Susan Baldwin


Relevant Degree Programs


Graduate Student Supervision

Doctoral Student Supervision (Jan 2008 - Mar 2019)
Microbial communities in field-based biological reactors treating mining-influenced water (2015)

Metals, sulfate, nitrate and ammonia are the main chemical constituents of mining-influenced water (MIW). Biological reactors are attractive for low-cost treatment of MIW. But their successful performance relies on having microbial consortia with the metabolic potential to remove the contaminants of concern. This study undertook to explore the microbial communities in two types of field-based systems that successfully treat MIW: Semi-passive biochemical reactors (BCR) removing metals and sulfate; Active biological reactors removing ammonia and nitrate in the presence of metals. Pyrotag sequencing of 16S rRNA genes was performed for 80 samples from four BCRs. Although they were located at different mine sites, the BCRs shared several taxonomic groups. Sulfate-reducing microorganisms (SRM) were restricted to Deltaproteobacteria and only a few Clostridium genera. Core SRM were specialized, often poorly characterized genera, also prevalent at other metal-contaminated sites. The BCRs were populated by both acetate-consuming SRM and methanogens. SRM were more prevalent in some BCRs than methanogens, which are potential competitors. The structure of the microbial community in a BCR containing pulp and paper biosolids as carbon source was different from that in the other BCRs. Network analysis revealed that the putative keystone microorganisms in this BCR were phylogenetically different from those in the other BCRs. According to correlation analysis of these keystone microorganisms, a hypothetical model proposed that keystone microorganisms in BCR3 employ different mechanisms (antagonistic) than keystones in the other BCRs to regulate the structure of microbial community. The microbial communities within mine nitrogen-removing bioreactors shared several taxonomic groups with those in non-mine related nitrogen-removing facilities. The mine system selected for archaeal (rather than bacterial) ammonia oxidizer and denitrifying populations. The denitrifying population was enriched and a metagenomic study revealed genes encoding enzymes involved in metal metabolism (e.g. arsenite oxidation, mercury reduction) that were related to denitrifiers such as Rhodobacter sp., Thiobacillus sp., Burkholderia sp., Methylotenera sp., and Variovorax sp. Sequences related to taxa capable of aerobic denitrification, autotrophic denitrification, nitrifier denitrification, and anammox were found. The microbiology of the influent water had a significant impact on the microbial composition of the nitrogen-removing bioreactors.

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Complex biochemical reactors for selenium and sulphate reduction : organic material biodegradation and microbial community shifts (2014)

Biochemical reactors using complex organic materials for treatment of mine-affected waters are attractive low-cost solutions, but their widespread adoption is severely limited by poor reliability and limited longevity. This is in part due to lack of guidance on which organic materials to use, their degradation over time, and how this affects the microbial community composition, which in turn influences reactor performance. Continuous-flow column bioreactors containing differing ratios of a wood, hay and manure mixture were operated for 159 to 430 days including successful and decline phases of performance. Reactor performance, detailed organic matter composition and microbial community structure were measured for reactors with different wood to hay ratios and after different times of operation. Reactors with more hay than wood reduced sulphate from 500 mg/L to less than 100 mg/L and selenium from 20.3 µg/L to less than 0.2 µg/L with a retention time of 14 days for the whole period of operation. Whereas reactors with a high wood to hay ratio operated successfully for 100-200 days after which their performance fluctuated. Increase in more readily available organic compounds with decrease in recalcitrant fibrous materials was charted over time and correlated with changes in microbial community composition. More hemicellulose and α-cellulose were consumed in the bioreactors with more hay content. Lignin content remained the same for the wood rich bioreactors, and increased in the hay-rich columns. Ash content in bioreactors with either organic mixture increased over time. The labile components, determined as neutral detergent and water soluble compounds, fluctuated cyclically. The microbial communities that evolved in the bioreactors were distinctly different from those present initially. At the early stages, the communities were rich in organic matter degraders classified in the Bacteroides, Parabacteroides and Ruminococcaceae taxonomic groups. There was a shift towards Methanogens and Mollicutes and Spirochaetes classified groups for the longer running bioreactors. Sulphate reducing bacteria were mostly Desulfobulbus and Desulfovibrio related and they were more prevalent in the presence of high sulphate throughout the reactor history.

