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The Figure 3 caption does not include the correct legend colors. The corrected Figure 3 caption reads: Figure 3. Diversity measures at the site scale in each estuary: α-site (red bars, mean and SD), γ- site (green bars) and β-site (blue bars). Sites: 1 to 10. Significant Spearman correlation (r) between diversity measures at each estuary is included in left corner of graphs. doi:10.1371/journal.pone.0065575.g003

Coastal ecosystems are often stressed by non-point source and cumulative effects that can lead to local-scale community homogenisation and a concomitant loss of large-scale ecological connectivity. Here we investigate the use of β-diversity as a measure of both community heterogeneity and ecological connectivity. To understand the consequences of different environmental scenarios on heterogeneity and connectivity, it is necessary to understand the scale at which different environmental factors affect β-diversity. We sampled macrofauna from intertidal sites in nine estuaries from New Zealand's North Island that represented different degrees of stress derived from land-use. We used multiple regression models to identify relationships between β-diversity and local sediment variables, factors related to the estuarine and catchment hydrodynamics and morphology and land-based stressors. At local scales, we found higher β-diversity at sites with a relatively high total richness. At larger scales, β-diversity was positively related to γ-diversity, suggesting that a large regional species pool was linked with large-scale heterogeneity in these systems. Local environmental heterogeneity influenced β-diversity at both local and regional scales, although variables at the estuarine and catchment scales were both needed to explain large scale connectivity. The estuaries expected a priori to be the most stressed exhibited higher variance in community dissimilarity between sites and connectivity to the estuary species pool. This suggests that connectivity and heterogeneity metrics could be used to generate early warning signals of cumulative stress.

Disturbance-mediated species loss has prompted research considering how ecosystem functions are changed when biota is impaired. However, there is still limited empirical evidence from natural environments evaluating the direct and indirect (i.e. via biota) effects of disturbance on ecosystem functioning. Oxygen deficiency is a widespread threat to coastal and estuarine communities. While the negative impacts of hypoxia on benthic communities are well known, few studies have assessed in situ how benthic communities subjected to different degrees of hypoxic stress alter their contribution to ecosystem functioning. We studied changes in sediment ecosystem function (i.e. oxygen and nutrient fluxes across the sediment water-interface) by artificially inducing hypoxia of different durations (0, 3, 7 and 48 days) in a subtidal sandy habitat. Benthic chamber incubations were used for measuring responses in sediment oxygen and nutrient fluxes. Changes in benthic species richness, structure and traits were quantified, while stress-induced behavioral changes were documented by observing bivalve reburial rates. The initial change in faunal behavior was followed by non-linear degradation in benthic parameters (abundance, biomass, bioturbation potential), gradually impairing the structural and functional composition of the benthic community. In terms of ecosystem function, the increasing duration of hypoxia altered sediment oxygen consumption and enhanced sediment effluxes of NH(4)(+) and dissolved Si. Although effluxes of PO(4)(3-) were not altered significantly, changes were observed in sediment PO(4)(3-) sorption capability. The duration of hypoxia (i.e. number of days of stress) explained a minor part of the changes in ecosystem function. Instead, the benthic community and disturbance-driven changes within the benthos explained a larger proportion of the variability in sediment oxygen- and nutrient fluxes. Our results emphasize that the level of stress to the benthic habitat matters, and that the link between biodiversity and ecosystem function is likely to be affected by a range of factors in complex, natural environments.

Background Estuaries are highly productive ecosystems that can export organic matter to coastal seas (the ‘outwelling hypothesis’). However the role of this food resource subsidy on coastal ecosystem functioning has not been examined. Methodology/Principal Findings We investigated the influence of estuarine primary production as a resource subsidy and the influence of estuaries on biodiversity and ecosystem functioning in coastal mollusk-dominated sediment communities. Stable isotope values (δ13C, δ15N) demonstrated that estuarine primary production was exported to the adjacent coast and contributed to secondary production up to 4 km from the estuary mouth. Further, isotope signatures of suspension feeding bivalves on the adjacent coast (Dosinia subrosea) closely mirrored the isotope values of the dominant bivalves inside the estuaries (Austrovenus stutchburyi), indicating utilization of similar organic matter sources. However, the food subsidies varied between estuaries; with estuarine suspended particulate organic matter (SPOM) dominant at Tairua estuary, while seagrass and fringing vegetation detritus was proportionately more important at Whangapoua estuary, with lesser contributions of estuarine SPOM. Distance from the estuary mouth and the size and density of large bivalves (Dosinia spp.) had a significant influence on the composition of biological traits in the coastal macrobenthic communities, signaling the potential influence of these spatial subsidies on ecosystem functioning. Conclusions/Significance Our study demonstrated that the locations where ecosystem services like productivity are generated are not necessarily where the services are utilized. Further, we identified indirect positive effects of the nutrient subsidies on biodiversity (the estuarine subsidies influenced the bivalves, which in turn affected the diversity and functional trait composition of the coastal sediment macrofaunal communities). These findings highlight the importance of integrative ecosystem-based management that maintains the connectivity of estuarine and coastal ecosystems.

