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PERN - Pan-European Rhizosphere Network

European - Russian initiative on Banking Rhizosphere Micro-Organisms


BCCM/MUCL

ALL-RUSSIAN COLLECTION OF MICROORGANISMS (VKM),
SKRYABIN INSTITUTE OF BIOCHEMISTRY AND PHYSIOLOGY OF MICROORGANISMS (IBPM)

Всероссийская коллекция микроорганизмов (ВКМ),
Институт биохимии и физиологии микроорганизмов им. Г.К. Скрябина (ИБФМ)

 

VKM (http://vkm.ru) operates since 1980 as a Department of the Skryabin Institute of Biochemistry and Physiology of Microorganisms (http://ibpm.ru) at the Pushchino Biological Research Center. VKM offers services which involve supply of cultures on request, deposition of cultures, including deposition for patent purposes, deposition of type strains associated with description of new taxa, as well as contract research on  identification, safe keeping of cultures, etc. Since 1987, VKM operates as International Depositary Authority for the preservation of patented strains under the Budapest Treaty. VKM is a member of the European Culture Collections' Organisation (ECCO) and the World Federation for Culture Collections (WFCC).
VKM is one of the Russia’s largest service collections in the field of non-medical microbiology. The collection maintains about 20 000 strains, including type and reference strains. Nearly 7.000 strains are presented in the on-line VKM-Catalogue (http://www.vkm.ru/Catalogue.htm). The working VKM depositories (not yet included in the Catalogue) contain hundreds strains of different phyla isolated from the rhizosphere and plants of various agricultural and pristine plant species, including endemic, rare and endangered ones.
VKM encompasses several research teams specializing in taxonomy and ecology of micro-organisms (bacteria, including actinobacteria, archeae, fungi, yeasts), as well as working groups concerned with preservation and bioinformatics. The VKM staff has experience in the study of microbial diversity, classification and identification of microorganisms of different phyla using molecular and culture-based  techniques, including 16S rRNA and multi-locus sequence analysis, real-time PCR, MALDI-TOF mass spectrometry, and relevant methods and equipments for determination of chemotaxonomic characteristics, such as the composition of cell wall amino acids and sugars, fatty acid profile, composition of isoprenoid  quinones, etc. The VKM staff has experience in WEB-processing and data banking, as well as in the intellectual property issues and regulatory framework in Russia. The research results of VKM are reflected in publications available at http://www.vkm.ru/.
The VKM team has been involved in several European and International projects in the past, funded by INTAS, CRDF and ISTC. Currently it is also participant in the FP7 project MIRRI (Microbial Resource Research Infrastructure).

KEY PERSONS INVOLVED IN THE PROJECT

Dr. Lyudmila I. Evtushenko, Head of VKM; current research interests are focused on bacterial diversity and systematics, mainly actinobacteria. She authored and co-authored many research and review papers, including  several chapters in ‘The Prokaryotes’ and ‘Bergey’s Manual of Systematic Bacteriology’. A member of  Subcommittee on the taxonomy of Suborder Micrococcineae and Subcommittee on the taxonomy of the Streptomycetaceae of the International Committee on Systematics of Prokaryotes (ICSP); served on Editorial board of the International Journal of Systematic and Evolutionary Microbiology (2003-2007).
Alexander N. Vasilenko, IT specialist, experienced in WEB-processing and databanking. He has been involved in development of VKM data bases and their integration with the BRC information resources, such as StrainInfo and WDCM. A member of CODATA task group " Advancing Informatics for Microbiology".
Dr. Oleg S. Stupar, Head of the information and coordination group at VKM; has experience in the Russian regulatory system and Intellectual Property Right issues. He is a member of Executive board of World Federation for Culture Collections (WFCC).
Prof. Lev V. Kalakoustkii, currently employed as VKM Coordinating Officer. A distinguished microbiologist having considerable experience in interdisciplinary projects. At one time he served as member of the ABS Committee at CBD Secretariat.

