Showing papers in "Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology in 1998"
TL;DR: The potentials and limitations of these techniques will be discussed, and it will be indicated why their use in ecological studies has become so important.
Abstract: Here, the state of the art of the application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology will be presented. Furthermore, the potentials and limitations of these techniques will be discussed, and it will be indicated why their use in ecological studies has become so important.
2,181 citations
TL;DR: Divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species.
Abstract: Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among the ascomycetous yeasts were analyzed from D1/D2 sequence divergence. For comparison, the phylogeny of selected members of the Saccharomyces clade was determined from 18S rDNA sequences. Species relationships were highly concordant between the D1/D2 and 18S trees when branches were statistically well supported.
2,174 citations
TL;DR: It is argued that failure to differentiate clearly between use of the terms ‘viability’ and ‘culturability” in an operational versus a conceptual sense is fuelling the current debate, and an alternative operational terminology is suggested that replaces ‘VBNC’ with expressions that are internally consistent.
Abstract: In microbiology the terms 'viability' and 'culturability' are often equated. However, in recent years the apparently self-contradictory expression 'viable-but-nonculturable' ('VBNC') has been applied to cells with various and often poorly defined physiological attributes but which, nonetheless, could not be cultured by methods normally appropriate to the organism concerned. These attributes include apparent cell integrity, the possession of some form of measurable cellular activity and the apparent capacity to regain culturability. We review the evidence relating to putative VBNC cells and stress our view that most of the reports claiming a return to culturability have failed to exclude the regrowth of a limited number of cells which had never lost culturability. We argue that failure to differentiate clearly between use of the terms 'viability' and 'culturability' in an operational versus a conceptual sense is fuelling the current debate, and conclude with a number of proposals that are designed to help clarify the major issues involved. In particular, we suggest an alternative operational terminology that replaces 'VBNC' with expressions that are internally consistent.
604 citations
TL;DR: Using what data is available, it is estimated that thirty grams of forest soil contains over half a million species of bacteria, which suggests that the number ofspecies of bacteria in the world may be more than a thousand million.
Abstract: The diversity of bacteria in the world is very poorly known. Usually less than one percent of the bacteria from natural communities can be grown in the laboratory. This has caused us to underestimate bacterial diversity and biased our view of bacterial communities. The tools are now available to estimate the number of bacterial species in a community and to estimate the difference between communities. Using what data are available, I have estimated that thirty grams of forest soil contains over half a million species. The species difference between related communities suggests that the number of species of bacteria may be more than a thousand million. I suppose that the explanation for such a large number of bacterial species is simply that speciation in bacteria is easy and extinction difficult, giving a rate of speciation higher than the rate of extinction, leading to an ever increasing number of species over time. The idea that speciation is easy is justified from the results of recent experimental work in bacterial evolution.
284 citations
TL;DR: Biosurfactants may find applications in the near future in the environmental remediation industries, where the requirement for purified molecules is of less importance and the cost of production is considerably higher than for synthetic surfactants.
Abstract: Like other hydrocarbon-oxidising bacteria, rhodococci respond to the presence of alkanes by producing biosurfactant molecules to improve their ability to utilise these hydrophobic compounds as growth substrates. In the rhodococci these surfactants are predominantly glycolipids, the majority of which remain cell-bound during unrestricted growth. Most work has been done on the trehalose mycolates formed by Rhodococcus erythropolis, but nitrogen- limited conditions lead to the production of anionic trehalose tetraesters also.
228 citations
TL;DR: Experiments to identify the phenotypic bases of improved competitive fitness in twelve E. coli populations that evolved for thousands of generations in a defined environment, in which glucose was the limiting substrate, suggest that enhanced transport was an important target of natural selection in the evolutionary environment.
