Magnetic genes: Studying the genetics of biomineralization in magnetotactic bacteria

Many species of bacteria can manufacture materials on a finer scale than those that are synthetically made. These products are often produced within intracellular compartments that bear many hallmarks of eukaryotic organelles. One unique and elegant group of organisms is at the forefront of studies into the mechanisms of organelle formation and biomineralization. Magnetotactic bacteria (MTB) produce organelles called magnetosomes that contain nanocrystals of magnetic material, and understanding the molecular mechanisms behind magnetosome formation and biomineralization is a rich area of study. In this Review, we focus on the genetics behind the formation of magnetosomes and biomineralization. We cover the history of genetic discoveries in MTB and key insights that have been found in recent years and provide a perspective on the future of genetic studies in MTB.

Inorganic-organic hybrid coatings on stainless steel by layer-by-layer deposition and surface-initiated atom-transfer-radical polymerization for combating biocorrosion

To improve the biocorrosion resistance of stainless steel (SS) and to confer the bactericidal function on its surface for inhibiting bacterial adhesion and biofilm formation, well-defined inorganic-organic hybrid coatings, consisting of the inner compact titanium oxide multilayers and outer dense poly(vinyl-N-hexylpyridinium) brushes, were successfully developed. Nanostructured titanium oxide multilayer coatings were first built up on the SS substrates via the layer-by-layer sol-gel deposition process. The trichlorosilane coupling agent, containing the alkyl halide atom-transfer-radical polymerization (ATRP) initiator, was subsequently immobilized on the titanium oxide coatings for surface-initiated ATRP of 4-vinylpyridine (4VP). The pyridium nitrogen moieties of the covalently immobilized 4VP polymer, or P(4VP), brushes were quaternized with hexyl bromide to produce a high concentration of quaternary ammonium salt on the SS surfaces. The excellent antibacterial efficiency of the grafted polycations, poly(vinyl-N-pyridinium bromide), was revealed by viable cell counts and atomic force microscopy images of the surface. The effectiveness of the hybrid coatings in corrosion protection was verified by the Tafel plot and electrochemical impedance spectroscopy measurements.

Desulfovibrio frigidus sp. nov. and Desulfovibrio ferrireducens sp. nov., psychrotolerant bacteria isolated from Arctic fjord sediments (Svalbard) with the ability to reduce Fe(III)

Strains 18T, 61T and 77 were isolated from two permanently cold fjord sediments on the west coast of Svalbard. The three psychrotolerant strains, with temperature optima at 20-23 degrees C, were able to grow at the freezing point of sea water, -2 degrees C. The strains oxidized important fermentation products such as hydrogen, formate and lactate with sulfate as the electron acceptor. Sulfate could be replaced by sulfite, thiosulfate or elemental sulfur. Poorly crystalline and soluble Fe(III) compounds were reduced in sulfate-free medium, but no growth occurred under these conditions. In the absence of electron acceptors, fermentative growth was possible. The pH optimum for the strains was around 7.1. The DNA G+C contents were 43.3 and 42.0 mol% for strains 18T and 61T, respectively. Strains 18T, 61T and 77 were most closely related to Desulfovibrio hydrothermalis (95.0-95.7 % 16S rRNA gene sequence similarity). Strains 18T and 77, exhibiting 99.9 % sequence similarity, represent a novel species for which the name Desulfovibrio frigidus sp. nov. is proposed. The type strain is strain 18T (=DSM 17176T = JCM 12924T). Strain 61T was closely related to strains 18T and 77 (97.6 and 97.5 % 16S rRNA gene sequence similarity), but on the basis of DNA-DNA hybridization strain 61T represents a novel species for which the name Desulfovibrio ferrireducens sp. nov. is proposed. The type strain is strain 61T (=DSM 16995T = JCM 12925T).

