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Showing papers on "Bacteria published in 2001"


Journal ArticleDOI
TL;DR: The evolution of quorum sensing systems in bacteria could, therefore, have been one of the early steps in the development of multicellularity.
Abstract: ▪ Abstract Quorum sensing is the regulation of gene expression in response to fluctuations in cell-population density. Quorum sensing bacteria produce and release chemical signal molecules called autoinducers that increase in concentration as a function of cell density. The detection of a minimal threshold stimulatory concentration of an autoinducer leads to an alteration in gene expression. Gram-positive and Gram-negative bacteria use quorum sensing communication circuits to regulate a diverse array of physiological activities. These processes include symbiosis, virulence, competence, conjugation, antibiotic production, motility, sporulation, and biofilm formation. In general, Gram-negative bacteria use acylated homoserine lactones as autoinducers, and Gram-positive bacteria use processed oligo-peptides to communicate. Recent advances in the field indicate that cell-cell communication via autoinducers occurs both within and between bacterial species. Furthermore, there is mounting data suggesting that ba...

4,449 citations


Journal ArticleDOI
TL;DR: Changing the use of tetracyclines in human and animal health as well as in food production is needed if this class of broad-spectrum antimicrobials through the present century is to continue to be used.
Abstract: Tetracyclines were discovered in the 1940s and exhibited activity against a wide range of microorganisms including gram-positive and gram-negative bacteria, chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. They are inexpensive antibiotics, which have been used extensively in the prophlylaxis and therapy of human and animal infections and also at subtherapeutic levels in animal feed as growth promoters. The first tetracycline-resistant bacterium, Shigella dysenteriae, was isolated in 1953. Tetracycline resistance now occurs in an increasing number of pathogenic, opportunistic, and commensal bacteria. The presence of tetracycline-resistant pathogens limits the use of these agents in treatment of disease. Tetracycline resistance is often due to the acquisition of new genes, which code for energy-dependent efflux of tetracyclines or for a protein that protects bacterial ribosomes from the action of tetracyclines. Many of these genes are associated with mobile plasmids or transposons and can be distinguished from each other using molecular methods including DNA-DNA hybridization with oligonucleotide probes and DNA sequencing. A limited number of bacteria acquire resistance by mutations, which alter the permeability of the outer membrane porins and/or lipopolysaccharides in the outer membrane, change the regulation of innate efflux systems, or alter the 16S rRNA. New tetracycline derivatives are being examined, although their role in treatment is not clear. Changing the use of tetracyclines in human and animal health as well as in food production is needed if we are to continue to use this class of broad-spectrum antimicrobials through the present century.

3,647 citations


Journal ArticleDOI
25 Oct 2001-Nature
TL;DR: DNA microarrays show that gene expression in biofilm cells is similar to that in free-living cells but there are a small number of significant differences, which points to mechanisms of biofilm resistance to antibiotics.
Abstract: Bacteria often adopt a sessile biofilm lifestyle that is resistant to antimicrobial treatment. Opportunistic pathogenic bacteria like Pseudomonas aeruginosa can develop persistent infections. To gain insights into the differences between free-living P. aeruginosa cells and those in biofilms, and into the mechanisms underlying the resistance of biofilms to antibiotics, we used DNA microarrays. Here we show that, despite the striking differences in lifestyles, only about 1% of genes showed differential expression in the two growth modes; about 0.5% of genes were activated and about 0.5% were repressed in biofilms. Some of the regulated genes are known to affect antibiotic sensitivity of free-living P. aeruginosa. Exposure of biofilms to high levels of the antibiotic tobramycin caused differential expression of 20 genes. We propose that this response is critical for the development of biofilm resistance to tobramycin. Our results show that gene expression in biofilm cells is similar to that in free-living cells but there are a small number of significant differences. Our identification of biofilm-regulated genes points to mechanisms of biofilm resistance to antibiotics.

1,134 citations


Journal ArticleDOI
TL;DR: The fixation and long-term persistence of horizontally transferred genes suggests that they confer a selective advantage on the recipient organism, and the nature of this advantage remains unclear, but detailed examination of several cases of acquisition of eukaryotic genes by bacteria seems to reveal the evolutionary forces involved.
Abstract: Comparative analysis of bacterial, archaeal, and eukaryotic genomes indicates that a significant fraction of the genes in the prokaryotic genomes have been subject to horizontal transfer. In some cases, the amount and source of horizontal gene transfer can be linked to an organism's lifestyle. For example, bacterial hyperthermophiles seem to have exchanged genes with archaea to a greater extent than other bacteria, whereas transfer of certain classes of eukaryotic genes is most common in parasitic and symbiotic bacteria. Horizontal transfer events can be classified into distinct categories of acquisition of new genes, acquisition of paralogs of existing genes, and xenologous gene displacement whereby a gene is displaced by a horizontally transferred ortholog from another lineage (xenolog). Each of these types of horizontal gene transfer is common among prokaryotes, but their relative contributions differ in different lineages. The fixation and long-term persistence of horizontally transferred genes suggests that they confer a selective advantage on the recipient organism. In most cases, the nature of this advantage remains unclear, but detailed examination of several cases of acquisition of eukaryotic genes by bacteria seems to reveal the evolutionary forces involved. Examples include isoleucyl-tRNA synthetases whose acquisition from eukaryotes by several bacteria is linked to antibiotic resistance, ATP/ADP translocases acquired by intracellular parasitic bacteria, Chlamydia and Rickettsia, apparently from plants, and proteases that may be implicated in chlamydial pathogenesis.