Abstract: An important problem in microbial ecology is to identify those phenotypic attributes that are responsible for competitive fitness in a particular environment. Thousands of papers have been published on the physiology, biochemistry, and molecular genetics of Escherichia coli and other bacterial models. Nonetheless, little is known about what makes one genotype a better competitor than another even in such well studied systems. Here, we review experiments to identify the phenotypic bases of improved competitive fitness in twelve E. coli populations that evolved for thousands of generations in a defined environment, in which glucose was the limiting substrate. After 10000 generations, the average fitness of the derived genotypes had increased by ∼ 50% relative to the ancestor, based on competition experiments using marked strains in the same environment. The growth kinetics of the ancestral and derived genotypes showed that the latter have a shorter lag phase upon transfer into fresh medium and a higher maximum growth rate. Competition experiments were also performed in environments where other substrates were substituted for glucose. The derived genotypes are generally more fit in competition for those substrates that use the same mechanism of transport as glucose, which suggests that enhanced transport was an important target of natural selection in the evolutionary environment. All of the derived genotypes produce much larger cells than does the ancestor, even when both types are forced to grow at the same rate. Some, but not all, of the derived genotypes also have greatly elevated mutation rates. Efforts are now underway to identify the genetic changes that underlie those phenotypic changes, especially substrate specificity and elevated mutation rate, for which there are good candidate loci. Identification and subsequent manipulation of these genes may provide new insights into the reproducibility of adaptive evolution, the importance of co-adapted gene complexes, and the extent to which distinct phenotypes (e.g., substrate specificity and cell size) are affected by the same mutations.
178 citations
TL;DR: Evidence from 16S ribosomal RNA sequencing suggests that the genus Rhodococcus is still heterogeneous, and improved diagnostic methods are needed to distinguish between species.
Abstract: Various approaches that have been used in the development of a system of classification for the genus Rhodococcus are discussed. The application of chemotaxonomic, molecular systematic and numerical phenetic methods have greatly contributed to improvements in the systematics of rhodococci and related mycolic- acid containing actinomycetes. The genus currently encompasses twelve validly described species but improved diagnostic methods are needed to distinguish between them. In addition, evidence from 16S ribosomal RNA sequencing suggests that the genus is still heterogeneous.
131 citations
TL;DR: Polyphasic taxonomic analysis revealed considerable diversity among the deep sea rhodococci and evidence for recently diverged species or DNA groups.
Abstract: A large number of mycolate actinomycetes have been recovered from deep-sea sediments in the NW Pacific Ocean using selective isolation methods The isolates were putatively assigned to the genus Rhodococcus on the basis of colony characteristics and mycolic acid profiles The diversity among these isolates and their relationship to type strains of Rhodococcus and other mycolate taxa were assessed by Curie point pyrolysis mass spectrometry (PyMS) Three major (A, C, D) and two minor (B, E) groups were defined by PyMS Cluster A was a large group of isolates recovered from sediment in the Izu Bonin Trench (2679 m); Cluster C comprised isolates from both the Izu Bonin Trench (6390 and 6499 m) and from the Japan Trench (4418, 6048 and 6455 m) These Cluster C isolates showed close similarity to Dietzia maris and this was subsequently confirmed using molecular methods Cluster D contained isolates recovered from a sediment taken from a depth of 1168m in Sagami Bay and were identified as members of the terrestrial species Rhodococcus luteus Clusters B and E had close affinities with members of the genera Gordonia and Mycobacterium The presence of Thermoactinomyces in certain of the deep-sea sediments studied was indicative of the movement of terrestrial material into the ocean depths 16S ribosomal RNA gene sequence analyses produced excellent definition of most genera of the mycolata, and indicated that the among the deep sea isolates (1) were novel species of Corynebacterium, Gordonia and Mycobacterium, and (2) a Sea of Japan isolate the phylogenetic depth of which suggests the possibility of a new genus Polyphasic taxonomic analysis revealed considerable diversity among the deep sea rhodococci and evidence for recently diverged species or DNA groups
128 citations
TL;DR: Irrespective of the chemical ‘language’ employed, interference with either the synthesis or transmission of a quorum sensing signal molecule in pathogenic bacteria offers an exciting new strategy for controlling infection.
Abstract: Although it has been clear for some time that individual bacterial cells employ intra-cellular signalling systems to sense, integrate and process information from their surroundings, their widespread capacity to perceive information from other bacterial cells is only just beginning to be recognised. Recent work has established that diverse bacteria exploit a cell-cell communication device to regulate the transcription of multiple target genes. This communication device termed 'quorum sensing', depends on the production of one or more diffusible signal molecules termed 'autoinducers' or 'pheromones' which enable a bacterium to monitor its own cell population density. Quorum sensing is thus an example of multicellular behaviour in prokaryotes and regulates diverse physiological processes including bioluminescence, swarming, antibiotic biosynthesis, plasmid conjugal transfer and the production of virulence determinants in animal, fish and plant pathogens. In Gram-negative bacteria, the best understood family of signal molecules are the N-acylhomoserine lactones (AHLs) which vary predominantly in the presence or absence of an acyl chain C3 substituent (oxo- or hydroxy-) and length of the N-acyl side chain. However not all quorum sensing signal molecules are AHLs; in Gram-positive bacteria, they are often post-translationally modified peptides. Irrespective of the chemical 'language' employed, interference with either the synthesis or transmission of a quorum sensing signal molecule in pathogenic bacteria offers an exciting new strategy for controlling infection.
