The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples

Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world's oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metagenomic sequence data collected as part of the Sorcerer II Global Ocean Expedition (GOS) revealed a high abundance of viral sequences, representing approximately 3% of the total predicted proteins. Cluster analyses of the viral sequences revealed hundreds to thousands of viral genes encoding various metabolic and cellular functions. Quantitative analyses of viral genes of host origin performed on the viral fraction of aquatic samples confirmed the viral nature of these sequences and suggested that significant portions of aquatic viral communities behave as reservoirs of such genetic material. Distributional and phylogenetic analyses of these host-derived viral sequences also suggested that viral acquisition of environmentally relevant genes of host origin is a more abundant and widespread phenomenon than previously appreciated. The predominant viral sequences identified within microbial fractions originated from tailed bacteriophages and exhibited varying global distributions according to viral family. Recruitment of GOS viral sequence fragments against 27 complete aquatic viral genomes revealed that only one reference bacteriophage genome was highly abundant and was closely related, but not identical, to the cyanomyovirus P-SSM4. The co-distribution across all sampling sites of P-SSM4-like sequences with the dominant ecotype of its host, Prochlorococcus supports the classification of the viral sequences as P-SSM4-like and suggests that this virus may influence the abundance, distribution and diversity of one of the most dominant components of picophytoplankton in oligotrophic oceans. In summary, the abundance and broad geographical distribution of viral sequences within microbial fractions, the prevalence of genes among viral sequences that encode microbial physiological function and their distinct phylogenetic distribution lend strong support to the notion that viral-mediated gene acquisition is a common and ongoing mechanism for generating microbial diversity in the marine environment

Construction of a gene probe for the detection of P virus (Reoviridae) infections in decapod crustaceans.

The construction is described of a molecular probe to P virus, a double stranded RNA virus belonging to the Reoviridiae, which is an endemic pathogen of swimming crabs in British coastal waters and the Mediterranean. The probe hybridises to the P virus genome and can be easily produced in large quantities by PCR. It may be used by dot blotting or in situ hybridisation to specifically detect P virus in tissues and cells of natural or experimentally infected animals. Analyses of tissue samples with this probe show that the virus infects connective tissues of gills and hepatopancreas. This is the first gene probe to be constructed for a native viral pathogen of temperate water brachyurans and it will be useful to study virus ecology and virus-host interactions in vivo and in vitro. An understanding of these processes is essential to control and manage disease and, ultimately, to identify immune effecters capable of destroying viral pathogens. (C) 1999 Elsevier Science B.V. All rights reserved.</p

Construction of a gene probe for the detection of P virus (Reoviridae) infections in decapod crustaceans.

The construction is described of a molecular probe to P virus, a double stranded RNA virus belonging to the Reoviridiae, which is an endemic pathogen of swimming crabs in British coastal waters and the Mediterranean. The probe hybridises to the P virus genome and can be easily produced in large quantities by PCR. It may be used by dot blotting or in situ hybridisation to specifically detect P virus in tissues and cells of natural or experimentally infected animals. Analyses of tissue samples with this probe show that the virus infects connective tissues of gills and hepatopancreas. This is the first gene probe to be constructed for a native viral pathogen of temperate water brachyurans and it will be useful to study virus ecology and virus-host interactions in vivo and in vitro. An understanding of these processes is essential to control and manage disease and, ultimately, to identify immune effecters capable of destroying viral pathogens. (C) 1999 Elsevier Science B.V. All rights reserved.</p

Short-term responses of unicellular planktonic eukaryotes to increases in temperature and UVB radiation

Background: Small size eukaryotes play a fundamental role in the functioning of coastal ecosystems, however, the way in which these micro-organisms respond to combined effects of water temperature, UVB radiations (UVBR) and nutrient availability is still poorly investigated. Results: We coupled molecular tools (18S rRNA gene sequencing and fingerprinting) with microscope-based identification and counting to experimentally investigate the short-term responses of small eukaryotes (<6 mu m; from a coastal Mediterranean lagoon) to a warming treatment (+3 degrees C) and UVB radiation increases (+20%) at two different nutrient levels. Interestingly, the increase in temperature resulted in higher pigmented eukaryotes abundances and in community structure changes clearly illustrated by molecular analyses. For most of the phylogenetic groups, some rearrangements occurred at the OTUs level even when their relative proportion (microscope counting) did not change significantly. Temperature explained almost 20% of the total variance of the small eukaryote community structure (while UVB explained only 8.4%). However, complex cumulative effects were detected. Some antagonistic or non additive effects were detected between temperature and nutrients, especially for Dinophyceae and Cryptophyceae. Conclusions: This multifactorial experiment highlights the potential impacts, over short time scales, of changing environmental factors on the structure of various functional groups like small primary producers, parasites and saprotrophs which, in response, can modify energy flow in the planktonic food webs