title: A microbial community description of a heavy metal contaminated soil site

authors: Tan, Lin

subjects: heavy metal

abstract: Tui mine area, with extremely low pH (2.9-3.3) values and high-metal concentrations, is one of the most contaminated sites in NZ. The structure of the microbial community in different soil layers (Top, Middle and Bottom) of the Tui mine tailing was investigated using culture-based and molecular approaches. The zinc resistance of an Acidocella strain, isolated previously, was determined by culturing methods. Growth curves of Acidocella indicated that it could grow at up to 250mM ZnSO₄, and in the presence of 250mM MgSO₄, both growth and Zn²⁺ resistance were greatly enhanced with tolerance up to 750mM Zn²⁺. Acidophilic bacteria were isolated and enumerated on solid media, and were found to be related to Actinobacteridae and Gammaproteobacteria. By contrast, cloning and pyrosequencing analysis of the 16S rRNA genes revealed that Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans were the most common strains that occurred in the soil environment in all layers. From a clone library of the Top layer DNA, 69 out of 118 clone sequences were phylogenetically affiliated with the iron-oxidizing Leptospirillum ferrooxidans within the Nitrospira and 16 with Acidithiobacillus ferrooxidans within the Proteobacteria. A broadly similar result was obtained from pyrosequencing analysis. The most abundant OTU (21.9%) was affiliated with Leptospirillum ferrooxidans and the second most abundant (8.4%) affiliated with Acidithiobacillus ferrivorans. With the Bottom layer soil, 61.5% of the amplicons sequences in the pyrosequencing run had the closest match with Leptospirillum ferrooxidans and the second most abundant OTU (27.2% of sequences) were affiliated with Acidithiobacillus ferrivorans SS3. Both molecular approaches indicate that a diverse population of bacterial species (128 different species from pyrosequencing) exist in the Top layer soil with the Bottom layer soil having a lower in diversity (49 different species from pyrosequencing).

text: A microbial community description of a heavy metal contaminated soil site Tui mine area, with extremely low pH (2.9-3.3) values and high-metal concentrations, is one of the most contaminated sites in NZ. The structure of the microbial community in different soil layers (Top, Middle and Bottom) of the Tui mine tailing was investigated using culture-based and molecular approaches. The zinc resistance of an Acidocella strain, isolated previously, was determined by culturing methods. Growth curves of Acidocella indicated that it could grow at up to 250mM ZnSO₄, and in the presence of 250mM MgSO₄, both growth and Zn²⁺ resistance were greatly enhanced with tolerance up to 750mM Zn²⁺. Acidophilic bacteria were isolated and enumerated on solid media, and were found to be related to Actinobacteridae and Gammaproteobacteria. By contrast, cloning and pyrosequencing analysis of the 16S rRNA genes revealed that Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans were the most common strains that occurred in the soil environment in all layers. From a clone library of the Top layer DNA, 69 out of 118 clone sequences were phylogenetically affiliated with the iron-oxidizing Leptospirillum ferrooxidans within the Nitrospira and 16 with Acidithiobacillus ferrooxidans within the Proteobacteria. A broadly similar result was obtained from pyrosequencing analysis. The most abundant OTU (21.9%) was affiliated with Leptospirillum ferrooxidans and the second most abundant (8.4%) affiliated with Acidithiobacillus ferrivorans. With the Bottom layer soil, 61.5% of the amplicons sequences in the pyrosequencing run had the closest match with Leptospirillum ferrooxidans and the second most abundant OTU (27.2% of sequences) were affiliated with Acidithiobacillus ferrivorans SS3. Both molecular approaches indicate that a diverse population of bacterial species (128 different species from pyrosequencing) exist in the Top layer soil with the Bottom layer soil having a lower in diversity (49 different species from pyrosequencing).

year: 2012

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: An examination of DHB climate change policy and implementation: Responsiveness to Māori health

authors: Powell, Elisha

abstract: The impacts of climate change have become increasingly evident throughout the world and in Aotearoa. Frequency and intensity of extreme weather events such as flooding, coastal erosion, wildfires, and droughts are notably increasing. Climate-related disasters have devastating effects on human health, as is well documented in literature. These effects include cardiovascular disease, poorer mental health, food insecurity and water borne disease. 

Due to pre-existing health disparities, Māori are particularly vulnerable to the health impacts of climate change. Further, Māori have unique relationships with whenua wherein destruction of the natural environment will have a negative impact on the health of Māori people and communities. The health sector has an obligation to respond to Māori health in a way that honours Māori relationships with the environment and prioritises equitable health outcomes for Māori in climate change policy. 