 

 

 

ВКМ (http://www.vkm.ru) функционирует с 1980 года как отделение Института биохимии и физиологии микроорганизмов им. Г.К. Скрябина (http://www.ibpm.ru) в Биологическом исследовательском Центре г. Пущино. ВКМ предоставляет такие услуги как предоставление культур микроорганизмов, депонирование культур, включая депонирование в связи с патентной процедурой, депонирование новых типовых штаммов, контрактные исследования по идентификации, безопасное хранение микроорганизмов и др. С 1987г. ВКМ выполняет функции Международного депозитария для хранения запатентованых штаммов согласно нормам Будапештского Договора. ВКМ - член Европейской ассоциации коллекций культур (ECCO) и Всемирной Федерации Коллекций Культур (WFCC).
ВКМ - одна из крупнейших сервисных коллекций немедицинского профиля. Коллекция хранит приблизительно 20 000 штаммов, включая типовые и эталонные. Приблизительно 7.000 штаммов представлено в Каталоге ВКМ, доступном в Интернете по адресу http://www.vkm.ru/Catalogue.htm. Действующие депозитарии ВКМ, не включенные в Каталог, содержат сотни различных штаммов, изолированных из ризосферы и растений сельскохозяйственных и редких культур, включая эндемики.
ВКМ имеет несколько исследовательских коллективов, специализирующихся в таксономии и экологии микроорганизмов (бактерии, включая актинобактерии, а также археи, мицелиальные грибы и дрожжи). Коллективы специализируются также в хранении микроорганизмов и биоинформатике. Штат ВКМ имеет опыт в исследовании микробного разнообразия, классификации и идентификации различных микроорганизмов, используя молекулярные и другие технологии, такие как 16S rRNA, мильтилокусный анализ, PCR в режиме реального времени, MALDI-TOF, соответствующие методы и оборудование для определения хемотаксономических характеристик, таких как структура аминокислот и сахаров клеточной стенки, профиль жирных кислот, состав изопреноидных хитонов и т д. Штат ВКМ имеет опыт ведения баз данных и страниц сайтов, в положениях интеллектуальной собственности и правового регулирования в России. Результаты проводимых в ВКМ исследований представлены в публикациях, перечисленных на сайте http://www.vkm.ru/.
В прошлом команда ВКМ участвовала в ряде Европейских и других международных проектов, финансируемых INTAS, CRDF и ISTC. Сейчас ВКМ также участвует в общеевропейском проекте MIRRI (Microbial Resource Research Infrastructure) системы FP7.

Участники проекта

Доктор билогических наук Людмила Ивановна Евтушенко, руководитель ВКМ; в настоящее время её интерес обращен на разнообразие и систематику бактерий, и прежде всего, актинобактерий. Она - автор и соавтор многих исследовательских и обзорных работ, включая главы в серии ‘The Prokaryotes’ и ‘Bergey’s Manual of Systematic Bacteriology’. Член подкомитета таксономии в "Suborder Micrococcineae and Subcommittee on the taxonomy of the Streptomycetaceae" Международного Комитета Систематики Прокариотов(ICSP); член редакционной коллегии в International Journal of Systematic and Evolutionary Microbiology (2003-2007).
Александр Николаевич Василенко, специализируется в информационных технологиях (IT), Интернет и базах данных. Он разрабатывал базы данных ВКМ, интегрировал их в другие системы информационных ресурсов БРЦ, такие как StrainInfo и WDCM. Член рабочей группы CODATA "Advancing Informatics for Microbiology".
Доктор Олег Сергеевич Ступарь, руководитель группы Информатики и Координации; имеет опыт в Российской системе правового регулирования и в положениях интеллектуальной собственности, член исполнительного Комитета Всемирной Федерации Коллекций Культур (WFCC).
Профессор Лев Владимирович Калакуцкий, в настоящее время научный руководитель ВКМ. выдающийся микробиолог, имеющий огромный опыт в многоплановых проектах, член-корреспондент Российской академии наук. В прошлом был членом ABS Committee в секретариате CBD.

