Conditions For Microbial Growth Research Articles

Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER.

Precise control over microbial cell growth conditions could enable detection of minute phenotypic changes, which would improve our understanding of how genotypes are shaped by adaptive selection. Although automated cell-culture systems such as bioreactors offer strict control over liquid culture conditions, they often do not scale to high-throughput or require cumbersome redesign to alter growth conditions. We report the design and validation of eVOLVER, a scalable DIY framework that can be configured to carry out high-throughput growth experiments in molecular evolution, systems biology, and microbiology. We perform high-throughput evolution of yeast across systematically varied population density niches to show how eVOLVER can precisely characterize adaptive niches. We describe growth selection using time-varying temperature programs on a genome-wide yeast knockout library to identify strains with altered sensitivity to changes in temperature magnitude or frequency. Inspired by large-scale integration of electronics and microfluidics, we also demonstrate millifluidic multiplexing modules that enable multiplexed media routing, cleaning, vial-to-vial transfers and automated yeast mating.

Silvopastoral systems drive the nitrogen-cycling bacterial community in soil

ABSTRACT Intercropping tree legumes with forage grasses in a silvopastoral system can avoid pasture degradation benefiting the soil. In such a system, nitrogen (N) is supplied by symbiosis between legumes and bacteria. However, the pasture quality determines the action of free-living nitrogen-fixing bacteria, which possess nifH genes, which encode nitrogenase enzyme. Ammonium-oxidizing bacteria (AOB), involved in the nitrification step, can be evaluated by specific regions of the 16S rRNA corresponding to AOB. Thus, we investigated the influence of the introduction of tree legumes into a silvopastoral system on the community structure and abundance of total bacteria, diazotrophic bacteria and ammonium-oxidizing bacteria by DGGE (denaturing gradient gel electrophoresis) and real-time qPCR (quantitative PCR). The experiment involved nine plots of one hectare each, planted with sabia (Mimosa caesalpinifolia), a Gliricidia species (Gliricidia sepium), and a Brachiaria species (Brachiaria decumbens) in a randomized block design, forming three treatments: I-Brachiaria intercropped with sabia; II-Brachiaria intercropped with Gliricidia and III-Brachiaria only, with three replicates. The structures of the total bacterial and ammonium-oxidizing bacterial communities were influenced by tree legume introduction, possibly through modification of the soil chemical attributes. The copy numbers of total bacteria, ammonium-oxidizing bacteria and diazotrophic bacteria were higher in soils planted with legumes, which provided better conditions for microbial growth compared to planting with the Brachiaria species alone. Silvopastoral management with tree legumes improves the biological quality of soil, favouring the bacterial community linked to N-cycling.

Effects of Microbial Growth Conditions on Synthesis of Magnetite Nanoparticles using Indigenous Fe(III)-Reducing Bacteria

Recent researches have shown that microbe–metal interactions play an important role in metal cycling and biomineralization in subsurface environments. The objective of this research was to study the effects of microbial growth conditions for size control on the synthesis of magnetite nanoparticles using Fe(III)-reducing bacteria enriched from intertidal flat sediments in Korea. The microbial formation of the magnetite nanoparticles was examined under various incubation temperatures (8–35 °C), concentrations (20–60 mM) of magnetite precursor, medium pHs (6.5–8.5), and incubation times (0–3 weeks). The Fe(III)-reducing bacteria formed 2~10 nm-sized magnetite (Fe3O4) by reduction of 40 mM akaganeite, especially under the conditions at 25 °C and medium pH = 8.5 within a 1-week incubation time. The magnetite nanoparticles formed by microbial processes exhibited superparamagnetic behavior.

Natural limestone discolouration triggered by microbial activity-a contribution.

Colour is a major argument that drives the decision of an architect in a specific architecture project and one of the most important characteristics and perceptible aspects of natural building stones. “Blue” limestones are building rocks, with different geological ages, typically used in several countries, and are known for their vulnerability to alteration, which causes colour change and the occurrence of unaesthetic patterns. Owing to this vulnerability, the conservation-restoration works in monuments, or new buildings constructed with “blue” limestone is extremely costly. Considering that the main limitation of this lithological variation is the chromatic change, a multidisciplinary approach was envisaged in this study to allow a closer insight into the chemical and mineralogical alterations and the microbial communities. Results obtained suggest that the inorganic alteration in the “blue” limestone may create favourable conditions for microbial growth and could lead to an increment in deterioration process.

