title: Fine-scale cryogenic sampling of planktonic microbial communities: Application to toxic cyanobacterial blooms

authors: Puddick, Jonathan

abstract: A lack of fine-scale methods for sampling planktonic microbial populations hinders advancement in understanding the responses of these communities to environmental conditions. Current methods provide resolution at scales of centimeters to meters, but not at the millimeter-scale required to understand highly stratified communities. To address this we developed two cryogenic sampling tools to collect spatially-precise samples from aquatic environments while simultaneously preserving the microbial communities. The application of these samplers was examined over a 5.5 h period using a cyanobacterial scum (Microcystis) formed in experimental mesocosms. A cryogenic “surface snatcher” collected a discrete layer (ca. 1 mm) of surface water. Compared to conventional surface sampling methods, the surface snatcher samples contained up to 22-times more microcystin, indicating that less underlying water was incorporated into the sample. A cryogenic “cold finger” sampler was used to collect vertical profiles of the upper 40 mm of the water column. This profiler provided new insights into the fine-scale structure of Microcystis scums, demonstrating that more microcystin-producing Microcystis was contained in the surface 5 mm than the 35 mm below. The results also showed that upregulation of microcystin production was highly localized in the top 2.5 mm of the Microcystis scum. Our results demonstrate that extreme changes in cyanobacterial communities can occur over small distances, and indicate that sampling resolution is of great importance for improving knowledge on cyanobacterial blooms and toxin production. While this study focused on microcystin-producing Microcystis, the cryogenic sampling tools described here could be applied to any planktonic microbial community.

text: Fine-scale cryogenic sampling of planktonic microbial communities: Application to toxic cyanobacterial blooms A lack of fine-scale methods for sampling planktonic microbial populations hinders advancement in understanding the responses of these communities to environmental conditions. Current methods provide resolution at scales of centimeters to meters, but not at the millimeter-scale required to understand highly stratified communities. To address this we developed two cryogenic sampling tools to collect spatially-precise samples from aquatic environments while simultaneously preserving the microbial communities. The application of these samplers was examined over a 5.5 h period using a cyanobacterial scum (Microcystis) formed in experimental mesocosms. A cryogenic “surface snatcher” collected a discrete layer (ca. 1 mm) of surface water. Compared to conventional surface sampling methods, the surface snatcher samples contained up to 22-times more microcystin, indicating that less underlying water was incorporated into the sample. A cryogenic “cold finger” sampler was used to collect vertical profiles of the upper 40 mm of the water column. This profiler provided new insights into the fine-scale structure of Microcystis scums, demonstrating that more microcystin-producing Microcystis was contained in the surface 5 mm than the 35 mm below. The results also showed that upregulation of microcystin production was highly localized in the top 2.5 mm of the Microcystis scum. Our results demonstrate that extreme changes in cyanobacterial communities can occur over small distances, and indicate that sampling resolution is of great importance for improving knowledge on cyanobacterial blooms and toxin production. While this study focused on microcystin-producing Microcystis, the cryogenic sampling tools described here could be applied to any planktonic microbial community.

year: 2016

title: Barcoding of the cytochrome oxidase I (COI) indicates a recent introduction of Ciona savignyi into New Zealand and provides a rapid method for Ciona species discrimination

authors: Smith, Kirsty Fiona

subjects: Cryptic invasion

abstract: Mitochondrial cytochrome oxidase I (COI) gene sequencing (DNA barcoding) of Ciona specimens from New Zealand (NZ) led to the first record of the solitary ascidian Ciona savignyi in the Southern Hemisphere. We sought to quantify C. savignyi COI genetic diversity around the NZ archipelago and to compare this with diversity within C. savignyi's native range in the north-west Pacific. Ciona savignyi specimens were collected from two NZ sites and from three sites around Japan. COI sequences (595 bp) were amplified and measures of genetic diversity were calculated. Based on differences between their COI sequences we developed a PCR-based assay to distinguish C. savignyi from the morphologically similar C. intestinalis. A total of 12 C. savignyi COI haplotypes were recovered from the 76 samples. Of the four haplotypes observed in NZ, two were unique. From the 10 haplotypes observed in the Japan samples, eight were unique. The C. savignyi populations in Japan were found to contain higher haplotype diversity when compared with those in NZ. The NZ samples contained only a small subset of the haplotype variation of the Japan samples, however, NZ samples did harbor two haplotypes not observed in the Japan samples. A PCR-based assay developed from the COI sequences was able to reliably discriminate the two Ciona species. The low COI genetic diversity within the two NZ C. savignyi populations sampled is consistent with a founder effect associated loss of genetic diversity. The robust PCR-based assay for distinguishing C. savignyi and C. intestinalis may find application in ecological and taxonomic studies and can be applied to both archival materials and live animals.

