Search

Understanding evolutionary transitions in scleractinian corals is fundamental to predicting responses of coral reefs to climate change. We examine transitions between solitary and colonial corals i...

In this contribution we describe and illustrate 14 coral morphospecies collected from the early Miocene Siamaná (Aquitanian–Burdigalian) and Jimol (late Burdigalian) formations of the Cocinetas Basin in La Guajira Peninsula, northern Colombia. Eleven were identified as already established species including seven genera belonging to the families Mussidae, Pocilloporidae, Poritidae, Siderastreidae, and Milleporidae; the other three remain in open nomenclature. Nine of the 11 species identified (81%) are extinct. The remaining two living species,Siderastrea sidereaandMillepora alcicornis, are common on modern Caribbean reefs. Their presence in the Siamaná Formation extends their temporal range in the Caribbean region to the early Miocene. Most of the taxa described here were hermatypic and zooxanthellate corals of the order Scleractinia, with the exception of the fire coralMillepora alcicornis, of the order Anthothecata, family Milleporidae. The coral fauna recorded in the Siamaná and Jimol formations is typical of shallow and calm waters of the Oligocene–Miocene transition.

We document for the first time Miocene corals from the Siamaná and Jimol formations of the Cocinetas Basin in La Guajira Peninsula, northern Colombia. This is the first of two contributions dedicated to the description and detailed illustration of morphospecies collected during two scientific expeditions (2011, 2014) to the remote region. Here we report coral morphospecies attributed to the families Acroporidae, Agathiphylliidae, Astrocoeniidae, Caryophylliidae, Diploastraeidae, Merulinidae, and Montastraeidae. Eighteen species belonging to these seven families, included in nine genera, are described. Fifteen species are assigned to established taxa, while three remain in open nomenclature. Of the species identified, onlyMontastraea cavernosa(Linnaeus, 1767) exists today. The coral taxa described are typical of the Oligocene–Miocene transition and were important components of shallow-water reefs in the Caribbean and Gulf of Mexico region during this period. The occurrence ofAgathiphylliaspp.,Antiguastrea, andDiploastreaspp. confirms the presence of these genera in the Miocene of the Southern Caribbean. Coral assemblages suggest that the La Guajira coral community thrived in calm and shallow waters.

The coral fauna of the Tamiami Formation documents a northern expansion of reef development along the Florida Peninsula during the mid-Pliocene warm period (MPWP). Radiometric dating (U-Pb) of Solenastrea bournoni produced an age of 2.99 ± 0.11 Ma, constraining reef development to the MPWP and the peak of Plio-Pleistocene faunal turnover; subsequent to the final closure of the Central American Seaway (CAS) but prior to major Northern Hemisphere Glaciation (NHG). Coral faunal analyses are based on a total of 1614 coral specimens collected along a 165 km stretch of the west Florida coast, and included rarefaction and detrended correspondence analysis (DCA). A total of 60 coral species occur within the Tamiami Formation, with faunal assemblages ranging from 42 to 87% extinct taxa. The Tamiami collections can be split into a southern “reef” assemblage with high diversity of stenotopic taxa and a northern “non-reef” assemblage with lower diversity eurytopic taxa. The southern reef assemblage contains framework buildups of the dominant tropical taxa Stylophora affinis , Orbicella annularis , and Acropora cervicornis . We interpret enhanced west Florida reef development during the middle Pliocene to be a product of more equitable sea surface temperatures, and reduced salinity fluctuations associated with higher sea levels. While mean sea surface temperature estimates based on oxygen isotopic analysis of the coral Solenastrea bournoni (25.3 °C) are similar to present day values (26 °C), a completely flooded southern Florida Platform in the Pliocene would be less prone to salinity fluctuations associated with coastal runoff and extreme cold-water events during winter storms. While higher latitude range shifts of tropical reef corals associated with current global climate change have been documented elsewhere in the world, we do not foresee the West Florida Shelf being conducive to significant range shifts in tropical coral taxa or reef development within the coming century.

The depositional setting for northern most Atlantic coral reef development during the Mid-Pliocene Warm Period is a gentle sloping mixed carbonate–siliciclastic ramp. Five core transects document the distribution of the reef complex in an area approximately 65 by 12 km, and nine repetitive depositional facies are identified. Paleoecological and sedimentological evidence documents facies development along a water depth–energy gradient. The mid-Pliocene Tamiami Formation is characterized by coral boundstone developed over level skeletal rudstone depositional units dominated by mollusks. Hyotissa haitensis (Sowerby), one of the last Gryphaeid oysters, is the dominant fossil found in the most continuous skeletal facies and overlies deeper water green clay facies, the only facies with pelagic foraminifera. Ground penetrating radar documents reef depositional topography, onlapping stratigraphy and two episodes of reef growth. Two cycles of deposition are recognized, separated by subaerial exposure. The coral boundstone and the skeletal rudstone exhibit both high primary and secondary porosity and overlie the impermeable clay facies. The upper surface of the coral boundstone lies at ~ 4 m in elevation whereas contemporaneous estuarine deposits are found to the north at elevations of 20–25 m. High porosity bank reef complexes along a shallow dipping ramp provide an alternative to the standard model of reef and porosity development along the outer shelf margin. Understanding the differences in associated facies between these two depositional environments permits better interpretation of observed heterogeneities in subsurface geobodies associated with inner shelf and platform settings.