Biodegradation and metabolic pathway of sulfamethoxazole by a novel strain Acinetobacter sp.

In this study, a novel strain capable of degrading sulfamethoxazole (SMX) was isolated and identified as Acinetobacter sp. The effect of influencing factors, such as initial SMX concentration (5-240mg/L), temperature (15-35°C), and pH (5-7), on SMX degradation was investigated. The results showed that when the initial SMX concentration was in the range of 5-240, the removal efficiency was 100%. The optimal condition for SMX biodegradation and microbial growth was determined to be 25°C and pH=7.0 in terms of the removal efficiencies of SMX and total organic carbon (TOC). Four metabolite compounds were detected during the process of SMX biodegradation, and the degradation pathways were tentatively proposed. In summary, Acinetobacter sp. was highly efficient in mineralizing SMX, which has the potential to be used for degrading SMX in water and wastewater.

Exploring potential pine litter biodegradability as a natural tool for low-carbon forestry

Litter decomposition has a remarkable role in the terrestrial C cycle not only for being an important C source of CO2 effluxes but also for leading soil organic matter (OM) formation with remarkable influences on sustainability of forest ecosystems, either broadleaf or coniferous. Thus, in order to evaluate the decomposability of litter from humid-temperate coniferous forests, two of the most widespread types of pine forests in the NW of Spain were selected (Pinus radiata D. Don, Pinus pinaster Ait.). In addition to litter characterization and solid state 13C NMR chemical structural identification, potential biodegradability and isotopic dynamics during the decomposition of litter from these two types of pine plantations were determined by using long-term controlled laboratory incubations (≈1year) under optimal environmental conditions for microbial growth (28°C and 80% moisture content). For both pine species, CO2 fluxes released during the experimental decomposition process fitted a common litter biodegradability model that considers two OM pools (labile and recalcitrant). The labile C pool represented 7.9% or 8.6% of the litter total C content in radiata or maritime pine forests, respectively, with the recalcitrant fraction showing averaged values close to 92% of the litter C. This recalcitrant pool had instantaneous mineralization rates between 80 and 170 times lower than the corresponding labile fraction. Radiata pine litter presented significantly higher instantaneous mineralization rates of the labile C pool compared with maritime litter (possibly related with their interspecific compositional differences, mean C/N ratio of 48 for radiata and 70 for maritime pine litter), which resulted in lower residence times for the former than the latter with an average half-life of 18days for radiata litter and of 34days for maritime litter. Multilinear regression modelling by combining the C mineralization indices and the biochemical characteristics of the litter as predictor variables of its potential biodegradability pointed to the labile C pool as the main driver of the whole litter decay process, since this parameter alone explained more than the 60% of the total variance. For both species, a brief 13C depletion was detected at the beginning of litter incubation and a negative significant correlation between litter 13C contents and early C fluxes was observed. Despite the already mentioned differences between radiata and maritime pine litter layers, the overall general findings on potential biodegradability suggest a similar short-to-medium term behaviour of the soil organic inputs for both types of forest ecosystems under the envisaged global warming challenge.

A comparative study of anaerobic fixed film baffled reactor and up-flow anaerobic fixed film fixed bed reactor for biological removal of diethyl phthalate from wastewater: a performance, kinetic, biogas, and metabolic pathway study

