This thesis examines sublethal stress responses in the common New Zealand estuarine bivalve, Austrovenus stutchburyi (cockle). The approach used throughout this thesis is a refinement of the biological indicator approach of Adams (1990), in which biomarker data are collected primarily at the individual and sub-organismal levels, but with additional measurements at the population and community levels. In this research several biochemical and physiological biomarkers are used to assess effects of contaminants on energetics, fecundity and growth of cockles. Adenylate energy charge (AEC) and total adenylate nucleotide pool (TANP) are biomarkers that have previously not been used with A. stutchburyi, and provide new information on energy cycling for this species. RNA concentration has also not previously been used with cockles, and this biomarker is correlated with growth. Glycogen concentration and condition indices are used to indicate reproductive potential and overall health. In order to fully investigate the utility of this comprehensive suite of biomarkers, their performance in laboratory and field situations was tested. Temporal variability in AEC, TANP and glycogen was analysed over two years for two populations of cockles in a northern harbour. The results indicated seasonal patterns for all biomarkers, with AEC reaching a maximum value in spring, TANP being lowest in winter, and glycogen concentration being high over spring and summer. Variability in biomarker response between cockles sampled at low tide and high tide was analysed in a laboratory experiment simulating exposure to air during low tide. Adenylate energy charge was found to be significantly lower in cockles after exposure to air for 4 hours, highlighting the importance of standardised collection protocols. These initial patterns, as well as spatial variability in biomarker response, were further investigated at several sites within a second harbour south of Auckland. There was little among site difference in glycogen concentration, and the data suggested that differences in site characteristics, such as sediment quality and type, were driving the mixed response patterns of AEC, TANP and condition. Because of inherent variability in field conditions, a series of laboratory experiments was then undertaken to assess responses under carefully controlled conditions. Cockles were challenged with PAHs, chlordane and tributyltin at two different doses, and biomarker response (AEC, TANP, glycogen and RNA) measured. One trial examined the effects of a one-off pulse of contaminant, in which sediment containing cockles was dosed at the outset of a 14-day experiment with a high concentration of contaminant. A daily dose of this same concentration of contaminant was supplied to the sediment for 14 days in a second trial to assess effects of a more continuous discharge. There were virtually no significant differences in biomarker response between treatments and controls for either trial, suggesting that the experimental setup may have been causing sublethal stress in some way. Finally, in order to maximise experimental control whilst maintaining environmental realism, a manipulative field experiment was undertaken in which cockles were transplanted from an uncontaminated site to a series of uncontaminated and contaminated sites in one of Auckland's major harbours. Biomarker response (AEC, TANP, glycogen and RNA) was measured in the transplanted and the autochthonous populations two weeks and eight weeks after transplantation. An ability to regulate adenylate nucleotides was detected, as cockles transplanted to contaminated sites had reduced TANP but maintained AEC levels. There were significant differences in glycogen and RNA among sites, with highest levels detected in cockles transplanted to an uncontaminated site. This suite of biomarkers showed great utility for use in environmental quality assessment. It is recommended that an approach such as that used in the Mussel Watch programme in the United States be employed for cockles, in order to monitor estuarine ecosystem health in New Zealand. The transplantation of cockles to estuaries where there are concerns about environmental quality, and the use of TANP, glycogen and RNA concentration to assess sublethal stress, has potential as a sensitive and cost-effective environmental monitoring technique for estuaries in New Zealand.

The eggs and larvae of the New Zealand snapper Pagrus auratus are pelagic with early buoyancy provided by dilute body fluids. The swimbladder begins to develop on the third day after hatch from a dorsal evagination of the gut tube. Communication w1h the gut is lost on about the tenth day following pneumatic inflation at around day eight. At this age the gas gland system appears fully functional and capable of secreting gas. By the age of settlement at around 30 days the swimbladder is a fully functional replica of the adult form except for the lack of a resorbent capillary system which does not develop until later in juvenile life. The swimbladder of the adult is of the euphysoclist form with a dorsally located resorbent oval area and sits high in the pleural cavity. The ventral tunica externa is firmly attached to the connective tissue lining the pleural space. The adult swimbladder displaces 5.6% of the volume of the body and its volume is regulated to provide near neutral buoyancy. The connective tissue integument provides almost no restriction to volume changes brought about by vertical movements of the fish and the swimbladder obeys Boyle's Law for physiological pressure changes. The ability of the connective tissue of the tunica externa to accommodate large tissue strains is due to massive regular crimping of otherwise straight collagen fibrils allowing reversible extensions up to 130%. In all other respects however the tissue structure of the tunica externa is consistent with a tissue providing an active mechanical role. The fibrillar morphology and physicochemical properties of swimbladder collagen is consistent with the vertebrate type I form however there are interesting variations in collagen form distributed throughout the swimbladder. Fibrillar morphology of the highly extensible tunica interna is significantly different to that of the tunica externa and appears to play very little mechanical rote. The extensibilty of the tunica externa appears to be regulated by physiological stress and related to the past history of tissue strain.

