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

Abstract

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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“…At week 0 (pre-crude oil spike), Actinobacteria represented 79.4% of sequences on average across microbiome types and 86.6% on average at week 6. This highlights the seemingly powerful constraints of abiotic soil parameters on bacterial taxonomy, supported by many environmental surveys of soil bacterial composition (e.g., [16][17][18][19]. Although we use a single soil substrate in this study, the abiotic environment appeared to lead to taxonomic convergence, and soil type has been shown to influence the trajectories of bacterial assemblages across a range of soil types following diesel contamination (18).…”

“…Although we use a single soil substrate in this study, the abiotic environment appeared to lead to taxonomic convergence, and soil type has been shown to influence the trajectories of bacterial assemblages across a range of soil types following diesel contamination (18). The nature of the soil environment appears to determine whether petroleum contamination will lead to dominance by Actinobacteria or Proteobacteria (18).…”

“…Defining functional redundancy in the soil microbiome is challenging. Although taxonomy has sometimes been correlated with function (18,51,52), these correlations tend to be confounded by differences in soil conditions. When starting with a single microbial strain, increasing microbial diversity is likely to increase carbon processing (as observed by Bell et al [22]) since there is a high chance of complementarity.…”

“…Biotic constraints such as plant root exudates (14), plant immune signaling (15), and competition from native microorganisms (4) can play important roles in shaping soil microbiomes, but, in general, soil bacterial composition follows predictable patterns based on abiotic constraints, such as physicochemical soil parameters (16)(17)(18)(19). These constraints complicate soil microbiome manipulation and may restrict our ability to alter microbiome trajectories.…”

Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada)

“…The primers contained 10-bp multiplex identifiers (MIDs) and adaptor sequences for Ion Torrent sequencing (Yergeau et al 2012;Bell et al 2013). Reactions were performed in 25-µl volumes containing: 10 ng of DNA, 0.3 µM of each primer, 0.4 mg ml -1 of bovine serum albumin, 0.2 µM of dNTPs and 0.05 U µl -1 of rTaq DNA polymerase (GE Healthcare).…”