title: Eutrophication effects on stream macrophytes

authors: Skovsholt, Louis Johansen

abstract: Macrophytes are large, autotrophic organisms residing in aquatic environments. In streams they play important roles as substrate, shelter, and food for higher trophic levels, alter water movements and perform biochemical transformations. Unfortunately, macrophyte diversity worldwide is under threat from multiple anthropogenic factors. Eutrophication, the process of nutrient enrichment following land use intensification, is a major driver of negative stream ecosystem change, often in combination with other anthropogenic pressures such as deforestation and introduction of non-native species. The current paradigm of macrophyte response to eutrophication notes the importance of the hydrological setting and substrate type, but always encompasses modification to competitive interactions between macrophyte growth forms as nutrient concentrations become less limiting and competition for light increases. However, details of the responses of macrophytes to increased nutrient inputs under multiple stressor environments are complex and still warrant investigation if effective guidance on macrophyte management is to be developed.
In this thesis, I have addressed questions related to nutrient concentrations at which macrophytes start to accrue excessive biomass, how this relates to community shifts, what these community shifts look like and how they may be modulated by other variables. Specifically, I have used a mix of field observations and mesocosm experiments to: 
i)	investigate differences in community composition of macrophyte communities in streams along a eutrophication gradient. 
ii)	experimentally explore how external nutrient concentrations affect internal nutrient status, and consequently the growth, morphology, and photosynthesis of stream macrophytes across a range of irradiances.
iii)	investigate if these responses lead to differences in competitive outcomes between species in mixed cultures. 
To investigate relationships between eutrophication and macrophytes in streams in Aotearoa New Zealand, I surveyed 30 lowland streams on the country’s North Island, focusing on the Waikato region. I targeted sites with as few confounding factors as possible by using existing stream classification data to select reaches in each stream that had low slope, were unshaded, and a discharge of around 1 m3 s-1. From those meeting these criteria I used a pre-existing, land-use based nutrient yield model to selected streams expected to provide a range of nutrient concentration. At each site I sampled nutrients (N and P) in water and sediment and analyzed the dominant macrophyte species for internal N and P content. I quantified community structure on five transects across each stream.
To explore links between environment and macrophytes I combined stream descriptors from national datasets in combination with the macrophyte community data and a list of trait scores of the encountered species in a RLQ multivariate analysis. The results showed a gradient in macrophyte community structure, a striking feature of which was the change in percentage of non-native species in the streams: eutrophic streams have almost no native species present. Additionally, many nutrient enriched streams were heavily clogged by macrophyte biomass, with species showing traits related to high performance and effective dispersal. A subsidiary gradient in the RLQ analysis, driven by nitrate and sediment phosphorous, saw a high presence of emergent species in eutrophic streams. This can be because the emergent species have a high nitrogen use efficiency compared to submerged species and can deal with a high turbidity by growing out of the water. A second subsidiary gradient, driven by water column phosphorous, correlated with eutrophic streams having a high degree of submerged non-native species; Ceratophyllum demersum, Egeria densa, Lagarosiphon major, and Elodea canadensis, all species that disperse primarily through fragmentation and can utilize bicarbonate as a carbon source. Phosphorous and carbon availability probably is a major driver for the presence of these species in these streams. 