BackgroundPhthalic acid esters, including diethyl phthalate (DEP), which are considered as top-priority and hazardous pollutants, have received significant attention over the last decades. It is vital for industries to select the best treatment technology, especially when the DEP concentration in wastewater is high. Meanwhile, anaerobic biofilm-based reactors are considered as a promising option. Therefore, in the present study, for the biological removal of DEP from synthetic wastewater, two different anaerobic biofilm-based reactors, including anaerobic fixed film baffled reactor (AnFFBR) and up-flow anaerobic fixed film fixed bed reactor (UAnFFFBR), were compared from kinetic and performance standpoints. As in the previous studies, only the kinetic coefficients have been calculated and the relationship between kinetic coefficients and their interpretation has not been evaluated, the other aim of the present study was to fill this research gap.ResultsIn optimum conditions, 90.31 and 86.91% of COD as well as 91.11 and 88.72% of DEP removal were achieved for the AnFFBR and UAnFFFBR, respectively. According to kinetic coefficients (except biomass yield), the AnFFBR had better performance as it provided a more favorable condition for microbial growth. The Grau model was selected as the best mathematical model for designing and predicting the bioreactors’ performance due to its high coefficients of determination (0.97 < R2). With regard to the insignificant variations of the calculated Grau kinetic coefficients (KG) when the organic loading rate (with constant HRT) increased, it can be concluded that both of the bioreactors can tolerate high organic loading rate and their performance is not affected by the applied DEP concentrations.ConclusionsBoth the bioreactors were capable of treating low-to-high strength DEP wastewater; however, according to the experimental results and obtained kinetic coefficients, the AnFFBR indicated higher performance. Although the AnFFBR can be considered as a safer treatment option than the UAnFFFBR due to its lower DEP concentrations in sludge, the UAnFFFBR had lower VSS/TSS ratio and sludge yield, which could make it more practical for digestion. Finally, both the bioreactors showed considerable methane yield; however, compared to the UAnFFFBR, the AnFFBR had more potential for bioenergy production. Although both the selected bioreactors achieved nearly 90% of DEP removal, they can only be considered as pre-treatment methods according to the standard regulations and should be coupled with further technology.

The Biodiversity of the Microbiota Producing Heat-Resistant Enzymes Responsible for Spoilage in Processed Bovine Milk and Dairy Products.

Raw bovine milk is highly nutritious as well as pH-neutral, providing the ideal conditions for microbial growth. The microbiota of raw milk is diverse and originates from several sources of contamination including the external udder surface, milking equipment, air, water, feed, grass, feces, and soil. Many bacterial and fungal species can be found in raw milk. The autochthonous microbiota of raw milk immediately after milking generally comprises lactic acid bacteria such as Lactococcus, Lactobacillus, Streptococcus, and Leuconostoc species, which are technologically important for the dairy industry, although they do occasionally cause spoilage of dairy products. Differences in milking practices and storage conditions on each continent, country and region result in variable microbial population structures in raw milk. Raw milk is usually stored at cold temperatures, e.g., about 4°C before processing to reduce the growth of most bacteria. However, psychrotrophic bacteria can proliferate and contribute to spoilage of ultra-high temperature (UHT) treated and sterilized milk and other dairy products with a long shelf life due to their ability to produce extracellular heat resistant enzymes such as peptidases and lipases. Worldwide, species of Pseudomonas, with the ability to produce these spoilage enzymes, are the most common contaminants isolated from cold raw milk although other genera such as Serratia are also reported as important milk spoilers, while for others more research is needed on the heat resistance of the spoilage enzymes produced. The residual activity of extracellular enzymes after high heat treatment may lead to technological problems (off flavors, physico-chemical instability) during the shelf life of milk and dairy products. This review covers the contamination patterns of cold raw milk in several parts of the world, the growth potential of psychrotrophic bacteria, their ability to produce extracellular heat-resistant enzymes and the consequences for dairy products with a long shelf life. This problem is of increasing importance because of the large worldwide trade in fluid milk and milk powder.

Time and temperature dependency of carbon dioxide triggered metal(loid) mobilization in soil

