title: Seasonal and spatial variations in bacterial communities from tetrodotoxin-bearing and non-tetrodotoxin-bearing clams

authors: Biessy, Laura

subjects: Science & Technology

abstract: Tetrodotoxin (TTX) is one of the most potent naturally occurring compounds and is responsible for many human intoxications worldwide. Paphies australis are endemic clams to New Zealand which contain varying concentrations of TTX. Research suggests that P. australis accumulate the toxin exogenously, but the source remains uncertain. The aim of this study was to identify potential bacterial TTX-producers by exploring differences in bacterial communities in two organs of P. australis: the siphon and digestive gland. Samples from the digestive glands of a non-toxic bivalve Austrovenus stutchburyi that lives amongst toxic P. australis populations were also analyzed. Bacterial communities were characterized using 16S ribosomal RNA gene metabarcoding in P. australis sourced monthly from the Hokianga Harbor, a site known to have TTX-bearing clams, for 1 year, from ten sites with varying TTX concentrations around New Zealand, and in A. stutchburyi from the Hokianga Harbor. Tetrodotoxin was detected in P. australis from sites all around New Zealand and in all P. australis collected monthly from the Hokianga Harbor. The toxin averaged 150 μg kg–1 over the year of sampling in the Hokianga Harbor but no TTX was detected in the A. stutchburyi samples from the same site. Bacterial species diversity differed amongst sites (p < 0.001, F = 5.9) and the diversity in siphon samples was significantly higher than in digestive glands (p < 0.001, F = 65.8). Spirochaetaceae (4–60%) and Mycoplasmataceae (16–78%) were the most abundant families in the siphons and the digestive glands, respectively. The bacterial communities were compared between sites with the lowest TTX concentrations and the Hokianga Harbor (site with the highest TTX concentrations), and the core bacterial communities from TTX-bearing individuals were analyzed. The results from both spatial and temporal studies corroborate with previous hypotheses that Vibrio and Bacillus could be responsible for the source of TTX in bivalves. The results from this study also indicate that marine cyanobacteria, in particular picocyanobacteria (e.g., Cyanobium, Synechococcus, Pleurocapsa, and Prochlorococcus), should be investigated further as potential TTX producers.

text: Seasonal and spatial variations in bacterial communities from tetrodotoxin-bearing and non-tetrodotoxin-bearing clams Tetrodotoxin (TTX) is one of the most potent naturally occurring compounds and is responsible for many human intoxications worldwide. Paphies australis are endemic clams to New Zealand which contain varying concentrations of TTX. Research suggests that P. australis accumulate the toxin exogenously, but the source remains uncertain. The aim of this study was to identify potential bacterial TTX-producers by exploring differences in bacterial communities in two organs of P. australis: the siphon and digestive gland. Samples from the digestive glands of a non-toxic bivalve Austrovenus stutchburyi that lives amongst toxic P. australis populations were also analyzed. Bacterial communities were characterized using 16S ribosomal RNA gene metabarcoding in P. australis sourced monthly from the Hokianga Harbor, a site known to have TTX-bearing clams, for 1 year, from ten sites with varying TTX concentrations around New Zealand, and in A. stutchburyi from the Hokianga Harbor. Tetrodotoxin was detected in P. australis from sites all around New Zealand and in all P. australis collected monthly from the Hokianga Harbor. The toxin averaged 150 μg kg–1 over the year of sampling in the Hokianga Harbor but no TTX was detected in the A. stutchburyi samples from the same site. Bacterial species diversity differed amongst sites (p < 0.001, F = 5.9) and the diversity in siphon samples was significantly higher than in digestive glands (p < 0.001, F = 65.8). Spirochaetaceae (4–60%) and Mycoplasmataceae (16–78%) were the most abundant families in the siphons and the digestive glands, respectively. The bacterial communities were compared between sites with the lowest TTX concentrations and the Hokianga Harbor (site with the highest TTX concentrations), and the core bacterial communities from TTX-bearing individuals were analyzed. The results from both spatial and temporal studies corroborate with previous hypotheses that Vibrio and Bacillus could be responsible for the source of TTX in bivalves. The results from this study also indicate that marine cyanobacteria, in particular picocyanobacteria (e.g., Cyanobium, Synechococcus, Pleurocapsa, and Prochlorococcus), should be investigated further as potential TTX producers.