Anthropogenic climate change compromises reef growth as a result of increasing temperatures and ocean acidification. Scleractinian corals vary in their sensitivity to these variables, suggesting species composition will influence how reef communities respond to future climate change. Because data are lacking for many species, most studies that model future reef growth rely on uniform scleractinian calcification sensitivities to temperature and ocean acidification. In order to address this knowledge gap, calcification of twelve common and understudied Caribbean coral species was measured for two months under crossed temperatures (27°C, 30.3°C) and CO2 partial pressures (pCO2) (400, 900, 1300 μatm). Mixed effects models of calcification for each species were then used to project community-level scleractinian calcification using Florida Keys reef composition data and IPCC AR5 ensemble climate model data. Three of the four most abundant species, Orbicella faveolata, Montastraea cavernosa, and Porites astreoides, had negative calcification responses to both elevated temperature and pCO2. In the business-as-usual CO2 emissions scenario, reefs with high abundances of these species had projected end-of-century declines in scleractinian calcification of >50% relative to present-day rates. Siderastrea siderea, the other most-common species, was insensitive to both temperature and pCO2 within the levels tested here. Reefs dominated by this species had the most stable end-of-century growth. Under more optimistic scenarios of reduced CO2 emissions, calcification rates throughout the Florida Keys declined

The fast growing calcareous skeletons of zooxanthellate reef corals (z corals) represent unique environmental proxy archives through their oxygen and carbon stable isotope composition (δ18O, δ13C). In addition, the accretion of the skeleton itself is ultimately linked to the environment and responds with variable growth rates (extension rate) and density to environmental changes. Here we present classical proxy data (δ18O, δ13C) in combination with calcification records from 15 massive z corals. The z corals were sampled from four interglacial units of the Florida carbonate platform (USA) dated approximately 3.2, 2.9, 1.8 and 1.2 Ma (middle Pliocene to early Pleistocene). The z corals (Solenastrea, Orbicella, Porites) derive from unlithified shallow marine carbonates and were carefully screened for primary preservation suited for proxy analysis. We show that skeletal accretion responded with decreasing overall calcification rates (decreasing extension rate but increasing density) to warmer water temperatures. Under high annual water temperatures, inferred from sub-annually resolved δ18O data, skeletal bulk density was high, but extension rates and overall calcification rates were at a minimum (endmember scenario 1). Maximum skeletal density was reached during the summer season giving rise to a growth band of high density within the annually banded skeletons (“high density band”, HDB). With low mean annual water temperatures (endmember scenario 2), bulk skeletal density was low but extension rates and calcification rates reached a maximum, and under these conditions the HDB formed during winter. Although surface water temperatures in the Western Atlantic warm pool during the interglacials of the late Neogene were ∼ 2 °C higher than they are in the present day, intermittent upwelling of cool, nutrient-rich water mitigated water temperatures off south-western Florida and created temporary refuges for z coral growth. Based on the sub-annually resolved δ18O and δ13C records, the duration of the upwelling episodes causing the endmember 2 conditions was variable and lasted from a few years to a number of decades. The episodes of upwelling were interrupted by phases without upwelling (endmember 1) which lasted for at least a few years and led to high surface water temperatures. This variable environment is likely one of the reasons why the coral fauna is dominated by the eurytopic genus Solenastrea, also a genus resistant to high turbidity. Over a period of ∼ 50 years, the oldest sub annually resolved proxy record available (3.2 Ma) documents a persistent occurrence of the HDB during winter. In contrast, the HDB forms in summer in modern z corals from the Florida reef tract. We suggest this difference should be tested as being the expression of a tendency towards decreasing interglacial upwelling since the middle Pliocene. The number of z coral sclerochronological records for the Plio-Pleistocene is still rather low, however, and requires more data and an improved resolution, through records from additional time slices. Nonetheless, our calcification data from the warm periods of past interglacials may contribute to predicting the effects of future ocean warming on z coral health along the Florida reef tract. The inconsistent timing of the HDB within single coral records or among specimens and time slices is unexpected and contrasts the common practice of establishing chronologies on the basis of the density banding.