Assessing the influence of CO2 on soil and aquifer geochemistry is a task of increasing interest when considering risk assessment for geologic carbon sequestration. Leakage and CO2 ascent can lead to soil acidification and mobilization of potentially toxic metals and metalloids due to desorption or dissolution reactions. We studied the CO2 influence on an Fe(III) (oxyhydr)oxide rich, gleyic Fluvisol sampled in close vicinity to a Czech mofette site and compared the short-term CO2 influence in laboratory experiments with observations on long-term influence at the natural site. Six week batch experiments with/without CO2 gas flow at 3 different temperatures and monitoring of liquid phase metal(loid) concentrations revealed two main short-term mobilization processes. Within 1 h to 1 d after CO2 addition, mobilization of weakly adsorbed metal cations occurred due to surface protonation, most pronounced for Mn (2.5–3.3 fold concentration increase, mobilization rates up to 278 ± 18 μg Mn kgsoil−1 d−1) and strongest at low temperatures. However, total metal(loid) mobilization by abiotic desorption was low. After 1–3 d significant Fe mobilization due to microbially-triggered Fe(III) (oxyhydr)oxide dissolution began and continued throughout the experiment (up to 111 ± 24 fold increase or up to 1.9 ± 0.6 mg Fe kgsoil−1 d−1). Rates increased at higher temperature and with a higher content of organic matter. The Fe(III) mineral dissolution was coupled to co-release of incorporated metal(loid)s, shown for As (up to 16 ± 7 fold, 11 ± 8 μg As kgsoil−1 d−1). At high organic matter content, re-immobilization due to resorption reactions could be observed for Cu. The already low pH (4.5–5.0) did not change significantly during Fe(III) reduction due to buffering from sorption and dissolution reactions, but a drop in redox potential (from > +500 mV to minimum +340 ± 20 mV) occurred due to oxygen depletion. We conclude that microbial processes following CO2 induction into a soil can contribute significantly to metal(loid) mobilization, especially at optimal microbial growth conditions (moderate temperature, high organic carbon content) and should be considered for carbon sequestration monitoring and risk assessment.

In situ Dynamics of O2, pH, Light, and Photosynthesis in Ikaite Tufa Columns (Ikka Fjord, Greenland)-A Unique Microbial Habitat.

The Ikka Fjord (SW Greenland) harbors a unique microbial habitat in the form of several hundred submarine tufa columns composed of ikaite, a special hexahydrate form of calcium carbonate that precipitates when alkaline phosphate- and carbonate-enriched spring water seeping out of the sea floor meets cold seawater. While several unique heterotrophic microbes have been isolated from the tufa columns, the microbial activity, and the boundary conditions for microbial growth in ikaite have remained unexplored. We present the first detailed in situ characterization of the physico-chemical microenvironment and activity of oxygenic phototrophs thriving within the ikaite columns. In situ underwater microsensor measurements of pH, temperature, and irradiance in the porous ikaite crystal matrix, revealed an extreme microenvironment characterized by low temperatures, strong light attenuation, and gradients of pH changing from pH 9 at the outer column surface to above pH 10 over the first 1–2 cm of the ikaite. This outer layer of the freshly deposited ikaite matrix contained densely pigmented yellow and green zones harboring a diverse phototrophic community dominated by diatoms and cyanobacteria, respectively, as shown by amplicon sequencing. In situ O2 measurements, as well as underwater variable chlorophyll fluorescence measurements of photosynthetic activity, demonstrated high levels of oxygenic photosynthesis in this extreme gradient environment with strong irradiance-driven O2 dynamics ranging from anoxia to hyperoxic conditions in the ikaite matrix, albeit the local formation of gas bubbles buffered the day-night dynamics of O2 in the tufa columns. The microbial phototrophs in the ikaite matrix are embedded in exopolymers forming endolithic biofilms that may interact with mineral formation and cementing of ikaite crystals.

Insights into the Virulence Traits of Streptococcus mutans in Dentine Carious Lesions of Children with Early Childhood Caries

Streptococcus mutans is an oral bacterium considered to play a major role in the development of dental caries. This study aimed to investigate the prevalence of S. mutans in active and arrested dentine carious lesions of children with early childhood caries and to examine the expression profile of selected S. mutans genes associated with survival and virulence, within the same carious lesions. Dentine samples were collected from 29 active and 16 arrested carious lesions that were diagnosed in preschool children aged 2-5 years. Total RNA was extracted from the dentine samples, and reverse transcription quantitative real-time PCR analyses were performed for the quantification of S. mutans and for analyses of the expression of S. mutans genes associated with bacterial survival (atpD, nox, pdhA) and virulence (fabM and aguD). There was no statistically significant difference in the prevalence of S. mutans between active and arrested carious lesions. Expression of the tested genes was detected in both types of carious dentine. The pdhA (p = 0.04) and aguD (p = 0.05) genes were expressed at higher levels in arrested as compared to active lesions. Our findings revealed that S. mutans is part of the viable microbial community in active and arrested dentine carious lesions. The increase in expression of the pdhA and aguD genes in arrested lesions is likely due to the unfavourable environmental conditions for microbial growth, inherent to this type of lesions.

