Staff Assessment Report EPA advice on application APP201895 – determination on the new organism status of Pseudomonas monteilii, Rhodococcus pyridinivorans, Paracoccus pantotrophus, and Nitrosomonas eutropha
June 2014
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EPA advice for application APP201895
Executive summary and recommendation
Application APP201895, submitted by Neil Pritchard of NPN Ltd., Napier, seeks a determination on the new organism status of four bacterial species (Pseudomonas monteilii, Rhodococcus pyridinivorans, Paracoccus pantotrophus and Nitrosomonas eutropha).
After reviewing the information, EPA staff recommend that the Hazardous Substances and New Organisms (HSNO) Decision Making Committee determines that Pseudomonas monteilii, Rhodococcus pyridinivorans, Paracoccus pantotrophus and Nitrosomonas eutropha are not new organisms for the purposes of the HSNO Act.
However, should new evidence be found regarding the new organism status of any of these organisms, new determinations can be sought.
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Table of Contents
Executive summary and recommendation ...... 2 Table of Contents ...... 3 1. Introduction ...... 4 2. Organism description...... 4 3. Summary and review of information ...... 5 4. Evaluation against statutory criteria ...... 11 5. Impact on international obligations ...... 12 References ...... 13 Appendix 1: Comments from MPI ...... 15 Appendix 2: Decision path for applications under Section 26 for determination as to whether an organism is a new organism ...... 17
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1. Introduction
1.1. The application from NPN Ltd. (the applicant) was submitted under section 26 of the HSNO Act (the Act) to determine whether the four bacterial species (Pseudomonas monteilii, Rhodococcus pyridinivorans, Paracoccus pantotrophus and Nitrosomonas eutropha) are new organisms for the purposes of the Act.
1.2. The applicant provided information with regard to the presence of the four bacterial species in New Zealand, albeit with few supporting references. The applicant provided some argument for the ubiquity of such organisms, particularly for P. monteilii, which was originally found in clinical isolates from humans, and is thus likely ubiquitous.
1.3. EPA staff have also searched the scientific literature and other local sources for evidence of the existence of these organisms both before and after 29 July 1998. Moreover, we have considered the histories of these organisms from the perspective of the taxonomic literature and the state of scientific knowledge regarding these species and their classification prior to 29 July 1998.
1.4. In response to the arguments in the application for the ubiquity of these organisms as evidence for presence in New Zealand, the EPA commissioned a report, The Biogeography of Environmental Microorganisms, by Clark Ehlers and Gavin Lear of the University of Auckland. This report considers and discusses the global ubiquity of bacterial species, both in general terms and specifically with regard to the four species that are the subject of this application.
1.5. Comment on the application was solicited from the Department of Conservation (DoC) and the Ministry for Primary Industries (MPI). DoC had no comment and MPI provided a response document to the application (Appendix 1).
1.6. EPA staff have evaluated the information in the application, the Report from the University of Auckland, the analysis and comment from MPI and other readily sourced information described above against the legislative criteria for determining whether P. monteilii, R. pyridinovorans, P. pantotrophus and N. eutropha are new organisms for the purposes of the Act.
2. Organism description
2.1. The four bacterial species that are the subject of this determination are unrelated, but most have nitrification (conversion of ammonia to nitrite and nitrate) and/or denitrification (conversion of nitrate to molecular nitrogen, nitrous oxide, or cellular components) ability. At least one species is capable of metabolising polycyclic aromatic hydrocarbons and another is capable of growth on hydrogen sulphide as a substrate.
