Dissertations / Theses on the topic 'Estuarine habitats'

In estuarine and other aquatic systems, it is possible for water to transport locally produced carbon (food) across habitat boundaries, and provide nutrition for animals remote from the carbon source. In estuarine and marine systems, early work examining the movement of carbon from saltmarsh habitats in the USA suggested that carbon may move large distances from inshore to offshore environments. Upon closer examination, however, evidence did not support this paradigm of large-scale carbon movement, referred to as the outwelling hypothesis, in some estuaries. Physical characteristics of estuaries in which large-scale carbon movement did not occur, such as restricted access to the sea, were proposed as a possible explanation, and for these estuaries, movement of carbon among estuarine habitats was considered more likely. A mosaic of saltmarsh and mangrove habitats dominate the subtropical barrier estuary of southern Moreton Bay, Queensland, but there have been no studies that examine the movement of carbon among habitats within this system. Previous studies that examine the movement of carbon have mostly been done in saltmarshes in the northern hemisphere or in tropical mangrove systems. Different vegetation and tidal regimes in temperate marshes of the northern hemisphere preclude generalisations of carbon movement to tropical and subtropical systems. Our understanding of carbon movement in tropical systems may extend to subtropical waters, but the saltmarsh-mangrove mosaic in the subtropics distinguishes them from their tropical counterparts. The mosaic of saltmarsh and mangrove habitats among the barrier islands of southern Moreton Bay thus provide a unique opportunity to examine the small-scale movement of carbon among adjacent habitats in a subtropical system. Stable isotopes of carbon have been used successfully to trace the transfer of carbon from autotrophs to consumers at a range of spatial scales. This method is able to distinguish among carbon sources where autotrophs have different ratios of 13C/12C, and consumers take on the ratio of their food source. The success of stable isotopes in clarifying food web processes, however, depends on isotope ratios changing in predictable ways as elements are processed. As isotope ratios may be influenced by changes in productivity, and differences in nutrient source, they may vary across small and large spatial scales that may confound interpretation of food web processes. In this study I measured small and large-scale spatial variability of three estuarine autotrophs (the saltmarsh grass, Sporobolus virginicus, the seagrass Zostera capricorni and the algal community epiphytic on Z. capricorni) and showed the small-scale spatial variability to be negligible and insufficient to preclude the use of carbon and nitrogen isotopes in food web studies. Large-scale variability was more pronounced and may be useful for spatial correlation of food webs for more mobile species. The small-scale homogeneity and clearly distinguished isotope ratios of the dominant autotrophs in adjacent saltmarsh and mangrove habitats in southeast Queensland are therefore ideally suited to the study of small-scale carbon movement between adjacent habitats. Carbon isotopes of estuarine invertebrates were used to estimate the movement of particulate carbon between adjacent saltmarsh and mangroves at the tens-of-metre scale. Carbon isotope values of two crab species (Parasesarma erythrodactyla and Australoplax tridentata) and two snail species (Salinator solida and Ophicardelus quoyi) in saltmarsh closely match those of the saltmarsh grass, and suggest that the movement and assimilation of carbon occurs at a scale much smaller than has previously been examined. In mangroves, the results of this study indicate that microphytobenthos with some contribution of mangrove carbon is the most likely food source for P. erythrodactyla and A. tridentata, although contribution of carbon from saltmarsh is also possible. Under this latter scenario, carbon movement in mangroves would be considered to occur at a scale larger than that in saltmarsh habitat. A study that examined the movement and assimilation of carbon by crabs and an estuarine slug (Onchidina australis) at a finer resolution (i.e. metres) supported the original findings and indicated that the movement and assimilation of carbon occurs 5 - 8 m either side of the saltmarsh-mangrove interface. At this small-scale, the movement and subsequent foraging of crabs among habitats, the movement of particulate carbon among habitats, or a combination of crab and particulate carbon movement are three alternative models that provide plausible explanations for the pattern in carbon isotope values of crabs. Crab movement among these habitats was measured using an array of pitfall traps perpendicular to the saltmarsh-mangrove interface. To test for carbon movement, samples of detritus were collected at 2 m intervals across this same interface and the carbon isotopes analysed. For the majority of crabs (up to 90% for both species), movement up or down the shore was less than 1 m from the place of initial capture. Thus, crab movement cannot explain the trend in carbon isotope values of crabs. The pattern in detrital isotope values was similar to that of crabs and indicates that the movement of particulate carbon across the saltmarsh-mangrove interface is the most likely explanation for crab isotope ratios. Sources of carbon for estuarine invertebrates can also depend on the size of the saltmarsh patches. Examination of the movement and assimilation of carbon by crabs in saltmarsh patches of different sizes adjacent to mangroves indicates that saltmarshes less than 0.3 ha in area are subsidised by the import of allochthonous carbon, most likely from mangroves. These findings contribute substantially to our understanding of the food web value of estuarine habitats and provide an important link between landscape and food web ecology. They also have important implications for determining the conservation value of estuarine habitats with respect to their functional (food web) value. The scale-dependent sampling used in this thesis also provides important evidence for the fine-scale movement of estuarine carbon that has not previously been examined.

In estuarine and other aquatic systems, it is possible for water to transport locally produced carbon (food) across habitat boundaries, and provide nutrition for animals remote from the carbon source. In estuarine and marine systems, early work examining the movement of carbon from saltmarsh habitats in the USA suggested that carbon may move large distances from inshore to offshore environments. Upon closer examination, however, evidence did not support this paradigm of large-scale carbon movement, referred to as the outwelling hypothesis, in some estuaries. Physical characteristics of estuaries in which large-scale carbon movement did not occur, such as restricted access to the sea, were proposed as a possible explanation, and for these estuaries, movement of carbon among estuarine habitats was considered more likely. A mosaic of saltmarsh and mangrove habitats dominate the subtropical barrier estuary of southern Moreton Bay, Queensland, but there have been no studies that examine the movement of carbon among habitats within this system. Previous studies that examine the movement of carbon have mostly been done in saltmarshes in the northern hemisphere or in tropical mangrove systems. Different vegetation and tidal regimes in temperate marshes of the northern hemisphere preclude generalisations of carbon movement to tropical and subtropical systems. Our understanding of carbon movement in tropical systems may extend to subtropical waters, but the saltmarsh-mangrove mosaic in the subtropics distinguishes them from their tropical counterparts. The mosaic of saltmarsh and mangrove habitats among the barrier islands of southern Moreton Bay thus provide a unique opportunity to examine the small-scale movement of carbon among adjacent habitats in a subtropical system. Stable isotopes of carbon have been used successfully to trace the transfer of carbon from autotrophs to consumers at a range of spatial scales. This method is able to distinguish among carbon sources where autotrophs have different ratios of 13C/12C, and consumers take on the ratio of their food source. The success of stable isotopes in clarifying food web processes, however, depends on isotope ratios changing in predictable ways as elements are processed. As isotope ratios may be influenced by changes in productivity, and differences in nutrient source, they may vary across small and large spatial scales that may confound interpretation of food web processes. In this study I measured small and large-scale spatial variability of three estuarine autotrophs (the saltmarsh grass, Sporobolus virginicus, the seagrass Zostera capricorni and the algal community epiphytic on Z. capricorni) and showed the small-scale spatial variability to be negligible and insufficient to preclude the use of carbon and nitrogen isotopes in food web studies. Large-scale variability was more pronounced and may be useful for spatial correlation of food webs for more mobile species. The small-scale homogeneity and clearly distinguished isotope ratios of the dominant autotrophs in adjacent saltmarsh and mangrove habitats in southeast Queensland are therefore ideally suited to the study of small-scale carbon movement between adjacent habitats. Carbon isotopes of estuarine invertebrates were used to estimate the movement of particulate carbon between adjacent saltmarsh and mangroves at the tens-of-metre scale. Carbon isotope values of two crab species (Parasesarma erythrodactyla and Australoplax tridentata) and two snail species (Salinator solida and Ophicardelus quoyi) in saltmarsh closely match those of the saltmarsh grass, and suggest that the movement and assimilation of carbon occurs at a scale much smaller than has previously been examined. In mangroves, the results of this study indicate that microphytobenthos with some contribution of mangrove carbon is the most likely food source for P. erythrodactyla and A. tridentata, although contribution of carbon from saltmarsh is also possible. Under this latter scenario, carbon movement in mangroves would be considered to occur at a scale larger than that in saltmarsh habitat. A study that examined the movement and assimilation of carbon by crabs and an estuarine slug (Onchidina australis) at a finer resolution (i.e. metres) supported the original findings and indicated that the movement and assimilation of carbon occurs 5 - 8 m either side of the saltmarsh-mangrove interface. At this small-scale, the movement and subsequent foraging of crabs among habitats, the movement of particulate carbon among habitats, or a combination of crab and particulate carbon movement are three alternative models that provide plausible explanations for the pattern in carbon isotope values of crabs. Crab movement among these habitats was measured using an array of pitfall traps perpendicular to the saltmarsh-mangrove interface. To test for carbon movement, samples of detritus were collected at 2 m intervals across this same interface and the carbon isotopes analysed. For the majority of crabs (up to 90% for both species), movement up or down the shore was less than 1 m from the place of initial capture. Thus, crab movement cannot explain the trend in carbon isotope values of crabs. The pattern in detrital isotope values was similar to that of crabs and indicates that the movement of particulate carbon across the saltmarsh-mangrove interface is the most likely explanation for crab isotope ratios. Sources of carbon for estuarine invertebrates can also depend on the size of the saltmarsh patches. Examination of the movement and assimilation of carbon by crabs in saltmarsh patches of different sizes adjacent to mangroves indicates that saltmarshes less than 0.3 ha in area are subsidised by the import of allochthonous carbon, most likely from mangroves. These findings contribute substantially to our understanding of the food web value of estuarine habitats and provide an important link between landscape and food web ecology. They also have important implications for determining the conservation value of estuarine habitats with respect to their functional (food web) value. The scale-dependent sampling used in this thesis also provides important evidence for the fine-scale movement of estuarine carbon that has not previously been examined.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environmental and Applied Science
Full Text

The role of autotrophic production in different coastal habitats in the production of fish in estuaries is an important consideration in coastal management and conservation. In the estuarine waters of the Australian east coast, many economically important fish species occur over mudflats lacking conspicuous vegetation. I used stable isotope analysis to examine where such fish ultimately derived their nutrition, in the subtropical waters of southern Moreton Bay, Queensland, Australia. I first tested traditional processing methodologies of autotroph samples, in this case of mangrove leaves, and examined variability in mangrove isotope values at different spatial scales. Mangrove leaves processed using time-consuming grinding showed no significant difference in isotope values than coarsely broken leaf fragments. Isotope values of green leaves were not meaningfully different from yellow or brown leaves that would normally be the leaves that actually dropped on to the sediment. Future analyses therefore can use green leaves, since they are more abundant and therefore more easily collected, and can simply be processed as whole leaf fragments rather than being ground to a powder. Carbon and nitrogen isotope values varied at several spatial scales. The proportion of variability partitioned at different scales varied depending on the species of mangrove and element (C or N) analysed. To properly represent a geographic area, isotope analysis should be done on leaves collected at different locations and, especially, from different trees within locations. The autotrophic source(s) supporting food webs leading to fish production on mudflats might be either in situ microphytobenthos or material transported from adjacent habitats dominated by macrophytes. I tested the importance of these sources by measuring ?13C values of 22 fish species and six autotroph taxa (microphytobenthos on mudflats, and seagrass, seagrass epiphytic algae, mangroves, saltmarsh succulents and saltmarsh grass in adjacent habitats) in Moreton Bay. I calculated the distribution of feasible contributions of each autotroph to fishes. All fish ?13C values lay in the enriched half of the range for autotrophs. For over 90% of fishes, the top three contributing autotrophs were seagrass, epiphytes and saltmarsh grass, with median estimates of approximately 60-90% from these sources combined. Seagrass was typically ranked as the main contributor based on medians, while epiphytic algae stood out based on 75th percentile contributions. The other three sources, including MPB, were ranked in the top three contributors for only a single fish. Organic matter from seagrass meadows is clearly important at the base of food webs for fish on adjacent unvegetated mudflats, either through outwelling of particular organic matter or via a series of predator-prey interactions (trophic relay). Modelling results indicate that saltmarsh grass (Sporobolus) also had high contributions for many fish species, but this is probably a spurious result, reflecting the similarity in isotope values of this autotroph to seagrass. Carbon from adjacent habitats and not in situ microphytobenthos dominates the nutrition for this suite of 22 fishes caught over mudflats. The ultimate autotrophic sources supporting production of three commercially important fish species from Moreton Bay were re-examined by further analysing carbon and nitrogen stable isotope data. Mean isotope values over the whole estuary for fish and autotroph sources were again modelled to indicate feasible combinations of sources. Variability in isotope values among nine locations (separated by 3-10 km) was then used as a further test of the likelihood that sources were involved in fish nutrition. A positive spatial correlation between isotope values of a fish species and an autotroph indicates a substantial contribution from the autotroph. Spatial correlations were tested with a newly developed randomisation procedure using differences between fish and autotroph values at each location, based on carbon and nitrogen isotopes combined in two-dimensional space. Both whole estuary modelling and spatial analysis showed that seagrass, epiphytic algae and particulate organic matter in the water column, potentially including phytoplankton, are likely contributors to bream (Acanthopagrus australis) nutrition. However, spatial analysis also showed that mangroves were involved (up to 33% contribution), despite a very low contribution based on whole estuary modelling. Spatial analysis for sand whiting (Sillago ciliata) demonstrated the importance of two sources, mangroves and microalgae on the mudflats, considered unimportant based on whole estuary modelling. No spatial correlations were found between winter whiting (Sillago maculata) and autotrophs, either because fish moved among locations or relied on different autotrophs at different locations. Spatial correlations between consumer and source isotope values provide a useful analytical tool for identifying the role of autotrophs in foodwebs, and were used here to demonstrate that organic matter from adjacent habitats, and in some cases also in situ production of microalgae, were important to fish over mudflats. Whilst recognising that production from several habitats is implicated in the nutrition of fishes over mudflats in Moreton Bay, clearly the major source is from seagrass meadows. Organic matter deriving from seagrass itself and/or algae epiphytic on seagrass is the most important source at the base of fisheries food webs in Moreton Bay. The importance of seagrass and its epiphytic algae to production of fisheries species in Moreton Bay reinforces the need to conserve and protect seagrass meadows from adverse anthropogenic influences.

