National Institute of Water and Atmospheric Research
Recent publications
Accurate species identification of harvested fishes is a central, yet often overlooked, component of fishery monitoring. This study examined the efficacy of using otolith shape to differentiate between the morphologically similar grenadiers Macrourus caml and M. whitsoni and validate species identifications by fishery observers within and adjacent to the Ross Sea region, Antarctica. Otolith shape information was collected from 610 M. caml and 329 M. whitsoni otoliths from research collections, where confidence in species identification was high, and 2558 samples collected by fishery observers from commercial longline catches. Univariate and linear discriminant analyses of research-collected samples revealed consistent differences in otolith shape between the two species, with otoliths of M. caml being larger and more elongate than those of M. whitsoni. No significant effect of collection depth or fishing season on otolith shape was evident for either species, and no significant effect of sampling location on otolith shape was evident for M. caml. Otolith shape of M. whitsoni varied slightly among sampling regions, although the extent of these differences was less than those between species. To validate observer identifications, a random forest (RF) model was trained using otolith shape data of 75% of the research collection samples, validated on the remaining 25%, and used to predict the species of fishery observer-collected samples. The RF model achieved high classification success for individuals from the research collections, with an Out-Of-Bag error rate of 5.97% for the training dataset. Overall classification success of individuals in the validation dataset was 96.2%, with 96.8% of M. caml and 94.8% of M. whitsoni correctly classified. Using this model, 90.6% of M. caml and 85.7% of M. whitsoni sampled by fishery observers were predicted as being correctly identified. Individual observer identification success ranged from 50.5% to 98.2%. The reliable and predictable differences in otolith shape observed between the two species indicates that our approach can be applied to ongoing or archived otolith collections to confirm species identification of fishery-sourced samples to improve the accuracy of fisheries monitoring, facilitate assignment of previously collected material to species level, develop high-confidence datasets for further biological analyses, and to understand and prioritise observer training needs. More broadly, our results highlight the potential for using otolith shape as an effective tool for assessing the accuracy of species identifications in fisheries sampling programs.
Estuaries are ecologically valuable ecosystems that process nutrients through complex biogeochemical processes. Here we identify drivers and inhibitors of nitrogen removal in unvegetated intertidal sandflats at six sites in Manukau Harbour (37° 2.00′S 174° 42.00′E) to quantify the exchange of solutes across the sediment-water interface, with nitrogen removal rates (NRR) measured at two contrasting sites (PI and CB) near and far, respectively, from an historical wastewater treatment plant. Solute fluxes were paired with sediment and macrofauna community data to identify drivers of ecosystem function. Fluxes of oxygen, nitrogen and phosphorous were found to vary among sites, with differences attributed to variation in sediment characteristics (grain size, chlorophyll a, organic content) and macrofauna community structure. Mean NRR was found to vary between sites (PI = 32.2 vs CB = 217.9 μmol N2/m²/h), with bioturbating macrofauna (bivalves Austrovenus stutchburyi and Macomona liliana), microphytobenthic biomass, and exposure to nutrients likely key contributing drivers.
We quantify the impacts of halogenated ozone-depleting substances (ODSs), greenhouses gases (GHGs), and short-lived ozone precursors on ozone changes between 1850 and 2014 using single-forcing perturbation simulations from several Earth System models with interactive chemistry participating in the CMIP6 Aerosol and Chemistry Model Intercomparison Project. We present the responses of ozone to individual forcings and an attribution of changes in ozone columns and vertically resolved stratospheric and tropospheric ozone to these forcings.
  • Courtney OgilvyCourtney Ogilvy
  • Rochelle ConstantineRochelle Constantine
  • Sarah J. BurySarah J. Bury
  • Emma L. CarrollEmma L. Carroll
Understanding the foraging ecology of animals gives insights into their trophic relationships and habitat use. We used stable isotope analysis to understand the foraging ecology of a critically endangered marine predator, the Māui dolphin. We analysed carbon and nitrogen isotope ratios of skin samples (n = 101) collected from 1993 to 2021 to investigate temporal changes in diet and niche space. Genetic monitoring associated each sample with a DNA profile which allowed us to assess individual and population level changes in diet. Potential prey and trophic level indicator samples were also collected (n = 166; 15 species) and incorporated in Bayesian mixing models to estimate importance of prey types to Māui dolphin diet. We found isotopic niche space had decreased over time, particularly since the 2008 implementation of a Marine Mammal Sanctuary. We observed a decreasing trend in ∂¹³C and ∂¹⁵N values, but this was not linear and several fluctuations in isotope values occurred over time. The largest variation in isotope values occurred during an El Niño event, suggesting that prey is influenced by climate-driven oceanographic variables. Mixing models indicated relative importance of prey remained constant since 2008. The isotopic variability observed here is not consistent with individual specialization, rather it occurs at the population level.
