidogens from Microbial Mat Associated with Groundwater Discharge in the Tunkin Valley. Microbiology. 2019; 88 (5):642-645.
Chicago/Turabian StyleA. P. Lukina; Yu. A. Frank; Denis Ivasenko; L. B. Glukhova; E. V. Danilova; Marat Avakyan; O. V. Karnachuk. 2019. "Isolation of New Thermophilic Sulfidogens from Microbial Mat Associated with Groundwater Discharge in the Tunkin Valley." Microbiology 88, no. 5: 642-645.
Viral particles have been detected in the underground biosphere where they could be one of the main factors impacting microbial diversity, biogeochemistry and evolution. To characterize the viral component in the deep subsurface biosphere, we sequenced the metagenome of subsurface aquifer located in the Tomsk region of Russia, sampled via 2.8-km-deep borehole 5P. The de novo assembly of metagenomics sequences yielded three circular genomes assigned to bacteriophages of the order Caudovirales. The annotated genome sequences of these bacteriophages have been deposited in the GenBank database under the accession numbers MK113949, MK113950 and MK113951.
Vitaly V. Kadnikov; Andrey V. Mardanov; Yulia A. Frank; Alexey V. Beletsky; Olga V. Karnachuk; Nikolai V. Ravin. Genomes of three bacteriophages from the deep subsurface aquifer. Data in Brief 2018, 22, 488 -491.
AMA StyleVitaly V. Kadnikov, Andrey V. Mardanov, Yulia A. Frank, Alexey V. Beletsky, Olga V. Karnachuk, Nikolai V. Ravin. Genomes of three bacteriophages from the deep subsurface aquifer. Data in Brief. 2018; 22 ():488-491.
Chicago/Turabian StyleVitaly V. Kadnikov; Andrey V. Mardanov; Yulia A. Frank; Alexey V. Beletsky; Olga V. Karnachuk; Nikolai V. Ravin. 2018. "Genomes of three bacteriophages from the deep subsurface aquifer." Data in Brief 22, no. : 488-491.
Almost all the known isolates of acidophilic or acid-tolerant sulphate-reducing bacteria (SRB) belong to the spore-forming genus Desulfosporosinus in the Firmicutes. The objective of this study was to isolate acidophilic/acid-tolerant members of the genus Desulfovibrio belonging to deltaproteobacterial SRB. The sample material originated from microbial mat biomass submerged in mine water and was enriched for sulphate reducers by cultivation in anaerobic medium with lactate as an electron donor. A stirred tank bioreactor with the same medium composition was inoculated with the sulphidogenic enrichment. The bioreactor was operated with a temporal pH gradient, changing daily, from an initial pH of 7.3 to a final pH of 3.7. Among the bacteria in the bioreactor culture, Desulfovibrio was the only SRB group retrieved from the bioreactor consortium as observed by 16S rRNA-targeted denaturing gradient gel electrophoresis. Moderately acidophilic/acid-tolerant isolates belonged to Desulfovibrio aerotolerans-Desulfovibrio carbinophilus-Desulfovibrio magneticus and Desulfovibrio idahonensis-Desulfovibrio mexicanus clades within the genus Desulfovibrio. A moderately acidophilic strain, Desulfovibrio sp. VK (pH optimum 5.7) and acid-tolerant Desulfovibrio sp. ED (pH optimum 6.6) dominated in the bioreactor consortium at different time points and were isolated in pure culture.
Dmitry Antsiferov; Tatiana S. Fyodorova; Anastasia A. Kovalyova; Anastasia Lukina; Yulia A. Frank; Marat Avakyan; David Banks; Olli H. Tuovinen; Olga V. Karnachuk. Selection for novel, acid-tolerant Desulfovibrio spp. from a closed Transbaikal mine site in a temporal pH-gradient bioreactor. Antonie van Leeuwenhoek 2017, 110, 1669 -1679.
AMA StyleDmitry Antsiferov, Tatiana S. Fyodorova, Anastasia A. Kovalyova, Anastasia Lukina, Yulia A. Frank, Marat Avakyan, David Banks, Olli H. Tuovinen, Olga V. Karnachuk. Selection for novel, acid-tolerant Desulfovibrio spp. from a closed Transbaikal mine site in a temporal pH-gradient bioreactor. Antonie van Leeuwenhoek. 2017; 110 (12):1669-1679.
