Carbonate mud is a major constituent of recent marine carbonate sediments and of ancient limestones, which contain unique records of changes in ocean chemistry and climate shifts in the geological past. However, the origin of carbonate mud is controversial and often problematic to resolve. Here we show that tropical marine fish produce and excrete various forms of precipitated (nonskeletal) calcium carbonate from their guts ("low" and "high" Mg-calcite and aragonite), but that very fine-grained (mostly < 2 μm) high Mg-calcite crystallites (i.e. > 4 mole % MgCO(3)) are their dominant excretory product. Crystallites from fish are morphologically diverse and species-specific, but all are unique relative to previously known biogenic and abiotic sources of carbonate within open marine systems. Using site specific fish biomass and carbonate excretion rate data we estimate that fish produce ∼6.1 × 10(6) kg CaCO(3)/year across the Bahamian archipelago, all as mud-grade (the < 63 μm fraction) carbonate and thus as a potential sediment constituent. Estimated contributions from fish to total carbonate mud production average ∼14% overall, and exceed 70% in specific habitats. Critically, we also document the widespread presence of these distinctive fish-derived carbonates in the finest sediment fractions from all habitat types in the Bahamas, demonstrating that these carbonates have direct relevance to contemporary carbonate sediment budgets. Fish thus represent a hitherto unrecognized but significant source of fine-grained carbonate sediment, the discovery of which has direct application to the conceptual ideas of how marine carbonate factories function both today and in the past.

Lionfish (Pterois volitans/miles) have invaded the majority of the Caribbean region within five years. As voracious predators of native fishes with a broad habitat distribution, lionfish are poised to cause an unprecedented disruption to coral reef diversity and function. Controls of lionfish densities within its native range are poorly understood, but they have been recorded in the stomachs of large-bodied Caribbean groupers. Whether grouper predation of lionfish is sufficient to act as a biocontrol of the invasive species is unknown, but pest biocontrol by predatory fishes has been reported in other ecosystems. Groupers were surveyed along a chain of Bahamian reefs, including one of the region's most successful marine reserves which supports the top one percentile of Caribbean grouper biomass. Lionfish biomass exhibited a 7-fold and non-linear reduction in relation to the biomass of grouper. While Caribbean grouper appear to be a biocontrol of invasive lionfish, the overexploitation of their populations by fishers, means that their median biomass on Caribbean reefs is an order of magnitude less than in our study. Thus, chronic overfishing will probably prevent natural biocontrol of lionfishes in the Caribbean.

Expert opinion was canvassed to identify crucial knowledge gaps in current understanding of climate change impacts on coral reef fishes. Scientists that had published three or more papers on the effects of climate and environmental factors on reef fishes were invited to submit five questions that, if addressed, would improve our understanding of climate change effects on coral reef fishes. Thirty-three scientists provided 155 questions, and 32 scientists scored these questions in terms of: (i) identifying a knowledge gap, (ii) achievability, (iii) applicability to a broad spectrum of species and reef habitats, and (iv) priority. Forty-two per cent of the questions related to habitat associations and community dynamics of fish, reflecting the established effects and immediate concern relating to climate-induced coral loss and habitat degradation. However, there were also questions on fish demographics, physiology, behaviour and management, all of which could be potentially affected by climate change. Irrespective of their individual expertise and background, scientists scored questions from different topics similarly, suggesting limited bias and recognition of a need for greater interdisciplinary and collaborative research. Presented here are the 53 highest-scoring unique questions. These questions should act as a guide for future research, providing a basis for better assessment and management of climate change impacts on coral reefs and associated fish communities.

The fisheries and biodiversity benefits of marine reserves are widely recognised but there is mounting interest in exploiting the importance of herbivorous fishes a tool to help ecosystems recover from climate change impacts. This approach might be particularly suitable for coral reefs which are acutely threatened by climate change yet the trophic cascades generated by reserves are strong enough that they might theoretically enhance the rate of coral recovery after disturbance. However, evidence for reserves facilitating coral recovery has been lacking. Here we investigate whether reductions in macroalgal cover, caused by recovery of herbivorous parrotfishes within a reserve, have resulted in a faster rate of coral recovery than in areas subject to fishing. Surveys of 10 sites inside and outside a Bahamian marine reserve over a 2.5 year period demonstrated that increases in coral cover, including adjustments for the initial size-distribution of corals, were significantly higher at reserve sites than that in non-reserve sites. Furthermore, macroalgal cover was significantly negatively correlated with the change in total coral cover over time. Recovery rates of individual species were generally consistent with small-scale manipulations on coral-macroalgal interactions, but also revealed differences that demonstrate the difficulties of translating experiments across spatial scales. Size-frequency data indicated that species which were particularly affected by high abundances of macroalgae outside the reserve had a population bottleneck restricting the supply of smaller corals to larger size classes. Importantly, because coral cover increased from a heavily degraded state, and recovery from such states has not previously been described, similar or better outcomes should be expected for many reefs in the region. Reducing herbivore exploitation as part of an ecosystem-based management strategy for coral reefs appears to be justified.