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Microbes involved in arsenic removal in passive treatment systems (2014)

Biogeochemical cycling of arsenic and speculation on mechanisms of arsenic removal are interest in the environmental remediation of contaminated sites.In the present study, combination of metagenomic molecular biology techniques with mineralogical analyses were used to study a biochemical reactor(BCR) that was successfully removing arsenic, zinc, copper and cadmium.First the metal and mineralogical content of the BCR solids was investigated. X-ray diffraction (XRD) and automated quantitative evaluation of minerals by scanning electron microscopy (QEMSCAN) were used formineralogical characterization. Analysis indicated that sulfates and sulfides were the predominant types of Zn and As minerals formed in the BCR.Arsenic minerals were detected as sulfides (arsenopyrite, tennantite), arsenates(wihelmkleinite), oxides (unknown zinc arsenic oxides) and zincarsenicsulfides, which showed evidence of metal adsorption on the surfaces of other solids such as silicates. Energy-dispersive X-ray spectroscopy verified that arsenic was associated with iron, zinc and sometimes cadmiumas arsenopyrite-type minerals. Using a SSU rRNA survey of the site, the following taxa were correlated with high metal content: Bacteroidetes, Synergistaceae, Victivallales, methanogens (Methanocorpusculum, Methanospirillum, Methanosarcina) and new phyla such as VadinHA17, M2PB4-65, candidate division WS6, RF3 and TM6. Next, enrichment culturing and arsenic chemical speciation monitoring were performed to assess potential for arsenic species transformationsin the BCR. Most predominant groups in the As(III) and As(V) media, were Simplicispira (β-proteobacterium) and Sedimentibacter (Firmicutes), respectively. Chemical arsenic speciation monitoring of the enrichments suggested that arsenite oxidation and arsenate reduction occurred. Thesegenera were not previously reported for arsenic transformation.Finally, functional metagenomic workflow was applied to study arsenic resistance genes. Functional screening and end-sequencing of large insert fosmid libraries demonstrated that arsenic(V) resistance genes were taxonomically widespread and different class of arsenic resistance genes relatedto periplasmic arsenate reduction, arsenite efflux, bioaccumulation (phosphate, metal transporters) and arsenite oxidation were present. Fewer geneswere associated with dissimilatory arsenate reduction and arsenic volatilization mechanisms. Methanomicrobia were predominant in the BCR and identification of methanogen-related arsenic resistance genes indicated that methanogens potentially played a role in arsenic removal inside the BCR.

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Developing biomarkers for mussel leukemia as tools for ecosystem health monitoring (2012)

The overall goal of this project was to develop biomarkers for mussel leukemia, a sublethal endpoint used in population health monitoring. The most common method for leukemia assessment is hematocytology, which is labour intensive and subject to bias. In this thesis, new biomarkers based on DNA ploidy detection and genotyping, were developed and compared with hematocytology. These new biomarkers would allow for more sensitive and efficient monitoring of near-shore ecosystems. Two Mytilus species, M. trossulus and M. edulis, were tested. Samples were obtained from Hopkins and Horseshoe Bay beaches, a mussel farm (Island Scallops, BC) and from caged mussels of the same origins submerged at a monitoring site in Burrard Inlet and a reference site off the Sunshine Coast.Three single nucleotide polymorphisms (SNPs) were detected within the coding region of p53 amplified from M. trossulus haemocyte cDNA, which were associated with leukemia. Many more polymorphic sites were found in M. edulis, some correlated with leukemia. Blocks in the p53 coding region sequences from late leukemic M. edulis were homologous with the M. trossulus p53 sequences, suggesting that hybridization may have contributed to increased disease susceptibility. Correlations between genotype and disease were not found in beach mussels or in either mussel species with early stages of leukemia.DNA content flow cytometry patterns for M. trossulus haemocytes could distinguish healthy animals from diseased for all stages of leukemia, including early ones, where haemolymph contains mixtures of healthy and neoplastic cells. No strong association was observed between ploidy and leukemia in M. edulis. This new method for M. trossulus leukemia detection is recommended for monitoring of marine ecosystems exposed to multiple stressors, for which leukemia is a valuable endpoint together with other biomarkers required for efficient environmental management.

