| evidence for unlinked rrn operons in the planctomycete pirellula marina. | southern hybridization of rrnas to chromosomal bamhi-digested dna of the eubacterium pirellula marina revealed the presence of two sets of 16s and 23s rrna genes. the two copies of the 23s rrna genes, located on 11- and about 13-kilobase (kb) inserts, were isolated from a lambda bacteriophage charon 35 library. the 11-kb fragment was cloned directly into pbr322, while a 5.4-kb bamhi-psti rdna subfragment of the approximately 13-kb insert was cloned into puc18. both recombinant plasmids, ppi1100 ... | 1989 | 2768196 |
| screening of a fosmid library of marine environmental genomic dna fragments reveals four clones related to members of the order planctomycetales. | a fosmid library with inserts containing approximately 40 kb of marine bacterial dna (j. l. stein, t. l. marsh, k. y. wu, h. shizuya, and e. f. delong, j. bacteriol. 178:591-599, 1996) yielded four clones with 16s rrna genes from the order planctomycetales. three of the clones belong to the pirellula group and one clone belongs to the planctomyces group, based on phylogenetic and signature nucleotide analyses of full-length 16s rrna genes. sequence analysis of the ends of the genes revealed a co ... | 1998 | 9687477 |
| a search for beta-lactamase in chlamydiae, mycoplasmas, planctomycetes, and cyanelles: bacteria and bacterial descendants at different phylogenetic positions and stages of cell wall development. | bacteria from different phylogenetic positions such as chlamydiae, mycoplasmas, planctomycetes and also endosymbiotic murein-containing cyanelles were investigated for the production of beta-lactamases. no beta-lactamase activity was found in bacteria lacking murein such as chlamydia pneumoniae, mycoplasma pneumoniae, pirellula marina and planctomyces maris. in the murein-containing cyanelles of cyanophora paradoxa no beta-lactamase activity could be detected. | 2000 | 10830893 |
| gene discovery within the planctomycete division of the domain bacteria using sequence tags from genomic dna libraries. | the planctomycetes comprise a distinct group of the domain bacteria, forming a separate division by phylogenetic analysis. the organization of their cells into membrane-defined compartments including membrane-bounded nucleoids, their budding reproduction and complete absence of peptidoglycan distinguish them from most other bacteria. a random sequencing approach was applied to the genomes of two planctomycete species, gemmata obscuriglobus and pirellula marina, to discover genes relevant to thei ... | 2002 | 12093378 |
| isolation of a bacterium resembling pirellula species from primary tissue culture of the giant tiger prawn (penaeus monodon). | during attempts to establish tissue cultures from hepatopancreas, heart, and hemolymph of the giant tiger prawn (penaeus monodon), using a medium including penicillin, streptomycin, and amphotericin b, bacterial contamination in the form of a sheet of growth attached to the tissue culture vessel was a persistent problem. contaminant bacteria were teardrop-shaped cells arranged in rosettes, and electron microscopy revealed buds, crateriform structures, and the absence of a peptidoglycan layer in ... | 1991 | 1781677 |
| unraveling the extent of diversity within the order planctomycetales. | the phylogenetic positions of 22 isolates that morphologically resemble members of the family planctomycetaceae were determined by sequence analysis of genes coding for 16s rrna. while nine and eight isolates could be assigned to the genera planctomyces and pirellula, respectively, three strains grouped near isosphaera pallida and one strain was closely related to gemmata obscuriglobus. no isolate was found to be related to a previously described species of any of the four genera at the species ... | 1995 | 7793948 |
| pirellula and om43 are among the dominant lineages identified in an oregon coast diatom bloom. | although bacterioplankton and phytoplankton are generally perceived as closely linked in marine systems, specific interactions between discrete bacterioplankton and phytoplankton populations are largely unknown. however, measurements of bacterioplankton distributions during phytoplankton blooms may indicate specific microbial lineages that are responding to phytoplankton populations, and potentially controlling them by producing allelopathic compounds. here we use a comprehensive molecular appro ... | 2006 | 16872400 |
| microbial community structure of sandy intertidal sediments in the north sea, sylt-rømø basin, wadden sea. | molecular biological methods were used to investigate the microbial diversity and community structure in intertidal sandy sediments near the island of sylt (wadden sea) at a site which was characterized for transport and mineralization rates in a parallel study (d. de beer, f. wenzhöfer, t. ferdelman, s.e. boehme, m. huettel, j.e.e. van beusekom, m.e. böttcher, n. musat, n. dubilier, transport and mineralization rates in north sea sandy intertidal sediments, sylt-romo basin, wadden sea, limnol. ... | 2006 | 16431068 |
