ORCID Profile
0000-0002-4220-9748
Current Organisations
University of Adelaide
,
Servatus Ltd
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Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/MF15361
Abstract: Biological surveys are needed to monitor and assess the health of ecosystems and the species within them. However, morphology-based bio ersity surveys can be invasive, time consuming and financially expensive. Recently, environmental (e)DNA sequencing has been demonstrated as a potential alternative to morphological-based surveys because it enables the rapid and inexpensive detection of multiple taxa from DNA present in the environment. Numerous studies have shown that eDNA-based bio ersity surveys can provide considerable information about aquatic ecosystem function and health. Therefore, this molecular method has the potential to improve how current aquatic biological surveys are conducted. Currently, most eDNA literature is aimed at an audience with a moderate to advanced knowledge of DNA sequencing, creating a barrier for many ecologists who lack DNA sequencing expertise but wish to apply such methods to their research. The aim of this review is to provide guidance to non-geneticists regarding sequencing eDNA for aquatic bio ersity surveys and to highlight the requirements that need to be considered before the technique can be effectively incorporated into biomonitoring programs. Specifically, we provide details and recommendations on some of the major principles, from s le collection to bioinformatic analyses. For those areas where specific recommendations cannot be given, we have provided references to suitable literature.
Publisher: Elsevier BV
Date: 12-2014
DOI: 10.1016/J.CHEMOSPHERE.2014.06.077
Abstract: Biofilm control in drinking water distribution systems (DWDSs) is crucial, as biofilms are known to reduce flow efficiency, impair taste and quality of drinking water and have been implicated in the transmission of harmful pathogens. Microorganisms within biofilm communities are more resistant to disinfection compared to planktonic microorganisms, making them difficult to manage in DWDSs. This study evaluates the impact of four unique drinking water treatments on biofilm community structure using metagenomic DNA sequencing. Four experimental DWDSs were subjected to the following treatments: (1) conventional coagulation, (2) magnetic ion exchange contact (MIEX) plus conventional coagulation, (3) MIEX plus conventional coagulation plus granular activated carbon, and (4) membrane filtration (MF). Bacterial biofilms located inside the pipes of each system were s led under sterile conditions both (a) immediately after treatment application ('inlet') and (b) at a 1 km distance from the treatment application ('outlet'). Bacterial 16S rRNA gene sequencing revealed that the outlet biofilms were more erse than those s led at the inlet for all treatments. The lowest number of unique operational taxonomic units (OTUs) and lowest ersity was observed in the MF inlet. However, the MF system revealed the greatest increase in ersity and OTU count from inlet to outlet. Further, the biofilm communities at the outlet of each system were more similar to one another than to their respective inlet, suggesting that biofilm communities converge towards a common established equilibrium as distance from treatment application increases. Based on the results, MF treatment is most effective at inhibiting biofilm growth, but a highly efficient post-treatment disinfection regime is also critical in order to prevent the high rates of post-treatment regrowth.
