Marine Genomics

Atmospheric deposition represents a major vector of both macro- and micro-nutrients to the oligotrophic open oceans, potentially imposing a profound impact on the functioning of the microbial community. Whereas bacterial responses to atmospheric deposition are being studied at the community level, corresponding functional changes are essentially unknown. Here we conducted a microcosm experiment coupled with metatranscriptomic analyses to elucidate taxonomic and functional profiles of the bacterial community in response to East Asian aerosols in the Western North Pacific Ocean (WNPO)...

The salmon louse Lepeophtheirus salmonis is a marine ectoparasite that has a detrimental impact on salmon farms. Genomic knowledge of adult stages is critical to understand the reproductive success and lifecycle completion of this species. Here, we report a comprehensive characterization of the L. salmonis miRNome with emphasis on the sex-differences of the parasite. Small-RNA sequencing was conducted on males and females, and mRNA-sequencing was also conducted to identify miRNA-targets at these stages. Based on bioinformatics analyses, 3101 putative miRNAs were found in L...

In January 1888, shortly after his Habilitation (Nov. 1887), Theodor Boveri came for the first time as guest investigator to the Naples Zoological Station. The last of his eight research stays took place in spring 1914, the year before his untimely death in 1915. The Naples Station was therefore a constant presence in all his scientific life. At least 20 of his publications are based on research done at Naples. In this paper, I will try to outline the unique working conditions that Boveri found at Naples. By 1888, the Naples Station was already an expanding, smoothly functioning organism...

Transcriptional regulation constitutes a rapid response of marine organisms facing stressful environmental conditions, such as the concomitant exposure to warming, ocean acidification and hypoxia under climate change. In previous studies, we investigated whole-organism physiological patterns and cellular metabolism in gill and muscle of the marine gastropod Haliotis fulgens in response to increasing temperature (18 °C to 32 °C at +3 °C per day) under hypoxia (50% air saturation), hypercapnia (1000 μatm pCO2 ) and both factors combined...

Gene regulatory networks account for the ability of the genome to program development in complex multi-cellular organisms. Such networks are based on principles of gene regulation by combinations of transcription factors that bind to specific cis-regulatory DNA sites to activate transcription. These cis-regulatory regions mediate logic processing at each network node, enabling progressive increases in organismal complexity with development. Gene regulatory network explanations of development have been shown to account for patterning and cell type diversification in fly and sea urchin embryonic systems, where networks are characterized by fast coupling between transcriptional inputs and changes in target gene transcription rates, and crucial cis-regulatory elements are concentrated relatively close to the protein coding sequences of the target genes, thus facilitating their identification...

Invasive parasites have been implicated in the declines of several freshwater species. The swim bladder nematode Anguillicola crassus was introduced into Europe in the 1980s and is considered a threat to the European eel (Anguilla anguilla). Infection affects stress resistance and swimming behaviour. European eels produce an immune response against the parasite during the late stages of infection and after repeated infections. We used RNA-seq to examine the molecular response to infection during the poorly understood early stage and identify expression of genes and associated processes that are modified in two immune organs of European eels 3 days post infection with A...

The present study addresses the microbiome of the first whale fall (YOKO 16) that has been described in the deep sea in the southern Atlantic Ocean (São Paulo Plateau; 4204 m depth), in terms of its metabolic uniqueness. Sets of ten thousand protein sequences from YOKO 16 and 29 public domain metagenomes (SRA and GenBank databases) that represent various marine, terrestrial and gut-associated microbial communities were analyzed. The determination of protein functionality, based on the KAAS server, indicated that the YOKO 16 microbiome has industrially-relevant proteins, such as proteases and lipases, that have low similarity (~50%) with previously-described enzymes...

The formalization of the idea of "Regulatory Genome" is a recent one. However, it stems from a long tradition in the study of how the genetic information is transferred between generations. Theodore Boveri suggested for the first time that the whole genome participates in the shaping of individuals. Through a long lineage of researchers, we have learned how this whole-genome activity is regulated, in space and time. It is, however, due to the insights and experimental approaches taken by different researchers, among them Eric Davidson and associates, that we understand the mechanistic basis of this regulation...

The marine diatom Phaeodactylum tricornutum is attractive for basic and applied diatom research. We isolated putative endogenous gene promoters derived from genes that are highly expressed in P. tricornutum: the fucoxanthin chlorophyll a/c-binding protein (FCP) C gene, the vacuolar ATP synthase 16-kDa proteolipid subunit (V-ATPase C) gene, the clumping factor A gene and the solute carrier family 34 member 2 gene. Five putative promoter regions were isolated, linked to an antibiotic resistance gene (Sh ble) and transformed into P...

Bivalves are frequently exposed to salinity and temperature fluctuations in the estuary. This study explored the molecular effect of these fluctuations by exposing Sydney rock oysters, (Saccostrea glomerata), native to Australia, to either low salinity, elevated temperature or a combined salinity and temperature stress. Following the exposures, RNA-Seq was carried out on the collected oyster tissues. Differential transcript analysis resulted in a total of 1473, 1232 and 2571 transcripts, which were differentially expressed in S...

