The production and use of manufactured metal (oxide) nanoparticles has exploded in recent years as they are exploited for their novel physical and chemical properties. Cerium oxide NPs (CeO2NPs) help increase combustion in diesel engines and their reported ability to scavenge free radicals has been exploited in therapeutic treatments. Silver NPs (AgNPs) are now used in consumer products such as socks and sticking plasters due to their antibacterial properties. Once released into the environment, their ultimate fate is predicted to be the oceans The aims of this thesis are to investigate the bioaccumulation and biological effects (oxidative stress and lipid peroxidation) of CeO2NPs and AgNPs on the mussel Mytilus edulis, and to understand the potential for trophic transfer of CeO2NPs to the crab Carcinus maenas, and subsequent induced biological effects. It was found in acute exposures that, at the suggested regulatory limit of 3mg/l, less than 5% of a CeO2NP dose will be accumulated by the digestive gland of M. edulis within 4 hours, before being depurated over at least 56 hours. There were no significant biological effects of CeO2NPs, yet larger, micron-size particles had significant anti-oxidant effects. Most effects were transitory, returning to normal levels after 24 hours. In uptake comparisons between AgNPs and Ag-nanorods (AgNRs) at 10μg/l (towards the regulatory limit of 1.9μg/l), AgNRs were accumulated in the digestive gland within 2 hours, but were depurated by 4 hours. Similarity in accumulation between AgNPs and ionic Ag – including continuous accumulation in the gills over 48 hours – suggested dissolution was mostly responsible for this. Both nanoforms instigated isolated oxidative stress responses over 4-24 hours, yet none were significantly worse than AgNO3, which instigated the greatest suite of significant oxidative stress responses. In trophic transfer experiments C. maenas accumulated CeO2NPs in the hepatopancreas at less than 1% of the fed dose. Stomach accumulation was high but transitory, with most particles removed in the faeces. Gills were also a site of accumulation and it was thought that the haemolymph provided a route of transit between the digestive organs and the respiratory organs. This novel experiment used NPs crafted from 140Ce; changes in isotopic ratios of Ce in the crab following trophic transfer could therefore be used to determine absolute increases in concentration against high, and highly variable, background concentrations. There were no significant biological effects following trophic transfer of these 140CeO2NPs. It was found that the current regulatory limits are predicted to be sufficient to protect M. edulis and C. maenas from acute exposure to CeO2NPs and AgNPs, yet chronic exposures should be investigated since the relationship between the uptake and elimination rate of NPs will determine the extent of bioaccumulation and biological effects.

Food webs in aquatic ecosystems can be dramatically altered by invasive species. Quagga mussels are prevalent invaders that compete with existing species and disrupt nutrient cycling. In 2012, the Quagga Mussel (Dreissena rostriformus bugensis) was introduced into Lake Powell and is expected to move throughout the reservoir in the near future. Stable isotope analysis is a powerful tool for characterizing food webs and trophic interactions. To predict the long-term effects of Quagga Mussels, we used stable isotope analysis of primary producers, primary consumers, prey fish species, and predator fish species in Lake Powell to determine food web structure. Quagga Mussel are positioned to disrupt the pelagic arm of the food web by interfering with the link between phytoplankton and herbivorous zooplankton. This will likely have negative impacts on pelagic fish such as striped bass (Morone saxatilis) and threadfin shad (Dorosoma petenense). Quagga Mussel may also boost benthic productivity in the littoral zone by diverting nutrients from the water column to the benthos. This may have positive impacts on littoral fishes such as largemouth bass (Micropterus salmoides), smallmouth bass (Micropterus dolomieu), bluegill (Lepomis macrochirus), and green sunfish (Lepomis cyanellus).

