O2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters

The acidification of water in mining areas is a global environmental issue primarily catalyzed by sulfur-oxidizing bacteria (SOB). Little is known about microbial sulfur cycling in circumneutral pH mine tailing impoundment waters. Here we investigate biological sulfur oxidation over four years in a mine tailings impoundment water cap, integrating aqueous sulfur geochemistry, genome-resolved metagenomics and metatranscriptomics. The microbial community is consistently dominated by neutrophilic, chemolithoautotrophic SOB (relative abundances of ~76% in 2015, ~55% in 2016/2017 and ~60% in 2018). Results reveal two SOB strategies alternately dominate across the four years, influencing acid generation and sulfur speciation. Under oxic conditions, novel Halothiobacillus drive lower pH conditions (as low as 4.3) and lower [S₂O₃^2-] via the complete Sox pathway coupled to O₂. Under anoxic conditions, Thiobacillus spp. dominate in activity, via the incomplete Sox and rDSR pathways coupled to NO₃^-, resulting in higher [S₂O₃^2-] and no net significant acidity generation. This study provides genomic evidence explaining acidity generation and thiosulfate accumulation patterns in a circumneutral mine tailing impoundment and has significant environmental applications in preventing the discharge of sulfur compounds that can impact downstream environments. These insights illuminate opportunities for in situ biotreatment of reduced sulfur compounds and prediction of acidification events using gene-based monitoring and in situ RNA detection.

Phage-encoded ribosomal protein S21 expression is linked to late-stage phage replication

The ribosomal protein S21 (bS21) gene has been detected in diverse viruses with a large range of genome sizes, yet its in situ expression and potential significance have not been investigated. Here, we report five closely related clades of bacteriophages (phages) represented by 47 genomes (8 curated to completion and up to 331 kbp in length) that encode a bS21 gene. The bS21 gene is on the reverse strand within a conserved region that encodes the large terminase, major capsid protein, prohead protease, portal vertex proteins, and some hypothetical proteins. Based on CRISPR spacer targeting, the predominance of bacterial taxonomic affiliations of phage genes with those from Bacteroidetes, and the high sequence similarity of the phage bS21 genes and those from Bacteroidetes classes of Flavobacteriia, Cytophagia and Saprospiria, these phages are predicted to infect diverse Bacteroidetes species that inhabit a range of depths in freshwater lakes. Thus, bS21 phages have the potential to impact microbial community composition and carbon turnover in lake ecosystems. The transcriptionally active bS21-encoding phages were likely in the late stage of replication when collected, as core structural genes and bS21 were highly expressed. Thus, our analyses suggest that the phage bS21, which is involved in translation initiation, substitutes into the Bacteroidetes ribosomes and selects preferentially for phage transcripts during the late-stage replication when large-scale phage protein production is required for assembly of phage particles.

Alum Addition Triggers Hypoxia in an Engineered Pit Lake

Here, we examine the geobiological response to a whole-lake alum (aluminum sulfate) treatment (2016) of Base Mine Lake (BML), the first pilot-scale pit lake established in the Alberta oil sands region. The rationale for trialing this management amendment was based on its successful use to reduce internal phosphorus loading to eutrophying lakes. Modest increases in water cap epilimnetic oxygen concentrations, associated with increased Secchi depths and chlorophyll-a concentrations, were co-incident with anoxic waters immediately above the fluid fine tailings (FFT) layer post alum. Decreased water cap nitrate and detectable sulfide concentrations, as well as increased hypolimnetic phospholipid fatty acid abundances, signaled greater anaerobic heterotrophic activity. Shifts in microbial community to groups associated with greater organic carbon degradation (i.e., SAR11-LD12 subclade) and the SRB group Desulfuromonodales emerged post alum and the loss of specialist groups associated with carbon-limited, ammonia-rich restricted niches (i.e., MBAE14) also occurred. Alum treatment resulted in additional oxygen consumption associated with increased autochthonous carbon production, watercap anoxia and sulfide generation, which further exacerbate oxygen consumption associated with on-going FFT mobilized reductants. The results illustrate the importance of understanding the broader biogeochemical implications of adaptive management interventions to avoid unanticipated outcomes that pose greater risks and improve tailings reclamation for oil sands operations and, more broadly, the global mining sector.

Isotopic and Chemical Assessment of the Dynamics of Methane Sources and Microbial Cycling during Early Development of an Oil Sands Pit Lake

Water-capped tailings technology (WCTT) is a key component of the reclamation strategies in the Athabasca oil sands region (AOSR) of northeastern Alberta, Canada. The release of microbial methane from tailings emplaced within oil sands pit lakes, and its subsequent microbial oxidation, could inhibit the development of persistent oxygen concentrations within the water column, which are critical to the success of this reclamation approach. Here, we describe the results of a four-year (2015-2018) chemical and isotopic (δ¹³C) investigation into the dynamics of microbial methane cycling within Base Mine Lake (BML), the first full-scale pit lake commissioned in the AOSR. Overall, the water-column methane concentrations decreased over the course of the study, though this was dynamic both seasonally and annually. Phospholipid fatty acid (PLFA) distributions and δ¹³C demonstrated that dissolved methane, primarily input via fluid fine tailings (FFT) porewater advection, was oxidized by the water column microbial community at all sampling times. Modeling and under-ice observations indicated that the dissolution of methane from bubbles during ebullition, or when trapped beneath ice, was also an important source of dissolved methane. The addition of alum to BML in the fall of 2016 impacted the microbial cycling in BML, leading to decreased methane oxidation rates, the short-term dominance of a phototrophic community, and longer-term shifts in the microbial community metabolism. Overall, our results highlight a need to understand the dynamic nature of these microbial communities and the impact of perturbations on the associated biogeochemical cycling within oil sands pit lakes.

