| 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 |
| 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 natural view of microbial biodiversity within hot spring cyanobacterial mat communities. | this review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. for example, none of 31 unique 16s rrna sequences detected in the octopus spring mat, yellowstone national park, matches t ... | 1998 | 9841675 |
| isolation of gemmata-like and isosphaera-like planctomycete bacteria from soil and freshwater. | new cultured strains of the planctomycete division (order planctomycetales) of the domain bacteria related to species in the genera gemmata and isosphaera were isolated from soil, freshwater, and a laboratory ampicillin solution. phylogenetic analysis of the 16s rrna gene from eight representative isolates showed that all the isolates were members of the planctomycete division. six isolates clustered with gemmata obscuriglobus and related strains, while two isolates clustered with isosphaera pal ... | 2002 | 11772655 |
| 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 |
| 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 |
| formation of multilayered photosynthetic biofilms in an alkaline thermal spring in yellowstone national park, wyoming. | in this study, glass rods suspended at the air-water interface in the runoff channel of fairy geyser, yellowstone national park, wy, were used as a substratum to promote the development of biofilms that resembled multilayered mat communities in the splash zone at the geyser's source. this approach enabled the establishment of the temporal relationship between the appearance of cyanobacteria, which ultimately formed the outer green layer, and the development of a red underlayer containing roseifl ... | 2009 | 19218404 |
| comparative analysis of two phenotypically-similar but genomically-distinct burkholderia cenocepacia-specific bacteriophages. | genomic analysis of bacteriophages infecting the burkholderia cepacia complex (bcc) is an important preliminary step in the development of a phage therapy protocol for these opportunistic pathogens. the objective of this study was to characterize kl1 (vb_bces_kl1) and ah2 (vb_bces_ah2), two novel burkholderia cenocepacia-specific siphoviruses isolated from environmental samples. | 2012 | 22676492 |
| transcriptional response of the model planctomycete rhodopirellula baltica sh1(t) to changing environmental conditions. | the marine model organism rhodopirellula baltica sh1(t) was the first planctomycete to have its genome completely sequenced. the genome analysis predicted a complex lifestyle and a variety of genetic opportunities to adapt to the marine environment. its adaptation to environmental stressors was studied by transcriptional profiling using a whole genome microarray. | 2009 | 19725962 |
| the cell cycle of the planctomycete gemmata obscuriglobus with respect to cell compartmentalization. | gemmata obscuriglobus is a distinctive member of the divergent phylum planctomycetes, all known members of which are peptidoglycan-less bacteria with a shared compartmentalized cell structure and divide by a budding process. g. obscuriglobus in addition shares the unique feature that its nucleoid dna is surrounded by an envelope consisting of two membranes forming an analogous structure to the membrane-bounded nucleoid of eukaryotes and therefore g. obscuriglobus forms a special model for cell b ... | 2009 | 19144151 |
| identification of bacteria in biofilm and bulk water samples from a nonchlorinated model drinking water distribution system: detection of a large nitrite-oxidizing population associated with nitrospira spp. | in a model drinking water distribution system characterized by a low assimilable organic carbon content (<10 microg/liter) and no disinfection, the bacterial community was identified by a phylogenetic analysis of rrna genes amplified from directly extracted dna and colonies formed on r2a plates. biofilms of defined periods of age (14 days to 3 years) and bulk water samples were investigated. culturable bacteria were associated with proteobacteria and bacteriodetes, whereas independently of culti ... | 2005 | 16332854 |
| combined use of 16s ribosomal dna and 16s rrna to study the bacterial community of polychlorinated biphenyl-polluted soil. | the bacterial diversity assessed from clone libraries prepared from rrna (two libraries) and ribosomal dna (rdna) (one library) from polychlorinated biphenyl (pcb)-polluted soil has been analyzed. a good correspondence of the community composition found in the two types of library was observed. nearly 29% of the cloned sequences in the rdna library were identical to sequences in the rrna libraries. more than 60% of the total cloned sequence types analyzed were grouped in phylogenetic groups (a c ... | 2001 | 11282645 |