Deep‐water corals are protected in the seas around New Zealand by legislation that prohibits intentional damage and removal, and by marine protected areas where bottom trawling is prohibited. However, these measures do not protect them from the impacts of a changing climate and ocean acidification. To enable adequate future protection from these threats we require knowledge of the present distribution of corals and the environmental conditions that determine their preferred habitat, as well as the likely future changes in these conditions, so that we can identify areas for potential refugia. In this study, we built habitat suitability models for 12 taxa of deep‐water corals using a comprehensive set of sample data and predicted present and future seafloor environmental conditions from an earth system model specifically tailored for the South Pacific. These models predicted that for most taxa there will be substantial shifts in the location of the most suitable habitat and decreases in the area of such habitat by the end of the 21st century, driven primarily by decreases in seafloor oxygen concentrations, shoaling of aragonite and calcite saturation horizons, and increases in nitrogen concentrations. The current network of protected areas in the region appear to provide little protection for most coral taxa, as there is little overlap with areas of highest habitat suitability, either in the present or the future. We recommend an urgent re‐examination of the spatial distribution of protected areas for deep‐water corals in the region, utilising spatial planning software that can balance protection requirements against value from fishing and mineral resources, take into account the current status of the coral habitats after decades of bottom trawling, and consider connectivity pathways for colonisation of corals into potential refugia.
Edge-of-field mitigations (EoFM) can reduce agricultural nutrient losses to surface water. To determine the feasibility and cost-effectiveness of EoFM, we developed a spatial–economic modelling approach and applied it in the Waituna Lagoon Catchment (Southland, New Zealand) to evaluate reductions in nitrogen (N) and phosphorus (P) loads, utilising three EoFMs: constructed wetlands, woodchip bioreactors and aluminised zeolite filters. Cost-effectiveness per targeted nutrient was calculated using a strategy that considers nutrient reduction potential and implementation costs of EoFM across all farms (catchment-collective approach), and a strategy requiring each farm to mitigate individually using their most cost-effective EoFM mitigations (farm-based approach). Our modelling showed that the load received from potentially EoFM eligible sub-catchments is 46% and 27% for overall N and overall P load, respectively. EoFM can achieve substantial reductions using a catchment-collective approach (max. 24% overall N load; max. 15% overall P load), but cannot on their own provide the reductions required to achieve the desired outcome (59% overall N and 53% overall P load). Catchment-collective approaches for EoFM placement become more cost effective than farm-based approaches when larger nutrient reductions are required (N >33%; P >30%; N&P combined load >16%, based on the received load from potentially EoFM eligible subcatchments).
Clouds and aerosols, as well as overhead ozone, can have large effects on ultraviolet (UV) irradiances. We use statistical methods to remove cloud effects and mean aerosol effects from spectral UV irradiance measurements to investigate the relationship between UV and total column ozone. We show that for fixed solar zenith angles (SZA), seasonal changes in ozone lead to marked changes in clear-sky UV irradiances. Such effects are larger at mid-latitudes than in the tropics. At mid-latitudes, the minimum ozone amount over the course of a year can be about 50 percent of its maximum, with the lowest values in autumn and the highest values in spring. These seasonal ozone changes lead to UV Index (UVI) values in autumn that can exceed those in spring at the same SZA by nearly a factor of two. Differences are even larger for UV spectra weighted by the action spectra for DNA-damaging UV, and for cutaneous previtamin D production. In some cases, the seasonal increase exceeds a factor of 4. The analysis experimentally demonstrates the limits of applicability of the concept of constant Radiative Amplification Factors (RAFs) for estimating effects of changes in ozone for some weighting functions. Changes in DNA-weighted UV and erythemally weighted UV are well represented by the published RAFs. However, there are large SZA dependencies in the case of UVB and vitamin D-weighted UV. For all weightings considered, RAFs calculated from the observations as a function of SZA show similar dependencies between sites, in good agreement with published values, independently of the ozone data source. Graphical abstract
Pastures represent about half of the global agricultural area and productivity losses from weeds are significant. The complex interactions between them and other pasture plants, livestock and the environment imply a need for innovative research that transforms pasture management. To this end, a horizon scan was conducted to identify relevant issues, questions, opportunities, and drivers. The drivers were ranked using three criteria: (1) is this a horizon (is the driver likely to become important in 10–20 years?); (2) will the research require stretchy science (is it currently not well addressed by the science community?); (3) is the research transformative (will successful scientific research in this area lead to significant changes to weed management in pastures?). We identified 11 major issues and 46 subordinate ones. The three highest ranked major issues were: (1) anticipated reductions in access to herbicides; (2) rethinking weed management under an ecosystem services paradigm; (3) responding to shifts in best practice and the regulations that are altering farm system planning to reduce farming’s environmental impacts. We conclude that fundamental interdisciplinary research is needed that addresses biosecurity and weed management issues, while reducing the environmental footprint of farming and maintaining productivity.
