Correlating the succession of microbial communities from Nigerian soils to petroleum biodegradation

Abstract

Whilst biodegradation of different hydrocarbon components has been widely demonstrated to occur by specialist oil-degrading bacteria, less is known about the impact on microbial communities as a function of oil composition by comparing the biodegradation of chemically complex fuels to synthetic products. The objectives of this study were (i) to assess the biodegradation capacity and succession of microbial communities isolated from Nigerian soils in media with crude oil or synthetic oil as sole sources of carbon and energy, and (ii) to assess the temporal variability of the microbial community size. Community profiling was done using 16 S rRNA gene amplicon sequencing (Illumina), and oil profiling using gas chromatography. The biodegradation of natural and synthetic oil differed probably due to the content of sulfur that may interfere with the biodegradation of hydrocarbons. Both alkanes and PAHs in the natural oil were biodegraded faster than in the synthetic oil. Variable community responses were observed during the degradation of alkanes and more simple aromatic compounds, but at later phases of growth they became more homogeneous. The degradation capacity and the size of the community from the more-contaminated soil were higher than those from the less-contaminated soil. Six abundant organisms isolated from the cultures were found to biodegrade oil molecules in pure cultures. Ultimately, this knowledge may contribute to a better understanding of how to improve the biodegradation of crude oil by optimizing culturing conditions through inoculation or bioaugmentation of specific bacteria during ex-situ biodegradation such as biodigesters or landfarming.

Keywords: Degradation capacity; Oil biodegradation; PAHs; Pre-exposure; Soil microbial communities.

Fig. 1

Quantification of specific hydrocarbons (C₁₁-C₃₀ alkanes and the sixteen priority PAHs according to the US-Environment Protection Agency (EPA)) in crude oil degraded by two soil communities: a less-contaminated soil (L-soil) and a more-contaminated soil (M-soil) compared with a weathering control without bacterial inoculum (W control). (a) Concentration of alkanes. (b) Concentration of PAHs. 2-methylnaphthalene (2-MN), 1-methylnaphthalene (1-MN), acenaphthylene (Acy), acenaphthene (Ace), fluorene (F), phenanthrene (P), anthracene (Ant), fluoranthene (Fl), pyrene (Pyr), benzo(a)anthracene (BaAnt), chrysene (Chr), benzo(b)fluoranthene (BbFl), benzo(k)fluoranthene (BkFl), benzo(a)pyrene (BaPyr), dibenz(a,h)anthracene (DBahAnt), benzo(ghi)perylene (BghiPer), and indeno(1,2,3-C,D)pyrene (Ipyr). Results are averages of biological triplicates with the error bars shown. The PAH subplots show the aromatic ring numbers

Fig. 2

Quantification of synthetic oil molecules degraded by two soil communities, one from a less-contaminated soil (L-soil) and one from a more-contaminated soil (M-soil) compared with a weathering control without bacterial inoculum (W control). (a) Concentration of alkanes (C₁₁-C₃₀). (b) Concentration of the sixteen priority PAHs according to the US-Environment Protection Agency (EPA). 2-methylnaphthalene (2-MN), 1-methylnaphthalene (1-MN), acenaphthylene (Acy), acenaphthene (Ace), fluorene (F), phenanthrene (P), anthracene (Ant), fluoranthene (Fl), pyrene (Pyr), benzo(a)anthracene (BaAnt), chrysene (Chr), benzo(b)fluoranthene (BbFl), benzo(k)fluoranthene (BkFl), benzo(a)pyrene (BaPyr), dibenz(a,h)anthracene (DBahAnt), benzo(ghi)perylene (BghiPer), and indeno(1,2,3-C,D)pyrene (Ipyr). Results are averages of biological triplicate with the error bars shown. The PAH subplots show the aromatic ring numbers

Fig. 3

Diversity of two oil-contaminated soils incubated in mineral media with crude oil (spiked with EPA-PAHs) or a synthetic oil. L-soil is a less contaminated soil and M-soil is a more contaminated soil. (a) Alpha-diversity indices. Observed index represents the total number of OTUs per sample. Shannon index represents the relative abundance of each OTU. (b) Non-metric multidimensional scaling (NMDS) ordination of the Bray-Curtiss dissimilarity between communities. All NMDS2 values of communities from the L-soil were negative while the same values were positive in case of communities from the M-soil. A dotted line was added to separate the clustering affinity of the bacterial communities from both types of soil

Fig. 4

Quantification of specific hydrocarbons (C₁₁-C₃₀ alkanes and the sixteen priority PAH according to the US-Environment Protection Agency (EPA)) linked to community changes. The crude oil was degraded by two soils: one less-contaminated (L-soil) and another more-contaminated (M-soil) in comparison with a weathering control without bacterial inoculum (W control). The summation of alkanes and the summation of PAHs (a and b) are affiliated with the bar plots of the abundance of the microbial community composition at the genus level (c and d). Only the most abundant genera (the top 7) or family level (in cases of unclassified genera) are listed in the legends

Fig. 5

Quantification of hydrocarbons in a synthetic oil linked to community changes. The synthetic oil was degraded by two soils: one less-contaminated (L-soil) and another more-contaminated (M-soil) in comparison with a weathering control without bacterial inoculum (W control). The summation of alkanes (C₁₁-C₃₀) and the summation of the sixteen priority PAH according to the US-Environment Protection Agency (EPA) (a and b) are affiliated with the bar plots of the abundance of the microbial community composition at the genus level (c and d). Only the most abundant genera (the top 6) are listed in the legends

Fig. 6

Degradation of a synthetic oil by single species in isolation. Cultures were made using 10 mL of medium in 30 mL glass bottles closed with Teflon caps. Incubations were at 30 °C, shaking at 120 rpm for six months. The weathering control (W control) did not contain a bacterial inoculum. (a) Degradation of n-alkanes (C₁₁ to C₃₀). (b) Degradation of PAHs. 2-methylnaphthalene (2-MN), 1-methylnaphthalene (1-MN), acenaphthylene (Acy), acenaphthene (Ace), fluorene (F), phenanthrene (P), anthracene (Ant), fluoranthene (Fl), pyrene (Pyr), benzo(a)anthracene (BaAnt), chrysene (Chr), benzo(b)fluoranthene (BbFl), benzo(k)fluoranthene (BkFl), benzo(a)pyrene (BaPyr), dibenz(a,h)anthracene (DBahAnt), benzo(ghi)perylene (BghiPer), and indeno(1,2,3-C,D)pyrene (Ipyr). Results are averages of biological triplicate with the error bars shown