How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?

Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non‐overlapping assemblages rather than subsets of one another. As a result, non‐saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false‐negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA.     

Clumped versus scattered: how does the spatial correlation of disturbance events affect biodiversity?

In this study, we systematically explore the effects of rate and spatial correlation (level of clumping) of disturbance events on a community of sessile species differing in their life history traits. A spatially explicit individual-based model shows that long-term coexistence is very sensitive to spatial correlation when the trade-off in life history traits includes differences in dispersal distances. Highest biodiversity emerges at highly correlated disturbances of intermediate rates. Diversity peaks shift to larger rates when clumping decreases. Scattered disturbances lead to competitive exclusion. Interestingly, we observed additional peaks in the diversity–disturbance curves at certain levels of clumping. Thus, subject to the differences in life history traits, particular combinations of disturbance rate and spatial correlation may enable subsets of species to coexist, which opens new possibilities for explaining diversity. Our results suggest that observation of high biodiversity under spatially correlated disturbances points to a competition–colonisation trade-off, which includes dispersal distances.     

Older species: a rejuvenation on coral reefs?

Aim To discuss the theory that the present high species diversity and apomorphic character of the coral reef ecosystem is because of the historic accumulation of basal species from marginal habitats. Location The Indo‐West Pacific Ocean. Methods The examination of biogeographical patterns from the standpoint of paleontology, phylogeny, genetics, and empirical data. Results Fossil patterns from several clades indicate a gradient of increasing average generic age that extends outward from the high diversity reefs. Successful species that give rise to new species, genera, and families apparently originate from high diversity locations. The tropics have been a major source of evolutionary novelty, not simply a refuge that has accumulated diversity. Many plesiomorphic clades, that once dominated the shallow tropics, are now limited to the deep sea and other safe places. Recent research on several tropical fish families indicates that more apomorphic species inhabit the high diversity reefs. Genetic studies suggest that a decrease in genetic variation extends from the diversity centre toward the outer reaches of the Indo‐West Pacific. Empirical data show that it is extremely difficult for species from low diversity areas to invade places of higher diversity. Main conclusions There is no convincing evidence to indicate that basal species from marginal habitats have been able to accumulate on the coral reefs. Once such species have been displaced from a high diversity environment, there is apparently no return. The evolutionary innovations that contribute to the origination of new phyletic lines take place under conditions of high diversity and maximum competition.     

Do elevated nutrients and organic carbon on Philippine reefs increase the prevalence of coral disease?

Characterizations of Philippine coral diseases are very limited. The two most common, ulcerative white spot disease (UWS) and massive Porites growth anomalies (MPGA), target the genus Porites, a dominant reef-building genus. This is the first investigation in the Philippines to detect positive correlations between coral disease, nutrient levels, and organic carbon. A total of 5,843 Porites colonies were examined. Water and sediment samples were collected for analyses of nutrients (total nitrogen and phosphorus) and total organic carbon at 15 sites along a 40.5 km disease gradient, which was previously shown to positively correlate with human population levels. Results suggest that outbreaks of UWS and MPGAs are driven by elevated nutrient and organic carbon levels. Although the variables analyzed could be proxies for other causative agents (e.g., high sediment levels), the results provide quantitative evidence linking relatively higher coral disease prevalence to an anthropogenically impacted environment.     

Are conservation units in the Caatinga biome,Brazil, efficient in the protection of biodiversity? An analysis based on the drosophilid fauna

Biodiversity is believed to be low in regions with vegetation that has adapted to water stress. Additionally, there is little interest by authorities in establishing and expanding conservation units in these areas. In Brazil, the Caatinga and the Cerrado biomes comprise this xerophilous vegetation. In both, climate is tropical and the dry season is long and well-defined. The Caatinga is the Brazilian biome with the smallest area protected by conservation units. This study evaluates the efficacy of conservation units in the Caatinga biome based on abundance and richness of drosophilids. Flies were collected inside and outside these areas. In total, approximately 23,000 flies of 32 species were collected in six conservation and six non-conservation sites. Two non-described species occurred exclusively inside protected areas, underlining the importance of conservation efforts in the maintenance of biodiversity. Other species were recorded exclusively outside conservation areas, which emphasizes the importance of establishing and expanding conservation units in the Caatinga. Native species were significantly more abundant inside conservation units, though the richness was similar in protected and non-protected areas. Abundance of exotic species outside conservation areas was statistically different in comparison with that of native ones.     