| direct analysis of genes encoding 16s rrna from complex communities reveals many novel molecular species within the human gut. | the human intestinal tract harbors a complex microbial ecosystem which plays a key role in nutrition and health. although this microbiota has been studied in great detail by culture techniques, microscopic counts on human feces suggest that 60 to 80% of the observable bacteria cannot be cultivated. using comparative analysis of cloned 16s rrna gene (rdna) sequences, we have investigated the bacterial diversity (both cultivated and noncultivated bacteria) within an adult-male fecal sample. the 28 ... | 1999 | 10543789 |
| cell wall and lipid composition of isosphaera pallida, a budding eubacterium from hot springs. | isosphaera pallida is an unusual gliding, budding eubacterium recently isolated from north american hot springs. electron micrographs of ultrathin sections revealed a cell wall atypical of eubacteria: two electrondense layers separated by an electron-transparent layer, with no evident peptidoglycan layer. growth was not inhibited by penicillin. cell walls were isolated from sheared cells by velocity sedimentation. the rigid-layer fraction, prepared from cell walls by treatment with boiling 10% s ... | 1987 | 3584067 |
| lrs14 transcriptional regulators influence biofilm formation and cell motility of crenarchaea. | like bacteria, archaea predominately exist as biofilms in nature. however, the environmental cues and the molecular mechanisms driving archaeal biofilm development are not characterized. here we provide data suggesting that the transcriptional regulators belonging to the lrs14-like protein family constitute a key regulatory factor during sulfolobus biofilm development. among the six lrs14-like genes encoded by sulfolobus acidocaldarius, the deletion of three led to markedly altered biofilm pheno ... | 2013 | 23657363 |
| abundance, diversity, and depth distribution of planctomycetes in acidic northern wetlands. | members of the bacterial phylum planctomycetes inhabit various aquatic and terrestrial environments. in this study, fluorescence in situ hybridization (fish) was applied to assess the abundance and depth distribution of these bacteria in nine different acidic wetlands of northern russia. planctomycetes were most abundant in the oxic part of the wetland profiles. the respective cell numbers were in the range 1.1-6.7 × 10(7) cells g(-1) of wet peat, comprising 2-14% of total bacterial cells, and d ... | 2012 | 22279446 |
| the emergence and early evolution of biological carbon-fixation. | the fixation of co₂ into living matter sustains all life on earth, and embeds the biosphere within geochemistry. the six known chemical pathways used by extant organisms for this function are recognized to have overlaps, but their evolution is incompletely understood. here we reconstruct the complete early evolutionary history of biological carbon-fixation, relating all modern pathways to a single ancestral form. we find that innovations in carbon-fixation were the foundation for most major earl ... | 2012 | 22536150 |
| phylogenomics of prokaryotic ribosomal proteins. | archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. we developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 arch ... | 2012 | 22615861 |
| the dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes. | the ancestral set of eukaryotic genes is a chimera composed of genes of archaeal and bacterial origins thanks to the endosymbiosis event that gave rise to the mitochondria and apparently antedated the last common ancestor of the extant eukaryotes. the proto-mitochondrial endosymbiont is confidently identified as an α-proteobacterium. in contrast, the archaeal ancestor of eukaryotes remains elusive, although evidence is accumulating that it could have belonged to a deep lineage within the tack (t ... | 2014 | 24691961 |
| complete genome sequence of planctomyces brasiliensis type strain (dsm 5305(t)), phylogenomic analysis and reclassification of planctomycetes including the descriptions of gimesia gen. nov., planctopirus gen. nov. and rubinisphaera gen. nov. and emended descriptions of the order planctomycetales and the family planctomycetaceae. | planctomyces brasiliensis schlesner 1990 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 consisting of a proteinaceous layer rather than a peptidoglycan layer. the first strains of p. brasiliensis, including the type strain ifam 1448(t), were isolated from a water sample of lagoa ver ... | 2014 | 25780503 |
| 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 ... | 2016 | 27015628 |
