Iron-coproporphyrin III is a natural cofactor in bacterioferritin from the anaerobic bacterium Desulfovibrio desulfuricans

A bacterioferritin was recently isolated from the anaerobic sulphate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 [Romão et al. (2000) Biochemistry 39, 6841–6849]. Although its properties are in general similar to those of the other bacterioferritins, it contains a haem quite distinct from the haem B, found in bacterioferritins from aerobic organisms. Using visible and NMR spectroscopies, as well as mass spectrometry analysis, the haem is now unambiguously identified as iron-coproporphyrin III, the first example of such a prosthetic group in a biological system. This unexpected finding is discussed in the framework of haem biosynthetic pathways in anaerobes and particularly in sulphate-reducing bacteria.     

Identification of sulphate-reducing ectosymbiotic bacteria from anaerobic ciliates using 16S rRNA binding oligonucleotide probes

The identity of ectosymbiotic bacteria of some marine, free-living anacrobic ciliates (Metopus contortus, Caenomorpha levanderi and Parablepharisma sp.) was studied using fluorescent-dye-conjugated oligonucleotides complementary to short sequence elements of 16S ribosomal RNA. The ectosymbiotic bacteria of all species hybridized with a eubacterial probe and those of the two former mentioned species hybridized with a general probe for sulphate-reducing bacteria, but not to a probe specific for Desulfobacter. The results support indirect evidence suggesting that ectosymbiotic bacteria of anaerobic ciliates are sulphate-reducers which depend on host metabolites for substrates.Abbreviations DMSO dimethyl sulfoxide - PBS phosphate-buffered saline, 137 mM NaCl, 2.7 mM KCl, 4.3 mM Na₂HPO₄, 1.4 mM KH₂PO₄, pH: 7.3 - TEAA triethylamonium acetate - 1 x SSC standard sodium citrate buffer, 150 mM NaCl, 15 mM Na₂ citrate, pH: 7.0 - 1 x Denh Denhardts solution, 0.02% ficoll, 0.02% bovine serum albumine, 0.02% polyvinol-pyralidone     

Molecular analysis of a sulphate-reducing consortium used to treat metal-containing effluents

A sulphate-reducing consortium used in a bioprocess to remove toxic metals from solution as insoluble sulphides, was characterised using molecular (PCR-based) and traditional culturing techniques. After prolonged cultivation under anoxic biofilm-forming conditions, the mixed culture contained a low diversity of sulphate-reducing bacteria, dominated by one strain closely related to Desulfomicrobium norvegicum, identified by three independent PCR-based analyses. The genetic targets used were the 16S rRNA gene, the 16S-23S rRNA gene intergenic spacer region and the disulfite reductase (dsr) gene, which is conserved amongst all known sulphate-reducing bacteria. This organism was also isolated by conventional anaerobic techniques, confirming its presence in the mixed culture. A surprising diversity of other non-sulphate-reducing facultative and obligate anaerobes were detected, supporting a model of the symbiotic/commensal nature of carbon and energy fluxes in such a mixed culture while suggesting the physiological capacity for a wide range of biotransformations by this stable microbial consortium.     

Isolation and characterization of sulphate-reducing bacteria <Emphasis Type="Italic">Desulfovibrio vulgaris</Emphasis> from Vajreshwari thermal springs in Maharashtra,India

Sulphate-reducing bacteria (SRB) in the thermal springs of Vajreshwari were investigated with combined microbiological and molecular approaches. A sulphate-reducing bacteria medium containing lactate was used for enrichment and isolation, which yielded Gram negative, rod shaped, anaerobic, non-spore forming and motile bacteria capable of reducing sulphate to sulphide. These grew at temperatures ranging from 25 to 55 °C and could use pyruvate, lactate and ethanol as electron donors. Desulfoviridin was detected in all the isolates. The partial 16S rRNA and dissimilatory sulphite reductase (DSR) gene sequences of five representative isolates revealed that the strains belonged to the sulphur reducing bacterial species Desulfovibrio vulgaris.     

