title: Effects of copper sprays on microbial communities in kiwifruit orchard soils

authors: Dean, Fiona Patricia

abstract: There has been a significant increase in the use of antimicrobial copper sprays on kiwifruit orchards in the Western Bay of Plenty (WBOP) since the first outbreak of the bacterial vine disease Pseudomonas syringae pv. actinidiae (Psa-V) in 2010. Studies have revealed that an accumulation of copper in soil may adversely affect soil microorganisms, which are pivotal in essential soil functions such as nutrient assimilation.
The aim of this study was to determine whether or not the use of copper sprays on WBOP kiwifruit orchards has had detrimental effects on soil microorganisms and if this has resulted in changes to the structure of soil microbiological communities.
Soil was sampled from ten WBOP kiwifruit orchards with varying levels of copper but with similar physicochemical properties. These included five sets of two adjacent orchards, of which one was organic and the other conventional, and for which data was available on soil copper levels for 2011. 
DNA extracted from each soil was amplified with PCR and sequenced using Ion Torrent Sequencing technology. The resulting bacterial and archaeal sequences were binned into operational taxonomic units (OTUs) and the phylogeny of each was determined using the Ribosomal Database Project (RDP) Classifier. Soils were also analysed for a number of physicochemical properties including total, bioavailable and free ionic copper.
Non-metric Multidimensional Scaling (NMDS) and Multi-Response Permutation Procedures (MRPP) were used to examine dissimilarities between microbial communities in relation to soil copper levels, management practices and other physicochemical variables. Indicator species analyses were conducted on OTU abundance data to determine if particular OTUs were indicative of soils with the lowest and highest copper levels. Community data were also compared using a number of measures of diversity. Differences in physicochemical parameters between soils were analysed for significance using ANOVA and t-tests.
Results revealed that levels of total copper in soils have increased since 2011, with significant differences measured between each pair of orchards. Significant differences in soil microbial communities were also revealed, with pH identified as the main driver of community composition within and between orchards and differences between orchards were also largely explained by management practices. Relative abundances of Archaea were significantly higher in conventional orchards and in soils with the highest levels of copper. However, overall community dissimilarities were not found to be related to soil copper levels. Indicator species analysis revealed that soils with < 30 mg kg-1 of total copper had a greater abundance of Actinobacteria, whilst soils with > 60 mg kg-1 had a higher representation of Chlamydiae, Chloroflexi, and Thaumarchaeota. 
The conclusions of this research are that current copper levels in the study orchard soils have not significantly influenced soil microbial community composition and associated functions. However, the high number of influential variables confounded attempts at identifying differences due to copper alone. In addition, the lack of knowledge on the specific functions of individual taxa, make it very difficult to reveal the long-term implications of even subtle differences in community composition as a result of copper use.

text: Effects of copper sprays on microbial communities in kiwifruit orchard soils There has been a significant increase in the use of antimicrobial copper sprays on kiwifruit orchards in the Western Bay of Plenty (WBOP) since the first outbreak of the bacterial vine disease Pseudomonas syringae pv. actinidiae (Psa-V) in 2010. Studies have revealed that an accumulation of copper in soil may adversely affect soil microorganisms, which are pivotal in essential soil functions such as nutrient assimilation.
The aim of this study was to determine whether or not the use of copper sprays on WBOP kiwifruit orchards has had detrimental effects on soil microorganisms and if this has resulted in changes to the structure of soil microbiological communities.
Soil was sampled from ten WBOP kiwifruit orchards with varying levels of copper but with similar physicochemical properties. These included five sets of two adjacent orchards, of which one was organic and the other conventional, and for which data was available on soil copper levels for 2011. 
DNA extracted from each soil was amplified with PCR and sequenced using Ion Torrent Sequencing technology. The resulting bacterial and archaeal sequences were binned into operational taxonomic units (OTUs) and the phylogeny of each was determined using the Ribosomal Database Project (RDP) Classifier. Soils were also analysed for a number of physicochemical properties including total, bioavailable and free ionic copper.
Non-metric Multidimensional Scaling (NMDS) and Multi-Response Permutation Procedures (MRPP) were used to examine dissimilarities between microbial communities in relation to soil copper levels, management practices and other physicochemical variables. Indicator species analyses were conducted on OTU abundance data to determine if particular OTUs were indicative of soils with the lowest and highest copper levels. Community data were also compared using a number of measures of diversity. Differences in physicochemical parameters between soils were analysed for significance using ANOVA and t-tests.
Results revealed that levels of total copper in soils have increased since 2011, with significant differences measured between each pair of orchards. Significant differences in soil microbial communities were also revealed, with pH identified as the main driver of community composition within and between orchards and differences between orchards were also largely explained by management practices. Relative abundances of Archaea were significantly higher in conventional orchards and in soils with the highest levels of copper. However, overall community dissimilarities were not found to be related to soil copper levels. Indicator species analysis revealed that soils with < 30 mg kg-1 of total copper had a greater abundance of Actinobacteria, whilst soils with > 60 mg kg-1 had a higher representation of Chlamydiae, Chloroflexi, and Thaumarchaeota. 
The conclusions of this research are that current copper levels in the study orchard soils have not significantly influenced soil microbial community composition and associated functions. However, the high number of influential variables confounded attempts at identifying differences due to copper alone. In addition, the lack of knowledge on the specific functions of individual taxa, make it very difficult to reveal the long-term implications of even subtle differences in community composition as a result of copper use.

