| phylogenetic analysis of particle-attached and free-living bacterial communities in the columbia river, its estuary, and the adjacent coastal ocean. | the columbia river estuary is a dynamic system in which estuarine turbidity maxima trap and extend the residence time of particles and particle-attached bacteria over those of the water and free-living bacteria. particle-attached bacteria dominate bacterial activity in the estuary and are an important part of the estuarine food web. pcr-amplified 16s rrna genes from particle-attached and free-living bacteria in the columbia river, its estuary, and the adjacent coastal ocean were cloned, and 239 ... | 1999 | 10388721 |
| 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 |
| 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 |
| phylum verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum planctomycetes. | the phylum verrucomicrobia is a divergent phylum within domain bacteria including members of the microbial communities of soil and fresh and marine waters; recently extremely acidophilic members from hot springs have been found to oxidize methane. at least one genus, prosthecobacter, includes species with genes homologous to those encoding eukaryotic tubulins. a significant superphylum relationship of verrucomicrobia with members of phylum planctomycetes possessing a unique compartmentalized cel ... | 2009 | 19133117 |
| 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 |
| emerging roles for the ro 60-kda autoantigen in noncoding rna metabolism. | all cells contain an enormous variety of ribonucleoprotein (rnp) complexes that function in diverse processes. although the mechanisms by which many of these rnps contribute to cell metabolism are well understood, the roles of others are only now beginning to be revealed. a member of this latter category, the ro 60-kda protein and its associated noncoding y rnas, was discovered because the protein component is a frequent target of the autoimmune response in patients with the rheumatic diseases s ... | 2011 | 21823229 |
| perspective for aquaponic systems: "omic" technologies for microbial community analysis. | aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. in this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. the nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. in this particular field, the microbial research, the "omic" technologies will allow a broader scope of studies about a cu ... | 2015 | 26509157 |
| annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. | the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ... | 2011 | 24710297 |
| metagenomic analysis of a southern maritime antarctic soil. | our current understanding of antarctic soils is derived from direct culture on selective media, biodiversity studies based on clone library construction and analysis, quantitative pcr amplification of specific gene sequences and the application of generic microarrays for microbial community analysis. here, we investigated the biodiversity and functional potential of a soil community at mars oasis on alexander island in the southern maritime antarctic, by applying 454 pyrosequencing technology to ... | 2012 | 23227023 |
| 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 |
| 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 |
| electron tomography of the nucleoid of gemmata obscuriglobus reveals complex liquid crystalline cholesteric structure. | the nucleoid of the planctomycete gemmata obscuriglobus is unique within the bacteria in being both highly condensed and enclosed by a double-membrane nuclear envelope, seemingly analogous to the nucleus of eukaryotes. here we have applied electron tomography to study high-pressure frozen, cryosubstituted cells of g. obscuriglobus and found multiple nested orders of dna organization within the condensed nucleoid structure. detailed examination of the nucleoid revealed a series of nested arcs cha ... | 2012 | 22993511 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| planctomycetes as novel source of bioactive molecules. | marine environments are a fruitful source of bioactive compounds some of which are the newest leading drugs in medicinal therapeutics. of particular importance are organisms like sponges and macroalgae and their associated microbiome. planctomycetes, abundant in macroalgae biofilms, are promising producers of bioactive compounds since they share characteristics, like large genomes and complex life cycles, with the most bioactive bacteria, the actinobacteria. furthermore, genome mining revealed t ... | 2016 | 27570520 |
| evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. | the deaminase-like fold includes, in addition to nucleic acid/nucleotide deaminases, several catalytic domains such as the jab domain, and others involved in nucleotide and adp-ribose metabolism. using sensitive sequence and structural comparison methods, we develop a comprehensive natural classification of the deaminase-like fold and show that its ancestral version was likely to operate on nucleotides or nucleic acids. consequently, we present evidence that a specific group of jab domains are l ... | 2011 | 21890906 |
