title: Contrasting microbial communities across anthropogenic pollution gradients: MV Rena shipwreck versus urban pressures

authors: Reihana, Kiri

subjects: microbial

abstract: With the catastrophic environmental event that was the MV Rena ship wreck and oil spill in the Bay of Plenty area in 2011, a serendipitous opportunity to laterally explore a variety of impacts in the marine biosphere emerged. One of those opportunities is studied here; how microbial communities respond to stress in context of existing ambient local anthropogenic influences. The locational backdrop to this study is also relevant and provides an additional element of complexity as the Bay of Plenty region is located in the middle of the Taupo Volcanic Zone, hence microbial communities are likely to reflect the regional geology. Therefore a research project was possible where a pollutant gradient was selected based on a range of locations reflecting different elements of natural versus human long term and acute impact stresses. The concept was to establish a platform of preliminary study from which more detailed could follow. In addition this study aimed at providing a link between microbial environmental responses to stress in a context that could permit uptake of scientific evidence for cultural impact assessments given the strong cultural focus on MV Rena impacts by government and the public.
A significant element of the exploratory process was to identify methodologies which may be of use in ascribing microbial community composition with the microenvironment in a manner that allows comparison with research reported in the literature.
Review of all results showed that sites from widely varying geologies and environmental/stress condition were more similar than was initially predicted. This is in sharp contrast to expectations generated from the literature. 
At the sites of Astrolabe Reef (Otaiti) (impacted by the ship wreck, major oil spill and heavy metal pollution event) and Maketu (impacted by a eutrophic estuary), similar consortia transpired, despite strongly different sources of stress, substantiating the microbial biogeography theory: ‘Everything is everywhere’ and ‘the environment selects’. However at Tauranga Harbour long term human activity appears to have had a significant ‘additional’ effect on microbial communities. Our challenge has hence become one to separate out natural versus a range of anthropogenic stressors. 
Underlying the general overall trends, subtle community effects such as at Astrolabe Reef, which supported significantly different dominant communities to the other two sites. It was expected that Tauranga Harbour and Maketu Estuary (adjacent coastally), would be more similar. Of all the sites one at the impacted Maketu, site 1 (M1) and the impacted Tauranga site 2 (T2), were highly similar at 96% from statistical analysis suggesting, the original assumption of visually similar site characteristics (impacted sites with low residence time and thick algal matts) do support similar microbial communities. Substantiating the theory that ‘everything is everywhere’ at these two sites, even though the variables and elemental composition were dissimilar. 
Rare and abundant species were separated out and analysed to elucidate patterns or trends in the communities. Overall the abundant species clustered, into impacted versus non impacted sites, for the rare species Tauranga and Maketu clustered clearly following the same trend; while the Astrolabe reef sites clustered together. The clear differentiation in the rare species from the Astrolabe reef sites, suggests that those species may make up the endemic bacterial communities at Astrolabe Reef with additional effects of Rena pollution suggested at some of the sites close to the wreck.
A general discussion of the cultural and economic impacts of the Rena oil spill, gave context to the holistic human impacts sustained by the local Māori, specifically the disconnect of their precious livelihoods and unique relationship with the environment. These holistic concepts could compromise a thesis in themselves so in this report their definitions are by no means finite.     
This study attempted to interrelate both cultural, ecological biology and microbiology science components for the purpose of a more comprehensive investigation of microbial responses to the Rena oil spill and contrast these to local anthropogenic pressures. However being the first attempt to catalogue the previously unknown microbial communities in the Bay of Plenty area, meant that sample regimes, techniques, processing and analysis were all experimental. Despite this, effects attributable to the Rena were identified that lay beyond the large scale variability identified for Bay of Plenty microbial community assemblages. 
These research results provide an important primary contribution to microbial understandings in the New Zealand context, and as a baseline mapping exercise for the Bay of Plenty region.