1,118 citations


Journal ArticleDOI
TL;DR: To investigate the antimicrobial properties of phenolic compounds present in Finnish berries against probiotic bacteria and other intestinal bacteria, including pathogenic species.
Abstract: Aims: To investigate the antimicrobial properties of phenolic compounds present in Finnish berries against probiotic bacteria and other intestinal bacteria, including pathogenic species. Methods and Results: Antimicrobial activity of pure phenolic compounds representing flavonoids and phenolic acids, and eight extracts from common Finnish berries, was measured against selected Gram-positive and Gram-negative bacterial species, including probiotic bacteria and the intestinal pathogen Salmonella. Antimicrobial activity was screened by an agar diffusion method and bacterial growth was measured in liquid culture as a more accurate assay. Myricetin inhibited the growth of all lactic acid bacteria derived from the human gastrointestinal tract flora but it did not affect the Salmonella strain. In general, berry extracts inhibited the growth of Gram-negative but not Gram-positive bacteria. These variations may reflect differences in cell surface structures between Gram-negative and Gram-positive bacteria. Cloudberry, raspberry and strawberry extracts were strong inhibitors of Salmonella. Sea buckthorn berry and blackcurrant showed the least activity against Gram-negative bacteria. Conclusions: Different bacterial species exhibit different sensitivities towards phenolics. Significance and Impact of the Study: These properties can be utilized in functional food development and in food preservative purposes.

950 citations


Journal ArticleDOI
TL;DR: Criteria for in vitro selection of probiotic bacteria that may reflect certain in vivo effects on the host such as modulation of gastrointestinal tract microflora is developed.

904 citations


Journal ArticleDOI
TL;DR: Two 16S rRNA-directed oligonucleotide probes specific for the phylum and genus Nitrospira were developed and evaluated for suitability for fluorescence in situ hybridization (FISH) and used to investigate the in situ architecture of cell aggregates of Nitro Spira-like nitrite oxidizers in wastewater treatment plants.
Abstract: Uncultivated Nitrospira-like bacteria in different biofilm and activated-sludge samples were investigated by cultivation-independent molecular approaches. Initially, the phylogenetic affiliation of Nitrospira-like bacteria in a nitrifying biofilm was determined by 16S rRNA gene sequence analysis. Subsequently, a phylogenetic consensus tree of the Nitrospira phylum including all publicly available sequences was constructed. This analysis revealed that the genus Nitrospira consists of at least four distinct sublineages. Based on these data, two 16S rRNA-directed oligonucleotide probes specific for the phylum and genus Nitrospira, respectively, were developed and evaluated for suitability for fluorescence in situ hybridization (FISH). The probes were used to investigate the in situ architecture of cell aggregates of Nitrospira-like nitrite oxidizers in wastewater treatment plants by FISH, confocal laser scanning microscopy, and computer-aided three-dimensional visualization. Cavities and a network of cell-free channels inside the Nitrospira microcolonies were detected that were water permeable, as demonstrated by fluorescein staining. The uptake of different carbon sources by Nitrospira-like bacteria within their natural habitat under different incubation conditions was studied by combined FISH and microautoradiography. Under aerobic conditions, the Nitrospira-like bacteria in bioreactor samples took up inorganic carbon (as HCO3− or as CO2) and pyruvate but not acetate, butyrate, and propionate, suggesting that these bacteria can grow mixotrophically in the presence of pyruvate. In contrast, no uptake by the Nitrospira-like bacteria of any of the carbon sources tested was observed under anoxic or anaerobic conditions.

783 citations


Journal ArticleDOI
TL;DR: Results of rRNA gene surveys and lipid analyses of archaea and bacteria associated with methane seep sediments from several different sites on the Californian continental margin suggest that other bacteria and archaea are also involved in methane oxidation in these environments.
Abstract: The oxidation of methane in anoxic marine sediments is thought to be mediated by a consortium of methane-consuming archaea and sulfate-reducing bacteria. In this study, we compared results of rRNA gene (rDNA) surveys and lipid analyses of archaea and bacteria associated with methane seep sediments from several different sites on the Californian continental margin. Two distinct archaeal lineages (ANME-1 and ANME-2), peripherally related to the order Methanosarcinales, were consistently associated with methane seep marine sediments. The same sediments contained abundant 13C-depleted archaeal lipids, indicating that one or both of these archaeal groups are members of anaerobic methane-oxidizing consortia. 13C-depleted lipids and the signature 16S rDNAs for these archaeal groups were absent in nearby control sediments. Concurrent surveys of bacterial rDNAs revealed a predominance of delta -proteobacteria, in particular, close relatives of Desulfosarcina variabilis. Biomarker analyses of the same sediments showed bacterial fatty acids with strong 13C depletion that are likely products of these sulfate-reducing bacteria. Consistent with these observations, whole-cell fluorescent in situ hybridization revealed aggregations of ANME-2 archaea and sulfate-reducing Desulfosarcina and Desulfococcus species. Additionally, the presence of abundant 13C-depleted ether lipids, presumed to be of bacterial origin but unrelated to ether lipids of members of the order Desulfosarcinales, suggests the participation of additional bacterial groups in the methane-oxidizing process. Although the Desulfosarcinales and ANME-2 consortia appear to participate in the anaerobic oxidation of methane in marine sediments, our data suggest that other bacteria and archaea are also involved in methane oxidation in these environments.

