title: Remote sensing of dynamics and aboveground biomass of seagrass in Tauranga Harbor (Bay of Plenty), New Zealand

authors: Ha, Nam-Thang

subjects: Seagrass

abstract: Seagrasses are angiosperm plants that are completely adapted to life in seawater. They are distributed widely across the climatic regions, ranging from the tropics to temperate regions, in both inter-tidal and sub-tidal zones. Multiple ecosystem services are recognized as being supported by seagrass meadows, which recently has included appreciation role in carbon sequestration. Seagrass meadows, however, have been degraded in both terms of area and habitat quality across the globe, leading to a significant loss of ecosystem services and human livelihood support. This ongoing degradation has resulted in an urgent need to develop tools for assessing the temporal changes of extant meadows and accurate estimation of seagrass biological parameters, which will contribute to a sustainable conservation strategy into the future. 

This thesis describes the use of a range of freely available Earth observation products, including multi-spectral imagery from Landsat and Sentinel-2, and synthetic aperture radar (SAR) products from Sentinel-1, coupled with a range of machine learning (ML) and meta-heuristic optimization algorithms, to develop novel and advanced techniques for remote sensing of seagrass. The work used field validation data from Tauranga Harbor, New Zealand, and specifically targeted mapping, change detection, and estimation of seagrass distribution and biomass. 

The relatively small and patchy meadows of Zostera muelleri in this harbor can be mapped using a three-category classification (dense, sparse and none) with up to 91% accuracy for dense and 75% for sparse meadows using the machine learning algorithm Rotation Forest with Sentinel-2 imagery. Despite a slightly lower accuracy (90%), the algorithm Canonical Correlation Forest also shows merit for categorical seagrass mapping. Historic Landsat multispectral satellite data used with ML models was able to map accurately the change in distribution of seagrass meadows over 29 years (1989 - 2019). For this binary mapping application (presence/absence) the CatBoost model obtained over 90% accuracy. 

Historic imagery indicates an approximately 50% of seagrass loss, from 2,424 ha in the year 1989 down to 1,184 ha in the year 2019 in Tauranga Harbor. Most of the early loss was from the northern and southern parts of the harbor and results were consistent with published estimates of change based on aerial photography. 

In addition, a mapping scheme of seagrass distribution was developed from SAR data and a fusion of the multi-spectral and SAR data was developed for seagrass aboveground biomass (AGB) estimation. Optimal results were obtained using a combination of ML methods and metaheuristic optimization. The seagrass distribution was mapped at an accuracy over 90% using the Extreme Gradient Boost (XGB) whilst the AGB map at 10 m spatial resolution was produced at 75% accuracy using the XGB model together with Sentinel-2 images and Particle Swarm Optimization (PSO). 

The last part of the thesis describes the development of a web-based application to allow the advances in this research to be shared with a broader community and strengthen international and domestic collaboration in seagrass protection and conservation. 

This study provides in-depth and advanced methods for seagrass resource inventory, maximizing the utilization of remotely sensed data, state-of-the-art ML and metaheuristic optimization algorithms to accurately map distribution and estimate desired biophysical parameters. The proposed methods are open-source and applicable across the globe, providing a complete toolset for both scientist and managers in aquatic resource management.

text: Remote sensing of dynamics and aboveground biomass of seagrass in Tauranga Harbor (Bay of Plenty), New Zealand Seagrasses are angiosperm plants that are completely adapted to life in seawater. They are distributed widely across the climatic regions, ranging from the tropics to temperate regions, in both inter-tidal and sub-tidal zones. Multiple ecosystem services are recognized as being supported by seagrass meadows, which recently has included appreciation role in carbon sequestration. Seagrass meadows, however, have been degraded in both terms of area and habitat quality across the globe, leading to a significant loss of ecosystem services and human livelihood support. This ongoing degradation has resulted in an urgent need to develop tools for assessing the temporal changes of extant meadows and accurate estimation of seagrass biological parameters, which will contribute to a sustainable conservation strategy into the future. 

