There is a growing threat of habitat change in estuarine and coastal regions, yet there are few models that enable ecologists and resource managers to forecast the response of macrofaunal species to long-term changes in sediment type. This study details a novel strategy that enabled us to rapidly collect data on macrofaunal densities and sediment characteristics by sampling mud-to-sand transition zones in 19 estuaries. Species-specific models that predict probability of occurrence relative to sediment mud content were developed for 13 common macrofaunal species. However, the roles played by many macrofaunal species are influenced by density, not just occurrence. Over broad spatial scales, the constraint an environmental variable places on density can be represented by the upper (or lower) limit on density. Thus, the distribution of maximum density along the gradient from mud to sand was modelled as another indicator of a species' preference. Both the maximum and minimum values for number of taxa, number of individuals, Shannon-Wiener diversity and taxonomic distinctness were also modelled. For most variables, good models (r 2 > 0.6) were developed. The models developed for the different species exhibited a wide variety of functional forms, highlighting the potential variation in response to habitat change even for closely related species with similar natural history characteristics. Probability-of-occurrence models and maximum-density models for a specific species also varied in functional form, emphasising that changes in both occurrence and density need to be considered when predicting likely responses to changes in habitat.

The wider effects of fishing on marine ecosystems have become the focus of growing concern among scientists, fisheries managers and the fishing industry. The present review examines the role of habitat structure and habitat heterogeneity in marine ecosystems, and the effects of fishing (i.e. trawling and dredging) on these two components of habitat complexity. Three examples from New Zealand and Australia are considered, where available evidence suggests that fishing has been associated with the degradation or loss of habitat structure through the removal of large epibenthic organisms, with concomitant effects on fish species which occupy these habitats. With ever‐increasing demands on fish‐stocks and the need for sustainable use of fisheries resources, new approaches to fisheries management are needed. Fisheries management needs to address the sustainability of fish‐stocks while minimizing the direct and indirect impacts of fishing on other components of the ecosystem. Two long‐term management tools for mitigating degradation or loss of habitat structure while maintaining healthy sustainable fisheries which are increasingly considered by fisheries scientists and managers are: (1) protective habitat management, which involves the designation of protected marine and coastal areas which are afforded some level of protection from fishing; and (2) habitat restoration, whereby important habitat and ecological functions are restored following the loss of habitat and/or resources. Nevertheless, the protection of marine and coastal areas, and habitat restoration should not be seen as solutions replacing conventional management approaches, but need to be components of an integrated programme of coastal zone and fisheries management. A number of recent international fisheries agreements have specifically identified the need to provide for habitat protection and restoration to ensure long‐term sustainability of fisheries. The protection and restoration of habitat are also common components of fisheries management programs under national fisheries law and policy.

Commercial fishing is one of the most important human impacts on the marine benthic environment. One such impact is through disturbance to benthic habitats as fishing gear (trawls and dredges) are dragged across the seafloor. While the direct effects of such an impact on benthic communities appear obvious, the magnitude of the effects has been very difficult to evaluate. Experimental fishing‐disturbance studies have demonstrated changes in small areas; however, the broader scale implications attributing these changes to fishing impacts are based on long‐term data and have been considered equivocal. By testing a series of a priori predictions derived from the literature (mainly results of small‐scale experiments), we attempted to identify changes in benthic communities at the regional scale that could be attributed to commercial fishing. Samples along a putative gradient of fishing pressure were collected from 18 sites in the Hauraki Gulf, New Zealand. These sites varied in water depth from ∼17 to 35 m and in sediment characteristics from ∼1 to 48% mud and from 3 to 8.5 μg chlorophyll a/cm3. Video transects were used for counting large epifauna and grab/suction dredge and core sampling were used for collecting macrofauna. After accounting for the effects of location and sediment characteristics, 15–20% of the variability in the macrofauna community composition sampled in the cores and grab/suction dredge samples was attributed to fishing. With decreasing fishing pressure we observed increases in the density of echinoderms, long‐lived surface dwellers, total number of species and individuals, and the Shannon‐Weiner diversity index. In addition, there were decreases in the density of deposit feeders, small opportunists, and the ratio of small to large individuals of the infaunal heart urchin, Echinocardium australe. The effects of fishing on the larger macrofauna collected from the grab/suction dredge samples were not as clear. However, changes in the predicted direction in epifaunal density and the total number of individuals were demonstrated. As predicted, decreased fishing pressure significantly increased the density of large epifauna observed in video transects. Our data provide evidence of broad‐scale changes in benthic communities that can be directly related to fishing. As these changes were identifiable over broad spatial scales they are likely to have important ramifications for ecosystem management and the development of sustainable fisheries.

Sediment run-off from land has been recognised as a threat to the biodiversity of shallow estuarine and coastal areas. Extreme rainfall events can cause flooding and landslides, which may result in rapid deposition of fine terrigenous sediments and have serious impacts on benthic communities. We designed a field experiment to study the response of intertidal benthos to such depositions of terrigenous clay. The experiment was conducted at 2 contrasting intertidal sites: a sheltered muddy sand habitat and an exposed sand habitat influenced by wind waves. Terrigenous clay (50% water content) was deposited in replicated experimental plots (2 m diameter) at each site in layers 0, 3, 6 or 9 cm thick. The initial response of the resident macrofauna and subsequent recolonisation was monitored over a period of 408 d. Physical and chemical properties of the experimental plots and wave climate at each site were also measured. The experiment demonstrated highly deleterious effects of catastrophic terrigenous clay deposition on estuarine macrobenthic communities. At both sites following clay deposition, the numbers of individuals were reduced by more than 50% after 3 d and by more than 90% after 10 d, irrespective of clay thickness. Mud crabs Helice crassa were the only animals able to emerge through the clay layer. They also exhibited elevated densities in clay treatments over the course of the experiment. After 28 d, a storm occurred (maximum wave height 0.4 m, period = 6 s) which dispersed the clay deposits at the exposed sandy site. Recolonisation of the surficial sediments was rapid at the exposed site following this wind-wave disturbance. However, deeper-dwelling animals such as large bivalves had not recovered to levels observed in the control plots by the end of the experiment. At the more sheltered muddy sand site, the clay deposition resulted in long-lasting habitat change; Although the clay was gradually broken up and re-colonised by small crabs and surface dwelling macrofauna, recovery was still incomplete 408 d after deposition. The results emphasise the role of wind-wave disturbance and transport of sediments and macrofauna with bedload, and the importance of bioturbation by crabs as facilitators of macrobenthic recovery after disturbance.

Facilitation by habitat modifiers is common in ecological communities, but the potential for temporal and spatial variations in environmental conditions to modify the outcome of these interactions and influence the strength of feedbacks is poorly understood. Suspension-feeding bivalves are important habitat modifiers that can facilitate surrounding communities by providing refuge from predation and changing boundary flows and through the production of organically enriched biodeposits. However, numerous studies have highlighted the problem of finding generalizable patterns. We tested the strength and generality of the relationship between the large suspension-feeding bivalve Atrina zelandica and surrounding macrofauna and hypothesized that facilitation by Atrina is conditional and modulated by site-specific suspended sediment concentration (SSC), which influences the quantity and quality of biodeposit production. We found temporally consistent patterns of higher rates of biodeposition and increased abundance and species richness in close proximity to Atrina under low SSC conditions. Facilitation strength decreased with increasing SSC, suggesting that the facilitation effect of Atrina is reduced and reversed along this environmental stress gradient.