title: Biases in the metabarcoding of plant pathogens using rust fungi as a model system

authors: Makiola, Andreas

subjects: Cloning

abstract: Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost‐effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next‐generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large‐scale detection and quantification of rust fungi, but not for confirming the absence of species.

text: Biases in the metabarcoding of plant pathogens using rust fungi as a model system Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost‐effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next‐generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large‐scale detection and quantification of rust fungi, but not for confirming the absence of species.

year: 2018

title: Interactions between freshwater mussels and non-native species

authors: Moore, Thomas Peter

subjects: conservation

abstract: Biological invasions contribute to ecosystem change globally, with a disproportionate and intensified impact in freshwaters. This process is exacerbated in modified systems such as hydrogeneration reservoirs that promote favourable conditions for non-native species proliferation. One of the major threats from non-native species is the introduction of novel interactions that may be particularly impactful on species in affiliate (dependent) relationships and that have narrow habitat requirements during early life-stages. Freshwater mussels (Bivalvia: Unionida) are sessile benthic organisms in affiliate relationships with host fish on which they complete their ectoparasitic life-stage. Attached larvae (glochidia) transform on suitable fish hosts before dropping off as juveniles on surficial sediments. Significant disruption to such interactions may lead to local extinction if affiliate partners are unable to be replaced (i.e., by non-native fish) or the availability of critical life-supporting habitats is reduced (e.g., by non-native macrophytes). Non-native species may play a role in reducing recruitment leading to the adult-skewed mussel population size-structures commonly observed. Accordingly, this thesis contributes knowledge of the interactions between unionid mussels and non-native species in modified freshwater ecosystems, and provides information to assist in species and reservoir management for unionid mussel conservation.

The thesis outputs are presented as chapters that have been published in, submitted to, or prepared for scientific journals. A general introduction (Chapter 1) provides context for a global meta-analysis of non-native species and unionid mussel interactions that highlighted non-native fish and macrophytes as potential threats to New Zealand mussels (Chapter 2). Accordingly, a laboratory experiment on three non-native fish (brown bullhead catfish, Ameiurus nebulosus; rudd, Scardinius erythrophthalmus; and goldfish, Carassius auratus) found mussel glochidia were not transformed in ecologically viable numbers compared to a known host fish (Gobiomorphus cotidianus) for a New Zealand unionid (Echyridella menziesii; Chapter 3). This finding suggested that shifts towards fish communities dominated by non-native species have potential to disrupt the obligate glochidial life-stage of unionid mussels.

Dense beds of non-native macrophytes (Ceratophyllum demersum and Egeria densa) were found to produce adverse anoxic and hypoxic conditions potentially fatal to mussels in a field survey of Karāpiro, the most downstream in the Waikato River hydrogeneration reservoir chain (Chapter 4). Here, adverse conditions at the sediment-water interface in littoral zones were mediated by reservoir management of water-level and water-flow, and by macrophyte control via herbicide application in the lower-lacustrine section. A subsequent field survey extended the Chapter 4 results to show that effects of non-native macrophytes at the sediment-water interface depended on macrophyte species and overarching hydrology, whereby adult-skewed mussel population size-structures were present in the lower-lacustrine of Karāpiro but not in the upper-riverine section where recruitment was occurring (Chapter 5).

The final chapter combined previous findings to show how various hypothetical scenarios of fish and macrophyte invasions could operate separately (non-native fish only) or in combination to disrupt E. menziesii recruitment (Chapter 6). This hypothetical analysis highlighted the importance of considering the threats of both non-native fish and macrophytes, which operate primarily on different stages of the unionid life-cycle, in freshwater mussel conservation and management. Due to the long life-span of unionids, recognition of non-native species impacts contributing to adult-skewed mussel population size-structures may provide an opportunity to restore disrupted mechanisms supporting their recruitment before local extinction occurs. Globalisation and energy demand facilitate continued biotic homogenisation and loss of associated ecosystem services. In this context, the role of management in preventing and mitigating the impacts of biological invasions on sensitive species with affiliate relationships will become increasingly important in freshwater ecosystems in the future.

text: Interactions between freshwater mussels and non-native species Biological invasions contribute to ecosystem change globally, with a disproportionate and intensified impact in freshwaters. This process is exacerbated in modified systems such as hydrogeneration reservoirs that promote favourable conditions for non-native species proliferation. One of the major threats from non-native species is the introduction of novel interactions that may be particularly impactful on species in affiliate (dependent) relationships and that have narrow habitat requirements during early life-stages. Freshwater mussels (Bivalvia: Unionida) are sessile benthic organisms in affiliate relationships with host fish on which they complete their ectoparasitic life-stage. Attached larvae (glochidia) transform on suitable fish hosts before dropping off as juveniles on surficial sediments. Significant disruption to such interactions may lead to local extinction if affiliate partners are unable to be replaced (i.e., by non-native fish) or the availability of critical life-supporting habitats is reduced (e.g., by non-native macrophytes). Non-native species may play a role in reducing recruitment leading to the adult-skewed mussel population size-structures commonly observed. Accordingly, this thesis contributes knowledge of the interactions between unionid mussels and non-native species in modified freshwater ecosystems, and provides information to assist in species and reservoir management for unionid mussel conservation.