The global loss of marine ecosystem engineers has caused an unprecedented decline in biodiversity. Although wild shellfish habitats have been shown to support biodiverse ecosystems, little is known about how biodiversity is altered by restored shellfish habitats, particularly mussels. To explore the biodiversity response to restored mussel habitats we deposited mussels on the seafloor in 1.5 × 1.5 m plots across a gradient of benthic environments. To understand a holistic community response, this study looks at the response of three faunal classifications over 1 year: infauna, epifauna, and pelagic fauna, compared with adjacent control plots (no mussels). The restored mussel habitats recorded 42 times more demersal fish than control areas, while macroalgae and mobile benthic invertebrates had over a twofold increase in abundance. Overall, the addition of mussels to the seafloor resulted in a general reduction of infaunal abundance and biodiversity, but an increase in epifaunal and pelagic faunal abundances, specifically from those species that benefit from benthic habitat complexity and an increase in food availability. From a management perspective, we highlight location-specific differences to consider for future restoration efforts, including environmental conditions and potential observed factors such as nearby sources of species, particularly predators, and relevant demersal fish ranges. Ultimately, measuring biodiversity responses in small-scale studies will serve as a valuable guide for larger scale restoration efforts and this study recommends considerations to enhance biodiversity outcomes in restored mussel habitats.
Agricultural production has economic, environmental, social and cultural consequences beyond farm boundaries, but information about these impacts is not readily available to decision makers. This study applied the Land Use Suitability concept by carrying out an assessment of a region that has the potential for intensification of agricultural production, but where eutrophication of river and estuary receiving environments due to nitrogen enrichment is a significant issue. The assessment evaluated three indicators for each farmable land parcel in the region: productive potential (the inherent productive and economic potential of the parcel), relative contribution (the potential for the parcel to contribute nitrogen to receiving environments compared to other land parcels), and pressure (the load of nitrogen delivered to receiving environments compared to the loads that ensure environmental objectives are achieved). The study indicated that existing data, methods and models can be used to calculate the indicators under different choices for regional land-use intensity and receiving environment objectives. However, the spatial resolution and accuracy that is achievable may preclude using assessment outputs to make land use decisions at small spatial scales such as individual farms. In addition, the study highlighted that land use suitability is not an intrinsic property of a land parcel because it is dependent on choices about land use elsewhere in the landscape and the environmental objectives, and that land use suitability is inherently subjective because of decisions that concern how indicators are combined and weighted.
Identifying barriers to the effective use of science in coastal management of Aotearoa-New Zealand is easy, due to the present lack of complicated governance and management structures, coupled with an emphasis on funding science that includes pathways to implementation. This opinion piece discusses four areas that still hinder effective use of science, all of which are likely to be problematic for other countries. We initially focus on why the science may not be used related to: misunderstandings (linguistic and conceptual differences including indigenous world views); timing of information delivery; uncertainty surrounding the information (knowledge limitations and funding); and top-down constraints (legal systems, politics and institutional objectives). We use Aotearoa-New Zealand examples to demonstrate the barriers operating within each area and discuss three potential solutions. Importantly our analysis indicates that researchers alone cannot transcend these barriers; rather, we need to work as part of an ecosystem, requiring commitment from all society, extending beyond the usual suspects (management agencies). We believe that ecological and systems education from junior school levels through to universities have an important role to play in setting the context to overcome current barriers.
