| 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 |
| partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces. | distinct partitioning has been observed in the composition and diversity of bacterial communities inhabiting the surface and overlying seawater of three coral species infected with black band disease (bbd) on the southern caribbean island of curaçao, netherlands antilles. pcr amplification and sequencing of bacterial 16s rrna genes (rdna) with universally conserved primers have identified over 524 unique bacterial sequences affiliated with 12 bacterial divisions. the molecular sequences exhibite ... | 2002 | 11976091 |
| community structure of ammonia-oxidizing bacteria within anoxic marine sediments. | the potential for oxidation of ammonia in anoxic marine sediments exists through anaerobic oxidation by nitrosomonas-like organisms, utilizing nitrogen dioxide, coupling of nitrification, manganese reduction, and anaerobic oxidation of ammonium by planctomycetes (the anammox process). here we describe the presence of microbial communities with the potential to carry out these processes in a natural marine sediment system (loch duich, scotland). natural microbial communities of planctomycetales-v ... | 2003 | 12620817 |
| 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 |
| the origin of multicellularity in cyanobacteria. | cyanobacteria are one of the oldest and morphologically most diverse prokaryotic phyla on our planet. the early development of an oxygen-containing atmosphere approximately 2.45-2.22 billion years ago is attributed to the photosynthetic activity of cyanobacteria. furthermore, they are one of the few prokaryotic phyla where multicellularity has evolved. understanding when and how multicellularity evolved in these ancient organisms would provide fundamental information on the early history of life ... | 2011 | 21320320 |
| 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 |
| the atypical two-component sensor kinase lpl0330 from legionella pneumophila controls the bifunctional diguanylate cyclase-phosphodiesterase lpl0329 to modulate c-di-gmp synthesis. | a significant part of bacterial two-component system response regulators contain effector domains predicted to be involved in metabolism of c-di-gmp, a second messenger which plays a key role in many physiological processes. intracellular level of c-di-gmp is controlled by diguanylate cyclases (dgcs) and phosphodiesterases (pdes) activities associated with ggdef and eal domains, respectively. the legionella pneumophila lens genome displays 22 ggdef/eal domain-encoding genes. one of them, lpl0329 ... | 2011 | 21757706 |
| 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 |
| optimizing information in next-generation-sequencing (ngs) reads for improving de novo genome assembly. | next-generation-sequencing is advantageous because of its much higher data throughput and much lower cost compared with the traditional sanger method. however, ngs reads are shorter than sanger reads, making de novo genome assembly very challenging. because genome assembly is essential for all downstream biological studies, great efforts have been made to enhance the completeness of genome assembly, which requires the presence of long reads or long distance information. to improve de novo genome ... | 2013 | 23922726 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| genomic and biochemical analysis of the diaminopimelate and lysine biosynthesis pathway in verrucomicrobium spinosum: identification and partial characterization of l,l-diaminopimelate aminotransferase and udp-n-acetylmuramoylalanyl-d-glutamyl-2,6-meso-diaminopimelate ligase. | the gram-negative bacterium verrucomicrobium spinosum has attracted interest in recent years following the sequencing and annotation of its genome. comparative genomic analysis of v. spinosum using diaminopimelate/lysine metabolic genes from chlamydia trachomatis suggests that v. spinosum employs the l,l-diaminopimelate aminotransferase (dapl) pathway for diaminopimelate/lysine biosynthesis. the open reading frame corresponding to the putative dapl ortholog was cloned and the recombinant enzyme ... | 2012 | 22783236 |
| physiological characterization of an anaerobic ammonium-oxidizing bacterium belonging to the "candidatus scalindua" group. | the phylogenetic affiliation and physiological characteristics (e.g., ks and maximum specific growth rate [μmax]) of an anaerobic ammonium oxidation (anammox) bacterium, "candidatus scalindua sp.," enriched from the marine sediment of hiroshima bay, japan, were investigated. "candidatus scalindua sp." exhibits higher affinity for nitrite and a lower growth rate and yield than the known anammox species. | 2013 | 23584767 |
