Pyrosequence analysis of bacterial communities in aerobic bioreactors treating polycyclic aromatic hydrocarbon-contaminated soil

Abstract

Two aerobic, lab-scale, slurry-phase bioreactors were used to examine the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil and the associated bacterial communities. The two bioreactors were operated under semi-continuous (draw-and-fill) conditions at a residence time of 35 days, but one was fed weekly and the other monthly. Most of the quantified PAHs, including high-molecular-weight compounds, were removed to a greater extent in the weekly-fed bioreactor, which achieved total PAH removal of 76%. Molecular analyses, including pyrosequencing of 16S rRNA genes, revealed significant shifts in the soil bacterial communities after introduction to the bioreactors and differences in the abundance and types of bacteria in each of the bioreactors. The weekly-fed bioreactor displayed a more stable bacterial community with gradual changes over time, whereas the monthly-fed bioreactor community was less consistent and may have been more strongly influenced by the influx of untreated soil during feeding. Phylogenetic groups containing known PAH-degrading bacteria previously identified through stable-isotope probing of the untreated soil were differentially affected by bioreactor conditions. Sequences from members of the Acidovorax and Sphingomonas genera, as well as the uncultivated ‘‘Pyrene Group 2’’ were abundant in the bioreactors. However, the relative abundances of sequences from the Pseudomonas, Sphingobium, and Pseudoxanthomonas genera, as well as from a group of unclassified anthracene degraders, were much lower in the bioreactors compared to the untreated soil.

Biostimulation Reveals Functional Redundancy of Anthracene-Degrading Bacteria in Polycyclic Aromatic Hydrocarbon-Contaminated Soil

“…As attempts to isolate members of AG1 in our lab using traditional methods were unsuccessful, molecular methods were used to ascertain the response of these organisms to specific environmental conditions. While sequences from this group were abundant in the untreated soil, ranging from 4-10% of total bacterial 16S rRNA genes in pyrosequence libraries (Singleton et al, accepted for publication; Singleton et al, 2011), operation of the bioreactor resulted in a declining relative abundance of AG1 sequences, with a relative abundance after 140 days of 0.3% . Anthracene-degrading Variovorax and Pigmentiphaga sequences in the untreated soil similarly declined in relative abundance during bioreactor operation, decreasing from < 1% of sequences in the untreated soil to negligible or undetectable levels Jones et al, 2011b).…”

Identification of Anthraquinone-Degrading Bacteria in Soil Contaminated with Polycyclic Aromatic Hydrocarbons

“…6 mesh before being stored in the dark at 4°C until use. The processed soil (64% sand, 30% silt, 6% clay [pH 7.6]) was treated in a bench-scale, semicontinuous, aerobic, slurry-phase bioreactor (32); 20% of the treated soil slurry was replaced every 7 days with untreated, processed soil in a buffer containing 5 mM potassium phosphate (pH 7.5) supplemented with 2.5 mM NH 4 NO 3 ("reactor buffer"). The untreated, processed soil is also referred to below as "feed soil," and the material removed from the bioreactor is referred to as "treated soil."…”

Description of Immundisolibacter cernigliae gen. nov., sp. nov., a high-molecular-weight polycyclic aromatic hydrocarbon-degrading bacterium within the class Gammaproteobacteria, and proposal of Immundisolibacterales ord. nov. and Immundisolibacteraceae fam. nov.

“…A bacterial strain whose 16S rRNA gene sequence placed it phylogenetically within the cluster of SIP-derived PG2 sequences, designated TR3.2 T , was successfully isolated from an aerobic bioreactor-treated, PAH-contaminated soil from the site of a former manufactured gas plant in Salisbury, NC, USA [19]. Strain TR3.2 T was isolated through serial dilutions of bioreactor-treated soil onto a modified version of the aerobic cultivation medium for Sulfuritalea hydrogenivorans [20] using a layer of oversprayed pyrene as a carbon source; this medium was also used to obtain the PAH-degrading bacterium 'Rugosibacter aromaticivorans' Ca6 [21].…”