Marine embayments and estuaries play an important role in the ecology and life history of many fish species. Cockburn Sound is one of a relative paucity of marine embayments on the west coast of Australia. Its sheltered waters and close proximity to a capital city have resulted in anthropogenic intrusion and extensive seascape modification. This study aimed to compare the sampling efficiencies of baited videos and fish traps in determining the relative abundance and diversity of temperate demersal fish species associated with naturally occurring (seagrass, limestone outcrops and soft sediment) and modified (rockwall and dredge channel) habitats in Cockburn Sound. Baited videos sampled a greater range of species in higher total and mean abundances than fish traps. This larger amount of data collected by baited videos allowed for greater discrimination of fish assemblages between habitats. The markedly higher diversity and abundances of fish associated with seagrass and limestone outcrops, and the fact that these habitats are very limited within Cockburn Sound, suggests they play an important role in the fish ecology of this embayment. Fish assemblages associated with modified habitats comprised a subset of species in lower abundances when compared to natural habitats with similar physical characteristics. This suggests modified habitats may not have provided the necessary resource requirements (e.g. shelter and/or diet) for some species, resulting in alterations to the natural trophic structure and interspecific interactions. Baited videos provided a more efficient and non-extractive method for comparing fish assemblages and habitat associations of smaller bodied species and juveniles in a turbid environment.
Citation: Wakefield CB, Lewis PD, Coutts TB, Fairclough DV, Langlois TJ (2013) Fish Assemblages Associated with Natural and Anthropogenically-Modified Habitats in a Marine Embayment: Comparison of Baited Videos and Opera-House Traps. PLoS ONE 8(3): e59959. doi:10.1371/journal.pone.0059959
Editor: Sharyn Jane Goldstien, University of Canterbury, New Zealand
Received: December 4, 2012; Accepted: February 20, 2013; Published: March 21, 2013
Copyright: © 2013 Wakefield et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This research received funding from Fremantle Ports, Oceanica consulting and the Department of Fisheries, Government of Western Australia to assist with the environmental impact assessment for the Kwinana Quays port development in Cockburn Sound. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have the following interests: this study was partly funded by Oceanica Consulting. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials.
Marine embayments and estuaries provide important habitats during the life histories of many fish species , , . The evolutionary importance of these areas is evident through their role in facilitating genetic subdivision and divergence in marine and estuarine fish populations , for species that exhibit both high or low dispersal capabilities , . However, on a much shorter time scale, anthropogenic activities have modified their seascape through the addition of infrastructure (e.g. piers and rockwalls), removal of substrate (e.g. dredging and mining), or chemical (e.g. eutrophication) and biological (e.g. introduced species) contamination. Despite extensive examples of anthropogenic induced impacts , the ecological processes governing sheltered nearshore areas continue to come under stress from further coastal development. Given the ecological importance of embayments and estuaries it is important to understand how such impacts influence their faunal assemblages.
The capacity of anthropogenically-modified (hereafter referred to as modified habitats) seascapes to resemble natural habitats has been evaluated through comparisons of their faunal assemblages . Modified habitats have typically been shown to support a subset of fish species that occur in adjacent natural habitats with similar physical attributes (e.g. topography), and in relatively higher or lower abundances depending on species-specific requirements for shelter, reproduction and diet . Any significant change in the composition of fishes from that of a natural state should be considered an impact based on alterations to the trophic structure and other interspecific interactions which are likely to occur . Results of studies comparing species richness, abundance and composition between natural and modified habitats (ranging from artificial reefs to piers) are inconsistent and have been shown to be influenced by the materials used in their construction and the sampling method . Large habitat modifications could lead to significant changes in the ecological and/or physical (e.g. hydrodynamics) processes within these embayments and estuaries (e.g. influence spawning and recruitment processes, ).
Marine embayments are rare on the west coast of Australia. The temperate embayment of Cockburn Sound (32°12′ S, Fig. 1) is recognised as an important spawning and nursery area for many commercially and recreationally targeted fish and crab species , , , , . Cockburn Sound is located in close proximity (ca 20 km) to the only capital city along this extensive coastline (ca 3000 km). As such, this embayment supports competing human uses, including heavy industry, shipping, a naval base, aquaculture and commercial and recreational fishing, with further large-scale port developments proposed. Large-scale declines in seagrass cover (ca 80% loss) have been linked to development activities in this embayment , , . The few studies of the fish communities of Cockburn Sound have focussed on seagrass beds using beach seine nets, trawling and set (gill) nets , , ,  and soft sediments using trawling , . However, there have been no comparisons of the fish faunal composition using the same sampling method among the different natural and modified habitats, as not all the above methods are able to sample these various habitats effectively.
