Reactive transport modeling of subsurface arsenic removal systems in rural Bangladesh.

Subsurface Arsenic Removal (SAR) is a technique for in-situ removal of arsenic from groundwater. Extracted groundwater is aerated and re-injected into an anoxic aquifer, where the oxygen in the injected water reacts with ferrous iron in the aquifer to form hydrous ferric oxide (HFO). Subsequent extraction of groundwater contains temporarily lower As concentrations, because As sorbs onto the HFO. Injection, storage, and extraction together is called a cycle. A reactive transport model (RTM) was developed in PHREEQC to determine the hydrogeochemical processes responsible for As (im)mobilization during experimental SAR operation performed in Bangladesh. Oxidation of Fe(II) and As(III) were modeled using kinetic-rate expressions. Cation exchange, precipitation of HFO, and surface complexation, were modeled as equilibrium processes. A best set of surface complexation reactions and corresponding equilibrium constants was adopted from previous studies to simulate all 20 cycles of a SAR experiment. The model gives a reasonable match with observed concentrations of different elements in the extracted water (e.g., the r(2) value of As was 0.59 or higher). As concentrations in the extracted water are governed by four major processes. First, As concentration decreases in response to the elevated pH of injection water and likewise increases when native neutral pH groundwater flows in. Second, the sorption capacity for As increases due to the gradual buildup of HFO. Third, As sorption is enhanced by preferential removal of As(V). Fourth, competitive sorption of Si limits the capacity of freshly precipitated HFO for As sorption. Transferability of the developed reactive transport model was demonstrated through successful application of the model, without further calibration, to two additional SAR sites in Bangladesh. This gives confidence that the model could be useful to assess potential SAR performance at locations in Bangladesh based on local hydrogeochemical conditions.

Low nitrification rates in acid Scots pine forest soils are due to pH-related factors.

In a previous study, ammonia-oxidizing bacteria (AOB)-like sequences were detected in the fragmentation layer of acid Scots pine (Pinus sylvestris L.) forest soils (pH 2.9-3.4) with high nitrification rates (>11.0 microg g-1 dry soil week-1), but were not detected in soils with low nitrification rates (<0.5 microg g-1 dry soil week-1). In the present study, we investigated whether this low nitrification rate has a biotic cause (complete absence of AOB) or an abiotic cause (unfavorable environmental conditions). Therefore, two soils strongly differing in net nitrification were compared: one soil with a low nitrification rate (location Schoorl) and another soil with a high nitrification rate (location Wekerom) were subjected to liming and/or ammonium amendment treatments. Nitrification was assessed by analysis of dynamics in NH4+-N and NO3- -N concentrations, whereas the presence and composition of AOB communities were assessed by polymerase chain reaction-denaturing gradient gel electrophoresis and sequencing of the ammonia monooxygenase (amoA) gene. Liming, rather than ammonium amendment, stimulated the growth of AOB and their nitrifying activity in Schoorl soil. The retrieved amoA sequences from limed (without and with N amendment) Schoorl and Wekerom soils exclusively belong to Nitrosospira cluster 2. Our study suggests that low nitrification rates in acidic Scots pine forest soils are due to pH-related factors. Nitrosospira cluster 2 detected in these soils is presumably a urease-positive cluster type of AOB.

Acidophilic microbial communities associated with a natural, biodegraded hydrocarbon seepage.

Characterization of microbial communities present in a surface petroleum seep in which hydrocarbons have been biodegraded for thousands of years in order to improve the understanding on natural petroleum biodegradation. DNA was extracted from a natural, surface petroleum seep and subjected to culture independent analysis (rRNA gene-based denaturing gradient gel electrophoresis and phylogenetic analysis of clone libraries). Molecular analysis suggested dominance by acidophilic bacteria, especially Alphaproteobacteria (mainly bacteria related to Acidiphilium and Acidocella). Archaea were not detected, but fungi were present. pH of the samples was around 3.5. Acidophilic microbial communities are associated with an acidic petroleum seep. Microbial community structure analysis gives information on the environmental conditions under which petroleum biodegradation occurs. This knowledge could be applied to define conditions for specific cultivation or activity measurements. The activity of acidophilic micro-organisms deserves more attention with respect to their involvement in natural petroleum degradation. This knowledge will contribute to the design of oil bioremediation strategies for polluted acidic settings.

Presence of Nitrosospira cluster 2 bacteria corresponds to N transformation rates in nine acid Scots pine forest soils.

