Biosafety and the environmental uses of micro-organisms : conference proceedings.

223 Pages·2015·4.951 MB·English

by  OECD

Biosafety and the
Environmental Uses
of Micro-Organisms
COnfErEnCE PrOCEEdings
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Biosafety and the
Environmental Uses
of Micro-Organisms
CONFERENCE PROCEEDINGS
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3
FOREWORD –

Foreword
This publication constitutes the proceedings of the OECD conference on
the “Environmental Uses of Micro-Organisms: An Overview of the State-of-the-Art and
Implications for Biotechnology Risk/Safety Assessment”. This event, organised under the
auspices of OECD’s Working Group on the Harmonisation of Regulatory Oversight in
Biotechnology (WG-HROB), was held on 26-27 March 2012. A total of 100 participants
attended the conference, which was open to OECD delegates as well as external
scientists, regulators and interested individuals. It was developed in collaboration with the
OECD Co-operative Research Programme under the Trade and Agriculture Directorate.
OECD has undertaken activities related to the safety of the environmental uses of
transgenic organisms (also known as genetically-modified organisms) since the mid-
1980s. The Working Group was established in its current form in 1995. Since that time,
its programme of work has included activities related to the environmental risk/safety
assessment of transgenic organisms with a major focus on transgenic plants.
In addition to this core activity on agricultural crops, the Working Group has long had
a number of projects related to the safety of environmental applications involving micro-
organisms. This has resulted in a number of publications, some of them dealing with
specific groups of micro-organisms which have been used in environmental applications
such as Pseudomonas, Acidithiobacillus, Acinobacter and Baculoviruses. Other
publications have addressed issues of importance in the risk/safety assessment of bacteria
such as taxonomy, detection methods, horizontal gene transfer and pathogenicity factors.
There have been many scientific developments in recent years related to the use of
micro-organisms in the environment and the conference was an opportunity to provide an
overview of the current situation, focusing on concrete or expected developments
involving the use of transgenic micro-organisms in the environment.
Following the conference, the Working Group discussed the outcomes and identified
a number of areas in which the use of transgenic micro-organisms is either already
underway or is likely to be forthcoming in the near future. At the time of writing,
the Working Group has agreed to launch a project for developing a guidance document
on the use of micro-algae. This document will aim to provide background information
which could be used in an environmental risk assessment. As for the other topics
addressed at the conference, some may be included in the programme of work of
the Working Group at a later stage, but this will depend on the resources available.

BIOSAFETY AND THE ENVIRONMENTAL USES OF MICRO-ORGANISMS: CONFERENCE PROCEEDINGS © OECD 2015
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– ACKNOWLEDGEMENTS

Acknowledgements
This publication includes the outputs of the OECD conference on the Environmental
Uses of Micro-Organisms: An Overview of the State-of-the-Art and Implications for
Biotechnology Risk/Safety Assessment, held in March 2012. The conference was
organised by OECD’s Working Group on Harmonisation of Regulatory Oversight in
Biotechnology with the support of Co-operative Research Programme. The OECD
Secretariat is grateful to all members of the Working Group, including the Chair and co-
Chairs, for their work in preparing and attending the event. The contributions made
by both speakers and participants were invaluable. At the same time, special thanks must
go to Hans Bergmans (former Chair of the Sub-Working Group on Micro-organisms)
for his major contribution to the arrangements. Thanks are also due to OECD colleagues
Carl-Christian Schmidt, Janet Schofield and Nathalie Elisseou Leglise from the Co-
operative Research Programme who did much to support the conference. Jennifer Allain
prepared the manuscript for the publication. The arrangements for the conference were
managed by Peter Kearns, Bertrand Dagallier, Kazuyuki Suwabe and Takahiko Nikaido
of the OECD Secretariat, who were also responsible for editing this document.

