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Modulation of microbial consortia enriched from different polluted environments during petroleum biodegradation

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Abstract

Environmental microbial communities are key players in the bioremediation of hydrocarbon pollutants. Here we assessed changes in bacterial abundance and diversity during the degradation of Tunisian Zarzatine oil by four indigenous bacterial consortia enriched from a petroleum station soil, a refinery reservoir soil, a harbor sediment and seawater. The four consortia were found to efficiently degrade up to 92.0% of total petroleum hydrocarbons after 2 months of incubation. Illumina 16S rRNA gene sequencing revealed that the consortia enriched from soil and sediments were dominated by species belonging to Pseudomonas and Acinetobacter genera, while in the seawater-derived consortia Dietzia, Fusobacterium and Mycoplana emerged as dominant genera. We identified a number of species whose relative abundances bloomed from small to high percentages: Dietzia daqingensis in the seawater microcosms, and three OTUs classified as Acinetobacter venetianus in all two soils and sediment derived microcosms. Functional analyses on degrading genes were conducted by comparing PCR results of the degrading genes alkB, ndoB, cat23, xylA and nidA1 with inferences obtained by PICRUSt analysis of 16S amplicon data: the two data sets were partly in agreement and suggest a relationship between the catabolic genes detected and the rate of biodegradation obtained. The work provides detailed insights about the modulation of bacterial communities involved in petroleum biodegradation and can provide useful information for in situ bioremediation of oil-related pollution.

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Acknowledgements

This work was partly financially supported through grants from the Tunisian Ministry of Higher Education and Scientific Research and from the University of Monastir. The authors are grateful to Imed Cheraeif from laboratory of Biochemistry and Mass spectrometry at the Monastir Medical Faculty in Tunisia for his technical assistance and support in the chromatography analysis. We thank Regional Commissariat for the Agricultural Development of Monastir in Tunisia for the technical assistance in physicochemical analyses of soil samples. We are also grateful to Sotirios Vasileiadis for providing a number of R scripts used for bioinformatics analyses and graphs preparation.

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  1. Laboratory of Analysis, Treatment and Valorization of Environmental Pollutants and Products, Faculty of Pharmacy, Monastir University, Monastir, Tunisia

    Rahma Omrani & Dalila Saidane

  2. Dipartimento di Scienze e Tecnologie Alimentari per una filiera agroalimentare sostenibile (DiSTAS), Facoltà di Scienze Agrarie, Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy

    Giulia Spini & Edoardo Puglisi

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Correspondence to Edoardo Puglisi.

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Fig. S1

Gas chromatographic spectra collected after different incubation times (0, 1 and 8 weeks) with Zarzatine crude oil (ZCO). Peaks are labelled according to individual hydrocarbons with their carbon number (C9–C29). (a): chromatograms of control sample (medium with only ZCO); (b) microcosms K; (c) microcosms R; (d) microcosms S; (e) microcosms E. Two replicates per sample are reported. For the control (a), chromatograms at week 0 are reported, while for the inoculated microcosms (b-e) the two graphs above are the replicates at the 1st week, the two below the replicates at the 8th week. SD: External standard. Supplementary material 1 (DOCX 497 kb)

Fig. S2

Percentages of bacterial sequences correctly classified at different taxonomic depth. Data refer to 547,560 sequences identified as bacterial after PCR amplification of the V3-V4 16S rRNA region. Supplementary material 2 (DOCX 70 kb)

Fig. S3

Hierarchical clustering of sequences from all experiments classified at the genus level. Clusters were identified with the average linkage algorithm for taxa that contributed at least 5% to a single sample. Taxa that contributed less than this threshold were added to the sequence group denoted “other”. Supplementary material 3 (DOCX 303 kb)

Supplementary material 4 (DOCX 23 kb)

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Omrani, R., Spini, G., Puglisi, E. et al. Modulation of microbial consortia enriched from different polluted environments during petroleum biodegradation. Biodegradation 29, 187–209 (2018). https://doi.org/10.1007/s10532-018-9823-3

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