The relation between environmental factors and the presence of ammonia-oxidising bacteria (AOB), and its consequences for the N transformation rates were investigated in nine Scots pine (Pinus sylvestris L.) forest soils. In general, the diversity in AOB appears to be strikingly low compared to other ecosystems. Nitrosospira cluster 2, as determined by temporal temperature gradient electrophoresis and sequencing, was the only sequence cluster detected in the five soils with high nitrification rates. In the four soils with low nitrification rates, AOB-like sequences could not be detected. Differences in nitrification rates between the forest soils correlated to soil C/N ratio (or total N) and atmospheric N deposition.

Atrazine catabolism by a combined bacterial association (KRA30) under carbon- and nitrogen-limitations in a retentostat.

AIMS: Nutrient-limited atrazine catabolism study in continuous cultures with biomass retention to mimic in situ environmental conditions and thus gain insight of the efficacy of biosupplementation/biostimulation to eliminate reduced herbicide bioavailability. METHODS AND RESULTS: Carbon- and nitrogen-limited retentostat (1 and 5 l) cultivation of a combined atrazine (100 mg l-1)-catabolizing association KRA30 was made. As a nitrogen source, through citrate supplementation, increased herbicide catabolism resulted and was complete in the absence of NH4-N. Co-metabolism of the molecule in the presence of succinate was identified. Population characterization by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) indicated component species numerical dominance shifts in response to changes in nutrient limitation, mineral salts composition and biofilm formation, although the total species complement and catabolic potential were retained. CONCLUSIONS: Biomass and catabolic capacity maintenance, through cost-effective biosupplementation/biostimulation, should promote atrazine bioavailability and so ensure successful amelioration. SIGNIFICANCE AND IMPACT OF THE STUDY: All planning, implementation and monitoring of bioremediation programmes should be underpinned by a combination of molecular and (continuous) culture-based methods.

Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer.

Knowledge about the relationship between microbial community structure and hydrogeochemistry (e.g., pollution, redox and degradation processes) in landfill leachate-polluted aquifers is required to develop tools for predicting and monitoring natural attenuation. In this study analyses of pollutant and redox chemistry were conducted in parallel with culture-independent profiling of microbial communities present in a well-defined aquifer (Banisveld, The Netherlands). Degradation of organic contaminants occurred under iron-reducing conditions in the plume of pollution, while upstream of the landfill and above the plume denitrification was the dominant redox process. Beneath the plume iron reduction occurred. Numerical comparison of 16S ribosomal DNA (rDNA)-based denaturing gradient gel electrophoresis (DGGE) profiles of Bacteria and Archaea in 29 groundwater samples revealed a clear difference between the microbial community structures inside and outside the contaminant plume. A similar relationship was not evident in sediment samples. DGGE data were supported by sequencing cloned 16S rDNA. Upstream of the landfill members of the beta subclass of the class Proteobacteria (beta-proteobacteria) dominated. This group was not encountered beneath the landfill, where gram-positive bacteria dominated. Further downstream the contribution of gram-positive bacteria to the clone library decreased, while the contribution of delta-proteobacteria strongly increased and beta-proteobacteria reappeared. The beta-proteobacteria (Acidovorax, Rhodoferax) differed considerably from those found upstream (Gallionella, Azoarcus). Direct comparisons of cloned 16S rDNA with bands in DGGE profiles revealed that the data from each analysis were comparable. A relationship was observed between the dominant redox processes and the bacteria identified. In the iron-reducing plume members of the family Geobacteraceae made a strong contribution to the microbial communities. Because the only known aromatic hydrocarbon-degrading, iron-reducing bacteria are Geobacter spp., their occurrence in landfill leachate-contaminated aquifers deserves more detailed consideration.

Microorganisms with a taste for vanilla: microbial ecology of traditional Indonesian vanilla curing.

The microbial ecology of traditional postharvesting processing of vanilla beans (curing) was examined using a polyphasic approach consisting of conventional cultivation, substrate utilization-based and molecular identification of isolates, and cultivation-independent community profiling by 16S ribosomal DNA based PCR-denaturing gradient gel electrophoresis. At two different locations, a batch of curing beans was monitored. In both batches a major shift in microbial communities occurred after short-term scalding of the beans in hot water. Fungi and yeast disappeared, although regrowth of fungi occurred in one batch during a period in which process conditions were temporarily not optimal. Conventional plating showed that microbial communities consisting of thermophilic and thermotolerant bacilli (mainly closely related to Bacillus subtilis, B. licheniformis, and B. smithii) developed under the high temperatures (up to 65 degrees C) that were maintained for over a week after scalding. Only small changes in the communities of culturable bacteria occurred after this period. Molecular analysis revealed that a proportion of the microbial communities could not be cultured on conventional agar medium, especially during the high-temperature period. Large differences between both batches were observed in the numbers of microorganisms, in species composition, and in the enzymatic abilities of isolated bacteria. These large differences indicate that the effects of microbial activities on the development of vanilla flavor could be different for each batch of cured vanilla beans.

