Large-scale phenotyping of 1,000 fungal strains for the degradation of non-natural, industrial compounds

Fungal biotechnology is set to play a keystone role in the emerging bioeconomy, notably to address pollution issues arising from human activities. Because they preserve biological diversity, Biological Resource Centres are considered as critical infrastructures to support the development of biotechnological solutions. Here, we report the first large-scale phenotyping of more than 1,000 fungal strains with evaluation of their growth and degradation potential towards five industrial, human-designed and recalcitrant compounds, including two synthetic dyes, two lignocellulose-derived compounds and a synthetic plastic polymer. We draw a functional map over the phylogenetic diversity of Basidiomycota and Ascomycota, to guide the selection of fungal taxa to be tested for dedicated biotechnological applications. We evidence a functional diversity at all taxonomic ranks, including between strains of a same species. Beyond demonstrating the tremendous potential of filamentous fungi, our results pave the avenue for further functional exploration to solve the ever-growing issue of ecosystems pollution.

Large-scale phenotyping of 1,000 fungal strains for the degradation of non-natural, industrial compounds

Fungal biotechnology is set to play a keystone role in the emerging bioeconomy, notably to address pollution issues arising from human activities. Because they preserve biological diversity, Biological Resource Centres are considered as critical infrastructures to support the development of biotechnological solutions. Here, we report the first large-scale phenotyping of more than 1,000 fungal strains with evaluation of their growth and degradation potential towards five industrial, human-designed and recalcitrant compounds, including two synthetic dyes, two lignocellulose-derived compounds and a synthetic plastic polymer. We draw a functional map over the phylogenetic diversity of Basidiomycota and Ascomycota, to guide the selection of fungal taxa to be tested for dedicated biotechnological applications. We evidence a functional diversity at all taxonomic ranks, including between strains of a same species. Beyond demonstrating the tremendous potential of filamentous fungi, our results pave the avenue for further functional exploration to solve the ever-growing issue of ecosystem pollution.

Preserving the reference strains.

It is critical that storage of the living reference strains, on which the names and properties are based and the DNA sequenced to assign a name (the reference genetic resources), are preserved optimally to retain stability. The fact that less than 1% of microbial diversity can be grown sets enormous challenges for repositories (microbial domain biological resource centres or mBRCs). It is most often the case that it is an axenic culture of the reference genetic resource that is preserved but, for those organisms that cannot be grown or where molecular techniques are used to identify the organism, DNA should be stored. This task increases further when the microbiome is being studied, and environmental samples from whole communities are examined; mBRCs need to address how these can be preserved too. This chapter focuses on property retention, selecting the appropriate techniques for longterm survival and stability of characters. It covers the operations of mBRCs and the most appropriate technologies and mechanisms for stability testing and quality assurance. It addresses the preservation of microbial strains of the wide range of archaeal, bacterial (including cyanobacterial), yeast and fungal type and reference strains.

Preservation, Characterization and Exploitation of Microbial Biodiversity: The Perspective of the Italian Network of Culture Collections

Microorganisms represent most of the biodiversity of living organisms in every ecological habitat. They have profound effects on the functioning of any ecosystem, and therefore on the health of our planet and of human beings. Moreover, microorganisms are the main protagonists in food, medical and biotech industries, and have several environmental applications. Accordingly, the characterization and preservation of microbial biodiversity are essential not only for the maintenance of natural ecosystems but also for research purposes and biotechnological exploitation. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are crucial for the safeguarding and circulation of biological resources, as well as for the progress of life sciences. This review deals with the expertise and services of CCs, in particular concerning preservation and characterization of microbial resources, by pointing to the advanced approaches applied to investigate a huge reservoir of microorganisms. Data sharing and web services as well as the tight interconnection between CCs and the biotechnological industry are highlighted. In addition, guidelines and regulations related to quality management systems (QMSs), biosafety and biosecurity issues are discussed according to the perspectives of CCs and mBRCs.

International postal, quarantine and safety regulations

There are numerous legislative regulations that impact on microbiology, microbial Biological Resource Centres (mBRCs) and culture collections, with which all microbiologists must comply. These affect access for collection, handling, distribution/shipping and utilisation of microbial resources. Areas where regulations are triggered are international post, quarantine and safety. The legislation and supporting documents are often difficult to find and understand, therefore the World Federation for Culture Collections (WFCC) has a long history in providing advice and guidance to help compliance with such legislation. A visit to the WFCC library (http://www.wfcc.info/wfcc_library/) will provide information on postal requirements shipping dangerous goods and on control measures in place for biosecurity to control access to dangerous pathogens. This paper will update such communications and provide relevant information on: Health and Safety (H&S); Quarantine regulations; and Postal Regulations and Safety. Other papers in this special issue will address elements that impact on distribution and use of microorganisms for example in packaging, legislation on the proliferation, distribution and misuse of dangerous pathogens, export licensing measures, the Convention on Biological Diversity and the Nagoya Protocol, ownership of Intellectual Property Rights (IPR) and the provision of safety information to the recipient of microorganisms. The advice is generic and users are advised to refer to their own National guidance and implementation acts to ensure they are compliant. The work was compiled from authors' efforts in their management of an mBRC and most recently contributions to the EMBRIC project (http://www.embric.eu/) in particular Deliverable 6.1 ‘Microbial pipeline from environment to active compounds' (http://www.embric.eu/deliverables).