The role of autotrophic production in different coastal habitats in the production of fish in estuaries is an important consideration in coastal management and conservation. In the estuarine waters of the Australian east coast, many economically important fish species occur over mudflats lacking conspicuous vegetation. I used stable isotope analysis to examine where such fish ultimately derived their nutrition, in the subtropical waters of southern Moreton Bay, Queensland, Australia. I first tested traditional processing methodologies of autotroph samples, in this case of mangrove leaves, and examined variability in mangrove isotope values at different spatial scales. Mangrove leaves processed using time-consuming grinding showed no significant difference in isotope values than coarsely broken leaf fragments. Isotope values of green leaves were not meaningfully different from yellow or brown leaves that would normally be the leaves that actually dropped on to the sediment. Future analyses therefore can use green leaves, since they are more abundant and therefore more easily collected, and can simply be processed as whole leaf fragments rather than being ground to a powder. Carbon and nitrogen isotope values varied at several spatial scales. The proportion of variability partitioned at different scales varied depending on the species of mangrove and element (C or N) analysed. To properly represent a geographic area, isotope analysis should be done on leaves collected at different locations and, especially, from different trees within locations. The autotrophic source(s) supporting food webs leading to fish production on mudflats might be either in situ microphytobenthos or material transported from adjacent habitats dominated by macrophytes. I tested the importance of these sources by measuring ?13C values of 22 fish species and six autotroph taxa (microphytobenthos on mudflats, and seagrass, seagrass epiphytic algae, mangroves, saltmarsh succulents and saltmarsh grass in adjacent habitats) in Moreton Bay. I calculated the distribution of feasible contributions of each autotroph to fishes. All fish ?13C values lay in the enriched half of the range for autotrophs. For over 90% of fishes, the top three contributing autotrophs were seagrass, epiphytes and saltmarsh grass, with median estimates of approximately 60-90% from these sources combined. Seagrass was typically ranked as the main contributor based on medians, while epiphytic algae stood out based on 75th percentile contributions. The other three sources, including MPB, were ranked in the top three contributors for only a single fish. Organic matter from seagrass meadows is clearly important at the base of food webs for fish on adjacent unvegetated mudflats, either through outwelling of particular organic matter or via a series of predator-prey interactions (trophic relay). Modelling results indicate that saltmarsh grass (Sporobolus) also had high contributions for many fish species, but this is probably a spurious result, reflecting the similarity in isotope values of this autotroph to seagrass. Carbon from adjacent habitats and not in situ microphytobenthos dominates the nutrition for this suite of 22 fishes caught over mudflats. The ultimate autotrophic sources supporting production of three commercially important fish species from Moreton Bay were re-examined by further analysing carbon and nitrogen stable isotope data. Mean isotope values over the whole estuary for fish and autotroph sources were again modelled to indicate feasible combinations of sources. Variability in isotope values among nine locations (separated by 3-10 km) was then used as a further test of the likelihood that sources were involved in fish nutrition. A positive spatial correlation between isotope values of a fish species and an autotroph indicates a substantial contribution from the autotroph. Spatial correlations were tested with a newly developed randomisation procedure using differences between fish and autotroph values at each location, based on carbon and nitrogen isotopes combined in two-dimensional space. Both whole estuary modelling and spatial analysis showed that seagrass, epiphytic algae and particulate organic matter in the water column, potentially including phytoplankton, are likely contributors to bream (Acanthopagrus australis) nutrition. However, spatial analysis also showed that mangroves were involved (up to 33% contribution), despite a very low contribution based on whole estuary modelling. Spatial analysis for sand whiting (Sillago ciliata) demonstrated the importance of two sources, mangroves and microalgae on the mudflats, considered unimportant based on whole estuary modelling. No spatial correlations were found between winter whiting (Sillago maculata) and autotrophs, either because fish moved among locations or relied on different autotrophs at different locations. Spatial correlations between consumer and source isotope values provide a useful analytical tool for identifying the role of autotrophs in foodwebs, and were used here to demonstrate that organic matter from adjacent habitats, and in some cases also in situ production of microalgae, were important to fish over mudflats. Whilst recognising that production from several habitats is implicated in the nutrition of fishes over mudflats in Moreton Bay, clearly the major source is from seagrass meadows. Organic matter deriving from seagrass itself and/or algae epiphytic on seagrass is the most important source at the base of fisheries food webs in Moreton Bay. The importance of seagrass and its epiphytic algae to production of fisheries species in Moreton Bay reinforces the need to conserve and protect seagrass meadows from adverse anthropogenic influences.
Thesis (Masters)
Master of Philosophy (MPhil)
School of Environmental and Applied Science
Full Text

The following four broad aims were addressed in this study. (1) To ascertain whether the characteristics of the benthic macroinvertebrate assemblages within the different nearshore marine habitat types identified by Valesini et al. (2003) on the lower west coast of Australia differ significantly, and whether the pattern of those spatial differences matches those among the environmental characteristics that were used to distinguish those habitat types; (2) To develop a quantitative approach for classifying nearshore habitats in estuarine waters that employs readily-available data for a range of enduring environmental characteristics, and to use that approach to classify the various habitat types present in nearshore waters of the Swan-Canning Estuary on the lower west coast of Australia; (3) To test the hypothesis that the characteristics of the benthic macroinvertebrate assemblages in the in the Swan-Canning Estuary differ significantly among nearshore habitat types, and that the pattern of those differences matches that among the environmental characteristics used to distinguish those habitat types and (4) To test the hypothesis that, as a result of environmental changes in the Swan-Canning Estuary, the characteristics of the benthic macroinvertebrate assemblages at various habitats in this estuary in 1986/7 differ from those in 2003/4. To address the first aim, benthic macroinvertebrates were sampled seasonally for one year in the subtidal waters and intertidal zone (upper and lower swash zones) at the six nearshore habitat types that were identified by Valesini et al. (2003) on the lower west coast of Australia. The habitat types, which differed mainly in the extent of their exposure to wave activity and whether seagrass and/or nearshore reefs were present, had been distinguished quantitatively using values for a suite of seven statistically-selected enduring environmental characteristics. The faunal samples yielded a total of 121 species representing eight phyla, among which the Polychaeta, Malacostraca and Bivalvia were the most speciose classes and contributed ~ 38, 23 and 10%, respectively, to the total number of individuals. The total number of species and mean density of macroinvertebrates was far greater at the most protected habitat type (1), which also contained dense beds of seagrass, than at any other habitat type, i.e. 70 species and 209.2 individuals 0.1 m-2, compared to 32 species and 36.9 individuals 0.1 m-2 at the most exposed habitat type (6), which had a substrate comprised only of sand. Differences among habitat type influenced the benthic macroinvertebrate species composition to a greater extent than differences among either zones or seasons. Significantly different faunal compositions were detected among those latter two factors only at the most protected habitat type. The faunal assemblage at habitat type 1 was clearly the most distinct from those at the other five habitat types, particularly in the subtidal zone (R-statistics=0.642-0.831, p=0.1%), and was typified by five abundant polychaete species that were adapted to deposit-feeding. In contrast, the fauna at habitat type 6 was typified by four crustacean species and a species of bivalve and polychaete, whose mobility and tough external surface facilitated their survival and feeding in those turbulent waters. The extents of the differences in species composition among the six habitat types was significantly matched with that among the suite of enduring environmental characteristics that distinguished those habitat types, particularly in the case of the subtidal zone (Rho=0.676). Such results indicated that the environmental variables used to distinguish the nearshore habitat types could be used to reliably predict the types of benthic macroinvertebrate species likely to occur at any site along the lower west coast of Australia. The above biological validation of the nearshore marine habitat classification scheme developed by Valesini et al. (2003) provided the justification for the approach to the second broad aim of this study, namely to develop a quantitative scheme for classifying habitat types in the Swan-Canning Estuary. This approach was similar to that employed by Valesini et al. (2003) in that it considers that differences among habitat types are well reflected by differences in a suite of enduring environmental variables. However, it improves on that earlier method by employing a completely objective and quantitative approach. Thus, a large number of environmentally-diverse nearshore sites (102) were initially selected throughout the Swan-Canning Estuary and a suite of 13 enduring environmental variables quantified at each using remotely-sensed images of the estuary in a Geographic Information System. Such variables were chosen to reflect either (i) the type of substrate and submerged vegetation present, (ii) the extent of exposure to wave action or (iii) the location of the site within the estuary with respect to its vicinity to marine and fresh water sources. These data were then subjected to the CLUSTER routine and associated SIMPROF procedure in the PRIMER v6 multivariate statistical package to quantitatively identify those groups of sites that did not differ significantly in their environmental characteristics, and thus represented habitat types. Eighteen habitat types were identified, which were shown to well reflect spatial differences in a suite of non-enduring water quality and sediment characteristics that were measured in situ at a range of estuarine sites during both summer and winter in 2005 (Rho=0.683 and 0.740, respectively, p=0.1%). However, those latter environmental characteristics required far more time in the field and laboratory to quantify than the enduring variables used to identify the habitat types. Benthic macroinvertebrates were sampled during summer and winter in 2005 in the shallow subtidal regions (~1 m depth) at sites representing eight of the habitat types identified in the Swan-Canning Estuary. These samples contained a total of 51 and 36 species during summer and winter, respectively, and, in both seasons, represented nine phyla, namely Annelida, Crustacea, Mollusca, Sipuncula, Nematoda, Platyhelminthes, Cnidaria, Uniramia and Nemertea. The compositions of the benthic macroinvertebrate assemblages differed significantly among habitat types and, to a similar extent, between seasons (Global R-statistic=0.408 and 0.409, respectively, p=0.1%). However, the spatial differences were considerable greater in winter than in summer (Global R-statistic=0.536 vs 0.280, p=0.1%), presumably due to the greater spatial variation in particular non-enduring in situ environmental characteristics, such as redox depth and salinity. While the number of species, overall density and taxonomic distinctness of benthic macroinvertebrates also differed significantly among habitats, those variables differed to a greater extent between seasons, being greater in winter than in summer. While the measures of taxonomic distinctness tended to be greater at habitat types located in the lower to middle reaches, i.e. habitat types 6, 7, 9, 10, 13 and 18, than the upper reaches i.e. habitat types 1 and 3, the number of species and overall density reflected this trend only during winter. During summer, the mean numbers of species at habitat types 1, 3, 6 and 10 (3.4-6.0) were significantly lower than those at habitat types 7, 13, and 18 (8.8-10.9), whereas the overall density of benthic macroinvertebrates was far greater at habitat type 7 (32260 individuals 0.1 m-2)than at any other habitat type in this season (3135-18552 individuals 0.1 m-2). Overall, the greatest differences in assemblage composition occurred between those at habitat types 1 and 18 (R-statistic=0.669, p=0.1%), which were located in the uppermost region of the estuary and the lower reaches of the basin, respectively, and differed to the greatest extent in their enduring environmental characteristics. The assemblage at habitat type 1, and also that at habitat type 3, located just downstream, were relatively distinct from those at all other habitat types, particularly during winter (R-statistics=0.666-0.993, p=0.1%). The fauna at the first of these habitat types was relatively depauperate, containing low numbers of species and densities, and was characterised by the polychaetes Leitoscoloplos normalis and Ceratonereis aequisetis and the bivalve Arthritica semen. The assemblage at habitat type 3 was also characterised by those three species and the amphipod Paracorophium minor and the polychaete Boccardiella limnicola. In contrast, the assemblage at habitat type 18 was characterised by a more diverse assemblage, i.e. the polychaetes Capitella capitata, C. aequisetis, L. normalis and Pseudopolydora kempi, the amphipods, Grandidierella propodentata and Corophium minor and the bivalve Sanguinolaria biradiata. The number of species was among the highest at this habitat type during both seasons, which was also reflected in the high taxonomic diversity, and the overall density was the highest in winter and second highest in summer. Despite the above faunal differences, those between assemblages at habitat types 7 and 9, which were both located in the basin of the Swan-Canning Estuary, were similar in magnitude to those that occurred between pairs of habitat types located in two different regions of the estuary. Although both habitat types 7 and 9 were characterised by a similar suite of species, i.e. Oligochaete spp., C. aequisetis, C. capitata, C. minor, G. propodentata, L. normalis, and S. biradiata, the substantial differences in assemblage composition between these habitat types in both summer and winter (R-statistics=0.570 and 0.725, respectively) was due to marked differences in the relative contributions of each of these species. Significant and strong correlations were shown to exist in both summer and winter between the pattern of differences in the benthic macroinvertebrate assemblages among habitat types and that among the enduring environmental characteristics used to identify those habitat types (Rho=0.625 and 0.825, respectively, p=0.1%). Furthermore, these correlations were greater than those obtained between the benthic macroinvertebrate fauna and any combination of the non-enduring environmental characteristics (i.e. water quality and sediment parameters) recorded in situ at each habitat type (Rho=0.508 and 0.824, in summer and winter, respectively, p=o.1%). This demonstrates the greater capacity of surrogate enduring environmental characteristics to account for differences in the range of variables that may influence the distribution of benthic invertebrate fauna. Thus, the lists of characteristic benthic macroinvertebrate taxa produced for each of the eight habitat types studied in the Swan-Canning Estuary provide a reliable benchmark by which to gauge any future changes in those fauna. Moreover, these results indicate that the above habitat classification scheme can be used to reliably predict the types of benthic macroinvertebrate fauna that are likely to occur at any nearshore site of interest in this estuarine system. The final component of this study showed that the benthic macroinvertebrate assemblages at four sites in the middle reaches of the Swan-Canning Estuary in 2003/4 differed significantly from those recorded at the same sites in 1986/7. Such differences were reflected in (1) changes in the relative densities of a suite of ten species that were responsible for distinguishing the faunas in these two periods, (2) the absence of 22 rare species in 2003/4 (i.e. 42% of the number of species recorded in 1986/7), (3) the presence of 17 new species in 2003/4, including an abundant polychaete that is likely to have been introduced and (4) a far greater extent of seasonal variation in the number of species and densities of benthic macroinvertebrates in 2003/4. Such changes are likely to be related to lower sediment oxygen levels in certain seasons in 2003/4, as well as an altered hydrological regime due to increased temperatures and decreased rainfall in that more recent period. The fact that these changes have occurred within the Swan-Canning Estuary highlights the need for effective management tools, such as the habitat classification scheme and associated faunal survey undertaken in this study. Such data will provide a sound basis by which to examine the ways in which fauna vary spatially within the system, and allow for the establishment of comprehensive benchmarks for detecting future changes.

