Stable and Sporadic Symbiotic Communities of Coral and Algal Holobionts

Coral and algal holobionts are assemblages of macroorganisms and microorganisms, including viruses, Bacteria, Archaea, protists and fungi. Despite a decade of research, it remains unclear whether these associations are spatial-temporally stable of species-specific. We hypothesized that conflicting interpretations of the data arise from high noise associated with sporadic microbial symbionts overwhelming signatures of stable holobiont members. To test this hypothesis, the bacterial communities associated with three coral species (Acropora rosaria, Acropora hyacinthus and Porites lutea) and two algal guilds (crustose coralline algae and turf algae) from 131 samples were analyzed using a novel statistical approach termed the Abundance-Ubiquity (AU) test. The AU test determines whether a given bacterial species would be present given additional sampling effort (that is, stable) versus those species that are sporadically associated with a sample. Using the AU test, we show that coral and algal holobionts have a high-diversity group of stable symbionts. Stable symbionts are not exclusive to one species of coral or algae. No single bacterial species was ubiquitously associated with one host, showing that there is not strict heredity of the microbiome. In addition to the stable symbionts, there was a low-diversity community of sporadice symbionts whose abundance varied widely across individual holobionts of the same species. Identification of these two symbiont communities supports the holobiont model and calls into question the hologenome theory of evolution

Variability and host density independence in inductions-based estimates of environmental lysogeny.

Temperate bacterial viruses (phages) may enter a symbiosis with their host cell, forming a unit called a lysogen. Infection and viral replication are disassociated in lysogens until an induction event such as DNA damage occurs, triggering viral-mediated lysis. The lysogen-lytic viral reproduction switch is central to viral ecology, with diverse ecosystem impacts. It has been argued that lysogeny is favoured in phages at low host densities. This paradigm is based on the fraction of chemically inducible cells (FCIC) lysogeny proxy determined using DNA-damaging mitomycin C inductions. Contrary to the established paradigm, a survey of 39 inductions publications found FCIC to be highly variable and pervasively insensitive to bacterial host density at global, within-environment and within-study levels. Attempts to determine the source(s) of variability highlighted the inherent complications in using the FCIC proxy in mixed communities, including dissociation between rates of lysogeny and FCIC values. Ultimately, FCIC studies do not provide robust measures of lysogeny or consistent evidence of either positive or negative host density dependence to the lytic-lysogenic switch. Other metrics are therefore needed to understand the drivers of the lytic-lysogenic decision in viral communities and to test models of the host density-dependent viral lytic-lysogenic switch

The Marine Viromes of Four Oceanic Regions

Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct “marine-ness” quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure

On lumped models for thermodynamic properties of simulated annealing problems

The paper describes a new method for the estimation of thermodynamic properties for simulated annealing problems using data obtained during a simulated annealing run. The method works by estimating energy-to-energy transition probabilities and is well adapted to simulations such as simulated annealing, in which the system is never in equilibrium.Nous décrivons une nouvelle méthode pour estimer les propriétés thermodynamiques dans des problèmes de recuit simulé, méthode qui utilise des données acquises durant le recuit simulé. La méthode est basée sur l' estimation des probabilités de transition énergie-énergie et est bien adaptée à des simulations de type recuit simulé, dans lesquelles le système n'est jamais à l'équilibre

Reference-independent comparative metagenomics using cross-assembly: crAss

Item does not contain fulltextMOTIVATION: Metagenomes are often characterized by high levels of unknown sequences. Reads derived from known microorganisms can easily be identified and analyzed using fast homology search algorithms and a suitable reference database, but the unknown sequences are often ignored in further analyses, biasing conclusions. Nevertheless, it is possible to use more data in a comparative metagenomic analysis by creating a cross-assembly of all reads, i.e. a single assembly of reads from different samples. Comparative metagenomics studies the interrelationships between metagenomes from different samples. Using an assembly algorithm is a fast and intuitive way to link (partially) homologous reads without requiring a database of reference sequences. RESULTS: Here, we introduce crAss, a novel bioinformatic tool that enables fast simple analysis of cross-assembly files, yielding distances between all metagenomic sample pairs and an insightful image displaying the similarities. Availability and implementation: crAss is available as a web server at http://edwards.sdsu.edu/crass/, and the Perl source code can be downloaded to run as a stand-alone command line tool. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Viral and microbial community dynamics in four aquatic environments

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Types of Phages in the Four Metagenomes

<p>A new version of the Phage Proteomic Tree (left panel) was constructed from 510 complete phage and prophage genomes using the previously described method [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040368#pbio-0040368-b023" target="_blank">23</a>]. The metagenomic sequences were compared to the phage on the Phage Proteomic Tree using TBLASTX, and the colored bars on the right represent significant similarities (<i>E</i>-value < 0.0001). Names of prophages are in red and the <i>Prochlorococcus</i> phage genomes are in green. An electronic version of the tree and a FASTA list of phage and prophage genomes used to make the tree are available at the SDSU Center for Universal Microbe Sequencing website (<a href="http://scums.sdsu.edu/phage/Oceans" target="_blank">http://scums.sdsu.edu/phage/Oceans</a>).</p

Sampling Sites

<p>The circles represent the sampling locations in the Sargasso Sea (SAR), Gulf of Mexico (GOM), British Columbia (BBC), and the Arctic Ocean. The number of samples taken at each location and combined for sequencing, as well as the date and depth range, are shown in the boxes.</p