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Microbial processes and carbon utilization in high sulfate waters and sediments (2010)

The application of microorganisms for treating high sulfate effluents is proving to be an effective approach although the processes involved are not well understood. One example is the use of anaerobic passive systems such as mine pit lakes and subsurface flow wetlands. This work addresses the missing information on microbial processes in two high sulfate environments: a permanently stratified fjord and a subsurface flow wetland treating mine waste. In Nitinat Lake fjord, although sulfide was present, no significant sulfate reduction occurred and quantitative polymerase chain reaction (qPCR) of the dissimilatory sulfite reductase gene (dsr) detected very few sulfate-reducing bacteria (SRB). Instead, the small subunit rRNA phylogenetic analysis revealed almost complete domination by novel Arcobacter-related species in deep anoxic water. In contrast, substantial sulfate reduction was measured in the fjord sediments. A rate of 250 ± 60 nmol cm⁻³ d⁻¹ was determined, and 8.7 ± 0.7 x 10⁶ copies of dsr mL⁻¹ were found using quantitative PCR (qPCR). When the sediments were amended with carbon sources (acetate, lactate, or a mixture of compost, silage and molasses), acetate stimulated the highest rate of sulfate reduction. An operating passive treatment system remediating metal-containing seepage near the Teck smelter in Trail, B.C. was used for a study of five carbon materials (silage, pulp mill biosolids, compost, molasses with hay, and cattails) as potential substrates for passive systems. Phylogenetic analyses of SSU rRNA and dsr genes were performed, as well as qPCR and chemical analyses of carbon parameters including easily degradable material (EDM), dissolved and particulate organic carbon (DOC and TOC), particulate nitrogen (PN), and carbon to nitrogen ratio C/N. Silage showed highest sulfate-reducing potential. The results showed that the initial C/N ratio of organic materials correlated positively with the SRB activity. However, phylogenetic analysis determined that the majority of bacterial species belonged to Bacteroidetes and Firmicutes phyla likely involved in complex carbon degradation. The lack of SRB in the actual system suggests that processes other than sulfate reduction are responsible for metal removal.This study contributed to the understanding of microbial processes and therefore aids in improving design and monitoring of passive treatment systems.

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Master's Student Supervision (2010-2017)
Biological reduction of selenium oxyanions in the presence of nitrate anions using anaerobic microbes (2016)

Biological selenium reduction has emerged as a viable solution for the removal of toxic selenium from the environment. However, the presence of nitrate hinders selenium reduction by acting as a competitive electron acceptor. The present thesis investigated the use of local mine-impacted sediment as an inoculum for selenium reduction and studied the affect of nitrate on the removal of selenium. Sediment samples, impacted by mining activities, were collected from two vastly different sites of the Elk River Valley. These sediments namely; Goddard Marsh and Mature Tailing Coal, were enriched for selenium reducing bacterial consortium under high selenium and varying nitrate concentrations to put additional selection pressure. Ultimately, two cultures from Goddard Marsh enriched under low and high nitrate condition as well as one culture from Mature Tailing Coal enriched under moderate nitrate condition were used to access the affect of nitrate on selenium reduction using central composite design matrix. The extent of Se reduction was highest in the Goddard Marsh enrichment with no nitrate while enrichment with moderate and high nitrate reduced selenium poorly. ANOVA results from the CCD experiment in Goddard Marsh enrichment with no nitrate indicated no affect of nitrate in Se reduction. Two primer sets targeting the selenate redutase (serA) from Thauera selenatis and nitrite reductase (nirK) from denitrifying population were used to quantify the population of selenium reducing and denitrifying population in the CCD experiment. Q-PCR assay successfully quantified serA genes in the cultures and correlated well with the initial Se concentration. Furthermore, the selenium reducing ability of enrichment cultures were compared with the bio-stimulated native sediments. Native sediments efficiently removed selenium from the culture medium while enrichment cultures preferentially removed nitrate over selenium. Metagenomic sequencing revealed the presence of many putative selenium reducers in the native sediments while Pseudomonas were more prevalent in the enrichment cultures. Denitrification, sulfate reduction and selenium assimilation genes were abundant in most sequences indicating its role in the reduction of selenium and nitrate. Thus, our study shows that efficient reduction of selenium in the presence of nitrate is possible with biological system.