656 citations


Journal Article
TL;DR: Nonpathogenic rhizobacteria can induce a systemic resistance in plants that is phenotypically similar to pathogen induced systemic acquired resistance and is effective under field conditions and offers a natural mechanism for biological control of plant disease.
Abstract: Nonpathogenic rhizobacteria can induce a systemic resistance in plants that is phenotypically similar to pathogen induced systemic acquired resistance Rhizobacteria mediated induced systemic resistance has been demonstrated against fungi,bacteria,and viruses in Arabidopis,bean,camation,cucumber,radish,tobacco and tomato under conditions in which the inducing bacteria and the challenging pathogen remained spatially separated Bacteria induce plants to produce the JA and ethylene to develop the ISR And ISR is effective under field conditions and offers a natural mechanism for biological control of plant disease

565 citations


Journal ArticleDOI
TL;DR: The accumulation of resistant bacteria by the use of antibiotics in agriculture and veterinary medicine and the spread of such bacteria via agriculture and direct contamination are documented.

499 citations


Journal ArticleDOI
TL;DR: The accessibility of bound aflatoxin B1 to an antibody in an indirect competitive inhibition enzyme-linked immunosorbent assay suggests that surface components of these bacteria are involved in binding.
Abstract: Specific lactic acid bacterial strains remove toxins from liquid media by physical binding. The stability of the aflatoxin B1 complexes formed with 12 bacterial strains in both viable and nonviable (heat- or acid-treated) forms was assessed by repetitive aqueous extraction. By the fifth extraction, up to 71% of the total aflatoxin B1 remained bound. Nonviable bacteria retained the highest amount of aflatoxin B1. Lactobacillus rhamnosus strain GG (ATCC 53103) and L. rhamnosus strain LC-705 (DSM 7061) removed aflatoxin B1 from solution most efficiently and were selected for further study. The accessibility of bound aflatoxin B1 to an antibody in an indirect competitive inhibition enzyme-linked immunosorbent assay suggests that surface components of these bacteria are involved in binding. Further evidence is the recovery of around 90% of the bound aflatoxin from the bacteria by solvent extraction. Autoclaving and sonication did not release any detectable aflatoxin B1. Variation in temperature (4 to 37°C) and pH (2 to 10) did not have any significant effect on the amount of aflatoxin B1 released. Binding of aflatoxin B1 appears to be predominantly extracellular for viable and heat-treated bacteria. Acid treatment may permit intracellular binding. In all cases, binding is of a reversible nature, but the stability of the complexes formed depends on strain, treatment, and environmental conditions. Food contaminants entering the body through the oral route are directly exposed to the action of gut microflora. Normal healthy intestinal microflora contains many strains of lactic acid bacteria (LAB), some of which have been isolated, ascribed health benefits, and termed probiotic strains (22). The protective effect of LAB against food mutagens such as heterocyclic amines, N-nitroso compounds, and aflatoxins has been reported (8, 12, 19, 24, 27). Many of these studies have involved Lactobacillus strains, and physical binding has been proposed as one mechanism of mutagen removal. This study focuses on the nature of the binding of aflatoxin B1 (AFB1) by 12 LAB strains. The potent mycotoxin AFB1 is a secondary metabolite of Aspergillus fungi that grow on a variety of food and feed commodities at any stage during growth, harvest, storage, and transportation. The occurrence of aflatoxin contamination is global, with severe problems especially prevalent in developing countries (11). Aflatoxins are of great concern because of their detrimental effects on the health of humans and animals, including carcinogenic, mutagenic, teratogenic, and immunosuppressive effects (3). Aflatoxins are also of industrial importance due to the economic losses resulting from condemnation of contaminated crops, cheese defects, and impaired growth and feed efficiency of animals fed contaminated feeds. Consequently there is a great demand for

Journal ArticleDOI
TL;DR: Investigations showed that auto-sterilization induced by relatively high temperatures (60-55 degrees C) caused a significant change in bacterial communities, and gram-positive bacteria, especially micrococcus, spores of bacilli, and fungal propagules survived, and reached high concentrations in the compost.

