Pyrosequencing Analysis Reveals High Population Dynamics of the Soil Microcosm Degrading Octachlorodibenzofuran

Abstract

A deeper understanding of the microbial community structure is very important in bioremediation for polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs). However, this has been insufficiently addressed in previous studies. To obtain more information, we pyrosequenced the V4/V5 regions of the 16S rRNA genes of bacterial communities transited from polluted soil to batch microcosms that rapidly degraded high concentrations of octachlorodibenzofuran (OCDF). The analysis results contained an average of 11,842 reads per sample, providing the first detailed description of bacterial communities associated with PCDD/Fs. The community composition markedly changed to be concomitant with the degradation of OCDF, indicating that a distinctive population structure developed rapidly in the microcosm. Although oxygen gas was provided weekly to the microcosm, the growth of potential degraders, Sphingomonas, Pseudomonas, Rhodococcus, and Clostridium, was observed, but in consistently low quantities. While anaerobic Sedimentibacter initially emerged as an abundant pioneer, several aerobic participants, such as the genera Brevundimonas, Pseudoxanthomonas, and Lysobacter, exhibited a large increase in their 16S rRNA gene copies within the timeframe, which showed a temporal population dynamic, and indicated their collaborative contributions to the degradation of OCDF under hypoxic conditions. These results have provided a deeper insight into the microbial community structure and population dynamics of the OCDF-degrading microcosm.

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“…The compositions of bacterial populations were analysed using high-throughput sequencing of 16S rRNA amplicons as previously described 55 , 56 . The hypervariable V3–V4 region of the bacterial 16S rRNA gene was amplified using a barcoded fusion primer set (Table S4 ) with a thermal cycling program comprising an initial denaturation at 95 °C for 2 min, followed by 30–35 cycles of annealing starting at 65 °C (ending at 55 °C) for 15 s, and extension at 68 °C for 30 s. The amplicons in triplicate samples were pooled and purified using an AMPureXP PCR Purification Kit (Agencourt, Brea, CA, USA) and quantified using a Qubit dsDNA HS Assay Kit on a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).…”

Kinetic analysis of biological degradation for tetramethylammonium hydroxide (TMAH) in the anaerobic activated sludge system at ambient temperature

“…To profile the archaeal community structure, the archaeal 16S rRNA genes were amplified with the Archaea-specific primer set (ARC344f-mod and Arch958R-mod) [17] and subjected to a bar-coded high-throughput sequencing on a 454 GS Junior platform (Roche Applied Science, USA). The sequencing data were analysed with the RDP database as previously described [3].…”

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“…In Chen et al (2014), soil samples containing high concentration of OCDF were used for microcosm study and bacterial communities involved in OCDF degradation were monitored using high-throughput pyrosequencing. Bacterial community succession rapidly changed with consequent degradation of OCDF.…”