In geological outcrops and drill cores from reef frameworks, the skeletons of scleractinian corals are usually leached and more or less completely transformed into sparry calcite because the highly porous skeletons formed of metastable aragonite (CaCO3) undergo rapid diagenetic alteration. Upon alteration, ghost structures of the distinct annual growth bands often allow for reconstructions of annual extension ( = growth) rates, but information on skeletal density needed for reconstructions of calcification rates is invariably lost. This report presents the bulk density, extension rates and calcification rates of fossil reef corals which underwent minor diagenetic alteration only. The corals derive from unlithified shallow water carbonates of the Florida platform (south-eastern USA), which formed during four interglacial sea level highstands dated approximately 3.2, 2.9, 1.8, and 1.2 Ma in the mid-Pliocene to early Pleistocene. With regard to the preservation, the coral skeletons display smooth growth surfaces with minor volumes of marine aragonite cement within intra-skeletal porosity. Within the skeletal structures, voids are commonly present along centres of calcification which lack secondary cements. Mean extension rates were 0.44 ± 0.19 cm yr−1 (range 0.16 to 0.86 cm yr−1), mean bulk density was 0.96 ± 0.36 g cm−3 (range 0.55 to 1.83 g cm−3) and calcification rates ranged from 0.18 to 0.82 g cm−2 yr−1 (mean 0.38 ± 0.16 g cm−2 yr−1), values which are 50 % of modern shallow-water reef corals. To understand the possible mechanisms behind these low calcification rates, we compared the fossil calcification rates with those of modern zooxanthellate corals (z corals) from the Western Atlantic (WA) and Indo-Pacific calibrated against sea surface temperature (SST). In the fossil data, we found a widely analogous relationship with SST in z corals from the WA, i.e. density increases and extension rate decreases with increasing SST, but over a significantly larger temperature window during the Plio-Pleistocene. With regard to the environment of coral growth, stable isotope proxy data from the fossil corals and the overall structure of the ancient shallow marine communities are consistent with a well-mixed, open marine environment similar to the present-day Florida Reef Tract, but variably affected by intermittent upwelling. Upwelling along the platform may explain low rates of reef coral calcification and inorganic cementation, but is too localised to account also for low extension rates of Pliocene z corals throughout the tropical WA region. Low aragonite saturation on a more global scale in response to rapid glacial–interglacial CO2 cyclicity is also a potential factor, but Plio-Pleistocene atmospheric pCO2 is generally believed to have been broadly similar to the present day. Heat stress related to globally high interglacial SST only episodically moderated by intermittent upwelling affecting the Florida platform seems to be another likely reason for low calcification rates. From these observations we suggest some present coral reef systems to be endangered from future ocean warming.

Bacteriophages infect an estimated 1023 to 1025 bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub “superspreaders,” releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation. Two novel Escherichia coli phage superspreaders, SUSP1 and SUSP2, liberated four evolutionarily distinct plasmids with equal efficiency, including two close relatives of prominent antibiotic resistance vectors in natural environments. SUSP2 also mediated the extensive lateral transfer of antibiotic resistance in unbiased communities of soil bacteria from Maryland and Wyoming. Furthermore, the addition of SUSP2 to cocultures of kanamycin-resistant E. coli and kanamycin-sensitive Bacillus sp. bacteria resulted in roughly 1,000-fold more kanamycin-resistant Bacillus sp. bacteria than arose in phage-free controls. Unlike many other lytic phages, neither SUSP1 nor SUSP2 encodes homologs to known hydrolytic endonucleases, suggesting a simple potential mechanism underlying the superspreading phenotype. Consistent with this model, the deletion of endonuclease IV and the nucleoid-disrupting protein ndd from coliphage T4, a phage known to extensively degrade chromosomal DNA, significantly increased its ability to promote plasmid transformation. Taken together, our results suggest that phage superspreaders may play key roles in microbial evolution and ecology but should be avoided in phage therapy and other medical applications., IMPORTANCE Bacteriophages (phages), viruses that infect bacteria, are the planet’s most numerous biological entities and kill vast numbers of bacteria in natural environments. Many of these bacteria carry plasmids, extrachromosomal DNA elements that frequently encode antibiotic resistance. However, it is largely unknown whether plasmids are destroyed during phage infection or released intact upon phage lysis, whereupon their encoded resistance could be acquired and manifested by other bacteria (transformation). Because phages are being developed to combat antibiotic-resistant bacteria and because transformation is a principal form of horizontal gene transfer, this question has important implications for biomedicine and microbial evolution alike. Here we report the isolation and characterization of two novel Escherichia coli phages, dubbed “superspreaders,” that promote extensive plasmid transformation and efficiently disperse antibiotic resistance genes. Our work suggests that phage superspreaders are not suitable for use in medicine but may help drive bacterial evolution in natural environments.

Despite the importance of oolitic depositional systems as indicators of climate and reservoirs of inorganic C, little is known about the microbial functional diversity, structure, composition, and potential metabolic processes leading to precipitation of carbonates. To fill this gap, we assess the metabolic gene carriage and extracellular polymeric substance (EPS) development in microbial communities associated with oolitic carbonate sediments from the Bahamas Archipelago. Oolitic sediments ranging from high-energy 'active' to lower energy 'non-active' and 'microbially stabilized' environments were examined as they represent contrasting depositional settings, mostly influenced by tidal flows and wave-generated currents. Functional gene analysis, which employed a microarray-based gene technology, detected a total of 12,432 of 95,847 distinct gene probes, including a large number of metabolic processes previously linked to mineral precipitation. Among these, gene-encoding enzymes for denitrification, sulfate reduction, ammonification, and oxygenic/anoxygenic photosynthesis were abundant. In addition, a broad diversity of genes was related to organic carbon degradation, and N2 fixation implying these communities has metabolic plasticity that enables survival under oligotrophic conditions. Differences in functional genes were detected among the environments, with higher diversity associated with non-active and microbially stabilized environments in comparison with the active environment. EPS showed a gradient increase from active to microbially stabilized communities, and when combined with functional gene analysis, which revealed genes encoding EPS-degrading enzymes (chitinases, glucoamylase, amylases), supports a putative role of EPS-mediated microbial calcium carbonate precipitation. We propose that carbonate precipitation in marine oolitic biofilms is spatially and temporally controlled by a complex consortium of microbes with diverse physiologies, including photosynthesizers, heterotrophs, denitrifiers, sulfate reducers, and ammonifiers.