Journal ArticleDOI
TL;DR: The results of this study support the hypothesis that vaginal bacteria, not epithelial cells, are the primary source of lactic acid in the vagina.
Abstract: BACKGROUND: The origin of the lactic acid that acidifies the vagina is not well established. It is widely accepted that during times of high oestrogen (during the neonatal period and again during a woman’s reproductive years) large amounts of glycogen are deposited in the vaginal epithelium and that the glycogen is anaerobically metabolized to lactic acid. What is not established is whether lactic acid is primarily produced by vaginal bacteria or by vaginal epithelial cells. Human cells can make only L-lactate, while bacteria can produce both D- and L-, thus the D -t oL-lactate ratio can indicate the relative contribution of bacterially derived lactic acid. METHODS: In this study, we used chiral HPLC to examine the percentages of D- and L-lactate in vaginal secretions, in primary cultures of bacteria from these vaginal secretions, and in cultures of lactobacillus isolates of vaginal origin. RESULTS: We found that in most vaginal secretion samples, >50% of the lactic acid was the D-isoform (mean 55%, range 6–75%, n 14). CONCLUSIONS: Our results thus support the hypothesis that vaginal bacteria, not epithelial cells, are the primary source of lactic acid in the vagina.

Journal ArticleDOI
TL;DR: Determining the phylogenetic affiliation of sponge-associated microorganisms by 16S rRNA analysis facilitated the rational selection of culture media and isolation conditions to target specific groups of well-represented bacteria for laboratory culture.
Abstract: Molecular techniques were employed to document the microbial diversity associated with the marine sponge Rhopaloeides odorabile. The phylogenetic affiliation of sponge-associated bacteria was assessed by 16S rRNA sequencing of cloned DNA fragments. Fluorescence in situ hybridization (FISH) was used to confirm the presence of the predominant groups indicated by 16S rDNA analysis. The community structure was extremely diverse with representatives of the Actinobacteria, low-G+C gram-positive bacteria, the beta- and gamma-subdivisions of the Proteobacteria, Cytophaga/Flavobacterium, green sulfur bacteria, green nonsulfur bacteria, planctomycetes, and other sequence types with no known close relatives. FISH probes revealed the spatial location of these bacteria within the sponge tissue, in some cases suggesting possible symbiotic functions. The high proportion of 16S rRNA sequences derived from novel actinomycetes is good evidence for the presence of an indigenous marine actinomycete assemblage in R. odorabile. High microbial diversity was inferred from low duplication of clones in a library with 70 representatives. Determining the phylogenetic affiliation of sponge-associated microorganisms by 16S rRNA analysis facilitated the rational selection of culture media and isolation conditions to target specific groups of well-represented bacteria for laboratory culture. Novel media incorporating sponge extracts were used to isolate bacteria not previously recovered from this sponge.

Journal ArticleDOI
TL;DR: Bacterial binding of AFB1 by these strains was rapid, and more than 50% AFB1 was bound throughout a 72-h incubation period, which further support the ability of specific strains of lactic acid bacteria to bind selected dietary contaminants.

Journal ArticleDOI
TL;DR: Real-time PCR was used to quantify populations of ammonia-oxidizing bacteria representing the β subdivision of the classProteobacteria in samples of arable soil, both nitrogen fertilized and unfertilized from Mellby, Sweden, and showed that the concentration of template DNA released at various times remained constant after 10 to 100 s of bead beating.
Abstract: Real-time PCR was used to quantify populations of ammonia-oxidizing bacteria representing the β subdivision of the classProteobacteria in samples of arable soil, both nitrogen fertilized and unfertilized, from Mellby, Sweden. Primers and probes targeting a 16S ribosomal DNA region of the ammonia-oxidizing bacteria were designed and used. In the fertilized soil there were ∼6.2 × 107 ammonia-oxidizing bacteria per g of soil, three times more than the number of bacteria in the unfertilized soil. The lytic efficiency of bead beating in these soils was investigated by using populations of free or loosely attached bacteria, bacteria tightly bound to particles, and bacteria in nonfractionated samples. The shapes of the curves generated in these tests showed that the concentration of template DNA released at various times remained constant after 10 to 100 s of bead beating.

Journal ArticleDOI
TL;DR: This study indicates that the rhizosphere of salt marsh plants contains a diverse population of PAH-degrading bacteria, and the use of plant-associated microorganisms has the potential for bioremediation of contaminated sediments.
Abstract: Polycyclic aromatic hydrocarbon (PAH)-degrading bacteria were isolated from contaminated estuarine sediment and salt marsh rhizosphere by enrichment using either naphthalene, phenanthrene, or biphenyl as the sole source of carbon and energy. Pasteurization of samples prior to enrichment resulted in isolation of gram-positive, spore-forming bacteria. The isolates were characterized using a variety of phenotypic, morphologic, and molecular properties. Identification of the isolates based on their fatty acid profiles and partial 16S rRNA gene sequences assigned them to three main bacterial groups: gram-negative pseudomonads; gram-positive, non-spore-forming nocardioforms; and the gram-positive, spore-forming group, Paenibacillus. Genomic digest patterns of all isolates were used to determine unique isolates, and representatives from each bacterial group were chosen for further investigation. Southern hybridization was performed using genes for PAH degradation from Pseudomonas putida NCIB 9816-4, Comamonas testosteroni GZ42, Sphingomonas yanoikuyae B1, and Mycobacterium sp. strain PY01. None of the isolates from the three groups showed homology to the B1 genes, only two nocardioform isolates showed homology to the PY01 genes, and only members of the pseudomonad group showed homology to the NCIB 9816-4 or GZ42 probes. The Paenibacillus isolates showed no homology to any of the tested gene probes, indicating the possibility of novel genes for PAH degradation. Pure culture substrate utilization experiments using several selected isolates from each of the three groups showed that the phenanthrene-enriched isolates are able to utilize a greater number of PAHs than are the naphthalene-enriched isolates. Inoculating two of the gram-positive isolates to a marine sediment slurry spiked with a mixture of PAHs (naphthalene, fluorene, phenanthrene, and pyrene) and biphenyl resulted in rapid transformation of pyrene, in addition to the two- and three-ringed PAHs and biphenyl. This study indicates that the rhizosphere of salt marsh plants contains a diverse population of PAH-degrading bacteria, and the use of plant-associated microorganisms has the potential for bioremediation of contaminated sediments.

