Phylogeny of β-xylanases from Planctomycetes

Here, we present the results of a computational analysis of a group of hypothetical GH10 endo-β-xylanases from the Planctomycetes, a bacterial phylum with poorly characterized functional capabilities. These proteins are encoded in all analyzed genomes of heterotrophic Planctomycetes and form a phylogenetically distinct and tight cluster. In addition, we determined nucleotide sequences for endo-β-xylanase genes from five strains of Isosphaera-Singulisphaera group of the Planctomycetes. The trees constructed for the 16S rRNA genes and the inferred amino acid sequences of endo-β-xylanases were highly congruent, thus suggesting the vertical transfer of endo-β-xylanase genes and their functional importance in Planctomycetes.     

Temporal variability of coastal Planctomycetes clades at Kabeltonne station, North Sea

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 ~90% of the Planctomycetes reside in the >3-μm 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.     

粉粒氨氮和水分影响浮霉菌门群落的空间分化

【背景】来自浮霉菌门(Planctomycetes)的厌氧氨氧化菌是高氨污染系统安全脱氮的生态友好型微生物,但关于特定生态梯度下Planctomycetes群落结构功能的空间分化以及驱动分化的主要环境因子等问题尚未引起关注。【目的】阐明Planctomycetes群落结构空间分化及影响其分化的主要环境因子。【方法】运用16S rRNA基因高通量测序手段检测温带半干旱区河流系统砂质及粉质沉积物、粉砂质及粉质土壤Planctomycetes群落结构的空间分布变化,统计学方法分析粉粒等理化因子对Planctomycetes群落结构功能分化的影响。【结果】OM190_ub_oo. o1种群主要分布在寡营养的砂质沉积物中,仅由砂粒正向驱动;OM190_ooo. o2和SM1A02. ub5种群主要分布在中营养的粉砂质土壤中,由水分和pH等正向驱动;AKYG587.ub3、Pla4_lineage_oo...     

Different <Emphasis Type="Italic">Planctomycetes</Emphasis> diversity patterns in latitudinal surface seawater of the open sea and in sediment

The 16S rRNA gene approach was applied to investigate the diversity of Planctomycetes in latitudinal surface seawater of the Western Pacific Ocean. The results revealed that the Pirellula-Rhodopirellula-Blastopirellula clade dominated the Planctomycetes community at all surface seawater sites while the minority genera Gemmata and Planctomyces were only found at sites H5 and H2 respectively. Although the clone frequency of the PRB clade seemed stable (between 83.3% and 94.1%) for all surface seawater sites, the retrieved Pirellula-Rhodopirellula-Blastopirellula clade presented unexpected diversity. Interestingly, low latitude seawater appeared to have higher diversity than mid-latitudes. integral-LIBSHUFF software analysis revealed significantly different diversity patterns between in latitudinal surface seawater and in the sediment of South China Sea station M2896. Our data suggested that different hydrological and geographic features contributed to the shift of Planctomycetes diversity in marine environments. This is, to our knowledge, the first systematic assessment of Planctomycetes in latitudinal surface seawater of the open sea and the first comparison of diversity pattern between surface seawater and sediments and has broadened our understanding of Planctomycetes diversity in marine environments.     

Phylogenetic and metabolic diversity of Planctomycetes from anaerobic, sulfide- and sulfur-rich Zodletone Spring, Oklahoma

