| a phylogenetic analysis of the myxobacteria: basis for their classification. | the primary sequence and secondary structural features of the 16s rrna were compared for 12 different myxobacteria representing all the known cultivated genera. analysis of these data show the myxobacteria to form a monophyletic grouping consisting of three distinct families, which lies within the delta subdivision of the purple bacterial phylum. the composition of the families is consistent with differences in cell and spore morphology, cell behavior, and pigment and secondary metabolite produc ... | 1992 | 1384053 |
| distribution of multicopy single-stranded dna among myxobacteria and related species. | multicopy single-stranded dna (msdna) is a short single-stranded linear dna originally discovered in myxococcus xanthus and subsequently found in stigmatella aurantiaca. it exists at an estimated 500 to 700 copies per chromosome (t. yee, t. furuichi, s. inouye, and m. inouye, cell 38:203-209, 1984). we found msdna in other myxobacteria, including myxococcus coralloides, cystobacter violaceus, cystobacter ferrugineus (cbfe17), nannocystis exedens, and nine independently isolated strains of m. xan ... | 1985 | 3932332 |
| pcr-based preparation of 23s rrna-targeted group-specific polynucleotide probes. | dna coding for a variable region within domain iii of bacterial 23s rrna was used as the target for group-specific polynucleotide hybridization probes. the corresponding rdna was amplified in vitro by the pcr technique in combination with a pair of primers specific for flanking conserved target sites. the amplified fragments were cloned or used directly as probes. rna probes were generated by in vitro transcription of cloned or amplified rdna. the probes were labeled by incorporating modified nu ... | 1994 | 7524442 |
| a highly selective pcr protocol for detecting 16s rrna genes of the genus pseudomonas (sensu stricto) in environmental samples. | pseudomonas species are plant, animal, and human pathogens; exhibit plant pathogen-suppressing properties useful in biological control; or express metabolic versatilities valued in biotechnology and bioremediation. specific detection of pseudomonas species in the environment may help us gain a more complete understanding of the ecological significance of these microorganisms. the objective of this study was to develop a pcr protocol for selective detection of pseudomonas (sensu stricto) in envir ... | 1998 | 9647828 |
| intraspecific diversity of the 23s rrna gene and the spacer region downstream in escherichia coli. | the molecular microevolution of the 23s rrna gene (rrl) plus the spacer downstream has been studied by sequencing of different operons from some representative strains of the escherichia coli ecor collection. the rrl gene was fully sequenced in six strains showing a total of 67 polymorphic sites, a level of variation per nucleotide similar to that found for the 16s rrna gene (rrs) in a previous study. the size of the gene was highly conserved (2902 to 2905 nucleotides). most polymorphic sites we ... | 1999 | 10217757 |
| phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater. | the phylogenetic diversity of the bacterial communities supported by a seven-stage, full-scale biological wastewater treatment plant was studied. these reactors were operated at both mesophilic (28 to 32 degrees c) and thermophilic (50 to 58 degrees c) temperatures. community fingerprint analysis by denaturing gradient gel electrophoresis (dgge) of the pcr-amplified v3 region of the 16s rrna gene from the domain bacteria revealed that these seven reactors supported three distinct microbial commu ... | 2000 | 10966414 |
| low-molecular-weight plasmid of salmonella enterica serovar enteritidis codes for retron reverse transcriptase and influences phage resistance. | retron reverse transcriptases are unusual procaryotic enzymes capable of synthesis of low-molecular-weight dna by reverse transcription. all of the so-far-described dna species synthesized by retron reverse transcriptases have been identified as multicopy single-stranded dna. we have shown that salmonella enterica serovar enteritidis is also capable of synthesis of the low-molecular-weight dna by retron reverse transcriptase. surprisingly, salmonella serovar enteritidis-produced low-molecular-we ... | 2001 | 11292805 |
| characterization and description of anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. | five strains were isolated which form a physiologically and phylogenetically coherent group of chlororespiring microorganisms and represent the first taxon in the myxobacteria capable of anaerobic growth. the strains were enriched and isolated from various soils and sediments based on their ability to grow using acetate as an electron donor and 2-chlorophenol (2-cph) as an electron acceptor. they are slender gram-negative rods with a bright red pigmentation that exhibit gliding motility and form ... | 2002 | 11823233 |