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TABLE OF CONTENTS –

Table of contents
Abbreviations and acronyms ......................................................................................................... 11
Executive summary ......................................................................................................................... 13
Introduction: Micro-organisms, public health and the environment ........................................ 15
Outcomes of the OECD conference on the “Environmental Uses of Micro-Organisms” ............. 16
Prospects and potential new biosafety projects for the OECD ...................................................... 19
References ..................................................................................................................................... 20
Part I The use of micro-organisms in agriculture ........................................................................ 21
Chapter 1 Biofertilizers: Present and future use of transgenic micro-organisms ..................... 23
Introduction ................................................................................................................................... 24
Symbiotic biofertilizers ................................................................................................................. 26
Free-living or non-symbiotic biofertilizers ................................................................................... 27
Helper bacteria .............................................................................................................................. 31
Conclusion ..................................................................................................................................... 31
References ..................................................................................................................................... 32
Chapter 2 Phytosanitation and the development of transgenic biocontrol agents .................... 35
Introduction ................................................................................................................................... 36
Mechanisms of plant defense ........................................................................................................ 36
Biological control by indigenous and introduced micro-organisms .............................................. 36
Barriers to the wider use of biocontrol technology ....................................................................... 37
Why transgenic biocontrol agents? ............................................................................................... 38
Molecular genetic modifications to biocontrol agents .................................................................. 39
Case study: Introduction of phenazine genes into Pseudomonas spp. .......................................... 41
Conclusion ..................................................................................................................................... 42
References ..................................................................................................................................... 43
Chapter 3 Lessons of the impact of genetically engineered micro-organisms on
natural ecosystems like soil ............................................................................................................ 47
Introduction ................................................................................................................................... 48
The great plate count anomaly and methods that can overcome it ................................................ 49
The soil ecosystem – its natural (normal) status, functioning and resilience ................................ 50
The normal operating range of soil function as the grand descriptor of normality ....................... 51
Outlook .......................................................................................................................................... 54
References ..................................................................................................................................... 55

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Part II The use of microalgae for production purposes ............................................................... 57
Chapter 4 The need and risks of using transgenic microalgae for the production
of food, feed, chemicals and fuels .................................................................................................. 59
Importance of transgenic microalgae ............................................................................................ 60
Genetic modification of algae ....................................................................................................... 60
European regulations for working with genetically modified organisms ...................................... 64
Risks related to production systems of (GM-)algae ...................................................................... 64
References ..................................................................................................................................... 68
Chapter 5 The benefits and advantages of commercial algal biomass harvesting ..................... 73
Concept of bioremediation using microalgae with value-adding co-product development .......... 74
Taxonomic affiliations: Implications for potential end product use.............................................. 75
Considerations for strain selection for commercial-scale algal production .................................. 81
Cultivation considerations ............................................................................................................. 84
Harvest and process considerations ............................................................................................... 86
Conclusion ..................................................................................................................................... 88
References ..................................................................................................................................... 89
Chapter 6 Issues in the risk assessment of the use of microalgae for production
purposes ........................................................................................................................................... 93
Introduction ................................................................................................................................... 94
Activities of the Algae Working Group of the Biomass Research and Development Board ........ 94
Example: The Toxic Substances Control Act (TSCA).................................................................. 95
Issues identified by the United States Environmental Protection Agency .................................... 96
Conclusion ..................................................................................................................................... 97
References ..................................................................................................................................... 99