| olsg (sinac_1600) is an ornithine lipid n-methyltransferase from the planctomycete singulisphaera acidiphila. | ornithine lipids (ols) are phosphorus-free membrane lipids widespread in bacteria but absent from archaea and eukaryotes. in addition to the unmodified ols, a variety of ol derivatives hydroxylated in different structural positions has been reported. recently, methylated derivatives of ols were described in several planctomycetes isolated from a peat bog in northern russia, although the gene/enzyme responsible for the n-methylation of ol remained obscure. here we identify and characterize the ol ... | 2015 | 25925947 |
| genomic evolution of 11 type strains within family planctomycetaceae. | the species in family planctomycetaceae are ideal groups for investigating the origin of eukaryotes. their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. however, their genomic structures, potential abilities, and evolutionary status are still unknown. in this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family planctomycetaceae. then, we constructed phyl ... | 2014 | 24489782 |
| characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides. | bacterial microcompartments (bmcs) are organelles that encapsulate functionally linked enzymes within a proteinaceous shell. the prototypical example is the carboxysome, which functions in carbon fixation in cyanobacteria and some chemoautotrophs. it is increasingly apparent that diverse heterotrophic bacteria contain bmcs that are involved in catabolic reactions, and many of the bmcs are predicted to have novel functions. however, most of these putative organelles have not been experimentally c ... | 2014 | 24487526 |
| the 2-methylcitrate cycle is implicated in the detoxification of propionate in toxoplasma gondii. | toxoplasma gondii belongs to the coccidian subgroup of the apicomplexa phylum. the coccidia are obligate intracellular pathogens that establish infection in their mammalian host via the enteric route. these parasites lack a mitochondrial pyruvate dehydrogenase complex but have preserved the degradation of branched-chain amino acids (bcaa) as a possible pathway to generate acetyl-coa. importantly, degradation of leucine, isoleucine and valine could lead to concomitant accumulation of propionyl-co ... | 2013 | 23279335 |
| telmatocola sphagniphila gen. nov., sp. nov., a novel dendriform planctomycete from northern wetlands. | members of the phylum planctomycetes are common inhabitants of northern wetlands. we used barcoded pyrosequencing to survey bacterial diversity in an acidic (ph 4.0) sphagnum peat sampled from the peat bog obukhovskoye, european north russia. a total of 21189 bacterial 16s rrna gene sequences were obtained, of which 1081 reads (5.1%) belonged to the planctomycetes. two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been availab ... | 2012 | 22529844 |
| keys to eukaryality: planctomycetes and ancestral evolution of cellular complexity. | planctomycetes are known to display compartmentalization via internal membranes, thus resembling eukaryotes. significantly, the planctomycete gemmata obscuriglobus has not only a nuclear region surrounded by a double-membrane, but is also capable of protein uptake via endocytosis. in order to clearly analyze implications for homology of their characters with eukaryotes, a correct understanding of planctomycete structure is an essential starting point. here we outline the major features of such s ... | 2012 | 22586422 |
| genomic analysis indicates the presence of an asymmetric bilayer outer membrane in planctomycetes and verrucomicrobia. | bacteria of the phylum planctomycetes are of special interest for the study of compartmental cellular organization. members of this phylum share a very unusual prokaryotic cell plan, featuring several membrane-bound compartments. recently, it was shown that this cellular organization might extend to certain members of the phylum verrucomicrobia. the planctomycete cell plan has been defined as featuring a proteinaceous cell wall, a cytoplasmic membrane surrounding the paryphoplasm, and an intracy ... | 2012 | 22934092 |
| molecular signatures for the pvc clade (planctomycetes, verrucomicrobia, chlamydiae, and lentisphaerae) of bacteria provide insights into their evolutionary relationships. | the pvc superphylum is an amalgamation of species from the phyla planctomycetes, verrucomicrobia, and chlamydiae, along with the lentisphaerae, poribacteria, and two other candidate divisions. the diverse species of this superphylum lack any significant marker that differentiates them from other bacteria. recently, genome sequences for 37 species covering all of the main pvc groups of bacteria have become available. we have used these sequences to construct a phylogenetic tree based upon concate ... | 2012 | 23060863 |