To test inferences made from observational field investigations, growth, morphological, and photosynthetic responses to different levels of nutrient concentration were investigated in a new experimental mesocosm setup. The system comprised four flumes fed by local groundwater stripped of ions by a reverse osmosis system, then dosed with major ions, macro- and micronutrient elements in controlled amounts to ensure finely controlled growth conditions. 
The first experiment addressed hypotheses around the impact of nitrate concentration on growth of two pondweed species common to Aotearoa New Zealand, Potamogeton crispus and P. ochreatus, and possible interactions between nutrient and irradiance. Four nutrient concentrations (control ~0 µg NO3—N L-1, low ~20 µg NO3—N L-1, medium ~250 µg NO3—N L-1, and, high ~5000 µg NO3—N L-1) were combined with four light levels (67.7, 44.5, 30.9, and 7.8 mol photons m-2 d1) in a full factorial design. I measured internal nitrogen (N) and carbon (C) content, growth rates, and morphology and used pulse amplitude modulated fluorometry to make photosynthesis-irradiance curves. The four external nutrient concentrations gave rise to two distinct groupings of plants based on their final internal nutrient content: a high-N group (2-4 % N) from high and medium nitrate treatments and a low-N group (~1 % N) from the low and control nitrate treatments. High-N plants of both species had faster growth rates and grew wider and taller than the low-N plants, but P. crispus grew widest and branched more, especially at high light levels. Low light availability negated any significant difference between N groups and, notably, low-N individuals of P. ochreatus performed better in this treatment than those of P. crispus. In general, the native P. ochreatus performed better than the non-native P. crispus under low nutrient stress, and the latter was best at high light and high nutrients. The results suggest that P. crispus has a great proliferation potential in eutrophic areas, and that lowering resource levels can help manage not only macrophyte proliferation, but also invasive species. A potential competitive advantage can be inferred for P crispus in eutrophic, well-lit waters.
The second mesocosm experiment investigated competitive interactions between the non-native and native pondweed. Four nutrient treatments were again used (0, 40, 120, and 400 µg NO3—N L-1), combined with two light treatments (18 and 3 mol photons m-2 d-1) in a full factorial design. In each treatment I compared growth of each species when plated in monoculture and mixed culture pots. For each replicate, growth rate and morphological traits (main stem length, lateral spread, branching degree, and root length) were measured. Neither species performed differently in mixed- or mono-specific cultures, indicating no inter-specific interactions under the experimental conditions. Rather, in mixed culture plots the outcome, in terms of growth differentials between taxa, reflected the responses of each species to the treatment. Increasing irradiance tended to result in P. crispus outperforming P. ochreatus, while increasing nutrient levels shifted allowed P. ochreatus to outperform P. ochreatus, particularly at low irradiance. Based on the results of this study, there is no direct short term competitive suppression of either species by the other, but differences in trait expression at different resource levels/combinations might still lead to competitive exclusion in a more natural setting. 
In this thesis I have shown that macrophytes respond to increases in external nutrient level by taking up more nutrients, increasing growth and expressing morphological plasticity. This is species dependent, however, and it is these differences in the ability to respond that appear to shape the macrophyte communities in streams. Streams with high light and nutrient supplies are susceptible to high accrual of biomass by a subset of responsive species that may ultimately end up being the only species present in these streams. I found that the eutrophication threshold for nitrogen is quite low, below 250 µg NO3-N L 1. Macrophyte growth was evident at nitrate concentrations only seen in quite pristine streams and several nutrient species seem to determine community compositions in streams. Thus, management actions for the protection of stream ecosystems would benefit from managing resource levels in general rather than focusing on a specific stressor.