Saltmarsh is an important coastal habitat located in the littoral zone of estuaries. Australian saltmarsh area is decreasing due to agricultural and urban development and invasion by mangrove. The aim of the study was to assess the contribution made by saltmarsh as a habitat and a source of food items for fish. Three saltmarsh sites were studied, with Towra Point chosen as a site for detailed ecological study. When corrected for water volume, fish densities were found to be higher within the saltmarsh compared to the adjacent mangrove. Although the fish assemblages in saltmarshes differed significantly from mangroves the overall ratio between commercially and ecologically valuable species in these habitats are similar, a result suggesting the importance of temperate saltmarsh as habitat for economically important fish. Significant export of crab larva from saltmarsh (average crab larval abundance 2124.63 m-3 outgoing water) is a positive contribution to the estuarine food chain supplementing the nutritional requirements of estuarine fish. While the diet of the crabs producing this larvae seems dependant on the saltmarsh environment (given the contrasting isotopic signatures of Sesarma erythrodactyla in saltmarsh and mangrove, and the similarity of isotopic signatures in the saltmarsh for Sesarma erythrodactyla and Helograpsus haswellianus), the crabs do not seem to be dependent on any of the common species of saltmarsh plant, but rather depend on particulate organic matter (POM) derived from local and other sources. Crab larva are a prey item for many estuarine fish, including commercially important species, as evidenced by gut content analysis of fish visiting the saltmarsh flats during spring tides. The results strongly suggest that emphasis be given to ecosystembased management for an estuary rather than component (e.g., vegetation) based managed as defined by the Fisheries Management Act (1994) and the State Environmental Planning Policy 14.

Includes bibliographies.
This thesis examines the utilization of rocky intertidal, sandy-beach surf-zone and estuarine habits by fishes on the southwestern Cape coast of South Africa. It has there central objectives: 1) to determine the species composition, abundance, size structure and seasonality of fish and to examine the extent to which they are influenced by environmental factors; 2) to describe the diets and patterns of feeding of the fish and to assess their impact on the food resources; and 3) to determine the importance of these habitats as nursery areas for juvenile fish.

Estuarine habitats along the temperate south-eastern shores of Australia are generally made up of salt marsh, mangrove forests and seagrass beds. In urban areas these habitats have been progressively fragmented as a result of population increase and industrial expansion. Salt marshes in particular have been vulnerable to urban expansion and reclamation because of their close proximity to densely populated areas, while mangrove forests have been less often reclaimed because of frequent tidal inundation. The effect of reclamation of salt marshes on the biotic assemblages and functioning of mangrove forests with an adjacent salt marsh, park or bund wall was examined at nine separate locations on the Parramatta River, Sydney NSW. A mensurative approach was used to describe the patterns of distribution and abundance of macro fauna at several temporal and spatial scales. The implications for management are that salt marshes are an integral part of estuaries, and smaller patches of salt marsh are just as important as larger patches in maintaining the diversity of faunal assemblages and ecosystem functioning in mangrove forests in urban areas
Master of Science (Hons)

Abstract: The primary data sources for this study were (1) 17 years of commercial fish catch data from over 30 selected estuarine fish species or species groups; and (2) estuarine habitat maps for Queensland, Australia. Queensland appears to be the best study region as it had the largest extent of soft sediment estuarine habitats, comprising seagrass, salt marsh and mangroves, and offers long-term commercial fish catch data compared to other states in Australia. As a first step, the relationship between catch (both as catch-per-unit-effort (CPUE) and total catch) for commercially caught species in their dominant fisheries (trawl, line, net or pot fisheries) and estuarine geomorphic spatial metrics were extracted from digital habitat maps in geographic information systems (GIS). For preliminary analyses, I examined 13 geographical regions in Queensland based on their importance to commercial fisheries. Spatial metric characteristics such as Euclidean distance, patch density and landscape connectivity for 273 estuaries along the Queensland coast were then calculated within 90 fish catch grids, which provided inshore fish catch data from 21 species groups. The collective spatial characteristics of estuarine habitats such as size and structural connectivity showed significant correlation with fish catch, with r2 values > 0.7 for 17 commercial species groups. More detailed multiple regression analysis and non-metric multidimensional scaling (nMDS) plots showed significant links between geomorphic coastal features such as structural connectivity and nearshore fisheries production. The relationship was best explained by connectivity indices for mangroves, salt marsh and channels, further suggesting the fundamental importance of connected tidal wetlands to the fish catch. Climate-driven dependencies of fish catch were explored by using CPUE, rainfall, coastal air temperature and the Southern Oscillation Index (SOI) and catch time-series for specific combinations of climate, seasons and regions. Surplus production models where applied to the commercial fish catch data using the program CLIMPROD. In addition to habitat configuration, climate, particularly rainfall, played a major role in the species composition of the fish catch. Up to 30 % of Queensland’s total fish catch and up to 80 % of the barramundi catch variation for specific regions were explained by rainfall, often with a time-lag response to rainfall events. Temperature had similar influences on fish and prawn catches, with high temperatures having a negative effect on the prawn catch in the Gulf of Carpentaria. The importance of estuary-scale habitat connectivity to fish populations was assessed by studying fish movement in relation to the extent of flooding for several commercially and recreationally important species in and out of a small mangrove creek using a stationary passive integrated transponder (PIT) system, augmented by underwater digital video recorders (DVRs) for visual sensing. A high-resolution digital elevation model derived from airborne light detection and ranging (LIDAR) and aerial imagery was used to estimate inundation pattern of intertidal habitats to compare with movement of PIT tagged fish. Investigations of fish movement at a detailed scale confirmed the broad-scale findings that habitat connectivity and close spatial proximity of resources are key factors for estuary-dependent fish species in tide-dominated systems to access different habitats. Access to habitat resources such as mangroves is more limited in time than previously thought and is dependent on fish species and size, thus suggesting importance of other adjoining habitats. Fish species and size also affected time of residency and diel pattern of habitat use. The analyses presented in this thesis also allow an evaluation of the economic consequences of climate parameters on estuarine fisheries. Species-specificity in climate-catch relationships suggested a strong need to develop forecast models and manage estuaries for future climate change by adjusting the quota for the more sensitive species. In addition, my findings on the role of estuarine habitat connectivity could guide the construction of a network of protected marine areas of various structural configurations that can optimise ecosystem services. The demonstrated value of habitat connectivity further warns against future reduction of connectivity by habitat destruction and climate change. The new techniques developed for assessing the spatial ecology of estuarine fish and their habitat utilisation and site fidelity behaviour will assist evaluation of the role of estuarine habitat inter-dependencies in supporting coastal fish populations. The fish catch data set used for fisheries management is valid for broad-scale investigations. However, it can be insufficient for managing certain stocks, e.g., fish targeted by recreational fishers. Data sets can be significantly improved by in-corporating locally collected recreational fish catch data, which can provide detailed information for particular river systems and allow better assessments of potential overfishing. The results of this study suggest that sound ecosystem-based fisheries management requires a diversity of information, an improved catch record system, a species-specific approach to managing the impact of climate change, and ecologically meaningful protection areas with high habitat connectivity.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment.
Science, Environment, Engineering and Technology
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Les estuaires sont constitués d'une vaste mosaïque d'habitats naturels et semi-naturels. L'objectif de cette thèse est d'étudier les végétations et les paysages végétaux des systèmes estuariens atlantique en France, en essayant de comprendre le fonctionnement et les schémas de distribution des différentes unités de végétation. La présente étude tente de mettre au point un modèle théorique commun de fonctionnement et de gradients écologiques, afin de compléter la classification et la connaissance écologique des estuaires, et une aide au suivi et à l’évaluation de l’utilisation des sols, des impacts humains, en développant un modèle spatio-temporel prédictif fondé sur la végétation réelle et potentielle, et en utilisant l'approche dynamico-caténale. Dans 8 estuaires sélectionnés, nous avons effectué des travaux sur le terrain pour une superficie totale de 98 318 ha, mettant en évidence 2 séries de végétation et 4 géopermaséries, correspondant à 131 associations végétales, 60 alliances, 43 ordres et 28 classes. Nous avons cartographié la végétation de trois estuaires représentatifs, ce qui représente une superficie totale de 74 433 ha. Un schéma synthétique des paysages végétaux estuariens est proposé, en intégrant les gradients géographiques et écologiques et les formes géomorphologiques
Estuaries generally include a wide mosaic of natural and semi-natural habitats. The objective of this thesis is to study the vegetation and Plant Landscape of French Atlantic estuarine Systems, trying to understand the functioning and the plant distribution patterns. The present study tries to carry out a theoretical common model of functioning and ecological gradients, in order to make a basis to improve their classification and ecological studies, and to Help the monitoring and assessment of land uses, land forms transformation and human impacts : developping a spatio-temporal predictive model based on actual and potential vegetation, using the dynamico-catenal approach.The study area corresponds to the Atlantic French estuaries. In 8 selected estuaries, we undertook fieldworks for a total of 98315 ha, highlighting 2 vegetation series and 4 geopermaseries, corresponding to 131 plant associations, 60 alliances, 43 ordos and 28 classes. We mapped the vegetation of three representative estuaries for a total of 74433 ha. A synthetic scheme of estuary vegetation landscape is proposed, integrating geographical and ecological gradients as well as geomorphologic forms

There is a paucity of published information on fish utilization of salt marshes outside North America. This dissertation represents the first intensive examination of the ichthyofauna associated with salt marshes in southern Africa and examines the species composition, diversity, size structure, distribution and estuarine dependence of fishes that utilize salt marshes in the Kariega Estuary. The research was concentrated on Taylor's salt marsh, with comparative studies being conducted on other salt marshes and habitats within the marine dominated Kariega Estuary. The possible importance of salt marshes as feeding and refuge areas for fishes was examined, as was the role of salt marshes in the food web of the estuary. The fishes frequenting salt marshes in the Kariega Estuary were predominantly the juveniles of marine species, with Mugilidae being the dominant family. The ichthyofauna was distributed primarily in the intertidal creeks with very few specimens captured on the vegetated Spartina maritima and Sarcocomia perennis flats. The different reaches of the intertidal creek were characterised by distinct fish assemblages. The fish assemblages associated with the intertidal salt marsh creeks were significantly different from those found in the eelgrass beds, the other dominant intertidal habitat in the Kariega Estuary. The eelgrass beds were dominated by estuarine fish species and had a higher density and standing stock of fishes when compared to the salt marsh creeks. The diversity of fishes in the two habitats was however similar. The intertidal salt marsh creek ichthyofauna also differed significantly from that found in the main estuary channel. The creek ichthyofauna was dominated by 0+ juveniles while the main channel had many subadult and adult fishes. The channel habitat also had numerous large piscivorous fishes which were absent from the salt marsh creeks. The low number of piscivorous fishes, together with limited fish predation from other sources, may be the reason why salt marshes provide a refuge for juvenile fishes that frequent these habitats. Unlike previous studies on North American, Australian and European salt marshes, the dominant fish species that frequented Taylor's marsh were not recorded feeding extensively on the marsh, and those that did had a limited distribution. The role of fishes in the transfer of energy off the Kariega salt marshes is therefore likely to be minimal. A stable carbon isotope study on the dominant primary producers and consumers within the Kariega Estuary revealed that detritus originating from the high lying salt marsh plants Sarcocornia perennis and Chenolea diffusa was not utilized by fishes in the Kariega Estuary. Preliminary results indicated that the cord grass Spartina maritima may be an important energy source to the fishes in the Kariega Estuary, but further research is needed to confirm this.

From an increasing awareness of the risks posed by climate change emerge the need to model potential impacts on coasts at a high spatial resolution, broad spatial scales, and time scales that correspond to the widely used IPCC sea-level rise scenarios. Little previous work has been carried out at this scale in the UK. This thesis investigates the potential of ‘reduced complexity’ models as a tool to represent mesoscale impacts of sea-level rise on UK estuarine environments. The starting point for this work is the Sea Level Affecting Marshes Model (SLAMM), which has been widely used in the USA. The SLAMM source code is first modified to accommodate the different tidal sedimentary environments and habitats found in the UK, and evaluated in a pilot study of the Newtown estuary, Isle of Wight. The modified SLAMM is then applied to the more complex environments of the Suffolk estuaries and the Norfolk barrier coast in order to evaluate its ability to produce meaningful projections of intertidal habitat change under the UKCP09 scenarios. Validation is also attempted against limited known historic changes, while a comparison of the SLAMM outputs to a GIS-based approach is also undertaken. Given sufficient sedimentation data, this approach produces robust projections in landform and habitat change at a whole estuary scale, with visually powerful outputs to convey possible future changes to stakeholders and policy makers. Although the nature of the SLAMM outputs is more sophisticated than the GIS-based approach, SLAMM is shown to have some limitations. The most serious of them lies in the empirical nature of the various sub-models of intertidal deposition and erosion. Whilst these can be calibrated to give meaningful results for saltmarsh, the lack of a robust formulation for tidal flats means that SLAMM is unable to resolve key landform and habitat transition in estuaries.

