Biodiversity and the Role of Microbial Resource Centres

Lindsay I. Sly Professor School of Chemistry and Molecular Biosciences, University of Queensland

Paper prepared for presentation at the “ And World Food Security: Nourishing The Planet And Its People” conference conducted by the Crawford Fund for International Agricultural Research, Parliament House, Canberra, Australia, 30 August – 1 September, 2010

Copyright 2010 by Lindsay I. Sly. All rights reserved. Readers may make verbatim copies of this document for non-commercial purposes by any means, provided that this copyright notice appears on all such copies.

K EY B IODIVERSITY AND F OOD S ECURITY C HALLENGES

Biodiversity and the Role of Microbial Resource Centres

LINDSAY I. SLY School of Chemistry and Molecular Biosciences University of Queensland St Lucia, Queensland 4072, Australia Email: [email protected]

Micro-organisms were the first forms of life on and fuelling accelerated interest in biodiscovery. earth and have evolved into the most ecologically, The OECD is strongly promoting that biological genetically and metabolically diverse species resource centres are essential to underpin ad- known. Micro-organisms belong to all three Do- vances in , the life sciences and the mains of life: The Bacteria, Archaea and Eukarya bioeconomy. Microbial resource centres are more as well as the . They have shaped the than collections. They work within the Convention of the planet and continue to nurture and on Biological Diversity (CBD) that was imple- sustain the environment, plants and animals on mented to support the conservation and utilisation which human society depends. While we continue of biodiversity and recognises the principles of fair to face difficulties posed by emerging animal, and equitable benefit sharing. They preserve and plant and human pathogens, most micro- provide authenticated, genetically stable microbial organisms are beneficial. Exploitation of microbial and cell cultures, provide access to information on genetic diversity has been fundamental to ad- cultures and their characteristics, and undertake vances made in biodiscovery and biotechnology. identification and description of new species. In Micro-organisms are major sources of important Australia, the Council of Heads of Australian pharmaceutical and industrial products for world- Collections of Micro-organisms is collaborating wide community benefits in health, agriculture and with the NCRIS Atlas of Living Australia project to industry. Cultures of micro-organisms have been develop the Australian Microbial Resources essential for the production of enzymes, fermenta- Information Network (AMRiN) integrated collec- tion products and metabolites. With advances in tions database to provide access to information on , genes of micro-organisms and Australian microbial cultures for use in research, whole natural communities are being exploited industry, government and education.

EMERITUS PROFESSOR LINDSAY SLY was Profes- Importance of microbial diversity sor of Microbial Systematics and Microbial Ecology, Director of the Centre for Bacterial Micro-organisms were the first forms of life on Diversity and Identification, and Curator of the earth and have evolved into the most ecologically, Australian Collection of Micro-organisms at the genetically and metabolically diverse species University of Queensland where he undertook known. Micro-organisms belong to all three research and teaching of the biodiversity, physi- Domains of life: the Bacteria, Archaea and Eu- ology, metabolism and ecology of bacteria from karya (algae, fungi, and protozoa), as well natural and industrial environments. He has as the Viruses. They have shaped the evolution of made major contributions to knowledge of microbial diversity, to the understanding of the planet and continue to nurture and sustain the phylogentic relationships amongst species in environment, plants and animals on which human diverse bacterial and archaeal divisions, and to society depends. I have previously reviewed the the development of molecular tools for the importance of microbial diversity and the role of identification of bacteria. In 2001 his contribu- microbial resource centres (Sly 1998a) and the tions were recognised with the prestigious following highlights the important issues raised in international Bergey Award. He was president of that publication. the World Federation for Culture Collections from 1996 to2000 and is currently Chair, Coun- Micro-organisms are an essential component of cil of Heads of Australian Collections of Micro- biological diversity, without which there can be organisms. no sustainable ecosystems (Hawksworth 1991,

