Faculty of Science - Leading creativity and innovation in the sciences

AEO case studies

Find out what AEO is researching.

Mapping soil health from microbial genes

mapping soil health from microbial genes

The soil beneath our feet is a living and constantly changing environment, with microbes such as bacteria and fungi believed to control up to 80% of its functions. Dr Gavin Lear of the School of Biological Sciences, the University of Auckland, and Dr Fiona Curran-Cournane, of the Research Investigations and Monitoring Unit, Auckland Council, are developing a novel index of soil health and potential productivity by assessing its microbial DNA.

They are working with seven regional councils across the country to record variations in the diversity and spread of microbial genes that are known to provide vital ecosystem services, including nutrient storage and cycling, says Dr Curran-Cournane.  In the picture, she’s on the right, taking samples in a Coatesville strawberry patch with the help of colleague Ebrahim Hussain.

The scientists say that this approach may provide major advances over the usual council monitoring programmes, which tend to focus on soil chemistry such as measures of organic carbon, total nitrogen, soil acidity and porosity. Changes in these can be slow to provide warnings that soil is becoming severely degraded, while bacterial communities respond rapidly to environmental change.

“What we’re hoping to do is develop a process so that declines in soil health and fertility can be detected at a far earlier stage, before degradation is severe or perhaps irreversible,” says Dr Lear.  “In future, we’ll be able to inform land managers and land owners more quickly about the status of their soil resource and what they can do in terms of land management practice. It will help us maintain and improve soil health around New Zealand.”  In native bush sites that are undisturbed, microbial communities can also give us indications of the impact of climate change.

The pair says that without the university-council collaboration, the project, due to run for two years from July 2014, wouldn’t have got off the ground. Says Dr Curran-Cournane, “This is just one great example of how the Auckland Environment Observatory is supporting the development and application of novel and interesting scientific research.”

Measuring air and noise pollution in Auckland city

measuring air and noise pollution in Auckland city

Researchers from the University of Auckland, the National Institute of Water and Atmospheric Research and AUT University, supported by the Auckland Council-convened CBD Advisory Board, studied air quality and noise in the Queen St valley as part of a project called Personal Exposure to Noise and Air Pollution.

The research, released in May 2014, found that air pollution in many of Auckland's busy central-city streets was highly variable in time and space.  It suggested that the highest concentrations of pollutants were generally associated with heavy traffic flows, slow-moving traffic and intersections. Customs St near its intersection with Queen St found to have the highest levels of nitrogen dioxide of the 62 sites tested. Customs St was also found to have the highest noise levels in the study.

High nitrogen dioxide levels were also recorded in Queen, Albert, Victoria and Wellesley streets. Levels of all traffic pollutants measured in Kitchener St next to Albert Park and the pedestrian and vehicle "shared space" zones of Elliott and Lorne streets were significantly lower.

Study co-principal Jennifer Salmond, a senior lecturer in the University of Auckland’s School of Environment, says that for Auckland Council to achieve its vision for the city to be the world’s most liveable, it's important to understand how traffic emissions affect air quality.

“Our results also show that careful consideration of urban design and traffic management can produce significant improvements in air quality – concentrations of air pollutants in shared pedestrian zones were, on average, half those measured in nearby heavily-trafficked streets.

“We need to make air quality management a priority now, before traffic emissions get to the point where they do pose a serious problem.”

Data was collected as researchers, who included 15 postgraduate students, walked the streets carrying hand-held particle counters, carbon monoxide monitors, lapel noise dosimeters, hand-held sound level meters, and a global positioning system, as shown in the photograph. 

The atmospheric pollutants measured included particulate matter, carbon monoxide and nitrogen dioxide. Ultrafine particles were measured at a permanent Auckland Council monitoring site on Queen St.

Alongside the air quality work, Dr Kim Dirks from the University of Auckland’s School of Population Health, led an analysis of the city soundscape and how noise affected people’s experience of the city, using questionnaires and interviews with members of the public. 