2.2. These four bacterial species and their taxonomic histories are summarised in Table 1.
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Table 1: Species that are the subjects of this determination Species Synonym(s)
Pseudomonas monteilii (sp. nov., Elomari et al. Pseudomonas putida biovar A (Elomari et al. 1994) 1997)
Rhodococcus pyridinivorans (sp. nov., Yoon et Rhodococcus sp., strain PDB9T al. 2000)
Micrococcus denitrificans (Beijerinck & Minkman 1910), Paracoccus pantotrophus (comb. nov., Rainey Thiosphaera pantotropha (gen. nov., sp. nov., et al. 1999) Robertson & Kuenen 1983), Paracoccus denitrificans (Ludwig et al. 1993)
Nitrosomonas eutropha (sp. nov., Koops et al. Nitrosomonas sp., genospecies 10 1991)
3. Summary and review of information
Commissioned report: The Biogeography of Environmental Microorganisms 3.1. The EPA commissioned a report: The Biogeography of Environmental Microorganisms in response to arguments for ubiquity of the microorganisms in the application. In this report, hereafter referred to as the Ubiquity Report, Ehlers and Lear (2014), discuss global phenomena that cause the distribution of Archaea and Bacteria to widely dispersed locations on the globe. Among these are natural phenomena, such as the intercontinental transport of dust particles by wind and rain clouds, as well as unintentional transport by human beings, for example in ship ballast water or via air travel. The Ubiquity Report is attached for reference.
3.2. The Ubiquity Report also discusses the global distribution of each of the four species under consideration in this application. This information is discussed here under the heading for the individual organisms, alongside the evidence from the applicant and our own independent evaluation.
Pseudomonas monteilii
Identification of Pseudomonas monteilii 3.3. Pseudomonas monteilii was originally identified based on isolates from human clinical specimens, including placenta, stool, bile, biological fluid, bronchial aspirate, urine and pleural fluid (Elomari et al. 1997). However, the species is not known to be a human pathogen. Prior to 1997, P. monteilii was known as Pseudomonas putida Biovar A (Elomari et al. 1994). Like many other species of Pseudomonas, P. monteilii is fluorescent.
Evidence 3.4. There is no direct evidence that EPA staff are aware of that P. monteilii was known in New Zealand prior to 1998, not surprising since P. monteilii was only classified as a species in 1997 (Elomari et al. 1997). However, several New Zealand accessions of P. putida are found in the ICMP culture
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collection, dating back as far as 1968, all of them from plant or soil samples. Since nothing is specified about the particular strains isolated, it is possible that any or all of these strains could be P. monteilii, which is now known to be found in association with plants (see Table 2).
3.5. The applicant argues that since P. monteilii is associated with humans as demonstrated with numerous clinical isolates in a non-pathogenic context (Elomari et al. 1997), it is likely that P. monteilii was present in New Zealand prior to 1998.
3.6. MPI has taken the view that there is insufficient evidence in the application to determine that P. monteilii is not a new organism. MPI further takes the view that the reclassification of P. monteilii from P. putida (a species known not to be a new organism) is insufficient grounds to assert that P. monteilii is not a new organism.
3.7. The Ubiquity Report notes that this species is cosmopolitan, and it has been identified in wide-ranging sites and environments around the world (Table 2). Of particular note is the detection of P. monteilii in coastal sediment in Argentina, suggesting that this organism is found in seawater and is therefore likely globally ubiquitous, consistent with its presence in at least eight additional countries scattered across the globe.
Table 2. Reports of detection/identification of Pseudomonas monteilii (compiled from citations in the Ubiquity Report) Country Environment
France Clinical samples
Belgium Clinical samples
Japan Field, sewage, pond water, wheat rhizosphere
Argentina Coastal sediment
Taiwan Soil
China Soil, municipal wastewater
USA Wheat rhizosphere, household, rubbish, compost, bathroom drains
Senegal Plant-associated
India Soil
Rhodococcus pyridinovorans
Identification of Rhodococcus pyridinovorans 3.8. Rhodococcus pyridinovorans was isolated from a culture enriched for pyridine-degrading bacteria, derived from industrial wastewater in Korea (Yoon et al. 2000). As its name suggests, the species is capable of degrading high concentrations of pyridine, a toxin introduced to the environment through
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herbicide and insecticide use (Yoon et al. 2000). Rhodococcus pyridinovorans is also a denitrifying bacterium, reducing nitrate to nitrite (Yoon et al. 2000).
Evidence 3.9. MPI takes the view that there is insufficient evidence to suggest that R. pyridinovorans is not a new organism, citing the organism’s association with environments containing aromatic compounds and optimal growth temperatures of 30-37o C, as criteria weighing against its presence in New Zealand.
