Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene

Martin, Florence; Torelli, Stéphane; Paslier, Denis Le; Barbance, Agnès; Martin-Laurent, Fabrice; Bru, David; Geremia, R.; Blake, G.; Jouanneau, Yves

doi:10.1016/j.envpol.2011.11.032

Cited by 146 publications

(92 citation statements)

References 34 publications

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“…SIP has been used to identify phylogenetically diverse bacteria capable of growth on PAHs ranging from 2 to 4 rings, including naphthalene ( Jeon et al, 2003;Singleton et al, 2005;Yu and Chu, 2005;Gutierrez et al, 2011;Jones et al, 2011a;Uhlik et al, 2012), anthracene ( Jones et al, 2011b;Zhang et al, 2011bZhang et al, , 2012, phenanthrene (Singleton et al, 2005(Singleton et al, , 2007Cébron et al, 2011;Jones et al, 2011a;Martin et al, 2012), pyrene (Singleton et al, 2006(Singleton et al, , 2007Jones et al, 2008;Jones et al, 2011a), fluoranthene ( Jones et al, 2011a), and benz [a]anthracene ( Jones et al, 2011a). A previous SIP study was conducted in this lab to identify aerobic anthracenedegrading bacteria in PAH-contaminated soil sampled from the site of a former manufactured gas plant ( Jones et al, 2011b).…”

Section: Introductionmentioning

confidence: 99%

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

Singleton²,

Aitken³

2013

Environmental Engineering Science

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Stable-isotope probing was previously used to identify bacterial anthracene-degraders in untreated soil from a former manufactured gas plant site. However, subsequent pyrosequence analyses of total bacterial communities and quantification of 16S rRNA genes indicated that relative abundances of the predominant anthracene-degrading bacteria (designated Anthracene Group 1) diminished as a result of biological treatment conditions in lab-scale, aerobic bioreactors. This study identified Alphaproteobacterial anthracene-degrading bacteria in bioreactor-treated soil which were dissimilar to those previously identified. The largest group of sequences was from the Alterythrobacter genus while other groups of sequences were associated with bacteria within the order Rhizobiales and the genus Bradyrhizobium. Conditions in the bioreactor enriched for organisms capable of degrading anthracene which were not the same as those identified as dominant degraders in the untreated soil. Further, these data suggest that identification of polycyclic aromatic hydrocarbon-degrading bacteria in contaminated but untreated soil may be a poor indicator of the most active degraders during biological treatment.

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Section: Introductionmentioning

confidence: 99%

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

Singleton²,

Aitken³

2013

Environmental Engineering Science

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“…SIP, as introduced by Radajewski et al (2000), allows to access the nucleic acids of microorganisms participating in the degradation of 13 C-labeled compounds without culturing them in growth media. The method was suitable to detect and identify microorganisms involved in the degradation of different organic pollutants (Mahmood et al, 2005;Cupples and Sims, 2007;Martin et al, 2012;Uhlik et al, 2012), and, thus, it was selected to identify the actively phenol and DCP-degrading microbial community and compare their diversity from the three SOC variants selected for this study.…”

Section: Introductionmentioning

confidence: 99%

Importance of soil organic matter for the diversity of microorganisms involved in the degradation of organic pollutants