text: Eutrophication effects on stream macrophytes Macrophytes are large, autotrophic organisms residing in aquatic environments. In streams they play important roles as substrate, shelter, and food for higher trophic levels, alter water movements and perform biochemical transformations. Unfortunately, macrophyte diversity worldwide is under threat from multiple anthropogenic factors. Eutrophication, the process of nutrient enrichment following land use intensification, is a major driver of negative stream ecosystem change, often in combination with other anthropogenic pressures such as deforestation and introduction of non-native species. The current paradigm of macrophyte response to eutrophication notes the importance of the hydrological setting and substrate type, but always encompasses modification to competitive interactions between macrophyte growth forms as nutrient concentrations become less limiting and competition for light increases. However, details of the responses of macrophytes to increased nutrient inputs under multiple stressor environments are complex and still warrant investigation if effective guidance on macrophyte management is to be developed.
In this thesis, I have addressed questions related to nutrient concentrations at which macrophytes start to accrue excessive biomass, how this relates to community shifts, what these community shifts look like and how they may be modulated by other variables. Specifically, I have used a mix of field observations and mesocosm experiments to: 
i)	investigate differences in community composition of macrophyte communities in streams along a eutrophication gradient. 
ii)	experimentally explore how external nutrient concentrations affect internal nutrient status, and consequently the growth, morphology, and photosynthesis of stream macrophytes across a range of irradiances.
iii)	investigate if these responses lead to differences in competitive outcomes between species in mixed cultures. 
To investigate relationships between eutrophication and macrophytes in streams in Aotearoa New Zealand, I surveyed 30 lowland streams on the country’s North Island, focusing on the Waikato region. I targeted sites with as few confounding factors as possible by using existing stream classification data to select reaches in each stream that had low slope, were unshaded, and a discharge of around 1 m3 s-1. From those meeting these criteria I used a pre-existing, land-use based nutrient yield model to selected streams expected to provide a range of nutrient concentration. At each site I sampled nutrients (N and P) in water and sediment and analyzed the dominant macrophyte species for internal N and P content. I quantified community structure on five transects across each stream.
To explore links between environment and macrophytes I combined stream descriptors from national datasets in combination with the macrophyte community data and a list of trait scores of the encountered species in a RLQ multivariate analysis. The results showed a gradient in macrophyte community structure, a striking feature of which was the change in percentage of non-native species in the streams: eutrophic streams have almost no native species present. Additionally, many nutrient enriched streams were heavily clogged by macrophyte biomass, with species showing traits related to high performance and effective dispersal. A subsidiary gradient in the RLQ analysis, driven by nitrate and sediment phosphorous, saw a high presence of emergent species in eutrophic streams. This can be because the emergent species have a high nitrogen use efficiency compared to submerged species and can deal with a high turbidity by growing out of the water. A second subsidiary gradient, driven by water column phosphorous, correlated with eutrophic streams having a high degree of submerged non-native species; Ceratophyllum demersum, Egeria densa, Lagarosiphon major, and Elodea canadensis, all species that disperse primarily through fragmentation and can utilize bicarbonate as a carbon source. Phosphorous and carbon availability probably is a major driver for the presence of these species in these streams. 
To test inferences made from observational field investigations, growth, morphological, and photosynthetic responses to different levels of nutrient concentration were investigated in a new experimental mesocosm setup. The system comprised four flumes fed by local groundwater stripped of ions by a reverse osmosis system, then dosed with major ions, macro- and micronutrient elements in controlled amounts to ensure finely controlled growth conditions. 
The first experiment addressed hypotheses around the impact of nitrate concentration on growth of two pondweed species common to Aotearoa New Zealand, Potamogeton crispus and P. ochreatus, and possible interactions between nutrient and irradiance. Four nutrient concentrations (control ~0 µg NO3—N L-1, low ~20 µg NO3—N L-1, medium ~250 µg NO3—N L-1, and, high ~5000 µg NO3—N L-1) were combined with four light levels (67.7, 44.5, 30.9, and 7.8 mol photons m-2 d1) in a full factorial design. I measured internal nitrogen (N) and carbon (C) content, growth rates, and morphology and used pulse amplitude modulated fluorometry to make photosynthesis-irradiance curves. The four external nutrient concentrations gave rise to two distinct groupings of plants based on their final internal nutrient content: a high-N group (2-4 % N) from high and medium nitrate treatments and a low-N group (~1 % N) from the low and control nitrate treatments. High-N plants of both species had faster growth rates and grew wider and taller than the low-N plants, but P. crispus grew widest and branched more, especially at high light levels. Low light availability negated any significant difference between N groups and, notably, low-N individuals of P. ochreatus performed better in this treatment than those of P. crispus. In general, the native P. ochreatus performed better than the non-native P. crispus under low nutrient stress, and the latter was best at high light and high nutrients. The results suggest that P. crispus has a great proliferation potential in eutrophic areas, and that lowering resource levels can help manage not only macrophyte proliferation, but also invasive species. A potential competitive advantage can be inferred for P crispus in eutrophic, well-lit waters.
The second mesocosm experiment investigated competitive interactions between the non-native and native pondweed. Four nutrient treatments were again used (0, 40, 120, and 400 µg NO3—N L-1), combined with two light treatments (18 and 3 mol photons m-2 d-1) in a full factorial design. In each treatment I compared growth of each species when plated in monoculture and mixed culture pots. For each replicate, growth rate and morphological traits (main stem length, lateral spread, branching degree, and root length) were measured. Neither species performed differently in mixed- or mono-specific cultures, indicating no inter-specific interactions under the experimental conditions. Rather, in mixed culture plots the outcome, in terms of growth differentials between taxa, reflected the responses of each species to the treatment. Increasing irradiance tended to result in P. crispus outperforming P. ochreatus, while increasing nutrient levels shifted allowed P. ochreatus to outperform P. ochreatus, particularly at low irradiance. Based on the results of this study, there is no direct short term competitive suppression of either species by the other, but differences in trait expression at different resource levels/combinations might still lead to competitive exclusion in a more natural setting. 
In this thesis I have shown that macrophytes respond to increases in external nutrient level by taking up more nutrients, increasing growth and expressing morphological plasticity. This is species dependent, however, and it is these differences in the ability to respond that appear to shape the macrophyte communities in streams. Streams with high light and nutrient supplies are susceptible to high accrual of biomass by a subset of responsive species that may ultimately end up being the only species present in these streams. I found that the eutrophication threshold for nitrogen is quite low, below 250 µg NO3-N L 1. Macrophyte growth was evident at nitrate concentrations only seen in quite pristine streams and several nutrient species seem to determine community compositions in streams. Thus, management actions for the protection of stream ecosystems would benefit from managing resource levels in general rather than focusing on a specific stressor.