The characterisation of the universal features of intertidal zonation on rocky coasts (Stephenson and Stephenson 1949; 1952; 1954; 1961) has stimulated many attempts t o explain the factors responsible for the observed patterns of distribution. Initial investigations which were essentially confined to the effects of a single factor upon different species suggested that ecological position was often correlated with physiological response. Recent studies have indicated that the subtidal distributions of algae show characteristic patterns (Kitching 1941 ; Bergquist 1960; Kain 1960; 1971; Morgans 1961 ; McLean 1962; Schwenke 1966; Neushul 1967; Clark and Neushul 1967; Larkum et al.1967; John 1971). However, there have been relatively few attempts to examine in detail and subsequently integrate the physiological response to environmental factors of major belt-demarcating algae of the sublittoral . The four New Zealand species of Carpophyllum are inhabitants of the uppermost sublittoral and the sublittoral fringe (Bergquist 1960; Dromgoole 1965). This particular study was undertaken in an attempt to elucidate the subtle differences in response which determine the distribution limits characteristic of each species. There is little information on the biology of Carpophyllum with the exception of some anatomical and embryological work (Delf 1939; Dawson 1940; Naylor 1954) and an earlier investigation of C. maschalocarpum (Dromgoole 1965). Thus to provide a basis for physiological experiments preliminary studies were directed to the following aspects: ( i ) a brief review of the morphology, anatomy and taxonomy of the genus, ( ii ) growth of sporelings in laboratory culture using various seawater media, ( iii ) definition of the geographical and vertical limits of the four species and a general study of their ecology with emphasis on population distributions, periodicitiy of reproduction and plant composition in relation to environment. The physiological response of algae to environmental factors has been examined by previous workers at the protoplasmic level using the criterion of resistance (e.g. Biebl 1956, 1962; Kanwisher 1957); at the metabolic level by measurement of photosynthesis and respiration (e.g. Chapman 1961n) ; and at the level of the whole plant by growth rates in laboratory cultures (e.g. Kain 1965) or of selected individuals in the field (e.g. Klugh and Martin, 1927). Attempts to culture Carpophyllum were not entirely successful. An earlier investigation indicated that the growth rates of Carpophyllum in situ are difficult to assess (Dromgoole 1965) and hence the metabolic approach, which does allow some integration of response to several factors by means of carbon balance calculations (e.g. Brown and Johnson 1964), has been used extensively in this study. The metabolic activity of large brown algae varies considerably with age and part of plant (Clendenning and Sargent 1957a, b; Chapman 1961a). To eliminate sampling problems in Carpophyllum a cuvette allowing continuous long-term monitoring of oxygen exchange of a single piece of material was developed. This laboratory apparatus has shown that the photosynthesis and respiration of the various organs is sensitive to environmental changes in pH, C02 supply, oxygen tension, light , water flow, dehydration and temperature. The nature and possible causes of the response t o each factor were examined in detail as this was considered essential to any interpretation of their ecological significance. Finally, the information obtained from these gas exchange measurements has been integrated by means of metabolic balance calculations and a descriptive synthesis of field and laboratory results has provided a general picture of the biology of these plants.

The scope of the present work is the systematic revision of the Demospongiae of the N.Z. region, here defined as including North and South Is. and all outlying islands as far north as Three Kings and South to Auckland and Cambell Is. The Kermadec Is. are not considered as part of the N.Z. region, but the sponges recorded from these islands are revised in the sytematic account. At present, 243 species of Demospongiae are recorded for this region, these belonging to 124 genera and 35 families. Of this total 49 species have been described as new and forty-six species are recorded as new to the fauna in this work.