Chicago/Turabian StyleDmitry Antsiferov; Tatiana S. Fyodorova; Anastasia A. Kovalyova; Anastasia Lukina; Yulia A. Frank; Marat Avakyan; David Banks; Olli H. Tuovinen; Olga V. Karnachuk. 2017. "Selection for novel, acid-tolerant Desulfovibrio spp. from a closed Transbaikal mine site in a temporal pH-gradient bioreactor." Antonie van Leeuwenhoek 110, no. 12: 1669-1679.
V. V. Kadnikov; Yu. A. Frank; Andrey Mardanov; A. V. Beletskii; Denis Ivasenko; N. V. Pimenov; O. V. Karnachuk; Nikolai Ravin. Uncultured bacteria and methanogenic archaea predominate in the microbial community of Western Siberian deep subsurface aquifer. Microbiology 2017, 86, 412 -415.
AMA StyleV. V. Kadnikov, Yu. A. Frank, Andrey Mardanov, A. V. Beletskii, Denis Ivasenko, N. V. Pimenov, O. V. Karnachuk, Nikolai Ravin. Uncultured bacteria and methanogenic archaea predominate in the microbial community of Western Siberian deep subsurface aquifer. Microbiology. 2017; 86 (3):412-415.
Chicago/Turabian StyleV. V. Kadnikov; Yu. A. Frank; Andrey Mardanov; A. V. Beletskii; Denis Ivasenko; N. V. Pimenov; O. V. Karnachuk; Nikolai Ravin. 2017. "Uncultured bacteria and methanogenic archaea predominate in the microbial community of Western Siberian deep subsurface aquifer." Microbiology 86, no. 3: 412-415.
The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of five years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50oC. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surface flow. Community analysis by PCR-DGGE 16S rRNA genes profiling, repeatedly performed within five years, revealed several dominating phylotypes consistently found in the borehole water, and highly variable diversity of prokaryotes, brought to the surface with the borehole outflow. The major planktonic components of the microbial community were Desulfovirgula thermocuniculi and Methanothermobacter spp. The composition of the minor part of the community was unstable, and molecular analysis did not reveal any regularity in its variations, except some predominance of uncultured Firmicutes. Batch cultures with complex organic substrates inoculated with water samples were set in order to enrich prokaryotes from the variable part of the community. PCR-DGGE analysis of these enrichments yielded uncultured Firmicutes, Chloroflexi, and Ignavibacteriae. A continuous-flow microaerophilic enrichment culture with a water sample amended with acetate contained Hydrogenophilus thermoluteolus, which was previously detected in the microbial mat developing at the outflow of the borehole. Cultivation results allowed us to assume that variable components of the 3P well community are hydrolytic organotrophs, degrading buried biopolymers, while the constant planktonic components of the community degrade dissolved fermentation products to methane and CO2, possibly via interspecies hydrogen transfer. Occasional washout of minor community components capable of oxygen respiration leads to the development of microbial mats at the outflow of the borehole where residual dissolved fermentation products are aerobically oxidized. Long-term community analysis with the combination of molecular and cultivation techniques allowed us to characterize stable and variable parts of the community and propose their environmental roles.
Yulia A. Frank; Vitaly V. Kadnikov; Sergey N. Gavrilov; David Banks; Anna L. Gerasimchuk; Olga A. Podosokorskaya; Alexander Y. Merkel; Nikolai A. Chernyh; Andrey Mardanov; Nikolai Ravin; Olga Karnachuk; Elizaveta A. Bonch-Osmolovskaya. Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study. Frontiers in Microbiology 2016, 7, 2101 .
AMA StyleYulia A. Frank, Vitaly V. Kadnikov, Sergey N. Gavrilov, David Banks, Anna L. Gerasimchuk, Olga A. Podosokorskaya, Alexander Y. Merkel, Nikolai A. Chernyh, Andrey Mardanov, Nikolai Ravin, Olga Karnachuk, Elizaveta A. Bonch-Osmolovskaya. Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study. Frontiers in Microbiology. 2016; 7 ():2101.