Toxic effects of dissolved heavy metals on Desulfovibrio vulgaris and Desulfovibrio sp. strains

Biological treatment of metal-containing wastewaters with sulphate-reducing bacteria (SRB) is an attractive technique for the bioremediation of this kind of medium. In order to design a suitable engineering process to address this environmental problem, it is crucial to understand the inhibitory effect of dissolved heavy metals on these bacteria. Batch studies were carried out to evaluate the toxic effects of several heavy metal ions [Cr(III), Cu(II), Mn(II), Ni(II) and Zn(II)] on two cultures of SRB (Desulfovibrio vulgaris and Desulfovibrio sp.). The experimental data indicate that SRB show different responses to each metal. At the highest metal concentration tolerated for each metal, the precipitation levels for D. vulgaris were as follows: 24.7%-15 ppm Cr(III), 45%-4 ppm Cu(II), 60%-10 ppm Mn(II), 96%-8.5 ppm Ni(II) and 9%-20 ppm Zn(II). The corresponding values for Desulfovibrio sp. were: 25.5%-15 ppm Cr(III), 71%-4 ppm Cu(II), 66.2%-10 ppm Mn(II), 96.1%-8.5 ppm Ni(II) and 93%-20 ppm Zn(II). Results obtained in batch studies will be taken into account for the subsequent design of a sulphate-reducing bioreactor to reduce levels of heavy metals present in different types of contaminated media.

Isolation of sulfate-reducing bacteria from the terrestrial deep subsurface and description of Desulfovibrio cavernae sp. nov

Deep subsurface sandstones in the area of Berlin (Germany) located 600 to 1060 m below the surface were examined for the presence of viable microorganisms. The in situ temperatures at the sampling sites ranged from 37 to 45 degrees C. Investigations focussed on sulfate-reducing bacteria able to grow on methanol and triethylene glycol, which are added as chemicals to facilitate the long-term underground storage of natural gas. Seven strains were isolated from porewater brines in the porous sandstone. Three of them were obtained with methanol (strains H1M, H3M, and B1M), three strains with triethylene glycol (strains H1T, B1T, and B2T) and one strain with a mixture of lactate, acetate and butyrate (strain H1-13). Due to phenotypic properties six isolates could be identified as members of the genus Desulfovibrio, and strain B2T as a Desulfotomaculum. The salt tolerance and temperature range for growth indicated that the isolates originated from the indigenous deep subsurface sandstones. They grew in mineral media reflecting the in situ ionic composition of the different brines, which contained 1.5 to 190 g NaCl x l(-1) and high calcium and magnesium concentrations. The Desulfovibrio strains grew at temperatures between 20 and 50 degrees C, while the Desulfotomaculum strain was thermophilic and grew between 30 and 65 degrees C. The strains utilized a broad spectrum of electron donors and acceptors. They grew with carbon compounds like lactate, pyruvate, formate, n-alcohols (C1-C5), glycerol, ethylene glycol, malate, succinate, and fumarate. Some strains even utilized glucose as electron donor and carbon source. All strains were able to use sulfate, sulfite and nitrate as electron acceptors. Additionally, three Desulfovibrio strains reduced manganese oxide, the Desulfotomaculum strain reduced manganese oxide, iron oxide, and elemental sulfur. The 16S rRNA analysis revealed that the isolates belong to three different species. The strains H1T, H3M and B1M could be identified as Desulfovibrio indonesiensis, and strain B2T as Desulfotomaculum geothermicum. The other Desulfovibrio strains (H1M, H1-13, and B1T) showed identical 16S rDNA sequences and similarities as low as 93% to their closest relative, Desulfovibrio aminophilusT. Therefore, these isolates were assigned to a new species, Desulfovibrio cavernae sp. nov., with strain H1M as the type strain.

