Coastal marine habitat mapping using multi-beam acoustics, video data and a decision tree classifier on the temperate south-east Australian continental shelf

In this habitat mapping study, multi-beam acoustic data are integrated with extensive, precisely geo-referenced video validation data in a GIS environment to classify benthic substrates and biota at a 33km2 site in the near shore waters of Victoria, Australia. Using an automated decision-tree classification method, 5 representative biotic groups were identified in the Cape Nelson survey area using a combination of multi-beam bathymetry, backscatter and derivative products. Rigorous error assessment of derived, classified maps produced high overall accuracies (>85%) for all mapping products. In addition, a discrete multivariate analysis technique (kappa analysis) was used to assess classification accuracy. High-resolution (2.5m cell-size) representation of sea floor morphology and textural characteristics provided by multi-beam bathymetry and backscatter datasets, allowed the interpretation of benthic substrates of the Cape Nelson site and the communities of sessile organisms that populate them. Non-parametric multivariate statistical analysis (ANOSIM) revealed a significant difference in biotic composition between depth strata, and between substrate types. Incorporated with other descriptive measures, these results indicate that depth and substrate are important factors in the distributional ecology of the biotic communities at the Cape Nelson study site. BIOENV analysis indicates that derivatives of both multi-beam datasets (bathymetry and backscatter) are correlated with distribution and density of biotic communities. Results from this study provide new tools for research and management of the coastal zone.

In situ growth of Soletellina alba (Bivalvia: Psammobiidae) in response to detrital supply and mouth status in a seasonally-closed estuary

The supply of detritus is an important food source for many soft-sediment invertebrates, but its importance for their growth and condition is rarely, if ever, tested directly using manipulative field experiments. Therefore, we designed such a study to: (1) test the importance of fine particulate organic matter for the growth and condition of the infaunal bivalve Soletellina alba; (2) indirectly test the feeding mode of S. alba, which has been assumed to be a deposit feeder like other members of the same superfamily (Tellinoidea); (3) compare growth rates across two summers with contrasting patterns of estuary mouth opening/closing; and (4) compare the condition of individuals used in two field studies (i.e. present versus past) and a past laboratory study. Neither growth nor condition differed when organic content of the sediments was varied, which suggests that S. alba is either a suspension feeder or capable of switching modes of feeding. There was considerable interannual variation in growth with greater growth occurring during the summer with a longer period of mouth opening. This suggests that periods of mouth closure may reduce secondary production within seasonally-closed estuaries. Potential artefacts associated with laboratory trials were also identified, with laboratory bivalves exhibiting poorer condition than those used in two field trials. The present study provides no evidence that variable quantities and qualities of organic matter within the sediments influence the growth and condition of S. alba, but future studies should focus on food supplied via the water column when the estuary is open versus closed.

Where exactly do ground-foraging woodland birds forage? Foraging sites and microhabitat selection in temperate woodlands of southern Australia

Bird assemblages in woodlands of southern Australia are characterised by a high proportion of ground-foraging species, many of which are experiencing population declines. We examined the foraging sites of 13 species of ground-foraging birds, including four common species and nine declining species, in four study areas representing different woodland types. Microhabitat features were recorded within a 3-m radius of observed foraging points and compared with random points. Significant differences between foraging and random plots were detected for all but one species, clearly indicating selection for foraging habitat. However, levels of dissimilarity between foraging and random plots were low, suggesting that much of the woodland study area is suitable for foraging. Microhabitat features of particular importance for multiple species were a low density of trees and shrubs, a high cover of native herbs, and fallen timber on the ground. Sites amidst dense trees tended not to be used. Several species had more particular requirements, such as the Diamond Firetail (Stagonopleura guttata) for grass cover and the White-winged Chough (Corcorax melanorhamphos) for litter cover. There was no evidence that declining species showed a greater degree of selection or were more restricted in the availability of foraging microhabitats than common species. Several of the key attributes of preferred foraging sites, such as tree density, can be actively managed at the local scale. A heterogeneous ground layer is needed to provide suitable foraging habitat for the full suite of ground-foraging birds. Achieving suitable heterogeneity in present-day woodlands will require careful and active management of various disturbance processes.