| the stigmatella aurantiaca homolog of myxococcus xanthus high-mobility-group a-type transcription factor card: insights into the functional modules of card and their distribution in bacteria. | transcriptional factor card is the only reported prokaryotic analog of eukaryotic high-mobility-group a (hmga) proteins, in that it has contiguous acidic and at hook dna-binding segments and multifunctional roles in myxococcus xanthus carotenogenesis and fruiting body formation. hmga proteins are small, randomly structured, nonhistone, nuclear architectural factors that remodel dna and chromatin structure. here we report on a second at hook protein, card(sa), that is very similar to card and tha ... | 2003 | 12775690 |
| reverse transcription-pcr analysis of bottled and natural mineral waters for the presence of noroviruses. | a seminested reverse transcription-pcr method coupled to membrane filtration was optimized to investigate the presence of norovirus (nv) rna sequences in bottled and natural mineral waters. the recovery of viral particles by filtration varied between 28 and 45%, while the limit of detection of the overall method ranged from 6 to 95 viral particles. the assay was broadly reactive, as shown by the successful detection of 27 different viral strains representing 12 common genotypes of nvs. a total o ... | 2003 | 14602612 |
| at least 1 in 20 16s rrna sequence records currently held in public repositories is estimated to contain substantial anomalies. | a new method for detecting chimeras and other anomalies within 16s rrna sequence records is presented. using this method, we screened 1,399 sequences from 19 phyla, as defined by the ribosomal database project, release 9, update 22, and found 5.0% to harbor substantial errors. of these, 64.3% were obvious chimeras, 14.3% were unidentified sequencing errors, and 21.4% were highly degenerate. in all, 11 phyla contained obvious chimeras, accounting for 0.8 to 11% of the records for these phyla. man ... | 2005 | 16332745 |
| identification of (8s,9s,10s)-8,10-dimethyl-1-octalin, a key intermediate in the biosynthesis of geosmin in bacteria. | | 2008 | 18095691 |
| identification of (8s,9s,10s)-8,10-dimethyl-1-octalin, a key intermediate in the biosynthesis of geosmin in bacteria. | | 2008 | 18095691 |
| biochemistry and molecular genetics of the biosynthesis of the earthy odorant methylisoborneol in streptomyces coelicolor. | methylisoborneol (2) is a volatile organic compound produced by a wide variety of actinomycete soil organisms, myxobacteria, and cyanobacteria. it has an unusually low odor threshold and, together with geosmin, is responsible for the characteristic smell of moist soil as well as unpleasant taste and odor episodes associated with public water supplies and contamination of various foodstuffs, including fish, wine, and beer. despite considerable interest in detection and remediation of methylisobor ... | 2008 | 18563898 |
| biosynthesis of 2-methylisoborneol in cyanobacteria. | the production of odiferous metabolites, such as 2-methlyisoborneol (mib), is a major concern for water utilities worldwide. although mib has no known biological function, the presence of the earthy/musty taste and odor attributed to this compound result in the reporting of numerous complaints by consumers, which undermines water utility performance and the safe and adequate provision of potable waters. cyanobacteria are the major producers of mib in natural waters, by mechanisms that have heret ... | 2010 | 21174459 |
| biosynthesis of 2-methylisoborneol in cyanobacteria. | the production of odiferous metabolites, such as 2-methlyisoborneol (mib), is a major concern for water utilities worldwide. although mib has no known biological function, the presence of the earthy/musty taste and odor attributed to this compound result in the reporting of numerous complaints by consumers, which undermines water utility performance and the safe and adequate provision of potable waters. cyanobacteria are the major producers of mib in natural waters, by mechanisms that have heret ... | 2010 | 21174459 |
| fatty acid-related phylogeny of myxobacteria as an approach to discover polyunsaturated omega-3/6 fatty acids. | in an analysis of 47 aerobic myxobacterial strains, representing 19 genera in suborders cystobacterineae, nannocystineae, sorangiineae, and a novel isolate, "aetherobacter" sbsr008, an enormously diverse array of fatty acids (fas) was found. the distribution of straight-chain fatty acids (scfas) and branched-chain fatty acids (bcfas) supports the reported clustering of strains in the phylogenetic tree based on 16s rrna genes. this finding additionally allows the prediction and assignment of the ... | 2011 | 21317327 |
