Estimation of "Dehalococcoides" Populations in Lake Sediment Contaminated with Low Levels of Polychlorinated Dioxins

Abstract

Vertical profiles of polychlorinated dioxins and microbial biomass including "Dehalococcoides" populations in cores of sediment of Lake Suwa, Japan, were investigated. The core samples were analyzed in 3-cm intervals at 0-15 cm and 50 cm, where a sharp gradient of Eh from 5 to −110 mV with depth occurred. The concentration of polychlorinated dioxins was relatively constant at 0-15 cm, ranging from 7.6 to 8.3 ng (7.0-9.2 pg-TEQ [toxic equivalent]) g −1 dry wt, but decreased sharply at 50 cm. The total bacterial count was in the order of 10 8 to 10 9 g −1 dry wt, being highest at 3-6 cm and decreasing in the deeper sediment. A similar vertical profile was found for respiratory quinones with larger amounts of ubiquinones than menaquinones at 0-15 cm. Quantitative real-time PCR with a specific primer set showed that "Dehalococcoides" and its phylogenetic relatives occurred in the order of 10 4 g −1 (dry wt) at 0-12 cm but were absent at 50 cm. The amplified clones showed 91-100% similarity (mostly <94%) in sequence to a well-known dioxin-dechlorinating organism, "Dehalococcoides" sp. strain CBDB1. These results suggested that the surface sediment up to a depth of 12 cm provided favorable conditions for the growth and activity of both aerobic and anaerobic microorganisms including "Dehalococcoides". It is likely that a wide variety of "Dehalococcoides" and phylogenetic relatives thereof are omnipresent even in sediment with low levels of dioxins and play the primary role in dechlorinating organohalorides over a relatively wide range of Eh.

Biotransformation of Polychlorinated Dioxins and Microbial Community Dynamics in Sediment Microcosms at Different Contamination Levels

“…Mud samples taken from a core of sediment (depth 0-12 cm) of Lake Suwa 26) , Japan, were used as the seed for constructing microcosms. The samples were used immediately upon return to the laboratory.…”

“…Bulk DNA was extracted from the samples of sediment according to the protocol of Yoshida et al 60) with minor modifications as previously described 26) . The crude DNA extracted was further purified using a standard method including deprotenization with chloroform-isoamylalcohol and RNase treatment 37) .…”

Phylogenetic and Transcriptional Analyses of a Tetrachloroethene-Dechlorinating "Dehalococcoides" Enrichment Culture TUT2264 and Its Reductive-Dehalogenase Genes

“…The enrichment culture TUT2264 is unique in that it exhibits reductive dechlorination of chloroethenes despite its history, i.e., repeated enrichment with chloroaromatics such as 1,2,3-trichlorobenzene and fthalide from a polychlorinated-dechlorinating microcosm (10,17,18,42). In this study, we functionally characterized TUT2264 by measuring its chloroethene-dechlorinating activities, identifying rdhAs, and analyzing transcriptional levels in the presence of different chloroethenes.…”

“…Template DNAs were prepared as described above. The "Dehalococcoides"-specific primers used for real-time PCR were DHC793f (5'-GGGAGTATCGACCCTCTCTG-3') and DHC946r (5'-CGTTYCCCTTTCTGTTCACT-3') (18,42), which are capable of detecting diverse "Dehalococcoides" (17,18). PCR conditions were described by Futamata et al (10).…”

Nitrate removal performance of Diaphorobacter nitroreducens using biodegradable plastics as the source of reducing power

“…The transcripts of the nosZ gene, encoding for nitrous oxide reductase, were measured with a primer set of nosZ2f (5'-AAGCTCGACGACGCCATCGT-3') and nosZ2r (5'-CGGTCCTTGGAGAACTTGCA-3'), which were designed based on information from Khan et al [6]. The real-time qPCR assay was performed using a LightCycler FastStart DNA Master SYBR GREEN I kit (Roche Molecular Biochemicals, Indianapolis, USA) and a LightCycler system (Roche Diagnostics, Mannheim, Germany) according to the manufacturer's instructions and as described previously [24]. The PCR procedure consisted of pre-heating at 95°C for 10 min and 40 cycles of the reactions each of which consisted of denaturation at 95°C for 10 sec, annealing at 65°C for 4 sec, and extension at 72°C for 8 sec.…”