Baited video offers a non-extractive and effective method for describing and comparing fish communities across multiple habitats , . However, this method has had limited application within marine embayments and estuaries . Technological improvements have led to baited video equipment becoming more affordable and once acquired, the method is relatively inexpensive, can be easily repeated and can sample complex topography and sensitive habitats, such as seagrass . While traps are an extractive method, they have been used to effectively sample the fish communities and populations in various habitats , , , , . Comparisons between sampling efficiencies of baited video and commercial fish traps from tropical regions have demonstrated that baited video sampled higher numbers of species and abundances, and thus provided greater statistical power for detecting differences in the structure of fish communities . The majority of fish species that occur in Cockburn Sound are either smaller bodied or are typically juveniles , , compared with those sampled in the previous comparison by Harvey et al. .
Given Cockburn Sound is an important recruitment area for Pagrus auratus and Sillaginodes punctatus , , our objective was to investigate whether baited videos or traps were the more effective method for assessing small-bodied fish assemblages to determine their composition, relative abundances and associations with four natural (seagrass, limestone outcrops and soft sediment at<and >10 m depth) and two modified habitats (rockwall and dredged channels). As such, the ability of each method to discriminate fish species compositions, species richness and relative abundances at identical locations were investigated. The capacity of the modified habitats to function as natural habitats was assessed by comparing fish species compositions, species richness and relative abundances of fishes recorded in each habitat. If the two modified habitats were adequate substitutes for natural habitats in Cockburn Sound, it was hypothesised that based on the similarities of their physical characteristics, fish assemblages associated with rockwalls would resemble those of limestone outcrops, whereas assemblages in dredged channels would resemble those of soft sediment habitats.
Materials and Methods
Study Area and Sampling Regime
Cockburn Sound is a semi-enclosed marine embayment ca 16 km long by 9 km wide and has a sea surface area of ca 100 km2 and maximum depth of 23 m (Fig. 1). This embayment is bounded by the mainland to the east and south, Garden Island to the west and the shallow (<10 m) Parmelia Bank to the north (Fig. 1). The southern entrance of the sound has been partially closed through the construction of a rock-filled causeway in 1971–73. All margins of the sound have shallow banks (<10 m) comprising seagrass , small outcrops of limestone and extensive soft sediment (Fig. 1). Shipping channels have been dredged into the eastern and northern banks. A dominant feature of the benthos of Cockburn Sound is the deeper central basin (ca 20 m), which is a relatively uniform expanse of soft sediment (silt, Fig. 1). There is extensive industrial development and associated structures along the eastern margin of the sound and boat harbours at the south-eastern end of Garden Island (naval base), either side of the southern end of the causeway and in the north-east corner of the sound (Fig. 1).
Sampling was undertaken in June and July 2008. Baited videos were deployed over four days at 51 sites, followed one week later by traps at the same sites also over four days. Traps were intentionally used after baited videos, as the extraction of fish using traps could potentially reduce abundances and thus influence the results from the baited videos. Sampling sites were determined from ArcGIS© habitat maps (provided by Oceanica Consulting Pty Ltd) and targeted the major natural habitat types including sand banks (<10 m deep, eight sites), central sand basin (>10 m deep, 23 sites), seagrass (six sites) and limestone outcrops (seven sites, Fig. 1). Modified habitats including rockwalls (three sites) and dredged channels (four sites) were also sampled. Three replicate baited videos and traps were sampled concurrently 100–150 m apart at each site. The bait was refreshed for each baited video and trap set with ca 150 g of diced Australian pilchards (Sardinops sagax). Baited videos were left to record for 35 minutes, based on the effective duration determined by Morrison and Carbines . Traps were left to soak for 90 minutes as Ferrell and Sumpton , using the same type of traps, found catch rates of teleosts reached an asymptote after this period.
Baited Video and Trap Construction
The baited videos consisted of a single high definition (1920×1080 pixels) video camera (Canon HV20) placed in an underwater housing and fastened to a bar situated 75 cm from the floor and centrally within a galvanised-steel trapezium frame with the video orientated horizontally (Fig. 2). Bait was placed in a circular (13.5 cm diameter, 4 cm height) black plastic meshed container and suspended within the field of view 100 cm in front of the camera (Fig. 2). A rope and float for retrieval of the baited video was attached via a rope bridle at the top of the trapezium frame.
Scale reference: camera to bait holder 100 cm, floor to camera 75 cm and trap height 35 cm.
A pilot study was conducted to determine 1) an optimal length for the bait pole for baited videos to allow sufficient monitoring around the bait container in the turbid conditions, and 2) the most effective construction for fish traps. The different configurations of fish traps trialled included green vs black 25 mm stretched mesh over both a rounded opera-house trap (90 cm long, 60 cm wide and 35 cm high) and a rectangular trap (93 cm long, 57 cm wide and 33 cm high). The green meshed opera-house trap sampled a greater range of species at higher relative abundances, and was thus used for the remainder of the study. Each opera-house trap had a 10 cm diameter PVC ring spliced into each of the two openings that were located at either end. Two 25 mm square steel channels were attached to the base of each trap to provide ballast and rigidity, thereby minimising potential motion induced from water surge/currents (Fig. 2). Bait holders, identical to those used for the baited videos, were secured within the traps but offset from the two openings (Fig. 2). The traps were retrieved using a rope attached to a float on the waters surface, with the rope attached to the trap at the base midway along one side and perpendicular to the two openings.