Anaerobically grown <Emphasis Type="Italic">Thauera aromatica</Emphasis>, <Emphasis Type="Italic">Desulfococcus multivorans</Emphasis>, <Emphasis Type="Italic">Geobacter sulfurreducens</Emphasis> are more sensitive towards organic solvents than aerobic bacteria

The effect of seven important pollutants and three representative organic solvents on growth of Thauera aromatica K172, as reference strain for nitrate-reducing anaerobic bacteria, was investigated. Toxicity in form of the effective concentrations (EC50) that led to 50% growth inhibition of potential organic pollutants such as BTEX (benzene, toluene, ethylbenzene, and xylene), chlorinated phenols and aliphatic alcohols on cells was tested under various anaerobic conditions. Similar results were obtained for Geobacter sulfurreducens and Desulfococcus multivorans as representative for Fe³⁺-reducing and sulphate-reducing bacteria, respectively, leading to a conclusion that anaerobic bacteria are far more sensitive to organic pollutants than aerobic ones. Like for previous studies for aerobic bacteria, yeast and animal cell cultures, a correlation between toxicity and hydrophobicity (log P values) of organic compounds for different anaerobic bacteria was ascertained. However, compared to aerobic bacteria, all three tested anaerobic bacteria were shown to be about three times more sensitive to the tested substances.     

Toxic effects of toluene on the growth of activated sludge bacteria

Two bacteria were isolated from the activated sludge sample of a wastewater treatment plant in Dublin by enrichment culture technique with toluene as the sole source of carbon and energy. They were identified as Aeromonas caviae (To-4) and Pseudomonas putida (To-5). The growth of these bacteria depended on the manner in which toluene was supplied. In general, growth was better when toluene was supplied in the vapour phase. When toluene was added directly to the growth medium it was found to be toxic to the organisms but the toxic effect could be alleviated in the presence of other carbon sources and by the acclimation of the cells. The growth of To-4 on toluene has never been previously reported.     

Quorum Sensing,or How Bacteria “Talk” to Each Other

Reviewed are recent advances in studying the quorum-sensing systems, which regulate gene expression depending on population density. Low-molecular-weight acyl derivatives of L-homoserine lactone (N-AHL) freely diffuse through cell membranes and determine cell-to-cell communication in bacteria. The quorum-sensing systems have first been found to regulate bioluminescence in marine bacteria Photobacterium(Vibrio) fischeriand Vibrio harveyi. Such systems are widespread and control expression of genes for virulence factors, proteases, antibiotics, etc., in various Gram-negative bacteria, including plant, animal, and human pathogens. Quorum sensing is a prominent example of social behavior in bacteria, as signal exchange among individual cells allows the entire population to choose an optimal way of interaction with the environment and with higher organisms.     

Incidence of <Emphasis Type="Italic">Wolbachia</Emphasis> and <Emphasis Type="Italic">Cardinium</Emphasis> endosymbionts in the <Emphasis Type="Italic">Osmia</Emphasis> community in Korea

Sex ratio distorting endosymbionts induce reproductive anomalies in their arthropod hosts. They have recently been paid much attention as firstly texts of evolution of host-symbiont relationships and secondly potential biological control agents to control arthropod pests. Among such organisms, Wolbachia and Cardinium bacteria are well characterized. This study aims at probing such bacteria in the Osmia community to evaluate their potential utilization to control arthropod pests. Among 17 PCR tested species, Osmia cornifrons and a parasitic fly are infected with Wolbachia and a mite species is infected with Cardinium. Phylogenetic tree analyses suggest that horizontal transfer of the bacteria occurred between phylogenetically distant hosts.     

Activity of an isothiazolone biocide against Hormoconis resinae in pure and mixed biofilms

Biofilms containing single or mixed cultures of the fungus Hormoconis resinae and anaerobic sulphate-reducing bacteria (SRB) on stainless steel were incubated with an isothiazolone biocide (Kathon FP) at 28°C for 24 h. H. resinae within the biofilm was enumerated by immunofluorescence microscopy using specific antiserum, and SRB were assayed by culture. Fungal numbers in mixed biofilms were considerably reduced in comparison with those in pure biofilms. The biocide was shown to be effective against H. resinae in pure biofilms at 50 and 100 ppm, but in mixed biofilms only at the higher concentration. This concentration also reduced the sessile SRB numbers by 99%.P.S. Guiamet is with the Sección Biolectroquimica, INIFTA, Suc. 4, C.C. 16, 1900 La Plata, Argentina. C.C Gaylarde is with the Departamento de Solos, Fac. de Agronomia, UFRGS, Av. Bento Gonçalves, 7712, 91540-000 Porto Alegre, RS, Brazil     

Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria

Based upon their photosynthetic nature and the presence of a unique light-harvesting antenna structure, the chlorosome, the photosynthetic green bacteria are defined as a distinctive group in the Bacteria. However, members of the two taxa that comprise this group, the green sulfur bacteria (Chlorobi) and the filamentous anoxygenic phototrophic bacteria (Chloroflexales), are otherwise quite different, both physiologically and phylogenetically. This review summarizes how genome sequence information facilitated studies of the biosynthesis and function of the photosynthetic apparatus and the oxidation of inorganic sulfur compounds in two model organisms that represent these taxa, Chlorobium tepidum and Chloroflexus aurantiacus. The genes involved in bacteriochlorophyll (BChl) c and carotenoid biosynthesis in these two organisms were identified by sequence homology with known BChl a and carotenoid biosynthesis enzymes, gene cluster analysis in Cfx. aurantiacus, and gene inactivation studies in Chl. tepidum. Based on these results, BChl a and BChl c biosynthesis is similar in the two organisms, whereas carotenoid biosynthesis differs significantly. In agreement with its facultative anaerobic nature, Cfx. aurantiacus in some cases apparently produces structurally different enzymes for heme and BChl biosynthesis, in which one enzyme functions under anoxic conditions and the other performs the same reaction under oxic conditions. The Chl. tepidum mutants produced with modified BChl c and carotenoid species also allow the functions of these pigments to be studied in vivo.     

Culturable heterotrophic bacteria from the marine sponge <Emphasis Type="Italic">Dendrilla</Emphasis> <Emphasis Type="Italic">nigra</Emphasis>: isolation and phylogenetic diversity of actinobacteria

Culturable heterotrophic bacterial composition of marine sponge Dendrilla nigra was analysed using different enrichments. Five media compositions including without enrichment (control), enriched with sponge extract, with growth regulator (antibiotics), with autoinducers, and complete enrichment containing sponge extract, antibiotics, and autoinducers were developed. DNA hybridization assay was performed to explore host specific bacteria and ecotypes of culturable sponge-associated bacteria. Enrichment with selective inducers (AHLs and sponge extract) and regulators (antibiotics) considerably enhanced the cultivation potential of sponge-associated bacteria. It was found that Marinobacter (MSI032), Micromonospora (MSI033), Streptomyces (MSI051), and Pseudomonas (MSI057) were sponge-associated obligate symbionts. The present findings envisaged that “Micromonospora–Saccharomonospora–Streptomyces” group was the major culturable actinobacteria in the marine sponge D. nigra. The DNA hybridization assay was a reliable method for the analysis of culturable bacterial community in marine sponges. Based on the culturable community structure, the sponge-associated bacteria can be grouped (ecotypes) as general symbionts, specific symbionts, habitat flora, and antagonists.     

Oxidation of short-chain fatty acids by sulfate-reducing bacteria in freshwater and in marine sediments

Colony counts of acetate-, propionate- and l-lactate-oxidizing sulfate-reducing bacteria in marine sediments were made. The vertical distribution of these organisms were equal for the three types considered. The highest numbers were found just beneath the border of aerobic and anaerobic layers.Anaerobic mineralization of acetate, propionate and l-lactate was studied in the presence and in the absence of sulfate. In freshwater and in marine sediments, acetate and propionate were oxidized completely with concomitant reduction of sulfate. l-Lactate was always fermented. Lactate-oxidizing, sulfate-reducing bacteria, belonging to the species Desulfovibrio desulfuricans, and lactate-fermenting bacteria were found in approximately equal amounts in the sediments. Acetate-oxidizing, sulfate-reducing bacteria could only be isolated from marine sediments, they belonged to the genus Desulfobacter and oxidized only acetate and ethanol by sulfate reduction. Propionate-oxidizing, sulfate-reducing bacteria belonged to the genus Desulfobulbus. They were isolated from freshwater as well as from marine sediments and showed a relatively large range of usable substrates: hydrogen, formate, propionate, l-lactate and ethanol were oxidized with concomitant sulfate reduction. l-Lactate and pyruvate could be fermented by most of the isolated strains.     