Changes in the Caribbean coral fauna associated with Plio-Pleistocene extinctions are unique in that origination preceded extinction. This pattern is particularly evident in free-living solitary and flabello-meandroid (FSFM) corals. Here we use the stable isotopes of carbon and oxygen to assess the paleoautecology of pre-turnover FSFM corals from the Cibao Basin, northern Dominican Republic. We assess photosymbiosis and resource utilization within FSFM corals and how changing Neogene paleoclimatic and paleoceanographic conditions may have contributed to originations and extinctions within this unique ecological group. Measurements of[deltha]13C and [deltha]18O were compared between two known zooxanthellate coral species, two known azooxanthellate species, and six FSFM species of the Cibao Basin. Skeletal[deltha]13C provided the best indicator of resource utilization by FSFM corals. For both modern reef corals and Mio-Pliocene reef corals from the Cibao Basin, values of [deltha]13C fall between 0%o and -2%o whereas the [deltha]13C values of azooxanthellate corals generally fall between -3%o and -9%o. Both modern and fossil FSFM corals lie intermediate to these end members. FSFM values of [deltha]13C fall between -1%o and -4%o and suggest reduced photosymbiosis in comparison to typical reef corals. Reduced photosymbiosis of FSFM corals in comparison to reef corals is also reflected in a stronger covariation between [deltha]13C and [deltha]18O. Though FSFM corals are clearly utilizing translocated carbon from associated algal symbionts, the more depleated values of [deltha]13C and covariation with [deltha]18O suggest a greater dependence on heterotrophic feeding. This ecological lifestyle likely has made FSFM corals sensitive to changes in primary productivity that characterize the Caribbean Neogene.

Here we describe and illustrate 31 Miocene corals species from the Siamaná and Jimol Formations that were collected over two expeditions in the Guajira basin, Colombia during 2011 and 2014. Corals include 25 species, derived from 15 different genera and 12 families. Six of them remain with open nomenclature. From the 25 species found in the study area, 88% are extinct and the remaining under endanger status. Most of the species are hermatypic components of the Scleractinian order, with the exception of a member of the Milleporidae family. The corals described are composed of typical taxa from the Oligocene-Miocene transition, during which they were important components in building fringing and patch reefs in the circum-Caribbean/Gulf of Mexico region. The presence of typical Oligocene coral taxa such as Agathiphyllia spp., Antiguastrea sp., and Diploastrea spp. from La Guajira extend the distribution of these genera into the Miocene, adding a more recent geological presence in the Southern Caribbean. Coral assemblages suggest a development in clear, calm and shallow waters, under oligotrophic conditions and only moderate physical disturbance. Our descriptions represent the first effort to characterize the taxonomy of fossilized corals in Colombia.

Pleistocene sea-level change transformed staghorn corals into prolific reef builders that are sensitive to anthropogenic stressors., As one of the most prolific and widespread reef builders, the staghorn coral Acropora holds a disproportionately large role in how coral reefs will respond to accelerating anthropogenic change. We show that although Acropora has a diverse history extended over the past 50 million years, it was not a dominant reef builder until the onset of high-amplitude glacioeustatic sea-level fluctuations 1.8 million years ago. High growth rates and propagation by fragmentation have favored staghorn corals since this time. In contrast, staghorn corals are among the most vulnerable corals to anthropogenic stressors, with marked global loss of abundance worldwide. The continued decline in staghorn coral abundance and the mounting challenges from both local stress and climate change will limit the coral reefs’ ability to provide ecosystem services.

Enterococci, recommended at the U.S. federal level for monitoring water quality at marine recreational beaches, have been found to reside and grow within beach sands. However, the environmental and ecological factors affecting enterococcal persistence remain poorly understood, making it difficult to determine levels of fecal pollution and assess human health risks. Here we document the presence of enterococci associated with beach sediment biofilms at eight south Florida recreational beaches. Enterococcal levels were highest in supratidal sands, where they displayed a nonlinear, unimodal relationship with extracellular polymeric secretions (EPS), the primary component of biofilms. Enterococcal levels peaked at intermediate levels of EPS, suggesting that biofilms may promote the survival of enterococci but also inhibit enterococci as the biofilm develops within beach sands. Analysis of bacterial community profiles determined by terminal restriction fragment length polymorphisms showed the bacterial communities of supratidal sediments to be significantly different from intertidal and subtidal communities; however, no differences were observed in bacterial community compositions associated with different EPS concentrations. Our results suggest that supratidal sands are a microbiologically unique environment favorable for the incorporation and persistence of enterococci within beach sediment biofilms.

