Pore‐network modeling of biofilm evolution in porous media

The influence of bacterial biomass on hydraulic properties of porous media (bioclogging) has been explored as a viable means for optimizing subsurface bioremediation and microbial enhanced oil recovery. In this study, we present a pore network simulator for modeling biofilm evolution in porous media including hydrodynamics and nutrient transport based on coupling of advection transport with Fickian diffusion and a reaction term to account for nutrient consumption. Biofilm has non‐zero permeability permitting liquid flow and transport through the biofilm itself. To handle simultaneous mass transfer in both liquid and biofilm in a pore element, a dual‐diffusion mass transfer model is introduced. The influence of nutrient limitation on predicted results is explored. Nutrient concentration in the network is affected by diffusion coefficient for nutrient transfer across biofilm (compared to water/water diffusion coefficient) under advection dominated transport, represented by mass transport Péclet number >1. The model correctly predicts a dependence of rate of biomass accumulation on inlet concentration. Poor network connectivity shows a significantly large reduction of permeability, for a small biomass pore volume. Biotechnol. Bioeng. 2011;108: 2413–2423. © 2011 Wiley Periodicals, Inc.     

Xanthan degragation by biofilm in porous media

Biological activity in oil reservoirs can cause significant problems such as souring and plugging. This study focuses on the problem of polymer degradation and permeability reduction due to biofilm formation during polymer injection for improved oil recovery. Polymers are included in injection fluids to increase their viscosity. Results relating biological processes and polymer degradation to fluid‐dynamic conditions in a laboratory model porous medium are presented.

A transparent flow cell with an etched two‐dimensional network of pores served as a model porous medium. A sterile xanthan polymer and natural sea water solution were continuously injected into the porous medium. A bacterial culture capable of xanthan degradation was introduced into the cell by a single injection. Some of the cells from this culture attached to the pore walls forming an immobile bacterial culture, termed biofilm. The development of this biofilm, its xanthan degradation and its effect on permeability were measured.

The effects of injection rate and rate transitions were analyzed. Injection fluid viscosity was reduced by 30% after 5 min flow through the porous medium at the maximum steady state degradation rate observed. Permeability was significantly reduced by the xanthan degrading biofilm, causing an increase in pressure drop through the porous medium of up to 80%. Polymer injection in oil reservoirs may, therefore, have negative effects on oil recovery, unless efficient biofouling control is applied. The methodology presented may serve as a tool in the development of biofouling control measures in porous media.     

Selection of Bacteria with Favorable Transport Properties Through Porous Rock for the Application of Microbial-Enhanced Oil Recovery

This paper presents a bench-scale study on the transport in highly permeable porous rock of three bacterial species—Bacillus subtilis, Pseudomonas putida, and Clostridium acetobutylicum—potentially applicable in microbial-enhanced oil recovery processes. The transport of cells during the injection of bacterial suspension and nutrient medium was simulated by a deep bed filtration model. Deep bed filtration coefficients and the maximum capacity of cells in porous rock were measured. Low to intermediate (~10⁶/ml) injection concentrations of cellular suspensions are recommended because plugging of inlet surface is less likely to occur. In addition to their resistance to adverse environments, spores of clostridia are strongly recommended for use in microbial-enhanced oil recovery processes since they are easiest among the species tested to push through porous rock. After injection, further transport of bacteria during incubation can occur by growth and mobility through the stagnant nutrient medium which fills the porous rock. We have developed an apparatus to study the migration of bacteria through a Berea sandstone core containing nutrient medium.     