3.10. The Ubiquity Report again shows that this species has been identified/detected in widely dispersed locales and environments around the globe (Table 3). R. pyridinovorans is frequently associated with wastewater, effluent and environmentally degraded sites, all of which are found in New Zealand. Additionally, R. pyridinovorans has also been found in land suitable for farming in the Congo, consistent with its ability to grow at temperatures as low as 10o C (Yoon et al. 2000).
Table 3. Reports of detection/identification of Rhodococcus pyridinovorans (compiled from citations in the Ubiquity Report) Country Environment
Industrial wastewater, compost-packed biofilter (with identification of new Korea strains)
United Kingdom Effluent from a rubber additive plant
Congo Arable land
Hungary Oil-contaminated site
India Effluent sediment contaminated with pesticide
Paracoccus pantotrophus
Identification of Paracoccus pantotrophus 3.11. The history of the nomenclature of P. pantotrophus is circuitous. The species was originally described as an isolate from a denitrifying, sulphide-oxidising effluent-treatment pilot plant. The bacterium is a constitutively denitrifying sulphur-oxidising species capable of growing on a variety of substrates and it was thus named Thiosphaera pantotropha. Thiosphaera pantotropha was designated as the type strain of this new genus (Robertson & Kuenen 1983). At the time, T. pantotropha was noted as having striking morphological similarities to the species Paracoccus denitrificans (Robertson & Kuenen 1983).
3.12. Paracoccus denitrificans was originally described as Micrococcus denitrificans (Beijerinck & Minkman 1910), until its revision to P. denitrificans as the type species of the genus in 1969 (Davis et al. 1969). This revision was on the basis that, unlike true Micrococcus spp., this species forms rods in young cultures and it has a cell wall mucopeptide characteristic of Gram-negative bacteria (Baird-Parker 1965). However, usage of the name M. denitrificans continued in wide use for some time after this revision.
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3.12.1. As stated above, the “striking morphological and physiological similarities” between T. pantotropha and P. denitrificans led to a taxonomic re-examination of these two species. On the basis of identical 16S rDNA sequences, they were merged into P. denitrificans, with the later synonym, T. pantotropha, abandoned (Ludwig et al. 1993).
3.12.2. These species were again separated in 1999 based on molecular data (16S rDNA sequence) after the authenticity of the P. denitrificans strain used for comparison to T. pantotropha by Ludwig et al. (1993) was called into question and was confirmed to have been T. pantotropha, not P. denitrificans (Rainey et al. 1999).
3.12.3. However, the molecular sequence comparisons also showed that T. pantotropha was the closest relative of P. denitrificans, closer than other members of the genus Paracoccus. Therefore, T. pantotropha was combined into the genus Paracoccus with the name P. pantotrophus.
Evidence 3.13. Direct evidence for the presence of P. pantotrophus in New Zealand prior to 29 July 1998 is scant. A PhD Thesis published in 1971 describes the identification of Micrococcus denitrificans in municipal waste from the Mangere (Auckland) sewage treatment ponds (Brockett 1971). Micrococcus denitrificans had been reclassified as P. denitrificans in 1969, as described in 3.13, but the original name continued in use for some years after the reclassification. At the time of writing of that thesis, T. pantotropha (P. pantotrophus) had not yet been identified. Any members of this species observed at that time would presumably have been described as P. (or M.) denitrificans. It is thus possible, if not probable, that P. pantotrophus had in fact been observed at this time, particularly given the morphological similarities and substrate preferences between the species.
3.14. MPI takes the view that there is insufficient evidence to suggest that P. pantotrophus is not a new organism. MPI further notes that the application’s claim that this species was isolated from waste treatment plants in New Zealand is unsupported by a documented reference.
3.15. The Ubiquity Report provides substantial supporting evidence of the cosmopolitan nature of P. pantotrophus, which has been identified in a wide variety of sites around the world (Table 4).