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Sulfate, nitrate and selenium reduction in mining wastewater brine using anaerobic bacteria (2015)

The mining industry is a water usage intensive industry that generates large volumes of wastewater. This wastewater is technically difficult to treat when it is very saline. Large quantities of reagents are needed for chemical treatment, which is very expensive. The current thesis explores the possibility of using anaerobic bacteria to treat highly saline wastewater, as an alternative and more cost effective technology. Specifically, the concentrations of sulfate, nitrate and selenium were monitored, as these are constituents of concern at many mine sites. Samples of brine at different stages of a reverse osmosis treatment process were received from a mining company. Growth media for anaerobic bacteria were made according to the concentrations of chemicals present in the bine samples with certain amendments. Three sediment samples collected from different mine environments were tested as inocula for the experiment. Three growth conditions were also designed in order to determine the best suitable treatment conditions: condition #1 contains additional ammonia and iron salt as nutrients, condition #2 has only additional iron salt as nutrient and condition #3 has only zero-valent iron as an alternative additional iron source. DNA samples were extracted from culture sediments and analyzed using qPCR. Based on the results obtained, it was found that different combinations of inocula and growth condition were suitable for removing the most amount of sulfate, nitrate or selenium separately. In order to remove all three constituents at the same time, the best treatment was using inoculum collected from Mount Polley and adding only iron (II) chloride salt as nutrient besides carbon sources (condition #2).

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Oil sands process water and tailings pond contaminant transport and fate : physical, chemical and biological processes (2014)

The Alberta Oil Sands development has been in operation since the 1960s, where innovations in technology in bitumen extraction have resulted in adaptive management of environmental sensitivities to Oil Sands Process-affected Water (OSPW) and tailings. This research assessed all the potential processes that OSPW constituents might undergo in the tailings impoundments in order to theorize on their ultimate fate. A conceptual tailing pond model was created, the first of its kind as there have been no attempts in the existing literature, and a tool for future management of these facilities. The development of a model is quite complex where the objectives are defined (e.g. OSPW constituents) and the various physical, chemical, biological, geochemical, hydrological and limnological processes involved. This research was conducted by one individual, while such integration and analysis would typically be tackled by a team of multidisciplinary experts. The scope of this research included the OSPW produced from oil sands open-pit mining, extraction and processing of bitumen. The crushing of ore and chemical additives affect water chemistry through the release of ions, salts, metals and organic compounds. Oil sands mines generate process affected water high in contaminants and the high degree of water recycling further concentrates these substances. The spatial and geological focus comprised the Athabasca ore deposit, with special attention on the Fort McMurray area and particular examination of the Mildred Lake Settling basin. A thorough literature review was conducted where the data and concepts from various scientific sources were utilized as a basis in the creation of a Tailings Pond Model, to conceptualize the physical, chemical and biological processes within a typical tailings settling basin. All further refinement and upgrading of the bitumen, processing of coke or other by-products were out of scope. Technological innovations in bitumen extraction and assisted tailings consolidation have resulted in more complex constituent compositions. The physical, chemical and biological processes occurring within a tailings pond are multifaceted making it difficult to model the ultimate fates of various substances. Chemical oxidation and bacterial decomposition have been shown to decrease toxicity of certain contaminants of greater concern.

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On the interactions between naphthenic acids and inorganic minerals (2011)

Naphthenic acids are a family of carboxylic acids that are found in oil sands bitumen.These compounds partition to the aqueous phase during extraction andrefining and are toxic to various biota. The removal of these acids from solutionis difficult due to their low concentrations, complexity of the mixture and poor understandingof the behaviour of the mixed compounds. In particular, partitioningof these organic acids to solid surfaces is not well understood. Knowledge of thisequilibria would be helpful for potential process development.The research presented here describes the adsorption of two surrogate naphthenicacids onto inorganic minerals (copper sulphide and copper hydroxide). Decanoicacid and cyclohexane pentanoic acid were found to be insoluble in water atpH 3, leading to hydrophobic adsorption onto the minerals and the reaction vesselsurfaces. At pH 8.5, both acids formed insoluble copper-carboxylate complexeswhen mixed with the minerals. The hypothesized 2:1 acid:copper stoichiometrywas confirmed. The mechanism of complexation varied with the reaction conditions;both chelating and bridging complexes were observed in the resultantmetallo-organic solids. The relative hydrophobicity of the two NA surrogates wasalso found to contribute to the different adsorption trends.During the pH 8.5 reactions, the solution pHs were found to drop. The uncontrolleddecreases in pH had significant effect on the water-solid partition and onthe apparent mineral loading of the organics. It appears that soluble copper cationshave a higher extent of reaction with the carboxylate anions than does copper containedin the mineral solids. Quantification of these reactions is difficult; howeverthis research does enable conclusions about how the organic acids and inorganicminerals interact and sets the stage for future research.