121 citations
TL;DR: It is shown that rock inhabiting meristematic fungi are extremely tolerant against high temperatures, desiccation and osmotic stress, and Hortaea werneckii – hitherto only described as agent of human Tinea nigra – is shown to be the most tolerant rock inhabitant species tested.
Abstract: Black meristematic fungi together with lichens and cyanobacteria dominate the micro-flora of rock surfaces in arid and semi-arid environments of hot and cold deserts. This study shows that rock inhabiting meristematic fungi are extremely tolerant against high temperatures, desiccation and osmotic stress. Their temperature tolerance increases with increasing dehydration of the fungal thallus. Air dried mycelia of black yeasts stand temperatures up to 120 °C for at least 0.5 hours. As response to high temperatures multilayered cell walls are developed and trehalose is accumulated whereas the intracellular glycerol regulates the osmotic potential under NaCl stress. Strains from rock in moderate climate (North Germany) show the same tolerance than those isolated from the Mediterranean area. Hortaea werneckii – hitherto only described as agent of human Tinea nigra – is shown to be the most tolerant rock inhabiting species tested. Meristematic fungi cannot be pre-adapted to higher growth temperatures by increased incubation temperatures. Considering the results of this study the justification of the term ‘stress’ is discussed with regard to rock inhabiting fungi and their natural environment. Consequences for conservation treatments of monuments decayed by meristematic fungi are discussed on the basis of the ecophysiological properties of the fungi.
121 citations
TL;DR: The need for separate, DBT- and BTH-specific desulphurisation routes is rationalised in terms of the chemical differences between the two compounds.
Abstract: Desulphurising enzymes remove the sulphur moiety from an organosulphur molecule leaving the carbon skeleton intact. Two kinds of desulphurisation reaction are recognised. The dibenzothiophene (DBT)-specific pathway desulphurises DBT to inorganic sulphite and 2- hydroxybiphenyl (HBP), and the benzothiophene (BTH)-specific pathway desulphurises BTH to 2-(2′-hydroxyphenyl)ethan 1-al (HPEal) and probably inorganic sulphite. The DBT-desulphurisation pathway was originally identified in Rhodococcus erythropolis strain IGTS8 (ATCC 53968), and the BTH-desulphurisation pathway in Gordonia sp. strain 213E (NCIMB 40816). These organisms do not further metabolise the organic product of desulphurisation. In this article current knowledge of the biochemistry and genetics of the desulphurisation enzymes is reviewed. The need for separate, DBT- and BTH-specific desulphurisation routes is rationalised in terms of the chemical differences between the two compounds. The desulphurisation pathway is compared with other microbial DBT- degrading enzyme systems. Finally some comments are made concerning the application of desulphurisation enzymes for fuel desulphurisation and on the relevance of these enzymes to the ecology of the mycolata (sensu Chun et al, 1996).
TL;DR: It is emphasised that the mycolic acids in this complex form the basis of an outer lipid permeability barrier and the localisation and roles of other cell envelope components, notably complex free lipids, lipoglycans, proteins and lipoproteins are also considered.
Abstract: A knowledge of the organisation of the rhodococcal cell envelope is of fundamental importance if the environmental and biotechnological significance of these bacteria are to be understood and succesfully exploited. The genus Rhodococcus belongs to a distinctive suprageneric taxon, the mycolata, which includes among others the genera Corynebacterium, Mycobacterium and Nocardia. Members of this taxon exhibit an unusual complexity in their cell envelope composition and organisation compared to other Gram-positive bacteria. Models that describe the architecture of the mycobacterial cell envelope are extrapolated here to provide a model of the rhodococcal cell envelope. The rhodococcal cell envelope is dominated by the presence of an arabinogalactan cell wall polysaccharide and large 2-alkyl 3-hydroxy branched-chain fatty acids, the mycolic acids, which are covalently assembled into a peptidoglycan–arabinogalactan–mycolic acid matrix. This review further emphasises that the mycolic acids in this complex form the basis of an outer lipid permeability barrier. The localisation and roles of other cell envelope components, notably complex free lipids, lipoglycans, proteins and lipoproteins are also considered.