Chicago/Turabian StyleYulia A. Frank; Vitaly V. Kadnikov; Sergey N. Gavrilov; David Banks; Anna L. Gerasimchuk; Olga A. Podosokorskaya; Alexander Y. Merkel; Nikolai A. Chernyh; Andrey Mardanov; Nikolai Ravin; Olga Karnachuk; Elizaveta A. Bonch-Osmolovskaya. 2016. "Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study." Frontiers in Microbiology 7, no. : 2101.
Members of the genus Thermodesulfovibrio belong to the Nitrospirae phylum and all isolates characterized to date are neutrophiles. They have been isolated from terrestrial hot springs and thermophilic methanogenic anaerobic sludges. Their molecular signatures have, however, also been detected in deep subsurface. The purpose of this study was to characterize and analyze the genome of a newly isolated, moderately alkaliphilic Thermodesulfovibrio from a 2 km deep aquifer system in Western Siberia, Russia. The new isolate, designated N1, grows optimally at pH 8.5-9.0 and at 65 ºC. It is able to reduce sulfate, thiosulfate or sulfite with a limited range of electron donors such as formate, pyruvate and lactate. Analysis of the 1.93 Mb draft genome of strain N1 revealed that it contains a set of genes for dissimilatory sulfate reduction, including sulfate adenyltransferase, adenosine-5'-phosphosulfate reductase AprAB, membrane-bound electron transfer complex QmoABC, dissimilatory sulfite reductase DsrABC and sulfite reductase-associated electron transfer complex DsrMKJOP. Hydrogen turnover is enabled by soluble cytoplasmic, membrane-linked, and soluble periplasmic hydrogenases and a periplasmic formate dehydrogenase. The use of thiosulfate as an electron acceptor is enabled by a membrane-linked molybdopterin oxidoreductase. The N1 requirement for organic carbon sources corresponds to the lack of the autotrophic C1-fixation pathways. Comparative analysis of the genomes of Thermodesulfovibrio (T. yellowstonii, T. islandicus, T. аggregans, T. thiophilus, and strain N1) revealed a low overall genetic diversity and several adaptive traits. Consistent with an alkaliphilic lifestyle, a multisubunit Na+/H+ antiporter of the Mnh family is encoded in the Thermodesulfovibrio strain N1 genome. Nitrogenase genes were found in T. yellowstonii, T. aggregans, and T. islandicus, nitrate reductase in T. islandicus, and cellulose synthetase in T. aggregans and strain N1. Overall, our results provide genomic insights into metabolism of the Thermodesulfovibrio lineage in microbial communities of the deep subsurface biosphere
Yulia A. Frank; Vitaly V. Kadnikov; Anastasia P. Lukina; David Banks; Alexey Beletsky; Andrey Mardanov; Elena I. Sen’Kina; Marat Avakyan; Olga Karnachuk; Nikolai V. Ravin. Characterization and Genome Analysis of the First Facultatively Alkaliphilic Thermodesulfovibrio Isolated from the Deep Terrestrial Subsurface. Frontiers in Microbiology 2016, 7, 2000 .
AMA StyleYulia A. Frank, Vitaly V. Kadnikov, Anastasia P. Lukina, David Banks, Alexey Beletsky, Andrey Mardanov, Elena I. Sen’Kina, Marat Avakyan, Olga Karnachuk, Nikolai V. Ravin. Characterization and Genome Analysis of the First Facultatively Alkaliphilic Thermodesulfovibrio Isolated from the Deep Terrestrial Subsurface. Frontiers in Microbiology. 2016; 7 ():2000.
Chicago/Turabian StyleYulia A. Frank; Vitaly V. Kadnikov; Anastasia P. Lukina; David Banks; Alexey Beletsky; Andrey Mardanov; Elena I. Sen’Kina; Marat Avakyan; Olga Karnachuk; Nikolai V. Ravin. 2016. "Characterization and Genome Analysis of the First Facultatively Alkaliphilic Thermodesulfovibrio Isolated from the Deep Terrestrial Subsurface." Frontiers in Microbiology 7, no. : 2000.