Journal ArticleDOI
TL;DR: D.L. COUTEAU, A.R. GIBSON, G. WILLIAMSON and C.B. FAULDS.
Abstract: hydroxycinnamic acids, in the human large intestine. Methods and Results: Thirty-five isolates recovered after anaerobic batch culture incubation of human faecal bacteria in a chlorogenic acid-based medium were screened for cinnamoyl esterase activity. Six isolates released the hydroxycinnamate, ferulic acid, from its ethyl ester in a plate-screening assay, and these were identified through genotypic characterization (16S rRNA sequencing) as Escherichia coli (three isolates), Bifidobacterium lactis and Lactobacillus gasseri (two strains). Chlorogenic acid hydrolysing activities were essentially intracellular. These cinnamoyl esterase-producing organisms were devoid of other phenolic-degrading activities. Conclusions: The results show that certain gut bacteria, including some already recognized as potentially health-promoting (i.e. species belonging to the genera Bifidobacterium and Lactobacillus), are involved in the release of bioactive hydroxycinnamic acids in the human colon. Significance and Impact of the Study: Free hydroxycinnamates, including caffeic, ferulic and p-coumaric acids, exhibit antioxidant and anticarcinogenic properties both in vitro and in animal models. Given that the gut flora has a major role in human nutrition and health, some of the beneficial effects of phenolic acids may be ascribed to the microflora involved in metabolism.

Journal ArticleDOI
TL;DR: The results obtained for biogenic amine production by bacteria in a synthetic medium suggest that amino acid-decarboxylase activity is strain dependent rather than being related to specific species.

Journal ArticleDOI
TL;DR: The isolates obtained produced the phytohormone indoleacetic acid (IAA) in pure culture and this IAA production was enhanced in growth medium containing tryptophan and maximum increase in the root and shoot weight over control was observed in the plantlets inoculated with strain SC20.
Abstract: We report the isolation of nitrogen fixing, phytohormone producing bacteria from sugarcane and their beneficial effects on the growth of micropropagated sugarcane plantlets. Detection of the nitrogen fixing bacteria by ARA-based MPN (acetylene reduction assay-based most probable number) method indicated the presence of up to 106 bacteria per gram dry weight of stem and 107 bacteria per gram dry weight of root of field-grown sugarcane. Two nitrogen fixing bacterial isolates were obtained from stem (SC11, SC20) and two from the roots (SR12, SR13) of field-grown plants. These isolates were identified as Enterobacter sp. strains on the basis of their morphological characteristics and biochemical tests. The isolate SC20 was further characterized by 16S rRNA sequence analysis, which showed high sequence similarity to the sequence of Enterobacter cloacae and Klebsiella oxytoca. All the isolates produced the phytohormone indoleacetic acid (IAA) in pure culture and this IAA production was enhanced in growth medium containing tryptophan. The bacterial isolates were used to inoculate micro-propagated sugarcane in vitro where maximum increase in the root and shoot weight over control was observed in the plantlets inoculated with strain SC20. By using the15N isotope dilution technique, maximum nitrogen fixation contribution (28% of total plant nitrogen) was detected in plantlets inoculated with isolate SC20.

Journal ArticleDOI
TL;DR: Focus is placed on how Salmonella orchestrates acid tolerance by modulating the activities or levels of diverse regulatory proteins in response to pH stress, which results in induction of overlapping arrays of acid shock proteins that protect the cell against acid and other environmental stresses.

Journal ArticleDOI
TL;DR: Novel thiols found in those bacteria lacking glutathione are included, including glutathion amide and its perthiol, produced by phototrophic purple sulfur bacteria and apparently involved in their sulfide metabolism.
Abstract: ▪ Abstract Glutathione metabolism is associated with oxygenic cyanobacteria and the oxygen-utilizing purple bacteria, but is absent in many other prokaryotes. This review focuses on novel thiols found in those bacteria lacking glutathione. Included are glutathione amide and its perthiol, produced by phototrophic purple sulfur bacteria and apparently involved in their sulfide metabolism. Among archaebacteria, coenzyme M (2-mercaptoethanesulfonic acid) and coenzyme B (7-mercaptoheptanoylthreonine phosphate) play central roles in the anaerobic production of CH4 and associated energy conversion by methanogens, whereas the major thiol in the aerobic phototrophic halobacteria is γ-glutamylcysteine. The highly aerobic actinomycetes produce mycothiol, a conjugate of N-acetylcysteine with a pseudodisaccharide of glucosamine and myo-inositol, AcCys-GlcNα(1 → 1)Ins, which appears to play an antioxidant role similar to glutathione. Ergothioneine, also produced by actinomycetes, remains a mystery despite many years of...