Living stromatolites on the margins of Exuma Sound, Bahamas, are the only examples of modern stromatolites forming in open marine conditions similar to those that may have existed on Precambrian platforms. Six microbial mat types have previously been documented on the surfaces of stromatolites along the eastern side of Highborne Cay (Schizothrix, Solentia, heterotrophic biofilm, stalked diatom, tube diatom and Phormidium mats). Cycling of these communities create laminae with distinct microstructures. Subsurface laminae thus represent a chronology of former surface mats. The present study documents the effects of environmental factors on surface microbial communities of modern marine stromatolites and identifies potential causes of microbial mat cycling. Mat type and burial state at 43 markers along a stromatolitic reef on the margin of Highborne Cay were monitored over a two-year period (2005–2006). Key environmental parameters (i.e., temperature, light, wind, water chemistry) were also monitored. Results indicated that the composition of stromatolite surface mats and transitions from one mat type to another are controlled by both seasonal and stochastic events. All six stromatolite mat communities at Highborne Cay showed significant correlations with water temperature. Heterotrophic biofilms, Solentia, stalked diatom and Phormidium mats showed positive correlations with temperature, whereas Schizothrix and tube diatom communities showed negative correlations. A significant correlation with light (photosynthetically active radiation, PAR) was detected only for the heterotrophic biofilm community. No significant correlations were found between mat type and the monitored wind intensity data, but field observations indicated that wind-related events such as storms and sand abrasion play important roles in the transitions from one mat type to another. An integrated model of stromatolite mat community cycling is developed that includes both predictable seasonal environmental variation and stochastic events. The long-term monitoring of mat communities on Highborne Cay stromatolites and the resulting model are an important step in understanding morphogenesis of modern marine stromatolites, with implications for interpreting patterns of stromatolite lamination in the geologic record.

The risk of global extinction of reef-building coral species is increasing. We evaluated extinction risk using a biological trait-based resiliency index that was compared with Caribbean extinction during the Plio-Pleistocene, and with extinction risk determined by the International Union for Conservation of Nature (IUCN). Through the Plio-Pleistocene, the Caribbean supported more diverse coral assemblages than today and shared considerable overlap with contemporary Indo-Pacific reefs. A clear association was found between extant Plio-Pleistocene coral genera and our positive resilience scores. Regional extinction in the past and vulnerability in the present suggests that Pocillopora, Stylophora and foliose Pavona are among the most susceptible taxa to local and regional isolation. These same taxa were among the most abundant corals in the Caribbean Pliocene. Therefore, a widespread distribution did not equate with immunity to regional extinction. The strong relationship between past and present vulnerability suggests that regional extinction events are trait-based and not merely random episodes. We found several inconsistencies between our data and the IUCN scores, which suggest a need to critically re-examine what constitutes coral vulnerability.

Temporal patterns are evaluated in Neogene reef coral assemblages from the Bocas del Toro Basin of Panama in order to understand how reef ecosystems respond to long-term environmental change. Analyses are based on a total of 1,702 zooxanthellate coral specimens collected from six coral-bearing units ranging in age from the earliest Late Miocene to the Early Pleistocene: (1) Valiente Formation (12–11 Ma), (2) Fish Hole Member of the Old Bank Formation (5.8–5.6 Ma), (3) La Gruta Member of the Isla Colon Formation (2.2–1.4 Ma), (4) Ground Creek Member of the Isla Colon Formation (2.2–1.4 Ma), (5) Mimitimbi Member of the Urraca Formation (1.2–0.8 Ma), and (6) Hill Point Member of the Urraca Formation (1.2–0.8 Ma). Over 100 coral species occur in the six units, with faunal assemblages ranging from less than 10% extant taxa (Valiente Formation) to over 85% extant taxa (Ground Creek Member). The collections provide new temporal constraints on the emergence of modern Caribbean reefs, with the La Gruta Member containing the earliest occurrence of large monospecific stands of the dominant Caribbean reef coral Acropora palmata, and the Urraca Formation containing the last fossil occurrences of 15 regionally extinct taxa. Canonical correspondence analysis of 41 Late Miocene to Recent reef coral assemblages from the Caribbean region suggests changes in community structure coincident with effective oceanic closure of the Central American Seaway (~3.5 Ma). These changes, including increased Acropora dominance, may have contributed to a protracted period of elevated extinction debt prior to the major peak in regional coral extinctions (~2–1 Ma).