Co-production of acetone and ethanol with molar ratio control enables production of improved gasoline or jet fuel blends.

The fermentation of simple sugars to ethanol has been the most successful biofuel process to displace fossil fuel consumption worldwide thus far. However, the physical properties of ethanol and automotive components limit its application in most cases to 10-15 vol% blends with conventional gasoline. Fermentative co-production of ethanol and acetone coupled with a catalytic alkylation reaction could enable the production of gasoline blendstocks enriched in higher-chain oxygenates. Here we demonstrate a synthetic pathway for the production of acetone through the mevalonate precursor hydroxymethylglutaryl-CoA. Expression of this pathway in various strains of Escherichia coli resulted in the co-production of acetone and ethanol. Metabolic engineering and control of the environmental conditions for microbial growth resulted in controllable acetone and ethanol production with ethanol:acetone molar ratios ranging from 0.7:1 to 10.0:1. Specifically, use of gluconic acid as a substrate increased production of acetone and balanced the redox state of the system, predictively reducing the molar ethanol:acetone ratio. Increases in ethanol production and the molar ethanol:acetone ratio were achieved by co-expression of the aldehyde/alcohol dehydrogenase (AdhE) from E. coli MG1655 and by co-expression of pyruvate decarboxylase (Pdc) and alcohol dehydrogenase (AdhB) from Z. mobilis. Controlling the fermentation aeration rate and pH in a bioreactor raised the acetone titer to 5.1 g L(-1) , similar to that obtained with wild-type Clostridium acetobutylicum. Optimizing the metabolic pathway, the selection of host strain, and the physiological conditions employed for host growth together improved acetone titers over 35-fold (0.14-5.1 g/L). Finally, chemical catalysis was used to upgrade the co-produced ethanol and acetone at both low and high molar ratios to higher-chain oxygenates for gasoline and jet fuel applications. Biotechnol. Bioeng. 2016;113: 2079-2087. © 2016 Wiley Periodicals, Inc.

Characterization of Bioaerosols and their Relation with OC, EC and Carbonyl VOCs at a Busy Roadside Restaurants-Cluster in New Delhi

Measurement of biological particles (bioaerosols) in ambient air is of great importance as it is directly linked with the health issues. However, data on the bioaerosols characterization are scarce. Here we report on the concentration and characterization of bioaerosols (including bacterial and fungal aerosols) as well as determination of organic and elemental carbon (OC and EC) in total suspended particulate matter (TSPM) at a busy roadside restaurants-cluster site in New Delhi. In addition, 14 carbonyl volatile organic compounds (carbonyl VOCs) were also measured and their relationship with bioaerosols and OC/EC is assessed. The culturable airborne bacterial and fungal concentrations (CAB and CAF) at restaurant area varied significantly in different seasons ranging from 1.7 x 10(4)-9.8 x 10(4) (averaged 6.3 x 10(4) +/- 2.6 x 10(4) cfu m(-3)) and 3.5 x 10(2)-9.5 x 10(3) (3.9 x 10(3) +/- 3.1 x 10(3) cfu m(-3)) cfu m(-3), respectively. Major concentration peaks of TSPM, OC, EC as well as bacterial and fungal aerosols were found in winter and spring seasons. These peaks can be attributed to the low atmospheric boundary layer (ABL) height and favourable meteorological conditions for microbial growth in winter and spring seasons in New Delhi. Good correlations (R-2 > 0.5) were observed between CAB, CAF, TSPM and OC. On the other hand, CAB and CAF were not found to be correlated with carbonyl compounds (R2 < 0.2) indicative of their diverse sources. The bacterial identification was done by 16s rDNA sequencing and the identified strains were Bacillus sp., Bacillus firmus, Bacillus licheniformis, Bacillus cereus, Bacillus pumilus, Acinetobacter sp. and Acinetobactor radioresistens gene. Predominant fungal genera identified were Aspergillus, Cladosporium, Alternaria and Fusarium, which are known for adverse health effects causing numerous allergic and pathogenic inflammations.