Can a thermally tolerant symbiont improve the future of Caribbean coral reefs?

The detrimental effect of climate change induced bleaching on Caribbean coral reefs has been widely documented in recent decades. Several studies have suggested that increases in the abundance of thermally tolerant endosymbionts may ameliorate the effect of climate change on reefs. Symbionts that confer tolerance to temperature also reduce the growth rate of their coral host. Here, we show, using a spatial ecosystem model, that an increment in the abundance of a thermally tolerant endosymbiont (D1a) is unlikely to ensure the persistence of Caribbean reefs, or to reduce their rate of decline, due to the concomitant reduction in growth rate under current thermal stress predictive scenarios. Furthermore, our results suggest that given the documented vital rates of D1a‐dominated corals, increasing dominance of D1a in coral hosts may have a detrimental effect by reducing the resilience of Caribbean reefs, and preventing their long‐term recovery. This is because Caribbean ecosystems appear to be highly sensitive to changes in the somatic growth rate of corals. Alternative outcomes might be expected in systems with different community‐level dynamics such as reefs in the Indo‐Pacific, where the ecological costs of reduced growth rate might be far smaller.     

Suppression of herbivory by macroalgal density: a critical feedback on coral reefs?

Coral reefs globally are in decline, with some reefs undergoing phase shifts from coral-dominance to degraded states dominated by large fleshy macroalgae. These shifts have been underpinned by the overharvesting of herbivorous fishes and represent a fundamental change in the physical structure of these reefs. Although the physical structure provided by corals is regarded as a key feature that facilitates herbivore activity, the influence of the physical structure of macroalgal stands is largely unknown. Using transplanted Sargassum, the largest coral reef macroalga, we created habitat patches of predetermined macroalgal density (0.25-6.23 kg m(-2)). Remote video cameras revealed both grazing and browsing fishes avoided high density patches, preferring relatively open areas with low macroalgal cover. This behaviour may provide a positive feedback leading to the growth and persistence of macroalgal stands; increasing the stability of phase shifts to macroalgae.     

Is surface orientation a determinant for colonisation patterns of vagile and sessile macrobenthos on artificial reefs?

In order to examine how substratum colonisation can affect community structure, a 1-year study was conducted at the Faro/Ancão artificial reef (Algarve, Portugal). In the study of hard substratum communities, motile species are usually neglected and only the conspicuous species are taken into account. Therefore, the development of vagile and sessile components of the epibiotic community were analysed separately. Differences between assemblages on horizontal surfaces, but not on vertical surfaces, were detected. Multivariate analysis detected differences in macrobenthic community structure either considering sessile or motile components. However, significant differences were only detected for vagile fauna. Moreover, this study suggests that for hard substratum communities, analysis of the vagile fauna is important and should be taken into account in the functioning of the artificial raft.     

Is surface orientation a determinant for colonisation patterns of vagile and sessile macrobenthos on artificial reefs?

In order to examine how substratum colonisation can affect community structure, a 1-year study was conducted at the Faro/Ancao artificial reef (Algarve, Portugal). In the study of hard substratum communities, motile species are usually neglected and only the conspicuous species are taken into account. Therefore, the development of vagile and sessile components of the epibiotic community were analysed separately. Differences between assemblages on horizontal surfaces, but not on vertical surfaces, were detected. Multivariate analysis detected differences in macrobenthic community structure either considering sessile or motile components. However, significant differences were only detected for vagile fauna. Moreover, this study suggests that for hard substratum communities, analysis of the vagile fauna is important and should be taken into account in the functioning of the artificial raft.     

Will the "new biology" affect the future of histopathology?

The technologies used in histopathology are changing as a consequence of the current revolutionary progress in several areas of biology. It is likely that general cancer management will improve because of the impact of molecular techniques and immunohistochemistry on tumor diagnosis and classification and on the determination of prognosis and response to therapy. Moreover, as therapies are starting to be modelled after the distinctive molecular characteristics of a specific tumor, the availability of molecular tests to all patients will become a matter of great importance.     

