Dispersal of a nearshore marine fish connects marine reserves and adjacent fished areas along an open coast

Marine species with pelagic larvae typically exhibit little population structure, suggesting long‐distance dispersal and high gene flow. Directly quantifying dispersal of marine fishes is challenging but important, particularly for the design of marine protected areas (MPAs). Here, we studied kelp rockfish (Sebastes atrovirens) sampled along ~25 km of coastline in a boundary current‐dominated ecosystem and used genetic parentage analysis to identify dispersal events and characterize them, because the distance between sedentary parents and their settled offspring is the lifetime dispersal distance. Large sample sizes and intensive sampling are critical for increasing the likelihood of detecting parent–offspring matches in such systems and we sampled more than 6,000 kelp rockfish and analysed them with a powerful set of 96 microhaplotype markers. We identified eight parent–offspring pairs with high confidence, including two juvenile fish that were born inside MPAs and dispersed to areas outside MPAs, and four fish born in MPAs that dispersed to nearby MPAs. Additionally, we identified 25 full‐sibling pairs, which occurred throughout the sampling area and included all possible combinations of inferred dispersal trajectories. Intriguingly, these included two pairs of young‐of‐the‐year siblings with one member each sampled in consecutive years. These sibling pairs suggest monogamy, either intentional or accidental, which has not been previously demonstrated in rockfishes. This study provides the first direct observation of larval dispersal events in a current‐dominated ecosystem and direct evidence that larvae produced within MPAs are exported both to neighbouring MPAs and to proximate areas where harvest is allowed.     

Distribution of the human faecal bacterium Bacteroides fragilis, its bacteriophages and their relationship to current sewage pollution indicators in bathing water

Although several bacteria are currently used as possible indicators of human pathogens in sewage-polluted sea water, they are often viewed as inadequate and especially inadequate as indicators of viral pathogens. This study investigates the distribution of Bacteroides fragilis and closely related Bacteroides spp. and their associated bacteriophages in sea water frequently used for recreational purposes. These organisms may provide a potentially more appropriate indicator. Bacteroides fragilis is one of about 10 species which are loosely placed together in the 'B. fragilis' group. Samples down-current from a sewage outfall were examined for the presence of B. fragilis group organisms and associated bacteriophages. Numbers were correlated with current bacterial and possible viral indicators at these sites. These B. fragilis group isolates were used as hosts to successfully isolate bacteriophages. The host range of these bacteriophages was investigated. It is hoped to expand this study by using these B. fragilis group hosts and their bacteriophages to identify a more suitable, European-wide, indicator of bacterial pathogens which can also be used to detect bacteriophages which are suitable as viral indicators.     

Spatiotemporal variations of inorganic nutrients along the Jiangsu coast,China, and the occurrence of macroalgal blooms (green tides) in the southern Yellow Sea

Large macroalgal blooms (i.e. green tides of Ulva prolifera) occurred in the southern Yellow Sea, China, yearly from 2007 to 2016. They were among the largest of such outbreaks around the world, and these blooms likely originated along the coast of the Jiangsu Province, China. Understanding the roles of nutrients in the onset of these macroalgal blooms is needed to identify their origin. This study analyzes the spatiotemporal variations in dissolved inorganic nitrogen and phosphorus (DIN and PO₄–P) and the N/P ratio along the Jiangsu coast from 1996 to 2014 during late-March to April, the months which corresponds to the pre-bloom period of green tides since 2007. A zone of high DIN and PO₄–P concentrations has developed along the Jiangsu coast, between the cities of Sheyang and Nantong, since 1996. There was an 18-year trend of increasing DIN concentrations during the pre-bloom period as well as a positive correlation between the U. prolifera biomass and DIN concentrations. Nutrient inputs from rivers and mariculture in the Jiangsu Province may have provided nitrogen that contributed the magnitude of macroalgal blooms that subsequently spread into the southern Yellow Sea.     

Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater

The human-specific HF183 Bacteriodes 16S rRNA genetic marker can be used to detect human faecal pollution in water environments. However, there is currently no method to quantify the prevalence of this marker in environmental samples. We developed a real-time polymerase chain reaction (PCR) assay using SYBR Green I detection to quantify this marker in faecal and environmental samples. To decrease the amplicon length to a suitable size for real-time PCR detection, a new reverse primer was designed and validated on human and animal faecal samples. The use of the newly developed reverse primer in combination with the human-specific HF183 primer did not decrease the specificity of the real-time PCR assay but a melting curve analysis must always be included. This new assay was more sensitive than conventional PCR and highly reproducible with a coefficient of variation of less than 1% within an assay and 3% between assays. As the Bacteroides species that carries this human-specific marker has never been isolated, a bacteria real-time assay was used to determine the detection efficiency. The estimated detection efficiency in freshwater ranged from 78% to 91% of the true value with an average detection efficiency of 83+/-4% of the true value. Using a simple filtration method, the limit of quantification was 4.7+/-0.3x10(5) human-specific Bacteroides markers per litre of freshwater. The aerobic incubation of the human-specific Bacteroides marker in freshwater for up to 24 days at 4 and 12 degrees C, and up to 8 days at 28 degrees C, indicated that the marker persisted up to the end of the incubation period for all incubation temperatures.     

Occurrence of Salmonella spp and Cryptosporidium spp in a French coastal watershed: relationship with fecal indicators

Cryptosporidium and Salmonella are pathogenic microorganisms that can cause severe gastrointestinal illness in humans. Because these organisms are potentially transmitted through natural waters, this study was carried out to estimate the concentrations of both pathogens in a French coastal watershed and to determine the relationships with fecal indicators. Water samples from nine wastewater treatment plants and eight rivers were analyzed. Although both pathogens and indicators are released from sewage effluents, no clear correlation was found between the two enteric pathogens nor between a given pathogen and fecal indicators. These results suggest that fecal indicators do not adequately indicate the presence of Cryptosporidium and Salmonella in natural waters and that pathogens and indicators may have different behaviors in the aquatic environment.     

Following the LINEs: an analysis of primate genomic variation at human-specific LINE-1 insertion sites

The L1 Ta subfamily of long interspersed elements (LINEs) consists exclusively of human-specific L1 elements. Polymerase chain reaction-based screening in nonhuman primate genomes of the orthologous sites for 249 human L1 Ta elements resulted in the recovery of various types of sequence variants for approximately 12% of these loci. Sequence analysis was employed to capture the nature of the observed variation and to determine the levels of gene conversion and insertion site homoplasy associated with LINE elements. Half of the orthologous loci differed from the predicted sizes due to localized sequence variants that occurred as a result of common mutational processes in ancestral sequences, often including regions containing simple sequence repeats. Additional sequence variation included genomic deletions that occurred upon L1 insertion, as well as successive mobile element insertions that accumulated within a single locus over evolutionary time. Parallel independent mobile element insertions at orthologous loci in distinct species may introduce homoplasy into retroelement-based phylogenetic and population genetic data. We estimate the overall frequency of parallel independent insertion events at L1 insertion sites in seven different primate species to be very low (0.52%). In addition, no cases of insertion site homoplasy involved the integration of a second L1 element at any of the loci, but rather largely involved secondary insertions of Alu elements. No independent mobile element insertion events were found at orthologous loci in the human and chimpanzee genomes. Therefore, L1 insertion polymorphisms appear to be essentially homoplasy free characters well suited for the study of population genetics and phylogenetic relationships within closely related species.     

Colonization and divergence: phylogeography and population genetics of the Atlantic coast beach mice

Barrier island taxa provide an opportunity to investigate recent evolutionary processes, such as colonization and isolation of recently diverged taxa, and provide important insights into understanding contemporary diversity and the assessment of conservation units. Using rapidly evolving genetic markers (mitochondrial DNA and microsatellites), we studied the Atlantic coast beach mouse subspecies (Peromyscus polionotus decoloratus, P. p. niveiventris, and P. p. phasma). Our data indicate that each of the extant coastal subspecies (P. p. niveiventris and P. p. phasma) is comprised of unique haplotypes indicative of their isolation, while the extinct subspecies, P. p. decoloratus, contain a single haplotype, which was shared with P. p. phasma. Moreover, all the coastal haplotypes originate from a single mainland haplotype found in central Florida, USA. The microsatellite data indicated high levels of genetic structure among our sampled populations. Additionally, these data group the populations into three distinct genetic clusters, with each of the extant coastal subspecies belonging to their own cluster and the mainland individuals forming a separate cluster. The extant Atlantic coast beach mice are on separate evolutionary trajectories, thus representative of separate taxonomic units. Therefore, the data support that two extant subspecies on the Florida Atlantic coast fit the Distinct Population Segment designation and should be managed and conserved as two separate independent units.     

