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 2 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. July 2014 3 EPA advice for application APP201895 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 July 2014 4 EPA advice for application APP201895 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. July 2014 5 EPA advice for application APP201895 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 July 2014 6 EPA advice for application APP201895 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.