Publisher: American Chemical Society (ACS)
Date: 14-08-2017
Abstract: Chronic exposure to environmental contaminants can induce heritable "transgenerational" modifications to organisms, potentially affecting future ecosystem health and functionality. Incorporating transgenerational epigenetic heritability into risk assessment procedures has been previously suggested. However, a critical review of existing literature yielded numerous studies claiming transgenerational impacts, with little compelling evidence. Therefore, contaminant-induced epigenetic inheritance may be less common than is reported in the literature. We identified a need for multigeneration epigenetic studies that extend beyond what could be deemed "direct exposure" to F1 and F2 gametes and also include subsequent multiple nonexposed generations to adequately evaluate transgenerational recovery times. Also, increased experimental replication is required to account for the highly variable nature of epigenetic responses and apparent irreproducibility of current studies. Further, epigenetic end points need to be correlated with observable detrimental organism changes before a need for risk management can be properly determined. We suggest that epigenetic-based contaminant studies include concentrations lower than current "EC
Publisher: Wiley
Date: 23-01-2012
DOI: 10.1111/J.1523-1739.2011.01813.X
Abstract: Increased education of consumers can be an effective tool for conservation of commercially harvested marine species when product labeling is accurate and allows an informed choice. However, generic labeling (e.g., as white fish or surimi) and mislabeling of seafood prevents this and may erode consumer confidence in seafood product labels in general. We used DNA barcoding to identify the species composition of two types of convenience seafood (i.e., products processed for ease of consumption): fish fingers (long pieces of fish covered with bread crumbs or batter, n = 241) and seafood sticks (long pieces of cooked fish, n = 30). In products labeled as either white fish or surimi, four teleost species were present. Less than 1.5% of fish fingers with species-specific information were mislabeled. Results of other studies show substantially more mislabeling (e.g., >25%) of teleost products, which likely reflects the lower economic gains associated with mislabeling of convenience seafood compared with whole fillets. In addition to species identification, seafood product labels should be required to contain information about, for ex le, harvesting practices, and our data indicate that consumers can have reasonable confidence in the accuracy of the labels of convenience seafood and thus select brands on the basis of information about current fisheries practice.
Publisher: American Society for Microbiology
Date: 15-09-2015
DOI: 10.1128/AEM.01297-15
Abstract: Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic licon sequencing. Here, licon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user s les were more similar to the source water than to the postdisinfection water. Three s le locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as Nitrospira , were detected. Burkholderiales were abundant in s les containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic licon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs.
Publisher: Wiley
Date: 05-1969
DOI: 10.1111/MEC.15055
Abstract: Microalgal bloom events can cause major ecosystem disturbances, devastate local marine economies, and endanger public health. Therefore, detecting and monitoring harmful microalgal taxa is essential to ensure effective risk management in waterways used for fisheries, aquaculture, recreational activity, and shipping. To fully understand the current status and future direction of algal bloom distributions, we need to know how populations and ecosystems have changed over time. This baseline knowledge is critical for predicting ecosystem responses to future anthropogenic change and will assist in the future management of coastal ecosystems. We explore a NGS metabarcoding approach to rapidly identify potentially harmful microalgal taxa in 63 historic and modern Australian marine port and ballast tank sediment s les. The results provide a record of past microalgal distribution and important baseline data that can be used to assess the efficacy of shipping guidelines, nutrient pollution mitigation, and predict the impact of climate change. Critically, eDNA surveys of archived sediments were able to detect harmful algal taxa that do not produce microscopic fossils, such as Chattonella, Heterosigma, Karlodinium, and Noctiluca. Our data suggest a potential increase in Australian harmful microalgal taxa over the past 30 years, and confirm ship ballast tanks as key dispersal vectors. These molecular mapping tools will assist in the creation of policies aimed at reducing the global increase and spread of harmful algal taxa and help prevent economic and public-health problems caused by harmful algal blooms.
Publisher: Elsevier BV
Date: 05-2016
Publisher: Informa UK Limited
Date: 31-05-2016
DOI: 10.1080/08927014.2016.1184255
Abstract: Biofouling in canals and pipelines used for hydroelectric power generation decreases the flow capacity of conduits. A pipeline rig was designed consisting of test sections of varying substrata (PVC, painted steel) and light levels (transparent, frosted, opaque). Stalk-forming diatoms were abundant in both the frosted and transparent PVC pipes but negligible in the painted steel and opaque PVC pipes. Fungi were slightly more abundant in the painted steel pipe but equally present in all the other pipes while bacterial ersity was similar in all pipes. Photosynthetically functional biofouling (mainly diatoms) was able to develop in near darkness. Different biological fouling compositions generated differing friction factors. The highest friction factor was observed in the transparent pipe (densest diatom fouling), the lowest peak friction for the opaque PVC pipe (lowest fouling biomass), and with the painted steel pipe (high fouling biomass, but composed of fungal and bacterial crusts) being intermediate between the opaque and frosted PVC pipes.
No related grants have been discovered for Jennifer Shaw.