Iridoviruses of copepods: their identification, estuarine ecology and host histopathology

Zooplankton Invertebrate Iridescent viruses (ZoopIIVs: Iridoviridae) were discovered infecting copepods. Assays were developed for monitoring an infectious ZoopIIV; and the virus ultrastructure and host infection sites were described. The pioneering work has advanced research methods and our knowledge of infectious viruses in the zooplankton that provide critical ecosystem services globally

Urbanisation and the ecology of powerful owls ninox strenua in outer Melbourne, Victoria

Historically, the Powerful Owl (Ninox strenua) has been seen as a southeastern Australian species restricted to, or most numerous in, dense gullies of tall open forests in hilly or mountainous areas of the coast and Great Divide. However, recent research has revealed that Powerful Owls may breed numerously and successfully in a wider range of habitats than previously believed, including the forests and woodlands within the metropolitan areas of some major cities.Here we report on the breeding of a number of pairs of Powerful Owls in the Yarra Valley, Victoria. Study sites ranged from relatively undisturbed, wet sclerophyll forest 80 km from central Melbourne, through dry sclerophyll, eucalypt-dominated open forest with some disturbance, to a highly disturbed urban parkland only 18 km from central Melbourne. We found that Powerful Owls breed successfully in some urban areas, but are limited in the amount of human disturbance they can tolerate near their nesting hollow. In the most heavily utilized section of the urban parkland, all breeding attempts were unsuccessful and in one year the young were apparently eaten by one of the parents. This followed construction of a timber boardwalk under the nest tree during the breeding season. The Powerful Owls subsequently moved to a more secluded nesting hollow and raised two young. Recommendations for management of Powerful Owls in urban areas are discussed in the context
of these results.

Linshuichonetes gen. nov., a new rugosochonetid (Brachiopoda) genus from the Liangshan Formation (Early Permian) in Sichuan, China, and its ecology

A new genus and species, Linshuichonetes elfinis, belonging to the Rugosochonetidae, is described from the Early Permian (Late Artinskian or early Kungurian) Liangshan Formation of the Yangtze block. The new genus is defined externally by the presence of fine, but delayed, capillation and a weak or absent median sulcus and fold and by the presence of a distinct posteromedian sinus on the ventral umbo; and internally by a lack of median, lateral and accessory septa in the dorsal interior; absence of vascular trunks in the ventral interior and the presence of distinct radiating rows of papillae in the interior of both valves, particularly an unusual clustered arrangement of papillae on the posteromedian portion of the dorsal interior. The local environment during the deposition of the Liangshan Formation appears to have been a restricted tidal flat or lagoon which experienced frequent sealevel fluctuations associated with the onset of the Yanghsingian transgression. The new species, L. elfinis, appears to have several morphological adaptations enabling successful exploitation of this environment. It was typically a very small and thin-valved species with a high surface area to volume ratio, an advantage in an oxygen restricted environment. The small size and numerous body spinules would have aided individuals to remain suspended at the top of the fine, soft substrate. It also dominated the brachiopod assemblage in the Liangshan Formation, comprising up to 94%of specimens within a bed. These factors indicate that the new species appears to be an opportunistic species.

Fire, energy, and the ecology of reptiles in semi-arid Australia

‬Fire dependent ecosystems cover over half of the world's land surface. Understanding the factors that determine the distribution of fauna in these systems is essential to biodiversity conservation. This thesis explores the ecology of reptiles in a fire-prone region.

Flying, fasting, and feeding in birds during migration: a nutritional and physiological ecology perspective

Unlike exercising mammals, migratory birds fuel very high intensity exercise (e.g., flight) with fatty acids delivered from the adipose tissue to the working muscles by the circulatory system. Given the primary importance of fatty acids for fueling intense exercise, we discuss the likely limiting steps in lipid transport and oxidation for exercising birds and the ecological factors that affect the quality and quantity of fat stored in wild birds. Most stored lipids in migratory birds are comprised of three fatty acids (16:0, 18:1 and 18:2) even though migratory birds have diverse food habits. Diet selection and selective metabolism of lipids play important roles in determining the fatty acid composition of birds which, in turn, affects energetic performance during intense exercise. As such, migratory birds offer an intriguing model for studying the implications of lipid metabolism and obesity on exercise performance. We conclude with a discussion of the energetic costs of migratory flight and stopover in birds, and its implications for bird migration strategies.

Life history and the ecology of stress: how do glucocorticoid hormones influence life-history variation in animals?

