Welcome to the IUMS 2022 Interactive Program

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Culture Collections and Sustainable Development Goals: WFCC’s Catalyst Role

İpek Kurtböke, WFCC PRESIDENT

Sustainable development goals (SDGs) defined by the United Nations (UN) in 2015, are intended to be achieved by 2030. The SDGs include: (1) no poverty, (2) zero hunger, (3) good health and well-being, (4) quality education, (5) gender equality, (6) clean water and sanitation, (7) affordable and clean energy, (8) decent work and economic growth, (9) industry, innovation and infrastructure, (10) reducing inequality, (11) sustainable cities and communities, (12) responsible consumption and production, (13) climate action, (14) life below water, (15) life on land, (16) peace, justice and strong institutions, (17) partnerships for goals.

One of the key contributing disciplines toward realization of these goals is microbiology. Understanding the functional roles of microorganisms thus have great importance than ever for design and implementation of environmentally friendly and microbially-mediated technologies. The World Federation for Culture Collections (WFCC) plays a major role in all matters related to biological resource centres (BRCs). Examples include (i) standardization and best practice guidelines, (ii) networking, capacity building and education, (iii) postal, quarantine and safety regulations (iv) IP, patent and commercialization, (v) access, policies and legal frameworks and (vi) sustainability of endangered collections. Moreover, WFCC places emphasis on genome level characterization of microorganisms as well as open access to such information. All these above listed aspects have importance as they form foundational platform for microbial biotechnologies to be utilized to achieve the SDGs. Moreover, the WFCC interacts with different global organizations to promote the importance and relevance of the BRCs to the SDGs with emphasis placed on the contributions and the impact BRCs can make on science, health, education, and society. This presentation will communicate WFCC’s catalyst role in linking different stakeholders and providing background support to key parties for timely delivery of the SDGs.

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WFCC-MIRCEN World Data Centre for Microorganisms (WDCM, http://www.wdcm.org/) has long been committed to facilitating the application of cutting-edge information technology to improve the interoperability of microbial data, promote the access and use of data and information, and coordinate international co-operation between culture collections, scientists and other user communities.

To help plenty of culture collections that cannot make their data available online, WDCM launched the Global Catalogue of Microorganisms (GCM) (http://gcm.wdcm.org/) project in 2012. Up to now, GCM (http://gcm.wdcm.org/) has become one of the largest data portals for public service microbial collections and several international culture collection networks, providing data retrieval, analysis, and visualization system for microbial resources. Furthermore, GCM gradually developed into a knowledge base linking taxonomy, phenotype, omics data as well as relative scientific papers and patents with its catalogue information, which currently has aggregated 527,215 strains and other holdings (plasmids and antibodys) deposited in 146 collections from 51 countries and regions.

WDCM announced the launching of Global Microbial Type Strain Genome and Microbiome Sequencing Project in the 7th WDCM Symposium, marking the GCM project has begun to enter a new stage (GCM 2.0). Focused on exploring the genomic information of microorganisms, this project has planned to sequence all uncovered prokaryotic type strains together with select eukaryotic type strains, construct a database for genomics data sharing, and also provide online data mining environment. Working groups responsible for selecting bacterial and fungal strains, drafting SOP, managing intellectual property right and legal issues and constructing database have already embarked on the pioneer stage of GCM 2.0. The project will establish a cooperation network for type strain sequencing and functional mining, and complete genome sequencing of over 10000 species of microbial type strains in five years.

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The Westerdijk Institute, formerly known as the Centraalbureau voor Schimmelcultures (CBS-KNAW) is holding the largest living filamentous fungi and yeast collections in the world. To maintain the collection, preserve, use and analyse strain data, efficiently, and finally to publish them on its website, the BioloMICS software was developed and is under constant improvement. BioloMICS allows curators, technicians, and sales managers to manage all the complex aspects associated with collection’s operations ranging from data entries, importations, exportations, stock management, label printing, report templates, workflows, data analyses and publications.

Our system is currently used worldwide by a large diversity of scientific and microbial collections including the Microbial Resources Research Infrastructure (MIRRI, www.mirri.org) that offers access to more than 400 000 microbial resources of 50+ European culture collections.

We have further developed the system to manage nomenclatural and taxonomic data and in 2004, Mycobank (www.mycobank.org) was created, which now serves as official repository for the publication of new fungal names including yeasts.

Our system can also be used to manage reference databases such as the one on yeast taxonomy (www.theyeasts.org) or the Atlas of Clinical Fungi (www.clinicalfungi.org).

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Over the past 8 years the Nagoya Protocol has significantly impacted the handling and management of microbial samples. The legal obligations of culture collections, depositors, and users can pose challenges for collection managers and scientists alike. However, there are simple procedures and compliance management strategies that can alleviate concerns and provider clarity along the microbial management chain. The Leibniz Institute DSMZ, as a Registered Collection, under the EU implementation of the Nagoya Protocol will provide some hands-on advice and practical experience gained in recent years. Furthermore, the on-going discussion around the expansion of benefit-sharing obligations to digital sequence information (DSI) will also be presented. Here, input from the scientific community, including IUMS members, is especially critical to bridge the gap between science and policymaking.

Background and Aims

High throughput environmental metabarcoding can unearth hidden microscopic biodiversity. After including environmental sequence data, the estimated global fungal diversity has increased from the commonly cited 1.5 million to 2.2-3.8 million, then to 6.3 million. However, a concern about the sequence-only analyses is that they tend to inflate the number of taxa. My lab has been uncovering a number of new fungal lineages from the pine barrens ecosystem, which is acidic and nutrient-poor. We aim to uncover new fungal taxa and understand fungal diversity using culture-based and culture-independent methods.

Methods

We collected plant roots from the New Jersey Pine Barrens. For culture-based method, we observed morphology, culture growth rate, sequenced the ITS, 18S, 28S, RPB2, ACT genes, performed phylogenetic analysis, and conducted the plant-fungal interaction experiment. For the culture-independent method, we did Illumina metabarcoding analysis of the ITS region.

Results

From the pine barrens fungal study, we observed that sequence-only analyses may overestimate the taxonomic level. For example, the new family Pygmaeomycetaceae (Umbelopsidales, Umbelopsidomycetes, Mucoromycotina, Mucoromycota) we uncovered from the pine barrens ecosystem corresponds to “clade GS23”, which was recognized as a “at least class-level” new lineage based on a sequence-only soil fungal survey.

Conclusions

The disparities between sequence-only and culture-based taxonomic analyses can be explained by the problems associated with environmental sequence analyses, such as short sequence length, low quality, and chimera. Further effort on linking cultures or specimens with sequence-only “dark taxa” will provide more data to recalibrate fungal diversity calculation and to work towards a more accurate global fungal diversity estimation.