Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir

Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes.     

Monitoring exogenous and indigenous bacteria by PCR-DGGE technology during the process of microbial enhanced oil recovery

A field experiment was performed to monitor changes in exogenous bacteria and to investigate the diversity of indigenous bacteria during a field trial of microbial enhanced oil recovery (MEOR). Two wells (26-195 and 27-221) were injected with three exogenous strains and then closed to allow for microbial growth and metabolism. After a waiting period, the pumps were restarted and the samples were collected. The bacterial populations of these samples were analyzed by denaturing gradient gel electrophoresis (DGGE) with PCR-amplified 16S rRNA fragments. DGGE profiles indicated that the exogenous strains were retrieved in the production water samples and indigenous strains could also be detected. After the pumps were restarted, average oil yield increased to 1.58 and 4.52 tons per day in wells 26-195 and 27-221, respectively, compared with almost no oil output before the injection of exogenous bacteria. Exogenous bacteria and indigenous bacteria contributed together to the increased oil output. Sequence analysis of the DGGE bands revealed that Proteobacteria were a major component of the predominant bacteria in both wells. Changes in the bacteria population in the reservoirs during MEOR process were monitored by molecular analysis of the 16S rRNA gene sequence. DGGE analysis was a successful approach to investigate the changes in microorganisms used for enhancing oil recovery. The feasibility of MEOR technology in the petroleum industry was also demonstrated.     

Microbial response to reinjection of produced water in an oil reservoir

The microbial response to produced water reinjection (PWRI) in a North Sea oil field was investigated by a combination of cultivation and culture-independent molecular phylogenetic techniques. Special emphasise was put on the relationship between sulphate-reducing bacteria (SRB) and nitrate-reducing bacteria (NRB), and results were used to evaluate the possibility of nitrate treatment as a souring management tool during PWRI. Samples were collected by reversing the flow of the injection water, which provided samples from around the injection area. The backflowed samples were compared to produced water from the same platform and to backflowed samples from a biocide-treated seawater injector, which was the previous injection water treatment of the PWRI well. Results showed that reinjection of produced water promoted growth of thermophilic SRB. Thermophilic fatty acid oxidising NRB and potential nitrate-reducing sulphide-oxidising bacteria were also found. The finding of thermophilic NRB makes nitrate treatment during PWRI possible, although higher nitrate concentration will be necessary to compensate for the increased SRB activity.     

Optimization of the anaerobic treatment of a waste stream from an enhanced oil recovery process

The aim of this work was to optimize the anaerobic treatment of a waste stream from an enhanced oil recovery (EOR) process. The treatment of a simulated waste water containing about 150 mg chemical oxygen demand (COD)/L of total petroleum hydrocarbons (TPH) and the saturation level of CO₂ was evaluated. A two-step anaerobic system was undertaken in the mesophilic temperature range (30-40 °C). The method of evolutionary operation EVOP factorial design was used to optimize pH, temperature and organic loading rate with the target parameters of CO₂ reduction and CH₄ production in the first reactor and TPH removal in the second reactor. The results showed 98% methanogenic removal of CO₂ and CH₄ yield of 0.38 L/gCOD in the first reactor and 83% TPH removal in the second reactor. In addition to enhancing CO₂ and TPH removal and CH₄ production, application of this method showed the degree of importance of the operational variables and their interactive effects for the two reactors in series.     

Water status indicators of lemon trees in response to flooding and recovery

Potted 2-year-old lemon trees [Citrus limon (L.) Burm. fil, cv. Verna] grafted on sour orange (C. aurantium L.) rootstock were subjected to flooding for 3 d. Control plants were irrigated daily to field capacity. Continuously (sap flow, trunk diameter fluctuations) and discretely (predawn and midday leaf water potential, leaf conductance) measured plant-based water status indicators were compared. The sensitivity of the maximum daily trunk shrinkage signal intensity to flooding and its behaviour during the recovery period demonstrated that this indicator is more feasible than the others for use in automatic irrigation. The responses to flooding of continuously and discretely measured plant-based water status indicators were very similar to those observed in response to drought stress indicating that it necessary to use soil water measurement automatic sensors to detect the cause of the stress. The results underlined the robustness of the compensation heat-pulse technique for estimating instantaneous and daily transpiration rates on flooding stress and recovery.     