Reef-building corals are susceptible to black band disease (BBD), an infection characterized by a cyanobacteria-dominated microbial mat that kills coral tissue. BBD mats infecting six scleractinian corals and one gorgonian were studied to assess and identify important microbes involved in the disease. Genotypic variability of dominant BBD cyanobacteria was analyzed at high resolution using cyanobacteria-specific terminal restriction fragment length polymorphism (TRFLP) analysis of the rRNA internal transcribed spacer (rRNA-ITS) region. Most coral species were dominated by one of two distinct genotypes of the common BBD cyanobacteria CD1C11. The BBD mat infecting the seafan Gorgonia ventalina Linnaeus, 1758 was dominated by different cyanobacteria genotypes (SFDC1 and SFDC2). Clone library sequencing and TRFLP analyses of rRNA genes and reverse-transcribed rRNA reveal the identity and activity of the most abundant BBD microbes. A potential role of these microbes in infection and immunity was studied by comparing the microbial communities of BBD mats to those associated with the healthy tissues of infected and non-infected corals. The dominant cyanobacteria genotype CD1C11 was detected on healthy tissues of several diseased coral species, as well as on healthy colonies showing no outward signs of disease. Other important constituents of the BBD mats included Rhodobacteraceae, Vibrionaceae, and Bacteroidetes. Several isolates were similar to genotypes associated with other coral diseases.

Statistical analyses of occurrence data based on collections made from scattered Caribbean sections over the past 20 years indicate that turnover occurred in the Caribbean reef coral fauna between the late Miocene and early Pleistocene. The collections have been identified using standardized procedures, and age-dates assigned using high-resolution chronostratigraphic methods. During turnover, ~80% of the > 100 species and 17 of the 41 genera that were living in the Caribbean during the early Pliocene became extinct, and > 60% of the species now living in the Caribbean originated. Turnover involved increased speciation beginning in the late Miocene and ended with a pulse of extinction in Plio-Pleistocene time. Turnover was preceded by faunal collapse during the late Oligocene to early Miocene, and it was followed by stasis during the late Pleistocene to Recent. During these preceding and succeeding intervals, reef development was at a maximum, although reef coral diversity was relatively low. As a consequence of origination preceding extinction during turnover, most modern Caribbean reef coral species originated before the Plio-Pleistocene peak of extinction, under quite different ecological conditions from those in which they have lived over the past million years. The unusual relationship between origination and extinction may have been caused by changes in productivity associated with emergence of the Central American Isthmus, followed by the onset of Northern Hemisphere glaciation.During turnover, faunal change was stepwise or gradual. Local assemblages consisted of a mix of extinct and living species, which varied in composition but not in richness. Important reef dominants such as Acropora palmata and A. cervicornis arose in the southern Caribbean and appear to have migrated northward. Faunal change took place in shallow exposed environments, before it occurred in deep protected environments that served as refuges. Plio-Pleistocene extinction was selective for corals with small colonies, and resulted in a faunal shift to the large, fast-growing species that dominate Caribbean reefs today.

An assemblage of planktonic foraminifera is described from 125 samples taken from the Cercado, Gurabo, and Mao Formations in the Cibao Valley, northern Dominican Republic. The primary objectives of this study are to establish a biochronologic model for the late Neogene of the Dominican Republic and to examine sea surface conditions within the Cibao Basin during this interval. The Cercado Formation is loosely confined to Zones N17 and N18 (∼ 7.0–5.9 Ma). The Gurabo Formation spans Zones N18 and N19 (∼ 5.9–4.5 Ma). The Mao Formation is placed in Zone N19 (∼ 4.5–3.6 Ma). Changes in the relative abundances of indicator species are used to reconstruct sea surface conditions within the basin. Increasing relative abundances of Globigerinoides sacculifer and Globigerinoides ruber , in conjunction with a decreasing relative abundance of Globigerina bulloides , suggests the onset of increasing sea surface temperature and salinity in conjunction with diminishing primary productivity at ∼ 6.0 Ma. Abrupt increases in the relative abundances of G. sacculifer and G. ruber at ∼ 4.8 Ma suggest a major increase in sea surface temperature and salinity in the early Pliocene. The most likely mechanism for these changes is isolation of the Caribbean Ocean through progressive restriction of Pacific–Caribbean transfer via the Central American Seaway. Periods of high productivity associated with upwelling events are recorded in the upper Cercado Formation (∼ 6.1 Ma) and in the middle Mao Formation (∼ 4.2 Ma) by spikes in G. bulloides and Neogloboquadrina spp. respectively. The timing of major increases in sea surface salinity and temperature as well as decreasing productivity (∼ 4.8 Ma) and periods of upwelling (∼ 6.1and 4.2 Ma) in the Cibao Basin generally corroborate previously suggested Caribbean oceanographic changes related to the uplift of Panama. Changes in sea surface conditions depicted by paleobiogeographic distributions in the Cibao Basin suggest that shoaling along the Isthmus of Panama had implications in a shallow Caribbean basin as early as 6.0 Ma. Major paleobiologic changes between ∼ 4.8 and 4.2 Ma likely represent the period of final closure of the CAS and a nearly complete disconnection between Pacific and Caribbean water masses. This study illustrates the use of planktonic foraminifera in establishing some paleoceanographic conditions (salinity, temperature, productivity, and upwelling) within a shallow water basin, outlining the connection between regional and localized oceanographic changes.