Glucocorticoids hormones (GCs) are intuitively important for mediation of age-dependent vertebrate life-history transitions through their effects on ontogeny alongside underpinning variation in life-history traits and trade-offs in vertebrates. These concepts largely derive from the ability of GCs to alter energy allocation, physiology and behaviour that influences key life-history traits involving age-specific life-history transitions, reproduction and survival. Studies across vertebrates have shown that the neuroendocrine stress axis plays a role in the developmental processes that lead up to age-specific early life-history transitions. While environmental sensitivity of the stress axis allows for it to modulate the timing of these transitions within species, little is known as to how variation in stress axis function has been adapted to produce interspecific variation in the timing of life-history transitions. Our assessment of the literature confirms that of previous reviews that there is only equivocal evidence for correlative or direct functional relationships between GCs and variation in reproduction and survival. We conclude that the relationships between GCs and life-history traits are complex and general patterns cannot be easily discerned with current research approaches and experimental designs. We identify several future research directions including: (i) integration of proximate and ultimate measures, including longitudinal studies that measure effects of GCs on more than one life-history trait or in multiple environmental contexts, to test explicit hypotheses about how GCs and life-history variation are related and (ii) the measurement of additional factors that modulate the effects of GCs on life-history traits (e.g. GC receptors and binding protein levels) to better infer neurendocrine stress axis actions. Conceptual models of HPA/I axis actions, such as allostatic load and reactive scope, to some extent explicitly predict the role of GCs in a life-history context, but are descriptive in nature. We propose that GC effects on life-history transitions, survival probabilities and fecundity can be modelled in existing quantitative demographic frameworks to improve our understanding of how GC variation influences life-history evolution and GC-mediated effects on population dynamics Lay Summary Functional Ecology

Ecology of epifaunal caridean shrimps in the Hopkins River estuary, and the role of estuaries in the life history of the atyid "Paratya Australiensis" Kemp, 1917 in south-eastern Australia

This study examined the factors affecting the distribution and abundance of epifaunal caridean shrimps in seagrass meadows of the Hopkins River estuary in south-western Victoria, Australia, and investigated the life history patterns of the freshwater Parana australiensis, found for the first time in estuaries. Adult and sub-adult shrimps were surveyed in seagrass meadows along the estuary over two years, and their planktonic larvae were surveyed in adjacent waters. Three species were collected. The marine Palaemon serenus occurred only near the mouth, summer to autumn, in high salinities. The marine/estuarine Macrobrachium intermedium occurred throughout the estuary. Adults were most abundant in late autumn, and least abundant in summer (unlike trends reported in marine meadows). Densities were higher and less variable in downstream meadows. P. australiensis occurred in the upper estuary all year, most abundantly in spring, due to migration from the river after peak discharge. Ovigerous females dominated, while males, showing less migration into the estuary, dominated above estuarine influence. Adults disappeared from the estuary in summer as salinity rose. Breeding period for P. australiensis was briefer in the estuary (September-December) than upstream (July-April). M. intermedium began breeding later in the upper estuary (November/December-March) than in the lower estuary (October-March), probably reflecting a physiological response to lower salinity, rather than an interaction with P. australiensis. No ovigerous P. serenus were found in the estuary. Larvae of P. australiensis and M intermedium occurred abundantly throughout the estuary, but P. serenus larvae did not. P. australiensis was an early coloniser to the plankton after peak discharge (November-December). Larvae concentrated in the deep saline layer at the head of the intruding salt wedge, thus probably maintaining longitudinal position. Diurnal vertical migrations were evident within the salt wedge, and in a deep pool above tidal influence. M. intermedium larvae occurred October-May in the lower estuary and November-April in the upper estuary, peaking in abundance one to two months after P. australiensis. They were associated with low surface flows and surface salinities greater than 10, over an anoxic deeper layer. All three species exhibited extended development of euryhaline larvae in the laboratory. Tolerances and optimal salinities of larvae of the three species reflected their distributions. M. intermedium was the most euryhaline species. P. australiensis larvae were tolerant of higher salinities than juveniles of adults: capable of developing in salinity of at least 15. Most P. australiensis juveniles recruited to the estuary November-December, after which numbers declined dramatically. After settlement, most recruits probably migrated upstream out of the estuary. Two cohorts of M. intermedium recruited to the estuary from larvae in summer (December and February), but some juveniles also migrated from adjacent coastal waters. Post-larval migration was at least as important a determinant of abundance as direct recruitment from estuarine, planktonic larvae in all three species. Distributions among seagrass meadows along the estuary were determined primarily by physico-chemical patterns driven by hydrological changes. Seasonal variations in salinity and temperature were strongly associated with seasonal variations in shrimp abundance. Salinity tolerances of adults of the three species reflected their distribution patterns. Biotic interactions were more important in determining distributions within meadows. P. australiensis, when abundant, were associated with seagrass biomass. M. intermedium were also, but when seagrass was sparsest and least extensive. The two species apparently partitioned the seagrass meadow according to depth in early summer. Laboratory experiments suggested P. australiensis was displaced from deeper water by M. intermedium. Preference for vegetative complexity and competition for position within meadows suggest the underlying importance of predation in regulating shrimp populations. A survey of south-eastern Australian estuaries found P. australiensis larvae abundant in all stable, open, well-developed, salt-wedge estuaries where adults were abundant. Adults were most abundant in low salinities among submerged leafy macrophytes. Reproductive traits of P. australiensis were compared in estuarine and fresh reaches of three rivers. Early in the breeding season, egg size was smaller, and (size-specific) egg number larger in estuaries than upstream. A trade-off between egg size and egg number resulted in no difference in total (size-specific) reproductive investment between locations. Reproductive investment tended to decrease at some locations over the breeding season, and this decrease was a result of decreased egg size in most cases. The decrease in reproductive investment probably reflected reduced food availability for the adult, while the reduced egg size was probably a response to improved conditions for larval development. In the Hopkins River, larger egg size at upstream sites was reflected in larger early stage larvae. Later stage larvae were larger in the estuary, suggesting more favourable conditions for larval development. Allozyme electrophoresis showed the P. australiensis populations in each of the three rivers to be distinct. Allozyme frequencies were not different within the Hopkins River, but upstream and estuarine locations in the Curdies and Gellibrand were different. Although some variation in reproductive traits within catchments may have been due to genotypic differences, trade-offs between egg size and number, and decreases in egg size over summer were probably due to plastic responses to environmental cues. It is proposed P. australiensis inhabits and reproduces in both estuarine and freshwater environments by plastic response to environmental conditions. Recruitment to estuaries is dependent on the presence of suitable adult, littoral habitat, and a stable salt wedge for larval retention. Estuaries are important recruitment sites for P. australiensis, potentially allowing an extra brood each year before riverine recruitment. Estuarine broods could constitute a large part of the total fecundity of P. australiensis females. Euryhaline larvae and estuarine recruitment of P. australiensis suggest marine transport of larvae between estuaries as a possible dispersal mechanism for Paratya species.