This thesis describes the use of a range of freely available Earth observation products, including multi-spectral imagery from Landsat and Sentinel-2, and synthetic aperture radar (SAR) products from Sentinel-1, coupled with a range of machine learning (ML) and meta-heuristic optimization algorithms, to develop novel and advanced techniques for remote sensing of seagrass. The work used field validation data from Tauranga Harbor, New Zealand, and specifically targeted mapping, change detection, and estimation of seagrass distribution and biomass. 

The relatively small and patchy meadows of Zostera muelleri in this harbor can be mapped using a three-category classification (dense, sparse and none) with up to 91% accuracy for dense and 75% for sparse meadows using the machine learning algorithm Rotation Forest with Sentinel-2 imagery. Despite a slightly lower accuracy (90%), the algorithm Canonical Correlation Forest also shows merit for categorical seagrass mapping. Historic Landsat multispectral satellite data used with ML models was able to map accurately the change in distribution of seagrass meadows over 29 years (1989 - 2019). For this binary mapping application (presence/absence) the CatBoost model obtained over 90% accuracy. 

Historic imagery indicates an approximately 50% of seagrass loss, from 2,424 ha in the year 1989 down to 1,184 ha in the year 2019 in Tauranga Harbor. Most of the early loss was from the northern and southern parts of the harbor and results were consistent with published estimates of change based on aerial photography. 

In addition, a mapping scheme of seagrass distribution was developed from SAR data and a fusion of the multi-spectral and SAR data was developed for seagrass aboveground biomass (AGB) estimation. Optimal results were obtained using a combination of ML methods and metaheuristic optimization. The seagrass distribution was mapped at an accuracy over 90% using the Extreme Gradient Boost (XGB) whilst the AGB map at 10 m spatial resolution was produced at 75% accuracy using the XGB model together with Sentinel-2 images and Particle Swarm Optimization (PSO). 

The last part of the thesis describes the development of a web-based application to allow the advances in this research to be shared with a broader community and strengthen international and domestic collaboration in seagrass protection and conservation. 

This study provides in-depth and advanced methods for seagrass resource inventory, maximizing the utilization of remotely sensed data, state-of-the-art ML and metaheuristic optimization algorithms to accurately map distribution and estimate desired biophysical parameters. The proposed methods are open-source and applicable across the globe, providing a complete toolset for both scientist and managers in aquatic resource management.

year: 2021

title: Benthic nutrient release from Auckland dune lakes

authors: Özkundakci, Deniz

abstract: New Zealand’s freshwater lakes are under pressure from land use intensification, discharge of nutrient contaminants and over-allocation of groundwater resources. Dune lakes are comparatively rare ecosystems formed by wind-blown sand which creates depressions or water impoundments. Often isolated and diversity depauperate, their geomorphological features can make them particularly vulnerable to anthropogenic eutrophication. Ecological models provide a tool for assessing potential strategies for remediation of lake eutrophication. However, they require an understanding of the drivers of water quality decline, including external and internal nutrient loading. The University of Waikato was contracted by Auckland Council to assess lake littoral groundwater infiltration rates and sediment nutrient release rates in seven dune lakes to support the development of ecological models for the lakes.  

Littoral groundwater infiltration was measured using custom moulded clear acrylic domes fitted with valves which allowed water passage into an attached collection bag. The chambers were deployed in the winter and of late spring of 2023. Depending on lake size and site suitability, between one and four chambers were deployed in the littoral zone (generally ~0.5m depth) of each lake and left in place for 24 hours. Net groundwater efflux was not detected by any of the chambers, while groundwater infiltration rates ranged from 1.0–7.4 L m-2 day-1. Assessment of groundwater nutrient concentrations was not feasible due to the volume of the chamber (16 L) and the deployment period required to determine infiltration rates. Littoral groundwater infiltration likely constitutes a significant proportion of the inflow to these lakes, and rates appear to be volumetrically proportional to the linear distance to the catchment boundary from the point of sampling, and to variance in catchment rainfall. Littoral infiltration rates responded quickly (<24 hours) to total precipitation preceding sampling; however, this may be partially due to the higher-than-average rainfall and soil saturation during the 2023 survey period. 