| a suite of citrate-derived siderophores from a marine vibrio species isolated following the deepwater horizon oil spill. | nearly all microbes require iron for growth. the low concentration of iron found in the ocean makes iron acquisition a particularly difficult task. in response to these low iron conditions, many bacteria produce low-molecular-weight iron-binding molecules called siderophores to aid in iron uptake. we report herein the isolation and structural characterization of a suite of amphiphilic siderophores called the ochrobactins-oh, which are produced by a vibrio species isolated from the gulf of mexico ... | 2011 | 22178670 |
| a suite of citrate-derived siderophores from a marine vibrio species isolated following the deepwater horizon oil spill. | nearly all microbes require iron for growth. the low concentration of iron found in the ocean makes iron acquisition a particularly difficult task. in response to these low iron conditions, many bacteria produce low-molecular-weight iron-binding molecules called siderophores to aid in iron uptake. we report herein the isolation and structural characterization of a suite of amphiphilic siderophores called the ochrobactins-oh, which are produced by a vibrio species isolated from the gulf of mexico ... | 2011 | 22178670 |
| Exploration and Mining of the Bacterial Terpenome. | Tens of thousands of terpenoids are present in both terrestrial and marine plants, as well as fungi. In the last 5-10 years, however, it has become evident that terpenes are also produced by numerous bacteria, especially soil-dwelling Gram-positive organisms such as Streptomyces and other Actinomycetes. Although some microbial terpenes, such as geosmin, the degraded sesquiterpene responsible for the smell of moist soil, the characteristic odor of the earth itself, have been known for over 100 ye ... | 2011 | 22039990 |
| Exploration and Mining of the Bacterial Terpenome. | Tens of thousands of terpenoids are present in both terrestrial and marine plants, as well as fungi. In the last 5-10 years, however, it has become evident that terpenes are also produced by numerous bacteria, especially soil-dwelling Gram-positive organisms such as Streptomyces and other Actinomycetes. Although some microbial terpenes, such as geosmin, the degraded sesquiterpene responsible for the smell of moist soil, the characteristic odor of the earth itself, have been known for over 100 ye ... | 2011 | 22039990 |
| sterol synthesis in diverse bacteria. | sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. however, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. phylogenomic studies have identified g ... | 2016 | 27446030 |
| isolation and identification of myxobacteria from saline-alkaline soils in xinjiang, china. | fifty-eight terrestrial and salt-tolerant myxobacteria were isolated from the saline-alkaline soils collected from xinjiang, china. based on the morphologies and the 16s rrna gene sequences, these isolates were assigned into 6 genera, myxococcus, cystobacter, corallococcus, sorangium, nannocystis and polyangium. all the strains grew better with 1% nacl than without nacl. some myxococcus strains were able to grow at 2% nacl concentration, suggesting that these strains may be particular type of te ... | 2013 | 23936436 |
| marine-derived myxobacteria of the suborder nannocystineae: an underexplored source of structurally intriguing and biologically active metabolites. | myxobacteria are famous for their ability to produce most intriguing secondary metabolites. till recently, only terrestrial myxobacteria were in the focus of research. in this review, however, we discuss marine-derived myxobacteria, which are particularly interesting due to their relatively recent discovery and due to the fact that their very existence was called into question. the to-date-explored members of these halophilic or halotolerant myxobacteria are all grouped into the suborder nannocy ... | 2016 | 27340488 |
| biodegradation of natural rubber and related compounds: recent insights into a hardly understood catabolic capability of microorganisms. | | 2005 | 15932971 |
| structure-to-function relationships of bacterial translocator protein (tspo): a focus on pseudomonas. | the translocator protein (tspo), which was previously designated as the peripheral-type benzodiazepine receptor, is a 3.5 billion year-old evolutionarily conserved protein expressed by most eukarya, archae and bacteria, but its organization and functions differ remarkably. by taking advantage of the genomic data available on tspo, we focused on bacterial tspo and attempted to define functions of tspo in pseudomonas via in silico approaches. a tspo ortholog has been identified in several fluoresc ... | 2014 | 25477872 |
| molecular phylogeny of archaea from soil. | cultivation methods have contributed to our present knowledge about the presence and diversity of microbes in naturally occurring communities. however, it is well established that only a small fraction of prokaryotes have been cultivated by standard methods and, therefore, the prokaryotes that are cultivated may not reflect the composition and diversity within those communities. of the two prokaryotic phylogenetic domains, bacteria and archaea, members of the former have been shown to be ubiquit ... | 1997 | 8990199 |