text: Contrasting microbial communities across anthropogenic pollution gradients: MV Rena shipwreck versus urban pressures With the catastrophic environmental event that was the MV Rena ship wreck and oil spill in the Bay of Plenty area in 2011, a serendipitous opportunity to laterally explore a variety of impacts in the marine biosphere emerged. One of those opportunities is studied here; how microbial communities respond to stress in context of existing ambient local anthropogenic influences. The locational backdrop to this study is also relevant and provides an additional element of complexity as the Bay of Plenty region is located in the middle of the Taupo Volcanic Zone, hence microbial communities are likely to reflect the regional geology. Therefore a research project was possible where a pollutant gradient was selected based on a range of locations reflecting different elements of natural versus human long term and acute impact stresses. The concept was to establish a platform of preliminary study from which more detailed could follow. In addition this study aimed at providing a link between microbial environmental responses to stress in a context that could permit uptake of scientific evidence for cultural impact assessments given the strong cultural focus on MV Rena impacts by government and the public.
A significant element of the exploratory process was to identify methodologies which may be of use in ascribing microbial community composition with the microenvironment in a manner that allows comparison with research reported in the literature.
Review of all results showed that sites from widely varying geologies and environmental/stress condition were more similar than was initially predicted. This is in sharp contrast to expectations generated from the literature. 
At the sites of Astrolabe Reef (Otaiti) (impacted by the ship wreck, major oil spill and heavy metal pollution event) and Maketu (impacted by a eutrophic estuary), similar consortia transpired, despite strongly different sources of stress, substantiating the microbial biogeography theory: ‘Everything is everywhere’ and ‘the environment selects’. However at Tauranga Harbour long term human activity appears to have had a significant ‘additional’ effect on microbial communities. Our challenge has hence become one to separate out natural versus a range of anthropogenic stressors. 
Underlying the general overall trends, subtle community effects such as at Astrolabe Reef, which supported significantly different dominant communities to the other two sites. It was expected that Tauranga Harbour and Maketu Estuary (adjacent coastally), would be more similar. Of all the sites one at the impacted Maketu, site 1 (M1) and the impacted Tauranga site 2 (T2), were highly similar at 96% from statistical analysis suggesting, the original assumption of visually similar site characteristics (impacted sites with low residence time and thick algal matts) do support similar microbial communities. Substantiating the theory that ‘everything is everywhere’ at these two sites, even though the variables and elemental composition were dissimilar. 
Rare and abundant species were separated out and analysed to elucidate patterns or trends in the communities. Overall the abundant species clustered, into impacted versus non impacted sites, for the rare species Tauranga and Maketu clustered clearly following the same trend; while the Astrolabe reef sites clustered together. The clear differentiation in the rare species from the Astrolabe reef sites, suggests that those species may make up the endemic bacterial communities at Astrolabe Reef with additional effects of Rena pollution suggested at some of the sites close to the wreck.
A general discussion of the cultural and economic impacts of the Rena oil spill, gave context to the holistic human impacts sustained by the local Māori, specifically the disconnect of their precious livelihoods and unique relationship with the environment. These holistic concepts could compromise a thesis in themselves so in this report their definitions are by no means finite.     
This study attempted to interrelate both cultural, ecological biology and microbiology science components for the purpose of a more comprehensive investigation of microbial responses to the Rena oil spill and contrast these to local anthropogenic pressures. However being the first attempt to catalogue the previously unknown microbial communities in the Bay of Plenty area, meant that sample regimes, techniques, processing and analysis were all experimental. Despite this, effects attributable to the Rena were identified that lay beyond the large scale variability identified for Bay of Plenty microbial community assemblages. 
These research results provide an important primary contribution to microbial understandings in the New Zealand context, and as a baseline mapping exercise for the Bay of Plenty region.

year: 2016

title: Kaitiakitanga: protecting New Zealand's native biodiversity

authors: Morad, Munir

subjects: geography

abstract: Species diversity is a very important component of a healthy ecosystem, and a necessary condition for long-term sustainable development. However, it is widely recognised that species extinction is on the increase in New Zealand, as biological diversity comes under pressure from landuse activity and environmental change.

text: Kaitiakitanga: protecting New Zealand's native biodiversity Species diversity is a very important component of a healthy ecosystem, and a necessary condition for long-term sustainable development. However, it is widely recognised that species extinction is on the increase in New Zealand, as biological diversity comes under pressure from landuse activity and environmental change.

year: 2000

title: Visualizing class probability estimators

authors: Frank, Eibe

subjects: computer science

abstract: Inducing classifiers that make accurate predictions on future data is a driving force for research in inductive learning. However, also of importance to the users is how to gain information from the models produced. Unfortunately, some of the most powerful inductive learning algorithms generate "black boxes"—that is, the representation of the model makes it virtually impossible to gain any insight into what has been learned. This paper presents a technique that can help the user understand why a classifier makes the predictions that it does by providing a two-dimensional visualization of its class probability estimates. It requires the classifier to generate class probabilities but most practical algorithms are able to do so (or can be modified to this end).

text: Visualizing class probability estimators Inducing classifiers that make accurate predictions on future data is a driving force for research in inductive learning. However, also of importance to the users is how to gain information from the models produced. Unfortunately, some of the most powerful inductive learning algorithms generate "black boxes"—that is, the representation of the model makes it virtually impossible to gain any insight into what has been learned. This paper presents a technique that can help the user understand why a classifier makes the predictions that it does by providing a two-dimensional visualization of its class probability estimates. It requires the classifier to generate class probabilities but most practical algorithms are able to do so (or can be modified to this end).

year: 2003-02-19