Effect of C/N ratio and salinity on power generation in compost microbial fuel cells

In this work, compost Microbial Fuel Cells (cMFCs) were used to generate electricity from a mix of fruit and vegetable wastes, and soil with different C/N ratios and salinities. Experiments were carried out in 500mL cMFCs equipped with carbon felt anodes and manganese dioxide cathodes. The cMFCs were loaded with fresh compost and operated at 20–23°C for up to 97days. The low C/N ratio (C/N 24) had a greater power production with a maximum power density of 5.29mW/m2 (71.43mW/m3), indicating a more favorable condition for microbial growth. High-saline cMFCs produced lower power, suggesting that their level of salinity (10g/L of NaCl) inhibited electricigenic microorganisms. The closed-circuit cMFC showed an improved degradation of organic matter by 6% to 8% compared to the control MFC operated in an open circuit mode (no external resistor attached).

THE INFLUENCE OF FUNGI CONTAMINATION ON THE AVIATION FUEL AND BIOCIDE INHIBITOR

Aviation fuel is one of the fractions of fuel oil containing hydrocarbons and trace materials in the form of organic salts. Distribution of aviation fuel to the aircraft allows the aviation fuel contaminated by water due to condensation. The presence of water, hydrocarbons and organic compounds are appropriate conditions for microbial growth. The growth of microbes among other fungi generates biomass that sould can be able block fi lter between fuel tank in aircraft to the engine and have fatal consequences for flight operation. An efforts to prevent the growth of fungi is to add biocides in aviation fuel, which is in this study using formalin. Fungi was used in this experiments consists of four species which were dominant in the aviation fuel that are: Paecilomyces sp.1, Paecilomyces sp.2, Aspergillus sp., Scytalidium sp., as will as a the of mixed cultures of four species of fungus. The concentration of formalin is used as biocide were 150 ppm, 250 ppm and 500 ppm. Parameter measured are dry weight of fungi and physical characteristic of aviation fuel including specific gravity, smoke point, freezing point, copper strip corrosion and flash point. Experiment result showed that the addition of formalin could prevent the growth of fungi in aviation fuel. For Paecilomyces sp.1 and Paecilomyces sp.2, formalin concentration of 150 ppm can prevent fungi growth in aviation fuel signifi cantly. It takes 500 ppm for Aspergillus sp. and 250 ppm for Scytalidium sp. The concentration of formalin 250 ppm and 500 ppm were inhibit the growth of mixed culture. Analysis of the physical properties of aviation fuel, showed that the use of formalin does not affect the quality of aviation fuel in all parameters tested and they meet the quality standards of aviation fuel issued by Ministry of Defence. This means that formalin can be used as biocide for aviation fuel.

Relationships between the density and activity of microbial communities possessing arylsulfatase activity and soil sulfate dynamics during the decomposition of plant residues in soil

A laboratory incubation experiment was performed to examine the changes of soil microbial communities possessing arylsulfatase (ARS) activity. Different plant residues were incorporated into soils, and the resulting changes in the density and ARS activity of these communities relative to the sulfate content were studied. Mustard, fescue and wheat plant residues with different biochemical compositions and carbon (C):sulfur (S) ratios ranging from 60 to 486 were tested. Soil lacking residues was included as a control. Among the tested residues, mustard was the most labile and the most rapidly mineralized, leading to a significant 67% increase in the soil microbial biomass C (SMBC) compared with the control. The incorporation of mustard into soil induced a significant shift in the balance of microbes possessing ARS activity (ie. ratio bacteria:fungi) with an increase in the bacterial component producing ARS (ARS-B) but no change in ARS activity. A principal component analysis revealed clear differences between the soil samples according to both the nature of the residues incorporated and the duration of incubation. The correlation coefficients between the different variables showed that the ARS-B:ARS-F ratio was strongly correlated with the soil sulfate content (r = 0.81, p < 0.05). However, ARS activity was more closely correlated with ARS-F density than with ARS-B density (r = 0.63, p < 0.05 and r = 0.29, p < 0.1, respectively). The relative stability of the soil ARS activity, regardless of the nature of the residues incorporated was likely due to non-limiting S conditions for microbial growth in the soil used in this study.