A multitude of biotic indices that represent environmental status have been developed over the past decades making status comparisons difficult. However, transferring an existing index to a new region can be problematic due to differing stressors, ecosystem components and lack of knowledge on regional species sensitivities. Here we assess whether calculating species sensitivities to specific stressors based on biological traits offers a solution. We use biological traits of macrofaunal species to assess sensitivity to suspended sediment concentrations and calculated the Benthic Quality Index (BQI) at 47 sites across a suspended sediment gradient. This trait-based modification of the BQI was well correlated (0.82) to suspended sediment. Problems previously highlighted, relating to trait plasticity and differential weightings of indifferent and beneficial species, were investigated but did not strongly affect results. A trait-based approach has the additional benefit that the data could be easily converted to evaluate ecosystem function.
Recent oceanographic observations have identified significant changes of intermediate water masses characterized by increased temperatures, lowered pH and deoxygenation. In order to improve our understanding as to how these changes may impact deep-sea ecosystems one important strategy is to reconstruct past oceanic conditions. Here we examine the applicability of the scleractinian cold-water coral Solenosmilia variabilis as a marine archive for the reconstructions of past intermediate water mass temperatures by using Lithium (Li)/Magnesium (Mg) ratios. In particular, our study addresses 1) the calibration of Li/Mg ratios against in-situ temperature data, 2) the reconstruction of past intermediate water mass temperatures using scleractinian coral fossil samples from the Brazilian continental margin and 3) the identification of intraspecies variability within the coral microstructure. Results showed that Li/Mg ratios measured in the skeletons of S. variabilis fit into existing Li/Mg-T calibrations of other cold-water scleractinian. Furthermore, the coral microstructure exhibits interspecies variability of Li/Ca and Mg/Ca ratios were also similar to what has been observed in other cold-water scleractinian corals, suggesting a similar biomineralization control on the incorporation of Li and Mg into the skeleton. However, the Li/Mg based temperature reconstruction using fossil samples resulted in unexpectedly high variations >10°C, which might not be solely related to temperature variations of the intermediate water mass over the last 160 ka on the Brazilian continental margin. We speculate that such temperature variability may be caused by vertical movements of the aragonite saturation horizon and the associated seawater pH changes, which in turn influence the incorporation of Li and Mg into the coral skeleton. Based on these results it is recommended that future studies investigating past oceanic conditions need to consider the carbonate system parameters and how they might impact the mechanisms of Li and Mg being incorporated into skeletons of cold-water coral species such as S. variabilis.
Subtropical and Subantarctic waters either side of the southern hemisphere Subtropical Front are considered iron-limited, suggesting production within the front is dependent on a supply of iron from atmospheric deposition, zonal advection of coastal water, or upwelling. We present the results from a one-day biogeochemical survey in Subtropical Water east of the North Island, New Zealand, in a region where mesoscale cyclonic and anticyclonic eddies entrain chlorophyll in filaments around the eddies. There was no significant relationship between upper-mixed layer chlorophyll and any physical or macronutrient quantity. However, chlorophyll was significantly positively correlated with dissolved iron. A simple model suggests that while vertical entrainment of iron into the upper mixed layer occurred, most of the dissolved iron in the eddy was due to entrainment of high-iron coastal water into low-iron offshore Subtropical Water, and that this iron supports primary production in otherwise iron-deficient water. We suggest that a significant component of the total primary production within the STF may be determined by mesoscale eddy induced lateral advection of iron.
