title: A validation study of phycocyanin sensors for monitoring cyanobacteria in cultures and field samples

authors: Hodges, Caroline Marie

subjects: Phycocycanin

abstract: Cyanobacteria are photosynthetic prokaryotes present in almost all terrestrial and aquatic environments. Under favourable conditions of high nutrient inputs, high water temperature and adequate light, they can rapidly multiply and form blooms. Cyanobacterial blooms are harmful to aquatic processes as they reduce the amount of irradiance within the water column and some have the ability to produce toxins which pose a risk to human and animal health. Cyanobacterial blooms are becoming prevalent worldwide as a result of increased anthropogenic influences. To enable accurate risk assessment of drinking water reservoirs, water bodies for recreational use and to assist in the understanding of bloom dynamics, cyanobacterial biomass must be quantified. Traditionally this was done via grab sampling, the use of microscopy and measurements of chlorophyll-a concentration using spectrophotometry. These methods do not allow samples to be collected and analysed at a frequency that provides meaningful spatial and temporal resolution. Additionally, they can be time consuming, expensive and require taxonomic expertise. 

Measurements of chlorophyll-a concentration can provide an estimate of overall phytoplankton biomass but cannot differentiate between eukaryotic cells and cyanobacteria. However, the fluorescent pigment phycocyanin is specific to cyanobacteria and has a unique fluorescence signature which can enable the estimation of cyanobacteria biomass. Methods to detect phycocyanin fluorescence have been integrated into handheld sensors which can be used as a proxy for estimation of cyanobacterial biomass in situ. However, robust validation of these sensors is rarely undertaken. Previous use of fluorescence sensors suggest that there may be multiple sources of interference of the optical signal. The aim of this study was to assess the performance of commercially-available phycocyanin sensors using a combination of culture-based laboratory experiments and a field investigation.

The laboratory studies showed strong linear relationships between phycocyanin and chlorophyll-a fluorescence from sensors and cyanobacterial biovolume obtained by microscopy. This was observed across a range of cell concentrations for solitary (e.g. Microcystis sp.) and filamentous species (e.g. Aphanizomenon sp.). However this linear relationship was not observed with colonial and some filamentous cyanobacteria (Microcystis sp., Nodularia spumigena, and Dolichospermum sp.). Further investigation suggested that the morphology of densely aggregated species inhibited the penetration of light into the colony, resulting in an underestimation of phycocyanin. These results highlight a potential limitation for the use of phycocyanin sensors in situ as colonial and filamentous cyanobacteria are often observed. Other potential limitations for the use of phycocyanin sensors include natural variations in light intensity which can cause photobleaching; reducing fluorescence, as well as increased variability of phycocyanin fluorescence with changes in temperature.  

Field experiments during this study showed that extracellular phycocyanin from lysed cells could in some instances account for more than 20% of the total phycocyanin fluorescence. The field study also showed a strong linear relationship between measurements of phycocyanin fluorescence and cyanobacterial biovolume. However measurements of chlorophyll-a were poorly correlated to cyanobacterial biovolume. The results from the field experiments indicate that phycocyanin sensors may be a valuable tool to monitor cyanobacteria biomass in the field. Collectively, this data highlights the potential for the use of phycocyanin sensors to obtain high frequency data on cyanobacterial biomass, while also demonstrating limitations for their use in situ. Further study is needed to determine more definitively the effects of these potential limitations on phycocyanin measurements and which supplementary parameters could be measured in order for the data collected to be more robust and informative.

text: A validation study of phycocyanin sensors for monitoring cyanobacteria in cultures and field samples Cyanobacteria are photosynthetic prokaryotes present in almost all terrestrial and aquatic environments. Under favourable conditions of high nutrient inputs, high water temperature and adequate light, they can rapidly multiply and form blooms. Cyanobacterial blooms are harmful to aquatic processes as they reduce the amount of irradiance within the water column and some have the ability to produce toxins which pose a risk to human and animal health. Cyanobacterial blooms are becoming prevalent worldwide as a result of increased anthropogenic influences. To enable accurate risk assessment of drinking water reservoirs, water bodies for recreational use and to assist in the understanding of bloom dynamics, cyanobacterial biomass must be quantified. Traditionally this was done via grab sampling, the use of microscopy and measurements of chlorophyll-a concentration using spectrophotometry. These methods do not allow samples to be collected and analysed at a frequency that provides meaningful spatial and temporal resolution. Additionally, they can be time consuming, expensive and require taxonomic expertise. 