| archaea-like genes for c1-transfer enzymes in planctomycetes: phylogenetic implications of their unexpected presence in this phylum. | the unexpected presence of archaea-like genes for tetrahydromethanopterin (h4mpt)-dependent enzymes in the completely sequence geiome of the aerobic marine planctomycete pirellula sp. strain 1 ("rhodopirellula baltica") and in the currently sequenced genome of the aerobic freshwater planctomycete gemmata obscuriglobus strain uqm2246 revives the discussion on the origin of these genes in the bacterial domain. we compared the genomic arrangement of these genes in planctomyetes and methylotrophic p ... | 2004 | 15693614 |
| taxonomic heterogeneity within the planctomycetales as derived by dna-dna hybridization, description of rhodopirellula baltica gen. nov., sp. nov., transfer of pirellula marina to the genus blastopirellula gen. nov. as blastopirellula marina comb. nov. and emended description of the genus pirellula. | ninety-seven strains of budding bacteria originating from various aquatic habitats and morphologically resembling planctomycetes were investigated taxonomically. taxonomic differentiation was based on dna-dna hybridization, physiological properties and chemotaxonomic tests. nineteen hybridization groups, containing 79 of the tested strains, were established. eighteen strains, however, did not fit into any of these groups. rhodopirellula baltica gen. nov., sp. nov. is described, with strain sh 1t ... | 2004 | 15388712 |
| arbovirus detection in insect vectors by rapid, high-throughput pyrosequencing. | despite the global threat caused by arthropod-borne viruses, there is not an efficient method for screening vector populations to detect novel viral sequences. current viral detection and surveillance methods based on culture can be costly and time consuming and are predicated on prior knowledge of the etiologic agent, as they rely on specific oligonucleotide primers or antibodies. therefore, these techniques may be unsuitable for situations when the causative agent of an outbreak is unknown. | 2010 | 21085471 |
| diversity and seasonal changes of uncultured planctomycetales in river biofilms. | cell counts of planctomycetes showed that there were high levels of these organisms in the summer and low levels in the winter in biofilms grown in situ in two polluted rivers, the elbe river and the spittelwasser river. in this study 16s rrna-based methods were used to investigate if these changes were correlated with changes in the species composition. planctomycete-specific clone libraries of the 16s rrna genes found in both rivers showed that there were seven clusters, which were distantly r ... | 2004 | 15345387 |
| comparative analysis of ribonuclease p rna of the planctomycetes. | the planctomycetes, order planctomycetales, are a distinct phylum of domain bacteria. genes encoding the rna portion of ribonuclease p (rnase p) of some planctomycete members were sequenced and compared with existing database planctomycete sequences. rnpb gene sequences encoding rnase p rna were generated by a conserved primer pcr strategy for planctomyces brasiliensis, planctomyces limnophilus, pirellula marina, pirellula staleyi strain atcc 35122, isosphaera pallida, one other isosphaera strai ... | 2004 | 15280311 |
| identification of planctomycetes with order-, genus-, and strain-specific 16s rrna-targeted probes. | a specific 16s rrna-targeted oligonucleotide probe (pir1223) for the genus pirellula and a species-specific probe (rb454) for pirellula sp. strain sh1 have been designed and optimized. together with the already existing order-specific probe pla886, the two newly designed probes were used to detect and identify planctomycetes, pirellulae, and close relatives of pirellula sp. strain sh1 in different habitats. with the help of these probes for detection and identification, bacteria of the genus pir ... | 2004 | 14994173 |
| in silico analysis of the sigma54-dependent enhancer-binding proteins in pirellula species strain 1. | the planctomycetes are a phylogenetically distinct group of bacteria, widespread in aquatic and terrestrial environments. their cell walls lack peptidoglycan and their compartmentalised cells undergo a yeast-like budding cell division process. many bacteria regulate a subset of their genes by an enhancer-dependent mechanism involving the alternative sigma factor sigma54 (rpon, sigman) in association with sigma54-dependent transcriptional activators known as enhancer-binding proteins (ebps). the ... | 2004 | 14757243 |
| structure and seasonal dynamics of hyporheic zone microbial communities in free-stone rivers of the western united states. | the hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox gradients, and having a heterotrophic food web based on the consumption of organic carbon entrained from surface waters. hyporheic microbial communities constitute the base of food webs in these environments and are important for maintaining a functioning lotic ecosystem. while microbial communities of rivers dominated by fine-grained sediments are relatively well studied, little is known about the struc ... | 2003 | 14708745 |
| molecular evidence for novel planctomycete diversity in a municipal wastewater treatment plant. | we examined anoxic and aerobic basins and an anaerobic digestor of a municipal wastewater treatment plant for the presence of novel planctomycete-like diversity. three 16s rrna gene libraries were constructed by using a 16s rrna-targeted universal reverse primer and a forward pcr primer specific for planctomyces: phylogenetic analysis of 234 16s rrna gene sequences defined 110 operational taxonomic units. the majority of these sequences clustered with the four known genera, pirellula (32%), plan ... | 2003 | 14660385 |