We investigated the phylogenetic diversity and metabolic capabilities of members of the phylum Planctomycetes in the anaerobic, sulfide-saturated sediments of a mesophilic spring (Zodletone Spring) in southwestern Oklahoma. Culture-independent analyses of 16S rRNA gene sequences generated using Planctomycetes-biased primer pairs suggested that an extremely diverse community of Planctomycetes is present at the spring. Although sequences that are phylogenetically affiliated with cultured heterotrophic Planctomycetes were identified, the majority of the sequences belonged to several globally distributed, as-yet-uncultured Planctomycetes lineages. Using complex organic media (aqueous extracts of the spring sediments and rumen fluid), we isolated two novel strains that belonged to the Pirellula-Rhodopirellula-Blastopirellula clade within the Planctomycetes. The two strains had identical 16S rRNA gene sequences, and their closest relatives were isolates from Kiel Fjord (Germany), Keauhou Beach (HI), a marine aquarium, and tissues of marine organisms (Aplysina sp. sponges and postlarvae of the giant tiger prawn Penaeus monodon). The closest recognized cultured relative of strain Zi62 was Blastopirellula marina (93.9% sequence similarity). Detailed characterization of strain Zi62 revealed its ability to reduce elemental sulfur to sulfide under anaerobic conditions, as well as its ability to produce acids from sugars; both characteristics may potentially allow strain Zi62 to survive and grow in the anaerobic, sulfide- and sulfur-rich environment at the spring source. Overall, this work indicates that anaerobic metabolic abilities are widely distributed among all major Planctomycetes lineages and suggests carbohydrate fermentation and sulfur reduction as possible mechanisms employed by heterotrophic Planctomycetes for growth and survival under anaerobic conditions.     

Spatiotemporal changes in the structure and composition of a less-abundant bacterial phylum (Planctomycetes) in two perialpine lakes

We used fingerprinting and cloning-sequencing to study the spatiotemporal dynamics and diversity of Planctomycetes in two perialpine lakes with contrasting environmental conditions. Planctomycetes, which are less-abundant bacteria in freshwater ecosystems, appeared to be structured in the same way as the entire bacterial community in these ecosystems. They were more diversified and displayed fewer temporal variations in the hypolimnia than in the epilimnia. Like the more-abundant bacterial groups in aquatic systems, Planctomycetes communities seem to be composed of a very small number of abundant and widespread operational taxonomic units (OTUs) and a large number of OTUs that are present at low abundance. This indicates that the concept of "abundant or core" and "rare" bacterial phylotypes could also be applied to less-abundant freshwater bacterial phyla. The richness and diversity of Planctomycetes were mainly driven by pH and were similar in both of the lakes studied, whereas the composition of the Planctomycetes community seemed to be determined by a combination of factors including temperature, pH, and nutrients. The relative abundances of the dominant OTUs varied over time and were differently associated with abiotic factors. Our findings demonstrate that less-abundant bacterial phyla, such as Planctomycetes, can display strong spatial and seasonal variations linked to environmental conditions and suggest that their functional role in the lakes studied might be attributable mainly to a small number of phylotypes and vary over space and time in the water column.     

Free-living and aggregate-associated Planctomycetes in the Black Sea

We examined the distribution of uncultured Planctomycetes phylotypes along depth profiles spanning the redox gradient of the Black Sea suboxic zone to gain insight into their respective ecological niches. Planctomycetes phylogeny correlated with depth and chemical profiles, implying similar metabolisms within phylogenetic groups. A suboxic zone sample was split into >?30 and ?30?μm fraction except for members of the Scalindua genus, which were apparently free-living. Sequences from Candidatus Scalindua, known to carry out the anammox process, formed two distinct clusters with nonoverlapping depth ranges. One cluster, only 97.1% similar to the named species, was present at high nitrite/nitrate and low ammonium concentrations in the upper suboxic zone. We propose this sequence type be named 'Candidatus Scalindua richardsii'. A second cluster, containing sequences more similar to 'Candidatus Scalindua sorokinii', was present at high ammonium and low nitrite conditions in the lower suboxic zone. Sequences obtained from the sulfidic zone (1000?m depth) yielded Planctomycetes from two uncharacterized Planctomycetacia clusters and three potentially new genera as well as sequences from the uncultured OP3 phylum.     

海洋浮霉状菌多样性与生态学功能研究进展

浮霉状菌为一个独立的细菌门,具独特的细胞结构与基因组组成,是一类重要的环境微生物。有趣的是,浮霉状菌在海洋环境中具多样的生态学功能,如参与海洋碳循环、海洋厌氧氨氧化过程、矿物质富聚作用、及藻赤潮等,现已成为国际海洋环境微生物研究最热门的领域之一。然而,目前国内对该细菌门的研究进展尚无综合报道,由此,本文综合最新和最重要的文献综述了海洋浮霉状菌多样性及生态学功能的最新进展,并结合自己的工作对该领域未来的研究进行了展望。     