year: 2020

title: Making better use of global discretization

authors: Frank, Eibe

subjects: computer science

abstract: Before applying learning algorithms to datasets, practitioners often globally discretize any numeric attributes. If the algorithm cannot handle numeric attributes directly, prior discretization is essential. Even if it can, prior discretization often accelerates induction, and may produce simpler and more accurate classifiers. 
As it is generally done, global discretization denies the learning algorithm any chance of taking advantage of the ordering information implicit in numeric attributes. However, a simple transformation of discretized data preserves this information in a form that learners can use. We show that, compared to using the discretized data directly, this transformation significantly increases the accuracy of decision trees built by C4.5, decision lists built by PART, and decision tables built using the wrapper method, on several bench-mark datasets. Moreover, it can significantly reduce the size of the resulting classifiers.
This simple technique makes global discretization an even more useful tool for data preprocessing

text: Making better use of global discretization Before applying learning algorithms to datasets, practitioners often globally discretize any numeric attributes. If the algorithm cannot handle numeric attributes directly, prior discretization is essential. Even if it can, prior discretization often accelerates induction, and may produce simpler and more accurate classifiers. 
As it is generally done, global discretization denies the learning algorithm any chance of taking advantage of the ordering information implicit in numeric attributes. However, a simple transformation of discretized data preserves this information in a form that learners can use. We show that, compared to using the discretized data directly, this transformation significantly increases the accuracy of decision trees built by C4.5, decision lists built by PART, and decision tables built using the wrapper method, on several bench-mark datasets. Moreover, it can significantly reduce the size of the resulting classifiers.
This simple technique makes global discretization an even more useful tool for data preprocessing

year: 1999

title: Ecological modelling of water quality management options in Lake Waahi to support Hauanga Kai species: Technical Report

authors: Allan, Mathew Grant

abstract: This report describes a numerical modelling approach for Lake Waahi to assess the effects of various future scenarios on water quality attributes known to affect the appearance of the lake’s multiple hauanga kai species across differing spatial scales. Hauanga kai refers to customary gathering and use of naturally occurring and cultivated foods. Numerical models were used to support shared learning and development of future scenarios in response to different management options and environmental pressures. The shallow lakes of the Waikato region have been particularly impacted by anthropogenic eutrophication. This is due to the fact that many of these lakes have already undergone a degree of natural eutrophication due to their geomorphic properties, such as their low elevation and shallow depth. The main contributing factors to water quality decline in shallow Waikato lakes have been identified as: high external nutrient and sediment loads, internal loading exacerbated by high sediment resuspension and bioturbation from pest fish (carp), reduced water depth due to installation of water control structures, reduction in wetland filtering potential due to draining, and stock access to wetlands. A 1-D hydrodynamics model, the General Ocean Turbulence Model was coupled to a complex ecological model (PClake) via the Framework for Aquatic Biogeochemical Models (FABM). FABM is an open source FORTAN-based code that facilitates the coupling of hydrodynamic and ecological models. FABM-PCLake is a redesigned PCLake. The consensus from the model simulations carried out in the study suggests that, for Lake Waahi to undergo restoration whereby the lake is restored to clear-water stable state, both external load needs to be reduced significantly by greater than 50%, along with changes in lake ecological structure, resulting from re-establishment of macrophytes aided by the control of carp biomass. These finding supports the general view within the literature that for lake restoration success, external load reduction (catchment load) is critical. Finally, if the ultimate goal of lake restoration in Lake Waahi is to address the decline in tuna (shortfin eel - Anguilla australis) biomass, a return to a clear-water stable state should facilitate improvement in tuna habitat and provide the conditions for development of a healthy eel population. Coupled modelling approaches will provide a more complete picture of potential responses of Hauanga kai species to land and lake management scenarios.

text: Ecological modelling of water quality management options in Lake Waahi to support Hauanga Kai species: Technical Report This report describes a numerical modelling approach for Lake Waahi to assess the effects of various future scenarios on water quality attributes known to affect the appearance of the lake’s multiple hauanga kai species across differing spatial scales. Hauanga kai refers to customary gathering and use of naturally occurring and cultivated foods. Numerical models were used to support shared learning and development of future scenarios in response to different management options and environmental pressures. The shallow lakes of the Waikato region have been particularly impacted by anthropogenic eutrophication. This is due to the fact that many of these lakes have already undergone a degree of natural eutrophication due to their geomorphic properties, such as their low elevation and shallow depth. The main contributing factors to water quality decline in shallow Waikato lakes have been identified as: high external nutrient and sediment loads, internal loading exacerbated by high sediment resuspension and bioturbation from pest fish (carp), reduced water depth due to installation of water control structures, reduction in wetland filtering potential due to draining, and stock access to wetlands. A 1-D hydrodynamics model, the General Ocean Turbulence Model was coupled to a complex ecological model (PClake) via the Framework for Aquatic Biogeochemical Models (FABM). FABM is an open source FORTAN-based code that facilitates the coupling of hydrodynamic and ecological models. FABM-PCLake is a redesigned PCLake. The consensus from the model simulations carried out in the study suggests that, for Lake Waahi to undergo restoration whereby the lake is restored to clear-water stable state, both external load needs to be reduced significantly by greater than 50%, along with changes in lake ecological structure, resulting from re-establishment of macrophytes aided by the control of carp biomass. These finding supports the general view within the literature that for lake restoration success, external load reduction (catchment load) is critical. Finally, if the ultimate goal of lake restoration in Lake Waahi is to address the decline in tuna (shortfin eel - Anguilla australis) biomass, a return to a clear-water stable state should facilitate improvement in tuna habitat and provide the conditions for development of a healthy eel population. Coupled modelling approaches will provide a more complete picture of potential responses of Hauanga kai species to land and lake management scenarios.

year: 2018