Measurements of chlorophyll-a concentration can provide an estimate of overall phytoplankton biomass but cannot differentiate between eukaryotic cells and cyanobacteria. However, the fluorescent pigment phycocyanin is specific to cyanobacteria and has a unique fluorescence signature which can enable the estimation of cyanobacteria biomass. Methods to detect phycocyanin fluorescence have been integrated into handheld sensors which can be used as a proxy for estimation of cyanobacterial biomass in situ. However, robust validation of these sensors is rarely undertaken. Previous use of fluorescence sensors suggest that there may be multiple sources of interference of the optical signal. The aim of this study was to assess the performance of commercially-available phycocyanin sensors using a combination of culture-based laboratory experiments and a field investigation.

The laboratory studies showed strong linear relationships between phycocyanin and chlorophyll-a fluorescence from sensors and cyanobacterial biovolume obtained by microscopy. This was observed across a range of cell concentrations for solitary (e.g. Microcystis sp.) and filamentous species (e.g. Aphanizomenon sp.). However this linear relationship was not observed with colonial and some filamentous cyanobacteria (Microcystis sp., Nodularia spumigena, and Dolichospermum sp.). Further investigation suggested that the morphology of densely aggregated species inhibited the penetration of light into the colony, resulting in an underestimation of phycocyanin. These results highlight a potential limitation for the use of phycocyanin sensors in situ as colonial and filamentous cyanobacteria are often observed. Other potential limitations for the use of phycocyanin sensors include natural variations in light intensity which can cause photobleaching; reducing fluorescence, as well as increased variability of phycocyanin fluorescence with changes in temperature.  

Field experiments during this study showed that extracellular phycocyanin from lysed cells could in some instances account for more than 20% of the total phycocyanin fluorescence. The field study also showed a strong linear relationship between measurements of phycocyanin fluorescence and cyanobacterial biovolume. However measurements of chlorophyll-a were poorly correlated to cyanobacterial biovolume. The results from the field experiments indicate that phycocyanin sensors may be a valuable tool to monitor cyanobacteria biomass in the field. Collectively, this data highlights the potential for the use of phycocyanin sensors to obtain high frequency data on cyanobacterial biomass, while also demonstrating limitations for their use in situ. Further study is needed to determine more definitively the effects of these potential limitations on phycocyanin measurements and which supplementary parameters could be measured in order for the data collected to be more robust and informative.

year: 2016

title: The physical and biological function of wood in New Zealand's forested stream ecosystems

authors: Baillie, Brenda Robin

subjects: wood

abstract: Since the arrival of humans approximately 1000 years before present (B. P.), New Zealand has lost approximately 80% of its forest cover and along with it, the contribution of wood to our aquatic ecosystems. The aim of this thesis was to undertake a large catchment-scale assessment of LW loadings, spatial distribution and morphological influence in an old-growth indigenous forest to provide some understanding on the natural characteristics of wood that would have been present in many river systems of New Zealand prior to human settlement. The second component of the thesis involved the experimental removal of wood from three small streams in order to provide some insight into what that loss of wood may have meant for fish and aquatic invertebrate communities. In the first part of the study, a catchment scale survey of large wood (LW) was completed in a 5thorder, old-growth forest river system. LW volumes ranged from 59-503 m³ ha⁻¹ and declined down the river system along with the number of LW pieces suspended across the channel and LW influence on channel morphology, whereas piece frequency, number of pieces in debris dams and length increased. Nearly half the pieces were influencing channel morphology, particularly wood accumulation, sediment storage, bank armouring, and pool formation. These key pieces were larger, longer and more stable than average. LW contribution to habitat complexity was highest in the middle to upper sections of the river system. Four key zones of wood distribution and influence were identified in the river system. Zonal boundaries were influenced by changes in transport capacity, fluvial processes and channel morphology. In the second part of the study, a field trial was established in three small forested streams to measure the influence of wood and its experimental removal on channel morphology, and indigenous fish and aquatic invertebrate communities. Prior to wood removal there were no significant differences in the total density of fish between wood pools (pools with wood cover), open pools and riffles. Total fish biomass was marginally significant with most of the fish biomass located in wood pools. At the species level, the density and biomass of banded kokopu (Galaxias fasciatus) and the weights of longfin eels (Anguilla dieffenbachii) were significantly higher in wood pools. Species richness, density and biomass of bluegill bullies (Gobiomorphus hubbsi), torrentfish (Cheimarrichthys fosteri) and the density of redfin bullies (Gobiomorphus huttoni) was highest in riffles. Differences in fish community composition were greatest between riffles and pools, whereas there was considerable overlap between the two pool types. Total invertebrate density was 70% higher in debris dams than riffles prior to wood removal, but this difference was not significant. Densities of Trichoptera (caddisfly) and Plecoptera (stonefly), and five aquatic invertebrate taxa were significantly higher in debris dams which also contained greater numbers of less common taxa (< 1% total catch) than riffles. Only Deleatidium sp. (Ephemeroptera) densities were significantly higher in riffles than in debris dams. Aquatic invertebrate communities in debris dams differed significantly from those in riffles and season had a significant influence on aquatic invertebrate community structure. Removal of wood and associated debris dams from the treatment sections in each of the three streams resulted in a simplified channel morphology, significantly increasing the length and area in riffles and reducing the area of pools. The impact on the fish community was greatest for the two larger fish, banded kokopu and large longfin eels, whose abundance declined in the treatment sections. At the reach scale, only banded kokopu biomass showed a significant decline following wood removal. Invertebrates were less affected by wood removal and associated loss of debris dams. Invertebrate composition in the remaining riffles in the treatment sections had a higher proportion of Ephemeroptera and lower proportions of Trichoptera, Plecoptera and Diptera with fewer rare species than remaining debris dams in the control sections, but there were no discernable effects on invertebrate densities and functional feeding groups at the reach scale. Public perception of wood in waterways is mainly negative and wood is managed primarily to reduce flood damage in New Zealand’s streams. With continued research and advocacy on the environmental benefits, careful planning and judicial use, there is the potential to make better use of wood to rehabilitate and enhance New Zealand’s stream environments. This thesis provides some insight into the contribution of wood to forested stream ecosystems in New Zealand and the implicit losses associated with forest removal. It also contributes to our global understanding on the role of wood, its contribution to habitat heterogeneity and influence on biological communities.