Part III The use of micro-organisms for bioremediation .......................................................... 101
Chapter 7 Designing bacteria for the environment: From trial and error to
earnest engineering ....................................................................................................................... 103
Introduction ................................................................................................................................. 104
Genetically modified organisms for the environment: What went wrong? ................................. 104
Think big: Global challenges ...................................................................................................... 106
The onset of systems biology ...................................................................................................... 107
Synthetic biology: The next frontier ........................................................................................... 108
New risks in sight? ...................................................................................................................... 110
References ................................................................................................................................... 110
Chapter 8 The intentional release of micro-organisms into the environment:
Challenges to commercial use ...................................................................................................... 115
Introduction ................................................................................................................................. 116
Remediation technologies ........................................................................................................... 117
Bioremediation ............................................................................................................................ 118
Technologies involved in bioremediation ................................................................................... 118
Environmental risks of bioremediation ....................................................................................... 120
Nature protection and the introduction into the environment of micro-organisms ..................... 121
Examples of use of released micro-organisms in bioremediation ............................................... 122
Challenges to commercial use of bioremediation technologies .................................................. 123
Conclusion ................................................................................................................................... 124
References ................................................................................................................................... 125
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Part IV The use of micro-organisms in cleaning products ........................................................ 127
Chapter 9 Microbial-based cleaning products in use and the potential role
of transgenic micro-organisms ..................................................................................................... 129
Introduction ................................................................................................................................. 130
Survey of microbes currently used in cleaning products ............................................................. 131
Potential human health and environmental issues ....................................................................... 134
Regulatory experiences in Canada with these products .............................................................. 136
Knowledge gap in the use of Microbial-based cleaning products ............................................... 137
Conclusion ................................................................................................................................... 138
References ................................................................................................................................... 139
Chapter 10 Microbes in cleaning products: Regulatory experience and
challenges for risk assessment...................................................................................................... 143
Introduction ................................................................................................................................. 144
Rationale of using micro-organisms in cleaning products .......................................................... 144
Products and applications ............................................................................................................ 145
Microbial cleaners in the context of legislation .......................................................................... 146
Health and environmental risks ................................................................................................... 148
Conclusion ................................................................................................................................... 151
References ................................................................................................................................... 153
Part V Environmental applications of microbial symbionts of insects ..................................... 157
Chapter 11 Use and release of mosquitoes for the control of dengue
transmission: A world-first trial in Australia............................................................................. 159
Introduction ................................................................................................................................. 160
The use of Wolbachia as a biocontrol agent ................................................................................ 160
Field releases of Wolbachia-mosquitoes in Australia: The regulatory process ........................... 163
Wolbachia establishment in north Queensland mosquito populations ........................................ 166
Future directions for Wolbachia .................................................................................................. 169
Alternative technological strategies for disease control .............................................................. 170
References ................................................................................................................................... 171
Chapter 12 Fighting malaria with engineered mosquito symbiotic bacteria ........................... 175
Introduction ................................................................................................................................. 176
Transgenic mosquitoes ................................................................................................................ 176
Paratransgenesis .......................................................................................................................... 177
Challenges ahead ......................................................................................................................... 179
References ................................................................................................................................... 179