 

References

 

Culture collections: from unstable existence to sustainable development, pp. 113-118. In:  Legal aspects of scientific and technical activities and innovations. Proceedings of the extended session and panel discussion, State Duma of Russian Federation, Moscow, 2011. [in Russian]. By: Kalakoutskii L.V.

Collections of microorganisms, pp. 39-47. In: Maintenance of biological diversity in Russia as basis for sustainable development of research and innovations. Proceedings of the Public Session of The Public Chamber of Russian Federation, 1st March 2011. Publ.: Russian Academy of Agricultural Sciences, Moscow, 2011. [in Russian] (ISBN 978-5-902178-52-1). By: Kalakoutskii L.V.

Biological resource centres: current status in Russia and the world, problems of organization, development prospects. Yu.A. Ovchinnikov bulletin of biotechnology and physical and chemical biology, 2011, 7: 28-40. [in Russian]. By:  Kalakoutskii, L.V., and S.M. Ozerskaya.
http://www.biorosinfo.ru/Vestnik/2010/Journal_2011_1.pdf

Current WFCC CC catalogues as a starting ground for networking efforts. WFCC Newsletter, 2011, 50: 5-15. Vasilenko A., S. Ozerskaya, and O. Stupar.
http://www.wfcc.info/pdf/newsletter/Newsletter%20No.50%20(Sep.%202011).pdf

Fungal DC: a database on fungal diversity in culture collections of the world. Inoculum, Supplement to Mycologia (Newsletter of the Mycological Society of America), 2010, 61(3): 1-5.By: Ozerskaya S.M., A. N. Vasilenko, B. Verslyppe, and P. Dawyndt.
http://msafungi.org/wp-content/uploads/Inoculum/61(3).pdf

Fungal diversity in GenBank: problems and possible solutions. Inoculum, Supplement to Mycologia (Newsletter of the Mycological Society of America) 2010, 61(4): 1-4. By: Ozerskaya S.M., Kochkina G.A., Ivanushkina N.E.
http://msafungi.org/wp-content/uploads/Inoculum/61(4).pdf

Fungal taxonomic diversity and bioinformatics-related issues, pp. 633-634. In: Proceedings of the 6th International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2012). NY, IEEE Service Center, 2012.        By: Vasilenko A.N. and S.M. Ozerskaya.

Long term preservation of fungal cultures in All-Russian Collection of Microorganisms (VKM), pp.17-66. In: Laboratory protocols in fungal biology:  current methods in fungal biology(Eds.: V. K. Gupta and M. G. Tuohy). Springer, NY, 2013. By: Ozerskaya S.M., Ivanushkina N.E., Kochkina G.A., Eremina S.S., Vasilenko A.N., Chigineva N.I. 
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Celerinatantimonas yamalensis sp. nov., a cold-adapted diazotrophic bacterium from a cold permafrost brine. International Journal of Systematic and Evolutionary Microbiology, 2013, 63: 4421–4427. By: Shcherbakova V., N. Chuvilskaya, E. Rivkina, N. Demidov, V. Uchaeva, S. Suetin, N. Suzina, and D. Gilichinsky.
doi: 10.1099/ijs.0.045997-0

Halotolerant bacteria of the genus Arthrobacter degrading polycyclic aromatic hydrocarbons. Russian Journal of Ecology, 2011, 42: 502-509. Plotnikova E.G., Yastrebova O.V., Anan’ina L.N., Dorofeeva L.V., Lysanskaya V.Ya., Demakov V.A.
DOI: 10.1134/S1067413611060130

Molecular characteristics of bacterial decomposers of biphenyl and identification of genes encoding α-subunit of biphenyl 2,3-dioxygenase. Microbiology (Moscow), 2014, 83 (in press). By: Shumkova E. S., O.D. Egorova, E.S. Korsakova, L.V. Dorofeeva, and E.G. Plotnikova
http://www.maik.ru/cgi-perl/search.pl?lang=eng&type=contents&name=micbio

Thalassospira permensis sp. nov., a novel halotolerant bacterium isolated from a naphthalene-utilizing consortium. Microbiology (Moscow). 2011, 80: 703–712. By: Plotnikova E. G., E.G., Anan'ina L.N., Krauzova V.I. Ariskina E.V., Prisyazhnaya N.V., Lebedev A.T., Demakov V.A., Evtushenko L.I.
DOI: 10.1134/S0026261711050109