Planctomycetes diversity associated with macroalgae

Planctomycetes associated with 12 macroalgae from the north coast of Portugal were isolated, using an improved method. A total of 138 isolates were found to comprise 10 operational taxonomic units (OTUs), with 65% of the strains being closely related to the species Rhodopirellula baltica. The other strains are probably new species or genera related to Rhodopirellula, Blastopirellula and Planctomyces. Some of the OTUs isolated are unique and have never been found before in previous studies. Catalyzed reporter deposition-FISH confirmed the presence of Planctomycetes on macroalgal surfaces. This study provides the first report of the cultured diversity of Planctomycetes on the epiphytic macroalgae community and presents clear evidence of their nutritional and intimate relationship.     

Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis

Porphyra is a macrophytic red alga of the Bangiales that is important ecologically and economically. We describe the genomes of three bacteria in the phylum Planctomycetes (designated P1, P2 and P3) that were isolated from blades of Porphyra umbilicalis (P.um.1). These three Operational Taxonomic Units (OTUs) belong to distinct genera; P2 belongs to the genus Rhodopirellula, while P1 and P3 represent undescribed genera within the Planctomycetes. Comparative analyses of the P1, P2 and P3 genomes show large expansions of distinct gene families, which can be widespread throughout the Planctomycetes (e.g., protein kinases, sensors/response regulators) and may relate to specific habitat (e.g., sulfatase gene expansions in marine Planctomycetes) or phylogenetic position. Notably, there are major differences among the Planctomycetes in the numbers and sub-functional diversity of enzymes (e.g., sulfatases, glycoside hydrolases, polysaccharide lyases) that allow these bacteria to access a range of sulfated polysaccharides in macroalgal cell walls. These differences suggest that the microbes have varied capacities for feeding on fixed carbon in the cell walls of P.um.1 and other macrophytic algae, although the activities among the various bacteria might be functionally complementary in situ. Additionally, phylogenetic analyses indicate augmentation of gene functions through expansions arising from gene duplications and horizontal gene transfers; examples include genes involved in cell wall degradation (e.g., κ-carrageenase, alginate lyase, fucosidase) and stress responses (e.g., efflux pump, amino acid transporter). Finally P1 and P2 contain various genes encoding selenoproteins, many of which are enzymes that ameliorate the impact of environmental stresses that occur in the intertidal habitat.     

Diversity patterns and isolation of Planctomycetes associated with metalliferous deposits from hydrothermal vent fields along the Valu Fa Ridge (SW Pacific)

The microbial diversity associated with diffuse venting deep-sea hydrothermal deposits is tightly coupled to the geochemistry of the hydrothermal fluids. Previous 16S rRNA gene amplicon sequencing (metabarcoding) of marine iron-hydroxide deposits along the Arctic Mid Ocean Ridge, revealed the presence of diverse bacterial communities associated with these deposits (Storesund and Øvreås in Antonie van Leeuwenhoek 104:569–584, 2013). One of the most abundant and diverse phyla detected was the enigmatic Planctomycetes. Here we report on the comparative analyses of the diversity and distribution patterns of Planctomycetes associated with metalliferous deposits from two diffuse-flow hydrothermal vent fields (Mariner and Vai Lili) from the Valu Fa Ridge in the Southwestern Pacific. Metabarcoding of 16S rRNA genes showed that the major prokaryotic phyla were Proteobacteria (51–73% of all 16S rRNA gene reads), Epsilonbacteraeota (0.5–19%), Bacteriodetes (5–17%), Planctomycetes (0.4–11%), Candidatus Latescibacteria (0–5%) and Marine Benthic Group E (Hydrothermarchaeota) (0–5%). The two different sampling sites differed considerably in overall community composition. The abundance of Planctomycetes also varied substantially between the samples and the sites, with the majority of the sequences affiliated with uncultivated members of the classes Planctomycetacia and Phycisphaerae, and other deep branching lineages. Seven different strains affiliated with the order Planctomycetales were isolated, mostly from the Vai Lili samples, where also the highest Planctomycetales diversity was seen. Most of the isolates were affiliated with the genera Gimesia, Rhodopirellula and Blastopirellula. One isolate was only distantly related to known cultured, but uncharacterized species within the Pir4 group. This study shows that the deep-sea Planctomycetes represent a very heterogeneous group with a high phylogenetic diversity and a substantial potential for novel organism discovery in these deep ocean environments.     