An investigation into some physical and biotic effects of flooding on reservoir mud previously subjected to a period of aerial exposure

A series of laboratory experiments were carried out in order to investigate the effects of selected physical and biotic processes on the substratum of a recently flooded gently sloping marginal zone of Plover Cove Reservoir, Hong Kong. The physical effects of disturbance of the sediments promoted the redistribution of organic matter, as shown by differences in the percentage of organic matter in the supernatant and residue resulting when reservoir mud was stirred. It is suggested that such a process would promote the transfer of allochthonous organic carbon from the marginal zone (the area of input of such material) to the rest of the water body. Substrate characteristics were also influenced by the activities of two species of benthic gastropod,Sinotaia quadrata andMelanoides tuberculata. These animals increased the rate of production of particles from soaked blocks of parent mud when compared with experimental treatments in the absence of snails. Additionally both species enhanced the production of aggregates from fine sediments with a particle size of less than 125 µm. The magnitudes of both processes were statistically significant. Laboratory observations showed thatM. tuberculata had a significantly faster rate of aggregate and fine particulate production thanS. quadrata and it is possible that the former species may have the capacity to modify the substrate characteristics of the newly flooded marginal zone of Plover Cove.Department of Zoology, The University of Hong Kong     

IFT proteins accumulate during cell division and localize to the cleavage furrow in Chlamydomonas

Intraflagellar transport (IFT) proteins are well established as conserved mediators of flagellum/cilium assembly and disassembly. However, data has begun to accumulate in support of IFT protein involvement in other processes elsewhere in the cell. Here, we used synchronous cultures of Chlamydomonas to investigate the temporal patterns of accumulation and localization of IFT proteins during the cell cycle. Their mRNAs showed periodic expression that peaked during S and M phase (S/M). Unlike most proteins that are synthesized continuously during G1 phase, IFT27 and IFT46 levels were found to increase only during S/M phase. During cell division, IFT27, IFT46, IFT72, and IFT139 re-localized from the flagella and basal bodies to the cleavage furrow. IFT27 was further shown to be associated with membrane vesicles in this region. This localization pattern suggests a role for IFT in cell division.     

Design of an ex vivo culture system to investigate the effects of shear stress on cardiovascular tissue

Mechanical forces are known to affect the biomechanical properties of native and engineered cardiovascular tissue. In particular, shear stress that results from the relative motion of heart valve leaflets with respect to the blood flow is one important component of their mechanical environment in vivo. Although different types of bioreactors have been designed to subject cells to shear stress, devices to expose biological tissue are few. In an effort to address this issue, the aim of this study was to design an ex vivo tissue culture system to characterize the biological response of heart valve leaflets subjected to a well-defined steady or time-varying shear stress environment. The novel apparatus was designed based on a cone-and-plate viscometer. The device characteristics were defined to limit the secondary flow effects inherent to this particular geometry. The determination of the operating conditions producing the desired shear stress profile was streamlined using a computational fluid dynamic (CFD) model validated with laser Doppler velocimetry. The novel ex vivo tissue culture system was validated in terms of its capability to reproduce a desired cone rotation and to maintain sterile conditions. The CFD results demonstrated that a cone angle of 0.5 deg, a cone radius of 40 mm, and a gap of 0.2 mm between the cone apex and the plate could limit radial secondary flow effects. The novel cone-and-plate permits to expose nine tissue specimens to an identical shear stress waveform. The whole setup is capable of accommodating four cone-and-plate systems, thus concomitantly subjecting 36 tissue samples to desired shear stress condition. The innovative design enables the tissue specimens to be flush mounted in the plate in order to limit flow perturbations caused by the tissue thickness. The device is capable of producing shear stress rates of up to 650 dyn cm(-2) s(-1) (i.e., maximum shear stress rate experienced by the ventricular surface of an aortic valve leaflet) and was shown to maintain tissue under sterile conditions for 120 h. The novel ex vivo tissue culture system constitutes a valuable tool toward elucidating heart valve mechanobiology. Ultimately, this knowledge will permit the production of functional tissue engineered heart valves, and a better understanding of heart valve biology and disease progression.     

