Elsevier

Science of The Total Environment

Volume 665, 15 May 2019, Pages 113-124
Science of The Total Environment

Microbial metabolic strategies for overcoming low-oxygen in naturalized freshwater reservoirs surrounding the Athabasca Oil Sands: A proxy for End-Pit Lakes?

https://doi.org/10.1016/j.scitotenv.2019.02.032Get rights and content

Highlights

  • Seeking to provide much needed insight into large landscape reclamation end-point objectives

  • Insights into natural microbial metabolism in the Athabasca Oil Sands region

  • In-situ geochemical and gene expression surveys to understand active biogeochemistry

  • Hydrocarbon impact on microbial metabolism and sediment geochemistry under sub-oxic conditions

Abstract

The success and sustainability of aquatic ecosystems are driven by the complex, cooperative metabolism of microbes. Ecological engineering strategies often strive to harness this syntrophic synergy of microbial metabolism for the reclamation of contaminated environments worldwide. Currently, there is a significant knowledge gap in our understanding of how the natural microbial ecology overcomes thermodynamic limitations in recovering contaminated environments. Here, we used in-situ metatranscriptomics and associated metataxonomic analyses on sediments collected from naturalized freshwater man-made reservoirs within the Athabasca Oil Sands region of Alberta, Canada. These reservoirs are unique since they are untouched by industrial mining processes and serve as representative endpoints for model landscape reconstruction. Results indicate that a microbial syntrophic cooperation has been established represented by the oxygenic and anoxygenic phototrophs, sustained through the efficient use of novel cellular mechanistic adaptations tailored to these unique thermodynamic conditions. Specifically, chemotaxis transcripts (cheY & MCPs-methyl-accepting chemotaxis proteins) were highly expressed, suggesting a highly active microbial response to gradients in environmental stimuli, resulting indirectly from hydrocarbon compound alteration. A high expression of photosynthetic activity, likely sustaining nutrient delivery to the similarly highly expressed methanogenic community acting in syntrophy during the breakdown of organics. Overall the more diversified functionality within sub-oxic sample locations indicates an ability to maintain efficient metabolism under thermodynamic constraints. This is the first study to holistically identify and characterize these types of in-situ, metabolic processes and address their thermodynamic feasibility within a global context for large landscape reconstruction. These characterizations of regional, natural landscapes surrounding the oil sands mining operation are severely lacking, but truly provide invaluable insight into end-point goals and targets for reclamation procedures.

Introduction

Microorganisms are the most diverse group of organisms on the planet, therefore the need to understand both diversity and metabolic capabilities in a range of environments is vital in characterizing their roles for shaping their surroundings (Cowan et al., 2015; Foght and Fedorak, 2015; Hua et al., 2015). Increasing our comprehension of microbial influences on ecosystem dynamics is crucial for not only understanding biodiversity itself, but is also extremely useful in the fields of bioengineering and bioremediation where these diverse microorganisms are considered workhorses in degrading, transforming or sequestering a range of contaminants (Callaghan, 2013; DiLoreto et al., 2016; Jin et al., 2012; Scott et al., 2014; VanMensel et al., 2017). Advancements in microbial genomics has allowed researchers to piece together not only microbial energy metabolism, but also identify novel biodegradation pathways by which microbes take complex reactants to a more reduced, bioavailable product (An et al., 2013; Embree et al., 2014; Haritash and Kaushik, 2009; Reid et al., 2018). Certain polycyclic aromatic hydrocarbons (PAHs), for example, have been degraded by microbes under both controlled laboratory and select in-situ research (Reid et al., 2018). Further, many marine-based studies to date have shown the ability of complex natural microbial populations to metabolize hydrocarbon compounds, though there remains little research characterizing these metabolic capabilities for inland, freshwater ecosystems (Kappell et al., 2014; Mason et al., 2012; Reid et al., 2018; Scott et al., 2014). Additionally, despite being theoretically preferred in oxygen-rich environments, research has revealed several unique and effective biodegradation pathways are utilized by microbes under sub-oxic (i.e. extremely low dissolved oxygen; sometimes coexisting with sulfides) conditions (Haritash and Kaushik, 2009). Though many of these pathways have yet to be characterized, several studies have begun to shed light on how co-metabolic activity and syntrophy between microbial groups is facilitating their ability to overcome thermodynamic hurdles in low-oxygen environments (Dolfing et al., 2008; Morris et al., 2013; Pernthaler et al., 2008). Many of these degradation pathways culminate in the production of byproducts such as methane, which can have significant impacts on global greenhouse gas emissions.

