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APP203741 Staff Assessment Report.Pdf EPA advice for application APP203741 Staff Assessment Report December 2018 APP203741: To determine the new organism status of Kineosporia rhizophila, Actinoplanes cyanea, Actinoplanes digitatis, Actinoplanes ferrugineus, Cryptosporangium arvum and Cryptosporangium japonicum Purpose To determine if Kineosporia rhizophila, Actinoplanes cyanea, Actinoplanes digitatis, Actinoplanes ferrugineus, Cryptosporangium arvum and Cryptosporangium japonicum are new organisms under section 26 of the HSNO Act Application number APP203741 Application type Statutory determination Applicant Anther Experimental Distillation Pty Limited Date formally received 14 November 2018 1 Executive Summary and Recommendation Application APP203741, submitted by Anther Experimental Distillation Pty Limited, seeks a determination on the new organism status of Kineosporia rhizophila, Actinoplanes cyanea, Actinoplanes digitatis, Actinoplanes ferrugineus, Cryptosporangium arvum and Cryptosporangium japonicum. After reviewing all of the available information and completing a literature search concerning the organisms, EPA staff recommend that Kineosporia rhizophila, Actinoplanes cyanea, Actinoplanes digitatis, Actinoplanes ferrugineus, Cryptosporangium arvum and Cryptosporangium japonicum are not new organisms for the purpose of the HSNO Act based on evidence that these organisms have been identified and present in New Zealand since before 29 July 1998 when the HSNO Act came into effect. The genetic sequencing evidence also strongly suggests that these six microorganisms are ubiquitous in nature based on the isolations of these organisms across global continents, varying environments and timeframes. 2 EPA advice for application APP203741 Table of Contents Introduction and background ……………………………………………………………4 Organism description…………………………………………………………………………4 Review of information………………………………………………………………………10 Recommendation……………………………………………………………………………..11 References…………………………………………………………………………………….....12 Appendix 1: Decision pathway……..…………………………………………………..14 3 Introduction and background On 14 November 2018, Anther Experimental Distillation Pty Limited applied to the EPA under section 26 of the HSNO Act seeking a determination on the new organism status of Kineosporia rhizophila, Actinoplanes cyanea, Actinoplanes digitatis, Actinoplanes ferrugineus, Cryptosporangium arvum and Cryptosporangium japonicum. The EPA requested comment on the application from the Department of Conservation (DOC) and the Ministry for Primary Industries (MPI). DOC and MPI did not have any comments to make on this application. The applicant considers these species as not new organisms and to support this claim the applicant provided evidence to demonstrate that each of these organisms is present in New Zealand based on identification of these organisms in soil samples collected in New Zealand. In addition, the applicant argues that these organisms are likely to be ubiquitous organisms given the isolation of these organisms across geographical continents, varying environments and timeframes. Section 2A(1) of the HSNO Act prescribes that a new organism is, in part, an organism belonging to a species that was not present in New Zealand immediately before 29 July 1998. Description of organisms Kineosporia rhizophila Kineosporia rhizophila is a motile, spore-bearing, actinomycete bacterial species and a member of the genus, Kineosporia, due to its morphological and chemotaxonomic characteristics such as the inclusion of menaquinone, phospholipid and cellular fatty acid compositions. Kineosporia have the ability to release flagellated zoospores at a certain stage in their life cycle (Goodfellow & Cross, 1984). These motile, zoosporic actinomycetes have been associated with river and lake water, river sediments, decaying plant material submerged in streams and cast up on lake shores, grass inhabiting streams, in soil and a glacier in the Himalayas (Hasegawa 1991; Kudo et al. 1998; Cross 1986; Willoughby 1969; Shivaji et al. 1997; Shivaji et al. 2011). Kineosporia spp. have also been isolated in high numbers from leaf litter, dry stream beds and from branches overhanging water in Britain, the United States of America, Japan and Australia (Radajewski & Duxbury, 2001; Cross, 1986; Kudo et al. 1998). Furthermore, Actinomycete species belonging to the genera Actinoplanes, Kineosporia and Cryptosporangium have been frequently isolated from leaf litter samples which suggests they may have a significant role in the degradation of plant material (Hop et al. 2011; Tamura et al. 1998; Makkar & Cross, 1982). Kineosporia rhizophila was originally isolated in 1998 by Kudo et al. from various plant samples in Japan. In the same year, Kudo et al. also isolated this species from the roots of galingale (Cyperus micromona) and fallen leaves in Saitama, Japan, sphagnum in Mt Mikuni in Gumma, Japan and leaves of cat-tail (Typha latifolia) (Kudo et al. 1998). 