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1992; Hawksworth and Colwell 1992; Sly 1994; recycling of the elements in nature, and are impor- Center for Microbial Ecology 1995; Staley et al. tant components of food webs. Micro-organisms 1997). It is estimated that at least 50% of the often have unique functions (e.g. nitrogen fixa- living biomass on the planet is microbial (Center tion, nitrification, denitrification, for Microbial Ecology 1995) yet probably < 0.1% chemolithoautotrophic carbon dioxide fixation, have been characterised. Micro-organisms provide methane formation and sulfate reduction) in the a major source of genetic information for molecu- biogeochemical cycles, in soil formation and in lar biology and biotechnology (Bull et al. 1992; climate regulation, and influence atmospheric Nisbet 1992; Center for Microbial Ecology 1995; composition (including greenhouse gases— Staley et al. 1997). While some micro-organisms Rogers and Whitman 1991). The first micro- are serious pathogens of humans, animals and organisms evolved over 3.8 billion years ago and plants and pose a threat to health, food security consequently exhibit the greatest breadth of ge- and food safety, most are beneficial and sustain netic and metabolic diversity on the planet, far the environment and soil health. Plants and ani- greater than that of the plants and animals com- mals depend on microbes to grow and perform bined (Center for Microbial Ecology 1995; Staley optimally. et al. 1997). Some are able to grow under extreme conditions, and also in anaerobic environments Most advances in knowledge of the function and that cannot sustain plant or animal life. Micro- role of micro-organisms have been derived from organisms often exhibit symbiotic relationships pure culture studies, while most advances on the with plants (e.g. Rhizobium, Frankia and my- ecology and interactions of micro-organisms are corrhizal fungi in plant roots) and with animals likely to come from the application of molecular (e.g. tube worms and mussels). Animals depend studies using signature DNA and rRNA probes. on micro-organisms in their intestinal tracts for These studies have highlighted many important digestion and for the production of nutrients and functions of micro-organisms in relation to agri- essential vitamins. cultural processes and food security. However, until we have more complete knowledge of mi- The genetic and metabolic diversity of micro- crobial species and functional diversity, decisions organisms has been exploited for many years in about the role of micro-organisms and their influ- biotechnological applications such as antibiotic ence on sustainable ecosystems are being made on production, food, food processing, alcoholic the basis of very incomplete information. Without beverages, fermented foods and waste treatment. a thorough knowledge of microbial diversity and Micro-organisms are the major sources of anti- ecology, decisions concerned with sustainability microbial agents and also produce other important are likely to be flawed. pharmaceutical and therapeutic compounds in- cluding antihelminthics, antitumour agents, Recent advances in molecular methods (Woese insecticides, immunosuppressants, immunomodu- 1987; Ward et al. 1990, 2008; Liesack and lators and vitamins worth $35–50 billion annually Stackebrandt 1992; Stackebrandt et al. 1993; in global sales (Center for Microbial Ecology Olsen et al. 1994; Amann et al. 1995; Hugenholtz 1995). and Pace 1998) have revealed the inability of traditional culturing methods to fully show the The scientific benefits of microbial diversity diversity of bacteria and other micro-organisms, research include a better understanding of the role and have shown that the species diversity in most and function of microbial communities in various terrestrial and aquatic environments is far greater terrestrial, marine and aquatic environments; a than expected. The vast majority of microbial better understanding of the sustainable ecology of diversity (> 90%) remains to be discovered and its plants and animals; improved capacity to maintain function determined as there are no or few cul- soil fertility and water quality; and a better under- tured representatives in an increasing number of standing of the full consequences of animal and phylogenetic lineages. Consequently, actions plant extinctio; and of perturbations on ecosys- which lead to loss of microbial diversity are likely tems. The economic and strategic benefits are the to result in the loss of valuable knowledge of our discovery of micro-organisms for exploitation in natural microbial resources and understanding of biotechnological processes for new antibiotic and sustainability drivers. therapeutic agents; probiotics; novel fine chemi- cals, enzymes and polymers for use in industrial Micro-organisms occupy important niches in all and scientific applications; for bioremediation of ecosystems and are responsible for much of the

