title: Resolving functional resilience of microbial communities to climate-induced change in the McMurdo Dry Valleys of Antarctica

authors: Rovisco Correia Goncalves Monteiro, Maria

subjects: Climate change

abstract: The McMurdo Dry Valleys of Antarctica are an abiotically driven ecosystem characterized by having a very simple trophic structure dominated by microbial communities, whose diversity is shaped by extreme abiotic gradients, particularly extreme aridity and oligotrophy. Regional isolation and dispersal limitations have concurrently led to the emergence of heterogeneous microbial communities with highly localized dominant taxa across the region. These taxa were selected based on specialized genetic and physiological adaptations accumulated during long-term isolation, which conferred an advantage to endure the physical and chemical stress. Models predict that over the coming decades, climate change will trigger hydrological changes in the system with potential consequences for its microbial communities and, subsequently, ecosystem-level processes. The capacity of the Antarctic microbiome to absorb change while maintaining its structural and/or functional attributes will determine the extent to which predicted environmental changes will threaten the system's stability. 
This research starts by developing and validating a space-for-time sampling approach using variations in geochemical factors that follow alterations in water availability as time progresses and to which biological communities respond. This approach was replicated across the six major lakes in the Wright and Taylor valleys, and builds on previous examples of environmental gradients, which used arbitrary distance-based metrics as sampling design, incorporating significant yet uncharacterized in situ geochemical variability. The approach developed here enabled the acquisition of a comprehensive dataset that predicts, with confidence, that future hydrological changes will significantly alter the composition and diversity  of microbial communities historically adapted to arid and oligotrophic conditions. The latter will result in significant changes in the metabolic activity of pathways associated with carbon, nitrogen, phosphorous and sulphur cycles, with an increase in functional diversity and activity as the system becomes wetter. This work further provides first time evidence that carbon fixation via atmospheric chemosynthesis is the primary active pathway for carbon acquisition under extreme aridity in polar deserts, being replaced by photosynthetic carbon fixation with prolonged exposure to wetness.
To complement predictions made in situ using a space-for-time approach, this research incorporated temporal observations using manipulative experiments, performed in a Polar Desert Environmental Chamber (PDEC), to test the sensitivity and resilience of microbial communities to short-term wetting disturbances. It demonstrated that co-existing microbial taxa respond asynchronously during wetting and drying periods, which indicates dry soil communities comprise co-existing taxa with preferences for different environmental conditions. It also experimentally showed, for the first time, the capacity of microbial communities from this region to recover from short-term wetting events associated with the ability of dry-adapted taxa, mostly affiliated with Actinobacteriota and Acidobacteria phyla, to persist during the wetting period. 
Through the incorporation of large-scale spatial transects in conjunction with manipulative experiments, this research delivered a fundamental evidence-based anticipation of the compositional and functional aspects that are likely to change in the McMurdo Dry Valleys ecosystem in response to alterations in water dynamics as well as on the microbial attributes that enhance the ecosystem's functional resilience to climate change.

text: Resolving functional resilience of microbial communities to climate-induced change in the McMurdo Dry Valleys of Antarctica The McMurdo Dry Valleys of Antarctica are an abiotically driven ecosystem characterized by having a very simple trophic structure dominated by microbial communities, whose diversity is shaped by extreme abiotic gradients, particularly extreme aridity and oligotrophy. Regional isolation and dispersal limitations have concurrently led to the emergence of heterogeneous microbial communities with highly localized dominant taxa across the region. These taxa were selected based on specialized genetic and physiological adaptations accumulated during long-term isolation, which conferred an advantage to endure the physical and chemical stress. Models predict that over the coming decades, climate change will trigger hydrological changes in the system with potential consequences for its microbial communities and, subsequently, ecosystem-level processes. The capacity of the Antarctic microbiome to absorb change while maintaining its structural and/or functional attributes will determine the extent to which predicted environmental changes will threaten the system's stability. 
This research starts by developing and validating a space-for-time sampling approach using variations in geochemical factors that follow alterations in water availability as time progresses and to which biological communities respond. This approach was replicated across the six major lakes in the Wright and Taylor valleys, and builds on previous examples of environmental gradients, which used arbitrary distance-based metrics as sampling design, incorporating significant yet uncharacterized in situ geochemical variability. The approach developed here enabled the acquisition of a comprehensive dataset that predicts, with confidence, that future hydrological changes will significantly alter the composition and diversity  of microbial communities historically adapted to arid and oligotrophic conditions. The latter will result in significant changes in the metabolic activity of pathways associated with carbon, nitrogen, phosphorous and sulphur cycles, with an increase in functional diversity and activity as the system becomes wetter. This work further provides first time evidence that carbon fixation via atmospheric chemosynthesis is the primary active pathway for carbon acquisition under extreme aridity in polar deserts, being replaced by photosynthetic carbon fixation with prolonged exposure to wetness.
To complement predictions made in situ using a space-for-time approach, this research incorporated temporal observations using manipulative experiments, performed in a Polar Desert Environmental Chamber (PDEC), to test the sensitivity and resilience of microbial communities to short-term wetting disturbances. It demonstrated that co-existing microbial taxa respond asynchronously during wetting and drying periods, which indicates dry soil communities comprise co-existing taxa with preferences for different environmental conditions. It also experimentally showed, for the first time, the capacity of microbial communities from this region to recover from short-term wetting events associated with the ability of dry-adapted taxa, mostly affiliated with Actinobacteriota and Acidobacteria phyla, to persist during the wetting period. 
Through the incorporation of large-scale spatial transects in conjunction with manipulative experiments, this research delivered a fundamental evidence-based anticipation of the compositional and functional aspects that are likely to change in the McMurdo Dry Valleys ecosystem in response to alterations in water dynamics as well as on the microbial attributes that enhance the ecosystem's functional resilience to climate change.