Isomer-specific monitoring of naphthenic acids at an oil sands pit lake by comprehensive two-dimensional gas chromatography-mass spectrometry

Naphthenic acids (NAs) are persistent, toxic contaminants that are found to accumulate in oil sands process-affected water (OSPW) and tailings after bitumen extraction. A number of strategies for the reclamation of oil sands tailings are currently being tested, including the development of the first demonstration pit lake by Syncrude Canada, Base Mine Lake (BML). An important component of reclamation activities is understanding the source and cycling of NAs in such reclamation systems. However, NAs exist as a highly complex mixture of thousands of compounds which makes their analysis an ongoing challenge. Herein, comprehensive two-dimensional gas chromatography coupled to time of flight mass spectrometry (GC × GC/TOFMS) was used to analyze the methylated extracts of water samples from the water cap and fluid fine tailings (FFT) deposit of BML to characterize the variations in NA distributions between geochemical zones. A collection of (alkylated) monocyclic-, bicyclic-, adamantane-, and thiophene-type carboxylic acids were identified. Total relative abundances were calculated for each NA class (by summation of peak areas of all detected isomers) and minimal variability was detected in the water cap. Total relative abundances for each NA class were either similar or higher in the FFT, relative to the water cap. Examination of isomer distributions indicated that differences in abundance values were generally driven by variations in only one or two isomers of a given NA class. Furthermore, GC × GC revealed distinct isomer profiles were observed between two FFT samples and between the FFT and water cap. While it is not yet clear whether these differences are due to differences in sources of NAs or in their environmental processing, these results illustrate the capability of GC × GC to investigate these questions and thus contribute to the management of these compounds within reclamation or environmental systems.

Large freshwater phages with the potential to augment aerobic methane oxidation

There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC sequences show high similarity to (>90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus, Methylocystis and Methylobacter spp. In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host-phage relationships. Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. Thus, augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this potent greenhouse gas into the environment.

New Insights Into Acidithiobacillus thiooxidans Sulfur Metabolism Through Coupled Gene Expression, Solution Chemistry, Microscopy, and Spectroscopy Analyses

Here, we experimentally expand understanding of the reactions and enzymes involved in Acidithiobacillus thiooxidans ATCC 19377 S0 andS 2 ⁢ O 3 2 - metabolism by developing models that integrate gene expression analyzed by RNA-Seq, solution sulfur speciation, electron microscopy and spectroscopy. The A. thiooxidansS 2 ⁢ O 3 2 - metabolism model involves the conversion ofS 2 ⁢ O 3 2 - to SO 4 2 - , S0 andS 4 ⁢ O 6 2 - , mediated by the sulfur oxidase complex (Sox), tetrathionate hydrolase (TetH), sulfide quinone reductase (Sqr), and heterodisulfate reductase (Hdr) proteins. These same proteins, with the addition of rhodanese (Rhd), were identified to convert S0 to SO 3 2 - ,S 2 ⁢ O 3 2 - and polythionates in the A. thiooxidans S0 metabolism model. Our combined results shed light onto the important role specifically of TetH inS 2 ⁢ O 3 2 - metabolism. Also, we show that activity of Hdr proteins rather than Sdo are likely associated with S0 oxidation. Finally, our data suggest that formation of intracellularS 2 ⁢ O 3 2 - is a critical step in S0 metabolism, and that recycling of internally generated SO 3 2 - occurs, through comproportionating reactions that result inS 2 ⁢ O 3 2 - . Electron microscopy and spectroscopy confirmed intracellular production and storage of S0 during growth on both S0 andS 2 ⁢ O 3 2 - substrates.

Putative Mixotrophic Nitrifying-Denitrifying Gammaproteobacteria Implicated in Nitrogen Cycling Within the Ammonia/Oxygen Transition Zone of an Oil Sands Pit Lake

Anthropogenically-impacted environments offer the opportunity to discover novel microbial species and metabolisms, which may be undetectable in natural systems. Here, a combined metagenomic and geochemical study in Base Mine Lake, Alberta, Canada, which is the only oil sands end pit lake to date, revealed that nitrification was performed by members from Nitrosomonadaceae, Chloroflexi and unclassified Gammaproteobacteria “MBAE14.” While Nitrosomonadaceae and Chloroflexi groups were relatively abundant in the upper oxygenated zones, MBAE14 dominated the hypoxic hypolimnetic zones (approximately 30% of total microbial communities); MBAE14 was not detected in the underlying anoxic tailings. Replication rate analyses indicate that MBAE14 grew in metalimnetic and hypolimnetic water cap regions, most actively at the metalimnetic, ammonia/oxygen transition zone consistent with it putatively conducting nitrification. Detailed genomic analyses of MBAE14 evidenced both ammonia oxidation and denitrification into dinitrogen capabilities. However, the absence of known CO₂-fixation genes suggests a heterotrophic denitrifying metabolism. Functional marker genes of ammonia oxidation (amo and hao) in the MBAE14 genome are homologous with those conserved in autotrophic nitrifiers, but not with those of known heterotrophic nitrifiers. We propose that this novel MBAE14 inhabits the specific ammonia-rich, oxygen and labile organic matter-limited conditions occurring in Base Mine Lake which selectively favors mixotrophic coupled nitrifier denitrification metabolism. Our results highlight the opportunities to better constrain biogeochemical cycles from the application of metagenomics to engineered systems associated with extractive resource sectors.

Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria

Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, we describe two groups of Podoviridae phage that infect Fonsibacter A complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL (lysogenic strategy), shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete genomes and one draft genome of phage related to marine Pelagiphage HTVC010P and predicted a lytic strategy. The similarity in codon usage and cooccurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one group of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter and expand understanding of the ecology and evolution of these important bacteria.IMPORTANCE Fonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage.