Disease has dramatically reduced populations of the herbivorous urchin Diadema antillarum Philippi on Caribbean reefs, contributing to an increased abundance of macroalgae and reduction of coral cover. Therefore, recovery of D. antillarum populations is critically important, but densities are still low on many reefs. Among the many potential factors limiting these densities, the focus of this study is on predation pressure by fishes. Marine reserves provide opportunities to examine large-scale manipulations of predator-prey interactions and, therefore, D. antillarum densities were compared inside and outside a reserve in the Bahamas (Exuma Cays Land and Sea Park; ECLSP). Urchins and their fish predators were surveyed at nine sites inside and outside the ECLSP. Because of lower fishing effort, the total biomass of urchin predators, weighted by their dietary preferences for urchins, was significantly higher inside the ECLSP. Furthermore, fish community structure was significantly different inside the Park because of the increased biomass of the majority of species. No urchins were seen inside the ECLSP and this was significantly lower than the density of 0.04 urchin m-2 outside the Park. Regression analysis indicated that the relationship between the biomass of urchin predators and the proportion of transects containing urchins was non-linear, suggesting that small increases in fish biomass dramatically reduce urchin abundances. The link between lower density of urchins and higher density of their predators inside the ECLSP is strengthened by discounting five alternative primary mechanisms (variations in macroalgal cover, larval supply, environmental setting, density of other urchin species and abundance of predators not surveyed). Caribbean marine reserves have an important conservation role, but increased fish predation appears to reduce densities of D. antillarum. Urchins currently have limited functional significance on Bahamian reefs, but any future recovery of D. antillarum is likely to be limited in reserves, with potentially important ecological consequences. © Springer-Verlag 2009.

1. No-take reserves are a common tool for fisheries management and biodiversity conservation in marine ecosystems. Despite much discussion of their benefits, data documenting many reserve effects are surprisingly scarce. Several studies have also been criticized for a lack of rigour so that changes within reserves cannot be separated from underlying natural variation and attributed unequivocally to protection. 2. We sampled both benthic (video quadrats) and associated fish communities (underwater visual censuses) in a well-enforced reserve in the Bahamas. Sampling was explicitly stratified by habitat ('Montastraea reef' and 'gorgonian plain'). To distinguish reserve effects from natural variation, we compared changes inside and outside the reserve with those seen at equivalent spatial scales in other reef systems in the Bahamian archipelago that lack reserves. Reserve-level differences in benthic or fish communities not documented in other reef systems are categorized as 'robust' effects. 3. Robust reserve effects were limited to Montastraea reefs. The reserve supported an average of ≈ 15% more fish species per site compared to outside the reserve. This pattern was particularly driven by more large-bodied grouper, damselfish, and butterflyfish species inside the reserve. Increases in fish biomass and differences in community structure inside the reserve were limited to large-bodied groupers. Increased grazing pressure by parrotfishes in the reserve has lowered macroalgal cover, and caused previously undocumented changes in benthic community structure compared to sites outside the reserve. 4. Some reserve-level differences in fish communities were categorized as 'misleading' because equivalent differences were seen in other reef systems, and are likely to be caused by natural intra-habitat variation. Separation of robust and misleading results was only possible because of archipelago-scale sampling. 5. Synthesis and applications. The Bahamas represents a relatively lightly fished system within the Caribbean. However, cessation of fishing has still increased the mean number of species, the abundance of the most highly prized fishes and, through trophic cascades, altered benthic community structure. In certain habitats, reserves are clearly important for conserving fisheries and biodiversity. However, reserve effects must be explicitly separated from confounding variables to ensure conservation benefits are accurately identified and reported, and not oversold to managers and local stakeholders. © 2008 the Authors.