TL;DR: The current knowledge of rhodococci relating to gene transfer, recombination, plasmid replication and functions, cloning vectors and reporter genes, gene expression and its control, bacteriophages, insertion sequences and genomic rearrangements is reviewed.
Abstract: Eubacteria of the genus Rhodococcus are a diverse group of microorganisms commonly found in many environmental niches from soils to seawaters and as plant and animal pathogens. They exhibit a remarkable ability to degrade many organic compounds and their economic importance is becoming increasingly apparent. Although their genetic organisation is still far from understood, there have been many advances in recent years. Reviewed here is the current knowledge of rhodococci relating to gene transfer, recombination, plasmid replication and functions, cloning vectors and reporter genes, gene expression and its control, bacteriophages, insertion sequences and genomic rearrangements. Further fundamental studies of Rhodococcus genetics and the application of genetic techniques to the these bacteria will be needed for their continued biotechnological exploitation.
TL;DR: The successful resuscitation of bacterial cultures under laboratory conditions may need rather strictly defined parameters if it is to be successfully performed for the majority of cells in a population.
Abstract: It has been found previously that a significant number of Micrococcus luteus cells starved in a prolonged stationary phase (up to 2 months) and then held on the bench at room temperature without agitation for periods of up to a further 2–7 months can be resuscitated in liquid media which contained (statistically) no initially-viable (colony-forming) cells but which were fortified with sterile supernatant from the late logarithmic phase of batch growth. Here it was found that such resuscitation can be done only within a defined time period after taking the first sample from such cultures, necessarily involving agitation of the cells. The duration of this period depends on the age of the starved culture: cells kept on the bench for 3 months possess a 2 month period of resuscitability while cells starved for 6 months can be resuscitated only within 10 days after the beginning of sampling. It is suggested that the input of oxygen to the starved cultures while they are agitated may exert a negative influence on the cells, since cultures stored in anaerobic conditions (under nitrogen) had a more prolonged ’survival' time. The cells which experienced between 10 and 60 days of starvation on the bench could be resuscitated, although the number of resuscitable cells depended strongly on the concentration of yeast extract in the resuscitation medium. This concentration for cells stored on the bench for more than 2 months was 0.05% while ’1-month-old‘ cells displayed a maximum resuscitability in the presence of 0.01% of yeast extract. Application of the fluorescent probe propidium iodide revealed the formation of cells with a damaged permeability barrier if resuscitation was performed by using concentrations of yeast extract of 0.1% and above. Thus the successful resuscitation of bacterial cultures under laboratory conditions may need rather strictly defined parameters if it is to be successfully performed for the majority of cells in a population.
TL;DR: The results indicate that bioaugmentation with catabolic plasmids may be a viable means to enhance the bioremediation of soils which lack an adequate intrinsic ability to degrade a given xenobiotic.
Abstract: Few studies have been done to evaluate the transfer of catabolic plasmids from an introduced donor strain to indigenous microbial populations as a means to remediate contaminated soils. In this work we determined the effect of the conjugative transfer of two 2,4-D degradative plasmids to indigenous soil bacterial populations on the rate of 2,4-D degradation in soil. We also assessed the influence of the presence of 2,4-D on the number of transconjugants formed. The two plasmids used, pEMT1k and pEMT3k, encode 2,4-D degradative genes (tfd) that differ in DNA sequence as well as gene organisation, and confer different growth rates to Ralstonia eutropha JMP228 when grown with 2,4-D as a sole carbon source. In an agricultural soil (Ardoyen) treated with 2,4-D (100 ppm) there were ca. 107CFU of transconjugants per gram bearing pEMT1k as well as a high number of pEMT3k bearing transconjugants (ca. 106 CFU/g). In this soil the formation of a high number of 2,4-D degrading transconjugants resulted in faster degradation of 2,4-D as compared to the uninoculated control soil. In contrast, only transconjugants with pEMT1k were detected (at a level of ca. 103 CFU/g soil) in the untreated Ardoyen soil. High numbers of transconjugants that carried pEMT1k were also found in a second experiment done using forest soil (Lembeke) treated with 100 ppm 2,4-D. However, unlike in the Ardoyen soil, no transconjugants with pEMT3k were detected and the transfer of plasmid pEMT1k to indigenous bacteria did not result in a higher rate of decrease of 2,4-D. This may be because 2,4-D was readily metabolised by indigenous bacteria in this soil. The results indicate that bioaugmentation with catabolic plasmids may be a viable means to enhance the bioremediation of soils which lack an adequate intrinsic ability to degrade a given xenobiotic.