Desulfovibrio bastinii sp. nov. and Desulfovibrio gracilis sp. nov., moderately halophilic, sulfate-reducing bacteria isolated from deep subsurface oilfield water

Two moderately halophilic, mesophilic, sulfate-reducing bacteria were isolated from production-water samples from Emeraude Oilfield, Congo. Motile, vibrioid cells of SRL4225T grew optimally at a concentration of 4 % NaCl, at pH 5·8–6·2, with a minimal pH for growth of 5·2, showing that it is a moderately acidophilic bacterium. Cells of SRL6146T were motile, curved or vibrioid, long and thin rods. Optimal growth was obtained at a concentration of 5–6 % NaCl, at pH 6·8–7·2. The nutritional requirements showed that many of the characteristics of these strains overlap with those of known Desulfovibrio species. On the basis of 16S rRNA gene sequence analysis and DNA–DNA hybridization studies, both strains are members of the genus Desulfovibrio. However, they are not closely related to any species of the genus that have validly published names. It is therefore proposed that the two strains are members of two novel species of the genus Desulfovibrio with the names Desulfovibrio bastinii sp. nov. (type strain SRL4225T=DSM 16055T=ATCC BAA-903T) and Desulfovibrio gracilis sp. nov. (type strain SRL6146T=DSM 16080T=ATCC BAA-904T).

Desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir

A novel sulphate-reducing bacterium (Al1T) was recovered from a soured oil well in Purdu Bay, Alaska. Light and atomic force microscopy observations revealed that cells were Gram-negative, vibrio-shaped and motile by means of a single polar flagellum. The carbon and energy sources used by the isolate and the salinity, temperature and pH ranges facilitating its growth proved to be typical of a partial lactate-oxidizing, moderately halophilic, mesophilic, sulphate-reducing bacterium. Analysis of the fatty acid profile revealed that C(18 : 0), isoC(15 : 0) and isoC(17 : 1)omega7c were the predominant species. Fatty acid profile and complete 16S rRNA gene sequencing demonstrated the similarity between strain Al1T and members of the genus Desulfovibrio. The position of strain Al1T within the phylogenetic tree indicated that it clustered closely with Desulfovibrio vietnamensis DSM 10520T (98.9 % sequence similarity), a strain recovered from a similar habitat. However, whole-cell protein profiles, Fourier-transform infrared studies and DNA-DNA hybridization demonstrated that, in spite of the high level of 16S rRNA gene sequence similarity, there is sufficient dissimilarity at the DNA sequence level between D. vietnamensis DSM 10520T and strain Al1T (10.2 % similarity) to propose that strain Al1T belongs to a separate species within the genus Desulfovibrio. Based on the results obtained, the name Desulfovibrio alaskensis sp. nov. is therefore proposed, with Al1T (= NCIMB 13491T = DSM 16109T) as the type strain.

Iron corrosion by novel anaerobic microorganisms

Corrosion of iron presents a serious economic problem. Whereas aerobic corrosion is a chemical process, anaerobic corrosion is frequently linked to the activity of sulphate-reducing bacteria (SRB). SRB are supposed to act upon iron primarily by produced hydrogen sulphide as a corrosive agent and by consumption of 'cathodic hydrogen' formed on iron in contact with water. Among SRB, Desulfovibrio species--with their capacity to consume hydrogen effectively--are conventionally regarded as the main culprits of anaerobic corrosion; however, the underlying mechanisms are complex and insufficiently understood. Here we describe novel marine, corrosive types of SRB obtained via an isolation approach with metallic iron as the only electron donor. In particular, a Desulfobacterium-like isolate reduced sulphate with metallic iron much faster than conventional hydrogen-scavenging Desulfovibrio species, suggesting that the novel surface-attached cell type obtained electrons from metallic iron in a more direct manner than via free hydrogen. Similarly, a newly isolated Methanobacterium-like archaeon produced methane with iron faster than do known hydrogen-using methanogens, again suggesting a more direct access to electrons from iron than via hydrogen consumption.

