Genomic Characterization of Cyanophage vB_AphaS-CL131 Infecting Filamentous Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Reveals Novel Insights into Virus-Bacterium Interactions

While filamentous cyanobacteria play a crucial role in food web dynamics and biogeochemical cycling of many aquatic ecosystems around the globe, the knowledge regarding the phages infecting them is limited. Here, we describe the complete genome of the virulent cyanophage vB_AphaS-CL131 (here, CL 131), a Siphoviridae phage that infects the filamentous diazotrophic bloom-forming cyanobacterium Aphanizomenon flos-aquae in the brackish Baltic Sea. CL 131 features a 112,793-bp double-stranded DNA (dsDNA) genome encompassing 149 putative open reading frames (ORFs), of which the majority (86%) lack sequence homology to genes with known functions in other bacteriophages or bacteria. Phylogenetic analysis revealed that CL 131 possibly represents a new evolutionary lineage within the group of cyanophages infecting filamentous cyanobacteria, which form a separate cluster from phages infecting unicellular cyanobacteria. CL 131 encodes a putative type V-U2 CRISPR-Cas system with one spacer (out of 10) targeting a DNA primase pseudogene in a cyanobacterium and a putative type II toxin-antitoxin system, consisting of a GNAT family N-acetyltransferase and a protein of unknown function containing the PRK09726 domain (characteristic of HipB antitoxins). Comparison of CL 131 proteins to reads from Baltic Sea and other available fresh- and brackish-water metagenomes and analysis of CRISPR-Cas arrays in publicly available A. flos-aquae genomes demonstrated that phages similar to CL 131 are present and dynamic in the Baltic Sea and share a common history with their hosts dating back at least several decades. In addition, different CRISPR-Cas systems within individual A. flos-aquae genomes targeted several sequences in the CL 131 genome, including genes related to virion structure and morphogenesis. Altogether, these findings revealed new genomic information for exploring viral diversity and provide a model system for investigation of virus-host interactions in filamentous cyanobacteria. IMPORTANCE The genomic characterization of novel cyanophage vB_AphaS-CL131 and the analysis of its genomic features in the context of other viruses, metagenomic data, and host CRISPR-Cas systems contribute toward a better understanding of aquatic viral diversity and distribution in general and of brackish-water cyanophages infecting filamentous diazotrophic cyanobacteria in the Baltic Sea in particular. The results of this study revealed previously undescribed features of cyanophage genomes (e.g., self-excising intein-containing putative dCTP deaminase and putative cyanophage-encoded CRISPR-Cas and toxin-antitoxin systems) and can therefore be used to predict potential interactions between bloom-forming cyanobacteria and their cyanophages.Peer reviewe

A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales

In order to better understand the relationships among current Nostocales cyanobacterial blooms, eight genomes were sequenced from cultured isolates or from environmental metagenomes of recent planktonic Nostocales blooms. Phylogenomic analysis of publicly available sequences placed the new genomes among a group of 15 genomes from four continents in a distinct ADA Glade (Anabaena/Dolichospenruun/Aphanizomenon) within the Nostocales. This Glade contains four species-level groups, two of which include members with both Anabaena-like and Aphanizomenon-flos-aquae-like morphology. The genomes contain many repetitive genetic elements and a sizable pangenome, in which ABC-type transporters are highly represented. Alongside common core genes for photosynthesis, the differentiation of N-2-fixing heterocysts, and the uptake and incorporation of the major nutrients P, N and S, we identified several gene pathways in the pangenome that may contribute to niche partitioning. Genes for problematic secondary metabolites-cyanotoxins and taste-and-odor compounds-were sporadically present, as were other polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters. By contrast, genes predicted to encode the ribosomally generated bacteriocin peptides were found in all genomes

Food webs under changing biodiversity - Top-down control

Report on effects of changing predation pressure on benthic and pelagic specie

Morphology and distribution of phage-like particles in a eutrophic boreal lagoon* Virus-like particles Electron microscopy Curonian Lagoon

Abstract In this paper we present the results of direct observations of the morphology and size of phage-like particles by means of transmission electron microscopy (TEM) as a function of their spatial distribution in the shallow highly productive Curonian Lagoon of the Baltic Sea. In total, 26 morphologically different forms of phagelike particles were found. Different trends of distribution in terms of abundance, size and shape of virus-like particles were demonstrated. The total abundance of viruses varied from 1.91×10 7 ml −1 to 5.06×10 7 ml −1 . The virus to bacteria ratio (VBR) changed from 15.6 to 49 and was negatively associated with total bacterial numbers (r = −0.60; p < 0.05). The phages of family Myoviridae were the most diverse and were dominant at all stations

Absence of evidence for viral infection in colony-embedded cyanobacterial isolates from the Curonian Lagoon

The aim of the present study was to assess the frequency of viral infections in colony-embedded cells of the cyanobacteria Aphanizomenon flos-aquae and Microcystis aeruginosa collected from the brackish Curonian Lagoon. Natural and mitomycin C-treated A. flos-aquae and M. aeruginosa samples were examined for the presence of viruses and lysis by a combination of light-, epifluorescence and transmission electron microscopy techniques. Here we report a lack of evidence for virus infection, progeny formation and cell lysis in colony-embedded cells of A. flos-aquae and M. aeruginosa. These results indicated that viruses contribute little to the mortality of these cyanobacteria when the latter occur in colonies. Consequently, the results supported the hypothesis that colony formation can, at least temporarily, provide an efficient strategy for protection against virus-induced mortality. Finally, assuming that grazing has a negligible effect on colony-embedded cells in the Curonian Lagoon, we propose that most of the cyanobacterial biomass produced is lost from the pelagic food web by sedimentation

Morphology and distribution of phage-like particles in a eutrophic boreal lagoon

In this paper we present the results of direct observations of the morphology and size of phage-like particles by means of transmission electron microscopy (TEM) as a function of their spatial distribution in the shallow highly productive Curonian Lagoon of the Baltic Sea. In total, 26 morphologically different forms of phage-like particles were found. Different trends of distribution in terms of abundance, size and shape of virus-like particles were demonstrated. The total abundance of viruses varied from 1.91×107 ml-1 to 5.06×107 ml-1. The virus to bacteria ratio (VBR) changed from 15.6 to 49 and was negatively associated with total bacterial numbers (r = -0.60; p < 0.05). The phages of family Myoviridae were the most diverse and were dominant at all stations

Prototype-Based Contour Detection Applied to Segmentation of Phytoplankton Images

Novel prototype-based framework for image segmentation is introduced and successfully applied for cell segmentation in microscopy imagery. This study is concerned with precise contour detection for objects representing the Prorocentrum minimum species in phytoplankton images. The framework requires a single object with the ground truth contour as a prototype to perform detection of the contour for the remaining objects. The level set method is chosen as a segmentation algorithm and its parameters are tuned by differential evolution. The fitness function is based on the distance between pixels near contour in the prototype image and pixels near detected contour in the target image. Pixels “of interest correspond to several concentric bands of various width in outer and inner areas, relative to the contour. Usefulness of the introduced approach was demonstrated by comparing it to the basic level set and advanced Weka segmentation techniques. Solving the parameter selection problem of the level set algorithm considerably improved segmentation accuracy