Microbial sulfate reduction in acid mine drainage is still considered to be confined to anoxic conditions, although several reports have shown that sulfate-reducing bacteria (SRB) occur under microaerophilic or aerobic conditions. We have measured sulfate reduction rates of up to 60 nmol S cm−3day−1 in oxidized layers of gold mine tailings in Kuzbass (SW Siberia). A novel, acidophilic, copper-tolerant Desulfosporosinus sp. I2 was isolated from the same sample and its genome was sequenced. The genomic analysis and physiological data indicate the involvement of transporters and additional mechanisms to tolerate metals, such as sequestration by polyphosphates. Desulfosporinus sp. I2 encodes systems for a metabolically versatile life style. The genome possessed a complete Embden-Meyerhof pathway for glycolysis and gluconeogenesis. Complete oxidation of organic substrates could be enabled by the complete TCA cycle. Genomic analysis found all major components of the electron transfer chain necessary for energy generation via oxidative phosphorylation. Autotrophic CO2 fixation could be performed through the Wood-Ljungdahl pathway. Multiple oxygen detoxification systems were identified in the genome. Taking into account the metabolic activity and genomic analysis, the traits of the novel isolate broaden our understanding of active sulfate reduction and associated metabolism beyond strictly anaerobic niches.
Andrey Mardanov; Irina Panova; Alexey Beletsky; Marat Avakyan; Vitaly V. Kadnikov; Dmitry Antsiferov; David Banks; Yulia A. Frank; Nikolay V. Pimenov; Nikolai Ravin; Olga V. Karnachuk. Genomic insights into a new acidophilic, copper-resistantDesulfosporosinusisolate from the oxidized tailings area of an abandoned gold mine. FEMS Microbiology Ecology 2016, 92, fiw111 .
AMA StyleAndrey Mardanov, Irina Panova, Alexey Beletsky, Marat Avakyan, Vitaly V. Kadnikov, Dmitry Antsiferov, David Banks, Yulia A. Frank, Nikolay V. Pimenov, Nikolai Ravin, Olga V. Karnachuk. Genomic insights into a new acidophilic, copper-resistantDesulfosporosinusisolate from the oxidized tailings area of an abandoned gold mine. FEMS Microbiology Ecology. 2016; 92 (8):fiw111.
Chicago/Turabian StyleAndrey Mardanov; Irina Panova; Alexey Beletsky; Marat Avakyan; Vitaly V. Kadnikov; Dmitry Antsiferov; David Banks; Yulia A. Frank; Nikolay V. Pimenov; Nikolai Ravin; Olga V. Karnachuk. 2016. "Genomic insights into a new acidophilic, copper-resistantDesulfosporosinusisolate from the oxidized tailings area of an abandoned gold mine." FEMS Microbiology Ecology 92, no. 8: fiw111.
The paper describes a complex novel airlift plant for the simultaneous cleaning of water reservoir bottom sediments and water. The plant's design was tested in a model. Chemical analysis of the bottom sediments after experimental cleaning revealed a total oil content of 0.40–0.45 g kg−1, while the estimated initial oil content was around 16 g kg−1. This indicates a 35.5–40.0 times decrease in oil content.
Danil S. Vorobiev; Yulia A. Frank; Yury Noskov; Oleg E. Merzlyakov; Sergey P. Kulizhskiy. Novel technological solution for oil decontamination of bottom sediments. Water Practice and Technology 2016, 11, 139 -143.
AMA StyleDanil S. Vorobiev, Yulia A. Frank, Yury Noskov, Oleg E. Merzlyakov, Sergey P. Kulizhskiy. Novel technological solution for oil decontamination of bottom sediments. Water Practice and Technology. 2016; 11 (1):139-143.
Chicago/Turabian StyleDanil S. Vorobiev; Yulia A. Frank; Yury Noskov; Oleg E. Merzlyakov; Sergey P. Kulizhskiy. 2016. "Novel technological solution for oil decontamination of bottom sediments." Water Practice and Technology 11, no. 1: 139-143.
Dissimilatory sulfate reduction plays an important role in removal of dissolved metals from acidic mine waters. Although this process was convincingly shown to occur in acidic waste of metal recovery, few isolates of acidophilic/acid-tolerant sulfate reducers are known. We isolated a new acidophilic sulfidogen, strain BG, from the oxidized acidic waste of the Bom-Gorkhon tungsten deposit, Transbaikalia, Russia. Phylogenetic analysis of its 16S rRNA gene sequence made it possible to identify it as a member of the genus Desulfosporosinus. Unlike other known acidophilic sulfate reducers of this genus, strain BG was tolerant to high copper concentrations (up to 5 g/L), could grow on organic acids at low ambient pH, and formed crystalline copper sulfides (covellite and chalcopyrite). Molecular analysis of the phylotypes predominating in oxidized waste and in enrichment cultures confirmed the presence of various Desulfosporosinus strains.