Thiol-Based Selective Extraction Assay to Comparatively Assess Bioavailable Mercury in Sediments.

Bioaccumulation of methylmercury in the aquatic food web is governed in part by the methylation of inorganic divalent mercury (Hg(II)) by anaerobic microorganisms. In sulfidic settings, a small fraction of total Hg(II) is typically bioavailable to methylating microorganisms. Quantification of this fraction is difficult due to uncertainties in the speciation of Hg(II) and the mechanisms of uptake by methylating microbes. However, recent studies have shown that the bioavailable fraction is likely to include a portion of Hg(II) associated with solid phases, that is, nanostructured mercuric sulfides. Moreover, addition of thiols to suspensions of methylating cultures coincides with increased uptake into cells and methylmercury production. Here, we present a thiol-based selective extraction assay to provide information on the bioavailable Hg fraction in sediments. In the procedure, sediment samples were exposed to a nitrogen-purged solution of glutathione (GSH) for 30 min and the amount of GSH-leachable mercury was quantified. In nine sediment samples from a marine location, the relative GSH-leachable mercury concentration was strongly correlated to the relative amount of methylmercury in the sediments (r2=0.91, p<0.0001) across an order of magnitude of methylmercury concentration values. The approach was further applied to anaerobic sediment slurry microcosm experiments in which sediments were cultured under the same microbial growth conditions but were amended with multiple forms of Hg with a known spectrum of bioavailability. GSH-leachable Hg concentrations increased with observed methylmercury concentrations in the microcosms, matching the trend of species bioavailability in our previous work. Results suggest that a thiol-based selective leaching approach is an improvement compared with other proposed methods to assess Hg bioavailability in sediment and that this approach could provide a basis for comparison of sites where Hg methylation is a concern.

Effect of physico-chemical and operating conditions on the growth and activity of Acidithiobacillus ferrooxidans in a simulated heap bioleaching environment

Recent understanding of microbial retention within heap bioleaching systems has highlighted the importance of quantifying microbial growth and activity in both the bulk flowing solution and in the ore-associated phases. Typically, industrial heap bioleaching operations report variations in process conditions such as inoculum preparation and concentration and elevated copper concentrations in the recycled irrigation solution. In this paper, a mini-column reactor system containing pre-constructed and agglomerated, low-grade ore samples representing grab samples from a larger heap, were used to investigate the effect of a selection of physico-chemical and operating conditions on microbial growth, colonisation and substrate utilisation kinetics, considering both the planktonic and sessile populations of Acidithiobacillus ferrooxidans. The factors studied included inoculum size, inoculum cultivation conditions, availability of ferrous iron in the bulk flowing solution and copper concentration in the bulk flowing solution. The microbial population in the interstitial phase, i.e. associated with, but not bound to, the ore, remained the most abundant within the heap under all physico-chemical conditions considered. A comparison of the tests with different inoculum sizes found that a smaller inoculum size resulted in an increased delay in microbial growth and ferrous iron oxidation, but similar apparent maximum specific growth rates and iron oxidation rates. In contrast to the microbial culture grown on pyrite, a delay in microbial activity was observed for the culture grown on ferrous iron. However, greater microbial cell densities were reached, in the interstitial and attached phases compared with the pyrite-grown culture. The introduction of 6gL−1 cupric ions into the feed solution containing 0.2gL−1 ferric iron resulted in decreased microbial growth rate in the interstitial phase but not in the attached phase. Where the pyrite culture was pre-exposed to cupric ion, the microbial growth rate in the interstitial and attached phases was significantly enhanced. Nevertheless, the presence of cupric ion in the irrigation solution resulted in a decrease in microbial ferrous iron oxidation rate, irrespective of pre-culture conditioning. This study emphasises the important role played by the stagnant interstitial phase during the colonisation of a low-grade heap, particularly under adverse conditions for microbial growth and activity. It also highlights the role of inoculum culture conditions on the potential trade-off between increased heap colonisation and increased lag periods in microbial activity during heap start-up.

