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Topilina YS, Luk'yanova EA, Glukhova LB, Shurupova MN, Gerasimchuk AL, Frank YA, Antsiferov DV. Beneficial Effect of the New Leptodophora sp. Strain on Development of Blueberry Microclones in the Process of Their Adaptation. Microorganisms 2023; 11:1406. [PMID: 37374907 DOI: 10.3390/microorganisms11061406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
The paper searches for new solutions for the development of highbush blueberry orchards (Vaccinium corymbosum L. (1753)) in Western Siberia. All species of the genus Vaccinium display special symbiotic mycorrhizal associations with root systems-ericoid mycorrhiza, which essentially enhances the formation of adventitious and lateral roots. For the first time, we obtained pure cultures of micromycetes associated with the roots of wild species of the family Ericaceae in the Tomsk region, Russia. With regard to the data of molecular genetic analysis of the ITS region sequence, we selected the BR2-1 isolate based on its morphophysiological traits, which was assigned to the genus Leptodophora. Representatives of this genus typically enter into symbiotic relationships with heathers to form ericoid mycorrhizae. We studied the effect of strain BR2-1 on the development of microclones of the highbush blueberry var. Nord blue during their in vitro adaptation and showed its beneficial effect on growth and shoot formation in young plants. Experiments performed using submerged and solid-state methods showed that the most optimal method for commercial production of BR2-1 is cultivation on grain sterilized by boiling, followed by spore washing.
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Affiliation(s)
- Yulia S Topilina
- Biological Institute, National Research Tomsk State University, Lenina Ave., 36, 634050 Tomsk, Russia
- LLC Darwin, Str. Vysockogo Vladimira, 28, 634040 Tomsk, Russia
| | | | - Lubov B Glukhova
- Biological Institute, National Research Tomsk State University, Lenina Ave., 36, 634050 Tomsk, Russia
- LLC Darwin, Str. Vysockogo Vladimira, 28, 634040 Tomsk, Russia
| | - Margarita N Shurupova
- Biological Institute, National Research Tomsk State University, Lenina Ave., 36, 634050 Tomsk, Russia
| | - Anna L Gerasimchuk
- Biological Institute, National Research Tomsk State University, Lenina Ave., 36, 634050 Tomsk, Russia
| | - Yulia A Frank
- Biological Institute, National Research Tomsk State University, Lenina Ave., 36, 634050 Tomsk, Russia
- LLC Darwin, Str. Vysockogo Vladimira, 28, 634040 Tomsk, Russia
| | - Dmitry V Antsiferov
- Biological Institute, National Research Tomsk State University, Lenina Ave., 36, 634050 Tomsk, Russia
- LLC Darwin, Str. Vysockogo Vladimira, 28, 634040 Tomsk, Russia
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Frank YA, Vorobiev DS, Vorobiev ED, Samarinova AA, Antsiferov DV, Strezov V. Ability of benthic oligochaetes to bury microplastics in aquatic bottom sediments. Sci Total Environ 2023; 857:159687. [PMID: 36306841 DOI: 10.1016/j.scitotenv.2022.159687] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/05/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Yulia A Frank
- Biological Institute, Tomsk State University, Tomsk, Lenina Ave., 36, 634050, Russian Federation.
| | - Danil S Vorobiev
- Biological Institute, Tomsk State University, Tomsk, Lenina Ave., 36, 634050, Russian Federation
| | - Egor D Vorobiev
- Biological Institute, Tomsk State University, Tomsk, Lenina Ave., 36, 634050, Russian Federation
| | - Alisa A Samarinova
- Laboratory for Laser Molecular Imaging and Machine Learning, Tomsk State University, Lenina Ave., 36, 634050, Russian Federation
| | - Dmitry V Antsiferov
- Biological Institute, Tomsk State University, Tomsk, Lenina Ave., 36, 634050, Russian Federation
| | - Vladimir Strezov
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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Frank YA, Vorobiev ED, Babkina IB, Antsiferov DV, Vorobiev DS. Microplastics in fish gut, first records from the Tom River in West Siberia, Russia. Tomsk State University Journal of Biology 2020. [DOI: 10.17223/19988591/52/7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
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 <0.15 to 2.00 mm. The vast majority of detected microplastic particles (almost 80%) were less than 0.15 mm by their largest dimension. These data provide the first evidence of microplastics in fish from the Ob River system.
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Gerasimchuk AL, Ivasenko DA, Bukhtiyarova PA, Antsiferov DV, Frank YA. Search for new cultured lipophilic bacteria in industrial fat-containing wastes. BIO Web Conf 2020. [DOI: 10.1051/bioconf/20202302012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fat-containing wastes that are generated as a result of industrial production of food products and are being accumulated in large quantities in wastewater and sewage treatment plants and present a serious environmental problem. Microorganisms that decompose various types of lipids may be potential candidates for creation of commercial bioformulations for fat destruction. The aim of the study was to obtain pure cultures of lipophilic bacteria from fat-containing wastes, to study their diversity and activity for the development of a biological product. As a result, 30 strains of different phylogenetic groups with lipolytic activity was obtained. The most isolated strains were represented by enterobacteria and pseudomonas members within the Gammaproteobacteria. Almost half of the isolated strains were closely related to conditionally pathogenic microorganisms such as Serratia, Klebsiella etc. Non-pathogenic strains and promising for biotechnology ones belonged to Pseudomonas citronellolis, P. nitroreducens, P. synxantha, P. extremaustralis, Bacillus subtilis, B. amyloliquefaciens, Brevibacillus brevis and Microvirgula sp.