B IODIVERSITY AND W ORLD F OOD S ECURITY 61 polluted environments and bioleaching and recov- Biological Resource Centres (OECD 2001, 2007). ery of minerals; as well as preparedness against Microbial resource centres are more than collec- exotic and emerging pathogens of humans, ani- tions. They work within the CBD that was mals and plants. implemented to support the conservation and utilisation of biodiversity and recognises the The signing of the Convention on Biological principles of fair and equitable benefit sharing. Diversity in 1992 (CBD) (UNEP 1992) focussed They preserve and provide authenticated, geneti- attention on the value of micro-organisms as cally stable microbial and cell cultures, provide sources of genetic information (Bull et al. 1992; access to information on cultures and their charac- Nisbet 1992; Center for Microbial Ecology 1995; teristics, and undertake identification and Staley et al. 1997). At about the same time the description of new species. The fundamental role development of molecular methods for detecting is the ex-situ conservation and supply of viable micro-organisms in the environment revealed the and genetically stable cultures and genes for poor state of knowledge of both cultured and non- scientific research and testing. Important cultures cultured microbial diversity (e.g. Ward et al. resulting from research are accessioned, studied 1990; Liesack and Stackebrandt 1992; Stacke- and conserved. These functions enable and add brandt et al. 1993; Amann et al. 1995; Hugenholtz value to research for applications in industry and and Pace 1996). Subsequently, extensive research biotechnology. Microbial resource centres also effort and substantial research funding has been maintain extensive databases and thus provide directed to the areas of microbial diversity, micro- access to information on cultures, their character- bial ecology and biotechnology in Asia, the istics, literature and DNA sequences, for example. European Community and the USA (Clutter 1995; They also are centres of taxonomic expertise for Staley et al. 1997). North–South attention has also identification and characterisation of micro- been directed towards collaborations with devel- organisms and provide training in taxonomy and oping countries in the tropical ‘megadiversity’ preservation. With the decline in the teaching and regions. In addition, many developing countries research training in microbial taxonomy in univer- have become appreciative of the need to explore, sities, microbial resource centres are likely to have protect and exploit their own microbial resources. an increasingly important role in taxonomy re- Australia is in a unique position to take advantage search training that needs to be recognised and of the wide range of ecological habitats of micro- funded accordingly. bial diversity within its own boundaries and in the Asia–Pacific region through collaboration (Hawk- Maintaining living microbial cultures requires sworth 1994). Access to microbial resources and specific conservation skills and quality assurance sovereign rights with respect to micro-organisms to ensure genetic stability. It is essential that in environmental samples and cultures in collec- microbial cultures are considered as a global tions have been the focus of international resource for the orderly progress of science and meetings (Kirsop and Hawksworth 1994; Sands technology. However, such a strategy necessitates 1994; WFCC 1996) Australia, like most signatory that each country meets its obligations wherever countries to the CBD, has been developing na- possible. There are strategic advantages for the tional and international protocols for access and ex-situ conservation of micro-organisms within benefit sharing. the country of origin. Worldwide there are almost 600 culture collections of micro-organisms in 68 Microbial resource centres countries registered with the WFCC World Data Centre on Micro-organisms Microbial resource centres have an extremely (http://www.wfcc.info/datacenter.html). These important role underpinning the conservation of collections hold 1.5 million cultures of micro- microbial biodiversity and enabling advances in organisms and cultured cell lines, with by far the agriculture, food security, biotechnology and majority being held in Europe, North America and education. They constitute essential scientific Asia. It is concerning that only 11 collections are infrastructure that maintains collections of cul- listed for Africa and none in the Pacific region. tures of micro-organisms—living libraries of our Currently there are 35 collections listed for Aus- natural scientific heritage. Depending on their tralia, down from 50 in 1998 (Sly 1998b). In research roles, services provided and quality 1998, these microbial resource centres in Austra- systems, they are also referred to as Microbial lia held 65 000 cultures and it is important that the Genetic Resource Centres, and more recently as microbial diversity in these collections is pro-