text: Barcoding of the cytochrome oxidase I (COI) indicates a recent introduction of Ciona savignyi into New Zealand and provides a rapid method for Ciona species discrimination Mitochondrial cytochrome oxidase I (COI) gene sequencing (DNA barcoding) of Ciona specimens from New Zealand (NZ) led to the first record of the solitary ascidian Ciona savignyi in the Southern Hemisphere. We sought to quantify C. savignyi COI genetic diversity around the NZ archipelago and to compare this with diversity within C. savignyi's native range in the north-west Pacific. Ciona savignyi specimens were collected from two NZ sites and from three sites around Japan. COI sequences (595 bp) were amplified and measures of genetic diversity were calculated. Based on differences between their COI sequences we developed a PCR-based assay to distinguish C. savignyi from the morphologically similar C. intestinalis. A total of 12 C. savignyi COI haplotypes were recovered from the 76 samples. Of the four haplotypes observed in NZ, two were unique. From the 10 haplotypes observed in the Japan samples, eight were unique. The C. savignyi populations in Japan were found to contain higher haplotype diversity when compared with those in NZ. The NZ samples contained only a small subset of the haplotype variation of the Japan samples, however, NZ samples did harbor two haplotypes not observed in the Japan samples. A PCR-based assay developed from the COI sequences was able to reliably discriminate the two Ciona species. The low COI genetic diversity within the two NZ C. savignyi populations sampled is consistent with a founder effect associated loss of genetic diversity. The robust PCR-based assay for distinguishing C. savignyi and C. intestinalis may find application in ecological and taxonomic studies and can be applied to both archival materials and live animals.

year: 2012

title: Stop playing up! A critical ethnography of health, physical education and (sub)urban schooling

authors: Fitzpatrick, Katie

subjects: Health

abstract: This thesis explores the place of health and physical education in the lives of Otara youth in New Zealand. Situated in the southern suburbs of New Zealand’s largest city, Otara, South Auckland is known for its cultural diversity, as well as for poverty and crime. It is home to large numbers of indigenous Maori and migrant Pasifika (Pacific Island) youth. Based on a year-long critical ethnography of a multiethnic high school, this thesis explores how these young people engage with and respond to the school subjects of health and physical education. It also discusses broader issues in their lives, including the social geographies within which they reside, and how they understand their bodies, sexuality, health, gender and physicalities. The subjects of health and physical education are compulsory in most schools internationally – in New Zealand they are directly linked in curriculum policy documents and in school practice – but share a somewhat uneasy relationship and differing historical positions. Considered low status in schools, these subjects are also conflated with narrow body and health norms, possibly problematic for young women, and/or are wedded to the social and cultural world of sport. Curriculum policy documents established in the last ten years offer the possibility of critical and social approaches to these subjects, but examples of critical practice remain rare. Health and physical education are thus compulsory, contentious, contradictory and complex subjects within contemporary schooling. Critical ethnographies of schooling are relatively scarce compared with conventional ethnographic accounts, but critical ethnographies of health and physical education (PE) are almost unheard of. The use of such a methodology in this study enabled an indepth account of Otara youth in the subjects of health and PE at school. It also provided a platform for storied accounts of how one teacher, Dan, enacted a critical and culturally connected pedagogy of health and PE with the young people in his classes. This thesis explores the complex potential for health and PE as key sites of learning for Pasifika and Maori youth. It examines health and PE as subjects that are both politically fraught and spaces of hope.

text: Stop playing up! A critical ethnography of health, physical education and (sub)urban schooling This thesis explores the place of health and physical education in the lives of Otara youth in New Zealand. Situated in the southern suburbs of New Zealand’s largest city, Otara, South Auckland is known for its cultural diversity, as well as for poverty and crime. It is home to large numbers of indigenous Maori and migrant Pasifika (Pacific Island) youth. Based on a year-long critical ethnography of a multiethnic high school, this thesis explores how these young people engage with and respond to the school subjects of health and physical education. It also discusses broader issues in their lives, including the social geographies within which they reside, and how they understand their bodies, sexuality, health, gender and physicalities. The subjects of health and physical education are compulsory in most schools internationally – in New Zealand they are directly linked in curriculum policy documents and in school practice – but share a somewhat uneasy relationship and differing historical positions. Considered low status in schools, these subjects are also conflated with narrow body and health norms, possibly problematic for young women, and/or are wedded to the social and cultural world of sport. Curriculum policy documents established in the last ten years offer the possibility of critical and social approaches to these subjects, but examples of critical practice remain rare. Health and physical education are thus compulsory, contentious, contradictory and complex subjects within contemporary schooling. Critical ethnographies of schooling are relatively scarce compared with conventional ethnographic accounts, but critical ethnographies of health and physical education (PE) are almost unheard of. The use of such a methodology in this study enabled an indepth account of Otara youth in the subjects of health and PE at school. It also provided a platform for storied accounts of how one teacher, Dan, enacted a critical and culturally connected pedagogy of health and PE with the young people in his classes. This thesis explores the complex potential for health and PE as key sites of learning for Pasifika and Maori youth. It examines health and PE as subjects that are both politically fraught and spaces of hope.

year: 2010