Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii.
ABSTRACT: Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of the marine Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean and plays an important role for global and biogeochemical processes. Here we describe the features of the R. mucosus strain DFL-24(T) together with its genome sequence and annotation generated from a culture of DSM 17069(T). The 4,247,724 bp containing genome sequence encodes 4,194 protein-coding genes and 57 RNA genes. In addition to the presence of four plasmids, genome analysis revealed the presence of genes associated with host colonization, DMSP utilization, cytotoxins, and quorum sensing that could play a role in the interrelationship of R. mucosus with the dinoflagellate A. ostenfeldii and other marine organisms. Furthermore, the genome encodes genes associated with mixotrophic growth, where both reduced inorganic compounds for lithotrophic growth and a photoheterotrophic lifestyle using light as additional energy source could be used.
Project description:The marine Roseobacter clade comprises several genera of marine bacteria related to the uncultured SAR83 cluster, the second most abundant marine picoplankton lineage. Cultivated representatives of this clade are physiologically heterogeneous, and only some have the capability for aerobic anoxygenic photosynthesis, a process of potentially great ecological importance in the world's oceans. In an attempt to correlate phylogeny with ecology, we investigated the diversity of Roseobacter clade strains from various marine habitats (water samples, biofilms, laminariae, diatoms, and dinoflagellate cultures) by using the 16S rRNA gene as a phylogenetic marker gene. The potential for aerobic anoxygenic photosynthesis was determined on the genetic level by PCR amplification and sequencing of the pufLM genes of the bacterial photosynthesis reaction center and on the physiological level by detection of bacteriochlorophyll (Bchl) a. A collection of ca. 1,000 marine isolates was screened for members of the marine Roseobacter clade by 16S rRNA gene-directed multiplex PCR and sequencing. The 42 Roseobacter clade isolates found tended to form habitat-specific subclusters. The pufLM genes were detected in two groups of strains from dinoflagellate cultures but in none of the other Roseobacter clade isolates. Strains within the first group (the DFL-12 cluster) also synthesized Bchl a. Strains within the second group (the DFL-35 cluster) formed a new species of Roseovarius and did not produce Bchl a under the conditions investigated here, thus demonstrating the importance of genetic methods for screening of cultivation-dependent metabolic traits. The pufL genes of the dinoflagellate isolates were phylogenetically closely related to pufL genes from Betaproteobacteria, confirming similar previous observations which have been interpreted as indications of gene transfer events.
Project description:We present the genome of Roseovarius mucosus strain SMR3, a marine bacterium isolated from the diatom Skeletonema marinoi strain RO5AC sampled from top layer sediments at 14 m depth. Its 4,381,426 bp genome consists of a circular chromosome and two circular plasmids and contains 4,178 coding sequences (CDSs).
Project description:Genome organization, plasmid content and localization of the pufLM genes of the photosynthesis reaction center were studied by pulsed-field gel electrophoresis (PFGE) in marine phototrophic Alphaproteobacteria. Both anaerobic phototrophs (Rhodobacter veldkampii and Rhodobacter sphaeroides) and strictly aerobic anoxygenic phototrophs from the Roseobacter-Sulfitobacter-Silicibacter clade (Roseivivax halodurans, Roseobacter litoralis, Staleya guttiformis, Roseovarius tolerans, and five new strains isolated from dinoflagellate cultures) were investigated. The complete genome size was estimated for R. litoralis DSM6996(T) to be 4,704 kb, including three linear plasmids. All strains contained extrachromosomal elements of various conformations (linear or circular) and lengths (between 4.35 and 368 kb). In strain DFL-12, a member of a putative new genus isolated from a culture of the toxic dinoflagellate Prorocentrum lima, seven linear plasmids were found, together comprising 860 kb of genetic information. Hybridization with probes against the pufLM genes of the photosynthesis gene cluster after Southern transfer of the genomic DNAs showed these genes to be located on a linear plasmid of 91 kb in R. litoralis and on a linear plasmid of 120 kb in S. guttiformis, theoretically allowing their horizontal transfer. In all other strains, the pufLM genes were detected on the bacterial chromosome. The large number and significant size of the linear plasmids found especially in isolates from dinoflagellates might account for the metabolic versatility and presumed symbiotic association with eukaryotic hosts in these bacteria.