Taphonomy of modern deep,cold‐temperate water coral reefs

Deep‐water corals are widely distributed along the cold‐temperate northeastern Atlantic continental margin. Despite the widespread occurrence of these aphotic coral constructions in deep shelf settings, the processes of framework formation and postmortem alterations which result in different preservational styles are still poorly known. Detailed mapping surveys on probably one of the largest Lophelia reef structures were carried out on the Sula Ridge, Mid‐Norwegian Shelf in 270 to 300 m depth. Side scan sonar records and camera surveys yield information at various scales of resolution on the reef complex which is more than 9 km long and up to 45 m high. Living Lophelia colonies effectively prevent colonization by other organisms and are successful in the rejection of passing detrital material from the soft tissue. In a healthy condition the coral is able to encrust repetitively attached organisms by selectively secreted sclerenchyme layers, thus, this defensive reaction results in the thickening of the skeleton. Early postmortem alteration in Lophelia colonies is introduced by the formation of a biofilm and Dodgella (fungi) infestation. The biofilm is associated with selective Fe‐Mn precipitation on the coral skeleton. This is the zone of intense attachment of sessile invertebrates such as serpulids, brachiopods, foraminifers and encrusting bryozoans. More advanced taphonomic stages show an increasing dominance in sponges which reduce the interskeletal framework porosity significantly. In addition, boring sponges excavate the thickly calcified Lophelia skeletons, thus leading to in situ collapsing structures on the sea floor. It is the intensity of sediment trapping biofilms and sponge colonization and the amount of imported detrital particles predominantly from the pelagial zone that control the generation of a pure coral rubble facies or the preservation of collapsed but mud‐rich detrital mounds.     

Biotic resistance on coral reefs? Direct and indirect effects of native predators and competitors on invasive lionfish

Coral Reefs - Biotic resistance is the ability of an ecological community to prevent or limit the establishment or success of non-indigenous species. Native species can confer resistance by...     

New taxonomy and niche partitioning on coral reefs: jack of all trades or master of some?

Recent taxonomic advances are challenging widely held theories of the ecology and evolution of coral reef Invertebrates and communities. Large numbers of sibling species have been discovered across a variety of higher taxa. Differences in distribution, behavior and life history characteristics among sibling species demonstrate that niche diversification is more finely tuned, and interactions among organisms more specific, than most reef ecologists believed previously. Ecological and evolutionary understanding depends on good taxonomy.     

Will transgenic plants adversely affect the environment?

Transgenic insecticidal plants based onBacillus thuringiensis (Bt) endotoxins, on proteinase inhibitors and on lectins, and transgenic herbicide tolerant plants are widely used in modern agriculture. The results of the studies on likelihood and non-likelihood of adverse effects of transgenic plants on the environment including: (i) effects on nontarget species; (ii) invasiveness; (iii) potential for transgenes to ‘escape’ into the environment by horizontal gene transfer; and (iv) adverse effects on soil biota are reviewed. In general, it seems that large-scale implementation of transgenic insecticidal and herbicide tolerant plants do not display considerable negative effects on the environments and, moreover, at least some transgenic plants can improve the corresponding environments and human health because their production considerably reduces the load of chemical insecticides and herbicides.     

Will coral reef sponges be winners in the Anthropocene?

Recent observations have shown that increases in climate change‐related coral mortality cause changes in shallow coral reef community structure through phase shifts to alternative taxa. As a result, sponges have emerged as a potential candidate taxon to become a “winner,” and therefore a numerically and functionally dominant member of many coral reef communities. But, in order for this to occur, there must be sufficient trophic resources to support larger populations of these active filter‐feeding organisms. Globally, climate change is causing an increase in sea surface temperatures (SSTs) and a decrease in salinity, which can lead to an intensification in the stratification of shallow nearshore waters (0–200 m), that affects both the mixed layer depth (MLD) and the strength and duration of internal waves. Specifically, climate change‐driven increases in SSTs for tropical waters are predicted to cause increased stratification, and more stabilized surface waters. This causes a shallowing of the MLD which prevents nutrients from reaching the euphotic zone, and is predicted to decrease net primary production (NPP) up to 20% by the end of the century. Lower NPP would subsequently affect multiple trophic levels, including shallow benthic filter‐feeding communities, as the coupling between water column productivity and the benthos weakens. We argue here that sponge populations may actually be constrained, rather than promoted, by climate change due to decreases in their primary trophic resources, caused by bottom‐up forcing, secondary to physical changes in the water column (i.e., stratification and changes in the MLD resulting in lower nutrients and NPP). As a result, we predict sponge‐dominated tropical reefs will be rare, or short‐lived, if they occur at all into the future in the Anthropocene.     