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Table 4. Reports of detection/identification of Paracoccus pantotrophus (compiled from citations in the Ubiquity Report) Country Environment
Netherlands Denitrifying, sulphide-oxidising effluent
China Sludge samples from contaminated water from an insecticide plant
South Korea Municipal wastewater
3.16. It was suggested in the Ubiquity Report that this species may require specific environments that contain high concentrations of ammonium and nitrate, since this species is capable of carrying out coupled nitrification (conversion of ammonia to nitrate) and denitrification (conversion of nitrate to nitrite and nitrite to molecular nitrogen) (Robertson et al. 1988; Ehlers & Lear 2014). The Mangere waste treatment ponds where “M. denitrificans” was identified in 1971 certainly qualify as such an environment.
Nitrosomonas eutropha
Identification of Nitrosomonas eutropha 3.17. The species Nitrosomonas eutropha was initially described in 1991, together with seven other species of Nitrosomonas (Koops et al. 1991). Prior to that time, Nitrosomonas europaea and N. cryotolerans were the only described members of this genus. Nitrosomonas eutropha is a nitrifying species commonly found in sewage and is highly ammonia-tolerant, capable of surviving ammonium concentrations as high as 0.6 moles/L.
Evidence 3.18. Nitrosomonas spp. was identified in the Mangere (Auckland) sewage ponds in the late 1960’s or early 1970’s (Brockett 1971). However, no attempt was made in this work to characterise these bacteria to the species level.
3.19. There is one other published study in which Nitrosomonas species were identified in New Zealand. This paper utilised ‘semi-quantitative’ PCR and Fluorescence In Situ Hybridisation (FISH) to establish the presence of Nitrosomonas in a dairy effluent treatment wetland (Silyn-Roberts & Lewis 2001). The DNA oligonucleotide primers used in the PCR were specific for 16S rDNA sequences common to essentially all nitrosomonads. The DNA oligonucleotide probe used for FISH was more specific, designed to detect N. europaea and N. eutropha. Both experiments demonstrated that a Nitrosomonas species was present in the wastewater, but they could not definitively identify N. eutropha from either experiment, since the probes could not distinguish between N. eutropha and N. europaea. This paper was also discussed in the Ubiquity Report, which suggested that N. eutropha was the detected species.
3.20. MPI takes the view that the Silyn-Roberts and Lewis (2001) paper constitutes sufficient evidence that N. eutropha is not a new organism.
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3.21. The Ubiquity Report examines the global distribution of N. eutropha, based on an extensive review of the scientific literature. Based on these reports, it appears that N. eutropha is found in ammonium-rich eutrophying (nutrient-enriched, generally from runoff) environments, as its name suggests. N. eutropha has been detected in countries around the globe (Table 5). Table 5. Reports of detection/identification of Nitrosomonas eutropha (compiled from citations in the Ubiquity Report) Country Environment
USA Municipal wastewater, “PondProtect®” (commercial product)
Central Europe Eutrophic lakes & rivers
Japan Municipal wastewater, acidic soil
Switzerland Ammonia-rich leachate
Spain Waste treatment
Korea Waste treatment
China Waste treatment
Denmark Waste treatment
3.22. As alluded to in the Ubiquity Report with its discussion of the commercial product PondProtect® (Novozymes) http://www.novozymes.com/en/solutions/agriculture/aquaculture/pages/pondprotect.aspx, N. eutropha is finding its way into applied use as a commercial product. In this instance, the bacteria are used to remove ammonia from aquariums and aquaculture systems (eg, prawn farms) via nitrification. Recently, an American biotechnology company, AOBiome (https://www.aobiome.com/company), has developed N. eutropha as a commercial spray to alter a person’s skin microbiome (https://www.aobiome.com/bacteria-new-black), with purported health and environmental benefits. AOBiome was recently highlighted in a New York Times article describing a reporter’s experience using the product (http://www.nytimes.com/2014/05/25/magazine/my-no-soap-no-shampoo-bacteria- rich-hygiene-experiment.html?_r=0). Both these products appear to be for sale globally, assuming compliance with local laws.