year: 2016

title: Improving our fitnesse: From concrete executions to partial specification

authors: Streader, David

subjects: computer science

abstract: Fitnesse and FIT [5] allow systems tests to be written by non-programmers using a Wiki or HTML style of input. However, there is little support for syntactic and semantic checks as the tests are being designed. This paper describes a support tool for designing table-based test cases that gives deep semantic analysis about a set of test cases. It uses a variety of strategies such as pairwise analysis, boundary value analysis and test case subsumption to suggest missing test cases and to generalise concrete tests into more abstract tests. The goal is to interactively improve the quality of test suites during the test design phase.

text: Improving our fitnesse: From concrete executions to partial specification Fitnesse and FIT [5] allow systems tests to be written by non-programmers using a Wiki or HTML style of input. However, there is little support for syntactic and semantic checks as the tests are being designed. This paper describes a support tool for designing table-based test cases that gives deep semantic analysis about a set of test cases. It uses a variety of strategies such as pairwise analysis, boundary value analysis and test case subsumption to suggest missing test cases and to generalise concrete tests into more abstract tests. The goal is to interactively improve the quality of test suites during the test design phase.

year: 2011-04-07

title: He Māori, He Turi, He Turi, He Māori. Advancing the aspirations of Māori Deaf with their indigenous Connections: A case study

authors: Dunn, Katie Merepaea

subjects: Māori Deaf

abstract: Indigenous peoples consider their connection to whenua (land), whakapapa (genealogy), te reo (language) and tikanga (cultural values) to be an integral part of their worldview (Mead, 2003 & Barlow, 1991).

The identity struggle for indigenous minorities living within a colonised environment has been well documented (Bishop, 1995; Smith G, 1997; Smith L, 1999, & Walker, 2004). The controversies over land, customs, culture and language are major issues to understanding and maintaining one’s own cultural identity and, when considering the Deaf indigenous minorities, the task seems colossal.

When a Māori individual belongs to the hearing majority, the ability to find a place to stand, a connection to one’s turangawaewae (standing place), whakapapa, and marae (village) can be a personal struggle; however, this can often be overcome through a shared experience, through communication at a whānau (family), hapū (sub tribe) and iwi (tribe) level.  However, when the individual is part of a double minority such as the Māori Deaf community, the ability to engage and establish a relationship to enhance their connection to their turangawaewae, can become difficult due to the need to communicate in three different languages: English, Māori and Sign Language.  These language issues can create barriers for the Deaf, Māori and hearing communities at a whānau, hapū and iwi level.

This thesis examines a series of workshops created to advance the indigenous connections and understanding within the Māori Deaf community and Te Ao Māori (Māori worldview). It explores how the integration of the Deaf and hearing, indigenous Māori language and New Zealand Sign Language along with practical workshops can assist the aspirations of Māori Deaf within the advancement of Te Ao Māori and Te Reo Māori.  Within this thesis I will undertake a series of interviews with participants who are at the forefront of the Māori Deaf community. A suggestion of moving forward to address the needs of the Māori Deaf community within the desire to connect to their Māori language and customs is also offered within this thesis.

text: He Māori, He Turi, He Turi, He Māori. Advancing the aspirations of Māori Deaf with their indigenous Connections: A case study Indigenous peoples consider their connection to whenua (land), whakapapa (genealogy), te reo (language) and tikanga (cultural values) to be an integral part of their worldview (Mead, 2003 & Barlow, 1991).

The identity struggle for indigenous minorities living within a colonised environment has been well documented (Bishop, 1995; Smith G, 1997; Smith L, 1999, & Walker, 2004). The controversies over land, customs, culture and language are major issues to understanding and maintaining one’s own cultural identity and, when considering the Deaf indigenous minorities, the task seems colossal.

When a Māori individual belongs to the hearing majority, the ability to find a place to stand, a connection to one’s turangawaewae (standing place), whakapapa, and marae (village) can be a personal struggle; however, this can often be overcome through a shared experience, through communication at a whānau (family), hapū (sub tribe) and iwi (tribe) level.  However, when the individual is part of a double minority such as the Māori Deaf community, the ability to engage and establish a relationship to enhance their connection to their turangawaewae, can become difficult due to the need to communicate in three different languages: English, Māori and Sign Language.  These language issues can create barriers for the Deaf, Māori and hearing communities at a whānau, hapū and iwi level.

This thesis examines a series of workshops created to advance the indigenous connections and understanding within the Māori Deaf community and Te Ao Māori (Māori worldview). It explores how the integration of the Deaf and hearing, indigenous Māori language and New Zealand Sign Language along with practical workshops can assist the aspirations of Māori Deaf within the advancement of Te Ao Māori and Te Reo Māori.  Within this thesis I will undertake a series of interviews with participants who are at the forefront of the Māori Deaf community. A suggestion of moving forward to address the needs of the Māori Deaf community within the desire to connect to their Māori language and customs is also offered within this thesis.

year: 2012