| identification of proteins likely to be involved in morphogenesis, cell division, and signal transduction in planctomycetes by comparative genomics. | members of the planctomycetes clade share many unusual features for bacteria. their cytoplasm contains membrane-bound compartments, they lack peptidoglycan and ftsz, they divide by polar budding, and they are capable of endocytosis. planctomycete genomes have remained enigmatic, generally being quite large (up to 9 mb), and on average, 55% of their predicted proteins are of unknown function. importantly, proteins related to the unusual traits of planctomycetes remain largely unknown. thus, we em ... | 2012 | 23002222 |
| analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle. | the planctomycetes, verrucomicrobia, chlamydiae (pvc) super-phylum contains bacteria with either complex cellular organization or simple cell structure; it also includes organisms of different lifestyles (pathogens, mutualists, commensal, and free-living). genome content evolution of this group has not been studied in a systematic fashion, which would reveal genes underlying the emergence of pvc-specific phenotypes. here, we analyzed the evolutionary dynamics of 26 pvc genomes and several outgro ... | 2012 | 23221607 |
| structure/function analysis of a type iii polyketide synthase in the brown alga ectocarpus siliculosus reveals a biochemical pathway in phlorotannin monomer biosynthesis. | brown algal phlorotannins are structural analogs of condensed tannins in terrestrial plants and, like plant phenols, they have numerous biological functions. despite their importance in brown algae, phlorotannin biosynthetic pathways have been poorly characterized at the molecular level. we found that a predicted type iii polyketide synthase in the genome of the brown alga ectocarpus siliculosus, pks1, catalyzes a major step in the biosynthetic pathway of phlorotannins (i.e., the synthesis of ph ... | 2013 | 23983220 |
| complete genome sequence of isosphaera pallida type strain (is1b). | isosphaera pallida (ex woronichin 1927) giovannoni et al. 1995 is the type species of the genus isosphaera. the species is of interest because it was the first heterotrophic bacterium known to be phototactic, and it occupies an isolated phylogenetic position within the planctomycetaceae. here we describe the features of this organism, together with the complete genome sequence and annotation. this is the first complete genome sequence of a member of the genus isosphaera and the third of a member ... | 2011 | 21475588 |
| microbial community responses to organophosphate substrate additions in contaminated subsurface sediments. | radionuclide- and heavy metal-contaminated subsurface sediments remain a legacy of cold war nuclear weapons research and recent nuclear power plant failures. within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. a promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments. | 2014 | 24950228 |
| assessing diversity of dna structure-related sequence features in prokaryotic genomes. | prokaryotic genomes are diverse in terms of their nucleotide and oligonucleotide composition as well as presence of various sequence features that can affect physical properties of the dna molecule. we present a survey of local sequence patterns which have a potential to promote non-canonical dna conformations (i.e. different from standard b-dna double helix) and interpret the results in terms of relationships with organisms' habitats, phylogenetic classifications, and other characteristics. our ... | 2014 | 24408877 |
| abundant trimethylornithine lipids and specific gene sequences are indicative of planctomycete importance at the oxic/anoxic interface in sphagnum-dominated northern wetlands. | northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant sphagnum mosses. recent studies have shown that planctomycetes appear to be involved in degradation of sphagnum-derived debris. novel trimethylornithine (tmo) lipids have recently been characterized as abundant lipids in various sphagnum wetland planctomycete isolates, but their occurrence in the environment has not yet been confirmed. we applied a combined intact polar lipid (ipl) and mole ... | 2015 | 26150465 |
| high diversity of planctomycetes in soils of two lichen-dominated sub-arctic ecosystems of northwestern siberia. | a wide variety of terrestrial ecosystems in tundra have a ground vegetation cover composed of reindeer lichens (genera cladonia and cetraria). the microbial communities of two lichen-dominated ecosystems typical of the sub-arctic zone of northwestern siberia, that is a forested tundra soil and a shallow acidic peatland, were examined in our study. as revealed by molecular analyses, soil and peat layers just beneath the lichen cover were abundantly colonized by bacteria from the phylum planctomyc ... | 2016 | 28066382 |