Data Collection and Analysis
Footage recorded from baited video were analysed using a custom interface (BRUVS version 2.1, developed by the Australian Institute of Marine Science) to incorporate data collected from the field, the timing of events, reference images of the seafloor and fish in the field of view. The habitat classifications determined from GIS maps were confirmed for each replicate from video images. Natural habitats were classified into four categories, i.e. shallow sand bank (<10 m, SP), deep sand basin (>10 m, SB), seagrass (GR) and limestone outcrops (LM), and modified habitats into two categories, i.e. rockwall (RW) and dredged channel (DG). Fish were identified to the lowest possible taxa. The relative abundance of each species was determined as the maximum number visible in the field of view at any one time (Nmax) for baited video and the number caught for traps. The mean relative abundance of all demersal fish and the total number of species recorded were compared for each habitat and method separately.
The multivariate analyses were performed in PRIMER with the PERMANOVA add-on (version 6.1.13, , ). The abundance measure of fish species at each site was calculated as the mean relative abundance (Nmax, baited videos; numbers, traps) for the three replicates. Considering the more efficient sampling method was to be used for future monitoring following the completion of this study, analyses of each data set were performed separately and thus relative abundances were not standardised between methods. Relative abundance data for both methods were fourth root transformed prior to analyses based on the gradient of the lineal relationship between the logarithms of standard deviation and mean abundances of species, to down-weight the contribution of the most dominant species . Given their tendency to emphasise species composition and relative abundance within community data, zero-adjusted Bray-Curtis and both modified Gower Log10 and Log2 resemblance measures were considered prior to analyses . The stress performance derived from Shepard Diagrams, that displayed the departure of pairwise distances from the best-fitting increasing regression line produced from non-metric multi-dimensional scaling (nMDS) ordination, indicated that baited video and trap data were better treated using a zero-adjusted Bray-Curtis similarity matrix .
Assemblage analysis was performed using permutational multivariate analysis of variance (PERMANOVA, ). An unconstrained ordination using principal coordinates analysis (PCO) combined with cluster analysis were used to determine fish assemblage groupings among sites. The significance of these groupings were assessed using a similarity profile test (SIMPROF, ). These groupings were compared to a constrained ordination using canonical analysis of principal coordinates (CAP), which maintained a priori habitat classifications. An appropriate subset of axis (m) for the CAP analysis was determined by maximising the leave-one-out allocation success (m = 5). The first squared canonical correlation (δ2) and leave-one-out allocation success were used as an indication of how well groups were discriminated within the CAP analysis, as they provide a useful statistical estimate of misclassification error and demonstrate how distinct groups of sites are in multivariate space . A Spearman correlation >0.35 was used as an arbitrary limit to display potential correlations between individual species abundances and habitats relative to the canonical axes.
When significant P values were obtained from pairwise tests using PERMANOVA for baited video data, similarity percentages (SIMPER) were used to identify significant distinguishing fish species. This criteria was based on dissimilarity to standard deviation ratios (Diss/SD) >2 and percentage contributions >10%. The mean relative abundance (±1 se) of distinguishing species was then compared between each habitat type. Mean relative abundances were also compared between habitats for the targeted species Pagrus auratus and Sillaginodes punctatus.
Numbers of Fish and Species Recorded by Baited Videos versus Traps
Based on the sum of Nmax values, baited videos sampled at least 3,944 individual fish from 43 species and 27 families compared with only 1,040 individuals from 27 species and 18 families in traps. There were only two species sampled by the traps that were not sampled by the baited videos (Platycephalus longispinis and Gymnapistes marmoratus), whereas there were 16 species sampled by baited videos that were not caught in traps. For all species caught by both methods, a greater number of individuals were recorded from baited videos than in the traps, with the exception of Pentapodus vitta. Similarly, for each habitat type the mean abundance and species richness recorded by baited videos were greater than those determined from traps, except at sand basin sites (Fig. 3). This was particularly evident for the modified habitats. In rockwall habitats, baited videos recorded an average of 22.2 fish per replicate (±7.2 se) from a total of 18 species, compared with <1 (±0.3 se) fish per replicate from four species caught by traps (Fig. 3). Likewise, in dredged channel habitats baited videos recorded an average of 13.3 fish per replicate (±6.6 se) from 10 species, compared to traps that captured an average of less than one fish per replicate (±0.6 se) from three species (Fig. 3). The lower mean abundances and species richness recorded by traps may be attributed to the fact that 31% of trap sets caught invertebrate piscivorous predators (predominantly Portunus pelagicus or Octopus spp.), which were likely to deter fish from entering.