O. V. Karnachuk; I. A. Kurganskaya; Marat Avakyan; Y. A. Frank; O. P. Ikkert; Roman Filenko; E. V. Danilova; N. V. Pimenov. An acidophilic Desulfosporosinus isolated from the oxidized mining wastes in the Transbaikal area. Microbiology 2015, 84, 677 -686.
AMA StyleO. V. Karnachuk, I. A. Kurganskaya, Marat Avakyan, Y. A. Frank, O. P. Ikkert, Roman Filenko, E. V. Danilova, N. V. Pimenov. An acidophilic Desulfosporosinus isolated from the oxidized mining wastes in the Transbaikal area. Microbiology. 2015; 84 (5):677-686.
Chicago/Turabian StyleO. V. Karnachuk; I. A. Kurganskaya; Marat Avakyan; Y. A. Frank; O. P. Ikkert; Roman Filenko; E. V. Danilova; N. V. Pimenov. 2015. "An acidophilic Desulfosporosinus isolated from the oxidized mining wastes in the Transbaikal area." Microbiology 84, no. 5: 677-686.
Yulia Frank; David Banks; Marat Avakyan; Dmitry Antsiferov; Petr Kadychagov; Olga Karnachuk. Firmicutesis an Important Component of Microbial Communities in Water-Injected and Pristine Oil Reservoirs, Western Siberia, Russia. Geomicrobiology Journal 2015, 33, 387 -400.
AMA StyleYulia Frank, David Banks, Marat Avakyan, Dmitry Antsiferov, Petr Kadychagov, Olga Karnachuk. Firmicutesis an Important Component of Microbial Communities in Water-Injected and Pristine Oil Reservoirs, Western Siberia, Russia. Geomicrobiology Journal. 2015; 33 (5):387-400.
Chicago/Turabian StyleYulia Frank; David Banks; Marat Avakyan; Dmitry Antsiferov; Petr Kadychagov; Olga Karnachuk. 2015. "Firmicutesis an Important Component of Microbial Communities in Water-Injected and Pristine Oil Reservoirs, Western Siberia, Russia." Geomicrobiology Journal 33, no. 5: 387-400.
O. V. Karnachuk; S. N. Gavrilov; Marat Avakyan; O. A. Podosokorskaya; Yu. A. Frank; E. A. Bonch-Osmolovskaya; I. V. Kublanov. Diversity of copper proteins and copper homeostasis systems in Melioribacter roseus, a facultatively anaerobic thermophilic member of the new phylum Ignavibacteriae. Microbiology 2015, 84, 135 -143.
AMA StyleO. V. Karnachuk, S. N. Gavrilov, Marat Avakyan, O. A. Podosokorskaya, Yu. A. Frank, E. A. Bonch-Osmolovskaya, I. V. Kublanov. Diversity of copper proteins and copper homeostasis systems in Melioribacter roseus, a facultatively anaerobic thermophilic member of the new phylum Ignavibacteriae. Microbiology. 2015; 84 (2):135-143.
Chicago/Turabian StyleO. V. Karnachuk; S. N. Gavrilov; Marat Avakyan; O. A. Podosokorskaya; Yu. A. Frank; E. A. Bonch-Osmolovskaya; I. V. Kublanov. 2015. "Diversity of copper proteins and copper homeostasis systems in Melioribacter roseus, a facultatively anaerobic thermophilic member of the new phylum Ignavibacteriae." Microbiology 84, no. 2: 135-143.
Using aquatic worms (Oligochaeta: Tubificidae) for oil decontamination of bottom sediments has been first considered. In a set of experiments on Claparede, 1862, worms survived the exposure to oil content as high as 16.72 g/kg; they died of natural causes. Vigorous silt agitation by worms (bioturbation) was observed: the silt layer thickened as compared with that in reference aquaria without worms. Besides, it tended to thicken with increasing oil content of sediments. Within 30 days reduced oil content by 1.20 to 1.72 times, or by 16.67 to 41.90% (a<0.05), compared with that in reference aquaria.
