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101. Gausemycins A,B: Cyclic Lipoglycopeptides from Streptomyces sp.**

Author

Tyurin, Anton P., primary, Alferova, Vera A., additional, Paramonov, Alexander S., additional, Shuvalov, Maxim V., additional, Kudryakova, Gulnara K., additional, Rogozhin, Eugene A., additional, Zherebker, Alexander Y., additional, Brylev, Vladimir A., additional, Chistov, Alexey A., additional, Baranova, Anna A., additional, Biryukov, Mikhail V., additional, Ivanov, Igor A., additional, Prokhorenko, Igor A., additional, Grammatikova, Natalia E., additional, Kravchenko, Tatyana V., additional, Isakova, Elena B., additional, Mirchink, Elena P., additional, Gladkikh, Elena G., additional, Svirshchevskaya, Elena V., additional, Mardanov, Andrey V., additional, Beletsky, Aleksey V., additional, Kocharovskaya, Milita V., additional, Kulyaeva, Valeriya V., additional, Shashkov, Alexander S., additional, Tsvetkov, Dmitry E., additional, Nifantiev, Nikolay E., additional, Apt, Alexander S., additional, Majorov, Konstantin B., additional, Efimova, Svetlana S., additional, Ravin, Nikolai V., additional, Nikolaev, Evgeny N., additional, Ostroumova, Olga S., additional, Katrukha, Genrikh S., additional, Lapchinskaya, Olda A., additional, Dontsova, Olga A., additional, Terekhov, Stanislav S., additional, Osterman, Ilya A., additional, Shenkarev, Zakhar O., additional, and Korshun, Vladimir A., additional

Published
2021
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102. Innentitelbild: Gausemycins A,B: Cyclic Lipoglycopeptides from Streptomyces sp. (Angew. Chem. 34/2021)

Author

Tyurin, Anton P., primary, Alferova, Vera A., additional, Paramonov, Alexander S., additional, Shuvalov, Maxim V., additional, Kudryakova, Gulnara K., additional, Rogozhin, Eugene A., additional, Zherebker, Alexander Y., additional, Brylev, Vladimir A., additional, Chistov, Alexey A., additional, Baranova, Anna A., additional, Biryukov, Mikhail V., additional, Ivanov, Igor A., additional, Prokhorenko, Igor A., additional, Grammatikova, Natalia E., additional, Kravchenko, Tatyana V., additional, Isakova, Elena B., additional, Mirchink, Elena P., additional, Gladkikh, Elena G., additional, Svirshchevskaya, Elena V., additional, Mardanov, Andrey V., additional, Beletsky, Aleksey V., additional, Kocharovskaya, Milita V., additional, Kulyaeva, Valeriya V., additional, Shashkov, Alexander S., additional, Tsvetkov, Dmitry E., additional, Nifantiev, Nikolay E., additional, Apt, Alexander S., additional, Majorov, Konstantin B., additional, Efimova, Svetlana S., additional, Ravin, Nikolai V., additional, Nikolaev, Evgeny N., additional, Ostroumova, Olga S., additional, Katrukha, Genrikh S., additional, Lapchinskaya, Olda A., additional, Dontsova, Olga A., additional, Terekhov, Stanislav S., additional, Osterman, Ilya A., additional, Shenkarev, Zakhar O., additional, and Korshun, Vladimir A., additional

Published
2021
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103. Inside Cover: Gausemycins A,B: Cyclic Lipoglycopeptides from Streptomyces sp. (Angew. Chem. Int. Ed. 34/2021)