The Potential Role of Halothiobacillus spp. in Sulfur Oxidation and Acid Generation in Circum-Neutral Mine Tailings Reservoirs

The biogeochemistry of acid mine drainage (AMD) derived from waste rock associated sulfide mineral oxidation is relatively well-characterized and linked to Acidithiobacillus spp.. However, little is understood about the microbial communities and sulfur cycling before AMD develops, a key component of its prevention. This study aimed to examine circum-neutral mining impacted water (MIW) communities and its laboratory enrichments for sulfur oxidizing bacteria (SoxBac). MIW in situ microbial communities differed in diversity, structure and relative abundance consistent with site specific variations in total aqueous sulfur concentrations (TotS; ~2-17 mM), pH (3.67-7.34), and oxygen (22-93% saturation). However, the sulfur oxidizer, Halothiobacillus spp. dominated seven of the nine total SoxBac enrichment communities (~76-100% relative abundance), spanning three of the four mines. The presence and relative abundance of the identified sixteen known and five unclassified Halothiobacillus spp. here, were the important clustering determinants across parent MIW and enrichment communities. Further, the presence of Halothiobacillus spp. was associated with driving the pH <4 in enrichment experiments, and the combination of specific Halothiobacillus spp. in the enrichments affected the observed acid to sulfate ratios indicating differential sulfur cycling. Halothiobacillus spp. also dominated the parent communities of the two acidic MIWs providing corroborating evidence for its active role in net acid generation within these waters. These results identify a putative indicator organism specific to mine tailings reservoirs and highlight the need for further study of tailings associated sulfur cycling for better mine management and environmental stewardship.

Profiling of individual naphthenic acids at a composite tailings reclamation fen by comprehensive two-dimensional gas chromatography-mass spectrometry

Naphthenic acids (NAs) are naturally occurring in the Athabasca oil sands region (AOSR) and accumulate in tailings as a result of water-based extraction processes. NAs exist as a complex mixture, so the development of an analytical technique to characterize them has been an on-going challenge. The aim of this study was to use comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry to monitor individual NAs within a wetland reclamation site in the AOSR. Samples were collected from four monitoring wells at the site and the extracts were found to contain numerous resolved isomers of classical (monocyclic-, bicyclic-, adamantane-, indane-, and tetralin-type carboxylic acids) and sulfur-containing NAs (thiamonocyclic- and thiophene-type carboxylic acids). The absolute abundances of the monitored NAs were compared between four monitoring wells and unique profiles were observed at each well. Few significant changes in absolute abundances were observed over the sampling period, with the exception of one well (Well 6A). In addition, isomeric percent compositions were calculated for each set of structural isomers, and one-way analysis of variance (ANOVA) and two-dimensional hierarchical cluster analysis revealed high spatial variation at the site. However, consistent distributions were observed at each of the monitoring wells for some sets of NA isomers (such as: adamantane NAs), which may be useful for forensic applications, such as identifying sources of contamination or demonstrating biodegradation. The methods and results presented in this study demonstrate the utility of monitoring individual NAs, since both changes in absolute abundances of individual NAs and the distribution of NA isomers have the ability to provide insight into their sources and the processes controlling their concentrations that are not only of relevance to the Alberta Oil Sands, but also to other petroleum deposits and environmental systems.

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from 13 bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the 13 newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth's ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.

Elucidating carbon sources driving microbial metabolism during oil sands reclamation

Microbial communities play key roles in remediation and reclamation of contaminated environments via biogeochemical cycling of organic and inorganic components. Understanding the trends in in situ microbial community abundance, metabolism and carbon sources is therefore a crucial component of effective site management. The focus of this study was to use radiocarbon analysis to elucidate the carbon sources driving microbial metabolism within the first pilot wetland reclamation project in the Alberta oil sands region where the observation of H₂S had indicated the occurrence of microbial sulphate reduction. The reclamation project involved construction of a three compartment system consisting of a freshwater wetland on top of a sand cap overlying a composite tailings (CT) deposit. Radiocarbon analysis demonstrated that both dissolved and sediment associated organic carbon associated with the deepest compartments (the CT and sand cap) was primarily fossil (Δ¹⁴C = -769 to -955‰) while organic carbon in the overlying peat was hundreds to thousands of years old (Δ¹⁴C = -250 to -350‰). Radiocarbon contents of sediment associated microbial phospholipid fatty acids (PLFA) were consistent with the sediment bulk organic carbon pools (Peat: Δ¹⁴C_PLFA = -257‰; Sand cap Δ¹⁴C_PLFA = -805‰) indicating that these microbes were using sediment associated carbon. In contrast, microbial PLFA grown on biofilm units installed in wells within the deepest compartments contained much more modern carbon that the associated bulk carbon pools. This implied that the transfer of relatively more modern carbon was stimulating the microbial community at depth within the system. Correlation between cellular abundance estimates based on PLFA concentrations and the Δ¹⁴C_PLFA indicated that the utilization of this more modern carbon was stimulating the microbial community at depth. These results highlight the importance of understanding the occurrence and potential outcomes of the introduction of relatively bioavailable carbon to mine wastes in order to predict and manage the performance of reclamation strategies.

pH and Organic Carbon Dose Rates Control Microbially Driven Bioremediation Efficacy in Alkaline Bauxite Residue