超低渗油藏微生物吞吐技术的矿场试验

【目的】通过对渭北低渗油藏内源微生物的研究,考察分离纯化的内源解烃菌产生表面活性剂和降解原油的能力、岩心驱替增油效率,同时验证其在超低渗油田单井吞吐矿场实验的应用效果,探讨微生物采油技术在超低渗油田提高采收率的工艺和可行性。【方法】采集超低渗油藏的油水样,应用油平板进行产表面活性剂解烃菌的分离,通过生理生化特性和16S r RNA基因序列分析对菌株进行种属鉴定,评价其油藏环境适应性,利用内源-外源功能微生物复配体系进行原油降解,在填砂管和岩心物模上进行驱油实验,将优化好的微生物复配体系应用于现场实施单井吞吐工艺的实验。【结果】从渭北某区块超低渗油藏的原油样品中分离得到一株铜绿假单胞菌(Pseudomonas aeruginosa),命名为WB-001。该菌株可使发酵液的表面张力降至29.04 m N/m,使渭北原油蜡质含量降至8.48%。填砂管实验表明WB-001与外源枯草芽胞杆菌OPUS-HOB-001(Bacillus subtilis)复配后,驱油效率较单纯水驱提高了9.72%;岩心驱替实验较水驱提高12.54%。微生物单井吞吐措施后,平均日产油由措施前的0.42 t增加到0.89 t,累计增油44.47 t;原油降粘率为11.70%,降凝率为9.41%,采出水表面张力降低幅度为18.93%。【结论】通过详细的室内评估和成功的矿场实验,证明微生物采油技术在超低渗油藏有一定的应用可行性,并为后续规模化应用提供了理论基础和物质基础,为超低渗油田的高效精细开发探索一条新的途径。     

Reduction of porous media permeability from in situ Leuconostoc mesenteroides growth and dextran production

In situ growth of bacteria in a porous medium can alter the permeability of that media. This article reveals that the rate of permeability alteration can be controlled by the inoculation strategy, nutrient concentrations, and injection rates. Based on experimental observations a phenomenological model has been developed to describe the inoculation of the porous medium, the in situ growth of bacteria, and the permeability decline of the porous medium. This model consists of two phases that describe the bacteria in the porous medium: (1) the nongrowth phase in which cell transport and retention are occurring; and (2) the growth phase in which the retained cells grow and plug the porous media. Transition from the transport phase to the growth phase is governed by the growth lag time of the cells within the porous medium. The importance of the inoculum injection strategy and the nutrient injection strategy is illustrated by the model. (c) 1996 John Wiley & Sons, Inc.     

模拟油藏条件下内源微生物群落空间分布规律

【背景】油藏内源微生物群落是开展内源微生物驱油技术的物质基础,由于油藏多孔介质取样技术难度大、成本高,实施内源微生物驱油后从注入端到产出端多孔介质中的内源微生物空间分布规律尚不明确。【目的】通过室内长岩心连续驱替实验模拟油藏内源微生物驱油过程,分析实施后不同空间位点油砂上吸附的内源微生物群落结构,揭示从注入端到产出端内源微生物群落的空间分布规律。【方法】借助高通量测序技术及荧光定量PCR技术解析不同空间位点油砂原位微生物群落信息。【结果】注入端到产出端不同空间位点生态环境的差异及菌属间的相互作用造成油藏内源微生物群落空间分布差异,存在明显的好氧、厌氧空间演替变化规律。岩心前端主要存在一些好氧类的产生物表面活性剂类微生物如假单胞菌属,岩心中部主要存在兼性和厌氧类的微生物如地芽孢杆菌、厌氧杆菌属,岩心末端主要分布严格厌氧类细菌和产甲烷古菌,厌氧类微生物代谢产生的H2、CO2和乙酸分子可以为产甲烷古菌提供代谢底物。【结论】通过室内物模油砂研究,首次明确了内源微生物群落在多孔介质中从注入端到产出端的空间分布规律,证实油藏内源微生物的好氧、厌氧空间接替分布规律,深化了对油藏内源微生物的认识。     

Towards optimum permeability reduction in porous media using biofilm growth simulations

While biological clogging of porous systems can be problematic in numerous processes (e.g., microbial enhanced oil recovery—MEOR), it is targeted during bio‐barrier formation to control sub‐surface pollution plumes in ground water. In this simulation study, constant pressure drop (CPD) and constant volumetric flow rate (CVF) operational modes for nutrient provision for biofilm growth in a porous system are considered with respect to optimum (minimum energy requirement for nutrient provision) permeability reduction for bio‐barrier applications. Biofilm growth is simulated using a Lattice‐Boltzmann (LB) simulation platform complemented with an individual‐based biofilm model (IbM). A biomass detachment technique has been included using a fast marching level set (FMLS) method that models the propagation of the biofilm–liquid interface with a speed proportional to the adjacent velocity shear field. The porous medium permeability reduction is simulated for both operational modes using a range of biofilm strengths. For stronger biofilms, less biomass deposition and energy input are required to reduce the system permeability during CPD operation, whereas CVF is more efficient at reducing the permeability of systems containing weaker biofilms. Biotechnol. Bioeng. 2009;103: 767–779. © 2009 Wiley Periodicals, Inc.     