Sediment nutrient release rates were determined using benthic incubation chambers deployed at or near the deepest point of each lake during the spring of 2023. Four dark chambers were deployed in each lake for between 32–68 hours, water samples were pumped from each chamber and analysed for dissolved nutrients. Lakes Kawaupaku, Ōkaihau, Te Kanae and Whatihua were strongly stratified with anoxic bottom waters and sediment nutrient release rates could not be determined. Bottom water samples taken at the time of chamber deployment in these lakes found ammonium and nitrate concentrations were high (>0.2 mg N L-1) but dissolved reactive phosphorus (DRP) concentrations were near or below detection limits (<0.004 mg P L-1); indicating that internal lake phosphorus loading was likely limited in comparison to nitrogen loading.  

The shallow, polymictic nature of the Tomarata, Spectacle and Slipper lakes provided more suitable conditions for determination of in situ sediment nutrient fluxes, although a second deployment in Lake Tomarata was conducted in August 2024. The measured nutrient flux rates, maximum nutrient flux rates and half saturation constants for ammonium and dissolved reactive phosphorus are presented in the table below. The low phosphorus release rates may be due to low external phosphorus loading, associated with episodic sediment loading from the mostly ephemeral surface inflows to the lakes. These findings align with previous work carried out in Lake Tomarata demonstrating the sedimental total phosphorus (TP) pool to have a low redox sensitive phosphorus fraction despite sediment iron content being reasonably high (Waters, 2022). 

Prolonged stratification of lakes Kawaupaku, Ōkaihau, Te Kanae and Whatihua provided limited opportunity to directly assess internal nutrient loading. However, external phosphorus loading to these lakes is likely to be constrained as they are primarily groundwater fed with small, ephemeral surface inflows. In addition, hypolimnetic DRP concentrations and sediment phosphorus release rates determined for lakes Tomarata, Slipper and Spectacle indicate that internal phosphorus loading is low compared to other New Zealand lakes. External nitrogen loading is likely to be more substantial than phosphorus loading, but internal loading also appears to be lower than average. These findings underscore the distinct processes driving nitrogen and phosphorus loading, and consequently nutrient concentrations in the lakes studied. They also provide data critical for the parameterisation of subsequent water quality models, which might be used to inform land use practices through comprehensive scenario testing of various management options.

text: Benthic nutrient release from Auckland dune lakes New Zealand’s freshwater lakes are under pressure from land use intensification, discharge of nutrient contaminants and over-allocation of groundwater resources. Dune lakes are comparatively rare ecosystems formed by wind-blown sand which creates depressions or water impoundments. Often isolated and diversity depauperate, their geomorphological features can make them particularly vulnerable to anthropogenic eutrophication. Ecological models provide a tool for assessing potential strategies for remediation of lake eutrophication. However, they require an understanding of the drivers of water quality decline, including external and internal nutrient loading. The University of Waikato was contracted by Auckland Council to assess lake littoral groundwater infiltration rates and sediment nutrient release rates in seven dune lakes to support the development of ecological models for the lakes.  

Littoral groundwater infiltration was measured using custom moulded clear acrylic domes fitted with valves which allowed water passage into an attached collection bag. The chambers were deployed in the winter and of late spring of 2023. Depending on lake size and site suitability, between one and four chambers were deployed in the littoral zone (generally ~0.5m depth) of each lake and left in place for 24 hours. Net groundwater efflux was not detected by any of the chambers, while groundwater infiltration rates ranged from 1.0–7.4 L m-2 day-1. Assessment of groundwater nutrient concentrations was not feasible due to the volume of the chamber (16 L) and the deployment period required to determine infiltration rates. Littoral groundwater infiltration likely constitutes a significant proportion of the inflow to these lakes, and rates appear to be volumetrically proportional to the linear distance to the catchment boundary from the point of sampling, and to variance in catchment rainfall. Littoral infiltration rates responded quickly (<24 hours) to total precipitation preceding sampling; however, this may be partially due to the higher-than-average rainfall and soil saturation during the 2023 survey period. 