Bioremediation of alkaline tailings, based on fermentative microbial metabolisms, is a novel strategy for achieving rapid pH neutralization and thus improving environmental outcomes associated with mining and refining activities. Laboratory-scale bioreactors containing bauxite residue (an alkaline, saline tailings material generated as a byproduct of alumina refining), to which a diverse microbial inoculum was added, were used in this study to identify key factors (pH, salinity, organic carbon supply) controlling the rates and extent of microbially driven pH neutralization (bioremediation) in alkaline tailings. Initial tailings pH and organic carbon dose rates both significantly affected bioremediation extent and efficiency with lower minimum pHs and higher extents of pH neutralization occurring under low initial pH or high organic carbon conditions. Rates of pH neutralization (up to 0.13 mM H⁺ produced per day with pH decreasing from 9.5 to ≤6.5 in three days) were significantly higher in low initial pH treatments. Representatives of the Bacillaceae and Enterobacteriaceae, which contain many known facultative anaerobes and fermenters, were identified as key contributors to 2,3-butanediol and/or mixed acid fermentation as the major mechanism(s) of pH neutralization. Initial pH and salinity significantly influenced microbial community successional trajectories, and microbial community structure was significantly related to markers of fermentation activity. This study provides the first experimental demonstration of bioremediation in bauxite residue, identifying pH and organic carbon dose rates as key controls on bioremediation efficacy, and will enable future development of bioreactor technologies at full field scale.

Sulfur Biogeochemistry of an Oil Sands Composite Tailings Deposit

Composite tailings (CT), an engineered, alkaline, saline mixture of oil sands tailings (FFT), processed sand and gypsum (CaSO₄; 1 kg CaSO₄ per m³ FFT) are used as a dry reclamation strategy in the Alberta Oil Sands Region (AOSR). It is estimated that 9.6 × 10⁸ m³ of CT are either in, or awaiting emplacement in surface pits within the AOSR, highlighting their potential global importance in sulfur cycling. Here, in the first CT sulfur biogeochemistry investigation, integrated geochemical, pyrosequencing and lipid analyses identified high aqueous concentrations of ∑H₂S (>300 μM) and highly altered sulfur compounds composition; low cell biomass (3.3 × 10⁶– 6.0 × 10⁶ cells g⁻¹) and modest bacterial diversity (H' range between 1.4 and 1.9) across 5 depths spanning 34 m of an in situ CT deposit. Pyrosequence results identified a total of 29,719 bacterial 16S rRNA gene sequences, representing 131 OTUs spanning19 phyla including 7 candidate divisions, not reported in oil sands tailings pond studies to date. Legacy FFT common phyla, notably, gamma and beta Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi were represented. However, overall CT microbial diversity and PLFA values were low relative to other contexts. The identified known sulfate/sulfur reducing bacteria constituted at most 2% of the abundance; however, over 90% of the 131 OTUs identified are capable of sulfur metabolism. While PCR biases caution against overinterpretation of pyrosequence surveys, bacterial sequence results identified here, align with phospholipid fatty acid (PLFA) and geochemical results. The highest bacterial diversities were associated with the depth of highest porewater [∑H₂S] (22–24 m) and joint porewater co-occurrence of Fe²⁺ and ∑H₂S (6–8 m). Three distinct bacterial community structure depths corresponded to CT porewater regions of (1) shallow evident Fe^(II) (<6 m), (2) co-occurring Fe^(II) and ∑H₂S (6–8 m) and (3) extensive ∑H₂S (6–34 m) (UniFrac). Candidate divisions GNO2, NKB19 and Spam were present only at 6–8 m associated with co-occurring [Fe^(II)] and [∑H₂S]. Collectively, results indicate that CT materials are differentiated from other sulfur rich environments by modestly diverse, low abundance, but highly sulfur active and more enigmatic communities (7 candidate divisions present within the 19 phyla identified).

S reactivity of an oil sands composite tailings deposit undergoing reclamation wetland construction

This study is the first to characterize the S stability of a composite tailings (CT) deposit undergoing pilot wetland reclamation in the Athabasca Oil Sands Region (AOSR, Alberta, Canada). As CT is sulfur, organic carbon and bacterially rich, the goal of this study was to characterize the in situ aqueous distribution of sulfur compounds across the wetland, sand cap and underlying CT zones of the deposit, in an effort to establish the potential for microbial sulfur cycling and generation of H2S, an explosive, corrosive and toxicity risk. Porewater samples from three depths spanning the different layers of the deposit, as well as wetland surface ponded water samples were collected for geochemical analyses (July and Sept 2013), and for microbial enrichments (both S reducing and S oxidizing bacteria) in June 2014. While porewater ΣH2S(aq) was detected at all depths across the three zones of the deposit, results identify that the sand cap layer required for construction, acts as a mixing zone generating the highest solution H2S concentrations (>500 uM or 18 mg/L) and H2S gas levels (over 100 and up to 180 ppm) observed. Porewater dissolved sulfate concentrations (0.14-6.97 mM) were orders of magnitude higher and did not correlate to the observed distribution of ΣH2S concentrations throughout the deposit. Unique to the sandcap, dissolved organic carbon positively correlated with the observed maxima of ΣH2S(aq) seen in this layer. The water management of the deposit is a critical factor in the observed S trends. Active dewatering of the CT resulted in migration of S rich water up into the sandcap, while downwelling labile organic carbon from the developing wetland acted in concert to stimulate microbial generation of the H2S in this structural layer to the highest levels observed. Functional enrichments identified that diverse S reducing and oxidizing microbial metabolisms are widespread throughout the deposit, indicating that these waste materials are biogeochemically reactive with implications for longterm stability. These results are of relevance to both the oil sands region, as well as other mine contexts where S rich wastes occur, identifying the need to consider the potential bacterially driven cycling of S and C in the generation of constituents of concern, as well as the water management of such waste deposits to minimize risk.