The nursery role hypothesis provides an approach for assessing the nursery function of habitat types within estuaries. This study attempted to assess the nursery value of the dominant estuarine habitats in the Bushmans Estuary for Rhabdosargus holubi (Steindachner 1881) by analysing habitat complexity, relative abundance and behaviour of R. holubi and using stomach contents analysis and dietary diatom composition as indicative of feeding habitat. Structural habitat complexity was assessed in Zostera capensis (Setchell) seagrass and Spartina maritima (Curtis Fernald) salt marsh by sampling above-ground stem density and length, and total cover per unit area (Ct/At). Dimensionless habitat complexity indices such as the interstitial spatial index (ISI) at three magnifications and fractal geometry at two magnifications were used to further analyse habitat complexity. Above-ground biomass (P<0.05) in each season and canopy height (P<0.001) were significantly higher in salt marsh than in seagrass whilst stem density was significantly higher in seagrass than in salt marsh in each season (P<0.001). Each dimensionless index indicated that complexity is notably higher in seagrass than in the salt marsh. Using dimensionless indices that analyse complexity at different spatial scales provided a better analysis of habitat complexity than canopy height and biomass as it allowed for direct comparisons between habitat types. Underwater video cameras were deployed in seagrass, salt marsh and sand flat habitats to assess the relative abundance and behaviour of R. holubi. The relative abundance of R. holubi was significantly higher in seagrass than salt marsh and sand flats, whilst the behaviour of R. holubi indicated a high degree of habitat use in structured habitats and a low degree of habitat use in unstructured sand flat habitats. This indicated that not only are juvenile R. holubi a vegetation-associated species, but also a species that prefers seagrass to salt marsh.

Dégradés par plusieurs siècles d’endiguement et menacés par les effets du changement climatique, les marais intertidaux européens font aujourd’hui l’objet d’un nombre croissant de restaurations par rétablissement des marées sur d’anciennes zones endiguées, suivant une tendance générale appelée dépoldérisation. Cette thèse décrit la trajectoire de restauration des marais intertidaux à partir des communautés de necton (i.e., poissons et crustacés décapodes), sur la base de deux sites dépoldérisés accidentellement dans l’estuaire de la Gironde : le marais de Mortagne et l’île Nouvelle. L’évolution du necton dans les marais dépoldérisés est caractérisée à travers une approche synchronique à l’échelle de la mosaïque des habitats estuariens. La composition du necton dans les marais dépoldérisés est en grande partie similaire à celles des milieux intertidaux naturels et se différencie nette-ment des marais endigués, où les espèces exotiques d’eau douce prospèrent. Les marais restaurés apparaissent particulièrement attractifs pour le mulet porc, Liza ramada. La distribution des traits fonctionnels au sein des communautés de poissons révèle un changement de structure fonctionnelle au cours de la dépoldérisation, le temps de restauration étant inféré à partir d’un gradient de naturalité des habitats estuariens. En particulier, la spécialisation, la dispersion et la richesse fonctionnelle augmentent au cours de la restauration. Concernant l’évolution des règles d’assemblage, aucune tendance claire ne se dégage : les patrons diffèrent selon les traits fonctionnels.La dynamique temporelle de la composition des communautés de necton dans l’un des sites dépoldérisés montre une succession de trois phases au cours des quatre années suivant la restauration. Un changement plus abrupt concernant l’abondance de certaines espèces et la structure fonctionnelle des communautés est identifié au milieude la seconde phase, moins de deux ans après la dépoldérisation. La cinétique de transformation des communautés est probablement ralentie par le drainage incomplet du site dans les premiers temps de la dépoldérisation. Les résultats de cette thèse permettent de mieux comprendre la trajectoire de restauration des marais intertidaux, sans intervention humaine, tout en soulignant les atouts et les limites de certains modèles théoriques utilisés en écologie de la restauration
European intertidal marshes have greatly declined during the past centuries because of land claim andhave recently been threatened by the effects of climate change. In recent years, an increasing number of tidal resto-ration projects have been implemented, following a global trend termed de-embankment. This thesis describes therestoration trajectory of tidally restored marshes from the response of nekton (i.e., fish and decapod crustaceans)based on two storm-breached study sites in the Gironde estuary : the Mortagne marsh and the Nouvelle island.Nekton assemblage composition of tidally restored marshes was described through a whole-estuary approach en-compassing natural, restored and dyked habitats. Nekton assemblages of tidally restored marshes showed highcompositional similarity with natural intertidal habitats and greatly departed from dyked marshes. Dyked marsheswere characterized by high occurrence of freshwater exotic taxa. Tidally restored marshes seemed particularly at-tractive for the thin-lipped grey mullet, Liza ramada. The functional traits’ distribution within fish communities revealeda change in functional structure in the course of restoration using the naturalness state of habitats as a proxy forrestoration time. Most notably, functional specialization, dispersion and richness increased with restoration time.No clear pattern of change was observed in community assembly over time ; trends chiefly varied with respect totraits. Temporal trends in one of the restored sites revealed three phases in the first four years of tide restoration.The abundance of several species and the community functional structure changed more steeply in the midst ofthe second phase, less than two years following tide restoration. Community turnover was probably delayed dueto incomplete drainage of the site in the early stages of restoration. The results of this thesis lead to a better un-derstanding of the restoration trajectory of tidal marshes without human intervention and highlight the strengths andweaknesses of some theoretical models used in restoration ecology

Les écosystèmes côtiers et estuariens sont extrêmement riches d’un point de vue biologique et écologique et abritent des habitats essentiels au maintien et au renouvellement des ressources marines d’intérêt halieutique. Parmi les altérations subies par ces écosystèmes, les proliférations de macroalgues opportunistes sont l’un des signes les plus visibles de l’eutrophisation dans plusieurs régions du monde, et particulièrement dans le nord-ouest de la France. Les processus à l’origine de ces proliférations sont relativement bien identifiés tandis que leurs conséquences écologiques - notamment sur l’ichtyofaune - restent mal connues et peu étudiées. L’objectif de cette thèse est de caractériser les effets des marées vertes sur la fonction d’habitat halieutique essentiel au renouvellement de l’ichtyofaune des zones côtières et estuariennes par une approche multi-échelleLes conséquences des marées vertes sur l’ichtyofaune ont tout d’abord été examinées à l’échelle de la communauté. Ensuite, les processus par lesquels cette perturbation affecte l’ichtyofaune ont été étudiés par une approche à l’échelle de l’individu. Cette étude s’est intéressée aux réponses des juvéniles à travers la sélection de l’habitat et la comparaison de leurs performances physiologiques entre un site contrôle et un site impacté. Au travers de ces deux approches, un impact négatif écologiquement significatif des marées vertes sur la qualité des habitats essentiels au renouvellement des ressources d’intérêt halieutique a été mis en évidence. Les conséquences des marées vertes sur l’ichtyofaune sont modul
Coastal and estuarine systems are highly productive areas that provide unique biological and ecological services and shelter essential habitats to numerous fisheries resources. Among the perturbations experienced by these ecosystems, proliferations of opportunistic macroalgae, commonly known as ‘green tides’, are one of the most obvious signs of eutrophication in coastal and estuarine areas, worldwide, and in Northwestern France in particular. The processes underlying macroalgal proliferations are almost identified whereas their ecological consequences - especially for ichthyofauna - remain poorly understood and understudied. The objective of this thesis is to characterise the effects of green tides on the role of coastal and estuarine habitats for ichthyofauna, on both the community and the individual scales.First, we investigated the consequences of green tides on ichthyofauna on the community scale. Then, we examined the processes which affect the ichthyofauna during green tides, on the individual scale. Marine juvenile fish responses were investigated based on habitat selection and comparison of individual performances between a control and an impacted site. Based on these two complementary approaches, we evidence ecological significant negative effects of green tides on the quality of essential fish habitats. The effects of green tides on ichthyofauna are modulated by the intensity and nature of macroalgal blooms, and are related to the fish habitat use and ecology. A decreasing gradient of sensibility to green tides is emphasised, from benthic to demersal and pelagi

Estuarine marshes are generally considered to be productive but not necessarily diverse ecosystems. During 24 consecutive months, I collected 65,000 fishes and decapods comprising over 65 species from the New Orleans Land Bridge, an estuarine salt marsh. My research details the distribution of nekton across five contiguous but geomorphically different regions, which I defined as “Areas”. This factor “Area” was significant in explaining community composition differences in 11 of the 24 months I evaluated. That is, during those 11 months community structure was different among the Areas. Specific “month” was also found to be a significant factor as community structure was found to differ among the months. No consistent abiotic factors were associated with community structure. These observations imply that a different set of factors are associated with community structure at the Area level than at the microhabitat level. Sampling of nekton in shallow estuarine salt marsh habitats was difficult. The cast net is a useful gear type for this type of sampling and can be readily standardized for each operator. Standardization of the area covered by the net allows density of collected nekton to be calculated. Little is known about the life cycle of one important estuarine dependent sport fish, tarpon (Megalops atlanticus), in southeastern Louisiana. This research details the presence of the major life stages of the species in Louisiana and suggests that it is capable of completing its life cycle in State waters. The presence of a spawning capable female and male tarpon is documented.

Understanding the geographic distribution of sea turtles within their sub-populations could enhance conservation and management, especially for sub-populations that are the most threatened. Isotope techniques have been used for this purpose and have become popular in the past decade, with an increasing year-to-year trend in published studies. Via systematic literature review of all studies using isotopes to understand sea turtle ecology, this thesis first presents a robust understanding of the current state of the science, identifying knowledge gaps and priorities for future sea turtle conservation research (Chapter 2). This identified that very few stable isotope studies aimed at understanding foraging distributions have been completed on threatened sub-populations of sea turtles, whereas those considered of least concern by the IUCN have been the focus of many. I aimed to address this mismatch between stable isotope studies and conservation needs by developing, validating, and applying a novel isotope technique to understand the foraging distribution of critically endangered South Pacific loggerhead turtles (Caretta caretta), and in doing so identifying critical habitats for priority management. The technique presented uses isotope ratios from commensal barnacle shells, which vary with temperature (SST) and salinity (SSS) rather than turtle diet. Barnacle shells are formed sequentially, storing chemical information about of the surrounding conditions at the time of formation. This makes it possible to assign a date to samples, and compare isotope ratios with the spatial and temporal distribution of sea water parameters (SST and SSS), if the growth of the animal is well understood. Thus, in this thesis I tested the applicability of using barnacles to understand sea turtle foraging distribution by quantifying barnacle growth rates (Chapter 3), regional relationships between barnacle isotopes (C and O) and SST & SSS (Chapter 5), and discriminating between foraging areas based on time dependent isoscapes for barnacle shell (Chapter 4, 5). Finally, the technique is applied to predict the home area of loggerhead turtles that nest in southern Queensland, Australia, identifying hotspots and relationships between nesting and foraging habitats (Chapter 6). This thesis demonstrates that isotopes from barnacle shells can be used to identify the origin and migration distances of host turtles at varying spatial scales, depending on water chemistry gradients present at the time and location of shell formation. In eastern Australia is it possible to assign turtles to home areas with >86% accuracy when areas are separated by at least 400 km (Chapter 4). Globally, many coastal areas are likely to offer similar or better resolution to this, while pelagic waters will typically offer lower resolution. This thesis also shows that estuarine habitats are important foraging habitats for adult loggerhead turtles, probably more so for southern foragers, while marine habitats are clearly important in northern Australia. Future research should focus on developing isoscapes for barnacle shell in other regions, and combining barnacle analyses with other methods to improve the achievable resolution. I also expect that this technique can be applied widely to other taxa and objects that carry commensal barnacles throughout marine journeys.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
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Le littoral du pays basque sur sa partie française n’a fait l’objet que de très peu d’études des communautés benthiques qu’il renferme. A l’exception des suivis mis en œuvre dans le cadre de la surveillance DCE des masses d’eau et de quelques études d’impact ponctuelles, les systèmes benthiques apparaissent peu investigués. Par ailleurs, du fait de sa sédentarité, ce compartiment biologique s’avère être un bon indicateur de suivi environnemental, intégrant les variations de l’environnement. L’étude de la macrofaune benthique permet en effet d’obtenir un signal relativement clair, susceptible de détecter une perturbation du système. Néanmoins, afin d’évaluer l’impact écologique d’une perturbation, il est nécessaire de distinguer la variabilité naturelle (intrinsèque au milieu) de celle liées à la perturbation elle-même (activités anthropiques).L’objectif majeur de ce travail de thèse a été l’étude de l’influence des conditions hydrodynamiques sur la structure, la répartition et la dynamique des communautés benthiques de substrat meuble du littoral basque français. Derrière cet objectif académique, cette étude, menée en entreprise, supportait également un profond besoin d’opérationnalité en répondant au déficit de connaissances locales.L’étude s’est appuyée sur un important effort d’échantillonnage. Quatre campagnes de prélèvements (une par saison) ont ainsi été répliquées pendant 2 ans au débouché de 3 estuaires du pays basque français, complétées par une année supplémentaire d’investigations sur l’Adour. Afin d’appréhender l’influence des facteurs abiotiques, les conditions hydrodynamiques ont été simulées à l’aide des modèles opérationnels développés dans le cadre du projet Européen LOREA.Les résultats indiquent une incidence prédominante des conditions hydrodynamiques (vagues et apports des fleuves), contrôlant la dynamique sédimentaire locale, sur la structure et la répartition des communautés benthiques côtières de substrat meuble. D’un point de vue temporel, une relative stabilité a été observée suggérant ainsi une certaine résilience de ces communautés face à une perturbation naturelle de leur milieu.L’exploitation des données biosédimentaires acquises au large de l’Adour, mises au regard du régime hydrologique du fleuve, des vagues et des opérations de clapage du port de Bayonne, confirme ces observations. En effet, bien qu’un effet des immersions puisse être observé, dans ce milieu à fort hydrodynamisme, les matériaux sont rapidement dispersés et la macrofaune récupère vite.Enfin, l’étude a permis de signaler pour la première fois au Sud du Golfe de Gascogne, dans le Pays Basque français, Grandidierella japonica (Stephensen, 1938), espèce d’amphipode de la famille des Aoridae native de la mer du Japon. L’étude préliminaire de son installation locale et des niches écologiques estuariennes impactées proposée dans la cadre ce travail nécessite encore d’être approfondie. Des données complémentaires, biologiques et environnementales, sont en effet nécessaires pour affiner et confirmer les résultats obtenus
Along the French Basque coast, soft-bottom communities are poorly described. Indeed, except for the monitoring program of water bodies carried out through the WFD and some isolated impact studies, benthic systems appear weakly investigated. However, macrobenthos are known to be an effective indicator to establish the ecological quality of coastal and estuarine waters. Due to their sedentary nature, benthic macrofauna integrates effects of environmental variations and provides a relatively clear signal, susceptible to detect a disturbance on the ecosystem. Nonetheless, to assess disturbance ecological impact, it is necessary to discriminate natural variability (intrinsic to the environment) from that related to anthropogenic activities.The main issue of this PhD is to investigate the hydrodynamic conditions effects on the structure, the distribution and the dynamic of the soft-bottom communities of the French Basque coast. Behind this academic objective, this study conducted in a private company also supported a deep operationality need in improving local knowledges.A substantial sampling effort was carried out during this study. Four biosedimentary field campaigns (one per season) were replicated for two years in the vicinity of the three main French Basque country estuaries, supplemented by another year of investigations at the Adour river mouth. In order to assess the influence of abiotic factors, the hydrodynamic conditions were simulated using the operational models developed in the framework of the European project LOREA.The results show a predominant influence of hydrodynamic conditions (wave and river inputs) controlling local sediment dynamics and thus the structure and distribution of benthic soft-bottom nearshore communities. In terms of temporal variation, a relative stability has been observed suggesting an ecological resilience from natural disturbances.The analysis of the biosedimentary data from the area located in the vicinity of the Adour river mouth in relation to river flow, wave climate and dredge spoil disposal activities of the Bayonne harbour corroborate these observations. Indeed, despite the fact that a dumping impact can be noticed within this high naturally exposed environment, dredged materials are rapidly dispersed and the macrofauna recovers quickly.Finally, through the study of the macrobenthic communities, the non-native amphipod Grandidierella japonica Stephensen, 1938 of the family Aoridae has been reported for the first time in the southern part of the Bay of Biscay, along the French Basque Country. The preliminary study of this species local installation and the estuarine impacted ecological niches still requires improvement. Complementary biological and environmental data are needed to improve and confirm the obtained results