Bivalve molluscs of the genus Mytilus are considered a model organism in ecotoxicology and are known to be well adapted to marine ecosystems affected by multiple anthropogenic factors, including pollution. In order to assess whether pollution interferes with the reproductive success of Mytilus and affects the diversity within and between populations, we sequenced the transcriptomes of 72 individuals from 9 populations of Mytilus galloprovincialis collected along a ca. 130-km north-south transect on the Western coast of the Iberian Peninsula...

Ascidians belonging to Phlebobranchia accumulate vanadium to an extraordinary degree (≤ 350 mM). Vanadium levels are strictly regulated and vary among ascidian species; thus, they represent well-suited models for studies on vanadium accumulation. No comprehensive study on metal accumulation and reduction in marine organisms in relation to their symbiotic bacterial communities has been published. Therefore, we performed comparative 16S rRNA amplicon sequence analyses on samples from three tissues (branchial sac, intestine, and intestinal lumen) involved in vanadium absorption, isolated from two vanadium-rich (Ascidia ahodori and Ascidia sydneiensis samea) and one vanadium-poor species (Styela plicata)...

The Crassostrea virginica oyster has biological and economic importance in the Gulf of Mexico, an area with a high extraction and production of hydrocarbons. Exposure to hydrocarbons affects the reproductive processes in bivalves. In C. virginica, the effect of hydrocarbons on the gonad of the undifferentiated organism has not been evaluated to determine the possible damage during the maturation process. To evaluate this effect, RNA-seq data was generated from C. virginica gonads exposed to a 200 μg/L of hydrocarbons at different exposure times (7, 14 and 21 days) and a control treatment (without hydrocarbons)...

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The Cortes geoduck Panopea globosa is a large bivalve with a high commercial value distributed from the southern Pacific coast of the Baja California Peninsula to the northern Gulf of California, inhabiting a wide range of subtropical temperatures. A new record of this species in shallower waters suggests that it can tolerate a warmer environment than previously thought. To better understand the whole-body and molecular response mechanisms to different temperatures, we assessed the metabolic rate of juvenile individuals exposed to chronic and acute thermal conditions and analyzed the transcriptomic response in ctenidial tissues...

Tolerance of organisms towards heterogeneous and variable environments is highly related to physiological flexibility. An effective strategy to enhance physiological flexibility is the expression of polymorphic enzymes. This seems to be the case in the brown shrimp Crangon crangon. It shows high reproduction rates, feeds opportunistically on endo- and epibenthic organisms, and is apparently well adapted to variable environmental conditions. Previous electrophoretic studies revealed a high level of polymorphism and no consistent phenotype of digestive enzymes between individuals...

The order of Cetacea with 88 species including Odontoceti (or toothed whales) and Mysticeti (or baleen whales) is the most specialized and diversified group of mammals. The blue whale with a maximum recorded length of 29.9 m for 173 t of weight is the largest animal known to have ever existed, and any dolphin's brain is most powerful and complex than any other brain in the animal kingdom, second only to primate's. Nevertheless, Cetacea are mammals that re-entered the oceans only a little over 50 million years ago, a relatively short time on the evolutionary scale...

Pyropia yezoensis is an economically important marine macroalgae, naturally distributed in the upper intertidal zone. Owing to the nature of its habitat, the thallus will periodically be exposed to seawater or atmosphere, and can lose up to 95% of its cellular water content. This makes the alga an ideal research model to investigate the mechanisms of desiccation tolerance. In this study, we investigated the response mechanisms to dehydration and rehydration stresses at the transcription level in Pyropia yezoensis...

Marine picoplankton, unicellular organisms with cell sizes up to 3 μm in diameter, numerically dominate marine ecosystems, encompassing Archaea, Bacteria, Eukarya (protists and fungi) as well as viruses. Autotrophic and heterotrophic picoplankton abundance and community composition with a focus on picoeukaryotes (PEs) were investigated in the winter of 2016 at three stations along a coast-to-offshore transect in the southern Adriatic Sea. Abundances were estimated by flow cytometry, while community composition by Illumina High-Throughput Sequencing (HTS) of 16S and 18S rRNA genes...

The plating coral, Agaricia lamarcki is a widely distributed species inhabiting reefs across the Caribbean basin and Florida. This species is of interest since it is considered a depth-generalist, found from 10 to 70 m. Given the scope of contemporary studies on this coral's population dynamics and physiology, as well as, the potential of mesophotic reefs to be refuge habitats for deteriorated shallow water reefs, we present the first de novo transcriptome assembly of an important mesophotic coral. Using next-generation paired-end sequencing (Illumina Hiseq4000; 2 × 150 bp), we obtained a total of 82,506,058 raw reads...