Molecular diversity of the copepod, Nannocalunus minor: Genetic evidence of species and population structure in the North Atlantic Ocean

The abundant calanoid copepod, Nannocalanus minor, is widespread from the Florida Straits (FS), throughout the Gulf Stream and the Sargasso Sea, to the eastern North Atlantic Ocean. Does the species represent a single, randomly-mating population across this extensive region, or does it comprise a number of genetically distinct populations or taxonomically distinct forms? What are patterns and pathways of dispersal of the copepod across the North Atlantic? These questions were addressed using population genetic analysis of DNA sequence variation of a 440 base-pair region of the mitochondrial 16S rRNA gene. This analysis separated N. minor into two genetically distinct types (distinguished by 10% sequence difference) that may represent the previously described N. m. forma major and N.m. forma minor. The two genetic types differed in size range and in geographic distribution: Type I individuals were larger and were most abundant in the western regions of the Gulf Stream; Type II individuals were smaller and became more abundant toward the eastern regions of the Gulf Stream. Significant differences in the size-frequency distributions of N. minor from different regions of the North Atlantic may result from mixtures of the two genetic types and environmental differences in food availability. Within N. minor Type I, mtDNA sequence variation defined 68 haplotypes among 155 individuals. The haplotype frequency distribution was skewed: there were 40 individuals of one haplotype, 31 individuals of a second, and 60 unique individuals. Haplotype diversity, h, was very similar across the sampled range: h = 0.886 in samples from the FS and 0.874 for samples from the Gulf Stream Meander Region (GSMR). Nucleotide diversity, pi, was significantly greater in the FS (pi = 0.00490) than in the GSMR (0.00414), largely due to a number of genetically divergent individuals. Haplotype abundances did not differ significantly either within the regions (among FS samples, P = 0.756; among GSMR samples, P = 0.336) or between the regions (P = 0.636). Molecular genetic analysis can reveal cryptic species among marine taxa, and is particularly useful for taxa characterized by morphological similarity

Characteristic Changes in Decidual Gene Expression Signature in Spontaneous Term Parturition

Background: The decidua has been implicated in the "terminal pathway" of human term parturition, which is characterized by the activation of pro-inflammatory pathways in gestational tissues. However, the transcriptomic changes in the decidua leading to terminal pathway activation have not been systematically explored. This study aimed to compare the decidual expression of developmental signaling and inflammation-related genes before and after spontaneous term labor in order to reveal their involvement in this process. Materials and Methods: Chorioamniotic membranes were obtained from normal pregnant women who delivered at term with spontaneous labor (TIL, n=14) or without labor (TNL, n=15). Decidual cells were isolated from snap-frozen chorioamniotic membranes with laser microdissection. The expression of 46 genes involved in decidual development, sex steroid and prostaglandin signaling, as well as pro- and anti-inflammatory pathways was analyzed using high-throughput quantitative real-time polymerase chain reaction (qRT-PCR). Chorioamniotic membrane sections were immunostained and then semi-quantified for five proteins, and immunoassays for three chemokines were performed on maternal plasma samples. Results: The genes with the highest expression in the decidua at term gestation included insulin-like growth factor-binding protein 1 (IGFBP1), galectin-1 (LGALS1), and progestogen-associated endometrial protein (PAEP); the expression of estrogen receptor 1 (ESR1), homeobox A11 (HOXA11), interleukin 1beta (IL1B), IL8, progesterone receptor membrane component 2 (PGRMC2), and prostaglandin E synthase (PTGES) was higher in TIL than in TNL cases; the expression of chemokine C-C motif ligand 2 (CCL2), CCL5, LGALS1, LGALS3, and PAEP was lower in TIL than in TNL cases; immunostaining confirmed qRT-PCR data for IL-8, CCL2, galectin-1, galectin-3, and PAEP; and no correlations between the decidual gene expression and the maternal plasma protein concentrations of CCL2, CCL5, and IL-8 were found. Conclusion: Our data suggests that with the initiation of parturition, the decidual expression of anti-inflammatory mediators decreases, while the expression of pro-inflammatory mediators and steroid receptors increases. This shift may affect downstream signaling pathways that can lead to parturition

Improved Resolution of Reef-Coral Endosymbiont (Symbiodinium) Species Diversity, Ecology, and Evolution through psbA Non-Coding Region Genotyping