B IODIVERSITY AND W ORLD F OOD S ECURITY 62 tected and the on-going loss stabilised. Culture collections in Australia primarily have institu- Table 1. Examples of areas where microbial resource tional roles and the host institutions are usually centres contribute to agriculture and food security universities, CSIRO and government laboratories, Plant endosymbionts (e.g. Rhizobium for biological together with a few industries (DEST 1966). Most nitrogen fixation) cultures are bacteria and fungi with minor hold- Plant growth-promoting bacteria ings of protozoa, algae, viruses, plasmids and vectors, and animal cell lines. A number of collec- Biocontrol agents (e.g. pathogens of weeds, fungi, insects) tions are engaged in plant pathology, taxonomy, mycorrhizal , insect microbiology, Inocula to restore soil health and nutrient release (e.g. forest microbiology, food science and ecology, as phosphorus) well as plant breeding and biodeterioration of Source of genes for plant improvement (e.g. insect significance to agriculture and food security. resistance) Reference cultures for food safety testing, quarantine, Key functions in agriculture and trade Reference cultures for animal and plant disease food testing Microbial resource centres have played a key role Enzymes for food improvement and processing in agricultural and food research over many Cultures for food fermentations and nutritional decades. The Food and Agriculture Organization supplements (FAO) recognises the important role of microbial Innovative biodiscovery genetic resources and microbial resource centres for productive agriculture and food security (FAO 2009) and also in understanding the consequences Table 2. Examples of significant international collections of climate change (Fujisaka et al. 2009). Exam- ples of areas where microbial resource centres National Collection of Plant Pathogenic Bacteria contribute to agriculture and food security are (UK) shown in Table 1. Table 2 lists examples of sig- CABI Genetic Resource Collection (UK) nificant international collections that have had a Centraal Bureau voor Schimmelcultures long-term involvement in the conservation and (Netherlands) supply of cultures for research and regulatory USDA ARS Culture Collections (USA) compliance. Not only do these collections provide valuable resources and expertise; the cultures American Type Culture Collection (USA) from this research are available for extension of Canadian Collection of Fungal Cultures (Canada) this research. The intersection of existing knowl- Agricultural Culture Collection of China (China) edge and resources with often new independent International Collection of Micro-organisms from discoveries frequently leads to accelerated innova- Plants (New Zealand) tion (e.g. development of PCR). Table 3 lists examples of significant Australian collections which continue to contribute to Australian micro- bial resources for agriculture, food microbiology, biotechnology. UNESCO, through its Microbial plant pathology, quarantine and trade. Resource Centres Network (MIRCEN), has fos- tered and supported the development of collections in developing countries and the train- Global networking initiatives ing of scientists in the management and The World Federation for Culture Collections maintenance of collections as well as long-term (WFCC) is the peak international body that fosters cryopreservation techniques. In 1972 the WFCC culture collections, their documentation and with the support of UNESCO and UNEP estab- networking. The WFCC and the OECD Director- lished the WFCC World Data Centre for Micro- ate for Science, Technology and Industry, organisms (WDCM) at the University of Queen- Committee for Scientific and Technological sland to document the metadata and species Policy (OECD 2001) recognise that biological holdings of the worlds’ microbial culture collec- resources in culture collections are a world re- tions. In 1986 the WDCM was transferred to the source that needs to be accessible across national RIKEN in Japan and subsequently to the National boundaries for the orderly progress of science and Institute of , and will move to the Insti-

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of the life sciences, biotechnology, industry and Table 3. Significant agricultural and food microbial education, and will allow Australia to join the collections in Australia emerging OECD Global Biological Resource Rhizobium Research Collections, Sydney, Adelaide, Centre Network (GBRCN). Perth Australian Legume Inoculants Research Unit, NSW Australian Microbial Resources Department of Primary Industries, Gosford Research Network BRIP Plant Pathology Herbarium Collection, The Australian Microbial Resources Research Queensland Primary Industries & Fisheries, Brisbane Network was established within the framework of CSIRO Food and Nutritional Sciences Collection, the ARC Research Network Seed Funding Pro- Sydney gram in 2004. While not receiving further funding IMVS Culture Collection, Institute of Medical and for the development of a full ARC Research Veterinary Science, Adelaide Network, the seed funding played an important Department of Agriculture & Food Western Australia catalytic role. The Research Network aims to Plant Pathogen Collection, Perth provide integrated electronic access to Australian Phytoplasma DNA Collection, Charles Darwin collections of micro-organisms and to bioinforma- University, Darwin tion databases to meet national strategic needs for Australian Wine Research Institute, Adelaide microbiological resources and to support the CSIRO Livestock Industries, Brisbane competitive development of the life sciences and Plant Pathology Herbarium Collections, New South biotechnology industries in Australia. This objec- Wales Agriculture, Orange tive is now being fulfilled through collaboration in Australian Collection of Micro-organisms, University the NCRIS ‘Atlas of Living Australia’ project. of Queensland, Brisbane The network links researchers and fosters the discovery and exploitation of Australian microbial resources and associated information. tute of Microbiology of the Chinese Academy of The Australian Microbial Resources Information Science in 2011. The WDCM remains the authori- Network (AMRIN) web site tative record of the worlds’ microbial resource (http://www.amrin.org/Home.aspx) has been centres and continues to adapt to new information developed to improve access to information technologies and develop to meet changing global sources and to facilitate scientific advances and needs. efficiency through collaboration. AMRiN will be further developed as a database hub within the The OECD has recognised the essential role of Atlas of Living Australia to integrate the data biological resource centres for the life sciences within Australia’s microbial culture collections. and biotechnology (OECD 2001) and has devel- Recently, AMRRN established the Council of oped best-practice guidelines for biological Heads of Australian Collections of Micro- resource centres (OECD 2007). To progress the organisms (CHACM) (http://www.chacm.org) as development of standards to implement the best- the peak body to foster and oversee the develop- practice guidelines, a demonstration project for a ment of microbial culture collections and Global Biological Resource Centre Network development of BRCs in Australia. (http://www.gbrcn.org/index.php) commenced in 2008 involving BRCs in 15 countries including Canada, United Kingdom, Netherlands, France, Atlas of Living Australia Belgium, Germany, Finland, Portugal, Spain, The ‘Atlas of Living Australia’ (ALA) Italy, China, Japan, Brazil, Uganda and Kenya. In (http://www.ala.org.au/) is a very welcome out- order to maximise Australia’s global collaboration come from the Australian National Collaborative and to provide world-class microbial resource Research Infrastructure Strategy (NCRIS) initia- centre facilities, there is an urgent need to develop tive to develop science infrastructure capacity for a network of OECD-compliant biological resource the future. NCRIS identified the need to have centres by establishment of purpose-built facilities access to information in Australia’s biological and or up-grading of suitable microbial culture collections to foster research and help in govern- collections (Sly 2008). This infrastructure will ment and community decision-making. The ALA enhance current and future progress in many areas is being developed in collaboration with the