TL;DR: Cell-free extracts of Nitrosomonas eutropha oxidized ammonia to nitrite with NO2 (N2O4) as electron acceptor with ammonia oxidation activity shown to be sensitive against oxygen and hydroxylamine occurred as an intermediate.
Abstract: Cell-free extracts of Nitrosomonas eutropha oxidized ammonia to nitrite with NO2 (N2O4) as electron acceptor. The ammonia oxidation activity was shown to be sensitive against oxygen. In the absence of oxygen ammonia and NO2 were consumed in a ratio of approximately 1:2 and hydroxylamine occurred as an intermediate. NO was released in amounts equimolar to the consumption of NO2. After passing the cell suspension through a French pressure cell and fractionating it by density gradient centrifugation using a linear sucrose gradient, two soluble and two membrane fractions were detectable. Highest ammonia oxidation activity was measured in the membrane fractions and highest hydroxylamine oxidation activity in the soluble fractions. The KS values of the ammonia oxidizing system in cell-free extracts was about 20 microns NH3 and remained unchanged between pH 7.25 to 8.25.
TL;DR: The promiscuous and selfish nature of plasmids is demonstrated by their ability to genetically engineer their host so that the host cell is best able to cope and survive in hostile environments.
Abstract: Studies on the origin and evolution of plasmids may provide valuable insights on the promiscuous nature of DNA. The first examples of the selfish nature of nucleic acids are exemplified by primordial oligoribonucleotides which evolved into primitive replicons. The propagation of these molecules were likely patterned after the current viral RNA ribozymes, which have been recently shown to possess RNA synthesizing and template mediated polymerizing capabilities in the absence of proteins. The parasitic nature of nucleic acids is depicted by satellite nucleic acid molecules associated with viruses. The satellite of adenovirus and tobacco ringspot virus serve as established examples: they contain no open reading frames. Comparative analysis of the replication origins of virions and plasmids show them to be conserved, originating from the simplest autocatalytic replicon to highly complex and evolved plasmids, replicating by a rolling circle mechanism. The eventual association of proteins with nucleic acids provided added efficiency and protective advantages for molecular perpetuation. The promiscuous and selfish nature of plasmids is demonstrated by their ability to genetically engineer their host so that the host cell is best able to cope and survive in hostile environments. Survival of the host ensures survival of the plasmid. Sequestering of genes by plasmids occurs when the environmental conditions negatively affect the host. The sequestering mechanism is fundamental and forms the outreach mechanisms to generate and propagate macromolecules of increasing size when necessary for survival. The level of sophistication of plasmids increases with the addition of new genes such as those that allow the host to occupy a specific environment normally inhospitable to the host cell. The vast range of plasmid types which have obtained genes interchangeably reflect the levels of sophistication achieved by these macromolecules. The Ti plasmid in Agrobacterium tumefaciens and the pSym and accessory plasmids in Rhizobium illustrate the level of complexity attained by replicons.
TL;DR: Several isolates belonging to the genus Rhodococcus have been shown in studies to be among the best candidates for acrylic acid preparation from acrylonitrile due to their stability and tolerance to high concentrations of this reactive and disruptive substrate.
Abstract: Rhodococci are ubiquitous in nature and their ability to metabolise a wide range of chemicals, many of which are toxic, has given rise to an increasing number of studies into their diverse use as biocatalysts. Indeed rhodococci have been shown to be especially good at degrading aromatic and aliphatic nitriles and amides and thus they are very useful for waste clean up where these toxic chemicals are present.
TL;DR: The crystal structure of one nitrile hydratase is now available and has revealed many interesting aspects of the enzyme structure in relationship to its catalytic activity and substrate selectivity.
