Phenanthrene‐Degrader Community Dynamics in Rhizosphere Soil from a Common Annual Grass

Miya, Ryan K.; Firestone, Mary K.

doi:10.2134/jeq2000.00472425002900020029x

Cited by 76 publications

(66 citation statements)

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“…These findings are consistent with previous reports that plant species differentially affect microbial community structure and composition in the bulk soil (31,38). Higher numbers of polycyclic aromatic hydrocarbon-degrading organisms and higher degradation rates have been detected in the bulk soil collected from planted treatments than in the bulk soil collected from unplanted treatments in rhizoremediation studies (30,44). These findings are promising indications that certain trees may positively affect the number of degrading microorganisms in a large volume of soil, beyond the immediate vicinity of the roots traditionally defined as the rhizosphere.…”

Section: Discussionsupporting

confidence: 92%

Polychlorinated Biphenyl (PCB)-Degrading Bacteria Associated with Trees in a PCB-Contaminated Site

Leigh

Prouzová

Macková

et al. 2006

Appl Environ Microbiol

235

134

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The abundance, identities, and degradation abilities of indigenous polychlorinated biphenyl (PCB)-degrading bacteria associated with five species of mature trees growing naturally in a contaminated site were investigated to identify plants that enhance the microbial PCB degradation potential in soil. Culturable PCB degraders were associated with every plant species examined in both the rhizosphere and root zone, which was defined as the bulk soil in which the plant was rooted. Significantly higher numbers of PCB degraders (2.7-to 56.7-fold-higher means) were detected in the root zones of Austrian pine (Pinus nigra) and goat willow (Salix caprea) than in the root zones of other plants or non-root-containing soil in certain seasons and at certain soil depths. The majority of culturable PCB degraders throughout the site and the majority of culturable PCB degraders associated with plants were identified as members of the genus Rhodococcus by 16S rRNA gene sequence analysis. Other taxa of PCB-degrading bacteria included members of the genera Luteibacter and Williamsia, which have not previously been shown to include PCB degraders. PCB degradation assays revealed that some isolates from the site have broad congener specificities; these isolates included one Rhodococcus strain that exhibited degradation abilities similar to those of Burkholderia xenovorans LB400. Isolates with broad congener specificity were widespread at the site, including in the biostimulated root zone of willow. The apparent association of certain plant species with increased abundance of indigenous PCB degraders, including organisms with outstanding degradation abilities, throughout the root zone supports the notion that biostimulation through rhizoremediation is a promising strategy for enhancing PCB degradation in situ.Polychlorinated biphenyls (PCBs) are toxic, persistent pollutants of worldwide concern whose cleanup using conventional methods like incineration or relocation to specialized landfills is often prohibitively expensive. An alternative strategy for in situ PCB removal is biodegradation by microorganisms capable of metabolizing PCBs. Although bioaugmentation of soil with degradative bacteria has been largely unsuccessful in achieving significant aerobic PCB degradation in the field (29), efforts to biostimulate indigenous PCB-degrading bacteria have been promising. Analogue enrichment with biphenyl has been shown to increase the numbers of aerobic PCB-degrading bacteria in soil microcosms (12, 51) and to enhance PCB degradation rates in soils (6, 12) and in situ sediments (18). Unfortunately, as a field remedial strategy, addition of biphenyl is problematic due to the low water solubility of biphenyl, the necessity of repeated application, and concerns about biphenyl toxicity. By capitalizing on the innate ability of plants to alter soil microbial community structure, rhizoremediation offers an attractive and affordable alternative means for long-term biostimulation of aerobic PCB degradation in situ.Rhizostimulation of aromatic poll...

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Section: Discussionsupporting

confidence: 92%

Polychlorinated Biphenyl (PCB)-Degrading Bacteria Associated with Trees in a PCB-Contaminated Site

Leigh

Prouzová

Macková

et al. 2006

Appl Environ Microbiol

235

134

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“…Plants in phytoremediation of hydrocarbon contaminants have been proposed to improve degradation conditions in soil (Kuiper et al, 2004), and some improvement in biodegradation has been observed in plant microcosms/microecosystems (Miya and Firestone, 2000). Plant-associated microbes, especially in the root zone, potentially play a central role in rhizoremediation (Parrish et al, 2004;White et al, 2006) because plants mediate a rhizosphere effect illustrated by plant-specific microbial communities (Smalla et al, 2001;Costa et al, 2006).…”