Summary The high incidence of coral disease in shallow coastal marine environments suggests seawater depth and coastal pollution have an impact on the microbial communities inhabiting healthy coral tissues. A study was undertaken to determine how bacterial commu- nities inhabiting tissues of the coral Montastraea annularis change at 5 m, 10 m and 20 m water depth in varying proximity to the urban centre and seaport of Willemstad, Curacao, Netherlands Antilles. Analy- ses of terminal restriction fragment length polymor- phisms (TRFLP) of 16S rRNA gene sequences show significant differences in bacterial communities of polluted and control localities only at the shallowest seawater depth. Furthermore, distinct differences in bacterial communities were found with increasing water depth. Comparisons of TRFLP peaks with sequenced clone libraries indicate the black band disease cyanobacterium clone CD1C11 is common and most abundant on healthy corals in less than 10 m water depth. Similarly, sequences belonging to a previously unrecognized group of likely phototrophic bacteria, herein referred to as CAB-I, were also more common in shallow water. To assess the influence of environmental and physiologic factors on bacterial community structure, canonical correspondence analysis was performed using explanatory variables associated with: (i) light availability; (ii) seawater pol- lution; (iii) coral mucus composition; (iv) the commu- nity structure of symbiotic algae; and (v) the photosynthetic activity of symbiotic algae. Eleven per cent of the variation in bacterial communities was accounted for by covariation with these variables; the most important being photosynthetically active radia- tion (sunlight) and the coral uptake of sewage-derived compounds as recorded by the d 15 N of coral tissue.

Bacterial communities inhabiting healthy tissues of the reef-building corals Diploria strigosa and Montastraea annularis were evaluated across a human-induced environmental gradient along the southern coast of Curacao, Netherlands Antilles. Variations in bacterial communities inhabiting coral tissues were determined using terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes, and the δ15N value of coral tissue was used to assess the relative amount of human contaminants at each reef locality. Bacterial communities of D. strigosa were more variable than M. annularis, but there were no systematic differences in the populations of healthy M. annularis and D. strigosa. The δ15N value of coral tissues showed as much as a 1.5‰ increase in the impacted versus the non-impacted localities. While M. annularis showed no significant variation in bacterial community structure due to local reef conditions, the bacterial communities of D. strigosa showed dramatic shifts in community structure. The most abundant bacterial taxa inhabiting D. strigosa display increased dominance at impacted localities. By linking variations in microbial communities with an understanding of variations in local environmental conditions, this study provides a means of assessing potential factors that may impact the microbial habitat of coral tissues as well as overall reef health.

The extent to which origination and selective extinction influenced the structure and dynamics of Caribbean coral reef communities is evaluated by comparing the diversity and distributional patterns of coral species in two Dominican Republic reef sequences prior to and following late Cenozoic Caribbean faunal turnover. The two sequences consist of the late Miocene Arroyo Bellaco reef of the Cibao Valley, northern Dominican Republic, and the late Pleistocene 125-ka reef terrace of the southern Dominican Republic. Samples were collected along 20-meter transects (10 Miocene, 10 Pleistocene); species identifications were made using standard sets of characters and morphometrics. In particular, species of Montastraea annularis-like corals were distinguished within each sequence using a 2-dimensional landmark technique involving average linkage cluster analysis, discriminant analyses, and non-parametric tests. Four Miocene and four Pleistocene species were recognized. Subsequent community analysis was t...

© 2014 Edmunds et al. The reduction in coral cover on many contemporary tropical reefs suggests a different set of coral community assemblages will dominate future reefs. To evaluate the capacity of reef corals to persist over various time scales, we examined coral community dynamics in contemporary, fossil, and simulated future coral reef ecosystems. Based on studies between 1987 and 2012 at two locations in the Caribbean, and between 1981 and 2013 at five locations in the Indo-Pacific, we show that many coral genera declined in abundance, some showed no change in abundance, and a few coral genera increased in abundance. Whether the abundance of a genus declined, increased, or was conserved, was independent of coral family. An analysis of fossil-reef communities in the Caribbean revealed changes in numerical dominance and relative abundances of coral genera, and demonstrated that neither dominance nor taxon was associated with persistence. As coral family was a poor predictor of performance on contemporary reefs, a trait-based, dynamic, multi-patch model was developed to explore the phenotypic basis of ecological performance in a warmer future. Sensitivity analyses revealed that upon exposure to thermal stress, thermal tolerance, growth rate, and longevity were the most important predictors of coral persistence. Together, our results underscore the high variation in the rates and direction of change in coral abundances on contemporary and fossil reefs. Given this variation, it remains possible that coral reefs will be populated by a subset of the present coral fauna in a future that is warmer than the recent past.

