MIRRI - Microbial Resource Research Infrastructure


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MIRRI NEWS | Issue 8

Editorial | Hunters & GatherersMicrobe Highlights | News & Events | Meet MIRRI


Prof. Erko Stackebrandt

Dear all,

at the end of 2016 it is time to draw our conclusions for the year: with Portugal having signed the MIRRI MoU supporting the establishment of MIRRI-ERIC legal structure there are now six European countries on board. Negotiations with Italy, Russia and Germany are still ongoing. Unfortunately, we did not convince national stakeholders to proceed with an application for a legal status of MIRRI this year but, as Albert Einstein once said, You never fail until you stop trying.” – we will continue our work as we still firmly believe that a microbial resource infrastructure is indispensable for Europe.
Despite the end of the EU funding period MIRRI is still listed on the ESFRI roadmap and there is still so much more to achieve. The discussion on a smooth implementation of articles of the Nagoya Protocol is high on the agenda of all MIRRI partners and they play a recognized role at the level of national authorities and the European Commission. Some of our partners are involved in the development of the new biotechnology standard (ISO/TC 276), others participate in the development of a common strategy for quality assurance across research infrastructures (within CORBEL), whilst others are still negotiating with their national stakeholders.
The spirit of MIRRI and our principles still influences the European life science landscape and will continue to do so in 2017.


Kind regards,

Erko Stackebrandt
MIRRI Coordinator


Hunters & Gatherers

Who are the people, “hunting” microorganisms and collating them in public culture collections? Where are they located? And why do they participate in MIRRI?
In today’s issue these questions will be answered by the Industrial Yeasts Collection (DBVPG)  and the Polish Collection of Microorganisms (PCM).

The Industrial Yeast Collection DBVPG is one of the oldest EU yeast collections: it was founded as “in-house collection” at the beginning of 1900 and rationalized and transformed into a service institution in 1970s. The acronym DBVPG was derived by the Italian name of the first hosting Institution: Dipartimento di Biologia Vegetale of Perugia - PG. It is specialized in the study and ex-situ conservation of yeasts and yeast-like microorganisms and offers services to the international scientific community and to other private Institutions. Among the services offered by the Collection DBVPG we can include: distribution of yeast cultures, safe and patent deposit of cultures, yeast taxonomy service, screening upon request for biotech properties, theoretical and practical training courses for researchers and stakeholders.
The DBVPG research programs principally focus on the taxonomy, biodiversity and biotechnology of yeasts.
Currently, the Collection DBVPG maintains over 6,000 yeast and yeast-like cultures representing a large percentage of the known species in four separate sections. A) Section 1: about 1,300 fermenting strains for wine, brewery, bakery industry, including over 1,000 cultures of Saccharomyces cerevisiae; B) Section 2: about 2,800 yeast strains isolated from over 300 different environmental and food-associated habitats during 60 years of ecological surveys. In particular about 1,000 cultures were isolated from worldwide cold habitats. These belong to over 400 species of about 90 genera, and are currently the object of large-scale screening surveys. C) Section 3: type strains and certified yeast cultures from other Collections. Over 1,600 certified cultures obtained through exchanges with other certified culture Collections. D) Section 4: Over 300 cultures belonging to the genus Prototheca isolated from Italy and some European countries.

The collection DBVPG is affiliated to World Federation of Culture Collection (WFCC), European Culture Collection Organization (ECCO), Global Catalogue of Microorganisms (GCM), and was the Italian node of the EEC program (BRIDGE-BAP): MINE (Microbial Information Network Europe). Since 1997 the Collection DBVPG has been accredited by the Italian Ministry of Trade as an IDA (International Depositary Authority) for the deposit of patented yeast and yeast-like fungi under the Budapest Convention.
Since 2012 the DBVPG is a Collaborating Party of MIRRI.