Microbially-driven strategies for bioremediation of bauxite residue

Globally, 3 Gt of bauxite residue is currently in storage, with an additional 120 Mt generated every year. Bauxite residue is an alkaline, saline, sodic, massive, and fine grained material with little organic carbon or plant nutrients. To date, remediation of bauxite residue has focused on the use of chemical and physical amendments to address high pH, high salinity, and poor drainage and aeration. No studies to date have evaluated the potential for microbial communities to contribute to remediation as part of a combined approach integrating chemical, physical, and biological amendments. This review considers natural alkaline, saline environments that present similar challenges for microbial survival and evaluates candidate microorganisms that are both adapted for survival in these environments and have the capacity to carry out beneficial metabolisms in bauxite residue. Fermentation, sulfur oxidation, and extracellular polymeric substance production emerge as promising pathways for bioremediation whether employed individually or in combination. A combination of bioaugmentation (addition of inocula from other alkaline, saline environments) and biostimulation (addition of nutrients to promote microbial growth and activity) of the native community in bauxite residue is recommended as the approach most likely to be successful in promoting bioremediation of bauxite residue.

Identification of individual thiophene-, indane-, tetralin-, cyclohexane-, and adamantane-type carboxylic acids in composite tailings pore water from Alberta oil sands

RATIONALE

Naphthenic acids (NAs) accumulate in oil sands process-affected water (OSPW) as a result of the water-based extraction processes, and represent one of the toxic fractions in OSPW. They exist as a complex mixture and so the development of an analytical method to characterize and quantify individual acids has been an on-going challenge. The multidimensional separation technique of two-dimensional gas chromatography (GC × GC) has the potential to provide a fingerprint of the sources of NAs and can potentially resolve individual analytes for target analysis. However, the identity and toxicity of a large proportion of the acids present in tailing waters are still unknown.

METHODS

Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry (GC × GC/TOFMS) was used to characterize NAs in a pore water sample from a Syncrude composite tailings (CT) deposit in Fort McMurray, Alberta, Canada. The extractable organic acid fraction was derivatized with diazomethane and the structures of selected resolved esters were elucidated through interpretation of their electron ionization (EI) mass spectra and, if available, confirmed by comparison with the spectra of reference standards.

RESULTS

The high resolving power of the GC × GC/TOFMS technique allowed for the structural elucidation of numerous as yet unidentified acids in the CT pore water sample such as carboxylic acids containing a thiophene, indane, tetralin or cyclohexane moiety. Seventeen members of the previously reported class of adamantane-type carboxylic acids in oil sands process water could also be identified in the sample.

CONCLUSIONS

This study underlines the complexity of naphthenic acid isomer distributions in composite tailings and provides a useful inventory of individual acids.

Diurnal floc generation from neuston biofilms in two contrasting freshwater lakes

Selective adaptation of biofilm-forming bacteria to the nutrient-rich but environmentally challenging conditions of the surface microlayer (SML) or neuston layer was evident in littoral regions of two physically and geochemically contrasting freshwater lakes. SML bacterial communities (bacterioneuston) in these systems were depleted in Actinobacteria, enriched in either Betaproteobacteria or Gammaproteobacteria, and either unicellular Cyanobacteria were absent or microbial mat forming Cyanobacteria enriched relative to communities in the underlying shallow water column (0.5 m depth). Consistent with the occurrence of biofilm-hosted, geochemically distinct microhabitats, As-, Fe-, and S-metabolizing bacteria including anaerobic taxa were detected only in the SML in both systems. Over diurnal time scales, higher wind speeds resulted in the generation of floc from SML biofilms, identifying a transport mechanism entraining SML accumulated microorganisms, nutrients, and contaminants into the underlying water column. The energy regime experienced by the SML was more important to floc generation as larger flocs were more abundant in the larger, oligotrophic lake (higher relative energy regime) compared to the sheltered, smaller lake, despite relatively higher concentrations of bacteria, organic carbon, Fe, and PO4(3-) in the latter system.

Microbial engineering of floc Fe and trace element geochemistry in a circumneutral, remote lake

Evaluation of lacustrine floc Fe, Pb, and Cd biogeochemistry over seasonal (summer, winter) and water column depth (metalimnetic, hypolimnetic) scales reveals depth-independent seasonally significant differences in floc Fe biominerals and trace element (TE: Pb, Cd) sequestration, driven by floc microbial community shifts. Winter floc [TE] were significantly lower than summer [TE], driven by declining abundance and reactivity of floc amorphous Fe((III))-(oxy)hydroxide (FeOOH) phases under ice ([FeOOH](summer) = 37-77 mgg(-1) vs [FeOOH](winter) = 0.3-7 mgg(-1)). Further, while high summer floc [FeOOH] was observed at both water column depths, winter floc was dominated by Fe((II)) phases. However, the observed seasonal change in the nature and concentrations of floc Fe-phases was independent of water column [Fe], O2, and pH and, instead, significantly correlated to floc bacterial community membership. Bioinformatic modeling (Unifrac, PCA analyses) of in situ and experimental microcosm results identified a temperature-driven seasonal turnover of floc microbial communities, shifting from dominantly putative Fe metabolisms within summer floc to wintertime ancillary Fe reducing and S metabolizing bacteria. This seasonal shift of floc microbial community functioning, significantly the wintertime loss of microbial Fe((II))-oxidizing capability and concomitant increases of sulfur-reducing bacteria, alters dominant floc Fe minerals from Fe((III)) to Fe((II)) phases. This resulted in decreased winter floc [TE], not predicted by water column geochemistry.