Journal ArticleDOI
TL;DR: The now available detailed insight into the organization of the Gram-positive protein secretion system and how it differs from the well-characterized system of Escherichia coli may in the future facilitate the exploitation of these organisms in the high level production of heterologous proteins.
Abstract: In contrast to Gram-negative bacteria, secretory proteins of Gram-positive bacteria only need to traverse a single membrane to enter the extracellular environment. For this reason, Gram-positive bacteria (e.g. various Bacillus species) are often used in industry for the commercial production of extracellular proteins that can be produced in yields of several grams per liter culture medium. The central components of the main protein translocation system (Sec system) of Gram-negative and Gram-positive bacteria show a high degree of conservation, suggesting similar functions and working mechanisms. Despite this fact, several differences can be identified such as the absence of a clear homolog of the secretion-specific chaperone SecB in Gram-positive bacteria. The now available detailed insight into the organization of the Gram-positive protein secretion system and how it differs from the well-characterized system of Escherichia coli may in the future facilitate the exploitation of these organisms in the high level production of heterologous proteins which, so far, is sometimes very inefficient due to one or more bottlenecks in the secretion pathway. In this review, we summarize the current knowledge on the various steps of the protein secretion pathway of Gram-positive bacteria with emphasis on Bacillus subtilis, which during the last decade, has arisen as a model system for the study of protein secretion in this industrially important class of microorganisms.

Journal ArticleDOI
TL;DR: The results suggest that some Cytophaga-like bacteria are also important in the decomposition of polymeric organic matter in the dissolved phase with implications for the accumu- lation of dissolved organic matter and pathways of carbon flow during phytoplankton blooms.
Abstract: The relationship between bacterial 16S rRNA gene composition and carbon metabolism was analyzed during an intense dinoflagellate bloom off the Southern California coast during the spring of 1997. Bacterial numbers and rate processes, chlorophyll a, and the dissolved and particulate organic matter pools were measured during the bloom to provide a framework within which to assess bacterial community composition. Free bacteria were numerically dominant, generally comprising >90% of the total, and were responsible for >70% of bacterial production. Attached bacteria had higher cell-specific growth rates than free bacteria (range = 0.5 to 15.1 and 0.7 to 2.5 d -1 , respectively) and had hydrolytic ectoenzyme activities at times more than an order of magnitude higher on a per cell basis. Denaturing gradient gel electrophoresis analysis of bacterial community composition indi- cated that: (1) the free and attached communities were distinct, and (2) marked shifts in bacterial community structure occurred concomitant with the peaks in attached enzyme activities, specific growth rates and DOC concentration. Of the 24 16S rDNA clones analyzed, 7 were related to the Cytophaga-like bacteria (CLB), 6 to the α-subclass and 5 to the γ-subclass of the Proteobacteria; 3 were related to oxygenic phototrophs, 2 were heteroduplexes and 1 was a possible chimera. While the α- and γ-Proteobacteria predominated in the <1.0 µm fraction, CLB were identified in both the free and attached fractions as well as among bacteria cultured from the same water, without overlap among these groups. The observation that distinct Cytophaga group sequences were present in the free versus attached fractions is counter to the current understanding that these organisms occupy a principally 'particle-specialist' niche. Our results suggest that some CLB are also important in the decomposition of polymeric organic matter in the dissolved phase with implications for the accumu- lation of dissolved organic matter and pathways of carbon flow during phytoplankton blooms.

Journal ArticleDOI
TL;DR: To investigate the populations of Bacteria and Archaea associated with metal-rich sediments from Green Bay, WI, nucleic acids were extracted and the phylogenetic relationships of cloned 16S rRNA genes were analysed.
Abstract: Biology is believed to play a large role in the cycling of iron and manganese in many freshwater environments, but specific microbial groups indigenous to these systems have not been well characterized. To investigate the populations of Bacteria and Archaea associated with metal-rich sediments from Green Bay, WI, we extracted nucleic acids and analysed the phylogenetic relationships of cloned 16S rRNA genes. Because nucleic acids have not been routinely extracted from metal-rich samples, we investigated the bias inherent in DNA extraction and gene amplification from pure MnO2 using defined populations of whole cells or naked DNA. From the sediments, we screened for manganese-oxidizing bacteria using indicator media and found three isolates that were capable of manganese oxidation. In the phylogenetic analysis of bacterial 16S rRNA gene clones, we found two groups related to known metal-oxidizing genera, Leptothrix of the beta-Proteobacteria and Hyphomicrobium of the alpha-Proteobacteria, and a Fe(III)-reducing group related to the Magnetospirillum genus of the alpha-Proteobacteria. Groups related to the metal-reducing delta-Proteobacteria constituted 22% of the gene clones. In addition, gene sequences from one group of methanogens and a group of Crenarchaeota, identified in the archaeal gene clone library, were related to those found previously in Lake Michigan sediments.