Author

Tyurin, Anton P., primary, Alferova, Vera A., additional, Paramonov, Alexander S., additional, Shuvalov, Maxim V., additional, Kudryakova, Gulnara K., additional, Rogozhin, Eugene A., additional, Zherebker, Alexander Y., additional, Brylev, Vladimir A., additional, Chistov, Alexey A., additional, Baranova, Anna A., additional, Biryukov, Mikhail V., additional, Ivanov, Igor A., additional, Prokhorenko, Igor A., additional, Grammatikova, Natalia E., additional, Kravchenko, Tatyana V., additional, Isakova, Elena B., additional, Mirchink, Elena P., additional, Gladkikh, Elena G., additional, Svirshchevskaya, Elena V., additional, Mardanov, Andrey V., additional, Beletsky, Aleksey V., additional, Kocharovskaya, Milita V., additional, Kulyaeva, Valeriya V., additional, Shashkov, Alexander S., additional, Tsvetkov, Dmitry E., additional, Nifantiev, Nikolay E., additional, Apt, Alexander S., additional, Majorov, Konstantin B., additional, Efimova, Svetlana S., additional, Ravin, Nikolai V., additional, Nikolaev, Evgeny N., additional, Ostroumova, Olga S., additional, Katrukha, Genrikh S., additional, Lapchinskaya, Olda A., additional, Dontsova, Olga A., additional, Terekhov, Stanislav S., additional, Osterman, Ilya A., additional, Shenkarev, Zakhar O., additional, and Korshun, Vladimir A., additional

Published
2021
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110. Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis

Author

Ravin, Nikolai V., Mardanov, Andrey V., Beletsky, Alexey V., Kublanov, Ilya V., Kolganova, Tatiana V., Lebedinsky, Alexander V., Chernyh, Nikolai A., Bonch-Osmolovskaya, Elizaveta A., and Skryabin, Konstantin G.

Subjects
Genomes -- Research, Hyperthermophiles -- Genetic aspects, Biological sciences
Abstract

Desulfurococcus kamchatkensis is an anaerobic organotrophic hyperthermophilic crenarchaeon isolated from a terrestrial hot spring. Its genome consists of a single circular chromosome of 1,365,223 bp with no extra-chromosomal elements. A total of 1,474 protein-encoding genes were annotated, among which 205 are exclusive for D. kamchatkensis. The search for a replication origin site revealed a single region coinciding with a global extreme of the nucleotide composition disparity curve and containing a set of crenarchaeon-type origin recognition boxes. Unlike in most archaea, two genes encoding homologs of the eukaryotic initiator proteins Orc1 and Cdc6 are located distantly from this site. A number of mobile elements are present in the genome, including seven transposons representing IS607 and IS200/IS605 families and multiple copies of miniature inverted repeat transposable elements. Two large clusters of regularly interspaced repeats are present; none of the spacer sequences matches known archaeal extrachromosomal elements, except one spacer matches the sequence of a resident gene of D. kamchatkensis. Many of the predicted metabolic enzymes are associated with the fermentation of peptides and sugars, including more than 30 peptidases with diverse specificities, a number of polysaccharide degradation enzymes, and many transporters. Consistently, the genome encodes both enzymes of the modified Embden-Meyerhof pathway of glucose oxidation and a set of enzymes needed for gluconeogenesis. The genome structure and content reflect the organism's nutritionally diverse, competitive natural environment, which is periodically invaded by viruses and other mobile elements.

Published
2009

113. Two New Species of Filamentous Sulfur Bacteria of the Genus Thiothrix , Thiothrix winogradskyi sp. nov. and ' Candidatus Thiothrix sulfatifontis' sp. nov.

Author

Ravin, Nikolai V., Rossetti, Simona, Beletsky, Alexey V., Kadnikov, Vitaly V., Rudenko, Tatyana S., Smolyakov, Dmitry D., Moskvitina, Marina I., Gureeva, Maria V., Mardanov, Andrey V., and Grabovich, Margarita Yu.

Subjects
SULFUR bacteria, FILAMENTOUS bacteria, NUCLEIC acid hybridization, WHOLE genome sequencing, CANDIDATUS
Abstract