This study represents the first in a series tracing the early evolution of a dominant Caribbean reef coral, the Montastraea ''annularis'' species complex, using a combination of morphometric and phylogenetic approaches. It focuses on Costa Rica and Panama; additional geographic locations and reef environments will be treated in subsequent work. To distinguish species, new landmark methods are developed by comparisons with genetically characterized modern colonies from Panama. The fossil material consists of transverse thin-sections of 94 well-preserved specimens of M. annularis-like corals collected in Plio-Pleistocene reef sequences in the Limon basin of Costa Rica and the Bocas del Toro basin of Panama. The landmarks comprise 27 spatially homologous points, which define the thickness and structure of the corallite wall and associated costosepta. Bookstein size and shape coordinates are analyzed using cluster analysis and canonical discriminant analysis, and a total of 10 morphotypes are distinguished. Cladistic analyses are performed using characters derived partially from morphometric data. A matrix consisting of 16 taxa and eight characters is analyzed using global parsimony and a sister group of two species as the outgroup. The results reveal two distinct evolutionary groups, which are distinguished by the new corallite wall characters. One group contains one modern species, and the other contains a second; the relationships of the third are poorly resolved. Despite the low number of equally parsimonious trees, high numbers of plesiomorphic taxa, long range extensions, and lack of agreement with genetic data indicate that the new characters alone are inadequate for completely interpreting evolutionary relationships, and more samples and characters are needed. Nevertheless, these preliminary results do show that three modern species of the M. ''annularis'' complex arose prior to accelerated extinction at the end of late Pliocene to early Pleistocene faunal turnover of Caribbean reef corals, and two may have originated younger than 4 Ma. Six or more new species may be represented in upper Pliocene to lower Pleistocene sequences in Costa Rica and Panama. Coexistence of predominantly pre- and post-turnover clades may have been responsible for the high diversity observed within the species complex in these two sequences.

Fecal indicator microbes, such as enterococci, are often used to assess potential health risks caused by pathogens at recreational beaches. Microbe levels often vary based on collection time and sampling location. The primary goal of this study was to assess how spatial and temporal variations in sample collection, which are driven by environmental parameters, impact enterococci measurements and beach management decisions. A secondary goal was to assess whether enterococci levels can be predictive of the presence of Staphylococcus aureus, a skin pathogen. Over a ten-day period, hydrometeorologic data, hydrodynamic data, bather densities, enterococci levels, and S. aureus levels including methicillin-resistant S. aureus (MRSA) were measured in both water and sand. Samples were collected hourly for both water and sediment at knee-depth, and every 6 h for water at waist-depth, supratidal sand, intertidal sand, and waterline sand. Results showed that solar radiation, tides, and rainfall events were major environmental factors that impacted enterococci levels. S. aureus levels were associated with bathing load, but did not correlate with enterococci levels or any other measured parameters. The results imply that frequencies of advisories depend heavily upon sample collection policies due to spatial and temporal variation of enterococci levels in response to environmental parameters. Thus, sampling at different times of the day and at different depths can significantly impact beach management decisions. Additionally, the lack of correlation between S. aureus and enterococci suggests that use of fecal indicators may not accurately assess risk for some pathogens.

Black band disease (BBD) is a virulent polymicrobial disease primarily affecting massive-framework-building species of scleractinian corals. While it has been well established that the BBD bacterial mat is dominated by a cyanobacterium, the quantitative composition of the BBD bacterial mat community has not described previously. Terminal-restriction fragment length polymorphism (T-RFLP) analysis was used to characterize the infectious bacterial community of the bacterial mat causing BBD. These analyses revealed that the bacterial composition of the BBD mat does not vary between different coral species but does vary when different species of cyanobacteria are dominant within the mat. On the basis of the results of a new method developed to identify organisms detected by T-RFLP analysis, our data show that besides the cyanobacterium, five species of the division Firmicutes , two species of the Cytophaga-Flexibacter-Bacteroides (CFB) group, and one species of δ-proteobacteria are also consistently abundant within the infectious mat. Of these dominant taxa, six were consistently detected in healthy corals. However, four of the six were found in much higher numbers in BBD mats than in healthy corals. One species of the CFB group and one species of Firmicutes were not always associated with the bacterial communities present in healthy corals. Of the eight dominant bacteria identified, two species were previously found in clone libraries obtained from BBD samples; however, these were not previously recognized as important. Furthermore, despite having been described as an important component of the pathogenetic mat, a Beggiatoa species was not detected in any of the samples analyzed. These results will permit the dominant BBD bacteria to be targeted for isolation and culturing experiments aimed at deciphering the disease etiology.

An exceptionally well-preserved aragonitic coral of the extinct species Goniopora hilli was collected from late Cenozoic sedimentary deposits in the Dominican Republic and dated using U-Pb techniques. Nine coralline subsamples yielded a 238 U/ 206 Pb– 207 Pb/ 206 Pb three-dimensional (3-D) inverse linear concordia age of 5.52 ± 0.15 (2σ) Ma, which, when coupled with 87 Sr/ 86 Sr ratios obtained from the same coral, allows for tighter constraints on temporal variability of marine species diversity prior to closure of the Central American Seaway. The recognition that pre-Quaternary aragonitic corals can be suitable for U-Pb dating creates new possibilities for refining the chronologies of late Cenozoic marine sedimentary sequences.