Presence of fish on the shallow flooded margins of a small intermittently open estuary in South Eastern Australia under variable flooding regimes

Shallow water habitats within estuarine systems are believed to be important areas for small fish. While a wide variety of shallow habitats have been studied, the land that becomes inundated by the damming effect after the closure of intermittently open mouths has previously been overlooked. Fish were sampled monthly from both the main channel and flood zone of an intermittently open estuary between July 2004 and June 2005 using minifyke nets during the day and at night. A total of 7,787 fish were collected during the study representing 13 species and 11 families. Philypnodon grandiceps was the most abundant species and, together with Atherinosoma microstoma, Pseudogobius olorum, and Galaxias maculatus, made up 94% of the total catch. Inundation of the flood zone occurred in two discrete forms associated with mouth condition, which consisted of sporadic flooding while the mouth was open, to long-term flooding for 6 months after its closure. Large numbers of fish were captured on the flood zone, which included nine species; however, A. microstoma dominated the catch. A distinct shift in the flood zone fish assemblage occurred between the two mouth conditions, which is likely associated with changes in hydro-period and food availability of the flood zone and physico-chemical parameters in the main channel. There was no longitudinal variation in the fish assemblage in both the main channel and flood zone; similarly, the diel period was found to have little effect on the fish assemblage. The total catch per unit effort did not vary across seasons and suggests that fish abundance within the estuary is stable throughout the year. Unlike other estuarine systems where shallow water fish assemblages may be structured by variations in tide and elevation within the Surrey, freshwater inflow and, more importantly, mouth condition appear to have the greatest influence in composition of the shallow water flood zone fish assemblage of intermittently open estuaries.

Victorian index of estuary condition : recommended themes and measures

Deakin University was engaged by the Department of Sustainability and Environment to develop an Index of Estuary Condition (IEC) for evaluating the environmental condition of Victorian estuaries. The Index will ultimately complement the existing Index of Stream Condition (ISC) by providing a consistent statewide assessment of the environmental condition of estuaries. This will better enable:

• Estuarine condition to be reported at regional, state and national levels.

• Prioritisation of resource allocation.

• Strategic evaluation of management interventions in estuaries.

Workshops involving participants with expertise in a variety of disciplines were convened to integrate learnings from assessment programs currently being developed interstate and overseas. This report synthesises and builds on the output from those workshops which:

• Identified key components (themes) of estuaries that contribute to estuarine condition.

• Contributed to development of a broad conceptual model for Victorian estuaries

• Identified possible measures of each theme

In keeping with the sub-indices of the ISC, six themes were identified for use in the IEC: Physical form, Hydrology, Water quality, Sediment, Flora and Fauna. Several measures within each theme are recommended to assess estuary condition.

Implementation of particular measures in the IEC partly depends on the investment required to both collect and interpret the required data. With regard to data collection, each measure was assessed according to whether there is an established sampling procedure, how frequently data need to be collected and the level of expertise required for collection and processing. For interpreting the data, measures were scored on whether baseline condition is established and whether descriptions and scores are developed which reflect the extent of deviation from that condition. These scores were used to indicate which measures are feasible to implement immediately and which require further investigation.

A trial of the recommended IEC measures in a selection of estuaries is recommended as it would provide an opportunity to test the measures and their suitability for application statewide. It is suggested that the trial is conducted in estuaries subject to various levels of threats within each of the four estuary classes described by Barton et al. (2008)

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.

Evaluation of the effectiveness of marine protected areas in temperate waters of Australasia