D. S. Vorob’Ev; Yu. A. Frank; S. V. Lushnikov; N. A. Zaloznyi; Yury Noskov. Oil decontamination of bottom sediments using Limnodrilus hoffmeisteri (Oligochaeta: Tubificidae). Contemporary Problems of Ecology 2010, 3, 15 -18.
AMA StyleD. S. Vorob’Ev, Yu. A. Frank, S. V. Lushnikov, N. A. Zaloznyi, Yury Noskov. Oil decontamination of bottom sediments using Limnodrilus hoffmeisteri (Oligochaeta: Tubificidae). Contemporary Problems of Ecology. 2010; 3 (1):15-18.
Chicago/Turabian StyleD. S. Vorob’Ev; Yu. A. Frank; S. V. Lushnikov; N. A. Zaloznyi; Yury Noskov. 2010. "Oil decontamination of bottom sediments using Limnodrilus hoffmeisteri (Oligochaeta: Tubificidae)." Contemporary Problems of Ecology 3, no. 1: 15-18.
The distribution and activity of sulfate-reducing bacteria (SRB) in the water column of the alpine meromictic Gek-Gel lake were studied. Apart from traditional microbiological methods based on cultivation and on measuring the process rates with radioactive labels, in situ fluorescent hybridization (FISH) was used, which enables identification and quantification without cultivating organisms. The peak rate of sulfate reduction, 0.486 µg S 1−1 day−1, was found in the chemocline at 33 m. The peak SRB number of 2.5×106 cells/ml, as determined by the most probable number method on selective media, was found at the same depth. The phylogenetic affiliation of the SRB, as determined by FISH, revealed the predominance of the Desulfovibrio spp., Desulfobulbus spp., and Desulfoarculus spp./Desulfomonile spp. groups. The numbers of spore-forming Desulfotomaculum spp. increased with depth. The low measured rates of sulfate reduction accompanied by high SRB numbers and the predominance of the groups capable of reducing a wide range of substrates permit us to assume utilization of electron acceptors other than sulfate as the main activity of the SRB in the water column.
O. V. Karnachuk; N. V. Pimenov; S. K. Yusupov; Yu. A. Frank; Ya. A. Puhakka; M. V. Ivanov. Distribution, diversity, and activity of sulfate-reducing bacteria in the water column in Gek-Gel lake, Azerbaijan. Microbiology 2006, 75, 82 -89.
AMA StyleO. V. Karnachuk, N. V. Pimenov, S. K. Yusupov, Yu. A. Frank, Ya. A. Puhakka, M. V. Ivanov. Distribution, diversity, and activity of sulfate-reducing bacteria in the water column in Gek-Gel lake, Azerbaijan. Microbiology. 2006; 75 (1):82-89.
Chicago/Turabian StyleO. V. Karnachuk; N. V. Pimenov; S. K. Yusupov; Yu. A. Frank; Ya. A. Puhakka; M. V. Ivanov. 2006. "Distribution, diversity, and activity of sulfate-reducing bacteria in the water column in Gek-Gel lake, Azerbaijan." Microbiology 75, no. 1: 82-89.
The purpose of this study was to characterize the distribution and activity of sulfate-reducing bacteria in tailings and sediments impacted by effluents from mining and smelting operations in the Norilsk area in northern Siberia. The Norilsk mining complex involves three smelter operations, a hydrometallurgical plant, and extensive tailings areas located in the permafrost zone. Sulfate reduction rates measured with a 35SO42− tracer technique under various in-situ conditions ranged from 0.05 to 30 nmol S cm−3 day−1. Acetate and glucose addition greatly stimulated sulfate reduction, whereas lactate had less effect. The most pronounced stimulation of sulfate reduction (6.5-fold) was observed with phosphate amendment. Most-probable-number (MPN) counts of sulfate-reducing bacteria in media with glucose, ethanol, lactate, and acetate as electron donors were generally highest at around 107 cells ml−1. The actual MPN counts varied with the sample, electron donor, and incubation conditions (pH 7.2 vs. pH 3.5; 28°C vs. 4°C). Enrichment cultures of sulfate-reducing bacteria were established from a sample that showed the highest rate of sulfate reduction. After multiple serial transfers, the dominant sulfate-reducers were identified by fluorescence in situ hybridization using genus and group-specific 16S rRNA-targeted oligonucleotide probes. Desulfobulbus spp. prevailed in ethanol and lactate enrichments and the Desulfosarcina-Desulfococcus group dominated in acetate and benzoate enrichments. Psychrophilic Desulfotalea-Desulfofustis and moderately psychrophilic Desulforhopalus spp. were identified in enrichments incubated at 4°C, but they were also found in mesophilic enrichments.