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4. Evaluation against statutory criteria
4.1. For an organism to be determined as “not new” under section 26 of the Act, the organism must be shown to lie outside the parameters of the definition of a new organism as defined in section 2A(1) of the Act: A new organism is- a) an organism belonging to a species that was not present in New Zealand immediately before 29 July 1998: b) an organism belonging to a species, subspecies, infrasubspecies, variety, strain, or cultivar prescribed as a risk species, where that organism was not present in New Zealand at the time of promulgation of the relevant regulation: c) an organism for which a containment approval has been given under this Act: ca) an organism for which a conditional release has been given: cb) a qualifying organism approved for release with controls: d) a genetically modified organism: e) an organism that belongs to a species, subspecies, infrasubspecies, variety, strain, or cultivar that has been eradicated from New Zealand.
4.2. The following Act criteria were not applicable to this determination as the four species under consideration in this application; have not been prescribed as risk species (section 2A(1)(b)); have not been approved to be held in containment or released with controls (sections 2A(1)(c), (ca) and (cb)); are not genetically modified organisms (section 2A(1)(d)); and have not been eradicated from New Zealand (section 2A(1)(e)).
4.3. Section 2A(1)(a) of the Act states that a new organism must belong to “a species that was not present in New Zealand immediately before 29 July 1998”. EPA staff have evaluated the information regarding these four bacterial species against this criterion.
4.4. Bacteria and Archaea are able to rapidly adapt, mutate, take up and lose genetic material via horizontal gene transfer. As such, they do not readily lend themselves to the traditional vertical transmission concepts of taxonomy as have been applied to animal and plant species (Staley 2009; Boto 2010).
4.5. Additionally, the sheer variety of bacteria that exist in nature, many of which have very similar characteristics, mean that bacterial species can be lumped under a single name until they are more carefully characterised. Such re-categorisation is commonplace in bacteriology (Staley 2009).
4.6. Fenchel (2005) comments on the artifice of the species concept, particularly as it applies to microorganisms, stating: “…a species simply represents the basic rank of classification as delimited by
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taxonomic experts and the reality of species is often overestimated. A species does not constitute an evolutionary unit.”
4.7. The tangible effect of this ever-changing knowledge and grasp of bacterial systematics means that bacterial species are often further characterised and are assigned new species names.
4.8. Moreover, there are well-established means by which bacteria, including non-sporulating species, are readily transported globally on wind-borne dust particles and/or water droplets. Humans are also vectors, particularly in the age of ready intercontinental air travel (Ehlers & Lear 2014).
4.9. The extensive and growing evidence of the ubiquity of a large number of free-living bacterial species has led to the view that “the environment selects, with dispersal effects”, as discussed in the Ubiquity Report (Ehlers & Lear 2014). This view is widely held among microbiologists (Fenchel & Finlay 2004).
4.10. Several lines of evidence and prevailing microbiological theory support the presence of these microbes in New Zealand prior to 29 July 1998:
Free-living bacteria (including the four species under consideration here as discussed above) are ubiquitous and they will grow where environmental conditions are suitable.
The bacterial species under consideration are widely distributed around the world, as documented in Section 3.
Bacterial species largely remain undetected until someone searches for them, and absence of evidence does not necessarily constitute evidence of absence.
At least three of these species may have been detected here but classified under an earlier, broader taxonomic classification.
The requisite environments that would support the growth of these microorganisms (ie, waste treatment plants, human aspirates, household environments, coastal sediment, etc.) exist in New Zealand.
4.11. EPA staff believe that there is sufficient weight of evidence that these species were present in New Zealand prior to 29 July 1998. We therefore recommend that Nitrosomonas eutropha, Rhodococcus pyridinovorans, Pseudomonas monteilii and Paracoccus pantotrophus should be deemed as not new organisms for the purposes of the Act.
5. Impact on international obligations
5.1. EPA staff are not aware of any international obligations that may be impacted by this determination.
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References
Baird-Parker A 1965. The classification of Staphylococci and Micrococci from world-wide sources. Journal of General Microbiology 38: 363-387.
Beijerinck M, Minkman D 1910. Bildung und verbrauch von stickstoffoxydul durch bakterien. Zentralblatt für bakteriologie, parasitenkunde, infektionskrankheiten und hygiene. Abteilung II 25: 30-63.
Boto L 2010. Horizontal gene transfer in evolution: facts and challenges. Proceedings of the Royal Society B: Biological Sciences 277(1683): 819-827.