In-situ, shotgun genomic approaches allow for whole population, unbiased characterizations, where targeted gene approaches and culturing studies can fall short in understanding the whole picture. These advancements are helping researchers understand how human impacts such as point-source and chronic pollution and even climate change are altering “natural” microbial diversity in various environments (Kimes et al., 2014; Reid et al., 2018; Weisener et al., 2017). Studies have revealed the plasticity of microbial function in response to contaminant presence, though there is generally a lack of studies simply characterizing microbial diversity and metabolic dynamics in naturally extreme environments (i.e. near hydrocarbon deposits; acidic springs; arctic tundra etc.) (Anantharaman et al., 2013; Brochier-Armanet and Moreira, 2015; Comte et al., 2013). It is these studies that could prove vital in the future, when large scale bioremediation efforts seek to determine an appropriate baseline reference, or target end-point from which to gauge bioremediation success. This is perhaps of no greater relevance than in northern Alberta, Canada, where one of the world's largest bitumen (i.e. oil) reserves is actively being mined (Reid et al., 2016a). In this unique geographic region, where bitumen naturally outcrops to the surface, there are also millions of liters of mining process-affected waters sitting in settling basins called tailings ponds. The large amount of bitumen extracted from the oil sands in the region creates large volumes of these process-affected materials (i.e. waste products), including water, sands, silts and clays, alongside a host of residual hydrocarbons and other contaminants. Government mandates that oil companies must perform reclamation practices once mining has ceased, and therefore much research is focused on identifying possible detoxification and reclamation strategies (Boudens et al., 2016; CEMA, 2012; Dhadli et al., 2012; Warren et al., 2016). End-Pit Lakes (EPLs) are one of the strategies being studied for the eventual remediation and reclamation of mines in the Athabasca Oil Sands region (CEMA, 2012). Given such diversity in the contaminant footprint in the region, it is imperative to understand the cumulative effects of multiple stressors on the natural environment (Lima and Wrona, 2019).

EPLs are large lake basins created in the remnants of open-pit mines, filled with a mixture of both processed mine waters and natural waters from the local rivers and tributaries (CEMA, 2012). Mimicking any natural lake system, these EPLs will be subject to not only depth, light, and oxygen variation, but also a host external and internal environmental stimulus. Recently, research has revealed the collective impact freshwater basins such as lakes, reservoirs and wetlands, have on global biogeochemical cycles, therefore forecasting the fate of future EPLs should be a vital area of research moving forward (Battin et al., 2009; Cole et al., 2007; Rooney et al., 2012; Trimmer et al., 2015). Early research on the first EPL (Base Mine Lake) - in the Athabasca Oil Sands region, has revealed similarities and differences to tailings environments, specifically noting increased nitrification activity (Risacher et al., 2018). What remains poorly defined and understood is the long-term fate of these EPLs, considering that their inevitably rich hydrocarbon footprint will influence their development towards an otherwise “normal” lake ecosystem biogeochemical signature. Additionally, there is still a poor understanding of how oil sands mining contributes to the contaminant signature in the surrounding natural landscape (Hodson, 2013; Kelly et al., 2009; Reid et al., 2018; Rooney et al., 2012). Within this context natural or man-made “analogues” are required. In northern Alberta, there are two man-made reservoirs that serve this purpose. They were created to divert water around mining operations, which could act as perfect simulation or end-point for matured EPLs. These reservoirs are created amidst the overburden of the same geologic formation from which the bitumen is extracted, therefore contain a natural hydrocarbon signature, largely void of additional anthropogenic input. These reservoirs are the closest representation of what a future EPLs will behave like, though remain unstudied in this context. The structural and functional diversity of the microbes studied here provide not only unbiased insight into the future biogeochemical characteristics of EPLs, but in a broader context, furthers our understanding of boreal, freshwater, meso- to oligotrophic lakes.

In this paper we collected a series of sediment cores in different redox conditions in two freshwater lakes/reservoirs within the Oil Sands footprint of Northern Alberta, Canada. Alongside measurements of PAH concentrations and accompanying physicochemical measurements, metatranscriptomics analyses were performed on the bed sediments to determine the in-situ biodegradation and general metabolic capabilities of the indigenous microbes. Metataxonomics analysis was also performed to gain insight into which microbes were associated with the metabolic processes observed through the gene expression analyses. Results aim to answer questions of how the indigenous microbial population deals with multiple stressors and varying environmental redox conditions.

Section snippets

Study systems and location

Ruth Lake (RL) and Poplar Creek Reservoir (PCR) are located in northern Alberta, Canada, adjacent to the Athabasca Oil Sands industrial sites (Fig. 1). Both water bodies are located on primarily organic lacustrine deposits, overlying glacial fluvial sediments, straddling the Clearwater and McMurray Formations (the Clearwater Formation overlies the McMurray Formation - the geologic formation constituting the minable bitumen of the Athabasca Oil Sands). These reservoirs were created in 1975, to

Geochemistry

The PAH signature observed at all sites is indicative of the heavy oil/bitumen deposit of the McMurray Formation (Table 1). PAH distributions were plotted to determine origin, and general trends with respect to substituted and unsubstituted compounds within each PAH family (Fig. 2). The approximate normal distribution of benz[a]anthracene/chrysene and naphthalene families of PAHs is indicative of petrogenic origin (oil products). Compared to the other PAH compounds measured, benzopyrene and

Conclusions

The microbial function and biogeochemical signatures observed in this study provide the first unbiased glimpse into the microbial ecology and metabolic processes that one day may be attributed to large, reclaimed freshwater lakes in the region, in the footprint of the McMurray Formation. Representing analogues to future EPLs, these results give insight into how natural landscapes behave in this region and provide biogeochemical targets for current and future reclamation projects. These types of

Acknowledgements

This project was funded in part by NSERC Discovery Grant 860006. The authors would also like to thank Environment and Climate Change Canada for their partial funding, logistical and field sampling support. They would also like to thank Genome Quebec for their support in RNAseq using their Illumina HiSeq 4000 platform.

Author contributions statement

T.R, I.G.D, S.R.C. and C.G.W all contributed to the writing and editing of the manuscript. All figures were produced by T.R. All authors reviewed the manuscript.

Competing interests

The authors declare no competing interests.

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