Picturing beach erosion and deposition trends using PSInSAR: an example from the non-barred southern west coast of India

Coastal dynamics can rapidly alter beach morphology. In some places, such as the non-barred southern west coast of India, studying changes to beach morphology is a relatively arduous task. Persistent Scatterer Interferometric Synthetic Aperture Radar (PSInSAR), a remote sensing technique that utilizes stacks of radar images for accurate long-term monitoring of ground features, allows for detailed observations of coastal morphodynamics. Twenty-two single look complex (SLC) synthetic aperture radar (SAR) Sentinel-1A images, acquired from 4 March 2016 to 3 June 2017, are used to monitor geomorphological processes such as coastal erosion and deposition. Ground deformation measurements from PSInSAR processing shows the coast stretching?~?70 km between Thaickal and Munambam is highly dynamic, characterized by phases of erosion and deposition. The highest negative displacement of ? 24.9 mm at Thaickal versus the?+?7.6 mm at Chellanam in the north show the co-existing milieus of erosion and deposition. PSInSAR results concur with corresponding Google Earth images. In addition, beach sediment texture and scanning electron microscope grain micro-texture in the beach segment further corroborate temporal phases of erosion and deposition. Two locations are identified as typical erosional sites, while one location typified deposition. Erosion and deposition or rebuilding of beaches, usually correspond respectively with the onset and offset of SW monsoon wave climate in the Arabian Sea. When zones of deposition are mainly located in the proximity of river and/or lake inlets, stretches characterized by erosion are distal to inlets. Linear regression analyses of displacement–time series plots were used to identify general erosion or depositional regimes along beach segments. Results from this study illustrate how PSInSAR is a capable and reliable processing tool for monitoring temporal phases of coastal morpho-dynamics.

     

Expansion of harmful brown tides caused by the pelagophyte,Aureoumbra lagunensis DeYoe et Stockwell,to the US east coast

Brown tides caused by the pelagophyte Aureoumbra lagunensis DeYoe et Stockwell have formed ecosystem disruptive algal blooms in shallow lagoons of Texas (TX), USA, for more than two decades but have never been reported elsewhere. During the summer of 2012, a dense brown tide occurred in the Mosquito Lagoon and northern Indian River Lagoon along the east coast of Florida (FL), USA. While chlorophyll a levels in this system have averaged 5 μg L⁻¹ during the past two decades, concentrations during this brown tide reached ∼200 μg L⁻¹. Concurrently, levels of nitrate were significantly lower than average and levels of dissolved organic nitrogen were significantly higher than average (p < 0.001 for both). Sequences of the 18S rRNA gene of the bloom community and of single cell isolates were identical to those of Aureoumbra lagunensis DeYoe et Stockwell from TX. The A. lagunensis brown tide in FL bloomed to densities exceeding 10⁶ cells mL⁻¹ (quantified with a species-specific immuno-label) from July through September, began to dissipate in October, but maintained densities exceeding 10⁵ cells mL⁻¹ in some regions through December of 2012. The decline of the bloom was associated with near-hypoxic conditions and more than 30 fish kills reported within the Mosquito Lagoon in September 2012, a number far exceeding all prior monthly reports in this system dating to 1996. Wild northern quahog populations (a.k.a. hard clam, Mercenaria mercenaria) suffered mass die offs during the brown tide and eastern oysters (Crassostrea virginica) that settled during 2012 were significantly smaller than prior years. Clearance rates of hard clams and eastern oyster were significantly reduced in the presence of Mosquito Lagoon bloom water and A. lagunensis monocultures isolated from the Mosquito Lagoon at densities of ∼10⁶ cells L⁻¹. The expansion of harmful brown tides caused by A. lagunensis to these estuaries represents a new threat to the US southeast coast.     

Seasonal variations in nematode assemblages on an Australian temperate ocean beach; the effect of heavy seas and unusually high tides

Free-living nematodes inhabiting a sandy beach exposed to strong ocean waves were sampled at bimonthly intervals for two years. Six 1.3-litre core samples were taken on each occasion down to a depth of 60 cm. The numbers of each species and their status as juveniles, males and females (with or without eggs) was recorded. In the common species all these stages occur throughout the year, but the population increases in the warmer months of the year and falls to a much lower level in winter. Most species are dispersed throughout the sand to a depth of at least 60 cm, but several species where almost always found below the water table at about 60 cm. The faunal composition of the nematode assemblages changed significantly from month to month. Additional samples were taken to monitor the effects of very strong waves coupled with a very high tide which remodelled the beach. The nematode fauna was partially reconstituted by this event. It is concluded that the intertidal beach fauna is a dynamic extension of the near shore sub-littoral nematode fauna.     