Sea-bed benthic-invertebrate assemblages of species within and proximal to an existing mussel farm off Taniwhanui Point, eastern Waiheke Island, are reported. Substratum type, whether predominantly mud, gravels or an admixture of the two, mud/gravels, is shown to influence infaunal species assemblage composition; the bivalve Theora lubrica, ostracods, amphipods and polychaetes characterise muddy substrata; polychaetes, particularly spionids and syllids, ostracods, amphipods, bivalves and ophiuroids characterise mud/gravel substrata; and diverse assemblages of polychaetes, bivalves, pagurid crabs, gastropods, ostracods, ophiuroids and nemertean worms characterise gravel substrata. Significant differences in sea-bed assemblages are reported along one transect inside and outside the farm over the three seasons during which surveys were conducted, summer, autumn, winter of 2008. Along the northern side of the mussel farm those sediments beneath the farm are characterised by greater abundances of polychaetes and crustaceans (Malacostraca), whereas sediments outside the farm are characterised by greater abundances of bivalves and ostracods. Sediments both inside and outside the north-eastern border of the farm during summer are characterised by similar abundances of polychaetes, bivalves and ostracods. Similarly, those sediments within and outside the farm along its southern border during summer are characterised by abundances of polychaetes, bivalves, crustaceans (Malacostraca) and gastropods. Measures of relative abundance, rarity and species richness are applied to sea-bed assemblages off eastern Waiheke Island to enable an appraisal of the spatial distribution of each within and outside the farm, and throughout the eastern Waiheke Island region. One of these measures, relative abundance, is then compared with other, albeit limited abundance data from previous soft-sediment surveys conducted throughout Hauraki Gulf. The most species rich and abundant sites off eastern Waiheke Island occur in gravelly substrata between Waiheke Island and Pakatoa Island, and between Rotoroa and Ponui Islands, in addition to beneath the southern portion of the existing mussel farm. Gravel-based substrata are recognised to be the most species rich and densely populated with invertebrates for this sediment type in Hauraki Gulf. Similarly, the muddy substrata off eastern Waiheke Island region appear to host more individuals and species than any other reported muddy substratum in Hauraki Gulf. The existing mussel farm is shown to significantly affect sea-bed communities, but in a manner that has not been previously reported in New Zealand. Species richness and abundance are greater beneath the farm, as are the proportions of very rare and uncommon taxa to more common and ubiquitous taxa. Sediments beneath the farm are not characterised by elevated abundances and richness of opportunistic species; and no obvious difference in sediment grain size is apparent along a transect extending from 20 m inside the farm to at least 110 m outside it. The biological footprint of the farm is limited, appearing to extend no further than 20 metres from the northern physical boundary of the farm; the gross sedimentary characteristics (grain size) do not differ significantly within and outside the farm. Within and immediately outside the farm species richness and abundance tend to increase during colder seasons; beneath the farm, species richness (d), abundance (N), Shannon index (H’) and Simpson index (1-λ’) were higher during May (autumn) and August (winter) than during February (summer); diversity values outside the farm were similar during summer and autumn, but species richness (d), evenness (J’), Shannon index (H’) and Simpson index (1-λ’) were all greater during winter. No opportunistic taxa are considered to be appropriate indicators of organically enriched environments, at least enrichment that can be intuitively linked to any direct effect of the existing mussel farm. One species, the heart urchin Echinocardium cordatum, only rarely occurs inside the physical farm boundary, so its relative abundance renders it an appropriate indicator species of mussel-farm impacts.

Symbiosis is one of the most widespread evolutionary strategies on Earth. In the deep-sea, symbioses between chemosynthetic bacteria and invertebrates are abundant at hydrothermal vents and cold seeps. These mutualisms, in which symbiont carbon fixation provides for host nutrition, are analogous to the ancient endosymbioses that resulted in the chloroplast and the eukaryotic mitochondrion. However, the evolutionary processes that led to the widespread dispersal of deep-sea organisms and the mechanisms by which symbioses are initiated and maintained are poorly characterized. This thesis examined the evolution of deep-sea mussels (Bathymodiolinae) and their chemosynthetic symbionts. Bathymodioline mussel taxonomy is in need of a comprehensive systematic revision because the majority of named genera do not constitute monophyletic groups. First, this thesis demonstrated that mussels found on the Northeast Pacific Ridges are members of Adipicola, a paraphyletic genus within Bathymodiolinae, refining the evolutionary history of this poorly characterized group. Second, an updated multi-locus phylogeny of bathymodiolines was presented and used to evaluate the statistical evidence for previously proposed hypotheses describing the directional evolution of bathymodioline traits. The results indicated that patterns of directional evolution in this group are not well supported and instead suggests that trait evolution has proceeded in a non-directional manner. Third, this thesis presented the first evidence of detection and abundance of bathymodioline symbionts in the deep-sea environment, providing direct evidence that these symbionts are environmentally acquired. Fourth, this thesis presented the first multi-locus phylogenies of bathymodioline symbionts and tested the hypothesis of environmental acquisition of symbionts in this group. The results demonstrated that symbiont and host lineages are decoupled, which is consistent with the environmental acquisition hypothesis. Finally, environmental acquisition implies that symbionts have opportunities to exchange genetic information with other bacterial strains and evidence for recombination in bathymodioline symbionts is also presented. This thesis advances our understanding of the evolutionary history of bathymodioline symbioses by clarifying host and symbiont evolutionary history and symbiont transmission strategy. In aggregate, these results suggest that bathymodiolines are more flexible with regard to the habitats they inhabit and the symbionts they harbor than previously understood.