| evaluation of two-dimensional difference gel electrophoresis for protein profiling. soluble proteins of the marine bacterium pirellula sp. strain 1. | two-dimensional gel electrophoresis (2de) is a central tool of proteome research, since it allows separation of complex protein mixtures at highest resolution. quantification of gene expression at the protein level requires sensitive visualization of protein spots over a wide linear range. two-dimensional difference gel electrophoresis (2d dige) is a new fluorescent technique for protein labeling in 2de gels. proteins are labeled prior to electrophoresis with fluorescent cydyes trade mark and di ... | 2003 | 12867748 |
| complete genome sequence of the marine planctomycete pirellula sp. strain 1. | 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 w ... | 2003 | 12835416 |
| in situ accessibility of small-subunit rrna of members of the domains bacteria, archaea, and eucarya to cy3-labeled oligonucleotide probes. | low accessibility of the rrna is together with cell wall impermeability and low cellular ribosome content a frequent reason for failure of whole-cell fluorescence hybridization with fluorescently labeled oligonucleotide probes. in this study we compare accessibility data for the 16s rrna of escherichia coli (gamma proteobacteria, bacteria) with the phylogenetically distantly related organisms pirellula sp. strain 1 (planctomycetes, bacteria) and metallosphaera sedula (crenarchaeota, archaea) and ... | 2003 | 12620867 |
| molecular and ultrastructural confirmation of classification of atcc 35122 as a strain of pirellula staleyi. | a freshwater isolate from campus lake, baton rouge, la, usa, strain atcc 35122 (= icpb 4362 = schmidt clpm white = tekniepe bt2 white), which had been proposed as a putative reference strain for 'planctomyces staleyi' (later reclassified as pirellula staleyi), has been re-examined to establish its relationship to the type strain of pirellula staleyi, atcc 27377t. 165 rrna sequencing confirms its very close relationship to atcc 27377t and its membership of the order planctomycetales. ultrastructu ... | 2002 | 12361271 |
| analysis of n-acetylglucosamine metabolism in the marine bacterium pirellula sp. strain 1 by a proteomic approach. | pirellula sp. strain 1 is a marine bacterium that can grow with the chitin monomer n-acetylglucosamine as sole source of carbon and nitrogen under aerobic conditions, and that is a member of the bacterial phylum planctomycetes. as a basis for the proteomic studies we quantified growth of strain 1 with n-acetylglucosamine and glucose, revealing doubling times of 14 and 10 h, respectively. studies with dense cell suspensions indicated that the capacity to degrade n-acetylglucosamine and glucose ma ... | 2002 | 12112844 |
| 16s-23s rdna intergenic spacer and 23s rdna of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection. | recently, anaerobic ammonium-oxidizing bacteria (aaob) were identified by comparative 16s rdna sequence analysis as a novel, deep-branching lineage within the planctomycetales. this lineage consists currently of only two, not yet culturable bacteria which have been provisionally described as candidatus 'brocadia anammoxidans' and candidatus 'kuenenia stuttgartiensis'. in this study, a large fragment of the rdna operon, including the 16s rdna, the intergenic spacer region (isr) and approximately ... | 2001 | 11553235 |
| cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell. | the organisation of cells of the planctomycete species pirellula marina, isosphaera pallida, gemmata obscuriglobus, planctomyces maris and "candidatus brocadia anammoxidans" was investigated based on ultrastructure derived from thin-sections of cryosubstituted cells, freeze-fracture replicas, and in the case of gemmata obscuriglobus and pirellula marina, computer-aided 3-d reconstructions from serial sections of cryosubstituted cells. all planctomycete cells display a peripheral ribosome-free re ... | 2001 | 11491082 |
| phylogenetic analysis of evolutionary relationships of the planctomycete division of the domain bacteria based on amino acid sequences of elongation factor tu. | sequences from the tuf gene coding for the elongation factor ef-tu were amplified and sequenced from the genomic dna of pirellula marina and isosphaera pallida, two species of bacteria within the order planctomycetales. a near-complete (1140-bp) sequence was obtained from pi. marina and a partial (759-bp) sequence was obtained for i. pallida. alignment of the deduced pi. marina ef-tu amino acid sequence against reference sequences demonstrated the presence of a unique 11-amino acid sequence moti ... | 2001 | 11443344 |
| novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16s rrna genes from bulk soil and rice roots of flooded rice microcosms. | using a newly developed 16s rrna gene (rdna)-targeted pcr assay with proposed group specificity for planctomycetes, we examined anoxic bulk soil of flooded rice microcosms for the presence of novel planctomycete-like diversity. for comparison, oxic rice roots were included as an additional sample in this investigation. the bacterial diversity detectable by this pcr assay was assessed by using a combined approach that included terminal restriction fragment length polymorphism (t-rflp) analysis an ... | 2001 | 11157225 |