An evaluation of the effectiveness of Marine Protected Areas (MPAs) in temperate waters of Australasia has been conducted for this thesis. The aim was to identify key elements needed in a strategy for establishment and management of MPA’s in temperate waters of Australasia. This aim was achieved by assessing how effective a sample of MPA’s has been in meeting the conservation objectives for their establishment and by identifying factors that have contributed to success or failure of the MPA’s in meeting these objectives. Particular attention was paid to the objectives of ecological sustainability and biodiversity preservation. A MPA for the purposes of this research was defined as an area of coastal or marine environment, with a substantial subtidal component, set aside by law primarily for conservation purposes. The study region encompassed the coastal zones of Victoria, Tasmania and South Australia (Australia) and New Zealand. The questions posed in order to address the aim of this thesis were; a) Have existing MPA’s been effective in achieving conservation objectives? b) What have been the important influences on effectiveness of existing MPA’s? c) What are the key elements required for implementation of effective MPA’s? The thesis is divided into three parts. Part I is a review of the literature on implementation and effectiveness of MPA’s. Part II presents a detailed evaluation of one MPA: Point Lonsdale Marine Reserve (PLMR), Victoria, Australia. Part in is an evaluation of a number of Australasian temperate MPA’s based on information provided in a survey of people involved in management of MPA’s, and from a variety of published and unpublished documents. The MPA’s are described, evidence about ecological effectiveness is presented and factors that have enhanced and limited the ability of these MPA’s to achieve conservation objectives are derived. A substantial amount of scientific evidence was found for increases in abundance, mean size and size range of fish and invertebrate populations within the boundaries of ‘no-take’ MPA’s, Some evidence was found for ‘spillover’ of adults and juveniles into adjacent fishing grounds. Ecological effects detected within ‘no-take’ MPA’s in Australasia matched those described in the literature. The abundance and mean size of a number of previously exploited species have increased, migration into adjacent fishing grounds has been documented, and species richness has increased in at least one MPA. The PLMR was established primarily to protect the scientifically significant intertidal rock platforms. The results of the case study suggest that this objective has been achieved. Opinions about effectiveness were obtained for 28 MPA’s. Of these 19 were considered to be achieving some objectives and 10 were considered to be performing well in terms of overall ecological effectiveness. Positive effects on biodiversity were generally assumed as a result of reduction of damaging anthropogenic effects on habitat. Many questionnaire respondents noted an increase in community awareness about and support for marine conservation as a result of proclamation of MPA’s, Overall, the results support the value of MPA’s for sustainability of fish stocks and preservation of biodiversity, but there is substantial doubt over whether some of the MPA’s are too small to maintain benefits in the long-term. ‘No-take’ MPA’s, particularly those more remote from the impacts of human activities, have been the most effective in achieving objectives. A number of interacting factors important to eventual success of MPA’s were identified. The most important enhancing factors identified for the PLMR were physical attributes that limit the extent of human use and a strong conservation ethic amongst many of the visitors to this marine reserve. Limiting factors were far more numerous. Of most concern is the inadequacy of at-site management. Almost half of visitors to the area were not aware of its marine reserve status, despite the fact many were frequent visitors. The need for better educational and interpretative material on-site is highlighted by the results of the PLMR visitor survey. A total of 56 factors that have enhanced effectiveness and 46 factors that have limited effectiveness of Australasian temperate MPA’s were identified. A number of factors were important in more than one MPA and this was used to derive a set of critical, or key, factors. For example, a conclusion of all three approaches used in this study is that failure to implement day-to-day management through lack of resources was a major constraint on effectiveness. The importance of MPA’s to marine conservation depends, in part, on how well they are managed. The key factors that influence MPA effectiveness were used as the basis for derivation of the main requirements for implementation of MPA’s that will be capable of meeting the objectives for their establishment. The most important needs are: • that ‘no-take’ areas surrounded by buffer zones form the basis for a system of MPA’s; • that a high level of protection is bestowed by legislation and regulations; • that a minimum size be set for the ‘no-take’ core areas; • that the selection of sites for MPA’s takes into account land-based impacts; • that institutional arrangements are developed specifically for MPA’s; • that funding for MPA’s is increased to enable effective management; • that day-to-day management is implemented in all MPA’s, with enforcement and education programs as priority areas; • that a monitoring program for one or more MPA in each 'State' is established to provide evidence of ecological effects of reservation; • that public and stakeholder involvement in development and implementation of MPA’s is encouraged as this will influence the degree of public support and compliance; • that community-based programs to educate the general public, stakeholders, the media and decision-makers about the value of MPA’s are essential; and • that measures to reduce financial impact on affected stakeholders be implemented.

Ecology and conservation of ground-foraging birds of temperate woodlands

Many ground-foraging birds are in serious decline. This research examined the distribution of these birds and revealed that they were most common in native pine woodlands of which little remains due to past clearing. The foraging habitat requirements of 13 species were documented providing valuable information for their conservation.