Between 1988 and 2014, otter trawls, seine nets, and plankton nets were deployed along the salinity gradients of 18 estuaries by the University of South Florida and the Florida Fish and Wildlife Research Institute (FWRI, a research branch of the Florida Fish and Wildlife Conservation Commission). The purpose of these surveys was to document the responses of aquatic estuarine biota to variation in the quantity and quality of freshwater inflows that were being managed by the Southwest Florida Water Management District (SWFWMD). In the present analyses, four community types collected by these gears were compared with a diversity of habitat factors to identify the factors with the greatest influence on beta diversity, and also to identify the factors that were most influential to important prey species and economically important species. The four community types were (1) plankton-net invertebrates, (2) plankton-net ichthyoplankton, (3) seine nekton, and (4) trawl nekton. The habitat factors were (1) vertical profiles of salinity, dissolved oxygen, pH, and water temperature taken at the time of the biological collections, (2) various characterizations of local habitat associated with seine and trawl deployments, (3) chlorophyll a, color, and turbidity data obtained from the STORET database (US Environmental Protection Agency), and (4) data that characterize the effects of freshwater inflow on different estuarine zones, including factors for freshwater inflow, freshwater turnover time, and temporal instability in freshwater inflow (flashiness). Only 13 of the 18 estuaries had data that were comprehensive enough to allow habitat-factor analysis. An existing study had performed distance-based redundancy analysis (dbRDA) and principle component analysis (PCA) for these data within 78 estuarine survey zones that were composited together (i.e., regardless of estuary of origin). Based on that study’s findings, the communities of primarily spring-fed and primarily surface-fed estuaries were analyzed separately in the present study. Analysis was also performed with the habitat factors grouped into three categories (water management, restoration, and water quality) based on their ability to be directly modified by different management sectors. For an analysis of beta diversity interactions with habitat factors, dbRDA (called distance-based linear modeling (DistLM) in the PRIMER software) was performed using PRIMER 7 software (Quest Research Limited, Auckland, NZ). The dbRDA indicated pH, salinity, and distance to the Gulf of Mexico (distance-to-GOM) usually explained the most variation in the biotic data. These results were compared with partial dbRDA using the Akaike Information Criterion (AIC) as the model selection criterion with distance-to-GOM held as a covariate to reduce the effect of differences in the connectivity of marine-derived organisms to the different estuaries; distance-to-GOM explained between 8.46% and 32.4% of the variation in beta diversity. Even with the variation from distance-to-GOM removed, salinity was still selected as most influential factor, explaining up to an additional 23.7% of the variation in beta diversity. Factors associated with the water-management sector were most influential (primarily salinity), followed by factors associated with the restoration sector (primarily factors that describe shoreline type and bottom type). For the analysis of individual species, canonical analysis of principal coordinates (CAP) was performed to test for significant difference in community structure between groups of sites that represented high and low levels of each factor. For those communities that were significantly different, an indicator value (IndVal) was calculated for each species for high and low levels of each factor. Among species with significant IndVal for high or low levels of at least one factor, emphasis was given to important prey species (polychaetes, copepods, mysids, shrimps, bay anchovy juveniles, and gammaridean amphipods) and to species of economic importance, including adults, larvae and juveniles of commercial and recreational fishes, pink shrimp, and blue crab. Shrimps, copepods and mysids were all associated with estuarine zones that had low percentages of wooded or lawn-type shoreline, a factor that may serve as a proxy for flood conditions, as lawns or trees were usually only sampled with seines at high water elevations and in the freshwater reaches of the estuaries. Many copepod and shrimp species were strongly associated with high flushing times, which suggests that if flushing times were too short in an estuarine zone, then these species or their prey would be flushed out. Multiple regression analysis was performed on each of the selected indicator species, using AIC as a selection criterion and distance-to-GOM as a covariate. As might be expected, the apparent influences of different habitat factors varied from species to species, but there were some general patterns. For prey species in both spring-fed and surface-fed estuaries, pH and flushing time explained a significant amount of variation. In surface-fed estuaries, the presence of oysters on the bottom also had a positive effect for many prey species. For economically important species, depth was important in both spring-fed and surface-fed estuaries. This suggested the importance of maintaining large, shallow areas, particularly in surface-fed estuaries. Another important factor in spring-fed estuaries was the percent coverage of the bottom with sand; however, a mixture of positive and negative coefficients on this factor suggested the importance of substrate variety. In surface-fed estuaries, flashiness also often explained substantial variation for many economically important species, usually with positive coefficients, possibly due to the importance of alternation between nutrient-loading and high-primary-productivity periods. When comparing the three management sectors, the restoration sector was the most explanatory. Several factors were averaged over entire estuaries due to data scarcity or due to the nature of the factors themselves. Specifically, the STORET data for chlorophyll, color, and turbidity was inconsistently distributed with in the survey areas and was not collected at the same time as the biological samples. Moreover, certain water-management factors such as freshwater-inflow rate and flashiness are inherently less dimensional than other factors, and could only be represented by a single observation (i.e., no spatial variation) at any point in time. Due to concern that reduced spatiotemporal concurrence/dimensionality was masking the influence of habitat factors, the community analysis was repeated after representing each estuary with a single value for each habitat factor. We found that far fewer factors were selected in this analysis; salinity was only factor selected from the water-management factors. Overall, the factor that explained the most variation most often was the presence of emergent vegetation on the shoreline. This factor is a good proxy for urban development (more developed areas have lower levels of emergent vegetation on the shoreline). Unlike the previous analysis, the restoration sector overwhelmingly had the highest R2 values compared with other management sectors. In general, these results indicate the seeming importance of salinity in the previous analysis was likely because it had a higher resolution compared with many other factors, and that the lack of resolution homogeneity did influence the results. Of the habitat factors determined to be most influential with the analysis of communities and individual species (salinity, pH, emergent vegetation and lawn-and-trees shoreline types, oyster and sand bottom types, depth, flashiness, and flushing time) most were part of an estuarine gradient with high values at one end of the estuary with a gradual shift to low values at the other end. Since many of the analyzed species also showed a gradient distribution across the estuary, the abundance and community patterns could be explained by any of the habitat factors with that same gradient pattern. Therefore, there is a certain limitation to determining which factors are most influential in estuaries using this type of regression-based analysis. Three selected factors that do not have a strong estuarine gradient pattern are the sand bottom type, depth, and flashiness. In particular, flashiness has a single value for each estuary so it is incapable of following the estuarine gradient. This suggests that flashiness has an important process-based role that merits further investigation of its effect on estuarine species.

As the southern sea otter (Enhydra lutris nereis) range expands into northern and southern California, it will encounter estuaries that have been historically occupied by sea otters. Understanding how otters use re-colonized estuarine environments will inform how estuaries might be managed to encourage future sea otter range expansion. This project addressed the question: how do southern sea otters use space in the unique estuarine habitats of Elkhorn Slough? I compared the locations and behaviors of 25 individual sea otters of different status (male, female, and female with pup) among eelgrass, saltmud, saltmarsh, tidal creek, and main channel habitats in Elkhorn Slough. From these data I created a synoptic model to predict space use for resident otters of Elkhorn Slough based on sex, behavior, home range, and habitat distribution. Ninety percent home ranges calculated from the model indicated that females used larger home ranges than males in the slough, but both sexes had smaller home range areas than otters using the rocky outer-coast habitats of the Monterey Peninsula. In Elkhorn Slough, important habitats associated with resting included tidal creeks (for females only) and eelgrass, whereas the main channel was important for foraging behaviors of both sexes. Although using land habitats, sea otters were most likely to be found within 50 m of water. Protection of similar resting and foraging habitats in prey-rich estuaries colonized in the future will promote southern sea otters recovery by allowing them to re-colonize historically important estuarine habitats.

Intertidal wetland habitats in southeastern Australia have changed significantly during the past sixty years. Mangrove habitats have expanded both seawards and landwards, the latter being at the expense of saltmarsh habitats. This relatively common phenomenon is generally suggested to be an outcome of sea-level rise. Several factors potentially responsible for this change are examined, including changes in mean sealevel during the past 50 to 100 years, changes in climate, population growth, catchment landuse, and estuary type. A protocol for mapping estuarine habitats was developed and implemented, incorporating the application of geographic information systems. Spatial and temporal coastal wetland habitat changes at nine sites along the New South Wales coast are illustrated. These habitat dynamics were shown to not correlate between sites. The results demonstrate that sea-level rise in this region cannot solely account for the extent of change during the past sixty years. With the exception of one site (Careel Bay), there have been no correlations between contemporary mean sea-level rise and mangrove incursion of the saltmarsh habitats at the study sites, or with rainfall patterns, at the scale of observation in this study, which was largely decadal. The only correlations determined during this study have been between population growth and coastal wetland habitat dynamics in some sites. In spite of saltmarsh habitat loss being a regional phenomenon, local factors appear to have a profound bearing on the rates of change. Neither contemporary mean sea-level rise, rainfall patterns, estuary type, catchment landuse, catchment natural cover nor population pressure can account solely for the patterns in the spatial and temporal dynamics of the coastal wetlands of New South Wales. It seems apparent that regional factors create preconditions favourable for mangrove incursion, but that localised conditions have been responsible for the extent of these incursions from site to site. That is, despite higher sea-level and greater rainfall, the extent of change has been determined by the unique characteristics of each site. The results have important implications for current estuary management practices in the state of New South Wales. The lack of spatial and temporal trends in coastal wetland habitat dynamics point to the need for management to be conducted on a localised, rather than regional scale. Additionally, anthropogenic influences must be carefully managed, since the extent of mangrove habitat expansion into saltmarsh areas is unlikely to be a natural occurrence.

Dusky kob Argyrosomus japonicus is a wide-ranging estuarine-dependent Sciaenid and an important fishery species throughout most of its distribution. It is one of South Africa’s most valuable coastal fishery species. High levels of juvenile exploitation in estuaries and ineffective management regulations have led to stock collapse, highlighting the need to better understand the spatial and temporal aspects of estuarine-dependency and multiple habitat use. Habitat connectivity is a critical property of estuarine-associated fishes and it therefore follows that knowledge of this link is fundamental in understanding population dynamics and the nursery role of estuarine and/or marine habitats. While dusky kob occur in both estuaries and nearshore coastal zones, limited information on connectivity among these habitats exists. The aim of this study is to assess the role of estuarine nursery habitats in the life cycle of the dusky kob by examining multiple habitat connectivity and determining the drivers associated with estuarine use. A total of 96 dusky kob (237–1280 mm total length) were tagged with acoustic transmitters in both the estuarine and marine environments of Algoa Bay, Eastern Cape, South Africa between May 2008 and September 2010. Their movements were monitored using a network of automated data-logging acoustic receivers deployed in the Sundays Estuary, seven neighbouring estuarine habitats, two commercial harbours and various sites within Algoa Bay. And more...

