Insights into Biodegradation Through Depth-Resolved Microbial Community Functional and Structural Profiling of a Crude-Oil Contaminant Plume

Abstract

Small-scale geochemical gradients are a key feature of aquifer contaminant plumes, highlighting the need for functional and structural profiling of corresponding microbial communities on a similar scale. The purpose of this study was to characterize the microbial functional and structural diversity with depth across representative redox zones of a hydrocarbon plume and an adjacent wetland, at the Bemidji Oil Spill site. A combination of quantitative PCR, denaturing gradient gel electrophoresis, and pyrosequencing were applied to vertically sampled sediment cores. Levels of the methanogenic marker gene, methyl coenzyme-M reductase A (mcrA), increased with depth near the oil body center, but were variable with depth further downgradient. Benzoate degradation N (bzdN) hydrocarbon-degradation gene, common to facultatively anaerobic Azoarcus spp., was found at all locations, but was highest near the oil body center. Microbial community structural differences were observed across sediment cores, and bacterial classes containing known hydrocarbon degraders were found to be low in relative abundance. Depth-resolved functional and structural profiling revealed the strongest gradients in the iron-reducing zone, displaying the greatest variability with depth. This study provides important insight into biogeochemical characteristics in different regions of contaminant plumes, which will aid in improving models of contaminant fate and natural attenuation rates.

Functional Gene Markers for Fumarate-Adding and Dearomatizing Key Enzymes in Anaerobic Aromatic Hydrocarbon Degradation in Terrestrial Environments

“…qPCR with FAE, bzdN and bamA gene primers has been repeatedly employed for the quantification of anaerobic aromatic hydrocarbon degraders in environmental samples [Beller et al, 2002[Beller et al, , 2008Fahrenfeld et al, 2014;Staats et al, 2011;Sun et al, 2014a;Winderl et al, 2008]. However, compared to cloning and sequencing, qPCR reactions need to fulfil even more rigid stringency criteria, while many of the primer sets used to date are highly degenerate ( table 1 ).…”

“…The results revealed a general consistency of key populations affiliated to known degraders within the genera Azoarcus and Geobacter detected via the different assays for the sites. Quantitative site monitoring of class I BCR ( bzdN ) genes of facultative anaerobes throughout the plume of the Bemidji crude oil spill has also recently been reported [Fahrenfeld et al, 2014], suggesting a significantly increased gene abundance close to the oil spill. It must be noted, however, that central catabolic genes such as bamA may be generally much more readily detectable in anoxic habitats than specific peripheral markers of aromatic hydrocarbon degradation, simply because benzoyl-CoA is a central intermediate not only in the anaerobic degradation of petrochemicals but also of humic acids, aromatic amino acids and lignin monomers [Andrade et al, 2012;Porter and Young, 2013].…”

“…The primer pair bzdNf/bzdNr, designed for amplifying a 700-bp fragment of the γ-subunit of the Azoarcustype class I BCR, has been successfully applied to DNA extracted from pure cultures and also contaminated sites, as well as the bcrCf/bcrCr primer pair, designed for amplifying a 800-bp fragment from the γ-subunit of the Thauera -type class I BCR [Fahrenfeld et al, 2014;Kuntze et al, 2011]. For class II BCRs, the developed bamBf/bamBr primers only yield a ∼ 300-bp gene fragment of the active subunit and several bamB homologues have been recovered [Löffler et al, 2011], suggesting its applicability on a more general level of class II BCR detection rather than as a detailed phylogenetic marker.…”

Comparison of bacterial and archaeal communities in depth-resolved zones in an LNAPL body

“…In contrast, directly analyzing in situ microbial communities at hydrocarbon-impacted sites potentially can lead to more field-relevant findings. Nextgeneration sequencing has enabled direct characterization of in situ microbial communities at selected hydrocarboncontaminated sites including sub-tidal sediment, estuary sediment, a railway refueling station, and a crude-oil contaminant plume (Acosta-González et al 2013;Fahrenfeld et al 2014;Sun et al 2013;Sutton et al 2013). Studies to date have not revealed a consistent set of hydrocarbon-associated microorganisms even when redox conditions are apparently similar; rather, characterized microbial communities vary substantially within and between sites.…”

Distribution of ammonia-oxidizing archaea and bacteria in plateau soils across different land use types

“…Soil shelters a huge density and diversity of microbes, which are believed to participate in a variety of biogeochemical processes (Dey et al 2012;Fahrenfeld et al 2014;Stroobants et al 2014). Nitrification process is of fundamental importance for nitrogen cycling in soil ecosystems.…”