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Part VI Environmental risk assessment of the deliberate release of engineered
micro-organisms ............................................................................................................................ 181
Chapter 13 Next generation sequencing-based metagenomics for monitoring
soil microbiota ............................................................................................................................... 183
Next-generation sequencing ........................................................................................................ 184
454 pyroseqencing ....................................................................................................................... 184
Bacterial species concept and its use of genome sequence in taxonomy and metagenomics ..... 185
Microbial community analysis: Conventional methods .............................................................. 186
Microbial community analysis: Metagenomics........................................................................... 187
Soil metagenomics: Practical applications .................................................................................. 188
Conclusion ................................................................................................................................... 189
References ................................................................................................................................... 190
Chapter 14 Reflection on environmental risk assessment of micro-organisms ....................... 197
Target of risk assessment ............................................................................................................ 198
Difficulty of using an analytical approach in assessing risk of micro-organisms
used in the environment .............................................................................................................. 198
References ................................................................................................................................... 202
Annex 14.A1: Text of paragraphs 8 and 9 of the Annex III to the Cartagena
Protocol on Biosafety .................................................................................................................. 204
Chapter 15 Risk assessment considerations of genetically modified micro-
organisms for releases .................................................................................................................. 207
Microbial community networks and resilience ........................................................................... 208
Risk assessments based on information on recipients ................................................................. 209
Environmental performance and containment............................................................................. 210
Horizontal gene transfer .............................................................................................................. 211
Conclusion ................................................................................................................................... 211
References ................................................................................................................................... 212
Chapter 16 Overarching issues in the environmental risk assessment of
deliberate release of transgenic micro-organisms ...................................................................... 215
Exploitation of bacterial diversity in the environment ................................................................ 216
Horizontal gene transfer of transgenic DNA ............................................................................... 217
Soil as a heterogeneous and complex environment ..................................................................... 219
References ................................................................................................................................... 220
Tables
Table 4.1. Overview of genetically transformed algal species ........................................................ 61
Table 4.2. Carotenoids produced by selected microalgae ................................................................ 62
Table 4.3. New products that have been made by algae through genetic modification ................... 63
Table 4.4. Important data for environmental risk assessments of algae .......................................... 67
Table 5.1. Taxonomic affiliation of algae ........................................................................................ 76
Table 5.2. Use of algal products and current market prices ............................................................. 79
Table 5.2. Use of algal products and current market prices (cont.) ................................................. 80
Table 5.3. Microalgal biochemical profiles in comparison to soy ................................................... 81
Table 5.4. Biodiesel properties of select microalgae calculated from FAME profiles .................... 82
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Table 5.5. Metal bioaccumulation (µg L-1) and effect of nutrient regime on fatty acid classes (%)
in a chlorophyte community dominated by Scenedesmus spp .................................................. 84
Table 5.6. Growth phase-dependent total lipid content, biomass productivity and lipid productivity
of four tropical microalgal species ............................................................................................ 87
Table 6.1. Overview of the Algae Working Group’s activities (2012) and participation ................ 95
Table 6.2. Summary of five main research categories for environmental risk assessments of
synthetic biology applications ................................................................................................... 98
Table 9.1. Micro-organisms used in cleaning products ................................................................. 132
Table 9.1. Micro-organisms used in cleaning products (cont.) ...................................................... 133
Table 14.1. Past OECD work on the environmental risk assessment of micro-organisms ............. 200
Table 14.2. Environmental use of microbes in the past .................................................................. 201
Figures
Figure 3.1. Representative example of a normal operating range of soils showing 3 of the 22
dimensions ................................................................................................................................ 53
Figure 4.1. Ideal microalga ............................................................................................................... 60
Figure 5.1. Concept of bioremediation using microalgae with value-adding co-product
development .............................................................................................................................. 75
Figure 5.2. Micrograph of the branching filamentous cyanobacterium Mastigocoleus sp. .............. 76
Figure 5.3. Salinity tolerance of Picochlorum atomus ...................................................................... 82
Figure 6.1. The interagency Algae Working Group ......................................................................... 95
Figure 7.1. Flowchart for the generation of genetically engineered catalysts in the era of systems
and synthetic biology .............................................................................................................. 109
Figure 8.1. Number of sites in the United States that require treatment for pollution .................... 116
Figure 8.2. Sampling of groundwater for determination of hydrocarbon contamination ............... 117
Figure 8.3. Range and weighting of industries that utilise bioremediation .................................... 119
Figure 8.4. Canadian draft guidelines for risk assessment for the release of micro-organisms into
the environment ...................................................................................................................... 121
Figure 8.5. Overview of public acceptability of controversial technologies (PACT), used to assist in
site-specific decision making about remediation technologies ............................................... 124
Figure 11.1. Schematic representation of the cytoplasmic incompatibility phenotype induced by
Wolbachia in Aedes aegypti mosquitoes ................................................................................. 161
Figure 11.2. Fluorescence in situ hybridisation of paraffin sections .............................................. 162
Figure 11.3. Regulatory pathway followed in Australia for the release of Wolbachia-infected
Aedes aegypti mosquitoes for the control of dengue .............................................................. 165
Figure 11.4. Location of the 2011 and 2012 Aedes aegypti release sites in north Queensland,
Australia .................................................................................................................................. 167
Figure 11.5. Increase in the frequency of Wolbachia-infected mosquitoes in Gordonvale and
Yorkeys Knob during the 2011 release ................................................................................... 168
Figure 14.1. Bilayered structure inherent in risk assessment related to micro-organisms .............. 198
Figure 14.2. Many factors other than LMOs influencing on biodiversity ...................................... 200
Figure 16.1. Metagenome exploitation ........................................................................................... 216
Figure 16.2. Visualisation of horizontal gene transfer in planta: Genetic approach ...................... 218
Figure 16.3. Visualisation of horizontal gene transfer in planta..................................................... 218

BIOSAFETY AND THE ENVIRONMENTAL USES OF MICRO-ORGANISMS: CONFERENCE PROCEEDINGS © OECD 2015