year: 2024-07-10

title: Propositionalisation of Profile Hidden Markov Models for Biological Sequence Analysis

authors: Mutter, Stefan

subjects: computer science

abstract: Hidden Markov Models are a widely used generative model for analysing sequence data. A variant, Profile Hidden Markov Models are a special case used in Bioinformatics to represent, for example, protein families. In this paper we introduce a simple propositionalisation method for Profile Hidden Markov Models. The method allows the use of PHMMs discriminatively in a classification task. Previously, kernel approaches have been proposed to generate a discriminative description for an HMM, but require the explicit definition of a similarity measure for HMMs. Propositionalisation does not need such a measure and allows the use of any propositional learner including kernel-based approaches. We show empirically that using propositionalisation leads to higher accuracies in comparison with PHMMs on benchmark datasets.

text: Propositionalisation of Profile Hidden Markov Models for Biological Sequence Analysis Hidden Markov Models are a widely used generative model for analysing sequence data. A variant, Profile Hidden Markov Models are a special case used in Bioinformatics to represent, for example, protein families. In this paper we introduce a simple propositionalisation method for Profile Hidden Markov Models. The method allows the use of PHMMs discriminatively in a classification task. Previously, kernel approaches have been proposed to generate a discriminative description for an HMM, but require the explicit definition of a similarity measure for HMMs. Propositionalisation does not need such a measure and allows the use of any propositional learner including kernel-based approaches. We show empirically that using propositionalisation leads to higher accuracies in comparison with PHMMs on benchmark datasets.

year: 2008

title: Ngā whakaaro o ngā ākonga: perspectives and experiences of Māori students in outdoor education in Aotearoa New Zealand

authors: Washbourn, Phil

subjects: Outdoor education

abstract: This study aims to develop an understanding of the perspectives and experiences of Māori students in a secondary school outdoor education programme in Aotearoa New Zealand. Lynch (2012) indicated that “there is a clear need, and wide scope, for research into: cultural elements of outdoor education programmes; cultural effects on participants; culturally appropriate research approaches and programme effects on, and experiences of, people who identify as Māori” (p.49). Outdoor education in Aotearoa New Zealand has been heavily influenced by ‘Eurocentric’ values and practices that contrast with those of Te Ao Māori. In line with a number of calls to re-envision the field, the perspectives and experiences of Māori and the incorporation of Te Ao Māori pedagogies are vital to the reconstruction of an integrated and inclusive Aotearoa New Zealand expression of Outdoor Education for the 21st century.
This study, guided by culturally responsive research methodology, used focus groups to investigate the opinions, thoughts and expectations of Māori students of outdoor education. Thematic analysis was used to analyse the focus group data, and four major themes were identified: the importance of shared experience and relationships to positive experiences of outdoor education; the distinctive practices of outdoor education make learning enjoyable and engaging; the importance to students of making connections with Te Ao Māori through experience, stories of places and history; and the complexity of engaging Māori in participation in outdoor education, including factors such as affordability, the influence of friends and whānau and prioritising educational pathways. A range of practices and approaches from Te Ao Māori are considered and presented, based on the contribution of the student participants, including pedagogical principles from Te Ao Māori such as wānanga, whanaungatanga and tauira. Suggestions for practice include developing connections within the community and experiencing Te Ao Māori learning contexts such as waka ama, noho marae and mahinga kai.

text: Ngā whakaaro o ngā ākonga: perspectives and experiences of Māori students in outdoor education in Aotearoa New Zealand This study aims to develop an understanding of the perspectives and experiences of Māori students in a secondary school outdoor education programme in Aotearoa New Zealand. Lynch (2012) indicated that “there is a clear need, and wide scope, for research into: cultural elements of outdoor education programmes; cultural effects on participants; culturally appropriate research approaches and programme effects on, and experiences of, people who identify as Māori” (p.49). Outdoor education in Aotearoa New Zealand has been heavily influenced by ‘Eurocentric’ values and practices that contrast with those of Te Ao Māori. In line with a number of calls to re-envision the field, the perspectives and experiences of Māori and the incorporation of Te Ao Māori pedagogies are vital to the reconstruction of an integrated and inclusive Aotearoa New Zealand expression of Outdoor Education for the 21st century.
This study, guided by culturally responsive research methodology, used focus groups to investigate the opinions, thoughts and expectations of Māori students of outdoor education. Thematic analysis was used to analyse the focus group data, and four major themes were identified: the importance of shared experience and relationships to positive experiences of outdoor education; the distinctive practices of outdoor education make learning enjoyable and engaging; the importance to students of making connections with Te Ao Māori through experience, stories of places and history; and the complexity of engaging Māori in participation in outdoor education, including factors such as affordability, the influence of friends and whānau and prioritising educational pathways. A range of practices and approaches from Te Ao Māori are considered and presented, based on the contribution of the student participants, including pedagogical principles from Te Ao Māori such as wānanga, whanaungatanga and tauira. Suggestions for practice include developing connections within the community and experiencing Te Ao Māori learning contexts such as waka ama, noho marae and mahinga kai.

year: 2018