Mining-Influenced Water (MIW) poses major environmental issues in New Zealand and worldwide due to a legacy of unmitigated mining activities. As conventional MIW treatment technologies can be very costly in terms of chemical and energy inputs, cheaper and environmentally-friendly alternative remediation strategies have been developed. These so-called passive treatment technologies include a range of engineered systems relying on biogeochemical processes able to mitigate the acidity and to immobilize the metals in MIW. The present research, built on previous work conducted at the University of Canterbury, investigated the use of waste materials in mesocosm lab-scale sulfate-reducing bioreactors (SRBR) to treat actual mining-influenced water (MIW) sourced at an active coal mine in New Zealand. Specifically, this study investigated using waste mussel shells as an alkaline amendment (instead of the more conventional material limestone), with organic waste materials such as wood byproducts and compost in complex substrate mixtures in upward-flow SRBR. The influence of hydraulic retention times of approximately 3 and 10 days (HRT; i.e. the contact time between the MIW and the substrate mixtures in the SRBR) on the treatment performances was also evaluated. Overall, each system successfully treated the MIW (e.g. increased the pH > 6 and removed >78 % of the metals, except Mn) during the first 5-month treatment period, while during the second 5-month period, the treatment systems containing limestone and/or operating at a short HRT started to show signs of decreased efficiency. Generally, the system containing mussel shell and operating at a long HRT was constantly the most efficient system. Over the whole 41-week period of treatment, key metal removal efficiencies ranged between 97.6 and 99.7 % (Al), 83.9 and 95.2 % (Fe), and 9.2 and 38.8 % (Mn). Sulfate removal, in terms of moles of sulfate removed per cubic meter of substrate per day, was on average below the design values of 0.3 mol/m3/d, and ranged between 0.03 and 0.55 mol/m3/d (median values were 0.26 to 0.3 mol/m3/d during the first 5-month period but dropped to 0.094 to 0.1 mol/m3/d during the second 5-month treatment period). The SRBR containing mussel shell instead of limestone resulted in significantly higher alkalinity generation (between 32 to 85 % higher) and higher metal removals (between 0.6 % higher for Al and 14 % higher for Ni). These results were mainly attributed to the unique mineralogy of the mussel shell which comprises of aragonite with traces of calcite, while limestone comprises of pure calcite with traces of quartz. The statistical analyses showed that the sulfate reduction was not significantly affected by the alkalinity source. Similarly, systems operating at a longer HRT (10 days instead of 3 days) showed better treatment performances than systems operating at a short HRT in terms of alkalinity generation (44 to 62% higher), metal removal (between 0.5 % higher for Al to 15 % higher for Ni, and between 17 to 23 % higher for Mn), and sulfate reduction (50 to 77 % higher). Overall, the systems operation on a longer HRT were dominated by a more reduced environment facilitating the precipitation of metal sulfides, while the reactors running on a shorter HRT were constantly maintained out of equilibrium by the continuous addition of fresh MIW. Chemical and mineralogical analyses performed on the spent substrates suggested that the metals were removed through precipitation as, and adsorption onto, metal sulfides (Fe, Zn, Ni, Cu), (oxy)hydroxides (Al, Fe, Zn), and carbonates (Mn, Zn). Mn, a metal known to be harder to remove from solution was likely removed through the precipitation of rhodochrosite (MnCO3) and via adsorption onto the organic matter. These results generally corroborated the results obtained using the geochemical modeling PHREEQC. Overall, this study showed that mussel shells are not only a sustainable and effective alternative to mined limestone, but their use in SRBR would also result in a better treatment of MIW. Additionally, even though an increase in HRT resulted in a better contaminant removal, a HRT of approximately 3 days was sufficient to remove about 80% of all metals (except Mn). Therefore, the difficult choice of an optimal HRT must balance the need to meet a specific effluent quality while keeping the treatment time reasonably short, and an intermediate retention time of approximately 6 days could be optimal.

The byssal adhesion mechanism of the biofouling species Dreissena polymorpha was investigated using a combination of studies on synthetic peptide mimics of tandem repeat sequences from byssal component Dreissena polymorpha foot protein 1 (Dpfp-1) and characterization of the regions of the byssus. A 20-residue fusion peptide incorporating two Dpfp-1 repeat sequences adopts a random coil and β-turn conformation in solution, and spontaneously forms a film at the solid-liquid interface in the presence of iron (III) cations. Infrared characterization of the byssus Amide I region showed that β-sheets dominate its secondary structure, although the proportion of different secondary structures varies between regions. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry of intact byssal regions identified previously unknown differences in the composition of byssal threads, plaques, and the adhesive interface, which are believed to correlate to the different roles of these components in the overall structure.