+ The science team’s co-principals were Ian Longley, (NIWA, air) Jennifer Salmond (The University of Auckland, air); Kim Dirks (The University of Auckland, air and noise); David Welch (The University of Auckland, noise); and Daniel Shepherd (AUT, noise). Stuart Grange was project manager.

Save our Kauri


In 2006, reports started mounting of dead and dying stands of kauri trees in the Waitakere Ranges. Foliage died, branches fell off, canopies thinned, and lesions at the base of trunks bled resin as the picture shows.

Investigations led to the discovery of kauri dieback, a new disease that spreads via microscopic water-borne spores (Phytophthora taxon Agathis, or PTA), in soil. The spores infect the roots and base of kauri trees, damaging the tissues that carry nutrients.  There is no cure and no treatment for the disease, which affects only New Zealand kauri. So far, little is known about PTA and its long-term impact on one of the country’s most iconic indigenous tree species.

University of Auckland ecologists George Perry and Bruce Burns are working with Auckland Council’s principal biosecurity adviser, Nick Waipara, to understand how kauri forests will respond to the large-scale loss of this species. Says Dr Burns: “We are looking at whether all kauri in a stand are affected long-term – or will some portion of the kauri population persist with PTA? Will such a depleted population allow kauri to retain a presence in these forests?”

Adds Dr Perry: “We are using measurements of stand structure and composition alongside demographic and statistical models to better understand the implications of the disease, and the extent to which these forests are or aren’t robust in the face of this pathogen.”

The research sites – Huapai, the Cascades, Huia and Piha – are all in the Waitakere area.  “It has been hypothesised that loss of kauri may result in other species, like rimu, becoming more abundant,” says Dr Perry, “but it is too early to say.” There will be no quick fix, and this is going to be a long project: “It has been set up with decadal dynamics in mind.”

+ Hear more about the project on National Radio’s programme Our Changing World here.

Other AEO collaborations

For the birds: Josie Galbraith’s PhD is investigating the effect that human feeding has on introduced bird communities and the potential for disease spread to native bird species. Outcomes will include the development of bird-feeding guidelines that mitigate risk. Supervisors: Dr Margaret Stanley and Associate Professor Jacqueline Beggs (School of Biological Sciences, University of Auckland); Associate Professor Darryl Jones (Griffith University, Australia.) Auckland Council advisors: Dr Nick Waipara and Dr Bethany Jackson.

Feral pigs and kauri dieback: This collaboration between Dr Cheryl Krull and Dr Margaret Stanley (School of Biological Sciences, University of Auckland) and Dr Imogen Bassett and Dr Nick Waipara (Auckland Council) is exploring the potential for feral pigs to spread kauri dieback disease.  

Weeds and climate change: Christine Sheppard’s PhD investigated the potential for introduced subtropical plants to become weeds under climate change. The research will help managers to future-proof weed-management decisions. Supervisors: Dr Margaret Stanley and Dr Bruce Burns (School of Biological Sciences, University of Auckland). Auckland Council advisor: Dr Nick Waipara.

Algal blooms: Sarah Roth’s MSc thesis explored algal bloom at Great Barrier Island (‘Green in the Pristine: Extensive subtidal bloom of Microdictyon umbilicatum at Great Barrier Island, northern New Zealand’). Supervisors: Dr Nick Shears (Leigh Marine Laboratory and the Department of Statistics, the University of Auckland) and Dr Jarrod Walker (Auckland Council).

Hauraki Gulf megafauna: Olivia Hamilton’s PhD research and Lily Kozmian-Ledward’s MSc research is using aerial surveys of the Hauraki Gulf to determine the abundance and distribution of  cetaceans and the distribution of seabirds, sharks, rays, fish and zooplankton aggregations in order to understand environmental drivers behind their habitat use and interactions.  This research will help inform marine spatial planning and set a benchmark for future surveys and measures of environmental change. Supervisors: Dr Rochelle Constantine (School of Biological Sciences and Institute of Marine Science), Associate Professor Rachel Fewster (Department of Statistics, the University of Auckland), Dr Cameron Walker (Faculty of Engineering, the University of Auckland) and Dr Leigh Torres (Oregon State University).