| identification of novel bacterial lineages as active members of microbial populations in a freshwater sediment using a rapid rna extraction procedure and rt-pcr. | a rapid method for the extraction of rna from the indigenous bacterial communities in environmental samples was developed. the method was tested using anoxic sediment samples from a productive freshwater lake (priest pot, cumbria, uk). the simple protocol yielded rrna and mrna of a purity suitable for amplification by reverse transcriptase pcr (rt-pcr). the integrity of the rt-pcr was demonstrated by amplifying 16s rrna and mrna for the mercury resistance regulatory gene merr. the diversity of 1 ... | 1999 | 10463164 |
| phylogenetic diversity, polyamine pattern and dna base composition of members of the order planctomycetales. | the 16s rdna sequences of 20 novel isolates of members of the order planctomycetales were compared to those of the type strains of described planctomycete species and 22 planctomycete isolates for which the 16s rdna sequences had been previously determined. the novel isolates could be assigned to several phylogenetically broad groups, four of which are defined by the genera gemmata, isosphaera, planctomyces and pirellula. to evaluate polyamines as a chemotaxonomic marker within this order, the p ... | 1999 | 10319492 |
| isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, penaeus monodon. | bacteria phenotypically resembling members of the phylogenetically distinct planctomycete group of the domain bacteria were isolated from postlarvae of the giant tiger prawn, penaeus monodon. a selective medium designed in the light of planctomycete antibiotic resistance characteristics was used for this isolation. planctomycetes were isolated from both healthy and monodon baculovirus-infected prawn postlarvae. the predominant colony type recovered from postlarvae regardless of viral infection s ... | 1997 | 8979353 |
| [high abundance of planctomycetes in anoxic layers of a sphagnum peat bog]. | the depth distribution of planctomycete abundance has been examined in six different sites of the sphagnum peat bog in bakchar, tomsk oblast, russia. in situ hybridization of peat with the fluorescently labeled oligonucleotide probes pla46 and pla886, reported to be group-specific for representatives of the phylum planctomycetes, revealed two distinct population maxima of these bacteria in all of the profiles examined. the first population maximum was detected in the uppermost, oxic layer of the ... | 2006 | 17205808 |
| complete nucleotide sequence of a 23s ribosomal rna gene from pirellula marina. | | 1988 | 3387225 |
| 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 numbe ... | 2006 | 17021241 |
| 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 heterotro ... | 2007 | 17545322 |
| different planctomycetes 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 seaw ... | 2008 | 18545964 |
| diversity of aerobic and anaerobic ammonia-oxidizing bacteria in marine sponges. | aerobic ammonia-oxidizing bacteria (aaob) are known to have an important function in the marine nitrogen cycle. anaerobic ammonium oxidation (anammox) carried out by some members of planctomycetales is also an important process in marine ecosystems. ammonia-monooxygenase gene (amoa) fragments were amplified to investigate the potential for nitrification and the diversity of the aaob in two marine sponges ircinia strobilina and mycale laxissima. all of the amoa sequences obtained from the two spo ... | 2010 | 19617876 |
| complete genome sequence of planctomyces limnophilus type strain (mü 290). | planctomyces limnophilus hirsch and müller 1986 belongs to the order planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall which is stabilized by a proteinaceous layer rather than a peptidoglycan layer. besides pirellula staleyi, this is the second completed genome sequence of the family planctomycetaceae. p. ... | 2010 | 21304691 |
| erratum to: complete genome sequence of pirellula staleyi type strain (atcc 27377). | | 2010 | 21304706 |
| temporal variability of coastal planctomycetes clades at station kabeltonne, 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 ribosomal rna (rrna) gene analysis and catalyzed reporter deposition fluorescence in situ hybridization (card-fish). generally planctomycetes are more abundant in summer and autumn ... | 2011 | 21642408 |
| complete genome sequence of pirellula staleyi type strain (atcc 27377). | pirellula staleyi schlesner and hirsch 1987 is the type species of the genus pirellula of the family planctomycetaceae. members of this pear- or teardrop-shaped bacterium show a clearly visible pointed attachment pole and can be distinguished from other planctomycetes by a lack of true stalks. strains closely related to the species have been isolated from fresh and brackish water, as well as from hypersaline lakes. here we describe the features of this organism, together with the complete genome ... | 2009 | 21304671 |