Project description:Many dinoflagellate species are notorious for the toxins they produce and ecological and human health consequences associated with harmful algal blooms (HABs). Dinoflagellates are particularly refractory to genomic analysis due to the enormous genome size, lack of knowledge about their DNA composition and structure, and peculiarities of gene regulation, such as spliced leader (SL) trans-splicing and mRNA transposition mechanisms. Alexandrium ostenfeldii is known to produce macrocyclic imine toxins, described as spirolides. We characterized the genome of A. ostenfeldii using a combination of transcriptomic data and random genomic clones for comparison with other dinoflagellates, particularly Alexandrium species. Examination of SL sequences revealed similar features as in other dinoflagellates, including Alexandrium species. SL sequences in decay indicate frequent retro-transposition of mRNA species. This probably contributes to overall genome complexity by generating additional gene copies. Sequencing of several thousand fosmid and bacterial artificial chromosome (BAC) ends yielded a wealth of simple repeats and tandemly repeated longer sequence stretches which we estimated to comprise more than half of the whole genome. Surprisingly, the repeats comprise a very limited set of 79-97 bp sequences; in part the genome is thus a relatively uniform sequence space interrupted by coding sequences. Our genomic sequence survey (GSS) represents the largest genomic data set of a dinoflagellate to date. Alexandrium ostenfeldii is a typical dinoflagellate with respect to its transcriptome and mRNA transposition but demonstrates Alexandrium-like stop codon usage. The large portion of repetitive sequences and the organization within the genome is in agreement with several other studies on dinoflagellates using different approaches. It remains to be determined whether this unusual composition is directly correlated to the exceptionally genome organization of dinoflagellates with a low amount of histones and histone-like proteins.
Project description:Salipiger mucosus Martínez-Cànovas et al. 2004 is the type species of the genus Salipiger, a moderately halophilic and exopolysaccharide-producing representative of the Roseobacter lineage within the alphaproteobacterial family Rhodobacteraceae. Members of this family were shown to be the most abundant bacteria especially in coastal and polar waters, but were also found in microbial mats and sediments. Here we describe the features of the S. mucosus strain DSM 16094(T) together with its genome sequence and annotation. The 5,689,389-bp genome sequence consists of one chromosome and several extrachromosomal elements. It contains 5,650 protein-coding genes and 95 RNA genes. The genome of S. mucosus DSM 16094(T) was sequenced as part of the activities of the Transregional Collaborative Research Center 51 (TRR51) funded by the German Research Foundation (DFG).
Project description:The complete mitochondrial genome sequence of the <i>Ptyas mucosus</i> was sequenced and reported for the first time using muscle tissue. The total length is 17?151?bp and sequence analysis showed its structure is in accordance with other snakes. The complete mitochondrial genome contains 2 rRNA genes, 21 tRNA genes, 13 protein-coding genes (PCGs), 2 control regions and 1 putative origin of L-strand replication. The gene order and nucleotide composition of <i>P. mucosus</i> are very similar with <i>E. bimaculata</i>, <i>E. anomala</i> and <i>E. schrenckii.</i> A phylogenetic tree of mitochondrial genomes indicated <i>P. mucosus</i> had the most closely relationship with <i>E. bimaculata</i>, and formed a monophyletic group with <i>E. bimaculata</i>, <i>E. anomala</i> and <i>E. schrenckii</i>.