The Polish Collection of Microorganisms (PCM) was established almost 50 years ago and from 1967 it is continuously operating at Hirszfeld Institute of Immunology and Experimental Therapy, PAS (Wrocław, Poland). In 1981 PCM joined the World Federation for Culture Collections (WFCC, registration No 106) and also became a founding member of European Culture Collections’ Organisation (ECCO). Fifteen years ago PCM received from World Intelectual Property Organiztion (WIPO) a status of the International Depositary Authority (IDA) for bacteria and bacteriophages for the patent purposes.
Our collection holds over 3,000 bacterial strains that cover a wide range of species with especially rich resources of Enterobacteriaceae family. This biological material serves as a valuable base for the conducted scientific projects, e.g. the studies on the structures of the bacterial surface antigens and their immunochemical properties. PCM keeps many potentially useful strains for diagnostic application and other microbiology-related domains. In addition, IIET PAS holds a unique bacteriophage collection that is actively used, not only for the scientific studies, but also as therapeutically material.

Lately, PCM was engaged in two EU projects and we performed modernization of our facilities to achieve the highest standards of microbial material identification, preservation and data collecting in an electronic platform.
From its origin PCM was cooperating with many scientific institutions in Poland and abroad. Recently, we extended our relations with the biotechnology companies that are interested in our resources, the identification services and a microbiological expertise.
From the very beginning PCM was actively engaged into MIRRI project and keeps the status of Collaborating Party. Firmly cooperating with Culture Collection of Industrial Microorganisms situated at Institute of Agricultural and Food Biotechnology (Warszawa, Poland), as a consortium SeCuRe, we expect to put a strong impact into future MIRRI performance. The project SeCuRe (National Node of MIRRI) is already situated on the Polish Roadmap for Research Infrastructure.


Microbe Highlights

In this issue, the series continues with highlights from MIRRI Collaborating Parties Culture Collection of Yeasts (CCY), Regional Specialised Collection of Alkanotrophic Microorganisms (IEGM) and Culture Collection of Algae at Goettingen University (SAG):

Taphrina gei-montani

Taphrina gei-montani (strains CCY 058-007-001 to CCY 058-007-005), a new species parasiting herbaceous Rosaceae

Members of the genus Taphrina, characteristic of a dimorphic lifestyle, are obligate parasites pathogenic to various vascular plants (economically important fruit trees, shrubs, herbaceus species and some ferns). A sexual state is strictly biotrophic with asci formations in the infected tissues, whereas an asexual can be cultivated on artificial yeast media in vitro.

Five strains of Taphrina gei-montany were isolated from the leaf tissues of Geum montanum L. (Rosaceae). Genetic analyses revealed that these isolates differ by 15 unique substitutions in the ITS region and by 6 substitutions in the rns gene from all other Taphrina species analysed. Taphrina gei-montani is also distinct from the other Taphrina species in the location of the asci within the host plant tissue. It forms asci irregularly in the subcuticular layer, which recline on the upper side of leaf tissue and causes locally demarcated convex/concave spots on living the leaves, stems and flowers. The species belongs to a resident microbiota of higher mountain latitudes and its availability depends only on the presence of the host plant. The type strain of T. gei-montani CCY 058-007-001T (= CBS 14159 = BU001) originates from the location Ľadové pleso (tarn), Vysoké Tatry, Slovakia (Petrýdesová et al. 2016).

Rhodococcus ruber IEGM 231 strain, an active hydrocarbon degrader and biosurfactant producer

Rhodococcus species are naturally occurring in diverse environments, including highly contaminated soils and waters, and even under oxygen- and nutrient-limited conditions. Their broad catabolic versatility, physiological and ecological adaptations to extreme environmental conditions imply a significant role of these microorganisms in both natural degradation of persistent pollutants and bioremediation of contaminated ecosystems. Some Rhodococcus species, particularly R. ruber, are able to grow using gaseous hydrocarbons (such as ethane, propane, butane, and acetylene) as sole carbon sources (Ivshina et al. (1995) Microbiology (Moscow). 64,507–513; Smith et al. 1999). Ivshina et al. (Microbiology (Moscow). 50,709–717) isolated large numbers of propane- and butane-degrading R. ruber from soil, rock, and groundwater associated with oil-bearing sites, suggesting that these gas-oxidizing rhodococci are indicative of hydrocarbon deposits and thus could be used in oil prospecting.