The metagenome of foulings from sulfidic spring "Serovodorodny" (Tatarstan, Russia), where members of the genus Thiothrix was observed, was sequenced. Representatives of the phyla Gammaproteobacteria, Cyanobacteria and Campilobacteriota dominated in the microbial community. The complete genome of Thiothrix sp. KT was assembled from the metagenome. It displayed 93.93–99.72% 16S rRNA gene sequence identity to other Thiothrix species. The average nucleotide identity (ANI) и digital DNA-DNA hybridization (dDDH) showed that the genome designated KT represents a new species within the genus Thiothrix, 'Candidatus Thiothrix sulfatifontis' sp. nov. KT. The taxonomic status has been determined of the strain Thiothrix sp. CT3, isolated about 30 years ago and not assigned to any of Thiothrix species due to high 16S rRNA gene sequence identity with related species (i.e., 98.8–99.4%). The complete genome sequence of strain CT3 was determined. The ANI between CT3 and other Thiothrix species was below 82%, and the dDDH values were less than 40%, indicating that strain CT3 belongs to a novel species, Thiothrix winogradskyi sp. nov. A genome analysis showed that both strains are chemo-organoheterotrophs, chemolithotrophs (in the presence of hydrogen sulfide and thiosulfate) and chemoautotrophs. For the first time, representatives of Thiothrix showed anaerobic growth in the presence of thiosulfate. [ABSTRACT FROM AUTHOR]

Published
2022
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117. Complete genome sequence of “candidatus syntrophocurvum alkaliphilum” strain B(2M), obtained from the metagenome of a salt-tolerant alkaliphilic anaerobic syntrophic butyrate-degrading consortium

Author

Mardanov, Andrey V. (author), Sorokin, Dimitry Y. (author), Beletsky, Alexey V. (author), Ravin, Nikolai V. (author), Mardanov, Andrey V. (author), Sorokin, Dimitry Y. (author), Beletsky, Alexey V. (author), and Ravin, Nikolai V. (author)

Abstract

A highly salt-tolerant and alkaliphilic syntrophic consortium that degrades butyrate under sulfate-reducing conditions was purified from a hypersaline soda lake in southwest Siberia. Here, we present the complete genome sequence of the syntrophic primary butyrate degrader in order to understand the molecular mechanisms of interaction between consortium members., BT/Environmental Biotechnology

Published
2020
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120. Wide distribution of Phycisphaera ‐like planctomycetes from WD2101 soil group in peatlands and genome analysis of the first cultivated representative

Author

Dedysh, Svetlana N., primary, Beletsky, Alexey V., additional, Ivanova, Anastasia A., additional, Kulichevskaya, Irina S., additional, Suzina, Natalia E., additional, Philippov, Dmitriy A., additional, Rakitin, Andrey L., additional, Mardanov, Andrey V., additional, and Ravin, Nikolai V., additional

Published
2020
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121. Genomic and Metabolic Insights into Two Novel Thiothrix Species from Enhanced Biological Phosphorus Removal Systems

Author

Mardanov, Andrey V., primary, Gruzdev, Eugeny V., additional, Smolyakov, Dmitry D., additional, Rudenko, Tatyana S., additional, Beletsky, Alexey V., additional, Gureeva, Maria V., additional, Markov, Nikita D., additional, Berestovskaya, Yulia Yu., additional, Pimenov, Nikolai V., additional, Ravin, Nikolai V., additional, and Grabovich, Margarita Yu., additional

Published
2020
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122. Genome sequence and analysis of the tuber crop potato