Sharks are considered top predators in many marine ecosystems, and can play an important role in structuring those communities. As a result, it is necessary to understand the factors that influence their abundance and distribution. This is particularly important as fishery managers develop fishery management plans for sharks that identify areas that serve as essential fish habitat (EFH). This includes nursery habitat where sharks are born and juveniles spend the early part of their life. However, our understanding of shark habitat use in the northeast Florida waters is limited. The goal of this thesis was to characterize the abundance and distribution of sharks in northeast Florida estuaries, and to examine the effect of abiotic and biotic factors affecting shark habitat use. A bottom longline survey conducted from 2009 – 2011 indicated that 11 shark species use the estuarine waters of northeast Florida during summer months. Atlantic sharpnose (Rhizoprionodon terraenovae), blacktip (Carcharhinus limbatus), bonnethead (Sphyrna tiburo), and sandbar sharks (Carcharhinus plumbeus) were the most abundant species and made up 87.1% of the total catch. Month, bottom water temperature, and depth were the most important factors determining the presence and abundance of these species. This study also examined the role of prey abundance in determining the abundance of Atlantic sharpnose sharks. The probability of catching an Atlantic sharpnose shark, and the abundance of Atlantic sharpnose sharks, were most influenced by site. Neither potential prey abundance nor preferred prey abundance were not significant factors effecting Atlantic sharpnose abundance. This may be a result of prey sampling not providing an accurate measure of the true availability of prey resources. Other factors, such as predation risk, may better explain habitat use patterns of Atlantic sharpnose sharks. Continued sampling will give a better understanding of the factors influencing shark habitat use in this area.

En la presente tesis doctoral se aborda el estudio de las comunidades de peces presentes en las zonas someras litorales del Mar Menor. La comunidad objeto de estudio estuvo conformada principalmente por individuos en estado de postlarva e individuos juveniles, junto con los adultos de especies de talla pequeña.Los objetivos planteados fueron:A) Caracterización específica de la ictiofauna.B) Análisis de la biología poblacional y relaciones con el hábitat de especies de peces bentónicos.C) Análisis de las relaciones entre los tipos de hábitats litorales y la comunidad de peces.Los resultados obtenidos ponen de manifiesto la elevada importancia de las zonas someras litorales de la laguna como hábitats esenciales para la multitud de especies ícticas, tanto aquellas que poseen interés pesquero comercial (familias Atherinidae, Mugilidae y Sparidae) como aquellas que presentan interés conservacionista (familias Cyprinodontidae y Syngnathidae).
The present PhD thesis investigates the small-sized fish assemblages in the shallow littoral areas of the Mar Menor coastal lagoon. The study was focused on juveniles of migrant fish species that recruit into the lagoon and short-lived resident fish species that spend their entire lives in it.The objectives were:A) To characterize the fish assemblages.B) To examine population biology and habitat associations of benthic fish species.C) To analyse the relationship between littoral habitat types and fish assemblages.The results pointed out the importance of shallow littoral areas of the lagoon as essential habitats for many fish species, both juvenile fish species of commercial interest (Atherinidae, Mugilidae and Sparidae families) and threatened fish species (Cyprinodontidae and Syngnathidae families).

Intertidal wetland habitats in southeastern Australia have changed significantly during the past sixty years. Mangrove habitats have expanded both seawards and landwards, the latter being at the expense of saltmarsh habitats. This relatively common phenomenon is generally suggested to be an outcome of sea-level rise. Several factors potentially responsible for this change are examined, including changes in mean sealevel during the past 50 to 100 years, changes in climate, population growth, catchment landuse, and estuary type. A protocol for mapping estuarine habitats was developed and implemented, incorporating the application of geographic information systems. Spatial and temporal coastal wetland habitat changes at nine sites along the New South Wales coast are illustrated. These habitat dynamics were shown to not correlate between sites. The results demonstrate that sea-level rise in this region cannot solely account for the extent of change during the past sixty years. With the exception of one site (Careel Bay), there have been no correlations between contemporary mean sea-level rise and mangrove incursion of the saltmarsh habitats at the study sites, or with rainfall patterns, at the scale of observation in this study, which was largely decadal. The only correlations determined during this study have been between population growth and coastal wetland habitat dynamics in some sites. In spite of saltmarsh habitat loss being a regional phenomenon, local factors appear to have a profound bearing on the rates of change. Neither contemporary mean sea-level rise, rainfall patterns, estuary type, catchment landuse, catchment natural cover nor population pressure can account solely for the patterns in the spatial and temporal dynamics of the coastal wetlands of New South Wales. It seems apparent that regional factors create preconditions favourable for mangrove incursion, but that localised conditions have been responsible for the extent of these incursions from site to site. That is, despite higher sea-level and greater rainfall, the extent of change has been determined by the unique characteristics of each site. The results have important implications for current estuary management practices in the state of New South Wales. The lack of spatial and temporal trends in coastal wetland habitat dynamics point to the need for management to be conducted on a localised, rather than regional scale. Additionally, anthropogenic influences must be carefully managed, since the extent of mangrove habitat expansion into saltmarsh areas is unlikely to be a natural

Gill nets and longlines were compared as shark nursery sampling methodologies in inshore waters of Georgia to (1) assess differences in gear selectivity, bias, and stress of capture and (2) determine potential relationships between habitat features and shark distribution and abundance. Gear selectivity varied between gears as a function of both species and life stage resulting in significantly different estimates of species and life stage compositions. Juvenile bonnetheads (Sphyrna tiburo) and young of the year blacktip sharks (Carcharhinus limbatus) experienced significantly higher stress from gill net capture than longline. Major sources of bias are thought to result from dietary preferences and individual size. Juvenile sandbar shark (C. plumbeus) distribution revealed a potential preference for creeks rather than sounds, between 0.32-0.8km wide and 4.02-8.05km from the ocean. Adult Atlantic sharpnose sharks (Rhizoprionodon terraenovae) appear to prefer larger, open sound waters closer to the ocean. A potential preference for locations in close proximity to jetties over those near oyster reefs was also observed for adult Atlantic sharpnose sharks, and while statistical significance was observed, a stronger pattern may exist, as sample sizes in this study were relatively small yet still able to detect a difference. Future investigations that quantify proportions of habitat availability and shark abundance in a given area may be more useful for identifying preferences for the structures observed in this study. This study also provides strong evidence of finetooth shark (C. isodon) primary and potentially secondary nursery habitat in areas that had not yet been documented. Findings from these investigations can be useful for managers seeking to maintain healthy coastal shark populations.

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Capes
Public awareness regarding environmental issues has increased in recent decades. The increasing number of impact assessment studies, management and conservation plans, as well as ecological monitoring studies, demand new and more efficient techniques. We collected fishes and environmental variables in three zones (upper, middle and lower) of a tropical estuary during ebb tide. The aim was to test for differences in fish assemblages along a gradient from freshwater to marine waters and to detect effects of habitat loss in the marginal areas of the estuary. Analyses in the sediment (granulometry, organic matter, dissolved oxygen) and water (dissolved oxygen, temperature, salinity and pH) in samples with different levels of habitat loss. We identified three categories of habitats and correlated with parameters of fish assemblages (density, biomass, richness, length and trophic guilds). A total of 77 species were recorded, forming two distinct fish assemblages, with family Eleotridae dominating in the upper, Gerreidae, Gobiidae and Tetraodontidae in the middle and lower estuary. Changes in the structure of fish assemblages as a reduction in density, biomass and richness were associated with habitat loss of natural features (muddy sediment replaced by sandy sediment, organic matter reduction). Dormitatus maculatus in upper estuary and Atherinella brasiliensis in the middle and lower estuary were the species that showed preference for the impacted areas and can serve as indicators of habitat loss due to silting marginal.
Salvador (BA)

A habitat corridor is a landscape feature that is hypothesized to promote dispersal between habitat patches that would otherwise be isolated, and promote population persistence. Habitat corridors have not been widely explored in marine and estuarine systems. We used artificial seagrass units (ASUs) placed on unstructured sediment in Middle Marsh and Drum Shoals, Back and Bogue Sounds, North Carolina to create seagrass patches (1m2 and 4m2) separated by bare sediment or connected by additional ASUs, which made up a habitat corridor. We assessed the interactive effects of habitat corridor (presence or absence) and interpatch distance (5m or 10m), as well as the ratio of corridor width to patch width upon dispersal of grass shrimp, Palaemonetes sp., and bay scallops, Argopecten irradians in seagrass. We conducted mark-recapture experiments where marked grass shrimp or bay scallops were placed in one patch from each treatment (donor patch). Regardless of the presence of a habitat corridor, interpatch distance, or ratio of corridor width to patch width, dispersal between seagrass patches for grass shrimp and bay scallops did not significantly vary. There was, however, a significant site effect with the number of scallops successfully dispersing between seagrass patches significantly higher at Drum Shoals than at Middle Marsh. The small spatial scales of this study and the perception of a homogeneous environment may explain the lack of a dispersal response by grass shrimp. Site-specific differences in bay scallop dispersal may have been due to varying flow at the two study sites. Tethering experiments were conducted concurrently with dispersal experiments to assess the interactive effects of habitat corridor and interpatch distance, as well as perimeter to area ratio, on predation-induced mortality of bay scallops. Habitat corridor, interpatch distance or perimeter to area ratio did not significantly influence predation-induced mortality of scallops; however, there was a significant site by interpatch distance interaction. Predation rates were greater in patches separated by 10m at Middle Marsh than at Drum Shoals, whereas predation was greater in patches separated by 5m at Drum Shoals than at Middle Marsh. The lack of predation response to habitat corridors may have been due to a prey refuge in size (the scallops used in this study were relatively large, 35mm-50mm), or relatively low replication (N = 5) or another biotic or environmental factor not measured during this study. Colonization experiments were conducted to assess the interactive effects of habitat corridor and interpatch distance upon the colonization of estuarine macrofauna in seagrass. Neither mean density nor species diversity of estuarine macrofauna, nor mean density of individual taxonomic groups was significantly influenced by the presence of habitat corridors or by interpatch distance. Mean densities of slow-, intermediate-, and rapid-level dispersers were also not significantly influenced by the presence of habitat corridors or interpatch distance. The lack of community-level response may be explained by the interaction of hydrodynamics and its influence on the perception of a homogeneous or heterogeneous environment by dispersing organisms. Although habitat corridors may promote animal movement between habitat patches in terrestrial systems and for certain marine predators, the results from the present study do not confirm that habitat corridors are used by estuarine macrofauna for dispersal or colonization at relatively small spatial (10s of m) and temporal (hours to one month) scales. The coupled effects of hydrodynamics and habitat use should be considered when investigating distribution and abundance patterns of organisms with different dispersal abilities.

Durant les premières années de leur vie, les juvéniles de nombreuses espèces de poissons plats, et en particulier la sole commune et la plie, fréquentent des zones de nourricerie côtières et estuariennes. Une fois leur maturité sexuelle atteinte, ils rejoignent l’aire de vie plus étendue des adultes, située sur le plateau continental et participent à la reproduction. L’emprise spatiale de ces nourriceries, très localisées, dépend notamment des apports en eau douce qui favorisent l’extension de la nourricerie vers le large et conduisent à un recrutement supérieur. Le lien entre les sources de matière organique, les populations invertébrés benthiques et les juvéniles de poissons plats étant complexe et mal connu dans ces milieux, il a été choisi d’étudier les relations trophiques et spatiales entre ces compartiments dans deux nourriceries différentes : l’estuaire de la Vilaine et la baie du Mont-Saint-Michel. La première partie de ce travail s’est attachée à décrire le réseau trophique benthique des juvéniles de poissons plats via l’analyse des isotopes stables (carbonne et azote) et des contenus digestifs. L’analyse spatio-temporelle de la signature isotopique du carbone des juvéniles de sole dans l’estuaire de la vilaine a indiqué une incorporation, variable selon le débit fluvial, de la matière organique d’origine terrigène dans le réseau trophique benthique. La baie du Mont-Saint-Michel, qui ne bénéficie pas d’autant d’apports en eau douce que les sytèmes purement estuariens, abrite une importante nourricerie pur les juvéniles de sole et de plie. Dans cette dernièe la production microphytobenthique issue des larges vasières intertidales (source autochtone de matière organique) a largement contribué au fonctionnement du réseau trophique des juvéniles de poissons plats
For a large proportion of flatfish species, and especially common sole and plaice, juveniles grow in restricted coastal and estuarine nursery grounds during their first years of life. Once their sexual maturity reached, they move to more extended adults habitat located on the continental shelf and contribute to the reproduction. Nursery grounds area depends on freshwater inputs which enhance the juvenile distribution to the open sea and the recruitment. The link between organic matter sources, benthic invertebrates populations that constitute their food supply and flatfish juveniles is complex and remains poorly known. Trophic and spatial interactions between these components have thus been investigated in two contrasted nursery grounds : the Vilaine estuary and the Mont-Saint-Michel bay. The first part of this project aimed to describe flatfish juveniles benthic food web using stable isotopes and gut contents analyses. Carbon stable isotope signatures in common sole juvenile in the vilaine estuary showed the incorporation of terrigenous organic matter into their benthic food wed. Furthermore, this assimilation varied according to Vilaine river flow. Conversely, the Mont-Saint-Michel bay receives little freshwater inputs, but supports an important nursery ground for plaice and common sole. In this nursery ground, microphytobenthos produced on the wide intertidal mudflats mainly contributed to flatfish juveniles food web. Combined utilisation of bot stable isotopes and gut contents analyses thus improved coastal and estuarine nursery grounds description : these analyses particularly pointed out the terrigeneous organic matter role and benthic diatoms production in the flatfish nursery grounds trophic functioning and the spatio-temporal variability of the respective influence of these two sources

The common snook, Centropomus undecimalis, is an estuarine dependent sport fish that relies upon subtidal wetlands as nursery habitat. Despite the economic and recreational significance of this species, there are portions of its life history and biology that are poorly understood, particularly its early life history. Understanding juvenile snook use of wetland habitats is crucial given the rapid loss and degradation of these areas to anthropogenic impacts. Young-of-the-year snook were collected in pond and creek habitats of a single wetland system to assess early life ecology and habitat use. Proxies of habitat quality were used to determine which habitats within a small spatial scale were optimal for young-of-the-year snook recruitment. Results indicated that even on a very small spatial scale, differences in habitat use were apparent, whereby smaller snook initially recruited to pond habitats and dedicated all energy into growth. Upon reaching a size of at least 40 mm SL snook began an ontogenetic habitat shift and moved to the tidal creek habitat. There, snook began to store energy, thus becoming more robust. Stable carbon and nitrogen isotopic analyses confirmed the ontogenetic habitat shift and revealed that snook have high site fidelity within the pond and creek habitats. Stable isotopic analysis also indicated that YOY snook appear to feed at the third trophic level consuming neonatal poecilliids and shrimp, and ultimately rely on benthic microalgae and particulate organic matter as basal resources. Results of this study advance the knowledge of juvenile snook ecology and will likely have implications for resource managers who are responsible for preserving and restoring wetland habitats upon which juvenile snook rely.