The numbers of fish species sampled from each habitat by each method are shown above bars. LM, limestone outcrops; GR, seagrass; SP, sand bank (<10 m); SB, sand basin (>10 m); RW, rockwall; DG, dredged channel.
Fish Assemblage Comparisons between Sampling Methods and Habitats
The fish assemblages differed significantly between sampling methods and among habitat types and an interaction was detected between these two variables (P = 0.001, Table 1). Within the natural habitats, both sampling methods recorded higher relative abundances and numbers of species in limestone outcrop and seagrass habitats (∼40 fish per replicate and >25 species) than sand bank and sand basin habitats (<4 fish per replicate and 10 species, Fig. 3). This was reflected in the pairwise comparisons, where based on data collected by baited videos, fish assemblages differed significantly between all natural habitats (P<0.025, Table 2), with the two soft sediment habitats, i.e. sand banks and sand basin, only marginally different (P = 0.041). Similar trends in pairwise comparisons were evident between natural habitats using trap data, except that fish assemblages in sand bank and sand basin habitats were not significantly different (Table 2). Fish assemblages associated with the two modified habitats were poorly sampled using traps compared to baited videos (Fig. 3). At the rockwall locations, baited videos recorded approximately half the relative abundance of fish than in limestone outcrop and seagrass habitats (40 vs 22 fish per replicate, Fig. 3). However, baited videos recorded markedly higher relative abundances of fish from dredged channels than sand bank and sand basin habitats (13 vs 3 fish per replicate, Fig. 3). Pairwise tests comparing fish assemblages of natural and modified habitats with similar physical characteristics, as recorded by baited videos, found no significant differences between dredged channels and both sand banks and sand basin habitats (P = 0.273 and 0.180, respectively) and between rockwall and limestone outcrop habitats (P = 0.215, Table 2). Fish assemblages recorded by baited videos in seagrass were significantly different from both modified habitats i.e. rockwalls and dredged channels (Table 2). While traps were also unable to detect a significant difference between dredged channel and soft sediment habitats (P>0.05), limestone outcrops and rockwall habitats did differ significantly (P = 0.026, Table 2).
Using an unconstrained PCO ordination and SIMPROF analysis, the natural habitat sites were distinguished into three main groups for both sampling methods at a Spearman correlation >0.35 using Bray-Curtis similarity (Fig. 4). According to the baited video data, these three groupings were clearly discriminated into seagrass, limestone outcrop and soft sediment (combining sand banks and sand basin, Fig. 4). Points for the rockwall habitats were located towards the top right of the plot, with one in each of the limestone outcrop and soft sediment groups and one within an overlap of the limestone outcrop and seagrass groups (Fig. 4). In contrast, the four dredged channel sites were dispersed with two sites in each of the limestone outcrop and soft sediment habitat groups (Fig. 4). According to the trap data, there was greater dispersion of natural and modified habitat sites within the PCO ordination, with many sites included in an overlap between groupings, which was not apparent in the analysis of the composition of fishes recorded by baited video (Fig. 4).
Habitat types include SP, sand bank (<10 m); SB, sand basin (>10 m); GR, seagrass; LM, limestone outcrops; RW, rockwall; DG, dredged channel.
Plots of the principal coordinates from the constrained CAP analysis showed closer clustering among sites from the same habitats for baited videos than traps (Fig. 5). This was confirmed by the higher values of leave-one-out allocation success and canonical correlation (δ2). Fish assemblages associated with natural habitats had an allocation success of 79.5% (δ2 = 0.88) when sampled by baited videos, compared to 54.5% (δ2 = 0.79) when sampled by traps. For the baited video data, the seagrass and limestone outcrop categories both had 100% allocation success, revealing the lower allocation success was due to misclassification between the two soft sediment groups (i.e. 62.5% for sand banks and 73.9% for sand basin habitats).
SP, sand bank (<10 m); SB, sand basin (>10 m); GR, seagrass; LM, limestone outcrops; RW, rockwall; DG, dredged channel. Fish species include Parequula melbournensis1, Pseudocaranx sp.2, Trachurus novaezelandie3, Pagrus auratus4, Pentapodus vitta5, Notolabrus parilus6, Coris auricularis7, Upeneichthys vlamingii8, Apogon rueppellii9, Arripis georgianus10, Meuschenia freycineti11, Acanthaluteres spilomelanurus12, Sillaginodes punctatus13, Pelates octolineatus14, Sphyraena novaehollandiae15, Torquigener pleurogramma16, Trygonorhina fasciata17, Myliobatis australis18, Scobinichthys granulatus19, Haletta semifasciata20.