Interaction of Escherichia coli B and B/4 and Bacteriophage T4D with Berea Sandstone Rock in Relation to Enhanced Oil Recovery

Much research and development is needed to recover oil reserves presently unattainable, and microbially enhanced oil recovery is a technology that may be used for this purpose. To address the problem of bacterial contamination in an oil field injection well region, we connected each end of a Teflon-sleeved Berea sandstone rock to a flask containing nutrient medium. By inoculating one flask with Escherichia coli B, we could observe bacterial growth in the uninoculated flask resulting from the transport and establishment of cells across the rock. Differences in bacterial populations occurred depending on whether bacteriophage T4D was first adsorbed to the rock. The results of these experiments indicate that the inhibition of bacterial establishment within a rock matrix is possible via lytic interaction. Some nonlytic effects are also implied by experiments with B/4 cells, which are T4D-resistant mutants of E. coli B. A 10 to 40% retention of T4 by the rock occurred when it was loaded with 10⁵ to 10⁶ PFU. We also describe a lysogenic system for possible use in microbially enhanced oil recovery techniques.     

Effect of biological activity on the movement of fluids through porous rocks and sediments and its application to enhanced oil recovery

Movement of fluids through geological porous media is an important factor in ore genesis, crude oil genesis, and in oil recovery from oil reservoirs. Such a movement may be beneficially affected by biological in situ activity. We have shown that once bacteria have been introduced into a porous medium, they are able to penetrate into their environment and multiply without decreasing significantly the rock's permeability. The limiting bacterial concentration, which may cause plugging, depends on the bacterial size, pore size, and pore size distribution of the reservoir rock. Microorganisms may, under anaerobic conditions, affect the composition of crude oil by increasing its asphaltenic fraction. In simulated systems microorganisms increased the recovery of the oil in place approximately five times. A bacterial consortium was more effective than a single pure bacterial strain.     

Transport of bacteria in porous media: II. A model for convective Transport and growth

A model is presented for the coupled processes of bacterial growth and convective transport of bacteria has been modeled using a fractional flow approach. The various mechanisms of bacteria retention can be incorporated into the model through selection of an appropriate shape of the fractional flow curve. Permeability reduction due to pore plugging by bacteria was simulated using the effective medium theory. In porous media, the rates of transport and growth of bacteria, the generation of metabolic products, and the consumption of nutrients are strongly coupled processes. Consequently, the set of governing conservation equations form a set of coupled, nonlinear partial differential equations that were solved numerically. Reasonably good agreement between the model and experimental data has been obtained indicating that the physical processes incorporated in the model are adequate. The model has been used to predict the in situ transport and growth of bacteria, nutrient consumption, and metabolite production. It can be particularly useful in simulating laboratory experiments and in scaling microbial-enhanced oil recovery or bioremediation processes to the field. (c) 1994 John Wiley & Sons, Inc.     

Dispersed oil disrupts microbial pathways in pelagic food webs

Most of the studies of microbial processes in response to the Deepwater Horizon oil spill focused on the deep water plume, and not on the surface communities. The effects of the crude oil and the application of dispersants on the coastal microbial food web in the northern Gulf of Mexico have not been well characterized even though these regions support much of the fisheries production in the Gulf. A mesocosm experiment was carried out to determine how the microbial community off the coast of Alabama may have responded to the influx of surface oil and dispersants. While the addition of glucose or oil alone resulted in an increase in the biomass of ciliates, suggesting transfer of carbon to higher trophic levels was likely; a different effect was seen in the presence of dispersant. The addition of dispersant or dispersed oil resulted in an increase in the biomass of heterotrophic prokaryotes, but a significant inhibition of ciliates, suggesting a reduction in grazing and decrease in transfer of carbon to higher trophic levels. Similar patterns were observed in two separate experiments with different starting nutrient regimes and microbial communities suggesting that the addition of dispersant and dispersed oil to the northern Gulf of Mexico waters in 2010 may have reduced the flow of carbon to higher trophic levels, leading to a decrease in the production of zooplankton and fish on the Alabama shelf.     