Although Māori face potentially severe health impacts due to climate change, there is limited literature that considers health sector climate change policy and its responsiveness to Māori health. In an effort to address this gap in literature, this thesis aims to examine whether there is existing District Health Board (DHB) policy focused on implementing institutional responses to climate change. Further, this research seeks to understand the extent to which any identified DHB climate change policy responds to Māori health. 

At the time of study, DHBs were responsible for providing and funding health services throughout Aotearoa. During the late stages of this research, the health sector underwent reform, and two health authorities have replaced DHBs. The implications of this research have important ramifications within the newly established health authorities. A dedicated Māori health authority will provide the health sector with the chance to advance health equity by acting on holistic understandings of health for Māori. These actions would establish health policy that recognises Māori health as fundamentally linked to the environment and therefore uniquely impacted by climate change. 

To achieve the aims of this thesis, two research methods were implemented. Initially, an environmental scan of 17 DHB websites was completed to identify climate change and Māori health policies. This was followed by qualitative interviews with three DHB staff from diverse localities. Additionally, tāngata whenua interviews from the wider research project named Haumanu Hauora, were analysed to ensure Māori understandings of climate change were included in this research (Masters-Awatere et al., 2022). 

Research findings provide insights that point to highly fragmented climate change policies across the health sector. There is a glaring lack of direction in the health sector's response to climate change throughout existing policy. Māori health policies were in place across all DHBs, however, lacked recognition of the interconnection between Māori health and the natural environment, and therefore the impacts of climate change. 

Although policy was fragmented across regions, there is potential to enhance both climate change and Māori health policies by recognising the interconnected nature of Māori health and climate change. This will necessitate a significant change in the health systems policy response to climate change that prioritises mātauranga Māori and addresses the ongoing impacts of colonisation.

text: An examination of DHB climate change policy and implementation: Responsiveness to Māori health The impacts of climate change have become increasingly evident throughout the world and in Aotearoa. Frequency and intensity of extreme weather events such as flooding, coastal erosion, wildfires, and droughts are notably increasing. Climate-related disasters have devastating effects on human health, as is well documented in literature. These effects include cardiovascular disease, poorer mental health, food insecurity and water borne disease. 

Due to pre-existing health disparities, Māori are particularly vulnerable to the health impacts of climate change. Further, Māori have unique relationships with whenua wherein destruction of the natural environment will have a negative impact on the health of Māori people and communities. The health sector has an obligation to respond to Māori health in a way that honours Māori relationships with the environment and prioritises equitable health outcomes for Māori in climate change policy. 

Although Māori face potentially severe health impacts due to climate change, there is limited literature that considers health sector climate change policy and its responsiveness to Māori health. In an effort to address this gap in literature, this thesis aims to examine whether there is existing District Health Board (DHB) policy focused on implementing institutional responses to climate change. Further, this research seeks to understand the extent to which any identified DHB climate change policy responds to Māori health. 

At the time of study, DHBs were responsible for providing and funding health services throughout Aotearoa. During the late stages of this research, the health sector underwent reform, and two health authorities have replaced DHBs. The implications of this research have important ramifications within the newly established health authorities. A dedicated Māori health authority will provide the health sector with the chance to advance health equity by acting on holistic understandings of health for Māori. These actions would establish health policy that recognises Māori health as fundamentally linked to the environment and therefore uniquely impacted by climate change. 

To achieve the aims of this thesis, two research methods were implemented. Initially, an environmental scan of 17 DHB websites was completed to identify climate change and Māori health policies. This was followed by qualitative interviews with three DHB staff from diverse localities. Additionally, tāngata whenua interviews from the wider research project named Haumanu Hauora, were analysed to ensure Māori understandings of climate change were included in this research (Masters-Awatere et al., 2022). 

Research findings provide insights that point to highly fragmented climate change policies across the health sector. There is a glaring lack of direction in the health sector's response to climate change throughout existing policy. Māori health policies were in place across all DHBs, however, lacked recognition of the interconnection between Māori health and the natural environment, and therefore the impacts of climate change. 

Although policy was fragmented across regions, there is potential to enhance both climate change and Māori health policies by recognising the interconnected nature of Māori health and climate change. This will necessitate a significant change in the health systems policy response to climate change that prioritises mātauranga Māori and addresses the ongoing impacts of colonisation.

year: 2025