The decline of coral reefs is well documented, yet a detailed understanding of the processes involved in the establishment, persistence, and ecology of the coral-dinoflagellate associations still remains largely unknown. The advent of molecular techniques has resulted in significant advances in understanding the molecular diversity present of symbiotic dinoflagellates from the genus Symbiodinium, but information concerning the functional, ecological, and biogeographical significance of this expanding symbiont diversity remains limited. This thesis therefore used molecular methodologies to uncover Symbiodinium diversity in Stylophora pistillata, Pocillopora damicornis, and Seriatopora hystrix at ecological scales, in response to thermal stress, and to long-term environmental shifts. In addition, all the molecular methods currently used in Symbiodinium research are critically reviewed to provide an important baseline for future studies. The application of ITS2-DGGE coupled with the integration of alternate speciation concepts and analyses showed great merit in assessing Symbiodinium diversity in S. pistillata, P. damicornis, and S. hystrix along a depth gradient (3 m to 18 m) at Heron Island on the Great Barrier Reef (Australia), and emphasizes that sampling regimes should focus on the role of symbionts within their functional habitat. S. pistillata associates with symbionts C78 or C35/a in shallow areas and C79 in the deep, but also harbors a generalist type C8/a that can be found at all depths. P. damicornis harbors C42/a in shallow areas while C33/a is generally found in deeper reef zones, although it is occasionally observed in the shallows. On the other hand, S. hystrix only harbors a single symbiont (C3/t) at all depths. The data from Chapter 2 therefore shows that closely related symbionts within a single clade can diverge rapidly under influence of ecological differentiation whereby each symbiont represents a separately evolving lineage that occupies a specific ecological niche. As such, closely related symbionts are likely to have evolved specializations that optimize performance within their environmental range. Previous studies have sought to explain the bleaching susceptibility of scleractinian corals as a function of the presence or absence of six major clades of Symbiodinium. In chapter 3 it is shown that sub-cladal types of clade C in S. pistillata differ in their response to thermal stress, and these differences are as large as those previously reported between different clades. Molecular (ITS2-DGGE) data is integrated with physiological measurements (PAM fluorometry, host protein, symbiont cell density) to investigate the response to stress (bleaching) and is directly related to fine-scale differences in symbiont-types. This suggests that the cladal distinction of Symbiodinium is insufficient to explain the highly variable responses commonly seen in reef-building corals. Furthermore, the results highlight that shifts in symbiont community within a host population are due to differential mortality rather than the uptake of novel symbionts. It therefore appears that changes in the thermal tolerance of corals by acquiring novel more resistant Symbiodinium to meet the challenges of global warming may be restricted, and as such cannot be expected to prevent large-scale reef degradation. Whilst most Symbiodinium cladal studies have focused on bleaching, Chapter 4 combines molecular (ITS2-DGGE) and physiological analyses (PAM fluorometry) to assess the flexibility of the coral–symbiont assemblages in S. pistillata, P. damicornis, and S. hystrix when faced with long-term shifts in key environmental conditions. To test this, a 32 month reciprocal transplant experiment was set-up on Heron Island, whereby corals were transplanted to a new light environment, i.e. shallow to deep, or deep to shallow. Although some host-symbiont combinations were able to shuffle sub-cladal symbiont types, almost all colonies reverted back to their original type within 7 to 12 months. Interestingly, transplanted colonies showed a broad acclimatory response by adjusting their physiological responses to those of the control colonies at the transplanted depth. However, those that persisted with sub-optimal symbiont types suffered disproportionate rates of mortality at the onset of additional stress (bleaching). This suggests that, despite their large acclimatory capacity, the holobiont was likely living at the limits of its tolerance range. As such, it appears that coral species cannot readily form a novel symbiotic unit by changing their symbiotic partner in response to prolonged periods of change, and it is therefore unlikely that they will be able to adjust their symbionts in an attempt to cope with changing global conditions. Finally, Chapter 5 reviews the different DNA markers (18S, 28S, ITS1, ITS2, cp23S) and screening methods (RFLP, LICOR, SSCP, DGGE, cloning-sequencing) currently applied to uncovering Symbiodinium diversity. Current rDNA markers are used to identify ancient or more recent evolutionary lineages and separate symbionts into broad groups such as clades, as well as uncovering fine-scale differences between ecologically different sub-cladal types. The 18S and 28S rDNA in combination with RFLP are appropriate for studies that focus on large groupings at the cladal level and may uncover broad biogeographical. However, studies on the ecology or physiology of host-symbiont associations clearly benefit from the capacity to detect the full level of variability present within a community (e.g. 28S-SSCP, ITS2-DGGE). Despite the suitability of the rDNA, it is an imperative that sequence information is combined with ecological data in order to accurately predict how each hostsymbiont combinations responds as a unit that is optimized to function within the range of its distribution. Symbiont types present in individual hosts are shown to be distinct cohesive groups that are not interchangeable on an ecological, functional and evolutionary scale. In summary, this thesis expands on the current knowledge of the role of Symbiodinium on coral reefs and introduces a number of novel concepts. It is imperative that effort and resources continue to be channelled to combine genetic and ecological studies on Symbiodinium, as they appear to be an important factor driving responses of their host. Although diversity assessments would benefit from the development of a single-copy molecular marker, it is important to continue utilizing current methodologies to increase our knowledge of coral-symbiont diversity if we are to understand and manage coral reefs in the short-term as environmental conditions continue to change.

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (leaves 88-102).

Thesis (M.S.)--University of North Carolina Wilmington, 2008. / Title from PDF title page (October 20, 2008) Includes bibliographical references (p. 101-106)

Thesis (M.Sc. Biological Sciences)--University of Waikato, 2007. / Title from PDF cover (viewed May 1, 2008). Includes bibliographical references (p. 52-59)

Thesis (M.Sc. (Zoology & Entomology)) - Rhodes University, 2008.

Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographic references (p. [116]-122).