Journal ArticleDOI
TL;DR: A microbial map of the 25 sourdoughs was plotted showing characteristic associations among lactic acid bacteria and differences in the lactic Acid bacteria species which were mainly due to the species of wheat flour, use of bakers yeast and type of bread.

Journal ArticleDOI
TL;DR: Survival of rainbow trout infected with vibriosis was improved 13-43% by six out of nine antagonistic strains tested in vivo, and the addition of live bacterial cultures to fish-rearing water may improve survival of the fish; however, in vitro antagonism could not completely predict an in vivo effect.
Abstract: The antibacterial properties of the indigenous microflora of rainbow trout (Oncorhynchus mykiss Walbaum) and the potential use of inhibitory bacteria as fish probiotics were investigated. A total of 1018 bacteria and yeasts were isolated on tryptone soy agar (TSA) from skin, gills and intestine. Forty-five of these inhibited growth of the fish pathogenic bacterium Vibrio anguillarum in a well diffusion assay. The antagonism was most prominent among Pseudomonas spp., as 28 (66%) of the antagonistic bacteria belonged to this genus, despite constituting only 15% of the total tested flora. As pseudomonads are typically siderophore producers, chrome azurol S (CAS) agar was used as a semi-selective medium for isolation of antagonistic bacteria. On this medium, 75% of the iron-chelating strains were inhibitory to V. anguillarum. Eight strains out of a subset of 11 antagonists caused a 3-6 log unit reduction in the density of V. anguillarum [measured by polymerase chain reaction (PCR) detection in a most probable number (MPN) regimen] in a broth co-culture assay. Survival of rainbow trout infected with vibriosis was improved 13-43% by six out of nine antagonistic strains tested in vivo. All disease-protecting strains were pseudomonads, isolated from CAS plates, whereas two Carnobacterium spp. that were antagonistic in in vitro well diffusion assays did not alter the accumulated mortality of rainbow trout. The addition of live bacterial cultures to fish-rearing water may thus improve survival of the fish; however, in vitro antagonism could not completely predict an in vivo effect. Further studies on the underlying mechanism of activity are required to design appropriate selection criteria for fish probiotic bacteria.

Journal ArticleDOI
TL;DR: It is concluded that n-hexane is activated at its second carbon atom by a radical reaction and presumably added to fumarate as a cosubstrate, yielding MPS as the first stable product.
Abstract: Alkanes as metabolites from organisms (10) and constituents of petroleum (49) and its refined products are widespread compounds in our environment. Containing exclusively apolar ς-bonds, alkanes are among the chemically least reactive compounds. Bacteria and fungi that utilize alkanes as growth substrates in the presence of molecular oxygen have been known for about 100 years (14, 15). Aerobic microorganisms all initiate the metabolism of alkanes by monooxygenase reactions. These enzymes generate a highly reactive oxygen species by partial reduction of O2, resulting in the introduction of a hydroxyl group into the alkane molecule by a radical mechanism (22, 51). The alkanol formed is further oxidized and metabolized via the β-oxidation pathway. It was shown only relatively recently that special types of bacteria, which are physiologically and phylogenetically distinct from previously described aerobic hydrocarbon-degrading microorganisms, degrade n-alkanes under strict exclusion of oxygen. n-Alkanes were anaerobically oxidized in pure cultures using sulfate (2, 3, 41, 43) or nitrate (18) as the electron acceptor or in enrichment cultures with sulfate (16) or nitrate (13, 39). Also, anaerobic conversion of long-chain n-alkanes to methane and CO2 in associations of enriched bacteria and archaea was demonstrated (4, 55). Oxidation of the isoprenoid-like alkane 2,5,9,13-tetramethylpentadecane (pristane) was demonstrated in a nitrate-reducing bacterial community (13). None of the hitherto isolated alkane-degrading anaerobic bacteria utilize aromatic hydrocarbons such as toluene, whereas anaerobic bacteria that degrade aromatic hydrocarbons do not utilize alkanes (24). First investigations into the anaerobic metabolism of n-alkanes were conducted with two phylogenetically related sulfate-reducing bacteria, strains Hxd3 and Pnd3 (3). Adaptation studies and analysis of cellular fatty acids with strain Hxd3 suggested that anaerobic degradation of alkanes does not occur via desaturation to 1-alkenes, a questionable mechanism that has been speculated about in some early studies on the possibility of anaerobic n-alkane degradation (for an overview, see reference 3). Strain Hxd3 formed mainly C-odd cellular fatty acids during growth with n-hexadecane and C-even cellular fatty acids during growth with n-heptadecane. One explanation for these fatty acid patterns was the assumption of an alteration in the carbon chain length during the initial anaerobic reactions by a C-odd carbon unit, e.g., by terminal addition of a one-carbon moiety. In strain Pnd3, however, cellular fatty acids were mainly C-even upon growth with C-even alkanes and mainly C-odd upon growth with C-odd alkanes; in addition, unidentified fatty acids were formed. The findings suggested different modes of initial reactions in the two n-alkane-degrading sulfate-reducing strains (3). Still, a common principle in the mechanism of initial reactions of n-alkanes in both strains was considered by assuming that the site of carbon addition may also be the subterminal position in the chain (3). In a third isolate of an n-alkane-degrading sulfate-reducing bacterium (strain AK-01), the n-alkanes serving as growth substrates influenced the pattern of cellular fatty acids in a similar manner as in strain Pnd3; in addition, 2-, 4-, and 6-methyl-branched fatty acids were identified (44). By labeling studies, the methyl branch of the fatty acids was shown to be the original terminal carbon of the n-alkane, suggesting addition of a carbon compound to the subterminal position (carbon-2) of the n-alkanes; the carboxyl group was not derived from bicarbonate (44). So far, no metabolites have been detected that could represent the direct product of the initial anaerobic reaction of an n-alkane. The present study was undertaken to identify such a metabolite and to gain insights into the mechanism of its formation. For the experiments, the recently isolated denitrifying strain HxN1 (18) was chosen. In contrast to other n-alkane-degrading anaerobic bacteria, strain HxN1 grows relatively rapidly (doubling time of 11 h under optimal conditions) and does not adhere to the insoluble alkane phase, so that cells can be harvested easily. Strain HxN1 utilizes n-alkanes with relatively short chains (C6 through C8) that are oxidized to CO2; other anaerobic n-alkane-degrading strains grow preferentially with chain lengths between C8 and C18. Recently, two-dimensional gel electrophoresis of cell extracts of strain HxN1 revealed specific formation of proteins during growth on n-hexane that were not formed on n-hexanoate. These proteins were therefore supposed to be specifically involved in initial reaction steps of n-alkanes. In the N terminus, one of these proteins exhibited a similarity to the small subunit (BssC) of benzylsuccinate synthase in denitrifying bacteria (A. Behrends, P. Ehrenreich, J. Heider, T. Hurek, S. Ratering, and F. Widdel, unpublished data). This enzyme activates toluene anaerobically by addition of the methyl group to fumarate, yielding benzylsuccinate (24), and there is evidence for the involvement of a glycyl radical in this reaction (17, 31; C. Leutwein, A. J. Pierik and J. Heider, personal communication). Hence, we expected a parallel between the mechanism of the initial reaction of n-alkanes and that of toluene in anaerobic bacteria. Still, a reaction of an alkane in the absence of oxygen would present a novel type of biochemical mechanism, because a saturated hydrocarbon is much less reactive than toluene. In this paper, we report the identification of (1-methylpentyl)succinate (MPS) formed during strictly anaerobic growth of strain HxN1 with nitrate and with n-hexane as the only organic substrate. Furthermore, an electron paramagnetic resonance (EPR) signal characteristic of a glycyl radical was detected in n-hexane-grown cells of strain HxN1. We therefore propose the formation of MPS from n-hexane and fumarate via a radical mechanism as the initial reaction in strain HxN1.