Olga Karnachuk; Nikolay V. Pimenov; Sandjar K. Yusupov; Yulia A. Frank; Anna Kaksonen; Jaakko A. Puhakka; Mikhail V. Ivanov; E. Börje Lindström; Olli H. Tuovinen. Sulfate Reduction Potential in Sediments in the Norilsk Mining Area, Northern Siberia. Geomicrobiology Journal 2005, 22, 11 -25.
AMA StyleOlga Karnachuk, Nikolay V. Pimenov, Sandjar K. Yusupov, Yulia A. Frank, Anna Kaksonen, Jaakko A. Puhakka, Mikhail V. Ivanov, E. Börje Lindström, Olli H. Tuovinen. Sulfate Reduction Potential in Sediments in the Norilsk Mining Area, Northern Siberia. Geomicrobiology Journal. 2005; 22 (1-2):11-25.
Chicago/Turabian StyleOlga Karnachuk; Nikolay V. Pimenov; Sandjar K. Yusupov; Yulia A. Frank; Anna Kaksonen; Jaakko A. Puhakka; Mikhail V. Ivanov; E. Börje Lindström; Olli H. Tuovinen. 2005. "Sulfate Reduction Potential in Sediments in the Norilsk Mining Area, Northern Siberia." Geomicrobiology Journal 22, no. 1-2: 11-25.
A sulfate-reducing bacterium, designated as strain R2, was isolated from wastewater of a ball-bearing manufacturing facility in Tomsk, Western Siberia. This isolate was resistant up to 800 mg Cu/l in the growth medium. By comparison, Cu-resistance of reference cultures of sulfate-reducing bacteria ranged from 50 to 75 mg Cu/l. Growth experiments with strain R2 showed that Cu was an essential trace element and, on one hand, enhanced growth at concentrations up to 10 mg/l but, on the other hand, the growth rate decreased and lag-period extended at copper concentrations of >50 mg/l. Phenotypic characteristics and a 1078 bp nucleotide sequence of the 16S rDNA placed strain R2 within the genus Desulfovibrio. Desulfovibrio R2 carried at least one plasmid of approximately of 23.1 kbp. A 636 bp fragment of the pcoR gene of the pco operon that encodes Cu resistance was amplified by PCR from plasmid DNA of strain R2. The pco genes are involved in Cu-resistance in some enteric and aerobic soil bacteria. Desulfovibrio R2 is a prospective strain for bioremediation purposes and for developing a homologous system for transformation of Cu-resistance in sulfate-reducing bacteria.
Olia V. Karnachuk; Svetlana Y. Kurochkina; Duongruitai Nicomrat; Yulia A. Frank; Denis Ivasenko; Elena A. Phyllipenko; Olli H. Tuovinen. Copper resistance in Desulfovibrio strain R2. Antonie van Leeuwenhoek 2003, 83, 99 -106.
AMA StyleOlia V. Karnachuk, Svetlana Y. Kurochkina, Duongruitai Nicomrat, Yulia A. Frank, Denis Ivasenko, Elena A. Phyllipenko, Olli H. Tuovinen. Copper resistance in Desulfovibrio strain R2. Antonie van Leeuwenhoek. 2003; 83 (1):99-106.
Chicago/Turabian StyleOlia V. Karnachuk; Svetlana Y. Kurochkina; Duongruitai Nicomrat; Yulia A. Frank; Denis Ivasenko; Elena A. Phyllipenko; Olli H. Tuovinen. 2003. "Copper resistance in Desulfovibrio strain R2." Antonie van Leeuwenhoek 83, no. 1: 99-106.