The influence of fluid shear on the structure and material properties of sulphate-reducing bacterial biofilms

Biofilms of sulphate-reducing Desulfovibrio sp. EX265 were grown in square section glass capillary flow cells under a range of fluid flow velocities from 0.01 to 0.4 m/s (wall shear stress, tau(w), from 0.027 to 1.0 N/m(2)). In situ image analysis and confocal scanning laser microscopy revealed biofilm characteristics similar to those reported for aerobic biofilms. Biofilms in both flow cells were patchy and consisted of cell clusters separated by voids. Length-to-width ratio measurements (l(c):w(c)) of biofilm clusters demonstrated the formation of more "streamlined" biofilm clusters (l(c):w(c)=3.03) at high-flow velocity (Reynolds number, Re, 1200), whereas at low-flow velocity (Re 120), the l(c):w(c) of the clusters was approximately 1 (l(c):w(c) of 1 indicates no elongation in the flow direction). Cell clusters grown under high flow were more rigid and had a higher yield point (the point at which the biofilm began to flow like a fluid) than those established at low flow and some biofilm cell aggregates were able to relocate within a cluster, by travelling in the direction of flow, before attaching more firmly downstream.

Antioxidative enzymes of sulfate-reducing bacterium desulfovibrio desulfuricans: superoxide dismutase and peroxidases

Extracts of Desulfovibrio desulfuricans B-1388 cells grown under anaerobic conditions displayed superoxide dismutase activity. The maximal activity was found during the stationary growth phase. The enzyme was virtually completely located in the periplasm fraction. D. desulfuricans B-1388 lacked catalase activity but contained active NADH- and NADPH-peroxidases. The activity of NADH-peroxidase depended on the physiological state of the culture. On changing the growth conditions (the presence of 5% CO in the gaseous phase), the activity of superoxide dismutase decreased.

Metabolism of explosive compounds by sulfate-reducing bacteria

The metabolism of various explosive compounds-1,3,5-trinitrobenzene (TNB), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazocine (HMX)-by a sulfate-reducing bacterial consortium, Desulfovibrio spp., was studied. The results indicated that the Desulfovibrio spp. used all of the explosive compounds studied as their sole source of nitrogen for growth. The concentrations of TNB, RDX, and HMX in the culture media dropped to below the detection limit (<0.5 ppm) within 18 days of incubation. We also observed the production of ammonia from the nitro groups of the explosive compounds in the culture media. This ammonia served as a nitrogen source for the bacterial growth, and the concentration of ammonia later dropped to <0.5 mg/L. The sulfate-reducing bacteria may be useful in the anaerobic treatment of explosives-contaminated soil.

Anaerobic degradation of 1,2-propanediol by a new Desulfovibrio strain and D. alcoholovorans

A sulfate-reducing bacterium, strain HDv, was isolated from the anoxic soil of a ricefield using lactate as electron donor. Cells were gram-negative, motile, nonsporulating curved rods, with single polar flagella. Substrates were incompletely oxidized to acetate and included glycerol, 1,2- and 1,3-propanediol. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, maleate, and malate were utilized as electron acceptors. Pyruvate, fumarate, maleate, malate and dihydroxyacetone were fermented. Desulfoviridin and c-type cytochromes were present. The DNA base composition was 66.6 +/- 0.3 mol% G+C. The isolate was identified as a Desulfovibrio sp.; its metabolic properties were somewhat different from those of previously described Desulfovibrio species. Comparative biochemical study of 1,2-propanediol dissimilation by the new isolate and Desulfovibrio alcoholovorans showed that NAD-dependent dehydrogenases play a key role in the catabolism of this substrate. The hypothetical pathways of 1,2-propanediol degradation by Desulfovibrio spp. are presented.

Desulfovibrio longus sp. nov., a sulfate-reducing bacterium isolated from an oil-producing well

A novel type of sulfate-reducing bacteria with unusual morphology was isolated from an oil-producing well in the Paris Basin. The cells of this bacterium, strain SEBR 2582T (T = type strain), are long, thin, flexible rods, contain desulfoviridin, and are physiologically similar to members of the genus Desulfovibrio. On the basis of 16S rRNA sequence data, this strain should be included in the genus Desulfovibrio. However, strain SEBR 2582T differs from other members of this genus morphologically, physiologically, and phylogenetically. Thus, a new species, Desulfovibrio longus sp. nov., is proposed for this organism.