Contrasting effects of habitat reduction,conversion and alteration on neutral and non neutral biological communities

While habitat transformation driven by human activities is the main driver of current biodiversity changes, there is still no framework to explore and forecast the effects of different types of habitat changes on the richness and composition of biological communities. To tackle this issue, we modeled the dynamics of a regional meta‐community, composed either of ecologically equivalent species (neutral model) or of generalist and specialist species (specialization model), and explored the impact of the overall reduction, patch conversion or alteration of an original habitat into one or several other habitats of different total carrying capacity on the community metrics at equilibrium. Our simulations reveal strong interactions between the community model considered (neutral or specialization model) and the type of habitat change. Under neutrality, the impact of habitat changes on richness can be approached by a power law species–individual relationship (SIR), which may at constant density be simplified into the widely used power law species–area relationship (SAR), independent of the type of change. However, in the presence of generalist and specialist species, we found that 1) while habitat reduction in area also leads to approximately power law SIRs and SARs, 2) patch conversion and alteration have more complex effects on regional species richness, and 3) habitat alteration elicits the functional homogenization of communities, involving a decrease of their average level of specialization.     

A pilot study to investigate the alteration of gut microbial profile in Dip2a knockout mice

International Microbiology - Accumulating evidence has pointed out that the gut-brain axis plays important roles in the etiology of autism spectrum disorder (ASD). Gut dysbiosis was reported in...     

Effect of exogenous inoculants on enhancing oil recovery and indigenous bacterial community dynamics in long-term field pilot of low permeability reservoir

Pseudomonas aeruginosa DN1 strain and Bacillus subtilis QHQ110 strain were chosen as rhamnolipid and lipopeptide producer respectively, to evaluate the efficiency of exogenous inoculants on enhancing oil recovery (EOR) and to explore the relationship between injected bacteria and indigenous bacterial community dynamics in long-term filed pilot of Hujianshan low permeability water-flooded reservoir for 26 months. Core-flooding tests showed that the oil displacement efficiency increased by 18.46% with addition of exogenous consortia. Bacterial community dynamics using quantitative PCR and high-throughput sequencing revealed that the exogenous inoculants survived and could live together with indigenous bacterial populations. They gradually became the dominant community after the initial activation, while their comparative advantage weakened continually after 3 months of the first injection. The bacterial populations did not exert an observable change in the process of the second injection of exogenous inoculants. On account of facilitating oil emulsification and accelerating bacterial growth with oil as the carbon source by the injection of exogenous consortia, γ-proteobacteria was finally the prominent bacterial community at class level varying from 25.55 to 32.67%, and the dominant bacterial populations were increased by 2–3 orders of magnitude during the whole processes. The content of organic acids and rhamnolipids in reservoir were promoted with the change of bacterial community diversity, respectively. Cumulative oil increments reached 26,190 barrels for 13 months after the first injection, and 55,947 barrels of oil had been accumulated in all of A20 wells block through two rounds of bacterial consortia injection. The performance of EOR has a cumulative improvement by the injection of exogenous inoculants without observable inhibitory effect on the indigenous bacterial populations, demonstrating the application potential in low permeability water-flooded reservoirs.     

Use of microelectrodes to investigate the effects of 2-chlorophenol on microbial activities in biofilms

In order to assess the applicability of using microelectrodes as a tool for inhibition tests, temporal and spatial inhibitory effects of 2-chlorophenol (2-CP) on O(2) respiration and nitrification activities in municipal wastewater biofilms were investigated using microelectrodes for O(2) and NH(4)(+). The time-course microelectrode measurements demonstrated that 2-CP inhibited O(2) respiration and nitrification activities within 6-18 min. The microbial activities were inhibited only in the upper 400 microm of the biofilms by 2-CP, and the bacteria present in the deeper parts of the biofilms were still active, probably due to limited penetration of 2-CP. These results could reasonably explain the difference in inhibitory ratios of the O(2) respiration and nitrification activities in the biofilms. O(2) respiration activity was incompletely inhibited, which was attributed to the presence of O(2) respiration activities in the deeper parts of the biofilm. In contrast, nitrification activity was significantly inhibited because ammonia-oxidizing bacteria were present in the upper parts of the biofilm. These results indicate that the microelectrodes with a very quick response time and a high spatial resolution are useful tools to study temporal and spatial inhibitory effects of inhibitors on in situ microbial activities in biofilms.     