year: 2022

title: Efficient tuning parameter selection by cross-validated score in high dimensional models

authors: Jung, Yoonsuh

abstract: As DNA microarray data contain relatively small sample size compared to the number of genes, high dimensional models are often employed. In high dimensional models, the selection of tuning parameter (or, penalty parameter) is often one of the crucial parts of the modeling. Cross-validation is one of the most common methods for the tuning parameter selection, which selects a parameter value with the smallest cross-validated score. However, selecting a single value as an ‘optimal’ value for the parameter can be very unstable due to the sampling variation since the sample sizes of microarray data are often small. Our approach is to choose multiple candidates of tuning parameter first, then average the candidates with different weights depending on their performance. The additional step of estimating the weights and averaging the candidates rarely increase the computational cost, while it can considerably improve the traditional cross-validation. We show that the selected value from the suggested methods often lead to stable parameter selection as well as improved detection of significant genetic variables compared to the tradition cross-validation via real data and simulated data sets.

text: Efficient tuning parameter selection by cross-validated score in high dimensional models As DNA microarray data contain relatively small sample size compared to the number of genes, high dimensional models are often employed. In high dimensional models, the selection of tuning parameter (or, penalty parameter) is often one of the crucial parts of the modeling. Cross-validation is one of the most common methods for the tuning parameter selection, which selects a parameter value with the smallest cross-validated score. However, selecting a single value as an ‘optimal’ value for the parameter can be very unstable due to the sampling variation since the sample sizes of microarray data are often small. Our approach is to choose multiple candidates of tuning parameter first, then average the candidates with different weights depending on their performance. The additional step of estimating the weights and averaging the candidates rarely increase the computational cost, while it can considerably improve the traditional cross-validation. We show that the selected value from the suggested methods often lead to stable parameter selection as well as improved detection of significant genetic variables compared to the tradition cross-validation via real data and simulated data sets.

year: 2016-02-08

title: Indigenous challenges to enhance freshwater governance and management in Aotearoa New Zealand - the Waikato river settlement

authors: Te Aho, Linda

subjects: New Zealand

abstract: Co-management of environmental resources is an idea that has been developing for some time in Aotearoa New Zealand as a strategy that recognises Indigenous interests in the environment, and the different ways that people view the world. The contest for control of New Zealand's rivers has generally arisen from successive governments purporting to secure rights based upon English common law. Precepts of that law were completely foreign to the Indigenous Maori who had their own conceptions of rivers. Through the eyes of the Maori, rivers have their own life force, their own spiritual energy and their own powerful identities. Rivers are inextricably linked to tribal identities. Over time a raft of policies was employed and legislation passed by parliament in the name of development and the national interest which did not take into account Maori understandings of the river and its ecosystems, nor their rights, interests, or authority. Excluded from decision-making processes, Maori have long brought matters to the attention of courts by using any basis to assert our rights and interests, and to have our concerns about the deteriorating health and wellbeing of our rivers taken seriously. The search for redress has been relentless. The Resource Management Act 1991 formalised a range of legal rights, but such rights can be meaningless if presented as just one of many other considerations that decision-makers have to take into account. This article explores the notion of collaborative management and the development of co-management models as a background to the emergent Waikato River settlement ± a legal solution embedded in the Waikato-Tainui Raupatu Claims (Waikato River) Settlement Act 2010 that generates a more robust opportunity to bring to an end a paradigm of exclusion and usher in a new era that promises enhanced governance and management of a significant waterway.

text: Indigenous challenges to enhance freshwater governance and management in Aotearoa New Zealand - the Waikato river settlement Co-management of environmental resources is an idea that has been developing for some time in Aotearoa New Zealand as a strategy that recognises Indigenous interests in the environment, and the different ways that people view the world. The contest for control of New Zealand's rivers has generally arisen from successive governments purporting to secure rights based upon English common law. Precepts of that law were completely foreign to the Indigenous Maori who had their own conceptions of rivers. Through the eyes of the Maori, rivers have their own life force, their own spiritual energy and their own powerful identities. Rivers are inextricably linked to tribal identities. Over time a raft of policies was employed and legislation passed by parliament in the name of development and the national interest which did not take into account Maori understandings of the river and its ecosystems, nor their rights, interests, or authority. Excluded from decision-making processes, Maori have long brought matters to the attention of courts by using any basis to assert our rights and interests, and to have our concerns about the deteriorating health and wellbeing of our rivers taken seriously. The search for redress has been relentless. The Resource Management Act 1991 formalised a range of legal rights, but such rights can be meaningless if presented as just one of many other considerations that decision-makers have to take into account. This article explores the notion of collaborative management and the development of co-management models as a background to the emergent Waikato River settlement ± a legal solution embedded in the Waikato-Tainui Raupatu Claims (Waikato River) Settlement Act 2010 that generates a more robust opportunity to bring to an end a paradigm of exclusion and usher in a new era that promises enhanced governance and management of a significant waterway.

year: 2010