Orientador : Henry Louis Spach
Coorientador : Alberto Teodorico Correia
Dissertação (mestrado) - Universidade Federal do Paraná, Setor de Ciências Biológicas, Programa de Pós-Graduação em Ecologia e Conservação. Defesa: Curitiba, 25/10/2016
Inclui referências : f. 35-42
Resumo: O robalo-peva (Centropomus parallelus) é uma espécie importante para a pesca comercial e recreativa no Brasil. Um estudo recente demonstrou que os juvenis desta espécie conseguem habitar ambientes de salinidade distinta ao longo do seu ciclo de vida. Contudo, uma vez que o conhecimento dos padrões migratórios e utilização do habitat por indivíduos são fundamentais na tomada de medidas adequadas para a conservação e manejo de uma espécie, é importante determinar se os indivíduos adultos desta espécie, sujeitos à exploração pesqueira, apresentam a mesma plasticidade ambiental. Nesse sentido, noventa adultos de robalo-peva foram coletados entre outubro de 2015 e março 2016 por meio da pesca por arpão e anzol no Complexo Estuarino de Paranaguá, Estado do Paraná, sul do Brasil. Três pontos de amostragem foram selecionados de acordo com um gradiente de salinidade conhecido: rio Cachoeira (ambiente oligohalino), rio Faisqueira (ambiente mesohalino) e Ponta do Poço (ambiente polialino). Os padrões de movimento foram inferidos a partir das concentrações de Sr:Ca e Ba:Ca obtidas ao longo do raio dos otólitos com o auxílio de uma microssonda de elétrons. A idade dos indivíduos foi estimada a partir da leitura dos anéis de crescimento anuais dos otólitos. Os dados sugerem oito diferentes padrões migratórios que mostram uma elevada plasticidade e adaptação ambiental a gradientes de salinidade distintos. Além disso, os dados também mostram que a maioria dos padrões migratórios incluem estuários como área de ocupação, isso evidencia a importância deste ambiente para a espécie, provavelmente devido à maior disponibilidade de alimentos e menor predação. Portanto a conservação desta espécie exige a preservação de ambientes de água doce e marinhos mas, principalmente, dos estuários, permitindo, desta forma, a conectividade entre habitats. Palavras-chave: Centropomidae; microquímica de otólitos; conectividade entre habitats; gradiente de salinidade; conservação e manejo de recursos pesqueiros
Abstract: The fat snook (Centropomus parallelus) is a species of importance to the commercial and recreational fisheries in Brazil. A recent study demonstrated that the early juveniles of this species can live in differently salinity environments throughout their lifecycle. Understanding of migratory patterns and habitat use by individuals are essential in the context of taking appropriate measures for the conservation and rational management of a species. Thus, it must be determined if the adults of this species, commercially exploited, have the same observed environmental plasticity. With this purpose ninety C. parallelus adults were collected between October 2015 and March 2016 using hook and spear fishing in Paranaguá Estuarine Complex, State of Paraná, South of Brazil. Three sampling sites were selected according to a known salinity gradient: Cachoeira River (oligohaline environment), Faisqueira River (mesohaline environment) and Ponta do Poço (polyhaline environment). The movement patterns were inferred from Sr:Ca and Ba:Ca concentrations recorded along the otoliths radius using a electron micro probe analyzer. The age of the individuals was estimated from the reading of the annual growth rings of otoliths. The data suggest eight different migration patterns that show a high plasticity and environmental adaptation to different salinity gradients. Furthermore, the data also show that almost migratory patterns include estuaries as an occupation area, suggesting the importance of these areas for the species, presumably due to the availability of food and lower predation pressure. Therefore the conservation of this species requires the preservation of freshwater and marine environments, but mainly estuaries, which allows the connectivity between habitats. Keywords: Centropomidae; otoliths microchemistry; habitat connectivity; salinity gradient; conservation and rational management

This study assessed the importance of overwash and breaching events on the ichthyofaunal community structure in the medium-sized temporarily open/closed Mpekweni Estuary located on the southeast coastline of southern Africa. The fish in the littoral zone of the estuary were sampled using a 5m seine net while the channel region was sampled using two nets, a smaller meshed 30m seine net to target the estuarine spawning species and the juvenile estuarine-dependant marine spawners, and a larger meshed 50m seine net to target the larger marine and freshwater spawning species. Intensive monthly sampling over two years provided data on selected physico-chemical and biological parameters. During the two year sampling period from November 2005 to October 2007 the estuary breached in late July 2006 and remained open till the sandbar re-formed across the mouth in late December 2006. Thus, sampling encompassed three open/closed phases 1) initial closed period, 2) open period and 3) re-closed period after the berm was re-formed. The open period was divided into two phases 1) the out-flow phase and 2) the tidal phase. A total of 36 fish species representing 19 families were sampled using the various seine nets employed during the investigation. In the littoral zone, the estuarine spawners (Estuarine Utilisation Category, [EUC] I), mainly the Gobiidae, Glossogobius callidus, dominated the samples numerically and by biomass. The smaller estuarine spawning species sampled in the channel were numerically dominated by Gilchristella aestuaria in conjunction with two other EUC I species, Atherina breviceps and G. callidus. The estuarine-dependant marine spawners (EUC II), however, dominated the ichthyofaunal biomass of the channel. The abundance and biomass of the larger species targeted were dominated by estuarine-dependant marine spawning species (EUC II), principally Rhabdosargus holubi. During the closed periods of the estuary, total fish abundance and biomass displayed weak seasonal patterns. The breaching event and subsequent open period was associated with a decrease in the total abundances of fish in the littoral zone and channel of the estuary, reflecting the out-flow of estuarine biomass-rich water into the marine environment. The breaching event coincided with a shift in the community composition of the ichthyofauna, reflecting the recruitment of marine spawning species into the estuary. Numerical analysis identified two distinct spatial fish communities within the estuary, a community associated with the mouth region and one comprising the rest of the estuary. The absence of any further spatial patterns in the ichthyofaunal community structure within the Mpekweni Estuary appear to be ascribed to the virtual absence of horizontal patterns in physico-chemical and biological parameters recorded in the system. Cohort analyses were employed to determine possible recruitment events for selected estuarine and marine spawning species. The estuarine spawning species displayed continuous recruitment patterns throughout the study, which appeared to be unaffected by the breaching event. Conversely, the larger marine spawning species displayed multiple cohorts, indicating non-continuous recruitment. Subsequent retrospective analysis of cohorts for the different species identified summer recruitment peaks that coincided with the breaching event and open period. Minor recruitment of marine spawning species also occurred during overwash events. The recruitment of ichthyofauna into the estuary was quantified during three distinct hydrological events: overwash, out-flow phase immediately after breaching and tidal phase during the period when the mouth was open. Estimates of fish recruitment were highest during the outflow phase immediately after the estuary breached and declined as the estuary became tidally inundated with marine water. Although not as high as the outflow and tidal phases, recruitment was evident during overwash events. Results of the current study highlight the importance of both breaching and overwashing events in structuring the ichthyofaunal community composition in a medium-sized southern African temporarily open/closed estuary. These results are broadly in agreement with similar studies conducted both locally and in other regions of the world.

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CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
A modelagem pode ser utilizada para determinar a distribuição de uma determinada espécie em uma área. Deste modo, pode auxiliar na conservação de espécies ameaçadas. Neste estudo, modelos foram utilizados para avaliar a influência do habitat, do tipo de presas capturadas por pescadores artesanais e do Valo Grande sobre a presença do boto-cinza na região do Complexo Estuarino Lagunar de Cananéia. Os dados foram coletados entre janeiro de 2012 a novembro de 2014, durante três 3 saídas de campo por estação do ano. Estas saídas de campo foram realizadas em quatro setores pré-definidos, que foram percorridos em transecções lineares. O setor II foi o de maior ocorrência de botos, provavelmente pela proximidade com o oceano adjacente. A distribuição entre os setores foi mais homogênea nas estações mais frias, onde os valores das variáveis ambientais são mais estáveis. Os maiores agrupamentos de animais também foram encontrados no inverno. Os botos foram avistados em diversos valores das variáveis ambientais analisadas. No entanto, as maiores ocorrências foram registradas em águas mais turvas; profundidades maiores que 10 metros; salinidade acima de 10 ppm; e águas mais frias e nas marés de sizígias. A presença do cerco-fixo no estuário também influenciou positivamente a ocorrência dos botos, que utilizam essa armadilha de pesca como barreira, minimizando a fuga das suas presas. A tainha foi a categoria de peixe que teve a maior associação com a presença dos botos, seguida pela guaivira e prejereba. Já o parati e o camarão estuarino apresentaram uma influência negativa com a presença do boto. O modelo preditivo do Valo Grande mostrou que a descarga de água doce influencia de maneira negativa na presença dos botos. Pelo exposto, fica claro que os botos-cinza apresentaram uma distribuição heterogênea dentro do estuário estudado e as áreas de maior concentração merecem maior atenção na elaboração de estratégias de conservação.
Niche modelling can be used to determine the distribution of a particular species in an enviromental space (ecological niche). It may be important to help to preserve endangered species. Therefore, in this study, niche modelling was used to evaluate the influence of: the habitat; the artisanal fishermen‟s catch species; and the Valo Grande on the presence of the Guiana dolphins (Sotalia guianensis) in the Estuarine Lagunar Complex of Cananéia, Brazil. The data were collected in three fieldworks per season, from January 2012 to November 2014. The fieldworks took place in four predefinied sectors. These sectors were sampled using a line-transect method. The presence of the Guiana dolphin was observed mostly on sector II. Probably because of the proximity to the adjacent ocean. The distribution among sectors was more homogeneous in the short cool season, when the environmental variables are more stable. The larger dolphin clusters were found during the winter. Guiana dolphins were sighted in a great diversity of environmental conditions. Nonetheless, the highest occurrences were recorded in cooler and turbid waters; depths greater than 10 meters; salinity above 10 ppm; and during spring tides (technically known in Portuguese as 'maré de sizígia'). Furthermore, the presence of an artisanal fish trap, known locally as cerco-fixo, has positively influenced the occurrence of Guiana dolphins in the estuary. The dolphins use cerco-fixo fish traps to corner shoals and reduce the escape routes of their prey. The mullet (Mugil brasiliensis) was the fish species which had the highest positive correlation with the presence of dolphins, followed by the leatherjacket (Oligoplites saurus) and the tripletail (Lobotes surinamensis). On the other hand, the white mullet (Mugil curema) and the whiteleg shrimp (Litopenaeus vannamei) had a negative correlation with the presence of the Guiana dolphin. The data collected on the Valo Grande Channel showed that freshwater discharges decrease the presence of Guiana dolphins. We can conclude that the Guiana dolphins have an heterogeneous distribution within the studied estuary. Therefore, the areas of greatest ocurrence deserve greater attention in the development of preservation strategies.

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Capes, Cnpq, Fapesb
Ambientes entremarés estuarinos são reconhecidos por seu grande valor ecológico e econômico. Nestes ambientes, muitas comunidades humanas utilizam os recursos naturais (e.g. mariscos, peixes) como principal fonte de renda e para própria alimentação. Nestes sistemas, assembleias macrobentônicas apresentam grande variação em sua distribuição espacial, devido à (i) variação de fatores ambientais como frações do sedimento, salinidade, matéria orgânica, declividade, e (ii) à variação de fatores biológicos, como processos de facilitação do assentamento de larvas, competição ou predação. Muitos estudos foram realizados em ambientes entremarés de estuários, entre esses, alguns foram realizados no gradiente entremarés (do corpo d’água em direção ao continente) e outros no gradiente estuarino ou longitudinal de salinidade (de regiões de água doce em direção ao mar). Estudos que buscam a descrição de padrões de zonação da macrofauna nos ambientes entremarés (i.e. no gradiente entremarés) são mais abundantes na literatura científica, especialmente em zonas temperadas. Estudos realizados em gradientes estuarinos, também mais comuns em zonas temperadas, sugeriram que a salinidade e as características do sedimento são os fatores que mais influenciam a estrutura das assembleias macrobentônicas. Contudo, estudos que abordam esses gradientes em ambientes entremarés tropicais são escassos. O objetivo do presente trabalho foi (i) caracterizar os padrões espaciais das assembleias macrobentônicas de habitats entremarés ao longo do gradiente estuarino dos principais tributários da Baía de Todos-os-Santos e, (ii) relacionar tais padrões com salinidade, CaCO3, matéria orgânica e frações sedimentares. Os rios Jaguaripe, Paraguaçu e Subaé foram amostrados ao longo do gradiente de salinidade, em 10 estações, com exceção do Subaé, no qual foram dispostas 11 estações. Em cada estação, foram coletadas amostras do sedimento, para determinação da granulometria e dos percentuais de CaCO3 e de matéria orgânica, e da macrofauna. Foram mensuradas a salinidade do corpo d’água e a salinidade intersticial do sedimento dos habitats entremarés. Os resultados apresentaram um padrão similar de estrutura e composição das assembleias macrobentônicas nos três estuários estudados, onde a salinidade foi a variável mais importante. Foi observado um padrão contínuo de assembleias ao longo do gradiente, cujos limites das distintas assembleias são de difícil determinação (i.e. seriação). Adicionalmente, foi observado que a riqueza de táxons ao longo dos gradiente geralmente decresceram em regiões dos estuários com maior aporte de água doce, concordando com alguns estudos pretéritos. Este foi o primeiro estudo que abordou a escala de gradiente estuarino em habitats entremarés tropicais com réplicas em três sistemas. São recomendados estudos futuros que contemplem uma variedade de escalas espaciais, com abordagem hierárquica, considerando o gradiente estuarino e o gradiente entremarés, bem como estudos manipulativos que avaliem o efeito de interações biológicas na estrutura e composição das assembleias estuarinas.
Spatial variation in the structure of macrobenthic assemblages on intertidal flats in temperate estuaries are known to be related to environmental factors such as salinity, sediment characteristics and topography. However, little attention has been given to the effect of the estuarine gradient in macrobenthic assemblages on tropical systems. This paper investigated the relationship between the spatial pattern of macrobenthic assemblages in intertidal habitats and the environmental variables in three tropical estuaries. The Jaguaripe, Paraguaçu and Subaé estuaries were sampled from march 2011 to march 2012. Data collection of macrofauna, salinity, sediment characteristics and organic matter content were obtained in the three estuarine gradient. The results showed a similar taxa replacement pattern along the estuarine gradients. Salinity was the main variable responsible for the structure of the benthic assemblages. There was a decrease of the number of taxa from the upper to low estuarine areas, similar to other studies at temperate and tropical zones. Future studies in tropical areas should consider hierarchical sampling schemes together with 14 functional approaches to strengthen knowledge about the functioning of intertidal estuarine environments.
Salvador