Charismatic marine mega-fauna: some recent discoveries and future challenges

 The last 20 years have been exciting times for scientists working with charismatic marine mega-fauna. Here recent advances are reviewed. There have been advances in both data gathering and data-analysis techniques that have allowed new insights into the physiological and behavioural ecology of free-ranging mega-faunal species; some marine mega-faunal species have now become model organisms for cutting edge approaches to identify the underlying mathematical properties of animal search patterns and hence the underlying behavioural processes (e.g. Levy flight versus Brownian motion); the implications of climate change have started to become more apparent with extended time-series of animal movements, abundance and performance; conservation issues have become integrated into marine planning and have resulted in the advent of extended networks of marine protected areas (MPAs) as well as large MPAs that span many 100,000 km2; and collaborative crossdisciplinary teams have started to reveal the importance of ocean currents in animal dispersal, the ontogeny of migration and population genetic structure. Looking to the future, increased data availability (e.g. through data sharing) will likely allow more holistic across-taxa analyses to become routine.
© 2013 Elsevier B.V. All rights reserved.

Feeding ecology of benthic invertebrates in an intermittently open estuary

Abundances of benthic invertebrates in the Hopkins River estuary were not affected by connection to the ocean, but by freshwater discharge and sediment properties. The bivalve Soletellina alba was identified as a suspension feeder. Invertebrate food sources were derived mainly from estuarine organic matter, but also contained marine and freshwater/terrestrial plants despite reduced river flow during drought conditions.

Coastal responses to estuarine discharge from intermittently open systems

This thesis is the first study to examine the interaction between estuarine discharge and coastal environments, for intermittent estuaries in Victoria. The study examined water quality, bacteria and seaweed communities and the diet of mussels, concluding that estuarine discharge is an important driver for the productivity of nearshore marine environments.

Freshwater influences on hydrology and seagrass dynamics of intermittent estuaries

Many temperate estuaries have intermittently open and closed mouths, a feature that is often related to intermittent freshwater input. These systems, often overlooked due to their small size, can have large hydrological variability over medium-term time scales.

This variability presents potential difficulties for estuarine species particularly where anthropogenic alterations to freshwater flows can cause large deviations from natural patterns of tidal influence and inundation of habitat.