| comprehensive analysis of the hepn superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and rna processing. | the major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks in large part to the advances of comparative genomics. typically, toxins evolve rapidly hampering the identification of these proteins by sequence analysis. here we analyze an unexpectedly widespread superfamily of toxin domains most of which possess rnase activity. | 2013 | 23768067 |
| wksl3, a new biocontrol agent for salmonella enterica serovars enteritidis and typhimurium in foods: characterization, application, sequence analysis, and oral acute toxicity study. | of the salmonella enterica serovars, s. enteritidis and s. typhimurium are responsible for most of the salmonella outbreaks implicated in the consumption of contaminated foods in the republic of korea. because of the widespread occurrence of antimicrobial-resistant salmonella in foods and food processing environments, bacteriophages have recently surfaced as an alternative biocontrol tool. in this study, we isolated a virulent bacteriophage (wksl3) that could specifically infect s. enteritidis, ... | 2013 | 23335772 |
| 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 |
| structural and biochemical characterization of a metagenome-derived esterase with a long n-terminal extension. | the genes encoding six novel esterolytic/lipolytic enzymes, termed lc-est1∼6, were isolated from a fosmid library of a leaf-branch compost metagenome by functional screening using tributyrin agar plates. these enzymes greatly vary in size and amino acid sequence. the highest identity between the amino acid sequence of each enzyme and that available from the database varies from 44 to 73%. of these metagenome-derived enzymes, lc-est1 is characterized by the presence of a long n-terminal extension ... | 2014 | 25348365 |
| structural and biochemical characterization of a metagenome-derived esterase with a long n-terminal extension. | the genes encoding six novel esterolytic/lipolytic enzymes, termed lc-est1∼6, were isolated from a fosmid library of a leaf-branch compost metagenome by functional screening using tributyrin agar plates. these enzymes greatly vary in size and amino acid sequence. the highest identity between the amino acid sequence of each enzyme and that available from the database varies from 44 to 73%. of these metagenome-derived enzymes, lc-est1 is characterized by the presence of a long n-terminal extension ... | 2014 | 25348365 |
| ether- and ester-bound iso-diabolic acid and other lipids in members of acidobacteria subdivision 4. | recently, iso-diabolic acid (13,16-dimethyl octacosanedioic acid) has been identified as a major membrane-spanning lipid of subdivisions 1 and 3 of the acidobacteria, a highly diverse phylum within the bacteria. this finding pointed to the acidobacteria as a potential source for the bacterial glycerol dialkyl glycerol tetraethers that occur ubiquitously in peat, soil, lakes, and hot springs. here, we examined the lipid composition of seven phylogenetically divergent strains of subdivision 4 of t ... | 2014 | 24928878 |
| linking activity and function to ecosystem dynamics in a coastal bacterioplankton community. | for bacterial communities containing hundreds to thousands of distinct populations, connecting functional processes and environmental dynamics at high taxonomic resolution has remained challenging. here we use the expression of ribosomal proteins (%rp) as a proxy for in situ activity of 200 taxa within 20 metatranscriptomic samples in a coastal ocean time series encompassing both seasonal variability and diel dynamics. %rp patterns grouped the taxa into seven activity clusters with distinct prof ... | 2014 | 24795712 |
| nickel-resistance determinants in acidiphilium sp. pm identified by genome-wide functional screening. | acidiphilium spp. are conspicuous dwellers of acidic, metal-rich environments. indeed, they are among the most metal-resistant organisms; yet little is known about the mechanisms behind the metal tolerance in this genus. acidiphilium sp. pm is an environmental isolate from rio tinto, an acidic, metal-laden river located in southwestern spain. the characterization of its metal resistance revealed a remarkable ability to tolerate high ni concentrations. here we report the screening of a genomic li ... | 2014 | 24740277 |
| prolyl oligopeptidase from the blood fluke schistosoma mansoni: from functional analysis to anti-schistosomal inhibitors. | blood flukes of the genus schistosoma cause schistosomiasis, a parasitic disease that infects over 240 million people worldwide, and for which there is a need to identify new targets for chemotherapeutic interventions. our research is focused on schistosoma mansoni prolyl oligopeptidase (smpop) from the serine peptidase family s9, which has not been investigated in detail in trematodes. | 2015 | 26039195 |