Project description:We showed that two very different manganese transporters occur in various important genera of marine bacteria. The ABC transporter encoded by sitABCD of the model Roseobacter-clade bacterium Ruegeria pomeroyi DSS-3 is required for Mn(2+) import and was repressed by the Mur (Manganese uptake regulator) transcriptional regulator in Mn-replete media. Most genome-sequenced Roseobacter strains contain SitABCD, which are in at least two sub-groups, judged by their amino-acid sequences. However, a few Roseobacters, for example, Roseovarius nubinhibens, lack sitABCD, but these contain another gene, mntX, which encodes a predicted inner membrane polypeptide and is preceded by cis-acting Mur-responsive MRS sequences. It was confirmed directly that mntX of Roseovarius nubinhibens encodes a manganese transporter that was required for growth in Mn-depleted media and that its expression was repressed by Mur in Mn-replete conditions. MntX homologues occur in the deduced proteomes of several bacterial species. Strikingly, all of these live in marine habitats, but are in distantly related taxonomic groups, in the ?- and ?-proteobacteria. Notably, MntX was prevalent in nearly all strains of Vibrionales, including the important pathogen, Vibrio cholerae. It also occurs in a strain of the hugely abundant Candidatus Pelagibacter (SAR11), and in another populous marine bacterium, Candidatus Puniceispirillum marinum (SAR116). Consistent with this, MntX was abundant in marine bacterial metagenomes, with one sub-type occurring in an as-yet unknown bacterial clade.
Project description:In seasonal environments, strong gradients of environmental parameters can shape life cycles of phytoplankton. Depending on the rate of environmental fluctuation, specialist or generalist strategies may be favored, potentially affecting life cycle transitions. The present study examined life cycle transitions of the toxin producing Baltic dinoflagellate Alexandrium ostenfeldii and their regulation by environmental factors (temperature and nutrients). This investigation aimed to determine whether genetic recombination of different strains is required for resting cyst formation and whether newly formed cysts are dormant. Field data (temperature and salinity) and sediment surface samples were collected from a site with recurrent blooms and germination and encystment experiments were conducted under controlled laboratory conditions. Results indicate a lack of seasonal germination pattern, set by an endogenous rhythm, as commonly found with other dinoflagellates from the Baltic Sea. Germination of quiescent cysts was triggered by temperatures exceeding 10°C and combined nutrient limitation of nitrogen and phosphorus or a drop in temperature from 16 to 10°C triggered encystment most efficiently. Genetic recombination was not mandatory for the formation of resting cysts, but supported higher numbers of resistant cysts and enhanced germination capacity after a resting period. Findings from this study confirm that A. ostenfeldii follows a generalist germination and cyst formation strategy, driven by strong seasonality, which may support its persistence and possibly expansion in marginal environments in the future, if higher temperatures facilitate a longer growth season.
Project description:Spirolides belong to a group of marine phycotoxins produced by the marine planktonic dinophyte Alexandrium ostenfeldii. Composed of an imine moiety and a spiroketal ring system within a macrocylcle, spirolides are highly diverse with toxin types that vary among different strains. This study aims to characterize the spirolides from clonal A. ostenfeldii strains collected from the Netherlands, Greenland and Norway by mass spectral techniques. The structural characterization of unknown spirolides as inferred from high-resolution mass spectrometry (HR-MS) and collision induced dissociation (CID) spectra revealed the presence of nine novel spirolides that have the pseudo-molecular ions m/z 670 (1), m/z 666 (2), m/z 696 (3), m/z 678 (4), m/z 694 (5), m/z 708 (6), m/z 720 (7), m/z 722 (8) and m/z 738 (9). Of the nine new spirolides proposed in this study, compound 1 was suggested to have a truncated side chain in lieu of the commonly observed butenolide ring in spirolides. Moreover, there is indication that compound 5 might belong to new spirolide subclasses with a trispiroketal ring configuration having a 6:5:6 trispiroketal ring system. On the other hand, the other compounds were proposed as C- and G-type SPX, respectively. Compound 7 is proposed as the first G-type SPX with a 10-hydroxylation as usually observed in C-type SPX. This mass spectrometry-based study thus demonstrates that structural variability of spirolides is larger than previously known and does not only include the presence or absence of certain functional groups but also involves the triketal ring system.