Next-Generation Sequencing of Microbial Communities in the Athabasca River and Its Tributaries in Relation to Oil Sands Mining Activities

Yergeau, Étienne; Lawrence, John R.; Sanschagrin, Sylvie; Waiser, Marley J.; Korber, Darren R.; Greer, Charles W.

doi:10.1128/aem.02036-12

Cited by 202 publications

(136 citation statements)

References 50 publications

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“…Sequencing was conducted on an Ion Torrent Personal Genome Machine using the Ion Xpress Template Kit (Life Technologies, Carlsbad, CA, USA) and the Ion 314 chip (Life Technologies) following the manufacturer's protocols. Ion Torrent sequencing has been shown to produce microbial community profiles that are highly comparable to those produced by 454 sequencing (Yergeau et al, 2012b).…”

Section: Microcosm Setup and Incubationmentioning

confidence: 99%

Predictable bacterial composition and hydrocarbon degradation in Arctic soils following diesel and nutrient disturbance

et al. 2013

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Increased exploration and exploitation of resources in the Arctic is leading to a higher risk of petroleum contamination. A number of Arctic microorganisms can use petroleum for growth-supporting carbon and energy, but traditional approaches for stimulating these microorganisms (for example, nutrient addition) have varied in effectiveness between sites. Consistent environmental controls on microbial community response to disturbance from petroleum contaminants and nutrient amendments across Arctic soils have not been identified, nor is it known whether specific taxa are universally associated with efficient bioremediation. In this study, we contaminated 18 Arctic soils with diesel and treated subsamples of each with monoammonium phosphate (MAP), which has successfully stimulated degradation in some contaminated Arctic soils. Bacterial community composition of uncontaminated, diesel-contaminated and diesel+MAP soils was assessed through multiplexed 16S (ribosomal RNA) rRNA gene sequencing on an Ion Torrent Personal Genome Machine, while hydrocarbon degradation was measured by gas chromatography analysis. Diversity of 16S rRNA gene sequences was reduced by diesel, and more so by the combination of diesel and MAP. Actinobacteria dominated uncontaminated soils with <10% organic matter, while Proteobacteria dominated higher-organic matter soils, and this pattern was exaggerated following disturbance. Degradation with and without MAP was predictable by initial bacterial diversity and the abundance of specific assemblages of Betaproteobacteria, respectively. High Betaproteobacteria abundance was positively correlated with high diesel degradation in MAP-treated soils, suggesting this may be an important group to stimulate. The predictability with which bacterial communities respond to these disturbances suggests that costly and time-consuming contaminated site assessments may not be necessary in the future.

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Section: Microcosm Setup and Incubationmentioning

confidence: 99%

Predictable bacterial composition and hydrocarbon degradation in Arctic soils following diesel and nutrient disturbance

et al. 2013

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“…Ion Torrent 16S rRNA sequencing Reverse-transcriptase (RT)-PCR of the partial 16S rRNA was performed using the universal primers F343 and R533 containing the 10-bp multiplex identifiers and adaptor sequences for Ion Torrent sequencing described previously (Yergeau et al, 2012;Bell et al, 2013). The sequencing of the pooled library was done using the Ion Torrent Personal Genome Machine system (Life Technologies).…”

Section: Nucleic Acid Extractionmentioning

confidence: 99%

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

et al. 2013

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The goal of phytoremediation is to use plants to immobilize, extract or degrade organic and inorganic pollutants. In the case of organic contaminants, plants essentially act indirectly through the stimulation of rhizosphere microorganisms. A detailed understanding of the effect plants have on the activities of rhizosphere microorganisms could help optimize phytoremediation systems and enhance their use. In this study, willows were planted in contaminated and non-contaminated soils in a greenhouse, and the active microbial communities and the expression of functional genes in the rhizosphere and bulk soil were compared. Ion Torrent sequencing of 16S rRNA and Illumina sequencing of mRNA were performed. Genes related to carbon and amino-acid uptake and utilization were upregulated in the willow rhizosphere, providing indirect evidence of the compositional content of the root exudates. Related to this increased nutrient input, several microbial taxa showed a significant increase in activity in the rhizosphere. The extent of the rhizosphere stimulation varied markedly with soil contamination levels. The combined selective pressure of contaminants and rhizosphere resulted in higher expression of genes related to competition (antibiotic resistance and biofilm formation) in the contaminated rhizosphere. Genes related to hydrocarbon degradation were generally more expressed in contaminated soils, but the exact complement of genes induced was different for bulk and rhizosphere soils. Together, these results provide an unprecedented view of microbial gene expression in the plant rhizosphere during phytoremediation.

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“…Each reverse primer was barcoded with a specific IonXpress sequence to identify samples. PCR amplicons were purified using QIAquick Gel Extraction Kit (Qiagen, Toronto, ON, Canada), pooled and sequenced using an Ion Torrent PGM system and a 316 chip with the Ion Sequencing 200 kit as described in Yergeau et al (2012). V5 amplicons were analyzed using the Mothur pipeline (Schloss et al, 2009).…”

Section: Sample Collectionmentioning

confidence: 99%

Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton

et al. 2014

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In this study, we used comparative metaproteomics to investigate the metabolic activity of microbial plankton inhabiting a seasonally hypoxic basin in the Northwest Atlantic Ocean (Bedford Basin). From winter to spring, we observed a seasonal increase in high-affinity membrane transport proteins involved in scavenging of organic substrates; Rhodobacterales transporters were strongly associated with the spring phytoplankton bloom, whereas SAR11 transporters were abundant in the underlying waters. A diverse array of transporters for organic compounds were similar to the SAR324 clade, revealing an active heterotrophic lifestyle in coastal waters. Proteins involved in methanol oxidation (from the OM43 clade) and carbon monoxide (from a wide variety of bacteria) were identified throughout Bedford Basin. Metabolic niche partitioning between the SUP05 and ARCTIC96BD-19 clades, which together comprise the Gamma-proteobacterial sulfur oxidizers group was apparent. ARCTIC96BD-19 proteins involved in the transport of organic compounds indicated that in productive coastal waters this lineage tends toward a heterotrophic metabolism. In contrast, the identification of sulfur oxidation proteins from SUP05 indicated the use of reduced sulfur as an energy source in hypoxic bottom water. We identified an abundance of Marine Group I Thaumarchaeota proteins in the hypoxic deep layer, including proteins for nitrification and carbon fixation. No transporters for organic compounds were detected among the thaumarchaeal proteins, suggesting a reliance on autotrophic carbon assimilation. In summary, our analyses revealed the spatiotemporal structure of numerous metabolic activities in the coastal ocean that are central to carbon, nitrogen and sulfur cycling in the sea.

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Next-Generation Sequencing of Microbial Communities in the Athabasca River and Its Tributaries in Relation to Oil Sands Mining Activities

Cited by 202 publications

References 50 publications

Predictable bacterial composition and hydrocarbon degradation in Arctic soils following diesel and nutrient disturbance

Predictable bacterial composition and hydrocarbon degradation in Arctic soils following diesel and nutrient disturbance

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton

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