Sediment nutrient release rates were determined using benthic incubation chambers deployed at or near the deepest point of each lake during the spring of 2023. Four dark chambers were deployed in each lake for between 32–68 hours, water samples were pumped from each chamber and analysed for dissolved nutrients. Lakes Kawaupaku, Ōkaihau, Te Kanae and Whatihua were strongly stratified with anoxic bottom waters and sediment nutrient release rates could not be determined. Bottom water samples taken at the time of chamber deployment in these lakes found ammonium and nitrate concentrations were high (>0.2 mg N L-1) but dissolved reactive phosphorus (DRP) concentrations were near or below detection limits (<0.004 mg P L-1); indicating that internal lake phosphorus loading was likely limited in comparison to nitrogen loading.  

The shallow, polymictic nature of the Tomarata, Spectacle and Slipper lakes provided more suitable conditions for determination of in situ sediment nutrient fluxes, although a second deployment in Lake Tomarata was conducted in August 2024. The measured nutrient flux rates, maximum nutrient flux rates and half saturation constants for ammonium and dissolved reactive phosphorus are presented in the table below. The low phosphorus release rates may be due to low external phosphorus loading, associated with episodic sediment loading from the mostly ephemeral surface inflows to the lakes. These findings align with previous work carried out in Lake Tomarata demonstrating the sedimental total phosphorus (TP) pool to have a low redox sensitive phosphorus fraction despite sediment iron content being reasonably high (Waters, 2022). 

Prolonged stratification of lakes Kawaupaku, Ōkaihau, Te Kanae and Whatihua provided limited opportunity to directly assess internal nutrient loading. However, external phosphorus loading to these lakes is likely to be constrained as they are primarily groundwater fed with small, ephemeral surface inflows. In addition, hypolimnetic DRP concentrations and sediment phosphorus release rates determined for lakes Tomarata, Slipper and Spectacle indicate that internal phosphorus loading is low compared to other New Zealand lakes. External nitrogen loading is likely to be more substantial than phosphorus loading, but internal loading also appears to be lower than average. These findings underscore the distinct processes driving nitrogen and phosphorus loading, and consequently nutrient concentrations in the lakes studied. They also provide data critical for the parameterisation of subsequent water quality models, which might be used to inform land use practices through comprehensive scenario testing of various management options.

year: 2025

title: Boat electrofishing survey of fish abundance in the Ohau Channel, Rotorua, in 2015

authors: Hicks, Brendan J.