16S rDNA-based characterization of BTX-catabolizing microbial associations isolated from a South African sandy soil.

In the presence of different selection pressures, particularly pH and electron donor concentration, indigenous microbial associations which catabolize selected petroleum hydrocarbon components (benzene, toluene and o-, m- and p-xylene (BTX)) were enriched and isolated from a petroleum hydrocarbon-contaminated KwaZulu-Natal sandy soil. Electron microscopy revealed that, numerically, rods constituted the majority of the populations responsible for BTX catabolism. Molecular techniques (polymerase chain reaction (PCR) and 16S rDNA fingerprinting by denaturing-gradient gel electrophoresis (DGGE)) were employed to explore the diversities and analyze the structures of the isolated microbial associations. Pearson product-moment correlation indicated that the different, but chemically similar, petroleum hydrocarbon molecules, effected the isolation of different associations. However, some similar numerically-dominant bands characterized the associations. A 30% similarity was evident between the m- and o-xylene-catabolizing associations regardless of the molecule concentration and the enrichment pH. PCR-DGGE was also used to complement conventional culture-based microbiological procedures for environmental parameter optimization. Band pattern differences indicated profile variations of the isolated associations which possibly accounted for the growth rate changes recorded in response to pH and temperature perturbations.

Growth, maintenance and fermentation pattern of the salt-tolerant lactic acid bacterium Tetragenococcus halophila in anaerobic glucose limited retention cultures.

The homofermentative lactic acid bacterium Tetragenococcus halophila showed mixed acid fermentation at low growth-rates under glucose limiting conditions and in the presence of 10% NaCl. Maximum growth yields in fermentors with cell retention were not affected by pH, but maintenance requirement was at pH 5.2 four times higher than at pH 7.0. Despite the high salt-concentration of the medium, maintenance requirements were low compared to other lactic acid bacteria. The possible causes of the observed differences in maintenance requirements are discussed.

Characterization of Tetragenococcus halophila Populations in Indonesian Soy Mash (Kecap) Fermentation.

Chinese- and Japanese-type fermented soy sauces are made of different plant materials. The lactic acid bacterium Tetragenococcus halophila is present and grows in both types. On the basis of the difference in sugar composition and content in the plant materials, differences in the populations of T. halophila bacteria were expected. However, obvious differences were found only regarding the utilization of l-arabinose. In the Chinese type, almost all isolates utilized l-arabinose, while in the Japanese type only 40% of the isolates did. Also, the population in the Japanese type was more heterogeneous regarding substrate utilization. Random amplified polymorphic DNA analysis revealed that the heterogeneous population at the Japanese-type industrial manufacturer was derived from only three strains at maximum. Genetic relatedness among isolates from different soy sauce manufacturers was low, but protein fingerprinting indicated that the isolates still belonged to one species.

Effects of phosphoglycerate kinase overproduction in Saccharomyces cerevisiae on the physiology and plasmid stability.

In this report the effects of phosphoglycerate kinase (PGK) overproduction on the physiology and plasmid stability in baker's yeast Saccharomyces cerevisiae containing the PGK1 gene on an episomal plasmid are described. This examination reveals that there is a preferred intracellular level for this enzyme, amounting to 10-15% of the total soluble protein. Strains containing the plasmid and the host strain were grown in non-selective batch cultures and continuous culture, under different growth conditions. Plasmid-containing yeast strains stabilize the copy number of the episomal plasmid at a level at which the PGK concentration is about 12%. This stabilization is due to an equilibrium between normal plasmid loss and selective pressure because of advantages resulting from the increased amount of PGK under glucose-limited conditions. During respiro-fermentative growth, PGK-overproducing cells showed an increased respiration rate and decreased fermentative activity, compared to the host strain. The PGK1 gene can be applied as a direct positive selection marker to obtain a high episomal plasmid stability during growth on glucose. The results are consistent with previously reported data on the physiology and gene stability of PGK-overproducing yeast cells that contain multiple copies of the PGK1 gene integrated into the genome.