Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil
Our objective was to study the bacterial community changes that determine enhanced removal of petroleum hydrocarbons from soils subjected to bioaugmentation with the hydrocarbon-degrading strains Rhodococcus erythropolis CD 130, CD 167, and their combination. To achieve this, a high-throughput seque...
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doaj-79bef5914431425293874dd702c4af622020-11-25T03:54:22ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-08-011110.3389/fmicb.2020.02106559027Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated SoilMagdalena Pacwa-Płociniczak0Paulina Biniecka1Kinga Bondarczuk2Zofia Piotrowska-Seget3Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, PolandInstitute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, PolandCentre for Bioinformatics and Data Analysis, Medical University of Bialystok, Białystok, PolandInstitute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, PolandOur objective was to study the bacterial community changes that determine enhanced removal of petroleum hydrocarbons from soils subjected to bioaugmentation with the hydrocarbon-degrading strains Rhodococcus erythropolis CD 130, CD 167, and their combination. To achieve this, a high-throughput sequencing of the 16S rRNA gene was performed. The changes in the bacterial community composition were most apparent the day after bacterial inoculation. These changes represented an increase in the percentage abundance of Rhodococcus and Pseudomonas genera. Surprisingly, members of the Rhodococcus genus were not present after day 91. At the end of the experiment, the bacterial communities from the CD 130, CD 167, and control soils had a similar structure. Nevertheless, the composition of the bacteria in the CD 130 + CD 167 soil was still distinct from the control. Metagenomic predictions from the 16S rRNA gene sequences showed that the introduction of bacteria had a significant influence on the predicted pathways (metabolism of xenobiotics, lipids, terpenoids, polyketides, and amino acids) on day one. On day 182, differences in the abundance of functional pathways were also detected in the CD 130 and CD 130 + CD 167 soils. Additionally, we observed that on day one, in all bioaugmented soils, the alkH gene was mainly contributed by the Rhodococcus and Mycobacterium genera, whereas in non-treated soil, this gene was contributed only by the Mycobacterium genus. Interestingly, from day 91, the Mycobacterium genus was the main contributor for the tested genes in all studied soils. Our results showed that hydrocarbon depletion from the analyzed soils resulted from the activity of the autochthonous bacteria. However, these changes in the composition and function of the indigenous bacterial community occurred under the influence of the introduced bacteria.https://www.frontiersin.org/article/10.3389/fmicb.2020.02106/fullpetroleum hydrocarbonsbioaugmentationsoil microbial communitieshigh-throughput sequencingmetagenome prediction |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Magdalena Pacwa-Płociniczak Paulina Biniecka Kinga Bondarczuk Zofia Piotrowska-Seget |
spellingShingle |
Magdalena Pacwa-Płociniczak Paulina Biniecka Kinga Bondarczuk Zofia Piotrowska-Seget Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil Frontiers in Microbiology petroleum hydrocarbons bioaugmentation soil microbial communities high-throughput sequencing metagenome prediction |
author_facet |
Magdalena Pacwa-Płociniczak Paulina Biniecka Kinga Bondarczuk Zofia Piotrowska-Seget |
author_sort |
Magdalena Pacwa-Płociniczak |
title |
Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil |
title_short |
Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil |
title_full |
Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil |
title_fullStr |
Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil |
title_full_unstemmed |
Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil |
title_sort |
metagenomic functional profiling reveals differences in bacterial composition and function during bioaugmentation of aged petroleum-contaminated soil |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2020-08-01 |
description |
Our objective was to study the bacterial community changes that determine enhanced removal of petroleum hydrocarbons from soils subjected to bioaugmentation with the hydrocarbon-degrading strains Rhodococcus erythropolis CD 130, CD 167, and their combination. To achieve this, a high-throughput sequencing of the 16S rRNA gene was performed. The changes in the bacterial community composition were most apparent the day after bacterial inoculation. These changes represented an increase in the percentage abundance of Rhodococcus and Pseudomonas genera. Surprisingly, members of the Rhodococcus genus were not present after day 91. At the end of the experiment, the bacterial communities from the CD 130, CD 167, and control soils had a similar structure. Nevertheless, the composition of the bacteria in the CD 130 + CD 167 soil was still distinct from the control. Metagenomic predictions from the 16S rRNA gene sequences showed that the introduction of bacteria had a significant influence on the predicted pathways (metabolism of xenobiotics, lipids, terpenoids, polyketides, and amino acids) on day one. On day 182, differences in the abundance of functional pathways were also detected in the CD 130 and CD 130 + CD 167 soils. Additionally, we observed that on day one, in all bioaugmented soils, the alkH gene was mainly contributed by the Rhodococcus and Mycobacterium genera, whereas in non-treated soil, this gene was contributed only by the Mycobacterium genus. Interestingly, from day 91, the Mycobacterium genus was the main contributor for the tested genes in all studied soils. Our results showed that hydrocarbon depletion from the analyzed soils resulted from the activity of the autochthonous bacteria. However, these changes in the composition and function of the indigenous bacterial community occurred under the influence of the introduced bacteria. |
topic |
petroleum hydrocarbons bioaugmentation soil microbial communities high-throughput sequencing metagenome prediction |
url |
https://www.frontiersin.org/article/10.3389/fmicb.2020.02106/full |
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