abstract: The aim of the survey was to provide on-going monitoring of the fish communities and abundance by boat electrofishing in the Ohau Channel, especially fish species that are taonga to Maori (eels, goldfish, and koura). In the current study, we present the findings from the ninth year of sampling (2015) and a summary of previous surveys.
We used the University of Waikato's 4.5 m-long, aluminium-hulled electrofishing boat to catch a total of total of 1,198 fish and koura (18.9 kg) at 13 sites on 2 December 2015, which comprised 2,671 lineal m and 10,684 m² in area. Koura (freshwater crayfish) and 6 fish species were present, with common bully the most abundant species (up to 45.5 fish 100 m⁻² at the site 6, edge habitat). Goldfish (up to 4.85 100 m⁻²) was the next most abundant species, with most goldfish at sites 7 and 12-13 in and around the side channel. Rainbow trout densities were up to 0.28 fish 100 m⁻². Mean bully density (11.41 fish 100 m⁻²) was much higher than for smelt (0.29 fish 100 m⁻²). Koura had a patchy distribution; only 3 individuals were caught at one site.
Comparing catches over the 9 years of sampling, the mean abundance of common bullies in 2015 was consistent with densities in most post-wall years (after 2007), but lower than in 2007 before wall closure (ANOVA P = 0.001). The cause of fluctuating bully abundance is not known, and was not accounted for by changes in water clarity expressed as black disc distance (BDD), water temperature, or water conductivity. Poor water clarity can reduce the efficiency of electrofishing, but high BDD did not correspond with high common bully densities. In 2015, smelt abundance had recovered somewhat from the low catch in 2014.
Goldfish biomass increased initially (2009-2010) because of targeted fishing in the excavated side branch (site 11), which has dense macrophytes and offers good habitat for goldfish. The continued rise in density from 2012 on, however, suggests a real increase in goldfish numbers. In 2012 and 2013 shortfin eels were caught, but no eels were caught in 2014 and only a single longfin eel was caught in 2015.
Analysis of fish densities before and after wall closure is hampered by the single data point before closure. However, we now have 9 years of post-wall data, and comparison of means suggest that the number of bullies has been lower since 2007. An obvious cause could be interruption of bully migration into the Ohau Channel from Lake Rotoiti by the wall. This suggests that the bully population in the Ohau Channel before wall construction and closure was a mixture of fish from lakes Rotorua and Rotoiti, and that recruitment from Rotoiti is now restricted. This hypothesis is testable with otolith microchemistry.

text: Boat electrofishing survey of fish abundance in the Ohau Channel, Rotorua, in 2015 The aim of the survey was to provide on-going monitoring of the fish communities and abundance by boat electrofishing in the Ohau Channel, especially fish species that are taonga to Maori (eels, goldfish, and koura). In the current study, we present the findings from the ninth year of sampling (2015) and a summary of previous surveys.
We used the University of Waikato's 4.5 m-long, aluminium-hulled electrofishing boat to catch a total of total of 1,198 fish and koura (18.9 kg) at 13 sites on 2 December 2015, which comprised 2,671 lineal m and 10,684 m² in area. Koura (freshwater crayfish) and 6 fish species were present, with common bully the most abundant species (up to 45.5 fish 100 m⁻² at the site 6, edge habitat). Goldfish (up to 4.85 100 m⁻²) was the next most abundant species, with most goldfish at sites 7 and 12-13 in and around the side channel. Rainbow trout densities were up to 0.28 fish 100 m⁻². Mean bully density (11.41 fish 100 m⁻²) was much higher than for smelt (0.29 fish 100 m⁻²). Koura had a patchy distribution; only 3 individuals were caught at one site.
Comparing catches over the 9 years of sampling, the mean abundance of common bullies in 2015 was consistent with densities in most post-wall years (after 2007), but lower than in 2007 before wall closure (ANOVA P = 0.001). The cause of fluctuating bully abundance is not known, and was not accounted for by changes in water clarity expressed as black disc distance (BDD), water temperature, or water conductivity. Poor water clarity can reduce the efficiency of electrofishing, but high BDD did not correspond with high common bully densities. In 2015, smelt abundance had recovered somewhat from the low catch in 2014.
Goldfish biomass increased initially (2009-2010) because of targeted fishing in the excavated side branch (site 11), which has dense macrophytes and offers good habitat for goldfish. The continued rise in density from 2012 on, however, suggests a real increase in goldfish numbers. In 2012 and 2013 shortfin eels were caught, but no eels were caught in 2014 and only a single longfin eel was caught in 2015.
Analysis of fish densities before and after wall closure is hampered by the single data point before closure. However, we now have 9 years of post-wall data, and comparison of means suggest that the number of bullies has been lower since 2007. An obvious cause could be interruption of bully migration into the Ohau Channel from Lake Rotoiti by the wall. This suggests that the bully population in the Ohau Channel before wall construction and closure was a mixture of fish from lakes Rotorua and Rotoiti, and that recruitment from Rotoiti is now restricted. This hypothesis is testable with otolith microchemistry.

year: 2016