Influences of natural and hydrological variability on seagrasses were examined in two central Victorian estuaries with anthropogenically-modified but naturally-intermittent freshwater flows and mouth openings. Comparisons were focused on differences between an estuary with artificially-augmented freshwater inflow and an adjacent system, in which the volume and timing of inflows were altered by a reservoir. Eight additional estuaries in the region were also used to provide a context for these two main sites.

Hydrological changes during the three-year field component were affected by the ending of a drought and then a major flood a year later as well as by ongoing anthropogenic flow reduction and augmentation. These influences on hydrology were associated with an initially high seagrass coverage that was substantially reduced and showed signs of recovery only in the system that was affected by lower inflows. Such influences and responses also changed seasonally but to a much lesser extent than the responses to stochastic climatic events.

Natural flows were intermittent and varied substantially between years. Flooding flows represented up to 89% of the long-term annual average flow. Water quality was broadly typical of the region, with the exception of low pH in some tributaries, especially those of Anglesea estuary. Anthropogenic changes to flow were most evident at times of low natural flows and resulted in longer and more frequent periods of zero inflow to Painkalac estuary and a continual base flow to Anglesea. This base flow, from ponds containing coal ash, neutralised waters flowing from upstream and increased conductivity, except at times of high natural flow.

A three-state conceptual model of the magnitude and variability of water levels, based largely on the degree of tidal influence was identified and quantitatively assessed for the two estuaries that were the main focus of the study. These states in turn had a large influence on the area and inundation of benthic habitat. Floods tended to open the mouths of estuaries, which then remained tidal given sufficient flow to overcome sedimentary processes at the mouths. Low and zero inflow was a precondition for closure of the mouths of the estuaries. When closed, differences in inflow resulted in different endpoints in salinity patterns. From an initial pattern similar to a classic ‘salt wedge’, Painkalac estuary, with reduced inflow, quickly destratified and gradually became more saline, at times hypersaline. Anglesea estuary, with augmented flow, tended to remain stratified for longer until becoming completely fresh, given a long enough period of closure.

Episodic changes in the water quality of the estuaries were associated with different components of the freshwater flow regimes. At high flows, fresh waters of low pH with a high metal load entered Anglesea estuary. Except during the largest flood, when the estuary was completely flushed, this water was neutralised at the halocline and resulting in precipitation of metals. High flows into Painkalac were associated with elevated concentrations of clay-sourced suspended solids. During a closed period, with zero flow, a release of sediment-bound nutrients triggered by anoxia was observed in Painkalac, followed by an algal bloom.

The large decline in seagrass extent that was observed in both estuaries was closely related to floods and the subsequent reductions in potential habitat associated with the tidal states that followed. Analysis of historical patterns of extent against rainfall records suggested that periods of drought and extended mouth closures were related to establishment and expansion of beds. This model was similar to that described for South African estuaries and contrasted with more-seasonal patterns reported for local marine embayments.

Rates of in situ decomposition of seagrass detritus showed a mix of seasonal and disturbance-driven patterns of change, depending on estuary. Variability of these rates on a scale of 100s of metres was typically not significant, but there were a few episodes that were highly significant. A negative correlation between decomposition rate and seagrass extent was also observed. A novel technique for assessing cellulose decomposition potential in sediment, adapted from soil science, proved to be a useful tool for estuarine research. Results from this component of the study highlighted both small-scale variability that was inconsistent through time, and also stable differences in decomposition potential between depths and estuaries that were consistent with differences in hydrological state and salinity.

Given the relative lack of knowledge about processes in intermittent estuaries, particularly those relating to changes in freshwater inflow, results from this study will be of value both locally and for similar systems elsewhere. Locally, it is likely that flow regimes to both Anglesea and Painkalac estuaries will be reduced, following closure of the mine power station at Anglesea and due to increased demand from the reservoir above Painkalac. There is potential to manage flows from each of these sources to minimise downstream effects. Regionally, and globally, there are many intermittent estuaries in areas with Mediterranean-type climates. It has been predicted that the climates of these regions will become drier but with an increase in intensity of storm events, both of which have ramifications for flow regimes to estuaries. It is hoped that results of this study will contribute to more informed management of intermittent estuaries in the context of these likely changes.