Evidence for the periplasmic location of hydrogenase in Desulfovibrio gigas

Hydrogenase has been found to be located in the periplasmic space of Desulfovibrio gigas, and it is proposed that hydrogenase plays an important and specific role in interspecies hydrogen transfer.

Sulfate reduction by a Desulfovibrio species isolated from sheep rumen

Several dissimilatory, sulfate-reducing bacteria were isolated from the rumen fluid of sheep fed purified diets containing sulfate. One isolate, strain D, was selected for characterization. This organism is a nonsporeforming, obligately anaerobic, mesophilic, nonmotile, gram-negative, straight rod. Cell-free extracts show absorption maxima for cytochrome c(3) and desulfoviridin, characteristic of Desulfovibrio. Carbohydrates, as a sole carbon source, will support growth. Lactate supports growth in the presence of sulfate, not in its absence, whereas glucose or pyruvate support growth either in the presence or absence of sulfate. The isolate has a deoxyribonucleic acid base composition of 61.2% guanine plus cytosine, which is similar to that of several other species of Desulfovibrio; however, it differs from previously described species in morphology, motility, and carbon source utilization. Cell-free extracts of this bacterium exhibit adenosine 5'-triphosphate-sulfurylase, adenosine-5'-phosphosulfate-reductase, and hydrogenase activity. After incubation of cell-free extracts with adenine 5'-triphosphate and (35)SO(4) (2-), adenosine-5'-phosphosulfate rather than 3'-phosphoadenosine-5'-phosphosulfate was shown to be labeled, indicating that the pathway of sulfate reduction in this organism is similar to that of other dissimilatory sulfate reducers. This is the first report of a Desulfovibrio sp. isolated from the rumen.

Fine structural observations of Desulfovibrio desulfuricans

Glutaraldehyde-fixed, platinum-carbon-shadowed whole mounts, and ultrathin sections of glutaraldehyde-OsO4-fixed cells of Desulfovibrio desulfuricans were observed by electron microscopy. The preparations demonstrated a typical Vibrio form with a single polar flagellum. The cell envelope and the formation of external blebs were shown to be similar to other gram-negative bacteria. The protoplast, apparently devoid of mesosomes or other membranous structures, was densely packed with ribosomes and contained a fibrous nucleoid. A specialized region near the flagellar end of the cell was commonly observed and termed the basal apparatus. Cell division appeared to be by constriction.

Sulfate-reducing bacterium with unusual morphology and pigment content

A dissimilatory sulfate-reducing bacterium was isolated which differed in morphology and pigment content from previously described species. The organism was mesophilic, obligately anaerobic, gram-negative, nonsporulating, long, and slender with one polar flagellum. Whole cells fluoresced red at neutral pH when excited with light at 365 nm owing to the presence of a pink pigment. Desulfoviridin was present. Reduced minus oxidized spectra of whole cells showed peaks in the position of a c-type cytochrome characteristic of Desulfovibrio species and peaks at about 629 and 603 nm. CO difference spectra showed the presence of a CO-binding pigment with a peak at 593 nm. Lactate and pyruvate supported growth in the presence of sulfate but not in its absence. Sulfate, sulfite, and thiosulfate served as electron acceptors for growth. Hydrogenase was present. The deoxyribonucleic acid had a buoyant density of 1.722 g/cm(3) and a guanosine plus cystosine molar percentage of total bases calculated by two different methods of 61.2 or 63.2.

Spontaneous spheroplast formation by Desulfovibrio aestuarii

Electron micrographs of sectioned spheroplasts of D. aestuarii have shown spontaneous spheroplast formation to be initiated by a separation of the cell wall to form an external projection or bleb. The transition to spheres occurs 4 to 6 days after exponential growth, is preceded by loss of sulfate-reducing ability, osmotic sensitivity, and viability, and is temperature dependent.