text: The physical and biological function of wood in New Zealand's forested stream ecosystems Since the arrival of humans approximately 1000 years before present (B. P.), New Zealand has lost approximately 80% of its forest cover and along with it, the contribution of wood to our aquatic ecosystems. The aim of this thesis was to undertake a large catchment-scale assessment of LW loadings, spatial distribution and morphological influence in an old-growth indigenous forest to provide some understanding on the natural characteristics of wood that would have been present in many river systems of New Zealand prior to human settlement. The second component of the thesis involved the experimental removal of wood from three small streams in order to provide some insight into what that loss of wood may have meant for fish and aquatic invertebrate communities. In the first part of the study, a catchment scale survey of large wood (LW) was completed in a 5thorder, old-growth forest river system. LW volumes ranged from 59-503 m³ ha⁻¹ and declined down the river system along with the number of LW pieces suspended across the channel and LW influence on channel morphology, whereas piece frequency, number of pieces in debris dams and length increased. Nearly half the pieces were influencing channel morphology, particularly wood accumulation, sediment storage, bank armouring, and pool formation. These key pieces were larger, longer and more stable than average. LW contribution to habitat complexity was highest in the middle to upper sections of the river system. Four key zones of wood distribution and influence were identified in the river system. Zonal boundaries were influenced by changes in transport capacity, fluvial processes and channel morphology. In the second part of the study, a field trial was established in three small forested streams to measure the influence of wood and its experimental removal on channel morphology, and indigenous fish and aquatic invertebrate communities. Prior to wood removal there were no significant differences in the total density of fish between wood pools (pools with wood cover), open pools and riffles. Total fish biomass was marginally significant with most of the fish biomass located in wood pools. At the species level, the density and biomass of banded kokopu (Galaxias fasciatus) and the weights of longfin eels (Anguilla dieffenbachii) were significantly higher in wood pools. Species richness, density and biomass of bluegill bullies (Gobiomorphus hubbsi), torrentfish (Cheimarrichthys fosteri) and the density of redfin bullies (Gobiomorphus huttoni) was highest in riffles. Differences in fish community composition were greatest between riffles and pools, whereas there was considerable overlap between the two pool types. Total invertebrate density was 70% higher in debris dams than riffles prior to wood removal, but this difference was not significant. Densities of Trichoptera (caddisfly) and Plecoptera (stonefly), and five aquatic invertebrate taxa were significantly higher in debris dams which also contained greater numbers of less common taxa (< 1% total catch) than riffles. Only Deleatidium sp. (Ephemeroptera) densities were significantly higher in riffles than in debris dams. Aquatic invertebrate communities in debris dams differed significantly from those in riffles and season had a significant influence on aquatic invertebrate community structure. Removal of wood and associated debris dams from the treatment sections in each of the three streams resulted in a simplified channel morphology, significantly increasing the length and area in riffles and reducing the area of pools. The impact on the fish community was greatest for the two larger fish, banded kokopu and large longfin eels, whose abundance declined in the treatment sections. At the reach scale, only banded kokopu biomass showed a significant decline following wood removal. Invertebrates were less affected by wood removal and associated loss of debris dams. Invertebrate composition in the remaining riffles in the treatment sections had a higher proportion of Ephemeroptera and lower proportions of Trichoptera, Plecoptera and Diptera with fewer rare species than remaining debris dams in the control sections, but there were no discernable effects on invertebrate densities and functional feeding groups at the reach scale. Public perception of wood in waterways is mainly negative and wood is managed primarily to reduce flood damage in New Zealand’s streams. With continued research and advocacy on the environmental benefits, careful planning and judicial use, there is the potential to make better use of wood to rehabilitate and enhance New Zealand’s stream environments. This thesis provides some insight into the contribution of wood to forested stream ecosystems in New Zealand and the implicit losses associated with forest removal. It also contributes to our global understanding on the role of wood, its contribution to habitat heterogeneity and influence on biological communities.