Comparative floc-bed sediment trace element partitioning across variably contaminated aquatic ecosystems

Significantly higher concentrations of Ag, As, Cu, Ni and Co are found in floc compared to bed sediments across six variably impacted aquatic ecosystems. In contrast to the observed element and site-specific bed sediment trace element (TE) partitioning patterns, floc TE sequestration is consistently dominated by amorphous oxyhydroxides (FeOOH), which account for 30-79% of floc total TE concentrations, irrespective of system physico-chemistry or elements involved. FeOOH consistently occur in significantly higher concentrations in floc than within bed sediments. Further, comparative concentration factors indicate significantly higher TE reactivity of floc-FeOOH relative to sediment-FeOOH in all systems investigated, indicating that both the greater abundance and higher reactivity of floc-FeOOH contribute to enhanced floc TE uptake. Results indicate that floc-organics (live cells and exopolymeric substances, EPS) directly predict floc-FeOOH concentrations, suggesting an organic structural role in the collection/templating of FeOOH. This, in turn, facilitates the sequestration of TEs associated with floc-FeOOH formation, imparting the conserved FeOOH "signature" on floc TE geochemistry across sites. Results demonstrate that the organic rich nature of floc exerts an important control over TE geochemistry in aquatic environments, ultimately creating a distinct solid with differing controls over TE behavior than bed sediments in close proximity (<0.5 m).

Physical and ecological controls on freshwater floc trace metal dynamics

Significantly higher concentrations of Ag, As, Cu, Co, Ni, and Pb are found in suspended floc compared to surficial bed sediments for a freshwater beach in Lake Ontario. Contrasting observed element-specific bed sediment metal partitioning patterns, floc sequestration for all elements is dominated by one substrate: amorphous oxyhydroxides. More specifically, floc metal scavenging is controlled by floc biogeochemical architecture. Floc organics, largely living microbial cells and associated exopolymeric substances (EPS), act as scaffolds for the collection and/or templating of amorphous Fe oxyhydroxides. While interactions between floc organics and amorphous Fe oxyhydroxides affected floc sorption behavior, specific element affinities and competition for these limited substrates was important for overall floc partitioning. Further, assessment of metal dynamics during stormy conditions indicated energy-regime driven shifts in floc and bed sediment partitioning that were specifically linked to the exchange of floc and bed sedimentary materials. These novel results demonstrate that the microbial nature of floc formation exerts an important control on floc metal dynamics distinguishable from surficial bed sediments and that hydrologic energy-regime is an important factor to consider in overall floc metal behavior, especially in beach environments.

An audit of transport conditions and arrival status of slaughter cattle shipped by road at an Ontario processor

This is an observational study to investigate slaughter cattle transportation conditions in Canada. Data collected include: length of time in transit; temperature variation; season; weather transport conditions; cattle weight; sex and whether sexes were separated on mixed loads; number of lots and whether lots were separated; cattle unloading speed; cattle handling score; trucker training and experience hauling cattle; ventilation; and condition of cattle at arrival. Information was collected on approximately 50 000 animals transported by 1363 trucks. All but 0.2% of trucks arrived within the 52 h allowable transport time before unloading required for rest, feed, and water. Most trucks (85.7%) were from within 8 h of the plant. Trucks surveyed were at or above the recommended space allowance 49% of the time. There were five non-ambulatory (unable to walk off the truck with or without assistance) or dead, 79 lame, and four animals that needed assistance of the 49 959 animals observed (0.4, 4.8 and 0.2%, respectively, of the trucks surveyed). However, these concerns were not necessarily a result of transportation, as animal health at loading was unknown. There were very few visible animal welfare concerns associated with the transportation of slaughter cattle in the population sampled. Key words: Cattle, transport, welfare, beef

Microbial architecture of environmental sulfur processes: a novel syntrophic sulfur-metabolizing consortia

Microbial oxidation of sulfur-rich mining waste materials drives acid mine drainage (AMD) and affects the global sulfur biogeochemical cycle. The generation of AMD is a complex, dynamic process that proceeds via multiple reaction pathways. The role of natural consortia of microbes in AMD generation, however, has received very little attention despite their widespread occurrence in mining environments. Through a combination of geochemical experimentation and modeling, scanning transmission X-ray microscopy, and fluorescent in situ hybridization, we show a novel interdependent metabolic arrangement of two ubiquitous and abundant AMD bacteria: chemoautotrophic sulfur-oxidizing Acidithiobacillus sp. and heterotrophic Acidiphilium sp. Highly reminiscent of anaerobic methane oxidation (AOM) consortia, these bacteria are spatially segregated within a planktonic macrostructure of extracellular polymeric substance in which they syntrophically couple sulfur oxidation and reduction reactions in a mutually beneficial arrangement that regenerates their respective sulfur substrates. As discussed here, the geochemical impacts of microbial metabolism are linked to the consortial organization and development of the pod structure, which affects cell-cell interactions and interactions with the surrounding geochemical microenvironment. If these pods are widespread in mine waters, echoing the now widespread discovery of AOM consortia, then AMD-driven CO(2) atmospheric fluxes from H(2)SO(4) carbonate weathering could be reduced by as much as 26 TgC/yr. This novel sulfur consortial discovery indicates that organized metabolically linked microbial partnerships are likely widespread and more significant in global elemental cycling than previously considered.

Microbial thiosulphate reaction arrays: the interactive roles of Fe(III), O2 and microbial strain on disproportionation and oxidation pathways

In this work, we experimentally evaluate pH and SO4(2-) dynamics associated with abiotic and microbial S2O3(2-) oxidation under varying [O2], [Fe(III)] and microbial strain/consortia (two pure strains, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, their consortia, and two enrichments from an acidic environmental system, Moose Lake 2002 and Moose Lake 2003). Results of the batch experiments demonstrate highly active microbial processing of S2O3(2-) while abiotic controls under identical experimental conditions remain static with no pH decrease. When abiotic controls were manually titrated with acid to achieve similar pH decreases to those occurring in the microbial treatments, different S pathways were involved. In particular, disproportionation is a substantial component of initial microbial S2O3(2-) processing, and is accelerated by the presence of Fe(III), indicating that recycling of S through intermediate oxidation states is likely to be widespread in acidic mine environments where high [Fe(III)] is common. Furthermore, the microbially mediated S reaction pathways were dependent on both environmental conditions and microbial strain/consortia, indicating that microbial community structure also plays a key role. Collectively, these results highlight the importance of microbial activity, their poor representation by abiotic S models, the likelihood that Fe(III), rather than O2, is a key control on microbial S processing in acid environments and the need to identify the microbial community/strain involved.