Abstract: Rhodococci have been shown to be capable of a very wide range of biotransformations. Of these, the conversion of nitriles into amides or carboxylic acids has been studied in great detail because of the biotechnological potential of such activities. Initial investigations used relatively simple aliphatic nitriles. These studies were quickly followed by the examination of the regio- and stereoselective properties of the enzymes involved, which has revealed the potential synthetic utility of rhodococcal nitrile biotransforming enzymes. Physiological studies on rhodococci have shown the importance of growth medium design and bioreactor operation for the maximal conversion of nitriles. This in turn has resulted in some truly remarkable biotransformation activities being obtained, which have been successfully exploited for commercial organic syntheses (e.g. acrylamide production from acrylonitrile). The two main types of enzyme involved in nitrile biotransformations by rhodococci are nitrile hydratases (amide synthesis) and nitrilases (carboxylic acid synthesis with no amide intermediate released). It is becoming clear that many rhodococci contain both activities and multiple forms of each enzyme, often induced in a complex way by nitrogen containing molecules. The genes for many nitrile-hydrolysing enzymes have been identified and sequenced. The crystal structure of one nitrile hydratase is now available and has revealed many interesting aspects of the enzyme structure in relationship to its catalytic activity and substrate selectivity.
TL;DR: It is indicated that sporulation and the synthesis of sterigmatocystin are co-regulated at a step previous to the brlA execution point.
Abstract: We analyzed the regulation of sterigmatocystin biosynthesis in wild type and mutant strains of Emericella nidulans (= Aspergillus nidulans). A positive correlation between both asexual and sexual sporulation and synthesis of the mycotoxin was observed. Those conditions which favored sporulation stimulated sterigmatocystin formation, and vice versa. Both processes were stimulated by light in a + genetic background. In contrast, they were inhibited by diaminobutanone, an inhibitor of ornithine decarboxylase. The effect of this inhibitor was partially reverted by putrescine addition. Partial supplementation of specific requirements to auxotrophic mutants allowed normal vegetative growth, but interfered with asexual sporulation and sterigmatocystin biosynthesis. Synthesis of the mycotoxin was neither affected in a brlA mutant or in developmental mutants blocked at later steps in sporulation. As in wild type strain, diaminobutanone inhibited sterigmatocystin biosynthesis and cleisthotecia formation in the brlA mutant, and its effect was reverted by addition of putrescine. The inhibitor also affected the transcription of brlA. Our results indicate that sporulation and the synthesis of sterigmatocystin are co-regulated at a step previous to the brlA execution point.
TL;DR: The results indicated that functional prophage genomes may be a common constituent of all bacterial genomes of the investigated strains.
Abstract: Several collections of natural isolates of the genus Salmonella and of the species Escherichia coli were studied for the release of viable temperate phages. The results indicated that functional prophage genomes may be a common constituent of all bacterial genomes of the investigated strains. About 99% of the Salmonella phages are capable of generalized transduction of chromosomal host markers and plasmids. The ratio of transducing E. coli phages is significantly lower.
TL;DR: Results indicated that a general intraspecific genetic diversity was globally distributed among all the population, however a very high level of diversity was found among strains nodulating different Medicago sativa varieties.
Abstract: We analysed the genetic diversity of 270 Sinorhizobium meliloti strains isolated from nodules of three different Medicago sativa varieties, planted in three different Italian soils, combining the Analysis of Molecular Variance (AMOVA) with the Random Amplified Polymorphic DNA (RAPD) technique to estimate variance among RAPD patterns with the aim to draw an objective description of the population genetic structure. Results indicated that a general intraspecific genetic diversity was globally distributed among all the population, however a very high level of diversity was found among strains nodulating different Medicago sativa varieties. Moreover the distribution of the RAPD haplotypes among the plant varieties also showed to be non-random. The overall data indicated that the plant genotype is a major factor in shaping the genetic structure of this natural Rhizobium population.
TL;DR: Crosses between genetically marked strains, and pulse-field gel electrophoresis of the chromosomal DNA of cells derived from individual spores revealed evidence of karyogamy, meiosis and even recombination in the basidiomyceteous Phaffia rhodozyma.
Abstract: Sexual activity was induced in the basidiomyceteous Phaffia rhodozyma (Xanthophyllomyces dendrorhous) by depletion of nitrogen from the culture medium. This activity involved both mating between two yeast cells and the formation of basidiospores. Mating is possibly started by a G1 phase arrest of the cell cycle, as in other yeasts. The life cycle exhibited homothallic features. Crosses between genetically marked strains, and pulse-field gel electrophoresis of the chromosomal DNA of cells derived from individual spores revealed evidence of karyogamy, meiosis and even recombination. The segregation ratio in tetrads pointed to diploid vegetative cells, which formed tetraploid zygotes and the immediate meiosis then gave rise to diploid progenies again. Apart from the type strain Phaffia rhodozyma CBS 5905, all the examined strains were able to sporulate.