Evaluation of antimicrobial activity of the lichens <Emphasis Type="Italic">Lasallia pustulata,Parmelia sulcata,Umbilicaria crustulosa</Emphasis>, and <Emphasis Type="Italic">Umbilicaria cylindrica</Emphasis>

The antimicrobial properties of acetone, methanol, and aqueous extracts of the lichens Lasallia pustulata, Parmelia sulcata, Umbilicaria crustulosa, and Umbilicaria cylindrica were studied comparatively in vitro. Antimicrobial activities of the extracts of different lichens were estimated by the disk diffusion test for Gram-positive bacteria, Gram-negative bacteria, and fungal organisms, as well as by determining the MIC (minimal inhibitory concentration). The obtained results showed that the acetone and methanol extracts of Lasallia pustulata, Parmelia sulcata, and Umbilicaria crustulosa manifest antibacterial activity against the majority of species of bacteria tested, in addition to selective antifungal activity. The MIC of lichen extracts was lowest (0.78 mg/ml) for the acetone extract of Lasallia pustulata against Bacillus mycoides. Aqueous extracts of all of the tested lichens were inactive. Extracts of the lichen Umbilicaria cylindrica manifested the weakest activity, inhibiting only three of the tested organisms.     

Change of Microbial Populations in a Suspended-sludge Reactor Performing Completely Autotrophic N-removal

Summary In recent years, several novel processes for N-removal almost without consumption of organic carbon under oxygen-limited conditions have been discovered, which may be a promising option for low-cost N-removal from ammonia-rich wastewater. In this study, a laboratory scale suspended-sludge reactor was continuously operated under low dissolved oxygen concentration. High N-removal efficiency and subsequently degradation of the reactor were observed. Molecular analysis based on a partial-16S rRNA gene library showed that, at the stage of high efficiency, the biomass was composed of Planctomycete-like bacteria (up to 40%) and heterotrophic organisms (approximately 60%) as well as a few ammonia-oxidizing bacteria and at the stage of degradation, the autotrophic ammonia-oxidizing bacteria were dominant (up to 70%) and Planctomycete-like bacteria were no longer found in the sludge. Three specific Planctomycete-16S rRNA-targeted probes were used for fluorescence in situ hybridization (FISH). The results showed that at the high-efficiency stage, Planctomycete-like bacteria, present at approximately 20% of the total bacteria, lay frequently in the middle of flocs, while the heterotrophic bacteria occurred within the outer layers. This work revealed that the change of the microbial populations is the key reason for reactor deterioration, and the heterotrophic bacteria probably play an important role in sustaining the biomass structure of the sludge.     

Competition for limiting amounts of oxygen between Nitrosomonas europaea and Nitrobacter winogradskyi grown in mixed continuous cultures

Chemolithotrophic nitrifying bacteria are dependent on the presence of oxygen for the oxidation of ammonium via nitrite to nitrate. The success of nitrification in oxygen-limited environments such as waterlogged soils, will largely depend on the oxygen sequestering abilities of both ammonium- and nitrite-oxidizing bacteria. In this paper the oxygen consumption kinetics of Nitrosomonas europaea and Nitrobacter winogradskyi serotype agilis were determined with cells grown in mixed culture in chemostats at different growth rates and oxygen tensions.Reduction of oxygen tension in the culture repressed the oxidation of nitrite before the oxidation of ammonium was affected and hence nitrite accumulated. K _m values found were within the range of 1–15 and 22–166 M O₂ for the ammonium- and nitrite-oxidizing cells, respectively, always with the lowest values for the N. europaea cells. Reduction of the oxygen tension in the culture lowered the half saturation constant K _m for oxygen of both species. On the other hand, the maximal oxygen consumption rates were reduced at lower oxygen levels especially at 0 kPa. The specific affinity for oxygen indicated by the V _max/K _m ratio, was higher for cells of N. europaea than for N. winogradskyi under all conditions studied. Possible consequences of the observed differences in specific affinities for oxygen of ammonium-and nitrite-oxidizing bacteria are discussed with respect to the behaviour of these organisms in oxygen-limited environments.     

Regulation of amino acid and glucose dissimilation in so-called ammonifiers and in other soil microorganisms

Pseudomonas acidovorans and P. putida, isolated from an enrichment culture with casein hydrolysate, and Agrobacterium radiobacter and Torulopsis sp., isolated from a glucose enrichment, were compared with respect to the physiology of ammonification. Decreasing ammonifying ability as well as increasing repression of the synthesis of amino acid degrading enzymes by glucose were found in the above order of organisms. In degradation sequences, observed with P. putida and A. radiobacter as test organisms, substances dissimilated prior to others had both, enhancing and repressing effects on the oxidation of the other compounds. This fact was parallelled by the observation, that in these two bacteria, glucose and single amino acids, when added to the same medium, exerted mutual repression of the synthesis of catabolic enzymes of their partners. The ecological significance of this type of regulation has been discussed.     