Biofilm hydrous manganese oxyhydroxides and metal dynamics in acid rock drainage

Biofilms in shallow, tailings-associated acid rock drainage (ARD) accumulated metals from May to September, indicating scavenging is stable within these biological solids over seasonal time frames. Results indicate a doubling (Mn, Cr) to over a 6-fold increase (Ni, Co) in biofilm metal concentrations. Biofilm oxygen and pH gradients measured over diel time scales with microelectrodes were observed to be both spatially and temporally variable, indicating that biofilms are highly dynamic geochemical environments. Biofilm metal retention and affinities were element specific indicating different processes control their sequestration. Metals were specifically scavenged by the organic constituents of the biofilm itself (Ni, Co) and associated biominerals of amorphous Mn oxyhydroxides (HMO; Ni, Co, and Cr). Results are consistent with sorption and coprecipitation processes controlling Ni and Co biofilm association, while Cr dynamics appear linked to those of Mn through redox processes. Biofilm HMO concentrations increased seasonally but showed significant diel fluctuations, indicating that both formation and dissolution processes occurred over rapid time scales in these biofilms. Biofilm HMO concentrations increased nocturnally but decreased during daylight hours to late afternoon minima. Under the geochemical conditions of the streams, observed HMO formation rates can only be explained by microbial catalysis. These results are the first to quantitatively examine microbial biofilm metal dynamics using microscale, geochemical techniques at both diel and seasonal time scales. They provide strong evidence for the significant role that microbial activity can play in metal geochemistry in natural environments.

New methods for the assessment of in vitro and in vivo stress cracking in biomedical polyurethanes

This article describes a new test method for the assessment of the severity of environmental stress cracking of biomedical polyurethanes in a manner that minimizes the degree of subjectivity involved. The effect of applied strain and acetone pre-treatment on degradation of Pellethane 2363 80A and Pellethane 2363 55D polyurethanes under in vitro and in vivo conditions is studied. The results are presented using a magnification-weighted image rating system that allows the semi-quantitative rating of degradation based on distribution and severity of surface damage. Devices for applying controlled strain to both flat sheet and tubing samples are described. The new rating system consistently discriminated between the effects of acetone pre-treatments, strain and exposure times in both in vitro and in vivo experiments. As expected, P80A underwent considerable stress cracking compared with P55D. P80A produced similar stress crack ratings in both in vivo and in vitro experiments, however P55D performed worse under in vitro conditions compared with in vivo. This result indicated that care must be taken when interpreting in vitro results in the absence of in vivo data.

Polydimethylsiloxane/polyether-mixed macrodiol-based polyurethane elastomers: biostability

A series of four thermoplastic polyurethane elastomers were synthesized with varying proportions of poly(hexamethylene oxide) (PHMO) and poly(dimethylsiloxane) (PDMS) macrodiols. The macrodiol ratios (by weight) employed were (% PDMS:% PHMO) 100:0, 80:20, 50:50 and 20:80. The weight fraction of macrodiol in each polymer was fixed at 60%. The mixed macrodiols were reacted with 4,4'-methylenediphenyl diisocyanate (MDI) and 1,4-butanediol (BDO) chain extender. The biostability of these polymers was assessed by strained subcutaneous implantation in sheep for three months followed by microscopic examination. Pellethane 2363-80A and 2363-55D were employed as control materials. The mechanical properties of the polymers were tested and discussed along with the biostability results. The results showed that soft, flexible PDMS-based polyurethanes with very promising biostability can be successfully produced using the mixed macrodiol approach. The formulation with 80% PDMS macrodiol produced the best result in terms of a combination of flexibility, strength and biostability.

Identification of the 1.4 kb and 4.0 kb messages for the lipoprotein associated coagulation inhibitor and expression of the encoded protein

Lipoprotein-Associated Coagulation Inhibitor (LACI) is a factor Xa dependent inhibitor of the factor VII(a)/Tissue Factor catalytic complex. Deduced from partial cDNA sequence, LACI's amino acid sequence has recently been reported. Northern blot analysis showed LACI cDNA hybridizes to RNAs of 1.4 and 4.0 kb in size. To complete the characterization of the LACI message(s), overlapping LACI cDNAs were isolated from a human endothelial cell library. Sequence analysis revealed the clones' inserts span 4023 bases of sequence, consisting of 381 bases of 5' untranslated sequence, an open reading frame of 912 bases, 2682 bases of 3' untranslated sequence and 48 bases of poly(A) sequence. In addition, a short 1.4 kb insert which encodes for LACI was found to contain 49 bases of 3' untranslated sequence and a 3' poly(A) tail. The 1.4 kb of sequence is contained in the 4.0 kb sequence, except for 14 bases of 5' sequence, suggesting that the LACI messages arise by the use of alternative termination and polyadenylation signals during processing. Northern blot analysis of RNA isolated from cells treated with actinomycin D showed both RNA species appear to be relatively stable. Using a bovine papilloma virus vector, LACI cDNA was transfected into mouse C127 fibroblasts. The recombinant LACI is recognized by polyclonal anti-LACI IgG, binds to factor Xa and inhibits VII(a)/Tissue Factor activity in a similar fashion as LACI purified from HepG2 cell conditioned media.