胜利油藏不同时间细菌群落结构的比较

利用聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)和构建16S rRNA基因克隆文库2种方法,对孤岛油田两口井(注水井G和采油井L)在相距9个月的2个时间点(A和B)所采集样品的细菌群落结构进行了比较。DGGE图谱聚类分析表明注水井在2个时间点的微生物群落结构相似性为48.1%,而采油井的相似性只有28.7%。16S rRNA基因克隆文库结果表明,A时间点样品G中的优势菌群为Betaproteobacteria、Gammaproteobacteria,还有Deferribacteres、Firmicutes、Bacteroidetes等;而样品L中,Gammaproteobacteria中的Moraxellaceae含量达到97%。B时间点G中除了优势菌Betaproteobacteria之外,Deferribacteres的数量显著增加,成为优势菌;而L在B时间点优势菌除Gammaproteobacteria外,还有Betaproteobacteria和Firmicutes。采油井中的微生物群落结构随时间发生了显著改变,而注水井变化不显著。这一结果部分揭示了微生物采油过程中地层微生物群落的变化规律,有助于进一步阐明微生物驱油的机理。     

Reactive Transport Modeling of Induced Selective Plugging by Leuconostoc Mesenteroides in Carbonate Formations

A process-based mechanistic reactive transport model was developed to understand how in-situ coupled processes and operational factors affect selective plugging of reactive carbonate formations by the fermenting bacteria Leuconostoc mesenteroides that produces a plugging polymer dextran. The growth and transport of L. mesenteroides and the associated (bio) geochemical reactions were simulated explicitly with enzyme activity at the field scale over spatial extents of hundreds of meters. Simulations were performed to explore controls on selective bioplugging of high permeability zones in a representative carbonate reservoir, a process that can be used to improve oil sweep efficiency through lower permeability layers. Simulation results indicate that dextran production and the effectiveness of plugging can be largely affected by sucrose and bacteria injection rates. Selective plugging of high permeability zones can only be achieved when the injection rates are high compared to the rates of dextran production. Otherwise, plugging only occurs at the vicinity of injection wells. Due to the dependence of enzyme activity on pH and the reactive nature of carbonate formations, the chemistry of the injection and the formation water is also important. The injection of sucrose and L. mesenteroides at the optimum pH for dextran production (5.2) leads to the dissolution of calcite and an increase in pH levels. However, the resulting pH does not suppress plugging with dextran. Lactic acid and CO₂ formed during the growth of L. mesenteroides buffers the pH of water to levels between 5.2 and 7.0 for continued dextran production. At neutral and basic pH levels, induced precipitation of calcite does not significantly modify the permeability profile at carbonate concentrations typically found in oilfield formation waters. This is the first work that examines the controlling parameters that affect selective plugging of carbonate formations at the field scale within the context of enhanced oil recovery. The demonstrated approach can be used to identify optimal operational conditions for enhanced oil recovery and other applications where selective plugging can be beneficial.     

Microbial selective plugging and enhanced oil recovery

Summary The ability of indigenous populations of microorganisms in Berea sandstone to improve the volumetric sweep efficiency and increase oil recovery by in situ growth and metabolism following the injection of nutrients was studied. Cores of differing permeabilities connected in parallel without crossflow and slabs of sandstone with differing permeabilities in capillary contact to allow crossflow were used. The addition of a sucrosenitrate mineral salts medium stimulated the growth and metabolism of microorganisms in the sandstone systems. This resulted in a preferential decrease in permeability in the core or slab with the higher initial permeability, diverted flow into the lower-permeability core or slab and improved the volumetric sweep efficiency. Injectivity into the slab with the lower initial permeability in the crossflow system increased during subsequent nutrient injections. Thus, microbial selective plugging does occur in laboratory systems that have the complex flow patterns observed in petroleum reservoirs without losing the ability to inject fluids into the formation. In situ microbial growth and metabolism increased oil recovery 10 to 38% of the original oil in place. Biogenic gas production accompanied oil production, and much of the gas was entrained within the produced oil suggesting that gas production was an important factor leading to increased oil recovery. Quantitation of the amount of phospholipid in the core confirmed that microbial growth preferentially occurred throughout the core with the higher initial permeability. These data showed that in situ microbial growth in the high-permeability regions improved not only the volumetric sweep efficiency but also the microscopic oil displacement efficiency.     