The byssal adhesion mechanism of the biofouling species Dreissena polymorpha was investigated using a combination of studies on synthetic peptide mimics of tandem repeat sequences from byssal component Dreissena polymorpha foot protein 1 (Dpfp-1) and characterization of the regions of the byssus. A 20-residue fusion peptide incorporating two Dpfp-1 repeat sequences adopts a random coil and β-turn conformation in solution, and spontaneously forms a film at the solid-liquid interface in the presence of iron (III) cations. Infrared characterization of the byssus Amide I region showed that β-sheets dominate its secondary structure, although the proportion of different secondary structures varies between regions. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry of intact byssal regions identified previously unknown differences in the composition of byssal threads, plaques, and the adhesive interface, which are believed to correlate to the different roles of these components in the overall structure.

Sea-bed benthic-invertebrate assemblages of species within and proximal to an existing mussel farm off Taniwhanui Point, eastern Waiheke Island, are reported. Substratum type, whether predominantly mud, gravels or an admixture of the two, mud/gravels, is shown to influence infaunal species assemblage composition; the bivalve Theora lubrica, ostracods, amphipods and polychaetes characterise muddy substrata; polychaetes, particularly spionids and syllids, ostracods, amphipods, bivalves and ophiuroids characterise mud/gravel substrata; and diverse assemblages of polychaetes, bivalves, pagurid crabs, gastropods, ostracods, ophiuroids and nemertean worms characterise gravel substrata. Significant differences in sea-bed assemblages are reported along one transect inside and outside the farm over the three seasons during which surveys were conducted, summer, autumn, winter of 2008. Along the northern side of the mussel farm those sediments beneath the farm are characterised by greater abundances of polychaetes and crustaceans (Malacostraca), whereas sediments outside the farm are characterised by greater abundances of bivalves and ostracods. Sediments both inside and outside the north-eastern border of the farm during summer are characterised by similar abundances of polychaetes, bivalves and ostracods. Similarly, those sediments within and outside the farm along its southern border during summer are characterised by abundances of polychaetes, bivalves, crustaceans (Malacostraca) and gastropods. Measures of relative abundance, rarity and species richness are applied to sea-bed assemblages off eastern Waiheke Island to enable an appraisal of the spatial distribution of each within and outside the farm, and throughout the eastern Waiheke Island region. One of these measures, relative abundance, is then compared with other, albeit limited abundance data from previous soft-sediment surveys conducted throughout Hauraki Gulf. The most species rich and abundant sites off eastern Waiheke Island occur in gravelly substrata between Waiheke Island and Pakatoa Island, and between Rotoroa and Ponui Islands, in addition to beneath the southern portion of the existing mussel farm. Gravel-based substrata are recognised to be the most species rich and densely populated with invertebrates for this sediment type in Hauraki Gulf. Similarly, the muddy substrata off eastern Waiheke Island region appear to host more individuals and species than any other reported muddy substratum in Hauraki Gulf. The existing mussel farm is shown to significantly affect sea-bed communities, but in a manner that has not been previously reported in New Zealand. Species richness and abundance are greater beneath the farm, as are the proportions of very rare and uncommon taxa to more common and ubiquitous taxa. Sediments beneath the farm are not characterised by elevated abundances and richness of opportunistic species; and no obvious difference in sediment grain size is apparent along a transect extending from 20 m inside the farm to at least 110 m outside it. The biological footprint of the farm is limited, appearing to extend no further than 20 metres from the northern physical boundary of the farm; the gross sedimentary characteristics (grain size) do not differ significantly within and outside the farm. Within and immediately outside the farm species richness and abundance tend to increase during colder seasons; beneath the farm, species richness (d), abundance (N), Shannon index (H’) and Simpson index (1-λ’) were higher during May (autumn) and August (winter) than during February (summer); diversity values outside the farm were similar during summer and autumn, but species richness (d), evenness (J’), Shannon index (H’) and Simpson index (1-λ’) were all greater during winter. No opportunistic taxa are considered to be appropriate indicators of organically enriched environments, at least enrichment that can be intuitively linked to any direct effect of the existing mussel farm. One species, the heart urchin Echinocardium cordatum, only rarely occurs inside the physical farm boundary, so its relative abundance renders it an appropriate indicator species of mussel-farm impacts.

Thesis (Ph. D.)--Oregon State University, 1995. / Typescript (photocopy). Includes bibliographical references (leaves 211-237). Also available online.

Thesis (M.Sc.)--Memorial University of Newfoundland, 2003. / Bibliography: leaves 63-71. Also available online.