| the combination of functional metagenomics and an oil-fed enrichment strategy revealed the phylogenetic diversity of lipolytic bacteria overlooked by the cultivation-based method. | metagenomic screening and conventional cultivation have been used to exploit microbial lipolytic enzymes in nature. we used an indigenous forest soil (ns) and oil-fed enriched soil (os) as microbial and genetic resources. thirty-four strains (17 each) of lipolytic bacteria were isolated from the ns and os microcosms. these isolates were classified into the (sub)phyla betaproteobacteria, gammaproteobacteria, firmicutes, and actinobacteria, all of which are known to be the main microbial resources ... | 2014 | 24859309 |
| matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity. | sulfatases cleave sulfate groups from various molecules and constitute a biologically and industrially important group of enzymes. however, the number of sulfatases whose substrate has been characterized is limited in comparison to the huge diversity of sulfated compounds, yielding functional annotations of sulfatases particularly prone to flaws and misinterpretations. in the context of the explosion of genomic data, a classification system allowing a better prediction of substrate specificity a ... | 2016 | 27749924 |
| molecular dissection of tatc defines critical regions essential for protein transport and a tatb-tatc contact site. | the twin arginine transport (tat) system transports folded proteins across the prokaryotic cytoplasmic membrane and the plant thylakoid membrane. tatc is the largest and most conserved component of the tat machinery. it forms a multisubunit complex with tatb and binds the signal peptides of tat substrates. here we have taken a random mutagenesis approach to identify substitutions in escherichia coli tatc that inactivate protein transport. we identify 32 individual amino acid substitutions that a ... | 2012 | 22742417 |
| diversity of nonribosomal peptide synthetase genes in the microbial metagenomes of marine sponges. | genomic mining revealed one major nonribosomal peptide synthetase (nrps) phylogenetic cluster in 12 marine sponge species, one ascidian, an actinobacterial isolate and seawater. phylogenetic analysis predicts its taxonomic affiliation to the actinomycetes and hydroxy-phenyl-glycine as a likely substrate. additionally, a phylogenetically distinct nrps gene cluster was discovered in the microbial metagenome of the sponge aplysina aerophoba, which shows highest similarities to nrps genes that were ... | 2012 | 22822366 |
| genome signature difference between deinococcus radiodurans and thermus thermophilus. | the extremely radioresistant bacteria of the genus deinococcus and the extremely thermophilic bacteria of the genus thermus belong to a common taxonomic group. considering the distinct living environments of deinococcus and thermus, different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor. their guanine-cytosine (gc) contents are similar; however, we hypothesized that their genomic signatures would be different. our findings indicate ... | 2012 | 22500246 |
| emergence and evolutionary analysis of the human ddr network: implications in comparative genomics and downstream analyses. | the dna damage response (ddr) is a crucial signaling network that preserves the integrity of the genome. this network is an ensemble of distinct but often overlapping subnetworks, where different components fulfill distinct functions in precise spatial and temporal scenarios. to understand how these elements have been assembled together in humans, we performed comparative genomic analyses in 47 selected species to trace back their emergence using systematic phylogenetic analyses and estimated ge ... | 2014 | 24441036 |
| the rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. | bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. by replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomal ... | 2015 | 25567229 |
| identification of anion channels responsible for fluoride resistance in oral streptococci. | recently, it has been reported that eric and crcb are involved in bacterial fluoride resistance. however, the fluoride-resistance mechanism in oral streptococci remains unclear. blast studies showed that two types of erics (eric1 and eric2) and two types of crcbs (crcb1 and crcb2) are present across 18 oral streptococci, which were identified in ≥ 10% of 166 orally healthy subjects with ≥ 0.01% of the mean relative abundance. they were divided into three groups based on the distribution of these ... | 2016 | 27824896 |
| gene-family extension measures and correlations. | the existence of multiple copies of genes is a well-known phenomenon. a gene family is a set of sufficiently similar genes, formed by gene duplication. in earlier works conducted on a limited number of completely sequenced and annotated genomes it was found that size of gene family and size of genome are positively correlated. additionally, it was found that several atypical microbes deviated from the observed general trend. in this study, we reexamined these associations on a larger dataset con ... | 2016 | 27527218 |
| it all starts with a sandwich: identification of sialidases with trans-glycosylation activity. | sialidases (3.2.1.18) may exhibit trans-sialidase activity to catalyze sialylation of lactose if the active site topology is congruent with that of the trypanosoma cruzi trans-sialidase (ec 2.4.1.-). the present work was undertaken to test the hypothesis that a particular aromatic sandwich structure of two amino acids proximal to the active site of the t. cruzi trans-sialidase infers trans-sialidase activity. on this basis, four enzymes with putative trans-sialidase activity were identified thro ... | 2016 | 27367145 |
