Terminal-restriction fragment length polymorphism analysis of biphenyl dioxygenase genes from a polychlorinated biphenyl-polluted soil

Capodicasa, Serena; Fedi, Stefano; Carnevali, Monica; Caporali, Leonardo; Viti, Carlo; Fava, Fabio; Zannoni, Davide

doi:10.1016/j.resmic.2009.10.001

Cited by 7 publications

(3 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The observed response of the microbial communities to PCBs is consistent with those of other studies that have evaluated microbial communities in PCB-laden soils [63][64][65][66] and estuarine sediments [21,67]. This study showed that the higher levels of PCBs in the sediments of Guánica Bay are associated with higher levels of organic carbon and also are associated with finer grained sediments, which is consistent with other studies [68][69][70][71].…”

Section: Discussionsupporting

confidence: 91%

Potential Impacts of PCBs on Sediment Microbiomes in a Tropical Marine Environment

Klaus

Kourafalou

Piggot

et al. 2016

JMSE

View full text Add to dashboard Cite

Within the tropical marine study site of Guánica Bay, Puerto Rico, polychlorinated biphenyls (PCBs) are subjected to coastal and oceanic currents coupled with marine microbial and geochemical processes. To evaluate these processes a hydrodynamic model was developed to simulate the transport of PCBs within nearshore and offshore marine areas of Guánica Bay. Material transport and circulation information from the model were matched with measurements from samples collected from within the bay. These samples, consisting of both intertidal and submerged sediments, were analyzed for physical characteristics (organic carbon, grain size, and mineralogy), microbial characteristics (target bacteria levels and microbial community analyses), presence of PCBs, and PCB-degrading enzymes. Results show that the bay geometry and bathymetry limit the mixing of the extremely high levels of PCBs observed in the eastern portion of the bay. Bay bottom sediments showed the highest levels of PCBs and these sediments were characterized by high organic carbon content and finer grain size. Detectable levels of PCBs were also observed within sediments found along the shore. Microbes from the bay bottom sediments showed a greater relative abundance of microbes from the Chloroflexi, phylum with close phylogenetic associations with known anaerobic PCB-degrading organisms. Based on quantitative PCR measurement of the biphenyl dioxygenase gene, the intertidal sediments showed the greatest potential for aerobic PCB degradation. These results elucidate particular mechanisms of PCB's fate and transport in coastal, tropical marine environments.

show abstract

Section: Discussionsupporting

confidence: 91%

Potential Impacts of PCBs on Sediment Microbiomes in a Tropical Marine Environment

Klaus

Kourafalou

Piggot

et al. 2016

JMSE

View full text Add to dashboard Cite

show abstract

“…Illumina high-throughput sequencing was performed to determine the diversity and composition of the bacterial communities in the sediment and enrichment samples (Capodicasa et al, 2009). PCR amplifications were conducted with the 515F/806R primer set that amplifies the V4 region of the 16S rRNA gene.…”

Section: Illumina High-throughput Sequencingmentioning

confidence: 99%

Culture‐dependent and culture‐independent characterization of potentially functional biphenyl‐degrading bacterial community in response to extracellular organic matter from Micrococcus luteus

Liu

Hashmi

et al. 2015

Microbial Biotechnology

View full text Add to dashboard Cite

Biphenyl (BP)-degrading bacteria were identified to degrade various polychlorinated BP (PCB) congers in long-term PCB-contaminated sites. Exploring BP-degrading capability of potentially useful bacteria was performed for enhancing PCB bioremediation. In the present study, the bacterial composition of the PCB-contaminated sediment sample was first investigated. Then extracellular organic matter (EOM) from Micrococcus luteus was used to enhance BP biodegradation. The effect of the EOM on the composition of bacterial community was investigated by combining with culture-dependent and culture-independent methods. The obtained results indicate that Proteobacteria and Actinobacteria were predominant community in the PCB-contaminated sediment. EOM from M. luteus could stimulate the activity of some potentially difficult-to-culture BP degraders, which contribute to significant enhancement of BP biodegradation. The potentially difficult-to-culture bacteria in response to EOM addition were mainly Rhodococcus and Pseudomonas belonging to Gammaproteobacteria and Actinobacteria respectively. This study provides new insights into exploration of functional difficult-to-culture bacteria with EOM addition and points out broader BP/PCB degrading, which could be employed for enhancing PCB-bioremediation processes.

show abstract

“…Such techniques seem promising for discovering novel biocatalysts, as only a tiny fraction of existing microorganisms are apparently culturable under laboratory conditions (3). Metagenomic approaches have been applied to characterize the diversity of dioxygenase sequences at a number of PCB-polluted sites (1,10,17). Sequences with high, as well as with low, similarities to those known from culturable organisms have been detected, depending on the examined site and probably also on the PCR primers used.…”

mentioning

confidence: 99%

Characterization of Biphenyl Dioxygenase Sequences and Activities Encoded by the Metagenomes of Highly Polychlorobiphenyl-Contaminated Soils

Standfuss-Gabisch

Al-Halbouni

Höfer

2012

Appl Environ Microbiol

View full text Add to dashboard Cite

ABSTRACTTotal extracted DNA from two heavily polychlorobiphenyl-contaminated soils was analyzed with respect to biphenyl dioxygenase sequences and activities. This was done by PCR amplification and cloning of a DNA segment encoding the active site of the enzyme. The translated sequences obtained fell into three similarity clusters (I to III). Sequence identities were high within but moderate or low between the clusters. Members of clusters I and II showed high sequence similarities with well-known biphenyl dioxygenases. Cluster III showed low (43%) sequence identity with a biphenyl dioxygenase fromRhodococcus jostiiRHA1. Amplicons from the three clusters were used to reconstitute and express complete biphenyl dioxygenase operons. In most cases, the resulting hybrid dioxygenases were detected in cell extracts of the recombinant hosts. At least 83% of these enzymes were catalytically active. Several amino acid exchanges were identified that critically affected activity. Chlorobiphenyl turnover by the enzymes containing the prototype sequences of clusters I and II was characterized with 10 congeners that were major, minor, or not constituents of the contaminated soils. No direct correlations were observed between on-site concentrations and rates of productive dioxygenations of these chlorobiphenyls. The prototype enzymes displayed markedly different substrate and product ranges. The cluster II dioxygenase possessed a broader substrate spectrum toward the assayed congeners, whereas the cluster I enzyme was superior in the attack ofortho-chlorinated aromatic rings. These results demonstrate the feasibility of the applied approach to functionally characterize dioxygenase activities of soil metagenomes via amplification of incomplete genes.

show abstract

Terminal-restriction fragment length polymorphism analysis of biphenyl dioxygenase genes from a polychlorinated biphenyl-polluted soil

Cited by 7 publications

References 27 publications

Potential Impacts of PCBs on Sediment Microbiomes in a Tropical Marine Environment

Potential Impacts of PCBs on Sediment Microbiomes in a Tropical Marine Environment

Culture‐dependent and culture‐independent characterization of potentially functional biphenyl‐degrading bacterial community in response to extracellular organic matter from Micrococcus luteus

Characterization of Biphenyl Dioxygenase Sequences and Activities Encoded by the Metagenomes of Highly Polychlorobiphenyl-Contaminated Soils

Contact Info

Product

Resources

About