Subaqueous spreading, a type of extensional mass transport that is characterized by a ridge and trough morphology, has been documented globally but is poorly understood. Subaqueous spreading is observed on gently inclined surfaces (typically <3°) when sediment bodies experience a sudden reduction of shear strength along their basal plane during clay softening or liquefaction of sands or silty sand sediment. Historically, spreading has been associated with very large landslides, but many unknown aspects of these mass movements have yet to be clarified. Does spreading influences the large catastrophic failure? What are the sedimentological and morphological aspects that contribute in initiating this process? These are some of the research questions that spurred the present work. Here, we introduce a database that incorporates information from thirty-two case studies, and use this to provide key insights into the sedimentary and morphological aspects of subaqueous spreading that will assist in the identification of spreading elsewhere. We find that subaqueous spreading is most common along passive glacial margins, but is also observed along active margins. The occurrence of contourites interlayered with glaciogenic deposits is, in most cases, associated with landslides (or landslide complexes) with spreading morphology. The database shows that seismic loading is commonly suggested to be the dominant trigger mechanism, although more geotechnical observations and modelling analysis would be needed to support this conclusion. We compare subaqueous spreading with terrestrial spreading, in particular to earthquake-related lateral spreading and clay landslides. We find that subaqueous spreading shares the same driving processes and potentially also some of the trigger mechanisms that are associated with the terrestrial spreading cases. Future work will be required to address the association between spreading and its occurrence on some of the largest landslides on Earth, its development mechanism, and its potential hazard implications.
The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. To determine how nitrogen cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes and transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively, and metagenomes and metatranscriptomes were analyzed from a subset of oxic and dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium) were prevalent and highly redundant, regardless of site-specific physicochemistry or nitrate availability, and present in 40% of reconstructed genomes, suggesting that nitrogen cycling is a core function of aquifer communities. Transcriptional activity for nitrification, denitrification, nitrite-dependent anaerobic methane oxidation and anaerobic ammonia oxidation (anammox) occurred simultaneously in oxic and dysoxic groundwater, indicating the availability of oxic-anoxic interfaces. Concurrent activity by these microorganisms indicates potential synergisms through metabolite exchange across these interfaces (e.g. nitrite and oxygen). Fragmented denitrification pathway encoding and transcription was widespread among groundwater bacteria, although a considerable proportion of associated transcriptional activity was driven by complete denitrifiers, especially under dysoxic conditions. Despite large differences in transcription, the capacity for the final steps of denitrification was largely invariant to aquifer conditions, and most genes and transcripts encoding N2O reductases were the atypical Sec-dependant type, suggesting energy-efficiency prioritization. Results provide insights into the capacity for cooperative relationships in groundwater communities, and the richness and complexity of metabolic mechanisms leading to the loss of fixed nitrogen.
Interpreting the links between transient in‐channel fine sediment storage and the dynamics of suspended sediment transport during flood events helps the understanding of river geomorphology, and also the impacts of fine sediment on water quality and bed habitats of rivers and downstream receiving environments. We present a unique physically based model of suspended sediment transport which is intimately coupled with fine sediment deposition and re‐entrainment processes within the gravel bed. This multi‐size fraction theory provides unique information about the effect of fine sediment size classes due to their dynamics and associated river bed changes in net deposition. The data from a series of flood events from the Oreti River, located in Southland, New Zealand were used to test the ability of this theory to provide a description of the dynamics of the fine sediment size distribution, their concentration, load, and rate of river bed deposition and re‐entrainment. After calibration of the model using the data from one flood event, the model provides good agreement between observed and modeled fine sediment concentration and event load for seven subsequent test events. One of the main applications of this theory in future is for routing suspended sediment concentration and changes on fine sediment deposition down a river network.
The inorganic chlorine (Cly) and odd nitrogen (NOy) chemical families influence stratospheric O3. In January 2020 Australian wildfires injected record‐breaking amounts of smoke into the southern stratosphere. Within 1–2 months ground‐based and satellite observations showed Cly and NOy were repartitioned. By May, lower stratospheric HCl columns declined by ∼30% and ClONO2 columns increased by 40%–50%. The Cly perturbations began and ended near the equinoxes, increased poleward, and peaked at the winter solstice. NO2 decreased from February to April, consistent with sulfate aerosol reactions, but returned to typical values by June ‐ months before the Cly recovery. Transport tracers show that dynamics not chemistry explains most of the observed O3 decrease after April, with no significant transport earlier. Simulations assuming wildfire smoke behaves identically to sulfate aerosols couldn't reproduce observed Cly changes, suggesting they have different composition and chemistry. This undermines our ability to predict ozone in a changing climate.
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381 members
Nicolas Fauchereau
  • Centre for Climate
Gustavo Olivares
  • Urban Air Quality and Health
Mike J Harvey
  • Centre for Atmosphere
Richard Lloyd McKenzie
  • Lauder Atmospheric Research Station
John S Clayton
  • Centre for Freshwater and Estuaries
Wellington, New Zealand