| multiple inter-kingdom horizontal gene transfers in the evolution of the phosphoenolpyruvate carboxylase gene family. | pepcase is a gene encoding phosphoenolpyruvate carboxylase that exists in bacteria, archaea and plants,playing an important role in plant metabolism and development. most plants have two or more pepcase genes belonging to two gene sub-families, while only one gene exists in other organisms. previous research categorized one plant pepcase gene as plant-type pepcase (ptpc) while the other as bacteria-type pepcase (btpc) because of its similarity with the pepcase gene found in bacteria. phylogeneti ... | 2012 | 23251445 |
| veillonella, firmicutes: microbes disguised as gram negatives. | the firmicutes represent a major component of the intestinal microflora. the intestinal firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. although most firmicutes are gram positive, members of the class negativicutes, including the genus veillonella, stain gram negative. veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerob ... | 2013 | 24976898 |
| 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 |
| f-/cl- selectivity in clcf-type f-/h+ antiporters. | many bacterial species protect themselves against environmental f(-) toxicity by exporting this anion from the cytoplasm via clc(f) f(-)/h(+) antiporters, a subclass of clc superfamily anion transporters. strong f(-) over cl(-) selectivity is biologically essential for these membrane proteins because cl(-) is orders of magnitude more abundant in the biosphere than f(-). sequence comparisons reveal differences between clc(f)s and canonical cl(-)-transporting clcs within regions that, in the canon ... | 2014 | 25070431 |
| dissemination of 6s rna among bacteria. | 6s rna is a highly abundant small non-coding rna widely spread among diverse bacterial groups. by competing with dna promoters for binding to rna polymerase (rnap), the rna regulates transcription on a global scale. rnap produces small product rnas derived from 6s rna as template, which rearranges the 6s rna structure leading to dissociation of 6s rna:rnap complexes. although 6s rna has been experimentally analysed in detail for some species, such as escherichia coli and bacillus subtilis, and w ... | 2014 | 25483037 |
| changes and recovery of soil bacterial communities influenced by biological soil disinfestation as compared with chloropicrin-treatment. | soil bacterial composition, as influenced by biological soil disinfestation (bsd) associated with biomass incorporation was investigated to observe the effects of the treatment on the changes and recovery of the microbial community in a commercial greenhouse setting. chloropicrin (cp) was also used for soil disinfestation to compare with the effects of bsd. the fusarium wilt disease incidence of spinach cultivated in the bsd- and cp-treated plots was reduced as compared with that in the untreate ... | 2013 | 23958081 |
| unification of cas protein families and a simple scenario for the origin and evolution of crispr-cas systems. | the crispr-cas adaptive immunity systems that are present in most archaea and many bacteria function by incorporating fragments of alien genomes into specific genomic loci, transcribing the inserts and using the transcripts as guide rnas to destroy the genome of the cognate virus or plasmid. this rna interference-like immune response is mediated by numerous, diverse and rapidly evolving cas (crispr-associated) proteins, several of which form the cascade complex involved in the processing of cris ... | 2011 | 21756346 |
| prokaryotic metabolic activity and community structure in antarctic continental shelf sediments. | the prokaryote community activity and structural characteristics within marine sediment sampled across a continental shelf area located off eastern antarctica (66 degrees s, 143 degrees e; depth range, 709 to 964 m) were studied. correlations were found between microbial biomass and aminopeptidase and chitinase rates, which were used as proxies for microbial activity. biomass and activity were maximal within the 0- to 3-cm depth range and declined rapidly with sediment depths below 5 cm. most-pr ... | 2003 | 12732510 |
| genome-based taxonomic classification of bacteroidetes. | the bacterial phylum bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16s rrna gene sequence. here we use a large collection of type-strain genomes from bacteroidetes and closely related ... | 2016 | 28066339 |
| two new families of the ftsz-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea. | several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling. here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the ftsz-tubulin superfamily. one of these families is limited in its spread to proteobacteria whereas the other is represented in ... | 2010 | 20459678 |
| relevance of gc content to the conservation of dna polymerase iii/mismatch repair system in gram-positive bacteria. | the mechanism of dna replication is one of the driving forces of genome evolution. bacterial dna polymerase iii, the primary complex of dna replication, consists of polc and dnae. polc is conserved in gram-positive bacteria, especially in the firmicutes with low gc content, whereas dnae is widely conserved in most gram-negative and gram-positive bacteria. polc contains two domains, the 3'-5'exonuclease domain and the polymerase domain, while dnae only possesses the polymerase domain. accordingly ... | 2013 | 24062730 |