The thesis outputs are presented as chapters that have been published in, submitted to, or prepared for scientific journals. A general introduction (Chapter 1) provides context for a global meta-analysis of non-native species and unionid mussel interactions that highlighted non-native fish and macrophytes as potential threats to New Zealand mussels (Chapter 2). Accordingly, a laboratory experiment on three non-native fish (brown bullhead catfish, Ameiurus nebulosus; rudd, Scardinius erythrophthalmus; and goldfish, Carassius auratus) found mussel glochidia were not transformed in ecologically viable numbers compared to a known host fish (Gobiomorphus cotidianus) for a New Zealand unionid (Echyridella menziesii; Chapter 3). This finding suggested that shifts towards fish communities dominated by non-native species have potential to disrupt the obligate glochidial life-stage of unionid mussels.

Dense beds of non-native macrophytes (Ceratophyllum demersum and Egeria densa) were found to produce adverse anoxic and hypoxic conditions potentially fatal to mussels in a field survey of Karāpiro, the most downstream in the Waikato River hydrogeneration reservoir chain (Chapter 4). Here, adverse conditions at the sediment-water interface in littoral zones were mediated by reservoir management of water-level and water-flow, and by macrophyte control via herbicide application in the lower-lacustrine section. A subsequent field survey extended the Chapter 4 results to show that effects of non-native macrophytes at the sediment-water interface depended on macrophyte species and overarching hydrology, whereby adult-skewed mussel population size-structures were present in the lower-lacustrine of Karāpiro but not in the upper-riverine section where recruitment was occurring (Chapter 5).

The final chapter combined previous findings to show how various hypothetical scenarios of fish and macrophyte invasions could operate separately (non-native fish only) or in combination to disrupt E. menziesii recruitment (Chapter 6). This hypothetical analysis highlighted the importance of considering the threats of both non-native fish and macrophytes, which operate primarily on different stages of the unionid life-cycle, in freshwater mussel conservation and management. Due to the long life-span of unionids, recognition of non-native species impacts contributing to adult-skewed mussel population size-structures may provide an opportunity to restore disrupted mechanisms supporting their recruitment before local extinction occurs. Globalisation and energy demand facilitate continued biotic homogenisation and loss of associated ecosystem services. In this context, the role of management in preventing and mitigating the impacts of biological invasions on sensitive species with affiliate relationships will become increasingly important in freshwater ecosystems in the future.

year: 2020

title: An old story, a new voice: Tertiary education in the Bay of Plenty region

authors: Amundsen, Diana Leigh

subjects: Bay of Plenty

abstract: In this article, I first critique neoliberal effects on the Aotearoa New Zealand tertiary education sector and then provide a close-up look at tertiary education in the Bay of Plenty region. Information is based on aspects of my doctoral research which was located across three tertiary education organisations comprising the Bay of Plenty Tertiary Education Partnership: The University of Waikato, Toi Ohomai Institute of Technology and, Te Whare Wānanga o Awanuiārangi.  The findings of this research examine connections across the partnership, delving into relevant aspects of universities, polytechnics and wānanga. I evaluate the historical, geographical, political and socio-cultural context of all three institutions. Lastly, I discuss campus connections between the partnership organisations. The emerging picture reveals an old story of expansion and growth with a new voice of tension between collaboration and competition in the face of a neoliberal education context. This article offers timely implications for contemporary and future University of Waikato campus connections and may appeal to academics, graduate students, policymakers and the general public.

text: An old story, a new voice: Tertiary education in the Bay of Plenty region In this article, I first critique neoliberal effects on the Aotearoa New Zealand tertiary education sector and then provide a close-up look at tertiary education in the Bay of Plenty region. Information is based on aspects of my doctoral research which was located across three tertiary education organisations comprising the Bay of Plenty Tertiary Education Partnership: The University of Waikato, Toi Ohomai Institute of Technology and, Te Whare Wānanga o Awanuiārangi.  The findings of this research examine connections across the partnership, delving into relevant aspects of universities, polytechnics and wānanga. I evaluate the historical, geographical, political and socio-cultural context of all three institutions. Lastly, I discuss campus connections between the partnership organisations. The emerging picture reveals an old story of expansion and growth with a new voice of tension between collaboration and competition in the face of a neoliberal education context. This article offers timely implications for contemporary and future University of Waikato campus connections and may appeal to academics, graduate students, policymakers and the general public.

year: 2019