The Rhodococcus ruber IEGM 231 strain was isolated from a water spring near an oil-extracting enterprise (Perm region, Russian Federation). The strain was shown to utilize propane, n-butane, and liquid alkanes; degrade mono- and polyaromatic hydrocarbons and heterocyclics; convert aryl alkyl sulfides into optically pure sulfoxides; transform beta-sitosterol into therapeutically prospective stigmast-4-en-3-one; produce nontoxic glycolipid biosurfactants; be highly resistant to heavy metals; and accumulate molybdenum and nickel. Trehalolipid biosurfactants produced by this strain express diverse imunomodulatory activities (Kuyukina et al. 2016). The whole genome of R. ruber IEGM 231 is now available at DDBJ/EMBL/GenBank (accession numbers CCSD01000001 to CCSD01000115) (Ivshina et al. 2014).

R. ruber IEGM 231. SEM image of cells (right), colonies grown on NA (middle) and mineral agar with hydrocarbons (left). © I. Ivshina


Strain SAG 192.80 described as epitype of astaxanthin producing green algal species Haematococcus pluvialis

Haematococcus pluvialis is an unicellular green algae that is often found in small, temporary freshwater bodies. Resting stages are formed in unfavourable conditions and contain high amounts of a blood-red coloured keto-carotenoid called astaxanthin. There is a high demand for this strong antioxidant substance in nutraceutic, aquaculture and cosmetic industry. Industrial production uses cultures of H. pluvialis as primary source of natural astaxanthin.
Different strains of H. pluvialis are known to differ considerably in their physiological characters, e.g. their ability to accumulate high amounts of astaxanthin at different temperatures.
An extensive molecular study on the intraspecific diversity in Haematococcus pluvialis now reveals distinct lineages within European strains (Allewaert et al. 2015). Better characterization of Haematococcus strains is now providing a solid phylogenetic framework for the selection of strains optimal for astaxanthin production in different climates.
An ITS rDNA phylogeny of a large set of European Haematococcus strains allowed the identification of three species of Haematococcus, two of them newly described. Strain SAG 192.80 shows typical morphology and is known for high astaxanthin production. It is now designated as epitype of the traditional species Haematococcus pluvialis because it is successfully cryopreserved and thus indefinitely stored at the Culture Collection of Algae at Göttingen University (SAG). Furthermore, its source location is closest to the type locality described by Flotow in 1844.

H. pluvialis (SAG 192.80)

News & Events

  • The MIRRI partner DSMZ organises a training workshop on its database BacDive on November 4, 2016 in Braunschweig (Germany). Participation is free of charge. For more details please visit the workshop website.
  • In summer 2016 the European Commission published the EC Guidance document on Regulation No 511/2014 that is intended to provide guidance on the scope of application and core obligations of the Regulation No 511/2014 on the compliance measures for users from the Nagoya Protocol.
  • The H2020 cluster project CORBEL, to which MIRRI is a partner, announces its 1st Open Call for Research Projects:
    The CORBEL Open Call invites researchers to apply to access technologies and services from more than 15 facilities from eight different research infrastructures across Europe. Selected projects will be allocated to so-called Access Tracks and gain unprecedented opportunities to utilise a wide range of high-end technologies and services. These include state-of-the-art offers from the fields of advanced imaging, biobanking, curated databases, marine model organisms, mouse mutant phenotyping, screening and medicinal chemistry, structural biology as well as systems biology.
    Projects will be supported at every stage, with CORBEL project managers on hand to help scientists navigate between different service providers and exploit the full potential of the offers available. The CORBEL consortium already launched its Innovation Office, consisting of a well-experienced team dealing with the special needs of industry (e.g. regarding IP issues, confidentiality agreements).
    Deadline for the submission of project proposals is November 30, 2016.
    Learn more about the CORBEL Open Call by visiting the project website.



Meet MIRRI @

  • ECCO XXXV Annual Meeting – Who/Where are we in 2016 and beyond, November 2-4, 2016 in Aberdeen (Scotland); lecture by R. Hurtado-Ortiz (CRBIP)
  • ESFRI-Roadmap Update 2018 in Horizon 2020, November 4, 2016 in Berlin (Germany); E. Stackebrandt (DSMZ)
  • EMBRIC Workshop “Best Practices for Biological Resource Centres – Long-term Preservation, Reproductuve Technology, Genetic Resources & Containment”, November 29-30, 2016 in Plymouth (UK); lecture by R. Hurtado-Ortiz (CRBIP)

This publication reflects the view only of the author(s), and the European Union cannot be held responsible for any use which may be made of the information contained therein.

European Strategy Forum on Research Infrastructures

This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 312251.