Distributions of Important and Distinguishing Fish Species among Habitats
Using data derived from baited videos, there were distinct groups of fish identified from CAP analysis with relative abundances significantly correlated (Spearman >0.35) with each of the three main natural habitat groups (i.e. seagrass, limestone outcrop and soft sediment, Fig. 5). There were eight fish species with relative abundances significantly correlated with seagrass (Apogon rueppellii, Arripis georgianus, Meuschenia freycineti, Acanthaluteres spilomelanurus, Sillaginodes punctatus, Pelates octolineatus, Sphyraena novaehollandiae and Torquigener pleurogramma, Fig. 5). Similarly, there were eight fish species with relative abundances significantly correlated with limestone outcrops (Parequula melbournensis, Pseudocaranx sp., Trachurus novaezelandie, Pagrus auratus, Pentapodus vitta, Notolabrus parilus, Coris auricularis and Upeneichthys vlamingii, Fig. 5). However, there were only two species of ray, Trygonorhina fasciata and Myliobatis australis, with relative abundances correlated with the soft sediment group, which most likely reflected the markedly lower abundances and species of fish recorded from these habitats (Fig. 5). In comparison, the CAP analysis of data derived from traps determined that only the relative abundances of a subset of fish species could be associated with seagrass from the other habitats (Fig. 5).
Based on SIMPER analysis using data derived from baited videos, there were three fish species, i.e. Torquigener pleurogramma, Pelates octolineatus and Meuschenia freycineti, that distinguished fish assemblages associated with seagrass from soft sediment and dredged habitats (contribution >10%, Diss/SD ratios >2.0). Only T. pleurogramma distinguished seagrass from limestone outcrop habitats. Notably, each of these three species occurred almost exclusively in seagrass (Fig. 6). There were three fish species including Pseudocaranx sp., Trachurus novaezelandie and Pentapodus vitta that distinguished assemblages between limestone outcrop and soft sediment habitats. Although the mean relative abundances of Pseudocaranx sp. and P. vitta were markedly higher in limestone outcrop and dredged channel habitats, they were also recorded consistently but at lower abundances in all other habitats (Fig. 6). In contrast, T. novaezelandie was recorded almost exclusively in limestone outcrop and rockwall habitats (Fig. 6).
DG, dredged channel; LM, limestone outcrops; RW, rockwall; SB, sand basin (>10 m); SP, sand bank (<10 m); GR, seagrass.
The distributions of the recreationally and commercially important P. auratus and S. punctatus were based on 134 and eight observations, respectively, from the 153 baited video replicates. All of the P. auratus except one individual were considered to belong to the 0+ age cohort (ca six months of age), based on their length relative to the size of the bait holder and known age-length relationship , . The relative abundance of juvenile P. auratus was highest in the dredged channel, and to a lesser extent, the limestone outcrop habitats, with occasional occurrences in the remaining habitats (Fig. 6). The ages of the eight S. punctatus observed by baited videos were indeterminate based on their relative length, they were however relatively small and most likely from young age classes. The individuals of that species were recorded in three of the six habitat types, including rockwall, seagrass and limestone outcrops (Fig. 6).
Baited videos recorded much greater relative abundances and numbers of fish species than opera-house traps from identical locations in four natural and two anthropogenically-modified habitats. As such, baited videos allowed for greater discrimination of fish assemblages between habitats and were thus considered to be a more efficient sampling method. It is likely that the capture of invertebrate piscivorous predators (i.e. crabs and octopus) in traps (31% of sets) greatly increased the likelihood of predator-prey interactions and thus reduced their sampling effectiveness . Such predator-prey interactions would have been overcome using baited videos, as it is likely the fish would have still been observed within the wide field of view during interactions. Baited video may have also sampled higher numbers of fish species by recording those that were attracted to the bait (evident through their feeding behaviour) as well as those that swam past, thereby increasing the numbers of predatory or scavenging species while also including herbivorous and omnivorous species . The baited video was also able to collect images of the habitat, which facilitated direct links between fish assemblages and their habitat associations that would have not been achieved from the use of traps alone . However, both baited videos and traps were only able to sample relative rather than absolute abundances of fish, given the complexities associated with estimating sampled area based on bait plume dispersal. In comparison, Morrison and Carbines  used a towed video method capable of estimating concentrations of juvenile teleosts by calculating swept area.
Fish assemblages sampled in natural habitats by baited videos were discriminated into three distinct groups, i.e. seagrass, limestone outcrops and soft sediment. Within the soft sediment group, there were only marginal differences between fish assemblages in habitats shallower (sand banks) or deeper (sand basin) than ten metres. In comparison, fish assemblages associated with natural habitats, as determined from traps, displayed weak discriminating power and tended to misclassify sites between the three groups, irrespective of whether analysis was constrained by a priori habitat classifications.