1. Theory is unclear about the optimal degree of isolation of habitat fragments where the aim is to maximise species richness. In a field-based microecosystem of Collembola and predatory and non-predatory mites, moss patches of the same total area were fragmented to varying degrees. The habitat was left for several months to allow the communities to approach a new state of equilibrium. 2. The species richness (in particular of predatory mites) of a given area of habitat was greater when it was part of a large mainland area than part of an island, in agreement with theory. 3. Conversely, species richness and abundance were largely unaffected by fragmentation of a fixed area of island habitat. In this case, it is suggested here that the advantages of several small patches (e.g. reduced impact of environmental stochasticity, wider range of habitats overall) were equally balanced by the advantages of a single large patch (e.g. reduced effect of demographic stochasticity, wider range of habitats within a single patch, reduced edge effect), or that both effects were small. 4. The shapes of rank-abundance curves were similar among the levels of fragmentation of a fixed area of island habitat, implying that fragmentation had little impact on community structure. Conversely, the species composition of non-predatory mites varied weakly, but significantly, by fragmentation. © Royal Entomological Society, 2005.

Specular reflection of solar radiation on non-flat water surfaces is a serious confounding factor for benthic remote sensing in shallow-water environments. This problem was recently overcome by Hochberg et al. who provided an effective method for the removal of 'sun glint' from remotely sensed images by utilization of the brightness in a near-infrared (NIR) band. Application of the technique was shown to give an increase in the accuracy of benthic habitat classification. However, as presented, the method is sensitive to outlier pixels, requires a time-consuming masking of land and cloud, and is not formulated in a manner leading to ease of implementation. We present a revised version of the method, which is more robust, does not require masking and can be implemented very simply. The practical approach described here will hopefully expedite the routine adoption of this effective and simple technique throughout the aquatic remote sensing community. © 2005 Taylor & Francis Group Ltd.

The coast of Honduras, Central America, represents the southern end of the Mesoamerican Barrier Reef System, although its marine resources are less extensive and studied than nearby Belize and Mexico. However, the coastal zone contains mainland reef formations, mangroves, wetlands, seagrass beds and extensive fringing reefs around its offshore islands, and has a key role in the economy of the country. Like most tropical areas, this complex of benthic habitats experiences limited annual variation in climatic and oceanographic conditions but seasonal and occasional conditions, particularly coral bleaching and hurricanes, are important influences. The effects of stochastic factors on the country's coral reefs were clearly demonstrated during 1998 when Honduras experienced a major hurricane and bleaching event. Any natural or anthropogenic impacts on reef health will inevitably affect other countries in Latin America, and vice versa, since the marine resources are linked via currents and the functioning of the system transcends political boundaries. Much further work on, for example, movement of larvae and transfer of pollutants is required to delineate the full extent of these links. Anthropogenic impacts, largely driven by the increasing population and proportion of people living in coastal areas, are numerous and include key factors such as agricultural run-off, over-fishing, urban and industrial pollution (particularly sewage) and infrastructure development. Many of these threats act synergistically and, for example, poor watershed management via shifting cultivation, increases sedimentation and pesticide run-off onto coral reefs, which increases stress to corals already affected by decreasing water quality and coral bleaching. Threats from agriculture and fishing are particularly significant because of the size of both industries. The desire to generate urgently required revenue within Honduras has also led to increased tourism which provides an overarching stress to marine resources since most tourists spend time in the coastal zone. Hence the last decade has seen a dramatic increase in coastal development, a greater requirement for sewage treatment and more demand for freshwater, particularly in the Bay Islands. Although coastal zone management is relatively recent in Honduras, it is gaining momentum from both large-scale initiatives, such as the Ministry of Tourism's 'Bay Islands Environmental Management Project', and national and international NGO projects. For example, a series of marine protected areas and legislative regulations have been established, but management capacity, enforcement and monitoring are limited by funding, expertise and training. Existing and future initiatives, supported by increased political will and environmental awareness of stakeholders, are vital for the long-term economic development of the country.

1. This paper describes a straightforward method for introducing species weightings into the calculation of a similarity matrix using the Bray-Curtis coefficient. Weighting may be required in order to provide differential emphasis in abundances on the basis of species' size, ecological importance, abundance or in mixing different data types. The similarity matrix can then be used for a range of multivariate analytical procedures, such as cluster analysis or ordination using non-metric multi-dimensional scaling (MDS). Such techniques are widely used for the identification of species' assemblages and habitats in marine resource and conservation assessment. 2. The weighting procedure was used to examine the effect of variable accuracy in species identification by trained volunteer divers conducting baseline surveys of reefal habitats in Belize. The accuracy of identification was found to vary asymmetrically between species. 3. The modified Bray-Curtis similarity coefficient was used to incorporate individual species weightings which are proportional to the frequency at which each species is correctly identified. The results of the study demonstrate the fundamental robustness of the Bray-Curtis similarity coefficient/multivariate approach which together, are insensitive to the asymmetric accuracy levels present in the data.