Multiple dispersal vectors drive range expansion in an invasive marine species

The establishment and subsequent spread of invasive species is widely recognised as one of the most threatening processes contributing to global biodiversity loss. This is especially true for marine and estuarine ecosystems, which have experienced significant increases in the number of invasive species with the increase in global maritime trade. Understanding the rate and mechanisms of range expansion is therefore of significant interest to ecologists and conservation managers alike. Using a combination of population genetic surveys, eDNA plankton sampling and hydrodynamic modelling we examined the patterns of introduction of the predatory Northern Pacific seastar (Asterias amurensis) and pathways of secondary spread within southeast Australia. Genetic surveys across the invasive range reveal some genetic divergence between the two main invasive regions and no evidence of ongoing gene flow; a pattern that is consistent with the establishment of the second invasive region via a human-mediated translocation event. In contrast hydrodynamic modelling combined with eDNA plankton sampling demonstrated that the establishment of range expansion populations within a region is consistent with natural larval dispersal and recruitment. Our results suggest that both anthropogenic and natural dispersal vectors have played an important role in the range expansion of this species in Australia. The multiple modes of spread combined with high levels of fecundity and a long larval duration in A. amurensis suggests it is likely to continue its range expansion and significantly impact Australian marine ecosystems.

Invertebrate larval dynamics in seasonally closed estuaries

Estuarine benthic assemblages are often numerically dominated by polychaetes. The limits of these populations are determined by larval, and probably to a lesser extent adult movement. A previous study (Newton 1996), indicated that planktonic polychaete larvae were very abundant over the summer months in the Hopkins River; however, the identification and source of these larvae was not known. Defining the extent of a population, and therefore the likelihood of that population recovering following a perturbation, is crucial for effective estuarine management. This study investigated both the likely source of the larvae, (i.e. estuarine or marine) and the extent of larval dispersal within and between estuaries by addressing the following questions: Which taxa produced the planktonic larvae? Are these taxa resident estuarine species? Are the larvae of different taxa evenly distributed within the estuary or do physicochemical parameters or other factors influence their abundance? Are the same larvae found in other estuaries along the coast? and Is there exchange of these larval taxa with the marine environment and other estuaries? Larvae were identified and described by culturing commonly occurring planktonic larvae until adult characteristics appeared. The spionids, Carazziella victoriensis and Prionospio Tatura, numerically dominated the plankton in the Hopkins and the spionid, Orthoprionospio cirriformia was recorded from the Hopkins, Curdies and Gellibrand estuaries. Two spionids, Carazziella sp. and Polydora sp. were identified from tidal waters. Mouth status and physicochemical conditions (salinity, temperature and dissolved oxygen) were monitored in each estuary. Whereas the Merri and Gellibrand estuaries were predominantly stratified over the sampling period, the Curdies was more often well mixed and the Hopkins varied from well mixed to stratified. The duration of mouth opening and hence the opportunity for larval exchange also varied in each estuary. The Merri River was closed for 13.5% of days over the study period, the Gellibrand River for 18.4%, the Hopkins River for 49% and the Curdies River for 71.0%. The distributions of larvae at spatial scales of metres, 100s of metres and kilometres were investigated within a single estuary. While the same larvae, C. victoriensis, P. Tatura and bivalve larvae, were found along the length of the Hopkins estuary the abundances varied at different spatial scales suggesting different processes were influencing the distribution of P. Tatura larvae, and C. victoriensis and bivalve larvae. The distribution of larvae between several estuaries was investigated by monitoring meroplankton at two sites at the mouth of each of the four estuaries approximately monthly (except for winter months). Different meroplanktonic assemblages were found to distinguish each estuary. Further, C. victoriensis and P. Tatura larvae were only recorded in the Hopkins but larvae of the spionid, Orthoprionopio cirriformia were detected in the Hopkins, Curdies and Gellibrand estuaries. The extent of larval exchange with other estuaries and the marine environment was determined by monitoring tidal waters. Settlement trays were also deployed to determine if larvae were moving into estuaries and settling but not recruiting. P. tatura larvae were not detected in the tidal waters of any estuary and while C. victoriensis and O. cirriformia were found in both flood and ebb tides there was no evidence of movement of theses taxa to other estuaries. Larvae of the spionids, Carazziella sp. and Polydora sp., were found in tidal waters of each estuary but were rarely detected in the plankton within the estuaries. Neither species was found as an adult in background cores from any estuary, nor with the exception of a few individuals in the Merri, were they detected in settlement trays in any estuary. I conclude that the source of the larvae of C. victoriensis, P. Tatura and O. cirriformia is estuarine and while C. victoriensis, and O. cirriformia move in and outh of the source estuary in tidal waters there was no evidence for movement to other estuaries. The spionids, Carazziella sp. and Polydora sp were considered to be marine and while they moved in and out of estuaries in tidal waters they did not usually settle in the estuaries. The results of this study are a crucial first step in the development of ecological models to better understand dispersal in seasonally closed estuaries that are typical of southern Australia. This study emphasises the unique physicochemical characteristics and biological assemblages within these estuaries and the need for estuarine management to reflect these differences.