TL;DR: The regulatory signals involved as well as the proteins recruited indicate that Shigella induces the formation of an adherence plaque at the cell surface in order to achieve entry.
Abstract: The pathogenesis of shigellosis is characterized by the capacity of the causative microorganism, Shigella, to invade the epithelial cells that compose the mucosal surface of the colon in humans. The invasive process encompasses several steps which can be summarized as follows: entry of bacteria into epithelial cells involves signalling pathways that elicit a macropinocitic event. Upon contact with the cell surface, S. flexneri activates a Mxi/Spa secretory apparatus encoded by two operons comprising about 25 genes located on a large virulence plasmid of 220 kb. Through this specialized secretory apparatus, Ipa invasins are secreted, two of which (IpaB, 62 kDa and IpaC, 42 kDa) form a complex which is itself able to activate entry via its interaction with the host cell membrane. Interaction of this molecular complex with the cell surface elicits major rearrangements of the host cell cytoskeleton, essentially the polymerization of actin filaments that form bundles supporting the membrane projections which achieve bacterial entry. Active recruitment of the protooncogene pp 60c-src has been demonstrated at the entry site with consequent phosphorylation of cortactin. Also, the small GTPase Rho is controlling the cascade of signals that allows elongation of actin filaments from initial nucleation foci underneath the cell membrane. The regulatory signals involved as well as the proteins recruited indicate that Shigella induces the formation of an adherence plaque at the cell surface in order to achieve entry. Once intracellular, the bacterium lyses its phagocytic vacuole, escapes into the cytoplasm and starts moving the inducing polar, directed polymerization of actin on its surface, due to the expression of IcsA, a 120 kDa outer membrane protein, which is localized at one pole of the microorganism, following cleavage by SopA, a plasmid-encoded surface protease. In the context of polarized epithelial cells, bacteria then reach the intermediate junction and engage their components, particularly the cadherins, to form a protrusion which is actively internalized by the adjacent cell. Bacteria then lyse the two membranes, reach the cytoplasmic compartment again, and resume actin-driven movement.
TL;DR: Transfer of plasmid RP4 to indigenous bacteria in bulk soil could only be detected in soil with nutrient amendment and transfer efficiencies detected in the barley spermosphere were among the highest reported from any natural environment.
Abstract: Transfer of plasmid RP4 to indigenous bacteria in bulk soil could only be detected in soil with nutrient amendment. Lack of physiological active donor and recipient cells was apparently one of the limiting factors in un-amended bulk soil. Plasmid transfer was detected both in the spermosphere and rhizosphere of barley seedlings. Transfer occured from seed coated donor bacteria (i) to introduced recipient bacteria and (ii) to indigenous bacteria present in soil. Plasmid transfer was also detected from donor bacteria introduced to the soil to seed coated recipient bacteria. Transfer efficiencies in the rhizosphere were significantly below the transfer efficiencies obtained in the spermosphere. The transfer efficiencies detected in the barley spermosphere were among the highest reported from any natural environment.
TL;DR: A role played by cell surface modifications of Thiobacillus ferrooxidans is suggested in imparting the copper tolerance to the cells and bioleaching of sulphide minerals.
Abstract: A strain of Thiobacillus ferrooxidans was adapted to grow at higher concentrations of copper by single step culturing in the presence of 20 g/L (0.314 mol/L) cupric ions added to 9K medium. Exposure to copper results in change in the surface chemistry of the microorganism. The isoelectric point of the adapted strain (pI=4.7) was observed to be at a higher pH than that of the wild unadapted strain(pI=2.0). Compared to the wild strain, the copper adapted strain was found to be more hydrophobic and showed enhanced attachment efficiency to the pyrite mineral. The copper adsorption ability of the adapted strain was also found to be higher than that of the wild strain. Fourier transform infrared spectroscopy of adapted cells suggested that a proteinaceous new cell surface component is synthesized by the adapted strain. Treatment of adapted cells with proteinase-K, resulted in complete loss of tolerance to copper, reduction in copper adsorption and hydrophobicity of the adapted cells. These observations strongly suggest a role played by cell surface modifications of Thiobacillus ferrooxidans in imparting the copper tolerance to the cells and bioleaching of sulphide minerals.
TL;DR: Several CO2-responsive random promoter lacZ fusions of unknown function have been isolated from a marine Synechococcus and a Pseudoalteromonas sp.