Ethanol production in an integrated process of fermentation and ethanol recovery by pervaporation

In ethanol fermentations inhibition of the microorganism by ethanol limits the amount of substrate in the feed that can be converted. In a process high feed concentrations are desirable to minimize the flows. Such high feed concentrations can be realized in integrated processes in which ethanol is recovered from the fermentation broth as it is formed. In this study ethanol recovery by pervaporation was coupled to glucose fermentations by baker's yeast. Pervaporation was carried out with commercial silicone based hollow-fibre membrane modules with relatively high fluxes. Three different types of process configurations with pervaporation were investigated. Two of these configurations also included cell retention by microfiltration, in order to optimize the productivity. In the systems with pervaporation a feed containing 360 kg/m³ glucose could be converted almost completely. This feed concentration is a factor three higher than in a process without ethanol recovery. The productivity was 14 kg/m³ h in a system with pervaporation only, and could be increased to 43 kg/m³ h in the system with all recycle by microfiltration. The kinetic data suggest that accumulation of inhibitory compounds occurs in the integrated system. The integrated process was relatively easy in operation.     

The influence of circadian rhythm during a sustained submaximal exercise and on recovery process.

The purpose of this study was to examine the time-of-day effects on muscle fatigue and recovery process following an isometric fatiguing contraction. Sixteen male subjects were tested at two times (06:00h and 18:00h) and were requested to perform a sustained submaximal contraction of the elbow flexors, consisting in maintaining 40% of their absolute strength as long as they could. Isometric maximal voluntary contractions (MVC) were performed before (Pre), immediately after (Post), and up to 10min after the endurance task. Endurance time, peak torque (PT) and electromyographic (EMG) activities of the biceps brachii and triceps brachii were recorded and analysed. Results showed that under Pre-test conditions, PT developed at 18:00h was higher than at 06:00h. No time-of-day effect appears for the endurance time and EMG activities during the test. No time-of-day effect was observed on either MVC or EMG recovery. From the results of this study, it seems that both muscle fatigue and recovery process are not time-of-day dependent. We conclude that circadian rhythm of the force do not influence the evaluation of muscle capacities during a submaximal exercise corresponding at 40% of MVC.     

Using an NMR metabolomics approach to investigate the pathogenicity of amyloid-beta and alpha-synuclein

Introduction

The pathogenicity at differing points along the aggregation pathway of many fibril-forming proteins associated with neurodegenerative diseases is unclear. Understanding the effect of different aggregation states of these proteins on cellular processes is essential to enhance understanding of diseases and provide future options for diagnosis and therapeutic intervention.

Objectives

To establish a robust method to probe the metabolic changes of neuronal cells and use it to monitor cellular response to challenge with three amyloidogenic proteins associated with neurodegenerative diseases in different aggregation states.

Method

Neuroblastoma SH-SY5Y cells were employed to design a robust routine system to perform a statistically rigorous NMR metabolomics study into cellular effects of sub-toxic levels of alpha-synuclein, amyloid-beta 40 and amyloid-beta 42 in monomeric, oligomeric and fibrillar conformations.

Results

This investigation developed a rigorous model to monitor intracellular metabolic profiles of neuronal cells through combination of existing methods. This model revealed eight key metabolites that are altered when neuroblastoma cells are challenged with proteins in different aggregation states. Metabolic pathways associated with lipid metabolism, neurotransmission and adaptation to oxidative stress and inflammation are the predominant contributors to the cellular variance and intracellular metabolite levels. The observed metabolite changes for monomer and oligomer challenge may represent cellular effort to counteract the pathogenicity of the challenge, whereas fibrillar challenge is indicative of system shutdown. This implies that although markers of stress are more prevalent under oligomeric challenge the fibrillar response suggests a more toxic environment.

Conclusion

This approach is applicable to any cell type that can be cultured in a laboratory (primary or cell line) as a method of investigating how protein challenge affects signalling pathways, providing additional understanding as to the role of protein aggregation in neurodegenerative disease initiation and progression.

     

The effects of flooding on the formation of ectomycorrhizae in Pinus sylvestris seedlings

Pinus sylvestris seedlings, grown in a vertical petri dish system, were inoculated with five different mycorrhizal fungi. Half of the root system in the petri dish was subjected to periodic flooding, and mycorrhizal colonization was studied. Thelephora terrestris, Laccaria laccata, and Hebeloma crustuliniforme were not sensitive to flooding, whereas Suillus flavidus and S. bovinus were highly sensitive. The latter failed to colonize the root even when flooded for only 2 min per day four times a week.