| phylogeny of rieske/cytb complexes with a special focus on the haloarchaeal enzymes. | rieske/cytochrome b (rieske/cytb) complexes are proton pumping quinol oxidases that are present in most bacteria and archaea. the phylogeny of their subunits follows closely the 16s-rrna phylogeny, indicating that chemiosmotic coupling was already present in the last universal common ancestor of archaea and bacteria. haloarchaea are the only organisms found so far that acquired rieske/cytb complexes via interdomain lateral gene transfer. they encode two rieske/cytb complexes in their genomes; on ... | 2012 | 22798450 |
| bringing planctomycetes into pure culture. | planctomycetes have been known since the description of planctomyces bekefii by gimesi at the beginning of the twentieth century (1924), although the first axenic cultures were only obtained in the 1970s. since then, 11 genera with 14 species have been validly named and five candidatus genera belonging to the anaerobic ammonium oxidation, anammox bacteria have also been discovered. however, planctomycetes diversity is much broader than these numbers indicate, as shown by environmental molecular ... | 2012 | 23335915 |
| global and targeted lipid analysis of gemmata obscuriglobus reveals the presence of lipopolysaccharide, a signature of the classical gram-negative outer membrane. | planctomycete bacteria possess many unusual cellular properties, contributing to a cell plan long considered to be unique among the bacteria. however, data from recent studies are more consistent with a modified gram-negative cell plan. a key feature of the gram-negative plan is the presence of an outer membrane (om), for which lipopolysaccharide (lps) is a signature molecule. despite genomic evidence for an om in planctomycetes, no biochemical verification has been reported. we attempted to det ... | 2016 | 26483522 |
| global and targeted lipid analysis of gemmata obscuriglobus reveals the presence of lipopolysaccharide, a signature of the classical gram-negative outer membrane. | planctomycete bacteria possess many unusual cellular properties, contributing to a cell plan long considered to be unique among the bacteria. however, data from recent studies are more consistent with a modified gram-negative cell plan. a key feature of the gram-negative plan is the presence of an outer membrane (om), for which lipopolysaccharide (lps) is a signature molecule. despite genomic evidence for an om in planctomycetes, no biochemical verification has been reported. we attempted to det ... | 2016 | 26483522 |
| 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 |
| sequence, structure and functional diversity of pd-(d/e)xk phosphodiesterase superfamily. | proteins belonging to pd-(d/e)xk phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, dna repair and trna-intron splicing. their malfunction in humans triggers severe diseases, such as fanconi anemia and xeroderma pigmentosum. to date there have been several attempts to identify and classify new pd-(d/e)kk phosphodiesterases using remote homology detection methods. such efforts are complicated, because the superfamily exhibit ... | 2012 | 22638584 |
| fluoride resistance and transport by riboswitch-controlled clc antiporters. | a subclass of bacterial clc anion-transporting proteins, phylogenetically distant from long-studied clcs, was recently shown to be specifically up-regulated by f(-). we establish here that a set of randomly selected representatives from this "clc(f)" clade protect escherichia coli from f(-) toxicity, and that the purified proteins catalyze transport of f(-) in liposomes. sequence alignments and membrane transport experiments using (19)f nmr, osmotic response assays, and planar lipid bilayer reco ... | 2012 | 22949689 |
| a molecular insight into algal-oomycete warfare: cdna analysis of ectocarpus siliculosus infected with the basal oomycete eurychasma dicksonii. | brown algae are the predominant primary producers in coastal habitats, and like land plants are subject to disease and parasitism. eurychasma dicksonii is an abundant, and probably cosmopolitan, obligate biotrophic oomycete pathogen of marine brown algae. oomycetes (or water moulds) are pathogenic or saprophytic non-photosynthetic stramenopiles, mostly known for causing devastating agricultural and aquacultural diseases. whilst molecular knowledge is restricted to crop pathogens, pathogenic oomy ... | 2011 | 21935414 |
| erratum to: complete genome sequence of pirellula staleyi type strain (atcc 27377). | | 2010 | 21304706 |
| 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 |
| 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 |
| differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient. | the hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. the microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. using a suite of methods (denaturing gradient gel electrophoresis, 16s rrna phylogeny, phospholipid fatty a ... | 2003 | 12957946 |
| novel major bacterial candidate division within a municipal anaerobic sludge digester. | in a previous study, we analyzed the molecular diversity of planctomycetales by pcr amplification and sequencing of 16s rrna clone libraries generated from a municipal wastewater plant, using planctomycete-specific and universal primer sets (r. chouari, d. le paslier, p. daegelen, p. ginestet, j. weissenbach, and a. sghir, appl. environ. microbiol. 69:7354-7363, 2003). only a small fraction (4%) of the 16s rrna gene sequences of the digester clone library corresponded to the planctomycetales div ... | 2005 | 15812049 |