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Comission on Gentic BACKGROUND STUDY PAPER NO. 64 March 2013 E Organización Food and Organisation des Продовольственная и de las Agriculture Nations Unies cельскохозяйственная Naciones Unidas Organization pour организация para la of the l'alimentation Объединенных Alimentación y la et l'agriculture United Nations Наций Agricultura COMMISSION ON GENETIC RESOURCES FOR FOOD AND AGRICULTURE STATUS AND TRENDS OF THE CONSERVATION AND SUSTAINABLE USE OF MICROORGANISMS IN AGROINDUSTRIAL PROCESSES By Iordanis Chatzipavlidis, Io Kefalogianni, Anastassia Venieraki1and Wilhelm Holzapfel2 This document has been prepared at the request of the Secretariat of the FAO Commission on Genetic Resources for Food and Agriculture, and in close collaboration with the FAO Rural Infrastructure and Agro-Industries Division, to facilitate the Commission’s discussions when it will review key issues in micro-organisms and invertebrates at its Fourteenth Regular Session. The content of this document is entirely the responsibility of the authors, and does not necessarily represent the views of the FAO or its Members. 1 Agricultural University of Athens, Department of Agricultural Biotechnology, GR-11855 Athens, Greece 2 Professor at the School of Life Sciences, Handong Global University, Pohang, Gyeongbuk, 791-708, The Republic of Korea This document is printed in limited numbers to minimize the environmental impact of FAO's processes and contribute to climate neutrality. Delegates and observers are kindly requested to bring their copies to meetings and to avoid asking for additional copies. Most FAO meeting documents are available on the Internet at www.fao.org BACKGROUND STUDY PAPER NO.64 ii TABLE OF CONTENTS Abbreviations and Acronyms v Executive Summary vii I. Introduction 1 I.1 Background and rationale 1 I.2. The demand for an environmentally friendly agriculture 1 I.2.1. The use of microorganisms in agro-industrial processes 2 I.3. Scope of the study 4 I.3.1. Objectives 4 I.3.2. Methodology 5 II. The current status and trends in the use of microorganisms in Agro-industrial processes 5 II.1. Microbes and microbial products 5 II.2. Biofertilizers 6 II.2.1. Microorganisms 6 II.3. Bio-pesticides 9 II.3.1. Global bio-pesticides market 10 II.3.2. Biological control agents 11 II.4. Effective Microorganisms (EM) 13 II.4.1. Application of EM 13 II.5. Composting agro-industrial wastes 15 II.5.1. Composition of agro-industrial wastes 15 II.5.2. Uses of agro-industrial wastes 16 II.6. Production of microbial metabolites 18 II.6.1. Substrate and methods 19 II.6.2. Organic acids 21 II.6.3. Flavour and aroma compounds 22 II.6.4. Enzymes 23 II.6.5. Fructooligosaccharides (FOS) 23 II.6.6. Bioactive compounds 23 II.6.7. Microbial pigments 25 II.6.8. Production of protein enriched feed 25 II.6.9. Polysaccharides 26 II.6.10. Bio-plastics 26 II.6.11. Bio-fuels 28 II.7. Bio-remediation 35 II.7.1. Bio-remediation of olive mill wastewater 36 II.8. Ensiling 38 II.9. Impact of climate change on the sustainable use and conservation of microorganisms in agro-industrial processes 38 II.9.1. Role of microorganisms in buffering climate change 39 II.9.2. Microbial biodiversity leads to ecosystem resilience and sustainability 40 II.9.3. Impact of climate change on microbes 40 II.9.4. Adaptability of microorganisms to a changing ecosystem – Impact of climate changes 41 II.9.5. Microbial resistance to climate change 41 II.9.6. Elevated temperature - global warming and its effect on severity of microbial pathogens 42 II.9.7. Effect of climate and environmental conditions on l iquid inocula 42 II.10. Can the use/application of microorganisms in agro-industrial BACKGROUND STUDY PAPER NO.64 iii processes mitigate the effects of climate-change in any way? 43 II.10.1. Involvement of biotechnology in climate- change adaptation and mitigation: Improving agricultural yield 43 II.10.2. Strategies for using microorganisms towards mitigating climate change 44 II.11. Future research on climate change and responses of microbial communities 45 II.11.1 Managing microbial communities to reduce carbon dioxide emissions 45 II.11.2. Managing microbial communities for generation of bio-fuels 45 II.11.3. Managing microbial communities to reduce methane emissions 46 II.11.4. Managing microbial communities to reduce N2O emissions 46 II.11.5. Microorganisms, process rates and climate models 48 II.12. Impacts of climate change - Gaps in knowledge – Recommendations 48 II.12.1. Gaps in key knowledge 49 II.12.2. Proposed key actions 50 II.12.3. Conclusions and implications 50 II.12.4 Monitoring and surveillance 52 II.12.5. Methods for characterising microbial species, communities and their functions 53 II.12.6. Standardised methods and metadata 53 II.12.7. Models for microbial function 53 II.13. Conclusions (climate) 53 III. The Conservation of Microorganisms used in Agro-industrial Processes 54 III.1. Importance of Biodiversity 54 III.1.1. Role of diversity in the use and conservation of microbes 55 III.1.2. Biodiversity: conservation and collections of microorganisms 56 III.2 Conservation practices 57 III.2.1. Organic agriculture 58 III.2.2. Integrated pest management 58 III.2.3. Biological control 60 III.2.4. Compost and soil organic matter 60 III.2.5. Culture collections 61 IV Looking forward : preparing for the future 63 IV.1. Organic agriculture 63 IV.1.1. Knowledge, skills and support 65 IV.1.2. Biofertilizers 66 IV.1.3. Use of Biofertilizers - recommendations 66 IV.2. Bio-pesticides – recommendations 71 IV.3. Bio-fuels – recommendations 76 IV.4. Compost - recommendations 78 IV.5. Microbial Metabolite- General Recommendations 78 IV.5.1 Agricultural biotechnology 79 IV.5.2. New sequencing technologies in characterisation of microbial diversity 80 IV.5.3. Nanotechnology 80 IV.5.4. Applications for new sequencing technologies 80 IV.5.5. Meta-approaches: metagenomics, metatranscripromics, metaproteomics 80 iv BACKGROUND STUDY PAPER NO.64 IV.6. Policies, Main Gaps 83 IV.6.1. Relative instances 84 IV.7. Questionnaires and analysis of interviews 85 V Conclusions and Future Prospects 88 V.1. Conclusions 88 V.2. Future Prospects 89 References 93 Glossary 106 Annex I 108 Uses of microorganisms in agro-industrial processes 108 Table I. Plant responses to inoculation with PGPR 108 Table II. Biocontrol agents for control of plant pathogens 116 Table III. Use of agro-industrial residues and by-products for the production of microbial metabolites 125 Annex II Country and regional examples on policies and main gaps in the industrial uses of microorganisms 135 List of Figures No. Title Page 1 Trends in the global market for microbes and microbial products, 2010-2016 (in US$ Millions) 5 2 Bio-pesticides: The Global Market (February 2010) 10 3 Total waste generation in the EU-27 by economic activity 15 4 Market share of products derived from microbes 19 5 Use of bio-plastics by region, 2008-2015 28 6 World bio-fuel production (Million tons oil equivalent) 28 7 Bio-fuel production in selected countries - Projection to 2016 29 8 Ethanol Production by feedstocks used 30 9 Estimated change in prices of bioethanol and biodiesel between the forthcoming and the previous decade 33 10 Trends in ethanol production from conversion of agricultural waste 34 11 A proposed framework for future research on climate change and ecological responses 47 12 Number of currently known living species of all organisms 55 13 World map of organic agriculture growth rates for 71 countries over a decade (2001-2011) 64 14 Which kind of bio-inoculants/biofertilizers or related products is most popular? 86 15 Which sectors are advising farmers on the application of bio-inoculants/biofertilizers or related products? 87 16 Who advices farmers when they apply bio-inoculants / biofertilizers and/or related products? 87 List of Tables No. Title Page 1 Microorganisms and their specific functions in agro-industrial processes 3 2 Conversion of lignocellulose into valuable products using Solid State Fermentation (SSF) 20 3 Questionnaire analysis (companies experts) 85 BACKGROUND STUDY PAPER NO.64 v Abbreviations and Acronyms AMF: Arbuscular Mycorrhizal Fungi ASPAC: Asian-Pacific ATMA: Agricultural Technology Management Agency B.: Bacillus BDAs: Biodiversity Development Agreements BIS: Bureau of India Standards BRCs: Biological Resource Centers CAGR: Compound Annual Growth Rate CAP: Common Agricultural Policy DNA: Deoxyribonucleic Acid E. coli: Escherichia coli EM: Effective Microorganisms EPA: Environmental Protection Agency EPS: extracellular polymeric substances FAO: Food and Agriculture Organization of the United Nations FOS: Fructooligosaccharides GHG: Greenhouse Gas GIA: Global Industry Analysis GMOs: Genetically Modified Rumen Microorganisms ICAR: Indian Council of Agricultural Research ICARDA: International Centre for Agricultural Research in Dry Areas INM: Integrated Nutrient Management IOC: International Oil Council IPM: Integrated Pest Management ISOPOM: Integrated Scheme of Oilseeds, Pulses, Maize and Oil palm LAB: Lactic Acid Bacteria LGT: Lateral Gene Transfer MDA: Multiple Displacement Amplification mRNA: messenger Ribonucleic Acid NABARD: National Bank for Agricultural and Rural Development NBDC: National Biofertilizer Development Centre NFM: Nitrogen Fixing Microbes NFSM: National food Security Mission NGO: Non-Governmental Organization NGS: Next-Generation Sequencing NPOF: National Project on Organic Farming OECD: Organization for Economic Cooperation and Development P.: Pseudomonas PCR: polymerase chain reaction PGPMs: plant growth-promoting microorganisms PGPRs:
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