Members of the bacterial phylum Planctomycetes are reported in marine water samples worldwide, but quantitative information is scarce. Here we investigated the phylogenetic diversity, abundance, and distribution of Planctomycetes in surface waters off the German North Sea island Helgoland during different seasons by 16S rRNA gene analysis and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Generally Planctomycetes are more abundant in samples collected in summer and autumn than in samples collected in winter and spring. Statistical analysis revealed that Planctomycetes abundance was correlated to the Centrales diatom bloom in spring 2007. The analysis of size-fractionated seawater samples and of macroaggregates showed that ϳ90% of the Planctomycetes reside in the >3-m size fraction. Comparative sequence analysis of 184 almost full-length 16S rRNA genes revealed three dominant clades. The clades, named Planctomyces-related group A, uncultured Planctomycetes group B, and Pirellula-related group D, were monitored by CARD-FISH using newly developed oligonucleotide probes. All three clades showed recurrent abundance patterns during two annual sampling campaigns. Uncultured Planctomycetes group B was most abundant in autumn samples, while Planctomyces-related group A was present in high numbers only during late autumn and winter. The levels of Pirellula-related group D were more constant throughout the year, with elevated counts in summer. Our analyses suggest that the seasonal succession of the Planctomycetes is correlated with algal blooms. We hypothesize that the niche partitioning of the different clades might be caused by their algal substrates.Planctomycetes are not planktonic fungi but a monophyletic group of Bacteria drawing increasing interest for microbial ecologists as well as evolutionary and cell biologists (12). On the basis of comparative 16S rRNA gene sequence analysis, this independent phylum belongs to the so-called Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum (55) that also includes the phylum Lentisphaerae, the candidate phylum Poribacteria (10), and the uncultured clade OP3. The grouping of these phyla into one superphylum is supported by unique features that distinguish its members from other members of the domain Bacteria, such as a peptidoglycan-free proteinaceous cell wall (25, 31), cellular compartmentalization (32, 33) and budding type of reproduction (12). Furthermore, Planctomycetes cells are often organized in a polar manner and attach to surfaces by nonprosthecate appendages (stalks) or holdfast structures.Although the first microscopic observation of rosette-forming "planktonic mycetes" was reported back in 1924 (58), pure cultures were not obtained until 1973 (51). Most strains have been isolated from marine, freshwater, and terrestrial habitats (2, 11, 13, 14, 26-28, 48, 57). Despite the recent success in isolating new members of the Planctomycetaceae (60), the phylum remains underrepresented in microbial culture collections. The Planctomyc...