et al. 2014

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Many organic pollutants are readily degradable by microorganisms in soil, but the importance of soil organic matter for their transformation by specific microbial taxa is unknown. In this study, sorption and microbial degradation of phenol and 2,4-dichlorophenol (DCP) were characterized in three soil variants, generated by different long-term fertilization regimes. Compared with a non-fertilized control (NIL), a mineral-fertilized NPK variant showed 19% and a farmyard manure treated FYM variant 46% more soil organic carbon (SOC). Phenol sorption declined with overall increasing SOC because of altered affinities to the clay fraction (soil particles o2 mm in diameter). In contrast, DCP sorption correlated positively with particulate soil organic matter (present in the soil particle fractions of 63-2000 lm). Stable isotope probing identified Rhodococcus, Arthrobacter (both Actinobacteria) and Cryptococcus (Basidiomycota) as the main degraders of phenol. Rhodococcus and Cryptococcus were not affected by SOC, but the participation of Arthrobacter declined in NPK and even more in FYM. 14 C-DCP was hardly metabolized in the NIL variant, more efficiently in FYM and most in NPK. In NPK, Burkholderia was the main degrader and in FYM Variovorax. This study demonstrates a strong effect of SOC on the partitioning of organic pollutants to soil particle size fractions and indicates the profound consequences that this process could have for the diversity of bacteria involved in their degradation.

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“…T he massive influx of novel sequence data derived from nextgeneration sequencing (NGS) technologies, in the context of both individual genomes (1) and metagenomes (2,3), has far outstripped efforts to link those sequences to specific organisms and biological functions (4). Techniques such as quantitative PCR (qPCR) (5), microarrays (6), clone libraries (7), and stable-isotope probing (8) have been used successfully to identify organisms potentially involved in biodegradation.…”

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confidence: 99%

Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil

Meier

Paterson

Lambert

2016

Appl Environ Microbiol

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Metagenomics allows the study of genes related to xenobiotic degradation in a culture-independent manner, but many of these studies are limited by the lack of genomic context for metagenomic sequences. This study combined a phenotypic screen known as substrate-induced gene expression (SIGEX) with whole-metagenome shotgun sequencing. SIGEX is a high-throughput promoter-trap method that relies on transcriptional activation of a green fluorescent protein (GFP) reporter gene in response to an inducing compound and subsequent fluorescence-activated cell sorting to isolate individual inducible clones from a metagenomic DNA library. We describe a SIGEX procedure with improved library construction from fragmented metagenomic DNA and improved flow cytometry sorting procedures. We used SIGEX to interrogate an aromatic hydrocarbon (AH)-contaminated soil metagenome. The recovered clones contained sequences with various degrees of similarity to genes (or partial genes) involved in aromatic metabolism, for example, nahG (salicylate oxygenase) family genes and their respective upstream nahR regulators. To obtain a broader context for the recovered fragments, clones were mapped to contigs derived from de novo assembly of shotgun-sequenced metagenomic DNA which, in most cases, contained complete operons involved in aromatic metabolism, providing greater insight into the origin of the metagenomic fragments. A comparable set of contigs was generated using a significantly less computationally intensive procedure in which assembly of shotgun-sequenced metagenomic DNA was directed by the SIGEX-recovered sequences. This methodology may have broad applicability in identifying biologically relevant subsets of metagenomes (including both novel and known sequences) that can be targeted computationally by in silico assembly and prediction tools.T he massive influx of novel sequence data derived from nextgeneration sequencing (NGS) technologies, in the context of both individual genomes (1) and metagenomes (2, 3), has far outstripped efforts to link those sequences to specific organisms and biological functions (4). Techniques such as quantitative PCR (qPCR) (5), microarrays (6), clone libraries (7), and stable-isotope probing (8) have been used successfully to identify organisms potentially involved in biodegradation. Substrate-induced gene expression (SIGEX) was proposed as a method for uncovering novel catabolic operons from metagenomes (9-12). SIGEX is a promoter trap method based on single-cell sorting of clones from a plasmid library using flow cytometry (FCM), where metagenomic clones of interest are identified by the increased expression of a downstream fluorescent reporter gene in the presence, but not in the absence, of an inducing compound. SIGEX was initially perceived as having great potential for mining genes from metagenomic samples in a high-throughput manner, without requiring prior knowledge of the sequences being screened for (13-15). However, SIGEX, and metagenomic promoter traps in general, has not lived up to this pote...

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Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene

Cited by 146 publications

References 34 publications

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

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

Importance of soil organic matter for the diversity of microorganisms involved in the degradation of organic pollutants

Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil

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