Ribosomal DNA sequence data abounds from numerous studies on the dinoflagellate endosymbionts of corals, and yet the multi-copy nature and intragenomic variability of rRNA genes and spacers confound interpretations of symbiont diversity and ecology. Making consistent sense of extensive sequence variation in a meaningful ecological and evolutionary context would benefit from the application of additional genetic markers. Sequences of the non-coding region of the plastid psbA minicircle (psbAncr) were used to independently examine symbiont genotypic and species diversity found within and between colonies of Hawaiian reef corals in the genus Montipora. A single psbAncr haplotype was recovered in most samples through direct sequencing (∼80–90%) and members of the same internal transcribed spacer region 2 (ITS2) type were phylogenetically differentiated from other ITS2 types by substantial psbAncr sequence divergence. The repeated sequencing of bacterially-cloned fragments of psbAncr from samples and clonal cultures often recovered a single numerically common haplotype accompanied by rare, highly-similar, sequence variants. When sequence artifacts of cloning and intragenomic variation are factored out, these data indicate that most colonies harbored one dominant Symbiodinium genotype. The cloning and sequencing of ITS2 DNA amplified from these same samples recovered numerically abundant variants (that are diagnostic of distinct Symbiodinium lineages), but also generated a large amount of sequences comprising PCR/cloning artifacts combined with ancestral and/or rare variants that, if incorporated into phylogenetic reconstructions, confound how small sequence differences are interpreted. Finally, psbAncr sequence data from a broad sampling of Symbiodinium diversity obtained from various corals throughout the Indo-Pacific were concordant with ITS lineage membership (defined by denaturing gradient gel electrophoresis screening), yet exhibited substantially greater sequence divergence and revealed strong phylogeographic structure corresponding to major biogeographic provinces. The detailed genetic resolution provided by psbAncr data brings further clarity to the ecology, evolution, and systematics of symbiotic dinoflagellates

Investigating Coral Bleaching in a Changing Climate: Our State of Understanding and Opportunities to Push the Field Forward

[First Paragraph] Coral reefs throughout the world are facing the consequences of large-scale changes in Earth’s climate. In particular, ocean warming is leading to frequent coral bleaching, which is threatening the long-term stability of coral reefs. Coral bleaching is a stress response that results in the disassociation of the mutualistic symbioses (i.e., dysbiosis) between corals and their endosymbiotic algae (Symbiodinium spp.). In the past two decades, there have been four substantial bleaching events, which have affected large geographic areas across the globe, including the worst recorded bleaching event on the Great Barrier Reef in 2016 (Berkelmans et al. 2004; Eakin et al. 2010; Stella et al. 2016). These large-scale bleaching events, in combination with many local-scale stressors, have contributed substantially to global declines in coral populations. In addition, bleaching may lead to compromised coral immunity, possibly resulting in additional mortality by a range of post-bleaching diseases (Maynard et al. 2015, Randall et al. 2014). Given their link to patterns of global-climate change and projections of increased warming in the coming decades, mass coral bleaching events are a key concern. In addition, current climate projections estimate that global bleaching is expected to occur annually by late this century, with more than 90% of reefs facing long-term degradation (Frieler et al. 2012). Furthermore, in locations such as the Caribbean, frequent thermal anomalies and consecutive annual bleaching events are expected to be common in less than 25 years (van Hooidonk et al. 2015). In fact, large-scale bleaching two years in a row was documented for the first time in 2014-2015 in Hawaii and in the Florida Keys. However, not all corals (and other symbiotic cnidarians) are equally susceptible to thermal stress, and some corals have been shown to recover from bleaching more quickly than others. Likewise, not all reefs are equally susceptible, and depending on local conditions, susceptibility can vary from one event to the next. Such variability in resilience could be a cornerstone to reef persistence over the coming century. However, the research needed to test this hypothesis remains to be performed

Stability of bedforms in laminar flows with free surface: from bars to ripples

International audienceThe present paper is devoted to the formation of sand patterns by laminar flows. It focuses on the rhomboid beach pattern, formed during the backswash. A recent bedload transport model, based on a moving-grains balance, is generalized in three dimensions for viscous flows. The water flow is modelled by the full incompressible Navier–Stokes equations with a free surface. A linear stability analysis then shows the simultaneous existence of two distinct instabilities, namely ripples and bars. The comparison of the bar instability characteristics with laboratory rhomboid patterns indicates that the latter could result from the nonlinear evolution of unstable bars. This result, together with the sensibility of the stability analysis with respect to the parameters of the transport law, suggests that the rhomboid pattern could help improving sediment transport models, so critical to geomorphologists

Transcriptional Response of Two Core Photosystem Genes in Symbiodinium spp. Exposed to Thermal Stress

Mutualistic symbioses between scleractinian corals and endosymbiotic dinoflagellates (Symbiodinium spp.) are the foundation of coral reef ecosystems. For many coral-algal symbioses, prolonged episodes of thermal stress damage the symbiont\u27s photosynthetic capability, resulting in its expulsion from the host. Despite the link between photosynthetic competency and symbiont expulsion, little is known about the effect of thermal stress on the expression of photosystem genes in Symbiodinium. This study used real-time PCR to monitor the transcript abundance of two important photosynthetic reaction center genes, psbA(encoding the D1 protein of photosystem II) and psaA (encoding the P700 protein of photosystem I), in four cultured isolates (representing ITS2-types A13, A20, B1, and F2) and two in hospite Symbiodinium spp. within the coral Pocillopora spp. (ITS2-types C1b-c and D1). Both cultured and in hospite Symbiodinium samples were exposed to elevated temperatures (32°C) over a 7-day period and examined for changes in photochemistry and transcript abundance. Symbiodinium A13 and C1b-c (both thermally sensitive) demonstrated significant declines in both psbA and psaA during the thermal stress treatment, whereas the transcript levels of the other Symbiodinium types remained stable. The downregulation of both core photosystem genes could be the result of several different physiological mechanisms, but may ultimately limit repair rates of photosynthetic proteins, rendering some Symbiodinium spp. especially susceptible to thermal stress

