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      Promotion of arsenic phytoextraction efficiency in the fern Pteris vittata by the inoculation of As-resistant bacteria: a soil bioremediation perspective

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          Abstract

          A greenhouse pot experiment was carried out to evaluate the efficiency of arsenic phytoextraction by the fern Pteris vittata growing in arsenic-contaminated soil, with or without the addition of selected rhizobacteria isolated from the polluted site. The bacterial strains were selected for arsenic resistance, the ability to reduce arsenate to arsenite, and the ability to promote plant growth. P. vittata plants were cultivated for 4 months in a contaminated substrate consisting of arsenopyrite cinders and mature compost. Four different experimental conditions were tested: (i) non-inoculated plants; (ii) plants inoculated with the siderophore-producing and arsenate-reducing bacteria Pseudomonas sp. P1III2 and Delftia sp. P2III5 (A); (iii) plants inoculated with the siderophore and indoleacetic acid-producing bacteria Bacillus sp. MPV12, Variovorax sp. P4III4, and Pseudoxanthomonas sp. P4V6 (B), and (iv) plants inoculated with all five bacterial strains (AB). The presence of growth-promoting rhizobacteria increased plant biomass by up to 45% and increased As removal efficiency from 13% without bacteria to 35% in the presence of the mixed inoculum. Molecular analysis confirmed the persistence of the introduced bacterial strains in the soil and resulted in a significant impact on the structure of the bacterial community.

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          Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species.

          Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.
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            16S ribosomal DNA amplification for phylogenetic study.

            A set of oligonucleotide primers capable of initiating enzymatic amplification (polymerase chain reaction) on a phylogenetically and taxonomically wide range of bacteria is described along with methods for their use and examples. One pair of primers is capable of amplifying nearly full-length 16S ribosomal DNA (rDNA) from many bacterial genera; the additional primers are useful for various exceptional sequences. Methods for purification of amplified material, direct sequencing, cloning, sequencing, and transcription are outlined. An obligate intracellular parasite of bovine erythrocytes, Anaplasma marginale, is used as an example; its 16S rDNA was amplified, cloned, sequenced, and phylogenetically placed. Anaplasmas are related to the genera Rickettsia and Ehrlichia. In addition, 16S rDNAs from several species were readily amplified from material found in lyophilized ampoules from the American Type Culture Collection. By use of this method, the phylogenetic study of extremely fastidious or highly pathogenic bacterial species can be carried out without the need to culture them. In theory, any gene segment for which polymerase chain reaction primer design is possible can be derived from a readily obtainable lyophilized bacterial culture.
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              Phytoremediation.

              Phytoremediation, the use of plants and their associated microbes for environmental cleanup, has gained acceptance in the past 10 years as a cost-effective, noninvasive alternative or complementary technology for engineering-based remediation methods. Plants can be used for pollutant stabilization, extraction, degradation, or volatilization. These different phytoremediation technologies are reviewed here, including their applicability for various organic and inorganic pollutants, and most suitable plant species. To further enhance the efficiency of phytoremediation, there is a need for better knowledge of the processes that affect pollutant availability, rhizosphere processes, pollutant uptake, translocation, chelation, degradation, and volatilization. For each of these processes I review what is known so far for inorganic and organic pollutants, the remaining gaps in our knowledge, and the practical implications for designing phytoremediation strategies. Transgenic approaches to enhance these processes are also reviewed and discussed.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                18 February 2015
                2015
                : 6
                : 80
                Affiliations
                [1] 1Department of Biotechnology, University of Verona Verona, Italy
                [2] 2Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa Pisa, Italy
                Author notes

                Edited by: Antonella Furini, University of Verona, Italy

                Reviewed by: Lena Ma, University of Florida, USA; Agnieszka Galuszka, Jan Kochanowski University, Poland

                *Correspondence: Silvia Lampis and Giovanni Vallini, Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy e-mail: silvia.lampis@ 123456univr.it ; giovanni.vallini@ 123456univr.it

                This article was submitted to Plant Biotechnology, a section of the journal Frontiers in Plant Science.

                Article
                10.3389/fpls.2015.00080
                4332284
                25741356
                81241944-21c3-4217-993d-77a6559c3f74
                Copyright © 2015 Lampis, Santi, Ciurli, Andreolli and Vallini.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 14 December 2014
                : 30 January 2015
                Page count
                Figures: 5, Tables: 2, Equations: 0, References: 73, Pages: 12, Words: 0
                Categories
                Plant Science
                Original Research Article

                Plant science & Botany
                arsenic,arsenopyrite cinders,phytoextraction,plant growth-promoting rhizobacteria,pteris vittata,rhizosphere-enhanced phytoremediation

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