Brockett O 1971. Some aspects of the microbiological activity of the Mangere oxidation ponds. PhD thesis, University of Auckland, Auckland.
Davis D, Doudoroff M, Stanier R, Mandel M 1969. Proposal to reject the genus Hydrogenomonas: taxonomic implications. International Journal of Systematic Bacteriology 19: 375-390.
Ehlers C, Lear G 2014. The Biogeography of Environmental Microorganisms EPA Contract Reference Number: AAN2014-130.
Elomari M, Izard D, Vincent P, Coroler L, Leclerc H 1994. Comparison of ribotyping analysis and numerical taxonomy studies of Pseudomonas putida Biovar A. Systematic and Applied Microbiology 17(3): 361-369.
Elomari M, Coroler L, Verhille S, Izard D, Leclerc H 1997. Pseudomonas monteilii sp. nov., isolated from clinical specimens. International Journal of Systematic Bacteriology 47(3): 846-852.
Fenchel T 2005. Cosmopolitan microbes and their ‘cryptic’ species. Aquatic Microbial Ecology 41: 49-54.
Fenchel T, Finlay BJ 2004. The ubiquity of small species: patterns of local and global diversity. Bioscience 54: 777-784.
Koops HP, Böttcher B, Möller UC, Pommerening-Röser A, Stehr G 1991. Classification of eight new species of ammonia-oxidizing bacteria: Nitrosomonas communis sp. nov., Nitrosomonas ureae sp. nov., Nitrosomonas aestuarii sp. nov., Nitrosomonas marina sp. nov., Nitrosomonas nitrosa sp. nov., Nitrosomonas eutropha sp. nov., Nitrosomonas oligotropha sp. nov. and Nitrosomonas halophila sp. nov. Journal of General Microbiology 137(7): 1689-1699.
Ludwig W, Mittenhuber G, Friedrich CG 1993. Transfer of Thiosphaera pantotropha to Paracoccus denitrificans. International Journal of Systematic Bacteriology 43(2): 363-367.
Rainey FA, Kelly DP, Stackebrandt E, Burghardt J, Hiraishi A, Katayama Y, Wood AP 1999. A re-evaluation of the taxonomy of Paracoccus denitrificans and a proposal for the combination Paracoccus pantotrophus comb. nov. International Journal of Systematic Bacteriology 49(2): 645-651.
Robertson LA, Kuenen JG 1983. Thiosphaera pantotropha gen. nov. sp. nov., a facultatively anaerobic, facultatively autotrophic sulphur bacterium. Journal of General Microbiology 129(9): 2847-2855.
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Robertson LA, van Niel EWJ, Torremans RAM, Kuenen JG 1988. Simultaneous nitrification and denitrification in aerobic chemostat cultures of Thiosphaera pantotropha. Applied and Environmental Microbiology 54(11): 2812-2818.
Silyn-Roberts G, Lewis G 2001. In situ analysis of Nitrosomonas spp. in wastewater treatment wetland biofilms. Water Research 35(11): 2731-2739.
Staley JT 2009 The phylogenomic species concept for Bacteria and Archaea. Microbe Magazine: http://www.microbemagazine.org/index.php?option=com_content&view=article&id=539:the- phylogenomic-species-concept-for-bacteria-and-archaea&catid=187&Itemid=361.
Yoon JH, Kang SS, Cho YG, Lee ST, Kho YH, Kim CJ, Park YH 2000. Rhodococcus pyridinivorans sp. nov., a pyridine-degrading bacterium. International Journal of Systematic and Evolutionary Microbiology 50(6): 2173-80.
LPSN – List of Prokaryotic Names with Standing in Nomenclature. http://www.bacterio.net/paracoccus.html. (See Note 1 under the Paracoccus denitrificans entry).