The sensitivity of the pseudomurein-containing genus Methanobacterium to inhibitors of murein synthesis

The sensitivity to inhibitors of various steps of murein synthesis was studied with six strains of methanogenic bacteria. Four of the strains belong to the genus Methanobacterium, which contains pseudomurein in its cell walls. This polymer-as well as murein-is not present in the two control organisms, Methanosarcina barkeri and Methanospirillum hungatii, which were found to be resistant to all inhibitors of murein synthesis. The four strains of Methanobacterium were resistant to the antibiotics fosfomycin, D-cycloserine, vancomycin, penicillin G and cephalosporin C, all of which inhibit the synthesis or function of the peptide subunits of murein. On the other hand, the four strains were susceptible to bacitracin, nisin, gardimycin and enduracidin. It is therefore assumed that the biosynthesis of murein and pseudomurein, respectively, may have some reactions of the so-called lipid cycle and the polymerization of the heteroglycan strands in common.     

Steady state and transient growth of autotrophic nitrifying bacteria

Growth of the autotrophic nitrifying bacteria Nitrosomonas europaea and Nitrobacter sp. was studied in continuous culture. Steady state growth kinetics of both organisms conformed with that predicted by chemostat theory, modified to account for maintenance energy requirement. Steady state data were used to calculate the maximum specific growth rate, the saturation constant for growth, the true growth yield and the maintenance coefficient. Transient growth was studied by imposing step changes in dilution rate. Step increases resulted in overshoots and oscillations in substrate concentration before establishment of a new steady state while step decreases in dilution rate were followed by monotonic changes in substrate concentration. The size of overshoots in substrate concentration following step increases in dilution rate was dependent on both the magnitude of the increase and of the dilution rate prior to the change.     

Isolation, Identification, and Activity of Mycoherbicidal Pathogens from Juvenile Broomrape Plants

Although there are reports of isolation of mycoherbicidal pathogens attacking the widespread broomrapes (Orobanche spp.) that parasitize legumes and vegetables, none is in use or available. This is despite there being no good method of controlling broomrapes in most crops other than by preplant fumigation with methyl bromide. Two highly parasitic fungi, Fusarium arthrosporioides strain E4a (CNCM I-164) and F. oxysporum strain E1d (CNCM I-1622), were isolated from nearly 100 organisms found on diseased, juvenile, emerging Orobanche flower stalks. A near-axenic polyethylene envelope system for culturing broomrape on tomato roots was used to ascertain pathogenicity of these strains. Both organisms fulfilled Koch's postulates for being primary pathogens. Their DNAs were analyzed and fingerprinted by restriction fragment length polymorphism and random amplified polymorphic DNA, showing that they are indeed different from each other and from many other Fusarium spp. and other formae speciales of F. oxysporum including a strain that attacks O. cumana on sunflowers. Both strains infect O. aegyptiaca, O. cernua, and O. ramosa, but not O. cumana. They did not infect any of the vegetable and legume crops tested and thus seem specific to Orobanche. Tomato plant roots dipped into a fungal spore and mycelial suspension and planted in broomrape-infested soil were protected for 6 weeks, as were tomato transplants in pot experiments. About 90% control was also achieved by posttransplant soil drench with fungal suspensions in pot experiments. These pathogens may be effective as seed, transplant, or soil-drench treatments of high-value vegetable and other crops.     

A 31P NMR study of the interaction of amphibian antimicrobialpeptides with the membranes of live bacteria

Summary Amphibian skin is a rich source of peptides that are specific to pathogens and act by disrupting bacterial membranes. Three antimicrobial peptides were isolated from the skin glands of Australian tree frogs,Litoria caerulea andLitoria genimaculata. NMR spectroscopy was used to observe changes induced by these peptides in the³¹P resonances of bacterial membranes in vivo. Caerin 1.1 and maculatin 1.1, both wide-spectrum antibiotics disrupted the membranes ofBacillus cereus andStaphylococcus epidermidis (Gram-positive), leading to an increase in the isotropic³¹P NMR signal. Caerin 4.1, a narrow-spectrum antibiotic, however, did not affect the³¹P spectra of these organisms. The results demonstrate the use of³¹P NMR to study the effects of membrane-disrupting agents on the membranes of live bacteria.