The phylum Planctomycetes is involved in important processes, such as the mineralization of algal biomass and the removal of nitrogen. Using a combination of 16S rRNA sequence analysis and in situ hybridization, we analyzed the diversity and dynamics of Planctomycetes in a shallow meso-eutrophic lake, Lago di Paola, Italy. Planctomycetes detected by the probe PLA46 accounted for 1 to 5% of prokaryotic picoplankton. Abundances were higher in the coastal lake than in the adjacent marine waters. In the surface waters of the lake, the numbers of Planctomycetes fluctuated greatly, reaching a maximum of 1.5 × 10 6 cells ml −1 in July. The hypoxic bottom waters had less variable cell abundances. The Planctomycetes counts were positively correlated with chlorophyll a concentrations, confirming the role of this phylum in the degradation of algal biomass. We obtained 70 almost full-length 16S rRNA gene sequences of Planctomycetes from 2 libraries. Four distinct clades could be identified. The Pirellula-related group F and the uncultured Planctomycetes group B both had the highest identity with sequences retrieved from marine habitats, whereas the Pirellula-related group E was affiliated with sequences known from freshwater and brackish water environments. The Planctomyces-related group A seems to have a wide habitat range. Catalyzed reported deposition fluorescence in situ hybridization with newly developed probes revealed abundances of the 4 clades in surface and bottom waters ranging from 1 × 10 3 to 5 × 10 4 cells ml −1. Together, the 4 clade-specific probes identified only about a quarter of the Planctomycetes detected by probe PLA46. This indicates that the diversity of Planctomycetes has not yet been fully explored. KEY WORDS: Coastal lake ecology · Planctomycetes · Bacterial diversity · FISH · CARD-FISH · 16S rRNA gene sequencing Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 65: [129][130][131][132][133][134][135][136][137][138][139][140][141] 2011 Most cultured strains have been isolated from marine, freshwater and terrestrial habitats (Bauld & Staley 1976, Franzmann & Skerman 1984, Giovannoni et al. 1987, Schlesner 1994, Wang et al. 2002. Despite the recent success in isolating new members of the Planctomycetes from aquatic (Fukunaga et al. 2009, Winkelmann & Harder 2009) and terrestrial habitats (Kulichevskaya et al. 2007(Kulichevskaya et al. , 2008(Kulichevskaya et al. , 2009, the phylum continues to be one of the least represented in microbial culture collections. Planctomycetes are most commonly heterotrophs (Fuerst 1995), with the notable exception being the autotrophic anammox bacteria, which catalyze anaerobic ammonia oxidation with nitrite (Strous et al. 1999).Studies based on molecular methods, such as 16S ribosomal RNA (rRNA) gene sequencing and fluorescence in situ hybridization (FISH), have revealed a broad distribution of Planctomycetes in aquatic environments. They have been detected in the marine water column (DeLong et al. 1993, Vergin...

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The Chlamydiae are a phylum of obligate intracellular bacteria comprising important human and animal pathogens, yet their occurrence in the environment, their phylogenetic diversity and their host range has been largely underestimated. We investigated the seasonality of environmental chlamydiae in a Tyrrhenian coastal lake. By catalysed reporter deposition fluorescence in situ hybridization, we quantified the small planktonic cells and detected a peak in the abundance of environmental chlamydiae in early autumn with up to 5.9 × 10(4) cells ml(-1) . Super-resolution microscopy improved the visualization and quantification of these bacteria and enabled the detection of pleomorphic chlamydial cells in their protist host directly in an environmental sample. To isolate environmental chlamydiae together with their host, we applied a high-throughput limited dilution approach and successfully recovered a Vexillifera sp., strain harbouring chlamydiae (93% 16S rRNA sequence identity to Simkania negevensis), tentatively named 'Candidatus Neptunochlamydia vexilliferae'. Transmission electron microscopy in combination with fluorescence in situ hybridization was used to prove the intracellular location of these bacteria representing the first strain of marine chlamydiae stably maintained alongside with their host in a laboratory culture. Taken together, this study contributes to a better understanding of the distribution and diversity of environmental chlamydiae in previously neglected marine environments.

Amoebae play an important ecological role as predators in microbial communities. They also serve as niche for bacterial replication, harbor endosymbiotic bacteria and have contributed to the evolution of major human pathogens. Despite their high diversity, marine amoebae and their association with bacteria are poorly understood. Here we describe the isolation and characterization of two novel marine amoebae together with their bacterial endosymbionts, tentatively named ‘Candidatus Occultobacter vannellae’ and ‘Candidatus Nucleophilum amoebae’. While one amoeba strain is related to Vannella, a genus common in marine habitats, the other represents a novel lineage in the Amoebozoa. The endosymbionts showed only low similarity to known bacteria (85–88% 16S rRNA sequence similarity) but together with other uncultured marine bacteria form a sister clade to the Coxiellaceae. Using fluorescence in situ hybridization and transmission electron microscopy, identity and intracellular location of both symbionts were confirmed; one was replicating in host-derived vacuoles, whereas the other was located in the perinuclear space of its amoeba host. This study sheds for the first time light on a so far neglected group of protists and their bacterial symbionts. The newly isolated strains represent easily maintainable model systems and pave the way for further studies on marine associations between amoebae and bacterial symbionts.