Habitat-specific type I polyketide synthases in soils and street sediments

  • Patrick HillEmail author
  • Jörn Piel
  • Stéphane Aris-Brosou
  • Václav Krištůfek
  • Christopher N. Boddy
  • Lubbert Dijkhuizen
Environmental Microbiology


Actinomycetes produce many pharmaceutically useful compounds through type I polyketide biosynthetic pathways. Soil has traditionally been an important source for these actinomycete-derived pharmaceuticals. As the rate of antibiotic discovery has decreased and the incidence of antibiotic resistance has increased, researchers have looked for alternatives to soil for bioprospecting. Street sediment, where actinomycetes make up a larger fraction of the bacterial population than in soil, is one such alternative environment. To determine if these differences in actinomycetal community structure are reflected in type I polyketide synthases (PKSI) distribution, environmental DNA from soils and street sediments was characterized by sequencing amplicons of PKSI-specific PCR primers. Amplicons covered two domains: the last 80 amino acids of the ketosynthase (KS) domain and the first 240 amino acids of the acyltransferase (AT) domain. One hundred and ninety clones from ten contrasting soils from six regions and nine street sediments from six cities were sequenced. Twenty-five clones from two earthworm-affected samples were also sequenced. UniFrac lineage-specific analysis identified two clades that clustered with actinomycetal GenBank matches that were street sediment-specific, one similar to the PKSI segment of the mycobactin siderophore involved in mycobacterial virulence. A clade of soil-specific sequences clustered with GenBank matches from the ambruticin and jerangolid pathways of Sorangium cellulosum. All three of these clades were found in sites >700 km apart. Street sediments are enriched in actinomycetal PKSIs. Non-actinomycetal PKSI pathways may be more chemically diverse than actinomycetal PKSIs. Common soil and street sediment PKIs are globally distributed.


Natural product discovery Polyketides Urban microbiology Bioprospecting Mycobactin 



Dr. Meng Wang was kind enough to translate the paper “Screening identifying and functional analysis of polyketide synthase I domains from soil and seawater of Yangshan Harbour” into English for us. We thank Dr. A. Poulain for providing the sample from Resolute Bay, Canada, Dr. Rashid Nazir for providing the Faisalabad Clock tower sample, Dr. Declan Hill for providing the street sample from Budapest, Hungary, and Keavin M. Stanford-Finnerty for the beach sand sample from Prince Edward Island, Canada. Our laboratory work was helped by Jean Bjornson of the Geography Dept of the University of Ottawa who assisted with soil analysis and Daniël van Middelkoop and Sarina de Roos who carried out cloning and sequencing as part of a work experience program for the School for Biomedical Laboratory Techniques in Groningen, The Netherlands. Funding for this work was provided by the NATO Programme Security Through Science ESP.EAP.CLG 981785, the Ministry of Education, Youth and Sports of the Czech Republic (LC06066, 2B06154), the Research Plan of the Institute of Soil Biology (AV 0Z 6066 0521), the Natural Sciences and Engineering Council of Canada, the Ministry of Research and Innovation, and the University of Ottawa.

Supplementary material

10295_2013_1362_MOESM1_ESM.pdf (412 kb)
Supplementary material 1 (PDF 411 kb) Fig. S1:A8-1 Cophylogeny
10295_2013_1362_MOESM2_ESM.pdf (403 kb)
Supplementary material 2 (PDF 403 kb) Fig. S2:A8-3 Cophylogeny
10295_2013_1362_MOESM3_ESM.pdf (397 kb)
Supplementary material 3 (PDF 397 kb) Fig. S3: A6 Cophylogeny
10295_2013_1362_MOESM4_ESM.pdf (402 kb)
Supplementary material 4 (PDF 402 kb) Fig. S4: A5 Cophylogeny
10295_2013_1362_MOESM5_ESM.pdf (398 kb)
Supplementary material 5 (PDF 397 kb) Fig. S5: Mbt Cophylogeny For all Cophylogenies, sequences in blue are from soil, in red from street sediments and in orange from earthworm-affected environments.
10295_2013_1362_MOESM6_ESM.xls (104 kb)
Supplementary material 6 (XLS 103 kb) Table S1: an Excel file with a description of environmental sequences
10295_2013_1362_MOESM7_ESM.xls (226 kb)
Supplementary material 7 (XLS 226 kb) Table S2: an Excel file with BLASTP matches of environmental sequences
10295_2013_1362_MOESM8_ESM.xls (48 kb)
Supplementary material 8 (XLS 48 kb) Table S3: an Excel file with a description of 99 comparable sequences from GenBank
10295_2013_1362_MOESM9_ESM.xlsx (11 kb)
Supplementary material 9 (XLSX 11 kb) Table S4: an Excel file comparing sequences from cosmopolitan nodes and known PKSI pathways


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Copyright information

© Society for Industrial Microbiology and Biotechnology 2013

Authors and Affiliations

  • Patrick Hill
    • 1
    Email author
  • Jörn Piel
    • 2
  • Stéphane Aris-Brosou
    • 1
  • Václav Krištůfek
    • 3
  • Christopher N. Boddy
    • 1
    • 4
  • Lubbert Dijkhuizen
    • 5
  1. 1.Department of BiologyUniversity of OttawaOttawaCanada
  2. 2.Institute of MicrobiologyEidgenössische Technische Hochschule (ETH) ZurichZurichSwitzerland
  3. 3.Biology Centre AS CR, v. v. i.-Institute of Soil BiologyČeské BudějoviceCzech Republic
  4. 4.Department of ChemistryUniversity of OttawaOttawaCanada
  5. 5.Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands

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