Evaluating the efficiency of DNA Metabarcoding to analyze the diet of Hippocampus guttulatus (Teleostea: Syngnathidae).

Seahorses are considered a flagship species for conservation efforts and due to their conservation status, improving knowledge on their dietary composition while applying a non-invasive approach, could be useful. Using Hippocampus guttulatus as a case study, the present study represents pioneering research into investigating the diet of seahorses by NGS-based DNA metabarcoding of fecal samples. The study developed and tested the protocol for fecal DNA metabarcoding during the feeding trials where captive seahorses were fed on a diet of known composition; the process was subsequently applied on fecal samples collected from wild individuals. The analysis of samples collected during the feeding trials indicated the reliability of the applied molecular approach by allowing the characterization of the effectively ingested prey. In the field study, among detected prey species, results revealed that the majority of the seahorse samples contained taxa such as Amphipoda, Decapoda, Isopoda, and Calanoida, while less common prey taxa were Gastropoda and Polyplacophora. As only a small amount of starting fecal material is needed and the sampling procedure is neither invasive nor lethal. The present study indicates DNA metabarcoding as useful for investigating seahorse diet and could help define management and conservation actions

Evaluating the efficiency of dna metabarcoding to analyze the diet of hippocampus guttulatus (Teleostea: Syngnathidae)

Seahorses are considered a flagship species for conservation efforts and due to their conservation status, improving knowledge on their dietary composition while applying a non-invasive approach, could be useful. Using Hippocampus guttulatus as a case study, the present study represents pioneering research into investigating the diet of seahorses by NGS-based DNA metabarcoding of fecal samples. The study developed and tested the protocol for fecal DNA metabarcoding during the feeding trials where captive seahorses were fed on a diet of known composition; the process was subsequently applied on fecal samples collected from wild individuals. The analysis of samples collected during the feeding trials indicated the reliability of the applied molecular approach by allowing the characterization of the effectively ingested prey. In the field study, among detected prey species, results revealed that the majority of the seahorse samples contained taxa such as Amphipoda, Decapoda, Isopoda, and Calanoida, while less common prey taxa were Gastropoda and Polyplacophora. As only a small amount of starting fecal material is needed and the sampling procedure is neither invasive nor lethal. The present study indicates DNA metabarcoding as useful for investigating seahorse diet and could help define management and conservation actions

Phytoplankton across Tropical and Subtropical Regions of the Atlantic, Indian and Pacific Oceans

Postprint4,411

Diversity and dynamics of a widespread bloom of the toxic dinoflagellate Alexandrium fundyense

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e22965, doi:10.1371/journal.pone.0022965.Historically, cosmopolitan phytoplankton species were presumed to represent largely unstructured populations. However, the recent development of molecular tools to examine genetic diversity have revealed differences in phytoplankton taxa across geographic scales and provided insight into the physiology and ecology of blooms. Here we describe the genetic analysis of an extensive bloom of the toxic dinoflagellate Alexandrium fundyense that occurred in the Gulf of Maine in 2005. This bloom was notable for its intensity and duration, covering hundreds of kilometers and persisting for almost two months. Genotypic analyses based on microsatellite marker data indicate that the open waters of the northeastern U.S. harbor a single regional population of A. fundyense comprising two genetically distinct sub-populations. These subpopulations were characteristic of early- and late-bloom samples and were derived from the northern and southern areas of the bloom, respectively. The temporal changes observed during this study provide clear evidence of succession during a continuous bloom and show that selection can act on the timescale of weeks to significantly alter the representation of genotypes within a population. The effects of selection on population composition and turnover would be magnified if sexual reproduction were likewise influenced by environmental conditions. We hypothesize that the combined effects of differential growth and reproduction rates serves to reduce gene flow between the sub-populations, reinforcing population structure while maintaining the diversity of the overall regional population.This work was supported by the National Institute of Environmental Health Sciences (1-P50-ES012742 to DMA and DLE), by the National Science Foundation through the Woods Hole Center for Oceans and Human Health (OCE-0430724), and by the ECOHAB program (NOAA Grant NA06NOS4780245)

Longer and less overlapping food webs in anthropogenically disturbed marine ecosystems: confirmations from the past

The human exploitation of marine resources is characterised by the preferential removal of the largest species. Although this is expected to modify the structure of food webs, we have a relatively poor understanding of the potential consequences of such alteration. Here, we take advantage of a collection of ancient consumer tissues, using stable isotope analysis and SIBER to assess changes in the structure of coastal marine food webs in the South-western Atlantic through the second half of the Holocene as a result of the sequential exploitation of marine resources by hunter-gatherers, western sealers and modern fishermen. Samples were collected from shell middens and museums. Shells of both modern and archaeological intertidal herbivorous molluscs were used to reconstruct changes in the stable isotopic baseline, while modern and archaeological bones of the South American sea lion Otaria flavescens, South American fur seal Arctocephalus australis and Magellanic penguin Spheniscus magellanicus were used to analyse changes in the structure of the community of top predators. We found that ancient food webs were shorter, more redundant and more overlapping than current ones, both in northern-central Patagonia and southern Patagonia. These surprising results may be best explained by the huge impact of western sealing on pinnipeds during the fur trade period, rather than the impact of fishing on fish populations. As a consequence, the populations of pinnipeds at the end of the sealing period were likely well below the ecosystem's carrying capacity, which resulted in a release of intraspecific competition and a shift towards larger and higher trophic level prey. This in turn led to longer and less overlapping food webs

MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences

Nucleotide sequences reference collections or databases are fundamental components in DNA barcoding and metabarcoding data analyses pipelines. In such analyses, the accurate taxonomic assignment is a crucial aspect, relying directly on the availability of comprehensive and curated reference sequence collection and its taxonomy information. The currently wide use of the mitochondrial cytochrome oxidase subunit-I (COXI) as a standard DNA barcode marker in metazoan biodiversity studies highlights the need to shed light on the availability of the related relevant information from different data sources and their eventual integration. To adequately address data integration process, many aspects should be markedly considered starting from DNA sequence curation followed by taxonomy alignment with solid reference backbone and metadata harmonization according to universal standards. Here, we present MetaCOXI, an integrated collection of curated metazoan COXI DNA sequences with their associated harmonized taxonomy and metadata. This collection was built on the two most extensive available data resources, namely the European Nucleotide Archive (ENA) and the Barcode of Life Data System (BOLD). The current release contains more than 5.6 million entries (3 9.1% unique to BOLD, 3.6% unique to ENA, and 572% shared between both), their related taxonomic classification based on NCBI reference taxonomy, and their available main metadata relevant to environmental DNA studies, such as geographical coordinates, sampling country and host species. MetaCOXI is available in standard universal formats ('fasta' for sequences & 'tsv' for taxonomy and metadata), which can be easily incorporated in standard or specific DNA barcoding and/or metabarcoding data analysis pipelines