The majority of habitat in Cockburn Sound is flat and relatively featureless soft sediment, particularly in the deep basin and eastern sand bank areas. Despite occupying the majority of the sound, fish assemblages recorded by baited video in these habitats comprised markedly fewer species (31% of species recorded) in relatively lower abundances. In comparison, the very limited area occupied by seagrass and limestone outcrop habitats had a 15 fold greater abundance of fish and comprised 60% and 65% of all species sampled, respectively. It thus appears important that to maintain fish diversity in Cockburn Sound, the natural seagrass and limestone outcrop habitats need to be conserved, particularly in light of the large scale and continued loss (>77%) of seagrass in this embayment .
The anthropogenically-modified habitats were poorly sampled by traps compared to baited videos. This was not surprising for rockwalls, as traps had to be located adjacent to them and relied on fish to leave the high vertical relief and complex shelter provided by the piles of large limestone blocks used in their construction. Baited video could overcome this by being orientated in the direction of the rockwall, thus identifying fish within this complex structure. Discrepancies in efficiency were however surprising for the low relief dredged channels, where the exposure of fish to baited videos and traps would have been similar. These inconsistencies provided little confidence in the ability of traps to provide useful comparisons between natural and modified habitats.
In regards to the overall fish abundance and species richness, the fish assemblages associated with modified habitats did resemble those of natural habitats with similar physical characteristics. Whereby, the overall abundances recorded using baited videos, were not significantly different between rockwall and limestone outcrops and between dredged channel and soft sediment habitats (sand banks and sand basin). Further investigation using PCO and SIMPROF analysis revealed subtle differences in fish assemblages sampled in rockwall sites, where assemblages were found to consist of a subset of species that were recorded from neighbouring natural habitats. This resulted in the three rockwall sites being grouped with one belonging to each of limestone outcrop and sand groups, and one combined within an overlap of limestone outcrop and seagrass groups. This suggests that fish assemblages sampled from rockwall habitat represented an altered composition from that associated with natural limestone outcrop habitat. Thus, the characteristics of rockwall habitat may not have provided the necessary resource requirements (e.g. shelter and/or diet) for some species, resulting in an alteration to the natural trophic structure and interspecific interactions , .
The fish assemblages sampled by baited video in dredged channel habitat showed mixed results, with two sites included within the soft sediment group, as was hypothesised, and two sites unexpectedly included within the limestone outcrop group. The two dredged channel sites that were grouped within the limestone outcrop group resulted from a high relative abundance of Pseudocaranx sp., P. auratus and P. vitta. The other two dredged channel sites that were included within the soft sediment group consisted of only T. fasciata from six replicates. The frequency of dredging of these channels in Cockburn Sound is low (ca every 8–10 years), which suggests a limited number of fish species will recolonise these disturbed areas, but their succession appears variable.
The results of this study support the use of baited videos over traps for broad fish ecology studies , and provided a non-extractive application for sampling of predominantly smaller bodied and juvenile fish species in sensitive or turbid environments. It also confirms the advantages of using baited videos for such studies compared to many traditional sampling techniques, such as line, trap and trawl , , , . This method would also be useful for collecting information on the relative abundance of 0+ aged recruits, thus contributing information on recruitment strength toward the stock assessments of exploited teleosts, e.g. P. auratus . In addition, this study provides sound quantitative data and repeatable methods for assessing changes in fish communities, which could contribute toward ecological assessments of developments involving anthropogenic modification of marine embayments.
We extend our gratitude to staff from the Department of Fisheries for providing logistical support. Thank you also to Bob Clarke for his useful suggestions regarding statistical analysis; and to Mike Travers and Jeff Norriss and two anonymous reviewers whose comments on earlier versions of the manuscript were greatly appreciated.
Conceived and designed the experiments: CBW PDL. Performed the experiments: CBW PDL TBC. Analyzed the data: CBW PDL DVF TJL. Wrote the paper: CBW PDL TBC DVF TJL.
- 1. Potter IC, Beckley LE, Whitfield AK, Lenanton RCJ (1990) Comparisons between the roles played by estuaries in the life cycles of fishes in temperate Western Australia and Southern Africa. Environ Biol Fishes 28: 143–178.
- 2. Sadovy Y, Cheung WL (2003) Near extinction of a highly fecund fish: the one that nearly got away. Fish and Fisheries 4: 86–99.
- 3. Wakefield CB (2010) Annual, lunar and diel reproductive periodicity of a spawning aggregation of snapper Pagrus auratus (Sparidae) in a marine embayment on the lower west coast of Australia. J Fish Biol 77: 1359–1378.
- 4. Watts RJ, Johnson MS (2004) Estuaries, lagoons and enclosed embayments: habitats that enhance population subdivision of inshore fishes. Mar Freshw Res 55: 641–651.
- 5. Ayvazian SG, Johnson MS, McGlashan DJ (1994) High levels of genetic subdivision of marine and estuarine populations of the estuarine catfish Cnidoglanis macrocephalus (Plotosidae) in southwestern Australia. Mar Biol 118: 25–31.