Isolation and characterization of Planctomycetes from the sediments of a fish farm wastewater treatment tank

The increasing ecological significance of Planctomycetes and the still limited knowledge of this group prompted us to obtain cultured isolates from the sediment of a treatment water recycling tank of a marine fish farm. Presence of strains from this group was assessed in the sediments and water column of the tank. Eleven isolates were obtained from the sediment sample by exploiting Planctomycetes natural resistance to several antibiotics and their capacity to degrade organic matter. Based on morphological characteristics and resistance to antibiotics, Planctomycetes were identified. Their phylogenetic affiliation was confirmed by the sequence analysis of the 16S rRNA gene that revealed the presence of a group of 6 isolates closely related to Rhodopirellula baltica and a cluster of 5 isolates with 97.7-97.9?% of similarity to this species, which probably are a different species of Rhodopirellula. ERIC-PCR profiles showed a higher discrimination within the two groups and allowed the identification of nine different genotypes within the isolated strains. This work corroborates the association of Rhodopirellula spp. with fish farm environments.     

Whole-genome reciprocal BLAST analysis reveals that planctomycetes do not share an unusually large number of genes with Eukarya and Archaea

The genome sequences of Rhodopirellula baltica, formerly Pirellula sp. strain 1, Blastopirellula marina, Gemmata obscuriglobus, and Kuenenia stuttgartiensis were used in a series of pairwise reciprocal best-hit analyses to evaluate the contested evolutionary position of Planctomycetes. Contrary to previous reports which suggested that R. baltica had a high percentage of genes with closest matches to Archaea and Eukarya, we show here that these Planctomycetes do not share an unusually large number of genes with the Archaea or Eukarya, compared with other Bacteria. Thus, best-hit analyses may assign phylogenetic affinities incorrectly if close relatives are absent from the sequence database.     

High ultraviolet C resistance of marine Planctomycetes

Planctomycetes are bacteria with particular characteristics such as internal membrane systems encompassing intracellular compartments, proteinaceous cell walls, cell division by yeast-like budding and large genomes. These bacteria inhabit a wide range of habitats, including marine ecosystems, in which ultra-violet radiation has a potential harmful impact in living organisms. To evaluate the effect of ultra-violet C on the genome of several marine strains of Planctomycetes, we developed an easy and fast DNA diffusion assay in which the cell wall was degraded with papain, the wall-free cells were embedded in an agarose microgel and lysed. The presence of double strand breaks and unwinding by single strand breaks allow DNA diffusion, which is visible as a halo upon DNA staining. The number of cells presenting DNA diffusion correlated with the dose of ultra-violet C or hydrogen peroxide. From DNA damage and viability experiments, we found evidence indicating that some strains of Planctomycetes are significantly resistant to ultra-violet C radiation, showing lower sensitivity than the known resistant Arthrobacter sp. The more resistant strains were those phylogenetically closer to Rhodopirellula baltica, suggesting that these species are adapted to habitats under the influence of ultra-violet radiation. Our results provide evidence indicating that the mechanism of resistance involves DNA damage repair and/or other DNA ultra-violet C-protective mechanism.     

Antimicrobial Activity of a Novel Freshwater Planctomycete Lacipirellula parvula PX69T

Microbiology - Planctomycetes are a phylogenetic group of bacteria with complex cell organization, large genomes and a wide spectrum of genome-encoded secondary metabolites. As suggested by...     

Genetic Determinants of Xylan Utilization in Humisphaera borealis M1803T,a Planctomycete of the Class Phycisphaerae

Microbiology - Planctomycetes of the class Phycisphaerae are aerobic and anaerobic heterotrophic bacteria that colonize a wide range of marine and terrestrial habitats. Their functional roles in...     

Detection of Chitinolytic Capabilities in the Freshwater Planctomycete Planctomicrobium piriforme

Microbiology - Members of the phylum Planctomycetes colonize a wide range of aquatic and terrestrial habitats, but their functional role in the environment remains poorly understood. One of the...