Tariq Siddique

Anaerobic biodegradation of longer-chain n-alkanes coupled to methane production in oil sands tailings.

Extraction of bitumen from mined oil sands ores produces enormous volumes of tailings that are stored in settling basins (current inventory ≥ 840 million m(3)). Our previous studies revealed that certain hydrocarbons (short-chain n-alkanes [C(6)-C(10)] and monoaromatics [toluene, o-xylene, m-xylene]) in residual naphtha entrained in the tailings are biodegraded to CH(4) by a consortium of microorganisms. Here we show that higher molecular weight n-alkanes (C(14), C(16), and C(18)) are also degraded under methanogenic conditions in oil sands tailings, albeit after a lengthy lag (~180 d) before the onset of methanogenesis. Gas chromatographic analyses showed that the longer-chain n-alkanes each added at ~400 mg L(-1) were completely degraded by the resident microorganisms within ~440 d at ~20 °C. 16S rRNA gene sequence analysis of clone libraries implied that the predominant pathway of longer-chain n-alkane metabolism in tailings is through syntrophic oxidation of n-alkanes coupled with CO(2) reduction to CH(4). These studies demonstrating methanogenic biodegradation of longer-chain n-alkanes by microbes native to oil sands tailings may be important for effective management of tailings and greenhouse gas emissions from tailings ponds.

Chapter 5: Impact of pesticides on soil microbial diversity, enzymes, and biochemical reactions.

Abstract Pesticides are extensively used in agriculture as a part of pest control strategies. Owing to their xenobiotics characteristics, pesticides may adversely affect the proliferation of beneficial soil microorganisms and their associated biotransformation in the soil. Inactivation of nitrogen‐fixing and phosphorus‐solubilizing microorganisms is observed in pesticide‐contaminated soils. Recent studies show that some pesticides disturb molecular interactions between plants and N‐fixing rhizobacteria and consequently inhibit the vital process of biological nitrogen fixation. Similarly, many studies show that pesticides reduce activities of soil enzymes that are key indicators of soil health. The applied pesticides may also influence many biochemical reactions such as mineralization of organic matter, nitrification, denitrification, ammonification, redox reactions, methanogenesis, etc. However, a few reports reveal some positive effects of applied pesticides on soil health. In this chapter, we attempt to analyze the impacts of pesticides on soil microbial communities, soil biochemical reactions, and soil enzymes.

Microbial Communities Involved in Methane Production from Hydrocarbons in Oil Sands Tailings

Microbial metabolism of residual hydrocarbons, primarily short-chain n-alkanes and certain monoaromatic hydrocarbons, in oil sands tailings ponds produces large volumes of CH(4) in situ. We characterized the microbial communities involved in methanogenic biodegradation of whole naphtha (a bitumen extraction solvent) and its short-chain n-alkane (C(6)-C(10)) and BTEX (benzene, toluene, ethylbenzene, and xylenes) components using primary enrichment cultures derived from oil sands tailings. Clone libraries of bacterial 16S rRNA genes amplified from these enrichments showed increased proportions of two orders of Bacteria: Clostridiales and Syntrophobacterales, with Desulfotomaculum and Syntrophus/Smithella as the closest named relatives, respectively. In parallel archaeal clone libraries, sequences affiliated with cultivated acetoclastic methanogens (Methanosaetaceae) were enriched in cultures amended with n-alkanes, whereas hydrogenotrophic methanogens (Methanomicrobiales) were enriched with BTEX. Naphtha-amended cultures harbored a blend of these two archaeal communities. The results imply syntrophic oxidation of hydrocarbons in oil sands tailings, with the activities of different carbon flow pathways to CH(4) being influenced by the primary hydrocarbon substrate. These results have implications for predicting greenhouse gas emissions from oil sands tailings repositories.