- 6. Johnson MS, Creagh S, Moran M (1986) Genetic subdivision of stocks of snapper, Chrysophrys unicolor, in Shark Bay, Western Australia. Aust J Mar Freshw Res 37: 337–345.
- 7. Orth RJ, Carruthers TJB, Dennison WC, Duarte CM, Fourqurean JW, et al. (2006) A global crisis for seagrass ecosystems. Bioscience 56: 987–996.
- 8. Clynick BG, Chapman MG, Underwood AJ (2008) Fish assemblages associated with urban structures and natural reefs in Sydney, Australia. Austral Ecol 33: 140–150.
- 9. Glasby TM, Connell SD (1999) Urban structures as marine habitats. Ambio 28: 595–598.
- 10. Wakefield CB, Fairclough DV, Lenanton RCJ, Potter IC (2011) Spawning and nursery habitat partitioning and movement patterns of Pagrus auratus (Sparidae) on the lower west coast of Australia. Fish Res 109: 243–251.
- 11. de Lestang S, Hall NG, Potter IC (2003) Changes in density, age composition, and growth rate of Portunus pelagicus in a large embayment in which fishing pressures and environmental conditions have been altered. J Crustac Biol 23: 908–919.
- 12. Breheny NB, Beckley LE, Wakefield CB (2012) Ichthyoplankton assemblages asscoiated with pink snapper (Pagrus auratus) spawning aggregations in coastal embayments of southwestern Australia. J R Soc West Aust 95: 103–114.
- 13. Lenanton RCJ (1974) The abundance and size composition of trawled juvenile snapper Chrysophrys unicolor (Quoy and Gaimard) from Cockburn Sound, Western Australia. Aust J Mar Freshw Res 25: 281–285.
- 14. Kendrick GA, Aylwarda MJ, Hegge BJ, Cambridge ML, Hillman K, et al. (2002) Changes in seagrass coverage in Cockburn Sound, Western Australia between 1967 and 1999. Aquat Bot 73: 75–87.
- 15. Cambridge ML, Chiffings AW, Brittan C, Moore L, McComb AJ (1986) Loss of seagrass in Cockburn Sound, Western Australia: II. Possible causes of seagrass decline. Aquat Bot 24: 269–285.
- 16. Silberstein K, Chiffings AW, McComb AJ (1986) The loss of seagrass in Cockburn Sound, Western Australia. III. The effect of epiphytes on productivity of Poidonia australis hook. F. Aquat Bot 24: 355–371.
- 17. Vanderklift MA (1996) Influence of adjacent seagrass on the fish assemblages off sandy beaches [Masters Thesis]. Western Australia: Edith Cowan University. 208 p.
- 18. Vanderklift MA, Jacoby CA (2003) Patterns in fish assemblages 25 years after major seagrass loss. Mar Ecol Prog Ser 247: 225–235.
- 19. Scott JK, Dybdahl RE, Wood WF (1986) The ecology of Posidonia seagrass fish communities in Cockburn Sound, Western Australia. Perth, Western Australia: Department of Conservation and Environment. Technical Series No. 11.
- 20. Dybdahl RE (1979) Technical report on fish productivity. An assessment of the marine faunal resources of Cockburn Sound. Perth, Western Australia: Department of Conservation and Environment, Report No. 4.
- 21. Penn JW (1977) Trawl caught fish and crustaceans from Cockburn Sound. Department of Fisheries and Wildlife Western Australia. Report No. 20. 24 p.
- 22. Johnston DJ, Wakefield CB, Sampey A, Fromont J, Harris D (2008) Developing long-term indicators for the sub-tidal embayment communities of Cockburn Sound. Western Australia: Department of Fisheries. Fisheries Research Report No. 181.
- 23. Harvey ES, McLean DL, Frusher S, Haywood MDE, Newman SJ, et al.. (2012) The use of BRUVs as a tool for assessing marine fisheries and ecosystems: a review of the hurdles and potential. University of Western Australia. FRDC Report Project No. 2010/002. 44 p.
- 24. Cappo M, Harvey E, Shortis M (2006) Counting and measuring fish with baited video techniques - an overview. Australian Society for Fish Biology Workshop Proceedings: 101–114.
- 25. Gladstone W, Lindfield S, Coleman M, Kelaher B (2012) Optimisation of baited remote underwater video sampling designs for estuarine fish assemblages. J Exp Mar Biol Ecol 429: 28–35.
- 26. Cappo M, Speare P, De’ath G (2004) Comparison of baited remote underwater video stations (BRUVS) and prawn (shrimp) trawls for assessments of fish biodiversity in inter-reefal areas of the Great Barrier Reef Marine Park. J Exp Mar Biol Ecol 302: 123–152.