| biomass yield efficiency of the marine anammox bacterium, "candidatus scalindua sp.," is affected by salinity. | the growth rate and biomass yield efficiency of anaerobic ammonium oxidation (anammox) bacteria are markedly lower than those of most other autotrophic bacteria. among the anammox bacterial genera, the growth rate and biomass yield of the marine anammox bacterium "candidatus scalindua sp." is still lower than those of other anammox bacteria enriched from freshwater environments. the activity and growth of marine anammox bacteria are generally considered to be affected by the presence of salinity ... | 2015 | 25740428 |
| evolutionary cell biology of division mode in the bacterial planctomycetes-verrucomicrobia- chlamydiae superphylum. | bacteria from the planctomycetes, verrucomicrobia, and chlamydiae (pvc) superphylum are exceptions to the otherwise dominant mode of division by binary fission, which is based on the interaction between the ftsz protein and the peptidoglycan (pg) biosynthesis machinery. some pvc bacteria are deprived of the ftsz protein and were also thought to lack pg. how these bacteria divide is still one of the major mysteries of microbiology. the presence of pg has recently been revealed in planctomycetes a ... | 2016 | 28018303 |
| dcia is an ancestral replicative helicase operator essential for bacterial replication initiation. | delivery of the replicative helicase onto dna is an essential step in the initiation of replication. in bacteria, dnac (in escherichia coli) and dnai (in bacillus subtilis) are representative of the two known mechanisms that assist the replicative helicase at this stage. here, we establish that these two strategies cannot be regarded as prototypical of the bacterial domain since dnac and dnai (dna[ci]) are present in only a few bacterial phyla. we show that dna[ci] was domesticated at least seve ... | 2016 | 27830752 |
| bioprospecting red sea coastal ecosystems for culturable microorganisms and their antimicrobial potential. | microorganisms that inhabit unchartered unique soil such as in the highly saline and hot red sea lagoons on the saudi arabian coastline, represent untapped sources of potentially new bioactive compounds. in this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (mn), microbial mat (mm), and barren soil (bs), collected from rabigh harbor lagoon (rhl) and al-kharrar lagoon (akl). the isolated bacteria were evaluated for their potential to produce bioactive c ... | 2016 | 27626430 |
| 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 |
| discovery strategies of bioactive compounds synthesized by nonribosomal peptide synthetases and type-i polyketide synthases derived from marine microbiomes. | considering that 70% of our planet's surface is covered by oceans, it is likely that undiscovered biodiversity is still enormous. a large portion of marine biodiversity consists of microbiomes. they are very attractive targets of bioprospecting because they are able to produce a vast repertoire of secondary metabolites in order to adapt in diverse environments. in many cases secondary metabolites of pharmaceutical and biotechnological interest such as nonribosomal peptides (nrps) and polyketides ... | 2016 | 27092515 |
| analysis of two domains with novel rna-processing activities throws light on the complex evolution of ribosomal rna biogenesis. | ribosomal biogenesis has been extensively investigated, especially to identify the elusive nucleases and cofactors involved in the complex rrna processing events in eukaryotes. large-scale screens in yeast identified two biochemically uncharacterized proteins, tsr3 and tsr4, as being key players required for rrna maturation. using multiple computational approaches we identify the conserved domains comprising these proteins and establish sequence and structural features providing novel insights r ... | 2014 | 25566315 |
| domain organization of dnase from thioalkalivibrio sp. provides insights into retention of activity in high salt environments. | our study indicates that dna binding domains are common in many halophilic or halotolerant bacterial dnases and they are potential activators of enzymatic activity at high ionic strength. usually, proteins adapt to high ionic strength by increasing the number of negatively charged residues on the surface. however, in dnases such adaptation would hinder the binding to negatively charged dna, a step critical for catalysis. in our study we demonstrate how evolution has solved this dilemma by engagi ... | 2015 | 26191053 |
| fuerstia marisgermanicae gen. nov., sp. nov., an unusual member of the phylum planctomycetes from the german wadden sea. | members of the phylum planctomycetes are ubiquitous bacteria that dwell in aquatic and terrestrial habitats. while planctomycetal species are important players in the global carbon and nitrogen cycle, this phylum is still undersampled and only few genome sequences are available. here we describe strain nh11(t), a novel planctomycete obtained from a crustacean shell (wadden sea, germany). the phylogenetically closest related cultivated species is gimesia maris, sharing only 87% 16s rrna sequence ... | 2016 | 28066393 |