Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats

S. Dealtry, G.C. Ding, V. Weichelt, V. Dunon, A. Schluter, M.C. Martini, M.F. Del Papa, A. Lagares, G.C.A. Amos, E.M.H. Wellington, W.H. Gaze, D. Sipkema, S. Sjoling, D. Springael, H. Heuer, J.D. Elsas, C. Thomas, K. Smalla

Research output: Contribution to journalArticleAcademicpeer-review

19 Citations (Scopus)

Abstract

IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC- DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are "hot spots'' of plasmids potentially carrying catabolic genes.
Original languageEnglish
Article numbere89922
JournalPLoS ONE
Volume9
Issue number2
DOIs
Publication statusPublished - 2014

Fingerprint

Ecosystem
plasmids
Screening
Plasmids
screening
habitats
DNA
Genes
Gene encoding
Gene Targeting
gene targeting
Southern Blotting
Pesticides
Southern blotting
Farms
Purification
Limit of Detection
detection limit
Pollution
pesticides

Keywords

  • resistance genes
  • naphthalene
  • pseudomonas
  • adaptation
  • prevalence
  • transposon
  • diversity
  • sediment
  • biobeds

Cite this

Dealtry, S. ; Ding, G.C. ; Weichelt, V. ; Dunon, V. ; Schluter, A. ; Martini, M.C. ; Del Papa, M.F. ; Lagares, A. ; Amos, G.C.A. ; Wellington, E.M.H. ; Gaze, W.H. ; Sipkema, D. ; Sjoling, S. ; Springael, D. ; Heuer, H. ; Elsas, J.D. ; Thomas, C. ; Smalla, K. / Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats. In: PLoS ONE. 2014 ; Vol. 9, No. 2.
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title = "Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats",
abstract = "IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC- DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are {"}hot spots'' of plasmids potentially carrying catabolic genes.",
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author = "S. Dealtry and G.C. Ding and V. Weichelt and V. Dunon and A. Schluter and M.C. Martini and {Del Papa}, M.F. and A. Lagares and G.C.A. Amos and E.M.H. Wellington and W.H. Gaze and D. Sipkema and S. Sjoling and D. Springael and H. Heuer and J.D. Elsas and C. Thomas and K. Smalla",
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year = "2014",
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Dealtry, S, Ding, GC, Weichelt, V, Dunon, V, Schluter, A, Martini, MC, Del Papa, MF, Lagares, A, Amos, GCA, Wellington, EMH, Gaze, WH, Sipkema, D, Sjoling, S, Springael, D, Heuer, H, Elsas, JD, Thomas, C & Smalla, K 2014, 'Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats' PLoS ONE, vol. 9, no. 2, e89922. https://doi.org/10.1371/journal.pone.0089922

Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats. / Dealtry, S.; Ding, G.C.; Weichelt, V.; Dunon, V.; Schluter, A.; Martini, M.C.; Del Papa, M.F.; Lagares, A.; Amos, G.C.A.; Wellington, E.M.H.; Gaze, W.H.; Sipkema, D.; Sjoling, S.; Springael, D.; Heuer, H.; Elsas, J.D.; Thomas, C.; Smalla, K.

In: PLoS ONE, Vol. 9, No. 2, e89922, 2014.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Dealtry, S.

AU - Ding, G.C.

AU - Weichelt, V.

AU - Dunon, V.

AU - Schluter, A.

AU - Martini, M.C.

AU - Del Papa, M.F.

AU - Lagares, A.

AU - Amos, G.C.A.

AU - Wellington, E.M.H.

AU - Gaze, W.H.

AU - Sipkema, D.

AU - Sjoling, S.

AU - Springael, D.

AU - Heuer, H.

AU - Elsas, J.D.

AU - Thomas, C.

AU - Smalla, K.

N1 - WOS:000331880700116

PY - 2014

Y1 - 2014

N2 - IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC- DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are "hot spots'' of plasmids potentially carrying catabolic genes.

AB - IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC- DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are "hot spots'' of plasmids potentially carrying catabolic genes.

KW - resistance genes

KW - naphthalene

KW - pseudomonas

KW - adaptation

KW - prevalence

KW - transposon

KW - diversity

KW - sediment

KW - biobeds

U2 - 10.1371/journal.pone.0089922

DO - 10.1371/journal.pone.0089922

M3 - Article

VL - 9

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 2

M1 - e89922

ER -