From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation

Abstract

Hydrocarbons are worldwide-distributed pollutants that disturb various ecosystems. The aim of this study was to characterize the short-lapse dynamics of soil microbial communities in response to hydrocarbon pollution and different bioremediation treatments. Replicate diesel-spiked soil microcosms were inoculated with either a defined bacterial consortium or a hydrocarbonoclastic bacterial enrichment and incubated for 12 weeks. The microbial community dynamics was followed weekly in microcosms using Illumina 16S rRNA gene sequencing. Both the bacterial consortium and enrichment enhanced hydrocarbon degradation in diesel-polluted soils. A pronounced and rapid bloom of a native gammaproteobacterium was observed in all dieselpolluted soils. A unique operational taxonomic unit (OTU) related to the Alkanindiges genus represented ϳ0.1% of the sequences in the original community but surprisingly reached >60% after 6 weeks. Despite this Alkanindiges-related bloom, inoculated strains were maintained in the community and may explain the differences in hydrocarbon degradation. This study shows the detailed dynamics of a soil bacterial bloom in response to hydrocarbon pollution, resembling microbial blooms observed in marine environments. Rare community members presumably act as a reservoir of ecological functions in high-diversity environments, such as soils. This rare-to-dominant bacterial shift illustrates the potential role of a rare biosphere facing drastic environmental disturbances. Additionally, it supports the concept of "conditionally rare taxa," in which rareness is a temporary state conditioned by environmental constraints.

Assessing Technical and Economic Feasibility of Complete Bioremediation for Soils Chronically Polluted with Petroleum Hydrocarbons

“…These enzymes include several dioxygenases, 1-acenaphthenol dehydrogenases, and salicylaldehyde dehydrogenases [46]. On the other hand, the genus Pseudomonas are also commonly present in hydrocarbon-contaminated environments [47][48][49] and their metabolism includes the degradation of various aliphatic and aromatic hydrocarbons [9,12,[50][51][52]. Both Pseudomonas and Acinetobacter strains are also well known to produce a wide variety of extracellular emulsifiers towards improving the bioavailability of hydrocarbons [53][54][55][56][57].…”

“…DN34). These strains were isolated from chronically hydrocarbon-contaminated soil located in the Aconcagua River (Valparaíso Region, Chile) and possess the ability to utilize a wide range of hydrocarbons as sole carbon sources [12]. In addition to their degrading potential, Acinetobacter sp.…”

“…AV treatment was carried out with the addition of a consortium of five bacterial strains that were previously isolated and characterized by our group [12,28]. The consortium was composed of two strains belonging to Pseudomonas and three strains from Acinetobacter genus.…”

“…To estimate the degradation of compounds belonging to the diesel range organics (DRO), including from C 12 to C 28 hydrocarbons (here after called TPH), quantification of hydrocarbons was performed every week, with exception of week number five after the beginning of the experiment. The procedure was accomplished as previously described [12], with minor modifications, injecting 2 µL of the sample in a gas chromatograph coupled with a flame ionization detector (GC-FID) (Clarus 680, PerkinElmer). Briefly, the injector temperature was 320°C, the detector temperature was 295°C, the flow was split less during injection at 10 ml min -1 .…”

“…Bioremediation techniques are often based on (i) natural bioattenuation, using indigenous microorganisms to degrade a pollutant; (ii) biostimulation, changing variables to enhance pollutant degradation by native communities; or (iii) bioaugmentation, using exogenous hydrocarbon clastic microorganisms [12]. Although bioremediation has gained increasing attention for being an environmentally sustainable, costeffective and a permanent alternative for treatment of contaminated soils with a wide range of pollutants, its contribution for the clean-up is still limited [13,14].…”