Functional significance of the Kunitz-type inhibitory domains of lipoprotein-associated coagulation inhibitor

Blood coagulation can be initiated when factor VII or VIIa, a plasma protease, binds to its essential cofactor, tissue factor (TF), and proteolytically activates factors IX and X, triggering a cascade of events which eventually leads to the formation of thrombin and a fibrin clot. Plasma contains a lipoprotein-associated coagulation inhibitor (LACI) which inhibits activated factor X (Xa) directly and, in a Xa-dependent way, inhibits VII(a)/TF activity, presumably by forming a quaternary Xa/LACI/VII(a)/TF complex. Sequence analysis of complementary DNA clones has shown that LACI contains three tandemly repeated Kunitz-type serine protease inhibitory domains. To investigate the relationship between these Kunitz structures and LACI function, we have used site-directed mutagenesis to produce altered forms of LACI in which the residue at the active-site cleft of each Kunitz domain has been individually changed. The second Kunitz domain is required for efficient binding and inhibition of Xa, and both Kunitz domains 1 and 2 are required for the inhibition of VIIa/TF activity; but alteration of the active-site residue of the third Kunitz domain has no significant effect on either function. We propose that in the putative inhibitory complex, Kunitz domain 1 is bound to the active site of VII(a)/TF and that Kunitz domain 2 is bound to Xa's active site.

The lipoprotein-associated coagulation inhibitor that inhibits the factor VII-tissue factor complex also inhibits factor Xa: insight into its possible mechanism of action

Blood coagulation is initiated when plasma factor VII(a) binds to its essential cofactor tissue factor (TF) and proteolytically activates factors X and IX. Progressive inhibition of TF activity occurs upon its addition to plasma. This process is reversible and requires the presence of VII(a), catalytically active Xa, Ca2+, and another component that appears to be associated with the lipoproteins in plasma, a lipoprotein-associated coagulation inhibitor (LACI). A protein, LACI(HG2), possessing the same inhibitory properties as LACI, has recently been isolated from the conditioned media of cultured human liver cells (HepG2). Rabbit antisera raised against a synthetic peptide based on the N-terminal sequence of LACI(HG2) and purified IgG from a rabbit immunized with intact LACI(HG2) inhibit the LACI activity in human serum. In a reaction mixture containing VIIa, Xa, Ca2+, and purified LACI(HG2), the apparent half-life (t1/2) for TF activity was 20 seconds. The presence of heparin accelerated the initial rate of inhibition threefold. Antithrombin III alpha alone had no effect, but antithrombin III alpha with heparin abrogated the TF inhibition. LACI(HG2) also inhibited Xa with an apparent t1/2 of 50 seconds. Heparin enhanced the rate of Xa inhibition 2.5-fold, whereas phospholipids and Ca2+ slowed the reaction 2.5-fold. Xa inhibition was demonstrable with both chromogenic substrate (S-2222) and bioassays, but no complex between Xa and LACI(HG2) could be visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Nondenaturing PAGE, however, showed that LACI(HG2) bound to Xa but not to X or Xa inactivated by diisopropyl fluorophosphate. Thus, LACI(HG2) appears to bind to Xa at or near its active site. Bovine factor Xa lacking its gamma-carboxyglutamic acid-containing domain, BXa(-GD), through treatment with alpha-chymotrypsin, was used to further investigate the Xa requirement for VIIa/TF inhibition by LACI(HG2). LACI(HG2) bound to BXa(-GD) and inhibited its catalytic activity against a small molecular substrate (Spectrozyme Xa), though at a rate approximately sevenfold slower than native BXa. Preincubation of LACI(HG2) with saturating concentrations of BXa(-GD) markedly retarded the subsequent inhibition of BXa. The VII(a)/TF complex was not inhibited by LACI(HG2) in the presence of BXa(-GD), and further, preincubation of LACI(HG2) with BXa(-GD) slowed the inhibition of VIIa/TF after the addition of native Xa. The results are consistent with the hypothesis that inhibition of VII(a)/TF involves the formation of a VIIa-TF-XA-LACI complex that requires the GD of XA.(ABSTRACT TRUNCATED AT 400 WORDS)

A model for evaluation of postural hypotension induced by drugs in conscious restrained normotensive rats

A rat model was developed for use in evaluating postural hypotensive activity of a compound. Conscious normotensive rats were restrained on a tilt board with special restrainers to avoid blocking limb circulation. Dose response curves were explored to delineate the potential postural hypotensive activity of a compound. In response to a 2-min 90 degree head-up tilt, only a negligible changes in blood pressure was observed in the control state. The conscious rat was therefore able instantaneously to compensate for postural change. This ability, however, was blocked by guanethidine. The compound induced a dose-related hypotension and a further, dose-dependent drop in blood pressure on tilt. Hydralazine, on the other hand, induced only dose-dependent hypotension, but no change in blood pressure response from control tilts. Since these findings appear to be in accord with human clinical data, this rat model may be suitable for use in evaluating potential postural hypotensive activity of compounds.

The importance of catecholamine uptake inhibition in the reversal of guanethidine blockade of adrenergic neurons

Adrenergic neuron blockade was induced by guanethidine in the pithed rat preparation. The pressor response to spinal electric stimulation was inhibited. The guanethidine blockade was reversed or prevented not only by tricyclic antidepressants but also by tripelennamine (an H1 antihistamine), tranylcypromine (a monoamine oxidase inhibitor) and viloxazine (a new antidepressant structurally unrelated to tricyclic antidepressants). Since these compounds all share neuronal uptake inhibitory activity, it seems that this property per se is sufficient to reverse/prevent the adrenergic neuron blockade induced by guanethdine.