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      Draft Genome Sequence of MCPA-Degrading Sphingomonas sp. Strain ERG5, Isolated from a Groundwater Aquifer in Denmark

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          Abstract

          Sphingomonas sp. strain ERG5 was isolated from a bacterial community, originating from a groundwater aquifer polluted with low pesticide concentrations. This bacterium degrades 2-methyl-4-chlorophenoxyacetic acid (MCPA) in a wide spectrum of concentrations and has been shown to function in bioaugmented sand filters. Genes associated with MCPA degradation are situated on a putative conjugative plasmid.

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          Molecular characteristics of xenobiotic-degrading sphingomonads.

          Lori Stolz (2008)
          The genus Sphingomonas (sensu latu) belongs to the alpha-Proteobacteria and comprises strictly aerobic chemoheterotrophic bacteria that are widespread in various aquatic and terrestrial environments. The members of this genus are often isolated and studied because of their ability to degrade recalcitrant natural and anthropogenic compounds, such as (substituted) biphenyl(s) and naphthalene(s), fluorene, (substituted) phenanthrene(s), pyrene, (chlorinated) diphenylether(s), (chlorinated) furan(s), (chlorinated) dibenzo-p-dioxin(s), carbazole, estradiol, polyethylene glycols, chlorinated phenols, nonylphenols, and different herbicides and pesticides. The metabolic versatility of these organisms suggests that they have evolved mechanisms to adapt quicker and/or more efficiently to the degradation of novel compounds in the environment than members of other bacterial genera. Comparative analyses demonstrate that sphingomonads generally use similar degradative pathways as other groups of microorganisms but deviate from competing microorganisms by the existence of multiple hydroxylating oxygenases and the conservation of specific gene clusters. Furthermore, there is increasing evidence for the existence of plasmids that only can be disseminated among sphingomonads and which undergo after conjugative transfer pronounced rearrangements.
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            Degradative plasmids from sphingomonads.

            Lori Stolz (2013)
            Large plasmids ('megaplasmids') are commonly found in members of the Alphaproteobacterial family Sphingomonadaceae ('sphingomonads'). These plasmids contribute to the extraordinary catabolic flexibility of this group of organisms, which degrade a broad range of recalcitrant xenobiotic compounds. The genomes of several sphingomonads have been sequenced during the last years. In the course of these studies, also the sequences of several plasmids have been determined. The analysis of the published information and the sequences deposited in the public databases allowed a first classification of these plasmids into a restricted number of groups according to the proteins involved in the initiation of replication, plasmid partition and conjugation. The sequence comparisons demonstrated that the plasmids from sphingomonads encode for four main groups of replication initiation (Rep) proteins. These Rep proteins belong to the protein superfamilies RepA_C (Pfam 04796), Rep_3 (Pfam 01051), RPA (Pfam 10134) and HTH-36 (Pfam 13730). The 'degradative megaplasmids' pNL2, pCAR3, pSWIT02, pCHQ1, pISP0, and pISP1, which code for genes involved in the degradation of aromatic hydrocarbons, carbazole, dibenzo-p-dioxin and γ-hexachlorocyclohexane, carry Rep proteins which either belong to the RepA_C- (plasmids pNL2, pCAR3, pSWIT02), Rep-3- (plasmids pCHQ1, pISP0) or RPA-superfamily (pISP1). The classification of these 'degradative megaplasmids' into three groups is also supported by sequence comparisons of the proteins involved in plasmid partition (ParAB) and the organization of the three genes on the respective plasmids. All analysed 'degradative megaplasmids' carry genes, which might allow a conjugative transfer of the plasmids. Sequence comparisons of these genes suggest the presence of at least two types of transfer functions, which either are closer related to the tra- or vir-genes previously described for plasmids from other sources. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.
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              Comparing metabolic functionalities, community structures, and dynamics of herbicide-degrading communities cultivated with different substrate concentrations.

              Sebastian R. Sørensen, Hemant K. Roy, Jens Aamand … (2012)
              Two 4-chloro-2-methylphenoxyacetic acid (MCPA)-degrading enrichment cultures selected from an aquifer on low (0.1 mg liter(-1)) or high (25 mg liter(-1)) MCPA concentrations were compared in terms of metabolic activity, community composition, population growth, and single cell physiology. Different community compositions and major shifts in community structure following exposure to different MCPA concentrations were observed using both 16S rRNA gene denaturing gradient gel electrophoresis fingerprinting and pyrosequencing. The communities also differed in their MCPA-mineralizing activities. The enrichments selected on low concentrations mineralized MCPA with shorter lag phases than those selected on high concentrations. Flow cytometry measurements revealed that mineralization led to cell growth. The presence of low-nucleic acid-content bacteria (LNA bacteria) was correlated with mineralization activity in cultures selected on low herbicide concentrations. This suggests that LNA bacteria may play a role in degradation of low herbicide concentrations in aquifers impacted by agriculture. This study shows that subpopulations of herbicide-degrading bacteria that are adapted to different pesticide concentrations can coexist in the same environment and that using a low herbicide concentration enables enrichment of apparently oligotrophic subpopulations.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 12 February 2015
                Publication date Collection: Jan-Feb 2015
                Volume: 3
                Issue: 1
                Electronic Location Identifier: e01529-14
                Affiliations
                [a ]Department of Environmental Science, Aarhus University, Roskilde, Denmark
                [b ]Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
                [c ]Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen, Denmark
                Author notes
                Address correspondence to Witold Kot, wk@ 123456envs.au.dk .
                Article
                Publisher ID: genomeA01529-14
                DOI: 10.1128/genomeA.01529-14
                PMC ID: 4333656
                PubMed ID: 25676756
                SO-VID: 40a1e857-106f-4893-9166-eaf16fce4720
                Copyright © Copyright © 2015 Nielsen et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

                History
                Date received : 30 December 2014
                Date accepted : 5 January 2015
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 10, Pages: 2, Words: 1096
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date January/February 2015
                access-type free

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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