Taxonomy,natural history and zoogeography of sand beach isopods from the coast of Southern Chile

Seven species of marine isopods were collected on sandy beaches of Southern Chile (from about 37° S until 42° S). From these, Excirolana hirsuticauda Menzies, Excirolana monodi Carvacho, Chaetilia paucidens Menzies, Macrochiridothea setifer Menzies and M. mehuinensis Jaramillo are known only from the Chilean coasts. Another species, Excirolana braziliensis Richardson, is known from other areas of American coasts. One species is identified here as Macrochiridothea aff. lilianae by its resemblance with M. lilianae Moreira from Southern Brazil. All these species are here briefly described and some aspects of their ecology added. Also Zoogeographic characterization of the studied area is discussed in relation to the distributional patterns of isopods living in them.     

A case study: fecal corticosteroid and behavior as indicators of welfare during relocation of an Asian elephant

This study was a preliminary investigation of an enzyme immunoassay for measuring fecal glucocorticoid metabolites in a male Asian elephant (Elephas maximus) by investigating changes in behavior and cortisol metabolite excretion associated with a putative stressful event. The study collected fecal samples for 10 days prior to, and 10 days after, 24-hr transport and relocation of the elephant to a new herd. The study measured cortisol metabolites using 2 enzyme immunoassays indicating a 389% and 340% increase in cortisol metabolite excretion following relocation. Maximal cortisol metabolite excretion occurred 2 days after relocation and remained elevated during establishment of the new herd. Stereotypic behavior increased approximately 400% after relocation. The relocation disturbed sleep patterns, the elephant spent less time sleeping during the night, and the elephant slept standing up. These results provide preliminary evidence that noninvasive monitoring of fecal cortisol metabolites can be used to investigate adrenal activity in Asian elephants and may be a safe, practical, and accurate welfare indicator.     

Diet of marine fish larvae and juveniles that use rocky intertidal pools at the Portuguese coast

The use of tidal pools during early ontogeny is likely to enhance growth, condition and survival chances of the transient marine fish larvae and juveniles that use them. However, the diet of such individuals within tidal pools is poorly known; this knowledge is important to understand why such high numbers of individuals use these environments in spring and summer on the Portuguese coast. Transient marine fishes were sampled monthly over a two‐year period in four tidal pools of a rocky reef on the west Portuguese coast. The diet composition in the tidal pools of the most abundant marine fish larvae/juveniles, Diplodus sargus and Atherina spp., were investigated. Stomach and gut contents of 483 individuals (354 D. sargus ranging in total length from 9 to 87 mm and 134 Atherina spp. ranging in total length from 10 to 31 mm) were analyzed and dietary indices estimated for the different developmental stages. The diet of D. sargus composed mainly harpacticoid copepods, chironomid larvae, ostracods, chironomid adults and amphipods; whereas the diet of Atherina spp. was mainly harpacticoid copepods, ostracods and gastropods. Along the ontogenetic development, the proportions and diversity of food items in the D. sargus diet varied. Importance of the harpacticoid copepods decreased with increasing fish size, while that of amphipods and isopods increased. Larvae and juvenile D. sargus and Atherina spp. found in rocky reef tidal pools are opportunistic consumers of a wide range of prey and thus take advantage of the high prey availability in these habitats.     

Global in scope and regionally rich: an IndiSeas workshop helps shape the future of marine ecosystem indicators

This report summarizes the outcomes of an IndiSeas workshop aimed at using ecosystem indicators to evaluate the status of the world??s exploited marine ecosystems in support of an ecosystem approach to fisheries, and global policy drivers such as the 2020 targets of the Convention on Biological Diversity. Key issues covered relate to the selection and integration of multi-disciplinary indicators, including climate, biodiversity and human dimension indicators, and to the development of data- and model-based methods to test the performance of ecosystem indicators in providing support for fisheries management. To enhance the robustness of our cross-system comparison, unprecedented effort was put in gathering regional experts from developed and developing countries, working together on multi-institutional survey datasets, and using the most up-to-date ecosystem models.     

Internal waves, primary production and the compensation depth of marine phytoplankton

Internal waves increase the average light intensity experiencedby phytoplankton and augment the compensation depth below whichno net photosynthesis occurs. These effects may be quite largein eutrophic waters with moderate or high light attenuationcoefficients. Data on internal waves and light attenuation canbe used to correct standard estimates of (new) primary productionin the lower euphotic zone based on uptake rates of carbon ornitrogen isotopes.