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Appendix 1: Comments from MPI
Comments Form to the EPA for New Organism Applications
Application Code: APP201895 Applicant Name: Neil Pritchard Application Category: Determine if an organism is a new organism Application Title: To determine if Pseudomonas monteilli, Rhodococcus pyridinivorans, Paracoccus pantotrophus and Nitrosomas eutropha are new organisms EPA Applications Contact: Tim Strabala Date: 8 July 2014 MPI Response Coordinator: Barry Wards Option to Speak in Support of this No Submission: Comments provided by: Barry Wards BASIS ON WHICH COMMENT IS PROVIDED
MPI submits these comments for consideration to the EPA on the following (where relevant to the type of application): Clarity of information; Information that MPI considers should be taken into consideration by the EPA; Adequacy of the proposed containment system, including suggestions for controls and amendments to proposed controls; and Enforceability of any proposed controls.
Matters relating to the application that are not within the scope of these comments may be provided to the EPA separately.
Comments
General Pseudomonas monteilli . It is MPI’s view that the applicant does not provide sufficient evidence to determine that Pseudomonas monteilli is not a new organism. . MPI is not able to provide any evidence supporting the premise that Ps. monteilli, more specifically those organisms that are now called Ps. monteilli, were present in New Zealand prior to 29 July 1998. . While it is correct that the genus Pseudomonas is a diverse and ecologically significant group of bacteria, that they are found in all of the major natural environments and have a universal distribution, MPI suggests that this is largely irrelevant as evidence supporting presence in New Zealand. It is widely acknowledged that the genus Pseudomonas is multigeneric and, for many years, taxonomic studies have sought to resolve its members into a classification based on more robust methodology. It is no surprise, therefore, that members of the genus are found everywhere.
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. Ps. monteilli is a result of those taxonomic changes, the new species name being proposed in 1997. The applicant has not provided any evidence to suggest that organisms that are now referred to as Ps. monteilli were present prior to 29 July 1998, specifically those organisms that may have been previously characterised as Ps. putida, which is the likely organism from which Ps. monteilli strains were originally grouped as.
Rhodococcus pyridinivorans . It is MPI’s view that the applicant does not provide sufficient evidence to determine that Rhodococcus pyridinivorans is not a new organism. . MPI is not able to provide any evidence supporting the premise that R. pyridinivorans, was present in New Zealand prior to 29 July 1998. . It is MPI’s understanding that R. pyridinivorans was first isolated and characterised from a industrial wastewater in Korea in 2000. The applicant provides no evidence that the species has been isolated in New Zealand or any evidence of detecting it in environments where it may be found. . While other members of the genus Rhodococcus are present in New Zealand, MPI suggests that this is insufficient evidence to indicate that R. pyridinivorans may be present now or prior to 29 July 1998. The unique characteristics of R. pyridinivorans, including its apparent presence in areas with aromatic compound contamination and its optimum growth temperature of 30-37oC, point further to it not being present in New Zealand.
Paracoccus pantotrophus . It is MPI’s view that the applicant does not provide sufficient evidence to determine that Paracoccus pantotrophus is not a new organism. . MPI is not able to provide any evidence supporting the premise that P. pantotrophus, was present in New Zealand prior to 29 July 1998. . The applicant states that P. pantotrophus has been isolated in New Zealand from waste treatment plants. No evidence has been provided to support this and the references supplied by the applicant do not support this statement. If P. Pantotrophus has been isolated in New Zealand, MPI expects that the applicant should supply evidentiary material to verify this.
Nitrosomonas eutropha . It is MPI’s view that the applicant does provide sufficient evidence to determine that Nitrosomonas eutropha is not a new organism. The published evidence of Silyn- Roberts and Lewis (2001) appears to support this. . MPI is not able to provide further evidence supporting the premise that N. eutrophus, was present in New Zealand prior to 29 July 1998. . While the applicant states that N. Eitropha is a common environmental bacterium found in New Zealand’s aquatic and terrestrial ecosystems, they provide little evidence to support this.
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Appendix 2: Decision path for applications under Section 26 for determination as to whether an organism is a new organism
Context
This decision path describes the decision-making process for applications under Section 26 for determination as to whether an organism is a new organism.
Introduction
The purpose of the decision path is to provide the HSNO decision maker1 with guidance so that all relevant matters in the HSNO Act and the Methodology have been addressed. It does not attempt to direct the weighting that the HSNO decision maker may decide to make on individual aspects of an application.