The ichthyofaunal community structure, population dynamics and movement patterns in the small temporarily open/closed (TOCE) Grant’s Valley estuary, situated along the Eastern Cape coastline, were investigated over the period May 2004 to April 2005. Community structure in the littoral zone was assessed, while growth of selected ichthyofaunal species was investigated using the MULTIFAN model. Population size was assessed using mark recapture models and movement within the estuary using the Hilborn (1990) model. Total ichthyofaunal densities and biomass within the littoral zone ranged between 0.31 to 21.45 fish m⁻² and 0.20 to 4.67 g wwt m⁻², with the highest values typically recorded during the summer. Results of the study indicated that the ichthyofaunal community structure within the estuary was closely linked to the mouth phase and the establishment of a link to the marine environment via overtopping events. In the absence of any link to the sea, the ichthyofaunal community was numerically dominated by estuarine resident species, mainly Gilchristella aestuaria and to a lesser extent, by the river goby, Glossogobius callidus which collectively comprised ca. 88% of all fish sampled. The establishment of the link to the marine environment contributed to an increased contribution of marine breeding species (e.g. Rhabdosargus holubi, Myxus capensis and Atherina breviceps) to the total ichthyofaunal abundances. In contrast, total ichthyofaunal biomass was almost always dominated by marine breeding species by virtue of their larger sizes. Results of hierarchical cluster analyses did not identify any spatial patterns in the ichthyofaunal community within the littoral zone. Results of MULTIFAN analysis indicated estuarine resident fish species bred over an extended period with peaks occurring in the summer months. Conversely, marine breeding fish were shown to recruit into the estuary following overtopping and breaching events. Results of the mark-recapture experiment indicated a population of ca. 12 000 (11 219 – 13 311) individuals greater than 50mm SL. Marine-breeding species (R. holubi, Monodactylus falciformis, and two mullet species) numerically dominated the ichthyofauna, possibly as a result of their effective use of overtopping events. The two mullet species, M. capensis and Liza richardsonii, and the Cape stumpnose, R. holubi moved extensively throughout the estuary, while the remaining species exhibited restricted movement patterns possibly due to the preference for refuge and foraging areas associated with reed beds. The observed movement patterns of individual fish species appeared to be associated with both foraging behaviour and habitat selection.

The following four broad aims were addressed in this study. (1) To ascertain whether the characteristics of the benthic macroinvertebrate assemblages within the different nearshore marine habitat types identified by Valesini et al. (2003) on the lower west coast of Australia differ significantly, and whether the pattern of those spatial differences matches those among the environmental characteristics that were used to distinguish those habitat types; (2) To develop a quantitative approach for classifying nearshore habitats in estuarine waters that employs readily-available data for a range of enduring environmental characteristics, and to use that approach to classify the various habitat types present in nearshore waters of the Swan-Canning Estuary on the lower west coast of Australia; (3) To test the hypothesis that the characteristics of the benthic macroinvertebrate assemblages in the in the Swan-Canning Estuary differ significantly among nearshore habitat types, and that the pattern of those differences matches that among the environmental characteristics used to distinguish those habitat types and (4) To test the hypothesis that, as a result of environmental changes in the Swan-Canning Estuary, the characteristics of the benthic macroinvertebrate assemblages at various habitats in this estuary in 1986/7 differ from those in 2003/4. To address the first aim, benthic macroinvertebrates were sampled seasonally for one year in the subtidal waters and intertidal zone (upper and lower swash zones) at the six nearshore habitat types that were identified by Valesini et al. (2003) on the lower west coast of Australia. The habitat types, which differed mainly in the extent of their exposure to wave activity and whether seagrass and/or nearshore reefs were present, had been distinguished quantitatively using values for a suite of seven statistically-selected enduring environmental characteristics. The faunal samples yielded a total of 121 species representing eight phyla, among which the Polychaeta, Malacostraca and Bivalvia were the most speciose classes and contributed ~ 38, 23 and 10%, respectively, to the total number of individuals. The total number of species and mean density of macroinvertebrates was far greater at the most protected habitat type (1), which also contained dense beds of seagrass, than at any other habitat type, i.e. 70 species and 209.2 individuals 0.1 m-2, compared to 32 species and 36.9 individuals 0.1 m-2 at the most exposed habitat type (6), which had a substrate comprised only of sand. Differences among habitat type influenced the benthic macroinvertebrate species composition to a greater extent than differences among either zones or seasons. Significantly different faunal compositions were detected among those latter two factors only at the most protected habitat type. The faunal assemblage at habitat type 1 was clearly the most distinct from those at the other five habitat types, particularly in the subtidal zone (R-statistics=0.642-0.831, p=0.1%), and was typified by five abundant polychaete species that were adapted to deposit-feeding. In contrast, the fauna at habitat type 6 was typified by four crustacean species and a species of bivalve and polychaete, whose mobility and tough external surface facilitated their survival and feeding in those turbulent waters. The extents of the differences in species composition among the six habitat types was significantly matched with that among the suite of enduring environmental characteristics that distinguished those habitat types, particularly in the case of the subtidal zone (Rho=0.676). Such results indicated that the environmental variables used to distinguish the nearshore habitat types could be used to reliably predict the types of benthic macroinvertebrate species likely to occur at any site along the lower west coast of Australia. The above biological validation of the nearshore marine habitat classification scheme developed by Valesini et al. (2003) provided the justification for the approach to the second broad aim of this study, namely to develop a quantitative scheme for classifying habitat types in the Swan-Canning Estuary. This approach was similar to that employed by Valesini et al. (2003) in that it considers that differences among habitat types are well reflected by differences in a suite of enduring environmental variables. However, it improves on that earlier method by employing a completely objective and quantitative approach. Thus, a large number of environmentally-diverse nearshore sites (102) were initially selected throughout the Swan-Canning Estuary and a suite of 13 enduring environmental variables quantified at each using remotely-sensed images of the estuary in a Geographic Information System. Such variables were chosen to reflect either (i) the type of substrate and submerged vegetation present, (ii) the extent of exposure to wave action or (iii) the location of the site within the estuary with respect to its vicinity to marine and fresh water sources. These data were then subjected to the CLUSTER routine and associated SIMPROF procedure in the PRIMER v6 multivariate statistical package to quantitatively identify those groups of sites that did not differ significantly in their environmental characteristics, and thus represented habitat types. Eighteen habitat types were identified, which were shown to well reflect spatial differences in a suite of non-enduring water quality and sediment characteristics that were measured in situ at a range of estuarine sites during both summer and winter in 2005 (Rho=0.683 and 0.740, respectively, p=0.1%). However, those latter environmental characteristics required far more time in the field and laboratory to quantify than the enduring variables used to identify the habitat types. Benthic macroinvertebrates were sampled during summer and winter in 2005 in the shallow subtidal regions (~1 m depth) at sites representing eight of the habitat types identified in the Swan-Canning Estuary. These samples contained a total of 51 and 36 species during summer and winter, respectively, and, in both seasons, represented nine phyla, namely Annelida, Crustacea, Mollusca, Sipuncula, Nematoda, Platyhelminthes, Cnidaria, Uniramia and Nemertea. The compositions of the benthic macroinvertebrate assemblages differed significantly among habitat types and, to a similar extent, between seasons (Global R-statistic=0.408 and 0.409, respectively, p=0.1%). However, the spatial differences were considerable greater in winter than in summer (Global R-statistic=0.536 vs 0.280, p=0.1%), presumably due to the greater spatial variation in particular non-enduring in situ environmental characteristics, such as redox depth and salinity. While the number of species, overall density and taxonomic distinctness of benthic macroinvertebrates also differed significantly among habitats, those variables differed to a greater extent between seasons, being greater in winter than in summer. While the measures of taxonomic distinctness tended to be greater at habitat types located in the lower to middle reaches, i.e. habitat types 6, 7, 9, 10, 13 and 18, than the upper reaches i.e. habitat types 1 and 3, the number of species and overall density reflected this trend only during winter. During summer, the mean numbers of species at habitat types 1, 3, 6 and 10 (3.4-6.0) were significantly lower than those at habitat types 7, 13, and 18 (8.8-10.9), whereas the overall density of benthic macroinvertebrates was far greater at habitat type 7 (32260 individuals 0.1 m-2)than at any other habitat type in this season (3135-18552 individuals 0.1 m-2). Overall, the greatest differences in assemblage composition occurred between those at habitat types 1 and 18 (R-statistic=0.669, p=0.1%), which were located in the uppermost region of the estuary and the lower reaches of the basin, respectively, and differed to the greatest extent in their enduring environmental characteristics. The assemblage at habitat type 1, and also that at habitat type 3, located just downstream, were relatively distinct from those at all other habitat types, particularly during winter (R-statistics=0.666-0.993, p=0.1%). The fauna at the first of these habitat types was relatively depauperate, containing low numbers of species and densities, and was characterised by the polychaetes Leitoscoloplos normalis and Ceratonereis aequisetis and the bivalve Arthritica semen. The assemblage at habitat type 3 was also characterised by those three species and the amphipod Paracorophium minor and the polychaete Boccardiella limnicola. In contrast, the assemblage at habitat type 18 was characterised by a more diverse assemblage, i.e. the polychaetes Capitella capitata, C. aequisetis, L. normalis and Pseudopolydora kempi, the amphipods, Grandidierella propodentata and Corophium minor and the bivalve Sanguinolaria biradiata. The number of species was among the highest at this habitat type during both seasons, which was also reflected in the high taxonomic diversity, and the overall density was the highest in winter and second highest in summer. Despite the above faunal differences, those between assemblages at habitat types 7 and 9, which were both located in the basin of the Swan-Canning Estuary, were similar in magnitude to those that occurred between pairs of habitat types located in two different regions of the estuary. Although both habitat types 7 and 9 were characterised by a similar suite of species, i.e. Oligochaete spp., C. aequisetis, C. capitata, C. minor, G. propodentata, L. normalis, and S. biradiata, the substantial differences in assemblage composition between these habitat types in both summer and winter (R-statistics=0.570 and 0.725, respectively) was due to marked differences in the relative contributions of each of these species. Significant and strong correlations were shown to exist in both summer and winter between the pattern of differences in the benthic macroinvertebrate assemblages among habitat types and that among the enduring environmental characteristics used to identify those habitat types (Rho=0.625 and 0.825, respectively, p=0.1%). Furthermore, these correlations were greater than those obtained between the benthic macroinvertebrate fauna and any combination of the non-enduring environmental characteristics (i.e. water quality and sediment parameters) recorded in situ at each habitat type (Rho=0.508 and 0.824, in summer and winter, respectively, p=o.1%). This demonstrates the greater capacity of surrogate enduring environmental characteristics to account for differences in the range of variables that may influence the distribution of benthic invertebrate fauna. Thus, the lists of characteristic benthic macroinvertebrate taxa produced for each of the eight habitat types studied in the Swan-Canning Estuary provide a reliable benchmark by which to gauge any future changes in those fauna. Moreover, these results indicate that the above habitat classification scheme can be used to reliably predict the types of benthic macroinvertebrate fauna that are likely to occur at any nearshore site of interest in this estuarine system. The final component of this study showed that the benthic macroinvertebrate assemblages at four sites in the middle reaches of the Swan-Canning Estuary in 2003/4 differed significantly from those recorded at the same sites in 1986/7. Such differences were reflected in (1) changes in the relative densities of a suite of ten species that were responsible for distinguishing the faunas in these two periods, (2) the absence of 22 rare species in 2003/4 (i.e. 42% of the number of species recorded in 1986/7), (3) the presence of 17 new species in 2003/4, including an abundant polychaete that is likely to have been introduced and (4) a far greater extent of seasonal variation in the number of species and densities of benthic macroinvertebrates in 2003/4. Such changes are likely to be related to lower sediment oxygen levels in certain seasons in 2003/4, as well as an altered hydrological regime due to increased temperatures and decreased rainfall in that more recent period. The fact that these changes have occurred within the Swan-Canning Estuary highlights the need for effective management tools, such as the habitat classification scheme and associated faunal survey undertaken in this study. Such data will provide a sound basis by which to examine the ways in which fauna vary spatially within the system, and allow for the establishment of comprehensive benchmarks for detecting future changes.