Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs)

Leigh, Mary Beth; Pellizari, Vivian H.; Uhlík, Ondřej; Sutka, R. L.; Rodrigues, Jorge L. M.; Ostrom, Nathaniel E.; Zhou, Jizhong; Tiedje, James M.

doi:10.1038/ismej.2007.26

Cited by 200 publications

(151 citation statements)

References 44 publications

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“…It is extremely difficult to detect microbial metabolic genes involved in contaminant degradation, as well as other important geochemical cycles, in a rapid and comprehensive way using conventional molecular ecology approaches. Microarray-based genomic technology provides a powerful tool for monitoring various microbial functional genes (Leigh et al, 2007;Yergeau et al, 2009;Liang et al, 2009a).…”

Section: Discussionmentioning

confidence: 99%

“…GeoChip 2.0 contains 24 243 oligonucleotide (50-mer) probes, which cover 410 000 genes in 4150 functional groups involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, as well as in organic contaminant degradation . Several studies have demonstrated that GeoChip is an ideal tool for dissecting the microbial community functional structure in both natural and contaminated environments (Leigh et al, 2007;Yergeau et al, 2007;Wu et al, 2008;Zhou et al, 2008;Van Nostrand et al, 2009;Wang et al, 2009;He et al, 2007He et al, , 2010Xu et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

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Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

et al. 2010

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To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

et al. 2010

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“…In a conceptually similar study, Leigh et al (2007) used MDA to increase the concentration of DNA that was labelled in a 13 C-biphenyl SIP incubation. MDA products were hybridized to the GeoChip, a microarray with probes targeting genes involved in aromatic hydrocarbon degradation (Leigh et al, 2007).…”

Section: Whole Community Genome Amplificationmentioning

confidence: 99%

“…MDA products were hybridized to the GeoChip, a microarray with probes targeting genes involved in aromatic hydrocarbon degradation (Leigh et al, 2007). One nanogram of DNA was amplified for microarray analysis, further underscoring the usefulness of MDA for studying the microbial ecology of low-biomass environments.…”

Section: Whole Community Genome Amplificationmentioning

confidence: 99%

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

2008

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Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR, microarray analysis and metagenomics to complex microbial populations. In the absence of suitable cultivation methods, it was not possible to obtain DNA samples from individual microorganisms. Recently, a method called multiple displacement amplification (MDA) has been used to circumvent these limitations by amplifying DNA from microbial communities in low-biomass environments, individual cells from uncultivated microbial species and active organisms obtained through stable isotope probing incubations. This review describes the development and applications of MDA, discusses its strengths and limitations and highlights the impact of MDA on the field of microbial ecology. Whole genome amplification via MDA has increased access to the genomic DNA of uncultivated microorganisms and low-biomass environments and represents a 'power tool' in the molecular toolbox of microbial ecologists.

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“…Connecting community structure with functions is one ultimate goal in microbial ecology (Leigh et al, 2007). Effects of pollution, or even more effect of plants, on the often very complex microbial communities in soil environments are challenging to depict.…”

Section: Treatment-specific Changes In Dioxygenases Tp Sipilä Et Almentioning

confidence: 99%

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

Sipilä

Keskinen²,

Akerman³

et al. 2008

The ISME Journal

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Genes encoding key enzymes of catabolic pathways can be targeted by DNA fingerprinting to explore genetic degradation potential in pristine and polluted soils. We performed a greenhouse microcosm experiment to elucidate structural and functional bacterial diversity in polyaromatic hydrocarbon (PAH)-polluted soil and to test the suitability of birch (Betula pendula) for remediation. Degradation of PAHs was analysed by high-performance liquid chromatography, DNA isolated from soil amplified and fingerprinted by restriction fragment length polymorphism (RFLP) and terminal restriction fragment length polymorphism (T-RFLP). Bacterial 16S rRNA T-RFLP fingerprinting revealed a high structural bacterial diversity in soil where PAH amendment altered the general community structure as well as the rhizosphere community. Birch augmented extradiol dioxygenase diversity in rhizosphere showing a rhizosphere effect, and further pyrene was more efficiently degraded in planted pots. Degraders of aromatic compounds upon PAH amendment were shown by the changed extradiol ring-cleavage community structure in soil. The RFLP analysis grouped extradiol dioxygenase marker genes into 17 distinct operational taxonomic units displaying novel phylogenetic clusters of ring-cleavage dioxygenases representing putative catabolic pathways, and the peptide sequences contained conserved amino-acid signatures of extradiol dioxygenases. A branch of major environmental TS cluster was identified as being related to Parvibaculum lavantivorans ring-cleavage dioxygenase. The described structural and functional diversity demonstrated a complex interplay of bacteria in PAH pollution. The findings improve our understanding of rhizoremediation and unveil the extent of uncharacterized enzymes and may benefit bioremediation research by facilitating the development of molecular tools to detect and monitor populations involved in degradative processes.

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Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs)

Cited by 200 publications

References 44 publications

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

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