Ocean acidification is a well recognised threat to marine ecosystems. High latitude regions are predicted to be particularly affected due to cold waters and naturally low carbonate saturation levels. This is of concern for organisms utilising calcium carbonate (CaCO(3)) to generate shells or skeletons. Studies of potential effects of future levels of pCO(2) on high latitude calcifiers are at present limited, and there is little understanding of their potential to acclimate to these changes. We describe a laboratory experiment to compare physiological and metabolic responses of a key benthic bivalve, Laternula elliptica, at pCO(2) levels of their natural environment (430 µatm, pH 7.99; based on field measurements) with those predicted for 2100 (735 µatm, pH 7.78) and glacial levels (187 µatm, pH 8.32). Adult L. elliptica basal metabolism (oxygen consumption rates) and heat shock protein HSP70 gene expression levels increased in response both to lowering and elevation of pH. Expression of chitin synthase (CHS), a key enzyme involved in synthesis of bivalve shells, was significantly up-regulated in individuals at pH 7.78, indicating L. elliptica were working harder to calcify in seawater undersaturated in aragonite (Ω(Ar) = 0.71), the CaCO(3) polymorph of which their shells are comprised. The different response variables were influenced by pH in differing ways, highlighting the importance of assessing a variety of factors to determine the likely impact of pH change. In combination, the results indicate a negative effect of ocean acidification on whole-organism functioning of L. elliptica over relatively short terms (weeks-months) that may be energetically difficult to maintain over longer time periods. Importantly, however, the observed changes in L. elliptica CHS gene expression provides evidence for biological control over the shell formation process, which may enable some degree of adaptation or acclimation to future ocean acidification scenarios.

High Antarctic coastal marine environments are comparatively pristine with strong environmental gradients, which make them important places to investigate biodiversity relationships. Defining how different environmental features contribute to shifts in beta-diversity is especially important as these shifts reflect both spatio-temporal variations in species richness and the degree of ecological separation between local and regional species pools. We used complementary techniques (species accumulation models, multivariate variance partitioning and generalized linear models) to assess how the roles of productivity, bio-physical habitat heterogeneity and connectivity change with spatial scales from metres to 100's of km. Our results demonstrated that the relative importance of specific processes influencing species accumulation and beta-diversity changed with increasing spatial scale, and that patterns were never driven by only one factor. Bio-physical habitat heterogeneity had a strong influence on beta-diversity at scales 40 km. Our analysis supports the emphasis on the analysis of diversity relationships across multiple spatial scales and highlights the unequal connectivity of individual sites to the regional species pool. This has important implications for resilience to habitat loss and community homogenisation, especially for Antarctic benthic communities where rates of recovery from disturbance are slow, there is a high ratio of poor-dispersing and brooding species, and high biogenic habitat heterogeneity and spatio-temporal variability in primary production make the system vulnerable to disturbance. Consequently, large areas need to be included within marine protected areas for effective management and conservation of these special ecosystems in the face of increasing anthropogenic disturbance.

Identifying the effects of stressors before they impact ecosystem functioning can be challenging in dynamic, heterogeneous 'real-world' ecosystems. In aquatic systems, for example, reductions in water clarity can limit the light available for photosynthesis, with knock-on consequences for secondary consumers, though in naturally turbid wave-swept estuaries, detecting the effects of elevated turbidity can be difficult. The objective of this study was to investigate the effects of shading on ecosystem functions mediated by sandflat primary producers (microphytobenthos) and deep-dwelling surface-feeding macrofauna (Macomona liliana; Bivalvia, Veneroida, Tellinidae). Shade cloths (which reduced incident light intensity by similar to 80%) were deployed on an exposed, intertidal sandflat to experimentally stress the microphytobenthic community associated with the sediment surface. After 13 weeks, sediment properties, macrofauna and fluxes of oxygen and inorganic nutrients across the sediment-water interface were measured. A multivariate metric of ecosystem function (MF) was generated by combining flux-based response variables, and distance-based linear models were used to determine shifts in the drivers of ecosystem function between non-shaded and shaded plots. No significant differences in MF or in the constituent ecosystem function variables were detected between the shaded and non-shaded plots. However, shading reduced the total explained variation in MF (from 64% in non-shaded plots to 15% in shaded plots) and affected the relative influence of M. liliana and other explanatory variables on MF. This suggests that although shade stress may shift the drivers of ecosystem functioning (consistent with earlier investigations of shading effects on sandflat interaction networks), ecosystem functions appear to have a degree of resilience to those changes.