Author

Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Zhang, Bo, Mu, Desheng, Ni, Peixiang, Zhang, Gengyun, Yang, Shuang, Li, Ruiqiang, Wang, Jun, Orjeda, Gisella, Guzman, Frank, Torres, Michael, Lozano, Roberto, Ponce, Olga, Martinez, Diana, De la Cruz, Germán, Chakrabarti, S. K., Patil, Virupaksh U., Skryabin, Konstantin G., Kuznetsov, Boris B., Ravin, Nikolai V., Kolganova, Tatjana V., Beletsky, Alexey V., Mardanov, Andrei V., Di Genova, Alex, Bolser, Daniel M., Martin, David M. A., Li, Guangcun, Yang, Yu, Kuang, Hanhui, Hu, Qun, Xiong, Xingyao, Bishop, Gerard J., Sagredo, Boris, Mejía, Nilo, Zagorski, Wlodzimierz, Gromadka, Robert, Gawor, Jan, Szczesny, Pawel, Huang, Sanwen, Zhang, Zhonghua, Liang, Chunbo, He, Jun, Li, Ying, He, Ying, Xu, Jianfei, Zhang, Youjun, Xie, Binyan, Du, Yongchen, Qu, Dongyu, Bonierbale, Merideth, Ghislain, Marc, del Rosario Herrera, Maria, Giuliano, Giovanni, Pietrella, Marco, Perrotta, Gaetano, Facella, Paolo, O’Brien, Kimberly, Feingold, Sergio E., Barreiro, Leandro E., Massa, Gabriela A., Diambra, Luis, Whitty, Brett R., Vaillancourt, Brieanne, Lin, Haining, Massa, Alicia N., Geoffroy, Michael, Lundback, Steven, DellaPenna, Dean, Buell, Robin C., Sharma, Sanjeev Kumar, Marshall, David F., Waugh, Robbie, Bryan, Glenn J., Destefanis, Marialaura, Nagy, Istvan, Milbourne, Dan, Thomson, Susan J., Fiers, Mark, Jacobs, Jeanne M. E., Nielsen, Kåre L., Sønderkær, Mads, Iovene, Marina, Torres, Giovana A., Jiang, Jiming, Veilleux, Richard E., Bachem, Christian W. B., de Boer, Jan, Borm, Theo, Kloosterman, Bjorn, van Eck, Herman, Datema, Erwin, te Lintel Hekkert, Bas, Goverse, Aska, van Ham, Roeland C. H. J., and Visser, Richard G. F.

Published
2011
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126. Frigoriglobus tundricola gen. nov., sp. nov., a psychrotolerant cellulolytic planctomycete of the family Gemmataceae from a littoral tundra wetland

Author

Kulichevskaya, Irina S., primary, Ivanova, Anastasia A., additional, Naumoff, Daniil G., additional, Beletsky, Alexey V., additional, Rijpstra, W. Irene C., additional, Sinninghe Damsté, Jaap S., additional, Mardanov, Andrey V., additional, Ravin, Nikolai V., additional, and Dedysh, Svetlana N., additional

Published
2020
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128. Microbial Processes and Microbial Communities in the Water Column of the Polar Meromictic Lake Bol’shie Khruslomeny at the White Sea Coast

Author

Savvichev, Alexander S., primary, Kadnikov, Vitaly V., additional, Rusanov, Igor I., additional, Beletsky, Alexey V., additional, Krasnova, Elena D., additional, Voronov, Dmitry A., additional, Kallistova, Anna Yu., additional, Veslopolova, Elena F., additional, Zakharova, Elena E., additional, Kokryatskaya, Nataliya M., additional, Losyuk, Galina N., additional, Demidenko, Nikolai A., additional, Belyaev, Nikolai A., additional, Sigalevich, Pavel A., additional, Mardanov, Andrey V., additional, Ravin, Nikolai V., additional, and Pimenov, Nikolay V., additional

Published
2020
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135. Lacipirellula parvula gen. nov., sp. nov., representing a lineage of planctomycetes widespread in low-oxygen habitats, description of the family Lacipirellulaceae fam. nov. and proposal of the orders Pirellulales ord. nov., Gemmatales ord. nov. and Isosphaerales ord. nov.

Author

Dedysh, Svetlana N., primary, Kulichevskaya, Irina S., additional, Beletsky, Alexey V., additional, Ivanova, Anastasia A., additional, Rijpstra, W. Irene C., additional, Damsté, Jaap S. Sinninghe, additional, Mardanov, Andrey V., additional, and Ravin, Nikolai V., additional

Published
2020
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136. Metagenomic data of the microbial community of lab-scale nitritation-anammox sequencing-batch bioreactor performing nitrogen removal from synthetic wastewater

Author

Mardanov, Andrey V., primary, Kotlyarov, Roman V., additional, Beletsky, Alexey V., additional, Nikolaev, Yury A., additional, Kallistova, Anna Yu., additional, Grachev, Vladimir A., additional, Berestovskaya, Yulia Yu, additional, Pimenov, Nikolai V., additional, and Ravin, Nikolai V., additional

Published
2019
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140. Targeted isolation based on metagenome‐assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere.