A standard proposal for biological resources centres

Purpose The purpose of this paper is to contribute to develop a standard providing requirements for managing the quality and competence of the biological resource centres (BRC). Design/methodology/approach The methodology for the standard setting was based on the principles of credibility, transparency, alignment and consistency. A justification study was performed to establish its objectives and scope, avoid overlap and prevent the risks in implementation. International documents providing rules for standard development were taken into consideration. Requirements were assembled from several standards and participation of interested parties was promoted. Findings No relevant international document exists covering fundamental issues for BRC operation. It is possible to develop a consistent and aligned standard, under a credible and transparent process that fits BRC purposes. Practical implications This standard will strengthen the BRC technical competence increasing its capability to provide authenticated high-quality biological materials – a crucial factor for biotechnological developments in the fields of health, agriculture and environment. It will serve as a basis for the BRC compliance assessment and the launch pad for establishing the global BRC network. Originality/value Original paper.

USMI Galaxy Demonstrator (UGD): a collection of tools to integrate microorganisms information

Due to the fragmentation of microbial information and the several branch of human activities encompassed by microorganism applications, a comprehensive approach for merging information on microbes is needed. Although on line service providers collect several data on microorganisms and provide services for microbial Biological Resource Centres (mBRCs), such services are still limited both in contents and aims. The USMI Galaxy Demonstrator (UGD), an implementation of the Galaxy framework exploiting the XML-based Microbiological Common Language (MCL), is meant to support researchers to make an integrated access to enriched information from microbial catalogues, as well as to help mBRC curators in validating and enriching the contents of their catalogues. Researchers and mBRC curators may exploit the UGD to avoid manual, potentially long, searches on the web and to identify and select microorganisms of interest. UGD tools are written in Python, version 2.7. They allow to enrich the basic information provided by catalogues with related taxonomy, literature, sequence and chemical compound data retrieved from some of the main databases on the basis of the strain number, i.e. the unique identifier for a given culture, and the species names. The data is retrieved by querying database Web Services using either the Simple Object Access Protocol (SOAP) or the Representational State Transfer (REST) access protocols. The MCL format provides a versatile way to archive and exchange data among mBRCs. Galaxy is a well-known, open, web-based platform which offers many tools to retrieve, manage and analyze different kind of information arising from any life science domain. By exploiting Galaxy flexibility,UGD implements some tools and workflows that can be used to find and integrate several information on microorganisms. UGD tools integrate basic information which may support mBRC staff in the insertion of all fundamental strain information in a proper format allowing integration and interoperability with external databases. They also extend the output by adding information on source materials, including species and strain numbers, and retrieve associated microorganisms which use a compound or an enzyme in whatever metabolic pathway by returning the accession number, synonyms, links to external databases, taxon name, and strain number of the requested molecule.

USMI Galaxy Demonstrator (UGD): a collection of tools to integrate microorganisms information

Due to the fragmentation of microbial information and the several branch of human activities encompassed by microorganism applications, a comprehensive approach for merging information on microbes is needed. Although on line service providers collect several data on microorganisms and provide services for microbial Biological Resource Centres (mBRCs), such services are still limited both in contents and aims. The USMI Galaxy Demonstrator (UGD), an implementation of the Galaxy framework exploiting the XML-based Microbiological Common Language (MCL), is meant to support researchers to make an integrated access to enriched information from microbial catalogues, as well as to help mBRC curators in validating and enriching the contents of their catalogues. Researchers and mBRC curators may exploit the UGD to avoid manual, potentially long, searches on the web and to identify and select microorganisms of interest. UGD tools are written in Python, version 2.7. They allow to enrich the basic information provided by catalogues with related taxonomy, literature, sequence and chemical compound data retrieved from some of the main databases on the basis of the strain number, i.e. the unique identifier for a given culture, and the species names. The data is retrieved by querying database Web Services using either the Simple Object Access Protocol (SOAP) or the Representational State Transfer (REST) access protocols. The MCL format provides a versatile way to archive and exchange data among mBRCs. Galaxy is a well-known, open, web-based platform which offers many tools to retrieve, manage and analyze different kind of information arising from any life science domain. By exploiting Galaxy flexibility,UGD implements some tools and workflows that can be used to find and integrate several information on microorganisms. UGD tools integrate basic information which may support mBRC staff in the insertion of all fundamental strain information in a proper format allowing integration and interoperability with external databases. They also extend the output by adding information on source materials, including species and strain numbers, and retrieve associated microorganisms which use a compound or an enzyme in whatever metabolic pathway by returning the accession number, synonyms, links to external databases, taxon name, and strain number of the requested molecule.