Abundance and Diversity of n-Alkane-Degrading Bacteria in a Forest Soil Co-Contaminated with Hydrocarbons and Metals: A Molecular Study on alkB Homologous Genes

Abstract

Unraveling functional genes related to biodegradation of organic compounds has profoundly improved our understanding of biological remediation processes, yet the ecology of such genes is only poorly understood. We used a culture-independent approach to assess the abundance and diversity of bacteria catalyzing the degradation of n-alkanes with a chain length between C(5) and C(16) at a forest site co-contaminated with mineral oil hydrocarbons and metals for nearly 60 years. The alkB gene coding for a rubredoxin-dependent alkane monooxygenase enzyme involved in the initial activation step of aerobic aliphatic hydrocarbon metabolism was used as biomarker. Within the area of study, four different zones were evaluated: one highly contaminated, two intermediately contaminated, and a noncontaminated zone. Contaminant concentrations, hydrocarbon profiles, and soil microbial respiration and biomass were studied. Abundance of n-alkane-degrading bacteria was quantified via real-time PCR of alkB, whereas genetic diversity was examined using molecular fingerprints (T-RFLP) and clone libraries. Along the contamination plume, hydrocarbon profiles and increased respiration rates suggested on-going natural attenuation at the site. Gene copy numbers of alkB were similar in contaminated and control areas. However, T-RFLP-based fingerprints suggested lower diversity and evenness of the n-alkane-degrading bacterial community in the highly contaminated zone compared to the other areas; both diversity and evenness were negatively correlated with metal and hydrocarbon concentrations. Phylogenetic analysis of alkB denoted a shift of the hydrocarbon-degrading bacterial community from Gram-positive bacteria in the control zone (most similar to Mycobacterium and Nocardia types) to Gram-negative genotypes in the contaminated zones (Acinetobacter and alkB sequences with little similarity to those of known bacteria). Our results underscore a qualitative rather than a quantitative response of hydrocarbon-degrading bacteria to the contamination at the molecular level.

Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil

“…As shown in rial), the degradation profiles at day 30 showed that decreases in the amount of aliphatic hydrocarbons had occurred for all the alkanes detected during the incubation with BP crude oil. This result is consistent with early studies with this and other strains of environmental mycobacteria on biodegradation of alkanes (36,(39)(40)(41). Among these identified alkanes, we selected 7 compounds, dodecane (C 12 ), tridecane (C 13 ), hexadecane (C 16 ), icosane (C 20 ), tetracosane (C 24 ), pentacosane (C 25 ), and octacosane (C 28 ), to monitor differences in degradation by the bacterium with time during incubation with BP crude oil.…”

Effects of different compost amendments on the abundance and composition of alkB harboring bacterial communities in a soil under industrial use contaminated with hydrocarbons

“…Previous studies revealed that alkB related sequences are present in a wide range of soil and water derived bacteria, such as Acinetobacter , Alcanivorax , Burkholderia , Mycobacterium , Pseudomonas , Rhodococcus and others (Van Beilen and Funhoff, 2007; Pérez-De-Mora et al, 2011). Furthermore, many alkB harboring bacteria (e.g., Mycobacterium and Nocardia ) carry in addition to the alk operon genes like almA which encodes for an enzyme that is involved in degrading of alkanes with a chain length of C 32 and longer (Feng et al, 2007).…”

Spatial Heterogeneity of Bacterial Communities in Sediments from an Infiltration Basin Receiving Highway Runoff

“…Previous research indicated that soil pH has the greatest influence on soil bacterial community composition, with positive correlation between soil pH and bacterial community structure [13,14,43]. Fan et al [13] found that fertilizer application reduced the soil pH and resulted in changes in ammonia-oxidizing bacterial composition and abundance.…”