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Australian biological collections communities in order to be internationally relevant and engaged in museums, herbaria, government, research insti- collaborative programs, collections will also need tutes and universities to provide integrated to meet emerging international OECD GBRCN electronic access to data and biological material best-practice standards that will in most cases for research and other applications. The ALA require improvements in facilities and staffing project enables free access to Australian biodiver- levels. There is a need to improve the future sity information online with the first public security of microbial resource centres by inclusion release of information scheduled for October in national and international infrastructure pro- 2010. The atlas will provide online access to grams. This move will help reverse the loss of biodiversity information from museums, herbaria collections and the microbial biodiversity when and biological collections, including information researchers retire or institutes change direction previously not available to the public, research and priorities. Exploitation of the untapped poten- literature, observations, maps and images. tial of microbial diversity and innovative biodiscovery will be fostered by the support of The development of the ALA is evidence of microbial resource centres. government recognition of the importance of this information for innovative science. However, to Making biological collections eligible for long- maximise the impact, funding is also required for term infrastructure funding will enable fulfillment maintenance and expansion of collections. This is of the recommendations to strengthen and support particularly so for microbial collections and culture collections of micro-organisms made in biological resource centres seeking compliance The National Strategy on the Conservation of with OECD GBRCN best practice guidelines for Australia’s Biological Diversity (1992), the House incorporation of quality systems for living mate- of Representatives Standing Committee on Pri- rial such as microbial and cell cultures. mary Industries and Regional Services report on Bioprospecting: Discoveries Changing the Future Issues, challenges and (2001), and the report on the Review of the Inno- recommendations vation System, Department of Innovation, Industry, Science and Research (Cutler 2008). Microbial resource centres underpin the life There is an urgent need to train and mentor the sciences and enable advances in agriculture, food next generation of taxonomists and curators of security, biotechnology and education, but their microbial resource centres. Many curators of important role needs more recognition and support collections are approaching retirement and many from government, funding agencies and host who have already retired are not being replaced. institutions. Apart from their fundamental role for Likely global changes (e.g. climate change) will the conservation of microbial biodiversity, they probably affect microbial ecology and species’ are necessary for the supply of reference control ranges and affect demand on microbial resource cultures essential for regulatory compliance for centres and their expertise. health and trade. Many government ministries and agencies support programs in agriculture, food, Various reports have called for accelerated re- health, quarantine, industry, science and education search on microbial diversity. Such an initiative which depend on taxonomic decisions and access would expand knowledge and opportunities for to standard cultures for quality assurance and biodiscovery and innovative agriculture and food regulatory compliance. There is also a growing industries. It would also help to reverse the de- need to manage impediments limiting exchange of cline in teaching and research training in cultures between researchers due to quarantine microbial taxonomy and ecology in universities. requirements, commercial IP, biosecurity, and One model which should be considered is the access and benefit-sharing protocols. establishment of ‘research centres of excellence’ in microbial diversity, taxonomy and ecology in New long-term infrastructure funding mechanisms collaboration with collections. This would assist are needed to support microbial resource centres. in training the next generation(s) of research Apart from the ex-situ conservation and supply of scientists and academics in microbial biodiversity current microbial genetic resources, there needs to and taxonomy to meet future challenges. As be more comprehensive accession of cultures used taxonomic expertise has been run down across the in research publications and publically funded biological disciplines, biological resource centres research projects than is currently the case. In will become the centres of taxonomic expertise to

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