In this document ‘section’ refers to sections of the HSNO Act, and ‘clause’ refers to clauses of the Methodology.
The decision path has two parts –
Flowchart (a logic diagram showing the process prescribed in the HSNO Act and the Methodology to be followed in making a decision), and Explanatory notes (discussion of each step of the process). Of necessity the words in the boxes in the flowchart are brief, and key words are used to summarise the activity required. The explanatory notes provide a comprehensive description of each of the numbered items in the flowchart, and describe the processes that should be followed to achieve the described outcome.
For proper interpretation of the decision path it is important to work through the flowchart in conjunction with the explanatory notes.
1 The HSNO decision maker refers to either the EPA Board or any committee or persons with delegated authority from the Board.
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Figure 1 Flowchart: Decision path for applications under Section 26 for determination as to whether an organism is a new organism
For proper interpretation of the decision path it is important to work through the flowchart in conjunction with the explanatory notes.
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Figure 1 Explanatory Notes
Item 1 Review the content of the application and all relevant information Review the application, Agency advice and any relevant information held by other Agencies, and advice from experts. Determine whether further information is required.
Item 2 Is this information sufficient to proceed? Review the information and determine whether or not there is sufficient information available to make a decision.
Item 3: Seek additional information If the HSNO decision maker considers that further information is required, then this may be sought either from the applicant (if there is an external applicant) or from other sources. If the HSNO decision maker considers that the information may not be complete but that no additional information is currently available, then the HSNO decision maker may proceed to make a determination2. If the application is not approved on the basis of lack of information (or if the organism is considered new) and further information becomes available at a later time, then the HSNO decision maker may choose to revisit this determination. In these circumstances the HSNO decision maker may choose to adopt a precautionary approach under section 7 of the Act.
Item 4: Identify scope of organism description The identification of the organism must be at an appropriate taxonomic classification. For applications involving potentially genetically modified organisms, the organism should be identified by describing the host organism and the processes to which it has been subjected to (for example injection with a non-replicative, non-integrative plasmid DNA vaccine).
Item 5:
Is it a GMO? Determine whether the organism is a GMO using the definitions in Section 2 of the Act and in the Hazardous Substances and New Organisms (Organisms Not Genetically Modified) Regulations 1998.
Item 6: Is the organism known to have been present in NZ immediately before 29 July 1998? Determine on the basis of the available information whether on balance of probabilities the organism is known to belong to a species that was present in New Zealand immediately prior to 29 July 1998. For the purposes of making a section 26 determination an organism is considered to be present in New Zealand if it can be established that the organism was permanently existing in New Zealand and was not present solely by way of being contained in a recognised safekeeping
2 Alternatively the application may lapse for want of information.
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EPA advice for application APP201895
facility, immediately prior to 29 July 1998. The key phrases ‘permanently existing, ‘recognised safekeeping facility’ and ‘immediately’ are defined in the Protocol Interpretations and Explanations of Key Concepts
Item 7: Is it prescribed as a risk species? Determine whether the organism has been prescribed as a risk species by regulation established under section 140(1)(h) of the Act. Note: at this point it may become apparent that the organism is an unwanted organism under the Biosecurity Act. If this is the case, then MAF BNZ and DOC may be advised (they may already have been consulted under items 1, 2 and 3).
Item 8: Was it present when prescribed? If the organism is prescribed as a risk species, determine whether it was present when it was prescribed. The organism is a new organism if it was not present in New Zealand at the time of the promulgation of the relevant regulation (Section 2A (1)(b) of the Act).
Item 9: Is it known to have been previously eradicated? Determine whether the organism is known to have been previously eradicated. Eradication does not include extinction by natural means but is considered to be the result of a deliberate act (see the interpretation in the Protocol Interpretations and Explanations of Key Concepts1.
Item 10: Has HSNO release without conditions approval been given under section 38 or 38I of the Act? If a HSNO release approval has been given under section 35 of the Act, then the organism remains a new organism. If a release approval has been given under section 38 of the Act then the organism is not a new organism. If a release approval has been given under section 38I of the Act, then if the approval has been given with controls then the organism remains a new organism, however, if this approval has been given without controls then it is not a new organism.
July 2014
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