Bioremediation and Phytoremediation of Pesticides: Recent Advances

The use of genetically modified or native microorganisms and plants to degrade or remove pollutants has emerged as a powerful technology for in situ remediation. An understanding of the genetic basis of the mechanisms of how microorganisms and plants biodegrade pollutants and how they interact with the environment is important for successful implementation of this technology. Recent studies have demonstrated that microbes and transgenic plants produce pesticide-degradaing enzymes that can mineralize different groups of pesticides and their metabolites with greater efficiency. This review describes the most recent progress in biotechnological approaches for enhancing the capability of microorganisms and plants through the characterization and transfer of pesticide-degrading genes, induction of catabolic pathways, and display of cell surface enzymes.

A first approximation kinetic model to predict methane generation from an oil sands tailings settling basin.

A small fraction of the naphtha diluent used for oil sands processing escapes with tailings and supports methane (CH(4)) biogenesis in large anaerobic settling basins such as Mildred Lake Settling Basin (MLSB) in northern Alberta, Canada. Based on the rate of naphtha metabolism in tailings incubated in laboratory microcosms, a kinetic model comprising lag phase, rate of hydrocarbon metabolism and conversion to CH(4) was developed to predict CH(4) biogenesis and flux from MLSB. Zero- and first-order kinetic models, respectively predicted generation of 5.4 and 5.1 mmol CH(4) in naphtha-amended microcosms compared to 5.3 (+/-0.2) mmol CH(4) measured in microcosms during 46 weeks of incubation. These kinetic models also predicted well the CH(4) produced by tailings amended with either naphtha-range n-alkanes or BTEX compounds at concentrations similar to those expected in MLSB. Considering 25% of MLSBs 200 million m(3) tailings volume to be methanogenic, the zero- and first-order kinetic models applied over a wide range of naphtha concentrations (0.01-1.0 wt%) predicted production of 8.9-400 million l CH(4) day(-1) from MLSB, which exceeds the estimated production of 3-43 million l CH(4) day(-1). This discrepancy may result from heterogeneity and density of the tailings, presence of nutrients in the microcosms, and/or overestimation of the readily biodegradable fraction of the naphtha in MLSB tailings.

Determinants of bacterial communities in Canadian agroforestry systems.

Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems.

Microbially-accelerated consolidation of oil sands tailings. Pathway I: changes in porewater chemistry

Dispersed clay particles in mine tailings and soft sediments remain suspended for decades, hindering consolidation and challenging effective management of these aqueous slurries. Current geotechnical engineering models of self-weight consolidation of tailings do not consider microbial contribution to sediment behavior, however, here we show that microorganisms indigenous to oil sands tailings change the porewater chemistry and accelerate consolidation of oil sands tailings. A companion paper describes the role of microbes in alteration of clay chemistry in tailings. Microbial metabolism in mature fine tailings (MFT) amended with an organic substrate (hydrolyzed canola meal) produced methane (CH4) and carbon dioxide (CO2). Dissolution of biogenic CO2 lowered the pH of amended MFT to pH 6.4 vs. unamended MFT (pH 7.7). About 12% more porewater was recovered from amended than unamended MFT during 2 months of active microbial metabolism, concomitant with consolidation of tailings. The lower pH in amended MFT dissolved carbonate minerals, thereby releasing divalent cations including calcium (Ca2+) and magnesium (Mg2+) and increasing bicarbonate (HCO−3) in porewater. The higher concentrations increased the ionic strength of the porewater, in turn reducing the thickness of the diffuse double layer (DDL) of clay particles by reducing the surface charge potential (repulsive forces) of the clay particles. The combination of these processes accelerated consolidation of oil sands tailings. In addition, ebullition of biogenic gases created transient physical channels for release of porewater. In contrast, saturating the MFT with non-biogenic CO2 had little effect on consolidation. These results have significant implications for management and reclamation of oil sands tailings ponds and broad importance in anaerobic environments such as contaminated harbors and estuaries containing soft sediments rich in clays and organics.