4 EPA advice for application APP203741 International isolates of this species also include from leaf litter in Vietnam (Sakiyama et al, 2009), soil in Japan (Hayakawa et al, 2000) and soil and leaf litter from West Java, Indonesia (Widyastuti et al. 2012). In addition, the applicant analysed soil survey studies that are similar to BASE1 surveys. These surveys consisted of 16S rRNA sequence analysis of microbial communities found in soil and other environments collected from locations around the world (Table 1). Using the 16S rRNA sequence of Kineosporia rhizophila the applicant performed several BLAST2 searches online and found the following results: Table 1: Global locations of endemic species and identity matched to 97 – 100% sequence similarity to Kineosporia rhizophila. Source Country % Identity Lichen China 99 Farm soil USA 99 Soil samples Argentina 97 Soil samples Canada 97 Soil France 97 Furthermore, the applicant provided two 16S rRNA sequencing reports (New Zealand and Australia) from Monash University which identified Kineosporia rhizophila from soil samples across a wide distribution of Australia and the North Island of New Zealand (Monash University Microbe Species Identity and Location report, 18 November 2015; Monash University Microbe Species Identity and Location Report, 24 August 2018). Actinoplanes cyanea Actinoplanes is a genus in the family of Micromonosporaceae. Bacteria within this genus have aerial mycelia and spherical, motile spores. Actinoplanes species produce the pharmaceutically important compounds valienamine (a precursor to the antidiabetic drug acarbose and the antibiotic validamycin), teicoplanin and ramoplanin. Actinoplanes cyanea (syn. Actinoplanes cyaneus) was first isolated from Siberian soil in 1977 by Terekhova et al. Unlike several other Actinoplanes species, this species lacks aerial 1 BASE: Biomes of Australian Soil Environment. BASE is a map of Australia’s soil microbial diversity. https://www.csiro.au/en/Research/Collections/ANH/Our-research/Soil-and-plant-interactions/Mapping-soil- biodiversity 2 BLAST: basic local alignment search tool. An algorithm used for comparing primary biological sequence information. 5 mycelium. The cell wall contains meso-diaminopimelic acid, arabinose, xylose and a non- identified analogue of diaminopimelic acid. On synthetic media, this species produces a soluble blue pigment. In 2007, Actinoplanes cyaneus was isolated from soil sites in the three Mongolian provinces of Tov, Uvs and Dornad (Enkh-Amgalan et al. 2012). These three provinces span west (Tov), central (Uvs) and far-eastern (Dornad) Mongolia. Other closely related Actinoplanes species have been isolated from soil close to the Marmore waterfalls in Terni, Italy. These isolates had a 97.6% gene sequence similarity to Actinoplanes cyanea (Kampfer et al. 2007). Furthermore, isolations in region of Liguria, Italy, showed a 99.3% gene sequence similarity to Actinoplanes cyanea strains (Wink et al. 2006). In addition, the applicant analysed soil survey studies that are similar to BASE surveys. These surveys consisted of 16S rRNA sequence analysis of microbial communities found in soil and other environments collected from locations around the world (Table 2). Using the 16S rRNA sequence of Actinoplanes cyanea the applicant performed several BLAST searches online and found the following results: Table 2: Global locations of endemic species and identity matched to 97 – 100% sequence similarity to Actinoplanes cyanea. Source Country % Identity Soil Russia 98 Sediment Greece 98 Marine sediments Iran 99 Soil France 97 Soil Canada 100 Soil Chile 100 The applicant provided two 16S rRNA sequencing reports (New Zealand and Australia) from Monash University which identified Actinoplanes cyanea from soil samples across a wide distribution of Australia and the North Island of New Zealand (Monash University Microbe Species Identity and Location report, 18 November 2015; Monash University Microbe Species Identity and Location Report, 24 August 2018). Actinoplanes digitatis Isolation of Actinoplanes digitatis (syn. Ampullariella digitata) has occurred from soil samples in Sheboygan, Michigan, United States in 1963 by J.N. Couch and from tree bark in Mt Taibai, China (European Nucleotide Archives). The applicant provided two 16S rRNA sequencing reports (New Zealand and Australia) from Monash University which identified Actinoplanes digitatis from soil samples across a wide 6 EPA advice for application APP203741 distribution of Australia and the North Island of New Zealand (Monash University Microbe Species Identity and Location report, 18 November
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