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      Phytomediated Biostimulation of the Autochthonous Bacterial Community for the Acceleration of the Depletion of Polycyclic Aromatic Hydrocarbons in Contaminated Sediments

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          Abstract

          Polycyclic aromatic hydrocarbons (PAHs) are a large group of organic contaminants causing hazards to organisms including humans. The objective of the study was to validate the vegetation of dredged sediments with Phragmites australis as an exploitable biostimulation approach to accelerate the depletion of PAHs in nitrogen spiked sediments. Vegetation with Phragmites australis resulted in being an efficient biostimulation approach for the depletion of an aged PAHs contamination (229.67 ± 15.56  μg PAHs/g dry weight of sediment) in dredged sediments. Phragmites australis accelerated the oxidation of the PAHs by rhizodegradation. The phytobased approach resulted in 58.47% of PAHs depletion. The effects of the treatment have been analyzed in terms of both contaminant depletion and changes in relative abundance of the metabolically active Gram positive and Gram negative PAHs degraders. The metabolically active degraders were quantified both in the sediments and in the root endospheric microbial community. Quantitative real-time PCR reactions have been performed on the retrotranscribed transcripts encoding the Gram positive and Gram negative large α subunit (RHD α) of the aromatic ring hydroxylating dioxygenases. The Gram positive degraders resulted in being selectively favored by vegetation with Phragmites australis and mandatory for the depletion of the six ring condensed indeno[1,2,3-cd]pyrene and benzo[g,h,i]perylene.

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          Real-Time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHDalpha) genes from Gram positive and Gram negative bacteria in soil and sediment samples.

          Real-Time PCR based assays were developed to quantify Gram positive (GP) and Gram negative (GN) bacterial populations that are capable of degrading the polycyclic aromatic hydrocarbons (PAH) in soil and sediment samples with contrasting contamination levels. These specific and sensitive Real-Time PCR assays were based on the quantification of the copy number of the gene that encodes the alpha subunit of the PAH-ring hydroxylating dioxygenases (PAH-RHDalpha), involved in the initial step of the aerobic metabolism of PAH. The PAH-RHDalpha-GP primer set was designed against the different allele types present in the data base (narAa, phdA/pdoA2, nidA/pdoA1, nidA3/fadA1) common to the Gram positive PAH degraders such as Rhodococcus, Mycobacterium, Nocardioides and Terrabacter strains. The PAH-RHDalpha-GN primer set was designed against the genes (nahAc, nahA3, nagAc, ndoB, ndoC2, pahAc, pahA3, phnAc, phnA1, bphAc, bphA1, dntAc and arhA1) common to the Gram negative PAH degraders such as Pseudomonas, Ralstonia, Commamonas, Burkholderia, Sphingomonas, Alcaligenes, Polaromonas strains. The PCR clones for DNA extracted from soil and sediment samples using the designed primers showed 100% relatedness to the PAH-RHDalpha genes targeted. Deduced from highly sensitive Real-Time PCR quantification, the ratio of PAH-RHDalpha gene relative to the 16S rRNA gene copy number showed that the PAH-bacterial degraders could represent up to 1% of the total bacterial community in the PAH-contaminated sites. This ratio highlighted a positive correlation between the PAH-bacterial biodegradation potential and the PAH-contamination level in the environmental samples studied.
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            Selection of specific endophytic bacterial genotypes by plants in response to soil contamination.

            Plant-bacterial combinations can increase contaminant degradation in the rhizosphere, but the role played by indigenous root-associated bacteria during plant growth in contaminated soils is unclear. The purpose of this study was to determine if plants had the ability to selectively enhance the prevalence of endophytes containing pollutant catabolic genes in unrelated environments contaminated with different pollutants. At petroleum hydrocarbon contaminated sites, two genes encoding hydrocarbon degradation, alkane monooxygenase (alkB) and naphthalene dioxygenase (ndoB), were two and four times more prevalent in bacteria extracted from the root interior (endophytic) than from the bulk soil and sediment, respectively. In field sites contaminated with nitroaromatics, two genes encoding nitrotoluene degradation, 2-nitrotoluene reductase (ntdAa) and nitrotoluene monooxygenase (ntnM), were 7 to 14 times more prevalent in endophytic bacteria. The addition of petroleum to sediment doubled the prevalence of ndoB-positive endophytes in Scirpus pungens, indicating that the numbers of endophytes containing catabolic genotypes were dependent on the presence and concentration of contaminants. Similarly, the numbers of alkB- or ndoB-positive endophytes in Festuca arundinacea were correlated with the concentration of creosote in the soil but not with the numbers of alkB- or ndoB-positive bacteria in the bulk soil. Our results indicate that the enrichment of catabolic genotypes in the root interior is both plant and contaminant dependent.
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              Functions of Macrophytes in Constructed Wetlands

              Hans Brix (1994)
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                Author and article information

                Journal
                Biomed Res Int
                Biomed Res Int
                BMRI
                BioMed Research International
                Hindawi Publishing Corporation
                2314-6133
                2314-6141
                2014
                7 August 2014
                : 2014
                : 891630
                Affiliations
                1Department of Biology, University of Pisa, 56126 Pisa, Italy
                2Teseco SpA, Via Carlo Ludovico Ragghianti 12, 56121 Pisa, Italy
                3STA srl, Via della Gherardesca 2, Ospedaletto, 56121 Pisa, Italy
                4Institute of Applied Research (Affiliated with University of Haifa), The Galilee Society, P.O. Box 437, 20200 Shefa-Amr, Israel
                5Tel Hai College, 12208 Upper Galilee, Israel
                Author notes

                Academic Editor: Daniele Daffonchio

                Author information
                http://orcid.org/0000-0002-8425-4491
                http://orcid.org/0000-0002-9592-8666
                http://orcid.org/0000-0001-9542-0806
                Article
                10.1155/2014/891630
                4142154
                b4df9503-12c0-4d0b-b0eb-eda037e46ac9
                Copyright © 2014 Simona Di Gregorio et al.

                This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 13 February 2014
                : 15 July 2014
                : 15 July 2014
                Categories
                Research Article

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