Molecular Mechanisms of Enhanced Bacterial Growth on Hexadecane with Red Clay

Abstract

Red clay was previously used to enhance bioremediation of diesel-contaminated soil. It was speculated that the enhanced degradation of diesel was due to increased bacterial growth. In this study, we selected Acinetobacter oleivorans DR1, a soil-borne degrader of diesel and alkanes, as a model bacterium and performed transcriptional analysis using RNA sequencing to investigate the cellular response during hexadecane utilization and the mechanism by which red clay promotes hexadecane degradation. We confirmed that red clay promotes the growth of A. oleivorans DR1 on hexadecane, a major component of diesel, as a sole carbon source. Addition of red clay to hexadecane-utilizing DR1 cells highly upregulated β-oxidation, while genes related to alkane oxidation were highly expressed with and without red clay. Red clay also upregulated genes related to oxidative stress defense, such as superoxide dismutase, catalase, and glutaredoxin genes, suggesting that red clay supports the response of DR1 cells to oxidative stress generated during hexadecane utilization. Increased membrane fluidity in the presence of red clay was confirmed by fatty acid methyl ester analysis at different growth phases, suggesting that enhanced growth on hexadecane could be due to increased uptake of hexadecane coupled with upregulation of downstream metabolism and oxidative stress defense. The monitoring of the bacterial community in soil with red clay for a year revealed that red clay stabilized the community structure.

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms

“…In contrast, the DP treatment, which exhibited the highest level of diesel biodegradation, was dominated by Proteobacteria and most often showed lower abundance of the genes involved in diesel biodegradation. This suggests that the enhancement of diesel biodegradation resulted not only from alteration of community structure but other effects as well, for example, promotion of bacterial growth 19 and upregulation of expression of genes related to alkane degradation and oxidative stress defense, as shown in our previous research 34 . It should be noted that the processed red clay used in this study did not contain organic nutrients, or nitrogen or phosphate fertilizers, and thus differed from the typical nutrient-rich soil used in traditional biostimulation strategies 35 .…”

Transcriptomic analysis of the highly efficient oil-degrading bacteriumAcinetobacter venetianusRAG-1 reveals genes important in dodecane uptake and utilization

“…Similarly, in DR1 both alkM genes were upregulated in hexadecane with alkMb exhibiting higher expression than alkMa (Jung et al. 2015 ). The Acinetobacter AlkMs might have evolved with overlapping substrate ranges with each performing optimally when degrading a specific range of carbon chain lengths.…”

“… 2013 ; Jung et al. 2015 ), an upregulation of genes homologous to iron uptake genes (ORF_2445, ORF_2118 and ORF_2945) was seen when RAG-1 was grown in dodecane relative to acetate. This is expected since the alkane monooxygenase is known to possess an iron-containing core.…”

“…It displays upregulation in hexadecane (Jung et al. 2015 ) and was hypothesized to aid in alkane uptake in DR1. The gene coding for OmpW (ORF_1329) in RAG-1 displayed 22% amino acid identity to AlkL in Gpo1 and was upregulated (3.5-fold) when grown in dodecane relative to acetate.…”

“…The alkane transcriptional response of the AlkM-containing Acinetobacter oleivorans DR1 identified upregulation of alkane metabolism, fatty acid metabolism, glyoxylate pathway and oxidative stress defense response genes (Jung et al. 2015 ). DR1 harbors two alkane monooxygenases with varied degrees of similarity to the alkane monooxygenases of RAG-1 (Supplementary Information 1, Supporting Information).…”