Pirellula sp. strain 1 (''Rhodopirellula baltica'') is a marine representative of the globally distributed and environmentally important bacterial order Planctomycetales. Here we report the complete genome sequence of a member of this independent phylum. With 7.145 megabases, Pirellula sp. strain 1 has the largest circular bacterial genome sequenced so far. The presence of all genes required for heterolactic acid fermentation, key genes for the interconversion of C1 compounds, and 110 sulfatases were unexpected for this aerobic heterotrophic isolate. Although Pirellula sp. strain 1 has a proteinaceous cell wall, remnants of genes for peptidoglycan synthesis were found. Genes for lipid A biosynthesis and homologues to the flagellar L-and P-ring protein indicate a former Gram-negative type of cell wall. Phylogenetic analysis of all relevant markers clearly affiliates the Planctomycetales to the domain Bacteria as a distinct phylum, but a deepest branching is not supported by our analyses. P irellula sp. strain 1, which is in the process of being validly described as ''Rhodopirellula baltica,'' is a marine, aerobic, heterotrophic representative of the globally distributed and environmentally important bacterial order Planctomycetales. Molecular microbial ecology studies repeatedly provided evidence that planctomycetes are abundant in terrestrial and marine habitats (1-5). For example, they inhabit phytodetrital macroaggregates in marine environments (6) and include one of the organisms known to derive energy from the anaerobic oxidation of ammonia (7). They catalyze important transformations in global carbon and nitrogen cycles. By their mineralization of marine snow particles planctomycetes have a profound impact on global biogeochemistry and climate by affecting exchange processes between the geosphere and atmosphere (8). From a phylogenetic perspective the order Planctomycetales forms an independent, monophyletic phylum of the domain Bacteria (9). It has recently been suggested to be the deepest branching bacterial phylum (10). Planctomycetes are unique in many other respects. Their cell walls do not contain peptidoglycan, the main structural polymer of most members of the domain Bacteria. They show a unique cell compartmentalization in which a single membrane separates a peripheral ribosome-free paryphoplasm from the inner riboplasm (pirellulosome). Within the riboplasm, all planctomycetes contain a condensed fibrillar nucleoid, which in Gemmata spp. is surrounded by a additional double membrane (11). These structures, together with an unusual fatty acid composition of the phospholipids, resemble eukaryotes rather than a representative of the bacterial domain (12).Characteristic for Planctomycetales are the polar cell organization and a life cycle with a polar, yeast-like cell division. Cells attach to surfaces at their vegetative poles by means of an excreted holdfast substance or stalks (13). Further unusual features are the crateriform structures on the cell surface of all planctomycetes (14). They appear as...

A basic problem of the metagenomic approach in microbial ecology is the assignment of genomic fragments to a certain species or taxonomic group, when suitable marker genes are absent. Currently, the (G + C)-content together with phylogenetic information and codon adaptation for functional genes is mostly used to assess the relationship of different fragments. These methods, however, can produce ambiguous results. In order to evaluate sequence-based methods for fragment identification, we extensively compared (G + C)-contents and tetranucleotide usage patterns of 9054 fosmid-sized genomic fragments generated in silico from 118 completely sequenced bacterial genomes (40 982 931 fragment pairs were compared in total). The results of this systematic study show that the discriminatory power of correlations of tetranucleotide-derived z-scores is by far superior to that of differences in (G + C)-content and provides reasonable assignment probabilities when applied to metagenome libraries of small diversity. Using six fully sequenced fosmid inserts from a metagenomic analysis of microbial consortia mediating the anaerobic oxidation of methane (AOM), we demonstrate that discrimination based on tetranucleotide-derived z-score correlations was consistent with corresponding data from 16S ribosomal RNA sequence analysis and allowed us to discriminate between fosmid inserts that were indistinguishable with respect to their (G + C)-contents.

Members of the Bacteroidetes, formerly known as the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum, are among the major taxa of marine heterotrophic bacterioplankton frequently found on macroscopic organic matter particles (marine snow). In addition, they have been shown to also represent a significant part of free-living microbial assemblages in nutrient-rich microenvironments. Their abundance and distribution pattern in combination with enzymatic activity studies has led to the notion that organisms of this group are specialists for degradation of high molecular weight compounds in both the dissolved and particulate fraction of the marine organic matter pool, implying a major role of Bacteroidetes in the marine carbon cycle. Despite their ecological importance, comprehensive molecular data on organisms of this group have been scarce so far. Here we report on the first whole genome analysis of a marine Bacteroidetes representative, 'Gramella forsetii' KT0803. Functional analysis of the predicted proteome disclosed several traits which in joint consideration suggest a clear adaptation of this marine Bacteroidetes representative to the degradation of high molecular weight organic matter, such as a substantial suite of genes encoding hydrolytic enzymes, a predicted preference for polymeric carbon sources and a distinct capability for surface adhesion.

Background: In the emerging field of environmental genomics, direct cloning and sequencing of genomic fragments from complex microbial communities has proven to be a valuable source of new enzymes, expanding the knowledge of basic biological processes. The central problem of this so called metagenome-approach is that the cloned fragments often lack suitable phylogenetic marker genes, rendering the identification of clones that are likely to originate from the same genome difficult or impossible. In such cases, the analysis of intrinsic DNA-signatures like tetranucleotide frequencies can provide valuable hints on fragment affiliation. With this application in mind, the TETRA web-service and the TETRA stand-alone program have been developed, both of which automate the task of comparative tetranucleotide frequency analysis.