Microbially-accelerated consolidation of oil sands tailings. Pathway II: solid phase biogeochemistry

Consolidation of clay particles in aqueous tailings suspensions is a major obstacle to effective management of oil sands tailings ponds in northern Alberta, Canada. We have observed that microorganisms indigenous to the tailings ponds accelerate consolidation of mature fine tailings (MFT) during active metabolism by using two biogeochemical pathways. In Pathway I, microbes alter porewater chemistry to indirectly increase consolidation of MFT. Here, we describe Pathway II comprising significant, direct and complementary biogeochemical reactions with MFT mineral surfaces. An anaerobic microbial community comprising Bacteria (predominantly Clostridiales, Synergistaceae, and Desulfobulbaceae) and Archaea (Methanolinea/Methanoregula and Methanosaeta) transformed FeIII minerals in MFT to amorphous FeII minerals during methanogenic metabolism of an added organic substrate. Synchrotron analyses suggested that ferrihydrite (5Fe2O3. 9H2O) and goethite (α-FeOOH) were the dominant FeIII minerals in MFT. The formation of amorphous iron sulfide (FeS) and possibly green rust entrapped and masked electronegative clay surfaces in amended MFT. Both Pathways I and II reduced the surface charge potential (repulsive forces) of the clay particles in MFT, which aided aggregation of clays and formation of networks of pores, as visualized using cryo-scanning electron microscopy (SEM). These reactions facilitated the egress of porewater from MFT and increased consolidation of tailings solids. These results have large-scale implications for management and reclamation of oil sands tailings ponds, a burgeoning environmental issue for the public and government regulators.

Reversed-phase liquid chromatographic method for analysis of endosulfan and its major metabolites

Abstract A high performance liquid chromatographic (HPLC) method suitable for the analysis of endosulfan and its metabolites in water and soil is described. Endosulfan is a contact and stomach insecticide, which is extremely toxic to fish, birds, and mammals. This method utilizes a µBondapak C18 reversed‐phase column and acetonitrile:water (70:30 v/v) or methanol:water (70:30 v/v) as a mobile phase. The maximum absorbance spectrum was obtained at 214 nm. Both mobile phases resolved the endosulfan isomers and their metabolites well (resolution R S > 1.5). Acetonitrile recovered α‐endosulfan (106 and 90%) and β‐endosulfan (103 and 80%), while methanol extracted α‐endosulfan (91 and 81%) and β‐endosulfan (72 and 56%) from water and soil slurry, respectively. Recovery of endosulfan sulfate, endosulfan diol, and endosulfan ether with acetonitrile was 99, 90, and 101% in water and 91, 81, and 90% in a soil slurry, respectively. The method has high selectivity towards the major metabolites of endosulfan. The method was optimized in extraction and chromatographic detection by HPLC.

Preferential methanogenic biodegradation of short-chain n-alkanes by microbial communities from two different oil sands tailings ponds.

Oil sands tailings ponds harbor diverse anaerobic microbial communities capable of methanogenic biodegradation of solvent hydrocarbons entrained in the tailings. Mature fine tailings (MFT) from two operators (Albian and CNRL) that use different extraction solvents were incubated with mixtures of either two (n-pentane and n-hexane) or four (n-pentane, n-hexane, n-octane and n-decane) n-alkanes under methanogenic conditions for ~600 d. Microbes in Albian MFT began methane production by ~80 d, achieving complete depletion of n-pentane and n-hexane in the two-alkane mixture and their preferential biodegradation in the four-alkane mixture. Microbes in CNRL MFT preferentially metabolized n-octane and n-decane in the four-alkane mixture after a ~80 d lag but exhibited a lag of ~360 d before commencing biodegradation of n-pentane and n-hexane in the two-alkane mixture. 16S rRNA gene pyrosequencing revealed Peptococcaceae members as key bacterial n-alkane degraders in all treatments except CNRL MFT amended with the four-alkane mixture, in which Anaerolineaceae, Desulfobacteraceae (Desulfobacterium) and Syntrophaceae (Smithella) dominated during n-octane and n-decane biodegradation. Anaerolineaceae sequences increased only in cultures amended with the four-alkane mixture and only during n-octane and n-decane biodegradation. The dominant methanogens were acetoclastic Methanosaetaceae. These results highlight preferential n-alkane biodegradation by microbes in oil sands tailings from different producers, with implications for tailings management and reclamation.