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Bukhtiyarova PA, Antsiferov DV, Brasseur G, Avakyan MR, Frank YA, Ikkert OP, Pimenov NV, Tuovinen OH, Karnachuk OV. Isolation, characterization, and genome insights into an anaerobic sulfidogenic Tissierella bacterium from Cu-bearing coins. Anaerobe 2019; 56:66-77. [PMID: 30776428 DOI: 10.1016/j.anaerobe.2019.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/27/2019] [Accepted: 02/14/2019] [Indexed: 01/19/2023]
Abstract
Recent reports on antimicrobial effects of metallic Cu prompted this study of anaerobic microbial communities on copper surfaces. Widely circulating copper-containing coinage was used as a potential source for microorganisms that had had human contact and were tolerant to copper. This study reports on the isolation, characterization, and genome of an anaerobic sulfidogenic Tissierella sp. P1from copper-containing brass coinage. Dissimilatory (bi)sulfite reductase dsrAB present in strain P1 genome and the visible absorbance around 630 nm in the cells suggested the presence of a desulfoviridin-type protein. However, the sulfate reduction rate measurements with 35SO42- did not confirm the dissimilatory sulfate reduction by the strain. The P1 genome lacks APS reductase, sulfate adenylyltransferase, DsrC, and DsrMK necessary for dissimilatory sulfate reduction. The isolate produced up to 0.79 mM H2S during growth, possibly due to cysteine synthase (CysK) and/or cysteine desulfhydrase (CdsH) activities, encoded in the genome. The strain can tolerate up to 2.4 mM Cu2+(150 mg/l) in liquid medium, shows affinity to metallic copper, and can survive on copper-containing coins up to three days under ambient air and dry conditions. The genome sequence of strain P1 contained cutC, encoding a copper resistance protein, which distinguishes it from all other Tissierella strains with published genomes.
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Affiliation(s)
- Polina A Bukhtiyarova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Dmitry V Antsiferov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Gael Brasseur
- Laboratoire de Chimie Bactérienne, CNRS, Mediterranean Institute of Microbiology, Marseille, France
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Yulia A Frank
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Olga P Ikkert
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Nikolay V Pimenov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia.
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Kadnikov VV, Mardanov AV, Ivasenko DA, Antsiferov DV, Beletsky AV, Karnachuk OV, Ravin NV. Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic microbial community. Sci Rep 2018; 8:6730. [PMID: 29712968 PMCID: PMC5928048 DOI: 10.1038/s41598-018-25146-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 04/17/2018] [Indexed: 12/05/2022] Open
Abstract
Thermal ecosystems associated with underground coal combustion sites are rare and less studied than geothermal features. Here we analysed microbial communities of near-surface ground layer and bituminous substance in an open quarry heated by subsurface coal fire by metagenomic DNA sequencing. Taxonomic classification revealed dominance of only a few groups of Firmicutes. Near-complete genomes of three most abundant species, ‘Candidatus Carbobacillus altaicus’ AL32, Brockia lithotrophica AL31, and Hydrogenibacillus schlegelii AL33, were assembled. According to the genomic data, Ca. Carbobacillus altaicus AL32 is an aerobic heterotroph, while B. lithotrophica AL31 is a chemolithotrophic anaerobe assimilating CO2 via the Calvin cycle. H. schlegelii AL33 is an aerobe capable of both growth on organic compounds and carrying out CO2 fixation via the Calvin cycle. Phylogenetic analysis of the large subunit of RuBisCO of B. lithotrophica AL31 and H. schlegelii AL33 showed that it belongs to the type 1-E. All three Firmicutes species can gain energy from aerobic or anaerobic oxidation of molecular hydrogen, produced as a result of underground coal combustion along with other coal gases. We propose that thermophilic Firmicutes, whose spores can spread from their original geothermal habitats over long distances, are the first colonizers of this recently formed thermal ecosystem.
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Affiliation(s)
- Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Denis A Ivasenko
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050, Tomsk, Russia
| | - Dmitry V Antsiferov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050, Tomsk, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050, Tomsk, Russia
| | - Nikolay V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.
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Mardanov AV, Panova IA, Beletsky AV, Avakyan MR, Kadnikov VV, Antsiferov DV, Banks D, Frank YA, Pimenov NV, Ravin NV, Karnachuk OV. Genomic insights into a new acidophilic, copper-resistantDesulfosporosinusisolate from the oxidized tailings area of an abandoned gold mine. FEMS Microbiol Ecol 2016; 92:fiw111. [DOI: 10.1093/femsec/fiw111] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 11/15/2022] Open
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