Application of MALDI-TOF mass spectrometry for differentiation of closely related species of the "Arthrobacter crystallopoietes" phylogenetic group. Microbiology (Moscow), 2012, 81: 696-701. By: Prisyazhnaya, N.V., E.G. Plotnikova, O.V. Bueva, E.S. Korsakova, L.V. Dorofeeva, E. N. Il'ina, A. T. Lebedev,  and L. I. Evtushenko.
DOI: 10.1134/S0026261712060136

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Production of antifungal cellobiose lipids by Trichosporon porosum. Mycopathologia, 2010, 169(2):117-123. By: Kulakovskaya, T. V., Golubev, W. I., Tomashevskaya, M. A., Kulakovskaya, E. V., Shashkov, A. S., Grachev, A. A., A. S. Chizhov, and Nifantiev, N. E.
DOI: 10.1007/s11046-009-9236-2

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Carbohydrate-containing cell wall polymers of some strains of the Bacillus subtilis group. Microbiology (Moscow), 2011, 80: 21-29. By: Streshinkaya G.M., A.S. Shashkov, N.V. Potekhina, Yu.I. Kozlova, E.M. Tul’skaya, S.M. Senchenkova, E.B. Kudryashova, and L.N. Anan’ina.
DOI: 10.1134/S0026261711010164

Teichoic acids of three type strains of the Bacillus subtilis group, Bacillus mojavensis VKM B-2650, Bacillus amyloliquefaciens subsp amyloliquefaciens VKM B-2582, and Bacillus sonorensis VKM B-2652.  Microbiology (Moscow), 2013, 82: 579-585. By: Potekhina, N.V., A.S. Shashkov, G.M. Streshinskaya, E.M. Tul'skaya, Y.I.  Kozlova,  S.N. Senchenkova, E.B. Kudryashova, and L.I. Evtushenko.
DOI: 10.1134/S002626171305010X

A novel type of teichoic acid from the cell wall of Bacillus subtilis VKM B-762. Carbohydr. Res., 2011, 346, 1173-1177. By: Shashkov A.,G. Streshinskaya, Yu. Kozlova, S. Senchenkova, N. Arbatsky, and E. Kudryashova.
http://dx.doi.org/10.1016/j.carres.2011.03.034  DOI: 10.1016/j.carres.2011.03.034

Cell wall teichoic acids of Bacillus licheniformis VKM B-511T, Bacillus pumilus VKM B-508T, and other strains previously assigned to Bacillus pumilus. Microbiology (Moscow), 2012, 81: 425-434. Streshinskaya G. M., Shashkov A. S., Kozlova Y. I., Tul’skaya E. M., Kudryashova E. B., Senchenkova S. N., Ariskina E. V., Evtushenko L. I., PotekhinaN. V.
DOI: 10.1134/S0026261712030125

Disaccharide 1-phosphate polymers of some representatives of Bacillus subtilis group. Biochemistry (Moscow), 2013, 78: 1146-1463. By: Potekhina N.V., Shashkov A.S., Streshinskaya G.M., Tul’skaya E.M., Senchenkova S.N., Kudryashova E.B., Dmitrenok A.S.
DOI: 10.1134/S000629791310009X

Teichuronic and teichulosonic acids of actinomycetes. Biochemisry (Moscow), 2011, 76: 736-744. By: Tul'skaya, E.M., A.S. Shashkov, G.M. Streshinskaya, S.N. Senchenkova, N.V. Potekhina, Y.I. Kozlova, and L.I. Evtushenko.
DOI: 10.1134/S0006297911070030