Author

Karnachuk, Olga V., Lukina, Anastasia P., Kadnikov, Vitaly V., Sherbakova, Viktoria A., Beletsky, Alexey V., Mardanov, Andrey V., and Ravin, Nikolai V.

Subjects
BIOSPHERE, BASE isolation system, SPIROCHETES, GENOMES, THERMOPHILIC bacteria, PHENOTYPES, MICROBIAL communities
Abstract

Most microorganisms from deep terrestrial subsurface remain yet uncultured. Recent achievements in recovery of metagenome‐assembled genomes (MAG) provide clues for improving cultivation via metabolic reconstructions and other genomic characteristics. Here we report the isolation in pure culture of a thermophilic spirochete with the use of MAGs binned from metagenomes of the deep (>2 km) aquifers broached by two artesian boreholes in Western Siberia. The organism constitutes a minor share in the aquifer microbial community and could not be cultivated by traditional techniques. The obtained two pure culture isolates along with three bacteria identified by MAGs represent a novel family‐level lineage in the order Brevinematales. Based on genomic and phenotypic characteristics the novel spirochete is proposed to be classified as Longinema margulisiae gen. nov., sp. nov. within a novel family, Longinemaceae fam. nov. Both cultivated strains, NST and N5R, are anaerobic hemoorganoheterotrophes growing by fermentation of starch and a few sugars. They can form recalcitrant round bodies under unfavourable growth conditions, which survive up to 15 min at 95°C and can revert to the original helical cells. We suggest that the round bodies may facilitate global distribution of this lineage, detected from molecular signaturesand colonization of subsurface environments. [ABSTRACT FROM AUTHOR]

Published
2021
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141. Hydrolytic capabilities as a key to environmental success: Chitinolytic and cellulolytic acidobacteriafrom acidic sub-arctic soils and boreal peatlands

Author

Belova, Svetlana E., Ravin, Nikolai V., Pankratov, Timofey A., Rakitin, Andrey L., Ivanova, Anastasia A., Beletsky, Alexey V., Mardanov, Andrey V., Sinninghe Damsté, Jaap S., Dedysh, Svetlana N., Organic geochemistry, and non-UU output of UU-AW members

Subjects
0301 basic medicine, Microbiology (medical), Peat, 030106 microbiology, lcsh:QR1-502, Polysaccharide, Microbiology, lcsh:Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Chitin, Soil pH, Botany, Bog, Original Research, chemistry.chemical_classification, geography, geography.geographical_feature_category, biology, Acidisarcina, Chitinase, 15. Life on land, biology.organism_classification, Acidobacteria, chemistry, Chitinolytic ability, biology.protein, Lichen-covered tundra, Bacteria, Genome annotation
Abstract

Members of the Acidobacteria are among the most efficient colonizers of acidic terrestrial habitats but the key traits underlying their environmental fitness remain to be understood. We analyzed indigenous assemblages of Acidobacteria in a lichen-covered acidic (pH 4.1) soil of forested tundra dominated by uncultivated members of subdivision 1. An isolate of these bacteria with cells occurring within saccular chambers, strain SBC82T, was obtained. The genome of strain SBC82T consists of a 7.11-Mb chromosome and four megaplasmids, and encodes a wide repertoire of enzymes involved in degradation of chitin, cellulose, and xylan. Among those, four secreted chitinases affiliated with the glycoside hydrolase family GH18 were identified. Strain SBC82T utilized amorphous chitin as a source of carbon and nitrogen; the respective enzyme activities were detected in tests with synthetic substrates. Chitinolytic capability was also confirmed for another phylogenetically related acidobacterium isolated from a Sphagnum peat bog, strain CCO287. As revealed by metatranscriptomic analysis of chitin-amended peat, 16S rRNA reads from these acidobacteria increased in response to chitin availability. Strains SBC82T and CCO287 were assigned to a novel genus and species, Acidisarcina polymorpha gen. nov., sp. nov. Members of this genus colonize acidic soils and peatlands and specialize in degrading complex polysaccharides.

Published
2018

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