Biogenic gas accumulations in Canada and China: geological characteristics and new insights

Generation of biogenic gas occurs under environmental conditions different from those of thermogenic gas (Rice and Claypool, 1981; Whiticar et al. 1986; Shurr et al., 2003). Microbial activity takes place at shallow depth in a semi-open system where sediments are not fully compacted, seal integrity is not well developed, and accumulation and leakage of microbial gas are competing processes. Thus the formation of a commercial biogenic gas field needs both sufficient microbial activity to maintain gas supply and an efficient entrapment mechanism to minimize gas leakage. This depends on not only the temperature and other microbial growth conditions, but also on the characteristics and internal architecture of both source and reservoir strata. A better understanding of the essential controls and optimal conditions for critical microbial activity, and for the efficient entrapment of gas generated, is important to successful exploration for biogenic resources. This Special Issue of the Bulletin of Canadian Petroleum Geology contains nine thematic research articles on microbial gas resources and their characteristics in the Western Canada Sedimentary Basin and selected Chinese basins. The nine articles are based on the results and findings from a comparative study of shallow biogenic gas resources in Canadian and Chinese basins conducted under a collaborative research agreement between PetroChina and the Geological Survey of Canada during 2010–2013. The agreement provided a unique opportunity to study shallow biogenic gas fields with different origins and characteristics in the two countries. The primary objective of the project is to better understand the critical geological controls on biogenically derived natural gas resources in shallow strata and their resource potential. The characteristics of the biogenic gas fields and available data for describing and quantifying the biogenic gas fields in the two countries are complimentary. The long production history and large amount of public data make the …

Diversity and factors controlling widespread occurrence of syn-rift Ladinian microbialites in the western Tethys (Triassic Catalan Basin, NE Spain)

The fault-block carbonate ramps of the Ladinian (Middle Triassic) Catalan Basin hosted a wide variety of microbial deposits which formed during a syn-rift stage. Stratigraphical and sedimentological analyses of these microbialites allow us to reconstruct two depositional models for such microbial deposits. Moreover new insights into the interplay between the intrinsic and extrinsic factors that controlled the widespread development of these microbialites are provided. Stromatolites, ooidal-muddy microbial laminites and thrombolites were analyzed on the basis of their geometry, lamination and textural attributes. These microbialites are distributed over two Transgressive–Regressive sequences and coexisted during the Fassanian (Early Ladinian) regressive stage. Later, stromatolites and ooidal-muddy microbial laminites developed during the Longobardian (Late Ladinian) transgressive stage. Three types of lamina couplets reflect distinct accretion processes linked to water chemistry, sediment supply and hydrodynamic conditions. Thrombolite textures were produced by accretionary, binding and encrusting processes (microbially mediated) and pervasive cementation.The widespread occurrence of microbial deposits is explained as a consequence of a biogeochemical cascade of events (e.g., anoxic/dysoxic seawater conditions, volcanic activity, upwelling of alkaline waters, nutrient concentrations, and microbial blooms), which promoted favorable conditions for microbial growth in the Tethys during the Ladinian. Furthermore, in the Catalan Basin, syn-rift fault induced subsidence and local water energy gradients exerted an essential role in the distribution of the three types of microbialites through space and time. Thrombolites were prone to grow in the hanging wall block of a half-graben (subtidal conditions), whereas stromatolites and ooidal-muddy microbial laminites flourished preferably in a foot wall block setting (intertidal–shallow subtidal conditions). However, the fact that thrombolites exhibit abundant botryoidal and isopachous fibrous marine cements, corrosion and significant microbial evidence allow us to hypothesize about the relationship between thrombolite occurrence and hydrothermal fault-controlled fluid circulation during the Triassic rifting.The two depositional models here proposed constitute a step forward the understanding of the platform-to-basin microbialite heterogeneity during the Ladinian. Furthermore this work sheds new light on the mechanisms that likely promoted microbialite development during a period of major ecological restructuration and complex oceanographic conditions.