Abstract: CO2 regulates gene expression across a diverse group of microorganisms including fungi, and both photosynthetic and non photosynthetic bacteria. The processes that CO2 regulates are diverse. Several CO2-responsive random promoter lacZ fusions of unknown function have been isolated from a marine Synechococcus and a Pseudoalteromonas sp., highlighting the wide effect of CO2 control in these organisms. Regulatory proteins have been described that mediate the CO2 response at transcription level in Bacillus anthracis, the group A streptococci and two Rhodobacter spp.. These regulatory proteins include: AcpA and AtxA that are involved in CO2 control of B. anthracis capsule and toxin production; Mga that regulates surface associated virulence factors in the group A streptococci; and RegB/A, a two component signal transduction system that responds to environmental stimuli including CO2, to regulate photosynthetic apparatus and CO2 fixation enzyme synthesis in Rhodobacter spp..
TL;DR: The increased understanding of bacterial behaviour that has resulted – and may further result – from these studies, can be used to fine-tune the beneficial activities of bacteria and/or more efficiently inhibit their deleterious ones.
Abstract: Among the signal transfer systems in bacteria two types predominate: two-component regulatory systems and quorum sensing systems. Both types of system can mediate signal transfer across the bacterial cell envelope; however, the signalling molecule typically is not taken up into the cells in the former type of system, whereas it usually is in the latter. The Two-component systems include the recently described (eukaryotic) phosphorelay systems; quorum sensing systems can be based upon autoinducers of the N-acylated homoserine lactones, and on autoinducers of a peptidic nature. A single bacterial cell contains many signalling modules that primarily operate in parallel. This may give rise to neural-network behaviour. Recently, however, for both types of basic signal transfer modules, it has been demonstrated that they also can be organised in series (i.e. in a hierarchical order). Besides their hierarchical position in the signal transduction network of the cell, the spatial distribution of individual signalling modules may also be an important factor in their efficiency in signal transfer. Many challenges lie hidden in future work to understand these signal transfer processes in more detail. These are discussed here, with emphasis on the mutual interactions between different signal transfer processes. Successful contributions to this work will require rigorous mathematical modelling of the performance of signal transduction components, and -networks, as well as studies on light-sensing signal transduction systems, because of the unsurpassed time resolution obtainable in those latter systems, the opportunity to apply repeated reproducible stimuli, etc. The increased understanding of bacterial behaviour that already has resulted--and may further result--from these studies, can be used to fine-tune the beneficial activities of bacteria and/or more efficiently inhibit their deleterious ones.
TL;DR: Heterologously expressed catR in vitro bound specifically to the intergenic region between catR and catA thereby providing a first indication for a possible involvement of CatR in the regulation of catechol catabolism.
Abstract: The catechol catabolic genes catABC from Rhodococcus opacus 1CP have previously been characterized by sequence analysis of the insert cloned on plasmid pRER1. Now, a 5.1-kb DNA fragment which overlaps with the insert of pRER1 was cloned, yielding pRER2, and subjected to sequencing. Besides three other open reading frames, a gene was detected ca 200 bp upstream of the catechol 1,2-dioxygenase gene catA, which is obviously transcribed divergently from catABC. The protein which can be deduced from this gene, CatR, resembles members of the PobR subfamily of IclR-type regulatory proteins. This finding was unexpected, as all catechol and chlorocatechol gene clusters known thus far from proteobacteria are under control of LysR-type regulators. It was not possible to inactivate catR by homologous recombination. However, heterologously expressed CatR in vitro bound specifically to the intergenic region between catR and catA thereby providing a first indication for a possible involvement of CatR in the regulation of catechol catabolism.
TL;DR: Phylogenetic analysis of nucleotide sequences from the D1/D2 domain of large subunit (26S) ribosomal DNA places C. arabinofermentans among the methanol-assimilating yeasts and most closely related to Candida ovalis.
Abstract: Candida arabinofermentans (type strain NRRL YB-2248, CBS 8468), a new yeast that ferments the pentose L-arabinose, is described. The three known strains of this new species were isolated from insect frass of pine and larch trees in the U.S. Phylogenetic analysis of nucleotide sequences from the D1/D2 domain of large subunit (26S) ribosomal DNA places C. arabinofermentans among the methanol-assimilating yeasts and most closely related to Candida ovalis. Strains of the new species produce 0.7-1.9 g/l ethanol from L-arabinose.