New cell wall glycopolymers of the representatives of the genus Kribbella. Carbohydr. Res., 2009, 344(16): 2255-2262. By: Shashkov, A. S., E. M. Tul'skaya, G. M. Streshinskaya, S. N. Senchenkova, A. N. Avtukh, and L. I. Evtushenko.
DOI: 10.1016/j.carres.2009.08.010
Novel teichulosonic acid from cell walls of some representatives of the genus Kribbella. Carbohydr. Res., 2011, 346: 2045-2051. By: Tul'skaya E.M., Streshinskaya G.M., Shashkov A.S., Senchenkova S.N., Avtukh A.N., Baryshnikova L.M., Evtushenko L.I.                                     DOI: 10.1016/j.carres.2011.06.003
Teichulosonic acid, an anionic polymer of a new class from the cell wall of Actinoplanes utahensis VKM Ac-674(T). Biochemistry (Moscow), 2012, 77: 511-517. 
By: Shashkov, A. S.,  G. M. Streshinskaya, Y. I. Kozlova,  E. M. Tul'skaya,  S. N. Senchenkova,  N. P. Arbatskii, O. V. Bueva, and L. I. Evtushenko.
DOI: 10.1016/j.carres.2012.02.011
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Structure of hexasaccharide 1-phosphate polymer from Arthrobacter uratoxydans VKM Ac-1979(T) cell wall. Biochemistry (Moscow), 2012. 77: 1294-1302. By: Potekhina, N. V., A. S. Shashkov, S. N. Senchenkova, L. V. Dorofeeva,  and L. I. Evtushenko.
DOI: 10.1134/S0006297912110089

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Description of Herbiconiux flava sp. nov., and emended description of the genus Herbiconiux. International Journal of Systematic and Evolutionary Microbiology,2012, 62: 795-799. By: HamadaM., C. Komukai, N. Tamura, L.I. Evtushenko, N.G. Vinokurova, andK.-i. Suzuki.
doi: 10.1099/ijs.0.031260-0

Yeast fungi in Picea abies (L.) Karst. needle litter. Microbiology (Moscow), 2010, 79: 385-389. By: Golubev, W. I. and M.A. Tomashevskaya.
DOI: 10.1134/S002626171003015X

Family Microbacteriaceae. In: Bergey's Manual of Systematic Bacteriology. Vol. 5:  The Actinobacteria,pp. 807-813 (Eds:  M. Goodfellow, P. Kämpfer, H.-J. Busse, M.E. Trujillo, K.-i. Suzuki, W.Ludwig and W.B. Whitman), Springer, NY, 2012. Evtushenko L.I.
ISBN 0-387-95042-7. http://www.bergeys.org/pubinfo.html

Genus Agreia, pp. 852-855. In:  Bergey's Manual of Systematic Bacteriology. Vol. 5:  The Actinobacteria, (Eds:   M. Goodfellow, P. Kämpfer, H.-J. Busse, M.E. Trujillo, K.-i. Suzuki, W.Ludwig and W.B. Whitman), Springer, NY, 2012. By: Evtushenko L.I.
ISBN 0-387-95042-7. http://www.bergeys.org/pubinfo.html

Genus Leifsonia, pp. 907-923. In: Bergey's Manual of Systematic Bacteriology. Vol. 5:  The Actinobacteria (Eds:   M. Goodfellow, P. Kämpfer, H.-J. Busse, M.E. Trujillo, K.-i. Suzuki, W.Ludwig and W.B. Whitman), Springer, NY, 2012. By: Evtushenko L.I.
ISBN 0-387-95042-7. http://www.bergeys.org/pubinfo.html

Genus Okibacterium, pp. 940-942. In: Bergey's Manual of Systematic Bacteriology. Vol. 5:  The Actinobacteria(Eds:   M. Goodfellow, P. Kämpfer, H.-J. Busse, M.E. Trujillo, K. Suzuki, W.Ludwig and W.B. Whitman), Springer, NY, 2012. Evtushenko L.I.
ISBN 0-387-95042-7. http://www.bergeys.org/pubinfo.html

Genus Rathayibacter, pp. 953-964. In: Bergey's Manual of Systematic Bacteriology. Vol. 5  The Actinobacteria,pp. 953-964 (Eds:   M. Goodfellow, P. Kämpfer, H.-J. Busse, M.E. Trujillo, K.-i. Suzuki, W.Ludwig and W.B. Whitman), Springer, NY, 2012. Evtushenko L.I. and L.V. Dorofeeva.
ISBN 0-387-95042-7. http://www.bergeys.org/pubinfo.html