- 27. Harvey ES, Newman SJ, Mclean DL, Cappo M, Meeuwig JJ, et al. (2012) Comparison of the relative efficiencies of stereo-BRUVs and traps for sampling tropical continental shelf demersal fishes. Fish Res 125–126: 108–120.
- 28. Travers MJ, Newman SJ, Potter IC (2006) Influence of latitude, water depth, day v. night and wet v. dry periods on the species composition of reef fish communities in tropical Western Australia. J Fish Biol 69: 987–1017.
- 29. Ferrell D, Avery R, Blount C, Hayes L, Pratt R (1994) The utility of small, baited traps for surveys of snapper (Pagrus auratus) and other demersal fishes. NSW Fisheries Research Institute, Cronulla.
- 30. Thrush SF, Schultz D, Hewitt JE, Talley D (2002) Habitat structure in soft-sediment environments and abundance of juvenile snapper Pagrus auratus. Mar Ecol Prog Ser 245: 273–280.
- 31. Jackson G, Burton C, Moran M, Radford B (2007) Distribution and abundance of juvenile pink snapper, Pagrus auratus, in the gulfs of Shark Bay, Western Australia, from trap surveys. Department of Fisheries, Western Australia. Fisheries Research Report No. 161.
- 32. Hyndes GA, Platell ME, Potter IC, Lenanton RCJ (1998) Age composition, growth, reproductive biology, and recruitment of king george whiting, Sillaginodes punctata, in coastal waters of southwestern Australia. Fish Bull 96: 258–270.
- 33. Cambridge ML, McComb AJ (1984) The loss of seagrass in Cockburn Sound, Western Australia. I. The time course and magnitude of seagrass decline in relation to industrial development. Aquat Bot 20: 229–243.
- 34. Morrison M, Carbines G (2006) Estimating the abundance and size structure of an estuarine population of the sparid Pagrus auratus, using towed camera during nocturnal periods of inactivity, and comparisons with conventional sampling techniques. Fish Res 82: 150–161.
- 35. Ferrell D, Sumpton W (1996) Assessment of the fishery for snapper (Pagrus auratus) in Queensland and New South Wales. Queensland: QDPI. FRDC 93/074. 143 p.
- 36. Clarke KR, Gorley RN (2006) PRIMER v6: User Manual/Tutorial. Plymouth, UK: PRIMER-E.
- 37. Anderson M, Gorley R, Clarke K (2008) PERMANOVA+ for PRIMER: guide to software and statistical methods. Plymouth, UK: Primer-E Ltd.
- 38. Clarke KR, Warwick RM (2001) Change in marine communities: an approach to statistical analysis and interpretation, 2nd edition. Plymouth, United Kingdom: PRIMER-E.
- 39. Anderson MJ, Crist TO, Chase JM, Velland M, Inouye BD, et al. (2011) Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist. Ecol Lett 14: 19–28.
- 40. Clarke KR, Somerfield PJ, Chapman MG (2006) On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray-Curtis coefficient for denuded assemblages. J Exp Mar Biol Ecol 330: 55–80.
- 41. Anderson MJ (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32–46.
- 42. Anderson MJ, Willis TJ (2003) Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology. Ecology 84: 511–525.
- 43. Wakefield CB (2006) Latitudinal and temporal comparisons of the reproductive biology and growth of snapper, Pagrus auratus (Sparidae), in Western Australia [Ph.D. Thesis]. Western Australia: Murdoch University. 162 p.
- 44. High WL, Ellis IE (1973) Underwater observations of fish behavior in traps. Helgol Wiss Meeresunters 24: 341–347.
- 45. Harvey ES, Cappo M, Butler JJ, Hall NG, Kendrick GA (2007) Bait attraction affects the performance of remote underwater video stations in assessment of demersal fish community structure. Mar Ecol Prog Ser 350: 245–254.
- 46. Walker DI, Kendrick GA, McComb AJ (2006) Decline and recovery of seagrass ecosystems - the dynamics of change. In: Larkum AWD, Orth RJ, Duarte CM, editors. Seagrasses: biology, ecology and conservation. Dordrecht, Netherlands: Springer. 551–565.
- 47. Langlois TJ, Fitzpatrick BR, Fairclough DV, Wakefield CB, Hesp SA, et al. (2012) Similarities between Line Fishing and Baited Stereo-Video Estimations of Length-Frequency: Novel Application of Kernel Density Estimates. PLoS ONE 7: e45973.
- 48. Wakefield CB, Moran MJ, Tapp NE, Jackson G (2007) Catchability and selectivity of juvenile snapper (Pagrus auratus, Sparidae) and western butterfish (Pentapodis vitta, Nemipteridae) from prawn trawling in a large marine embayment in Western Australia. Fish Res 85: 37–48.
- 49. Murphy HM, Jenkins GP (2010) Observational methods used in marine spatial monitoring of fishes and associated habitats: a review. Mar Freshw Res 61: 236–252.