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TL;DR: During their passage through the digestive tract of sterile grown maggots, the majority of E. coli was destroyed in the midgut, indicating that the feces were either sterile or contained only small numbers of bacteria.
Abstract: Green fluorescent protein-producing Escherichia coli were used to investigate the fate of bacteria in the alimentary tract of sterile grown maggots, Lucilia sericata (Meigen), using a laser scanning confocal microscope. A computer program was used to analyze the intensity of the fluorescence and to quantify the number of bacteria. The crop and the anterior midgut were the most heavily infected areas of the intestine. A significant decrease in the amount of bacteria was observed in the posterior midgut. The number of bacteria decreased even more significantly in the anterior hindgut and practically no bacteria were seen in the posterior end, near the anus. The viability of bacteria in the different gut sections was examined. It was shown that 66.7% of the crops, 52.8% of the midguts, 55.6% of the anterior hindguts, and 17.8% of posterior hindguts harbored living bacteria. In conclusion, during their passage through the digestive tract the majority of E. coli was destroyed in the midgut. Most of the remaining bacteria were killed in the hindgut, indicating that the feces were either sterile or contained only small numbers of bacteria.

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TL;DR: Phylogenetic analysis suggests that all NAD+‐dependent DNA ligases are closely related, but the ATP‐dependent enzymes have been acquired by Bacterial genomes on a number of separate occasions.
Abstract: DNA ligases join breaks in the phosphodiester backbone of DNA molecules and are used in many essential reactions within the cell. All DNA ligases follow the same reaction mechanism, but they may use either ATP or NAD+ as a cofactor. All Bacteria (eubacteria) contain NAD+-dependent DNA ligases, and the uniqueness of these enzymes to Bacteria makes them an attractive target for novel antibiotics. In addition to their NAD+-dependent enzymes, some Bacteria contain genes for putative ATP-dependent DNA ligases. The requirement for these different isozymes in Bacteria is unknown, but may be related to their utilization in different aspects of DNA metabolism. The putative ATP-dependent DNA ligases found in Bacteria are most closely related to proteins from Archaea and viruses. Phylogenetic analysis suggests that all NAD+-dependent DNA ligases are closely related, but the ATP-dependent enzymes have been acquired by Bacterial genomes on a number of separate occasions.