厌氧产表面活性剂微生物提高原油采收率的研究进展

微生物强化采油(microbial enhanced oil recovery,MEOR)是近年来在国内外发展迅速的一项提高原油采收率技术。微生物在油藏中高效生产表面活性剂等驱油物质是微生物采油技术成功实施的关键之一。然而,油藏的缺/厌氧环境严重影响好氧表面活性剂产生菌在油藏原位的生存与代谢活性;油藏注空气会增加开采成本,且注入空气的作用时效和范围难以确定。因此,开发厌氧产表面活性剂菌种资源并强化其驱油效率对于提高原油采收率具有重要意义。本文综述了国内外近年来利用厌氧产表面活性剂微生物提高原油采收率的研究进展,简述了微生物厌氧产表面活性剂的相关驱油机理、菌种资源开发现状以及油藏原位驱油应用进展,并对当前的研究提出了一些思考。     

油藏本源反硝化功能菌的产气作用(N2O)及对原油物性的影响

利用叠皿夹层培养法从新疆油田采出水中筛选到8株反硝化菌株T1、D1、D44、D46、D15、S1、S2、S6,经16S rDNA序列测定鉴定分析,这8株菌分别与施氏假单胞菌(T1、D1、D44)、恶臭假单胞菌(D46、D15)和铜绿假单胞菌(S1、S2、S6)相似,相似度均达到100%。通过室内批次培养试验,评价了这8株菌利用不同碳源的反硝化产气作用(N₂O)及对原油物性的影响。结果表明: 在以蔗糖为碳源时,产气量最大,以甘油为碳源时,产N₂O气浓度最高;菌株反硝化代谢过程导致原油体积膨胀和粘度降低,膨胀率与N₂O气体浓度呈显著正相关,相关系数为0.983,但与产气体积无相关性;铜绿假单胞菌株S1、S2、S6在以甘油为唯一碳源时产生少量表面活性剂(530～730 mg·L^-1),可降低表面张力并具有乳化原油的作用,但其产气量较少,对原油的膨胀与降粘作用低于其他反硝化菌株。研究提示,在筛选采油功能菌时,菌株反硝化产N₂O气体的能力应给予足够重视。     

Influence of a Rhamnolipid Biosurfactant on the Transport of Bacteria through a Sandy Soil

The objective of this study was to investigate the influence of an anionic rhamnolipid biosurfactant on the transport of bacterial cells through soil under saturated conditions. Three cell types with various hydrophobicities, i.e., Pseudomonas aeruginosa ATCC 9027, ATCC 27853, and ATCC 15442, were used in this study. In a series of experiments, columns packed with sterile sand were saturated with sterile artificial groundwater for 15 h, and then 3 pore volumes of (sup3)H-labeled bacterial suspensions with various rhamnolipid concentrations was pumped through the column. This was followed by 4 pore volumes of the rhamnolipid solution alone. The measured bacterial cell breakthrough curves were optimized by using an advection-dispersion transport model incorporating two-domain reversible sorption (instantaneous and rate limited) and with two first-order sink terms for irreversible adsorption. The influence of the rhamnolipid on the surface charge densities of the bacteria and the porous medium was also investigated. The results show that the rhamnolipid enhanced the transport of all cell types tested. For example, the rhamnolipid increased the recovery of the most hydrophilic strain, ATCC 9027, from 22.5 to 56.3%. Similarly, the recovery of ATCC 27853 increased from 36.8 to 49.4%, and the recovery of ATCC 15442, the most hydrophobic strain, increased from 17.7 to 40.5% in the presence of the rhamnolipid. The negative surface charge density of the porous medium was increased, while the surface charge density of the bacteria was not changed in the presence of the rhamnolipid. The model results suggest that the rhamnolipid predominantly affected irreversible adsorption of cells.     

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.     

A microscale model of bacterial and biofilm dynamics in porous media

A microscale model for the transport and coupled reaction of microbes and chemicals in an idealized two-dimensional porous media has been developed. This model includes the flow, transport, and bioreaction of nutrients, electron acceptors, and microbial cells in a saturated granular porous media. The fluid and chemicals are represented as a continuum, but the bacterial cells and solid granular particles are represented discretely. Bacterial cells can attach to the particle surfaces or be advected in the bulk fluid. The bacterial cells can also be motile and move preferentially via a run and tumble mechanism toward a chemoattractant. The bacteria consume oxygen and nutrients and alter the profiles of these chemicals. Attachment of bacterial cells to the soil matrix and growth of bacteria can change the local permeability. The coupling of mass transport and bioreaction can produce spatial gradients of nutrients and electron acceptor concentrations. We describe a numerical method for the microscale model, show results of a convergence study, and present example simulations of the model system.