DNA barcoding reveals the coral “laboratory-rat”, Stylophora pistillata encompasses multiple identities

Stylophora pistillata is a widely used coral “lab-rat” species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar-Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four clades diverged from one another 51.5-29.6 Mya, i.e., long before the closure of the Tethyan connection between the tropical Indo-West Pacific and Atlantic in the early Miocene (16–24 Mya) and should be recognised as four distinct species. These findings have implications for comparative ecological and/or physiological studies carried out using Stylophora pistillata as a model species, and highlight the fact that phenotypic plasticity, thought to be common in scleractinian corals, can mask significant genetic variation

Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region.

The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.We would like to thank the KAUST BioScience Core Lab and S. Neelamegam for 454 library generation and sequencing. We would also like to thank Y. Sawall and A. Al-Sofyani for provision and collection of coral samples, and three anonymous reviewers for helpful comments. This project was funded by a KAUST Academic Excellence Alliance (AEA) Award to CRV and CJH, baseline research funds to CRV and a National Science Foundation grant to TCL (OCE-09287664).This is the final published version. It first appeared at http://onlinelibrary.wiley.com/doi/10.1111/mec.12869/abstract

Diversity and Distribution of Symbiodinium Associated with Seven Common Coral Species in the Chagos Archipelago, Central Indian Ocean

The Chagos Archipelago designated as a no-take marine protected area in 2010, lying about 500 km south of the Maldives in the Indian Ocean, has a high conservation priority, particularly because of its fast recovery from the ocean-wide massive coral mortality following the 1998 coral bleaching event. The aims of this study were to examine Symbiodinium diversity and distribution associated with scleractinian corals in five atolls of the Chagos Archipelago, spread over 10,000 km 2. Symbiodinium clade diversity in 262 samples of seven common coral species, Acropora muricata, Isopora palifera, Pocillopora damicornis, P. verrucosa, P. eydouxi, Seriatopora hystrix, and Stylophora pistillata were determined using PCR-SSCP of the ribosomal internal transcribed spacer 1 (ITS1), PCR-DDGE of ITS2, and phylogenetic analyses. The results indicated that Symbiodinium in clade C were the dominant symbiont group in the seven coral species. Our analysis revealed types of Symbiodinium clade C specific to coral species. Types C1 and C3 (with C3z and C3i variants) were dominant in Acroporidae and C1 and C1c were the dominant types in Pocilloporidae. We also found 2 novel ITS2 types in S. hystrix and 1 novel ITS2 type of Symbiodinium in A. muricata. Some colonies of A. muricata and I. palifera were also associated with Symbiodinium A1. These results suggest that corals in the Chagos Archipelago host different assemblages of Symbiodinium types then their conspecifics from other locations in the Indian Ocean; and that future research will show whether these patterns in Symbiodinium genotypes may be due to local adaptation to specific conditions in the Chagos

Uptake, accumulation and metabolization of the antidepressant fluoxetine by Mytilus galloprovincialis

Fluoxetine, a selective serotonin re-uptake inhibitor (SSRI) antidepressant, is among the most prescribed pharmaceutical active substances worldwide. This study aimed to assess its accumulation and metabolization in the mussel Mytillus galloprovincialis, considered an excellent sentinel species for traditional and emerging pollutants. Mussels were collected from Ria Formosa Lagoon, Portugal, and exposed to a nominal concentration of fluoxetine (75 ng L-1) for 15 days. Approximately 1 g of whole mussel soft tissues was extracted with acetonitrile:formic acid, loaded into an Oasis MCX cartridge, and fluoxetine analysed by liquid chromatography with tandem mass spectrometry (LC-MSn). After 3 days of exposure, fluoxetine was accumulated in 70% of the samples, with a mean of 2.53 ng g(-1) dry weight (d.w.) and norfluoxetine was only detected in one sample (10%), at 3.06 ng g(-1) d.w. After 7 days of exposure, the accumulation of fluoxetine and norfluoxetine increased up to 80 and 50% respectively, and their mean accumulated levels in mussel tissues were up to 4.43 and 2.85 ng g(-1) d.w., respectively. By the end of the exposure period (15 days), both compounds were detected in 100% of the samples (mean of 9.31 and 11.65 ng g(-1) d.w., respectively). Statistical analysis revealed significant accumulation differences between the 3rd and 15th day of exposure for fluoxetine, and between the 3rd and 7th against the 15th day of exposure for norfluoxetine. These results suggest that the fluoxetine accumulated in mussel tissues is likely to be metabolised into norfluoxetine with the increase of the time of exposure, giving evidence that at these realistic environmental concentrations, toxic effects of fluoxetine in mussel tissues may occur. (C) 2016 Elsevier Ltd. All rights reserved