Family Nocardioidaceae, pp. 1189-1197.In:  Bergey's Manual of Systematic Bacteriology. Vol. 5:  The Actinobacteria. (Eds: M. Goodfellow, P. Kämpfer, H.-J. Busse, M.E. Trujillo, K.-i. Suzuki, W.Ludwig and W.B. Whitman), Springer, NY, 2012. Evtushenko L.I. and E.V. Ariskina.
ISBN 0-387-95042-7. http://www.bergeys.org/pubinfo.html

Genus Nocardioides, pp. 1197-1251.In: Bergey's Manual of Systematic Bacteriology. Vol. 5:  The Actinobacteria(Eds:   M. Goodfellow, P. Kämpfer, H.-J. Busse, M.E. Trujillo, K.-i. Suzuki, W.Ludwig and W.B. Whitman), Springer, NY, 2012. Evtushenko L.I., V.I. Кrausova V.I., and Y.W.  Yoon.
ISBN 0-387-95042-7. http://www.bergeys.org/pubinfo.html

Genus Kribbella, pp. 1268-1284 In: Bergey's Manual of Systematic Bacteriology. Vol. 5:  The Actinobacteria(Eds:   M. Goodfellow, P. Kämpfer, H.-J. Busse, M.E. Trujillo, K.-i. Suzuki, W.Ludwig and W.B. Whitman), Springer, NY,2012. Evtushenko L.I., and V.I. Krausova. ISBN 0-387-95042-7. http://www.bergeys.org/pubinfo.html

Evaluation of the taxonomic diversity of prosthecate bacteria belonging to the genera Brevundimonas and Caulobacter isolated from various eurasian ecosystems by analysis of the 16S rRNA genes. Microbiology (Moscow), 2011, 80: 403-410. Ariskina E.V., Chernousova E.Yu., Lapteva N.A., Akimov V.N.
DOI: 10.1134/S0026261711030027

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Phylogenetic study of Cryptococcus laurentii mycocinogenic strains. Mycological Progress, 2013, 12:  777-782. By: Yurkov, A.M., and W.I. Golubev.
DOI: 10.1007/s11557-012-0873-3

Mycocinotyping. Mykologia I Phytopathologia [Mycology and Phytopathology], 2012, 46(1): 3-13 [in Russian; Abstraict in English]. By: Golubev W.I.
ISSN 0026-3648.

Differentiation between aquatic and terrestrial Metschnikowia species based on their sensitivity to Pichia membranifaciens mycocins. Microbiology (Moscow), 2011, 80: 154-157. Golubev, W.
DOI: 10.1134/S0026261711010085
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Molecular genetic determinants of intraspecific polymorphism of the phytopathogenic fungus Cryphonectria parasitica. Russian Journal of Genetics, 2011, 47(3), 262-271. By: Popov A.P., A. A. Belov, N. E. Ivanushkina, I. L. Tsvetkov, and A.S. Konichev.
DOI: 10.1134/S1022795411030112

Modern approaches to systematics of the genus Сladosporium s. lat. Mykologia I Phytopathologia [Mycology and Phytopathology], 2013, 47(6):  349-357 [in Russian; Abstraict in English]. By: Ivanushkina, N.E.
ISSN 0026-3648.

Zygomycetes: recent developments in systematics, taxonomy and identification. Mykologia I Phytopathologia [Mycology and Phytopathology], 2012, 46(3): 161-171 [in Russian; Abstraict in English]. By: Kochkina, G.A.
ISSN 0026-3648.

Micromycetes in the connection with problems of biological safety. Problems in Medical Mycology (Moscow), 2011, 13(3): 3-12 [Paper in Russian]. By: Ozerskaya, S. M., N. E. Ivanushkina, and G.A. Kochkina.
http://www.rusmedserv.com/mycology/html/mapo_3_2011.pdf