Genetic diversity of Desulfovibrio spp. in environmental samples analyzed by denaturing gradient gel electrophoresis of [NiFe] hydrogenase gene fragments

The genetic diversity of Desulfovibrio species in environmental samples was determined by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified [NiFe] hydrogenase gene fragments. Five different PCR primers were designed after Comparative analysis of [NiFe] hydrogenase gene sequences from three Desulfovibrio species. These primers were tested in different combinations on the genomic DNAs of a variety of hydrogenase-containing and hydrogenase-lacking bacteria. One primer pair was found to be specific for Desulfovibrio species only, while the others gave positive results with other bacteria also. By using this specific primer pair, we were able to amplify the [NiFe] hydrogenase genes of DNAs isolated from environmental samples and to detect the presence of Desulfovibrio species in these samples. However, only after DGGE analysis of these PCR products could the number of different Desulfovibrio species within the samples be determined. DGGE analysis Of PCR products from differ ent bioreactors demonstrated up to two bands, while at least five distinguishable bands were detected in a microbial mat sample. Because these bands most likely represent as many Desulfovibrio species present in these samples, we conclude that the genetic diversity of Desulfovibrio species in the natural microbial mat is far greater than that in the experimental bioreactors

Desulfovibrio paquesii sp. nov., a hydrogenotrophic sulfate-reducing bacterium isolated from a synthesis-gas-fed bioreactor treating zinc- and sulfate-rich wastewater

A hydrogenotrophic, sulfate-reducing bacterium, designated strain SB1(T), was isolated from sulfidogenic sludge of a full-scale synthesis-gas-fed bioreactor used to remediate wastewater from a zinc smelter. Strain SB1(T) was found to be an abundant micro-organism in the sludge at the time of isolation. Hydrogen, formate, pyruvate, lactate, malate, fumarate, succinate, ethanol and glycerol served as electron donors for sulfate reduction. Organic substrates were incompletely oxidized to acetate. 16S rRNA gene sequence analysis showed that the closest recognized relative to strain SB1(T) was Desulfovibrio gigas DSM 1382(T) (97.5 % similarity). The G+C content of the genomic DNA of strain SB1(T) was 62.2 mol%, comparable with that of Desulfovibrio gigas DSM 1382(T) (60.2 mol%). However, the level of DNA-DNA relatedness between strain SB1(T) and Desulfovibrio gigas DSM 1382(T) was only 56.0 %, indicating that the two strains are not related at the species level. Strain SB1(T) could also be differentiated from Desulfovibrio gigas based on phenotypic characteristics, such as major cellular fatty acid composition (anteiso-C(15 : 0), iso-C(14 : 0) and C(18 : 1) cis 9) and substrate utilization. Strain SB1(T) is therefore considered to represent a novel species of the genus Desulfovibrio, for which the name Desulfovibrio paquesii sp. nov. is proposed. The type strain is SB1(T) (=DSM 16681(T)=JCM 14635(T)

Effectiveness of various sorbents and biological oxidation in the removal of arsenic species from groundwater

The AsIII and AsV adsorption capacity of biochar, chabazite, ferritin-based material, goethite and nano zerovalent iron was evaluated in artificial systems at autoequilibrium pH (i.e. MilliQ water without adjusting the pH) and at approximately neutral pH (i.e. TRIS-HCl, pH 7.2). At autoequilibrium pH, iron-based sorbents removed 200 ug L-1 As highly efficiently whereas biochar and chabazite were ineffective. At approximately neutral pH, sorbents were capable of removing between 17 and 100% of AsIII and between 3 and 100% of AsV in the following order: biochar,chabazite,ferritin-based material,goethite,nano zero-valent iron. Chabazite, ferritin-based material and nano zero-valent iron oxidised AsIII to AsV and ferritin-based material was able to reduce AsV to AsIII. When tested in naturally As-contaminated groundwater, a marked decrease in the removal effectiveness occurred, due to possible competition with phosphate and manganese. A biological oxidation step was then introduced in a one-phase process (AsIII bio-oxidation in conjunction with AsV adsorption) and in a two-phase process (AsIII bio-oxidation followed by AsV adsorption). Arsenite oxidation was performed by resting cells of Aliihoeflea sp. strain 2WW, and arsenic adsorption by goethite. The one-phase process decreased As in groundwater to 85 %, whereas the two-phase process removed up to 95%As, leaving in solution 6 ugL-1 As, thus meeting the World Health Organization limit (10 ug L-1). These results can be used in the scaling up of a twophase treatment, with bacterial oxidation of As combined to goethite adsorption

Thiomicrospira kuenenii sp. nov., and Thiomicrospira frisia sp. nov., two mesophilic obligately chemolithoautotrophic sulfur-oxidizing bacteria isolated from an intertidal mud flat

Two new members of the genus Thiomicrospira were isolated from an intertidal mud flat sample with thiosulfate as the electron donor and CO2 as carbon source. On the basis of differences in genotypic and phenotypic characteristics, it is proposed that strain JB-A1(T) (= DSM 12350(T)) and strain JB-A2(T) (= DSM 12351(T)) are members of two new species, Thiomicrospira kuenenii and Thiomicrospira frisia, respectively. The cells were Gram-negative vibrios or slightly bent rods. Strain JB-A1(T) was highly motile, whereas strain JB-A2(T) showed a much lower degree of motility combined with a strong tendency to form aggregates. Both organisms were obligately autotrophic and strictly aerobic. Nitrate was not used as electron acceptor. Chemolithoautotrophic growth was observed with thiosulfate, tetrathionate, sulfur and sulfide. Neither isolate was able to grow heterotrophically. For strain JB-A1(T), growth was observed between pH values of 4.0 and 7.5 with an optimum at pH 6.0, whereas for strain JB-A2(T), growth was observed between pH 4.2 and 8.5 with an optimum at pH 6.5. The temperature limits for growth were between 3.5 and 42 degrees C and 3.5 and 39 degrees C, respectively. The optimum growth temperature for strain JB-A1(T) was between 29 and 33.5 degrees C, whereas strain JB-A2(T) showed optimal growth between 32 and 35 degrees C. The mean maximum growth rate on thiosulfate was 0.35 h(-1) for strain JB-A1(T) and 0.45 h(-1) for strain JB-A2(T)