Seasonal monitoring of coral–algae interactions in fringing reefs of the Gulf of Aqaba, Northern Red Sea

This paper presents seasonal in situ monitoring data on benthic coverage and coral–algae interactions in high-latitude fringing reefs of the Northern Red Sea over a period of 19 months. More than 30% of all hermatypic corals were involved in interaction with benthic reef algae during winter compared to 17% during summer, but significant correlation between the occurrence of coral–algae interactions and monitored environmental factors such as temperature and inorganic nutrient availability was not detected. Between 5 and 10-m water depth, the macroalgae Caulerpa serrulata, Peyssonnelia capensis and filamentous turf algae represented almost 100% of the benthic algae involved in interaction with corals. Turf algae were most frequently (between 77 and 90% of all interactions) involved in interactions with hermatypic corals and caused most tissue damage to them. Maximum coral tissue loss of 0.75% day⁻¹ was observed for Acropora-turf algae interaction during fall, while an equilibrium between both groups of organisms appeared during summer. Slow-growing massive corals were more resistant against negative algal influence than fast-growing branching corals. Branching corals of the genus Acropora partly exhibited a newly observed phenotypic plasticity mechanism, by development of a bulge towards the competing organism, when in interaction with algae. These findings may contribute to understand the dynamics of phase shifts in coral reefs by providing seasonally resolved in situ monitoring data on the abundance and the competitive dynamic of coral–algae interactions.     

Experimental studies of rapid bioerosion of coral reefs in the Galápagos Islands

Experimental carbonate blocks of coral skeleton,Porites lobata (PL), and cathedral limestone (LS) were deployed for 14.8 months at shallow (5–6 m) and deep (11–13m) depths on a severely bioeroded coral reef, Champion Island, Galápagos Islands, Ecuador. Sea urchins (Eucidaris thouarsii) were significantly more abundant at shallow versus deep sites.Porites lobata blocks lost an average of 25.4 kg m^–2yr^–1 (23.71 m^–2yr^–1 or 60.5% decrease yr^–1). Losses did not vary significantly at depths tested. Internal bioeroders excavated an average of 2.6 kg m^–2 yr^–1 (2.41 m^–2 yr^–1 or 0.6% decrease yr^–1), while external bioeroders removed an average of 22.8 kg m^–2 yr^–1). (21.31 m^–2 yr^–1). or 59.9% decrease yr^–1). few encrusting organisms were observed on the PL blocks. Cathedral limestone blocks lost an average of 4.1 kg m^–2 yr^–1). (1.81 m^–2 yr^–1). or 4.6% decrease yr-'), also with no relation to depth. Internal bioeroders excavated an average of 0.6 kg m^–2 yr^–1). (0.31 m^–2 yr^–1). or 0.7% decrease yr^–1). and external bioeroders removed an average of 3.5 kg m^–2 yr^–1). (1.51 m^–2 yr^–1). or 3.9% decrease yr^–1). from the LS blocks. Most (57.6%) encrustation occurred on the bottom of LS blocks, and there was more accretion on block bottoms in deep (61.4 mg cm^–2 yr^–1). versus shallow (35.0 mg cm^–2 yr^–1) sites. External bioerosion reduced the average height of the reef framework by 0.2 cm yr^–1). for hard substrata (represented by LS) and 2.3 cm yr^–1). for soft substrata (represented by PL). The results of this study suggest that coral reef frameworks in the Galápagos Islands are in serious jeopardy. If rates of coral recruitment do not increase, and if rates of bioerosion do not decline, coral reefs in the Galápagos Islands could be eliminated entirely.     

Does the abundance of girellids and kyphosids correlate with cover of the palatable green algae,Ulva spp.? A test on temperate rocky intertidal reefs

This study assessed whether the abundance of girellids and kyphosids was related to cover of the palatable green algae, Ulva australis and Ulva compressa, on rocky intertidal reefs in Jervis Bay, New South Wales, Australia. No relationship was found between Ulva spp. cover and abundance of Girella tricuspidata, Girella elevata and Kyphosus sydneyanus during a period of relatively low Ulva spp. cover (i.e. February 2011 to March 2011), but during a period of significantly higher Ulva spp. cover (i.e. October 2011 to November 2011) there was a strong correlation between Ulva spp. cover and G. tricuspidata abundance. Spatial analysis indicated that the abundance of G. tricuspidata was consistent across time, suggesting G. tricuspidata were not moving between reefs in response to variation in Ulva spp. cover between periods but rather that large schools of G. tricuspidata resided on reefs that had relatively higher Ulva spp. cover at certain times of the year.