Section: Introductionmentioning

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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“…Such treatment generates a soil with modified characteristics, in which the resilience of biological functions has not yet been studied. Bioremediation, the use of microorganisms to clean up contaminated soil, is an environmentally safe solution for PAH removal (20,34) that can be accelerated by the positive effect of plants via the stimulation of microbial biodegradation in the rhizosphere (27,44,45,48,54) through root exudates (12,39). A major driving force for the rhizosphere effect is the massive input of organic substrate in soil, which can increase the bioavailability of PAHs but also induce a selection of rhizospheric communities (17,56) and increase the total activity, diversity, and number of bacteria (45,48,54,58), as well as the abundance of PAHdegrading bacteria populations (31,56).…”

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confidence: 99%

Influence of Vegetation on the In Situ Bacterial Community and Polycyclic Aromatic Hydrocarbon (PAH) Degraders in Aged PAH-Contaminated or Thermal-Desorption-Treated Soil

Cébron

Béguiristain

Faure

et al. 2009

Appl Environ Microbiol

108

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The polycyclic aromatic hydrocarbon (PAH) contamination, bacterial community, and PAH-degrading bacteria were monitored in aged PAH-contaminated soil (Neuves-Maisons [NM] soil; with a mean of 1,915 mg of 16 PAHs ⅐ kg ؊1 of soil dry weight) and in the same soil previously treated by thermal desorption (TD soil; with a mean of 106 mg of 16 PAHs ⅐ kg ؊1 of soil dry weight). This study was conducted in situ for 2 years using experimental plots of the two soils. NM soil was colonized by spontaneous vegetation (NM-SV), planted with Medicago sativa (NM-Ms), or left as bare soil (NM-BS), and the TD soil was planted with Medicago sativa (TD-Ms). The bacterial community density, structure, and diversity were estimated by real-time PCR quantification of the 16S rRNA gene copy number, temporal thermal gradient gel electrophoresis fingerprinting, and band sequencing, respectively. The density of the bacterial community increased the first year during stabilization of the system and stayed constant in the NM soil, while it continued to increase in the TD soil during the second year. The bacterial community structure diverged among all the plot types after 2 years on site. In the NM-BS plots, the bacterial community was represented mainly by Betaproteobacteria and Gammaproteobacteria. Polycyclic aromatic hydrocarbons (PAHs) are persistent organic pollutants associated with a wide range of anthropogenic activities (gas plants, wood preservation plants, waste incineration, coke production, and petrochemical industries). The intensive industrial coal mining during the 19th and 20th centuries in northern France caused contamination of large areas where the soil now needs to be remediated.Microbiological degradation is the chief process for natural elimination of PAHs from contaminated soil (9). A wide range of bacteria are able to degrade low-molecular-weight PAHs, such as naphthalene, phenanthrene, and anthracene, while the high-molecular-weight PAHs (with four or more fused aromatic rings) are more recalcitrant, and relatively few microorganisms are able to use them as a sole carbon source (8). The first hydroxylation step of the PAH ring is crucial to initiate an efficient biodegradation. This step is performed mainly by aerobic bacteria possessing a PAH-ring hydroxylating dioxygenase (PAH-RHD) system. Homologous PAH-RHD enzymes are encoded by specific genes present in both gram-positive (GP) and gram-negative (GN) bacterial species (22). Recently, we developed real-time PCR assays to quantify the functional genes encoding the catalytic ␣ subunit of the PAH-RHD (PAH-RHD ␣ ) enzyme. The quantifications were performed on soil DNA samples, giving important information about the PAH-degrading bacterial population present in various PAH-contaminated soils (7).High PAH degradation rates have been observed in laboratory experiments with strains or consortia isolated from PAHcontaminated soils (6, 33). However, in situ degradation is often a slower process due to environmental constraints and low availability of PAHs in aged, polluted ...

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Phenanthrene‐Degrader Community Dynamics in Rhizosphere Soil from a Common Annual Grass

Cited by 76 publications

References 0 publications

Polychlorinated Biphenyl (PCB)-Degrading Bacteria Associated with Trees in a PCB-Contaminated Site

Polychlorinated Biphenyl (PCB)-Degrading Bacteria Associated with Trees in a PCB-Contaminated Site

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

Influence of Vegetation on the In Situ Bacterial Community and Polycyclic Aromatic Hydrocarbon (PAH) Degraders in Aged PAH-Contaminated or Thermal-Desorption-Treated Soil

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