year: 2011

title: Kimihia, rangahaua ngā tikanga heke iho. He taonga huahua e riro mai: Exploring whakapapa as a tool towards a kaupapa Māori assessment framework in early childhood education

authors: Paki, Vanessa Anne

subjects: kaupapa Maori assessment

abstract: This study explores whakapapa as a tool, which can be used as a kaupapa Māori assessment framework in early childhood education, positioning kaupapa Māori theory as a paradigm base underpinning a philosophical and theoretical discourse towards assessment for children's learning. This thesis represents the culmination of a personal and professional journey, derived from the writer's longstanding interest in and commitment to kaupapa Māori early childhood education, and more specifically, philosophies and practices for assessment in this context. The study has canvassed a vast terrain of kaupapa Māori philosophy in its search for a theoretical grounding for a kaupapa Māori assessment framework for early childhood education.
Foundation to the study has been the premise that the notion of whakapapa serves as an overarching philosophical matrix, encompassing the interconnected realms of genealogy, spirituality, and knowledge that precede, surround, and embrace the Māori child. Throughout the thesis, diagrams are employed to demonstrate and model the whakapapa underpinning the conceptualisations being explored. After contextualising the study within a historical overview of the impact of colonisation of kaupapa Māori education and research, it is suggested that a re-examination of key concepts from tikanga Māori will illuminate transformative possibilities applicable to the study's focus on the development of a theoretical base for an assessment tool within kaupapa Māori early childhood settings. Drawing from the literature, the thesis re-positions the view of the Māori child to one of being nurtured within a philosophical construct underpinned and immersed in tikanga such as whakapapa, ira tangata, whanaungatanga, mana and tapu, and ako, providing a strongly Māori theoretical base for the envisioning of the assessment process. The outcome of this study is to propose an assessment framework, which embodies and reflects these core kaupapa Māori philosophies as praxis.

text: Kimihia, rangahaua ngā tikanga heke iho. He taonga huahua e riro mai: Exploring whakapapa as a tool towards a kaupapa Māori assessment framework in early childhood education This study explores whakapapa as a tool, which can be used as a kaupapa Māori assessment framework in early childhood education, positioning kaupapa Māori theory as a paradigm base underpinning a philosophical and theoretical discourse towards assessment for children's learning. This thesis represents the culmination of a personal and professional journey, derived from the writer's longstanding interest in and commitment to kaupapa Māori early childhood education, and more specifically, philosophies and practices for assessment in this context. The study has canvassed a vast terrain of kaupapa Māori philosophy in its search for a theoretical grounding for a kaupapa Māori assessment framework for early childhood education.
Foundation to the study has been the premise that the notion of whakapapa serves as an overarching philosophical matrix, encompassing the interconnected realms of genealogy, spirituality, and knowledge that precede, surround, and embrace the Māori child. Throughout the thesis, diagrams are employed to demonstrate and model the whakapapa underpinning the conceptualisations being explored. After contextualising the study within a historical overview of the impact of colonisation of kaupapa Māori education and research, it is suggested that a re-examination of key concepts from tikanga Māori will illuminate transformative possibilities applicable to the study's focus on the development of a theoretical base for an assessment tool within kaupapa Māori early childhood settings. Drawing from the literature, the thesis re-positions the view of the Māori child to one of being nurtured within a philosophical construct underpinned and immersed in tikanga such as whakapapa, ira tangata, whanaungatanga, mana and tapu, and ako, providing a strongly Māori theoretical base for the envisioning of the assessment process. The outcome of this study is to propose an assessment framework, which embodies and reflects these core kaupapa Māori philosophies as praxis.

year: 2007