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Design of bioreactor for reducing sulphate in cattle drinking water (2010)

A 5 litre laboratory-scale upflow anaerobic sludge blanket (UASB) bioreactor was constructed and operated for approximately one year to reduce sulphate in water using an agricultural byproduct, silage, as carbon source. The purpose of this water treatment system was to test the suitability of the UASB design to treat simulated ground water with high sulphate concentrations destined to be used as cattle drinking water. The UASB reactor design was selected after performing an extensive literature review of all available sulphate-reduction processes. A previous MASc project (Amber Brown, 2007) demonstrated the suitability of silage as a carbon source for sulphate reducing bacteria and, furthermore, in this thesis, fate of the organic compounds in the silage leachate during sulphate-reduction was determined. Six particular tests were performed in order to quantify the type of organics in the feed and effluent: chemical oxygen demand (COD), total organic carbon (TOC), total carbohydrates, total alcohols, total phenols, and selected organic and volatile fatty acids (VFA). The reactor ran continuously for approximately one year with a constant silage leachate feed COD concentration of 10,000 mg L₋−¹, and sulphate feed concentrations varying from 2,000 to 3,200 mg L−¹. The flow rates for each feed stream were maintained at ~0.5 mL min−¹ for silage leachate and ~1 mL min−¹ for sulphate feed for most of the experiment. The sulphate reduction rates (SRR) ranged from 368 to 845 mg L−¹ d−¹ and the amount of organics consumed was between 80-90%. Sulphide levels in the UASB bioreactor were consistently high for most of the experiment, ranging from 600-800 mg L−¹. When the sulphate feed concentration was increased to a maximum of 3,282 (± 27.22) mg L−¹, the sulphide concentration within the bioreactor reached a maximum of 1,273 (± 473.5) mg L−¹. A sulphide stripping column was introduced midway through the experiment in an attempt to reduce the sulphide concentration in the system. Short-term results were promising, however, prolonged sulphide removal in the system could not be maintained due to operational problems. Interestingly, during the last month of operation, despite the high sulphide levels, the SRR was at its highest with an upward trend.

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Development of an analytical tool for anaerobic digestion of organic wastes (2010)

Anaerobic digesters decompose organic matter biologically in the absence of oxygen. In some cases, in addition to waste management, the purpose of anaerobic digestion (AD) is to produce methane, which can be used for energy. In the Fraser Valley region, potentially 30 MW of energy can be generated through AD with the additional benefits of reduced odour, green house gas (GHG) emissions and soil and water contamination, which is produced currently from artificial fertilizers.The main goal of this research project is to develop an anaerobic digestion calculator that would assist farm and herd owners in the Lower Fraser Valley in making decisions on choosing suitable anaerobic digestion technologies for their own farms. The calculator is developed from Excel spreadsheets and graphical user interfaces (GUIs). These user interfaces take inputs, send the inputs to the corresponding spreadsheet cells, and block invalid inputs from causing calculation error. The new calculator uses the Lawrence and McCarty kinetic model to calculate substrate consumed during AD. This calculator takes hydraulic retention time (HRT) and feed, via animal counts, single-defined flow or mixing several waste sources, as inputs. From these inputs and default kinetic parameters, which can be modified, reactor size, biogas production rate, effluent characteristics, capital cost and revenue of the AD plant are calculated and summarized for users. Users can select one of the three possible digester configurations: completely-mixed, plug-flow and mixed plug-flow and heat and electricity co-generation or biogas upgrading. Currently the calculator is valid for simulating AD in the mesophilic temperature range only. Further modifications are needed to include other kinetic models, input more feed types and simulate thermophilic AD.

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Recent Tri-Agency Grants

The following is a selection of grants for which the faculty member was principal investigator or co-investigator. Currently, the list only covers Canadian Tri-Agency grants from years 2013/14-2016/17 and excludes grants from any other agencies.

  • Metagenomics to decipher underlying mechanisms of in situ bioremediation so as to verify successful environmental reclamation - Natural Sciences and Engineering Research Council of Canada (NSERC) - Engage Grants Program (2016/2017)
  • Improvement of passive biochemical reactors for selenium and sulphate removal at mine sites - Natural Sciences and Engineering Research Council of Canada (NSERC) - Collaborative Research and Development Grants - Project (2013/2014)
  • In situ bioremediation of high sulphate and sulphide environments - Natural Sciences and Engineering Research Council of Canada (NSERC) - Discovery Grants Program - Individual (2013/2014)

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