title: Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity.
abstract: Numerous therapeutically relevant small molecules have been identified from the screening of natural products (NPs) produced by environmental bacteria. These discovery efforts have principally focused on culturing bacteria from natural environments rich in biodiversity. We sought to assess the biosynthetic capacity of urban soil environments using a phylogenetic analysis of conserved NP biosynthetic genes amplified directly from DNA isolated from New York City park soils. By sequencing genes involved in the biosynthesis of nonribosomal peptides and polyketides, we found that urban park soil microbiomes are both rich in biosynthetic diversity and distinct from nonurban samples in their biosynthetic gene composition. A comparison of sequences derived from New York City parks to genes involved in the biosynthesis of biomedically important NPs produced by bacteria originally collected from natural environments around the world suggests that bacteria producing these same families of clinically important antibiotics, antifungals, and anticancer agents are actually present in the soils of New York City. The identification of new bacterial NPs often centers on the systematic exploration of bacteria present in natural environments. Here, we find that the soil microbiomes found in large cities likely hold similar promise as rich unexplored sources of clinically relevant NPs.
authors.affiliation: Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065.
authors.forename: Zachary
authors.identifier: 0000-0001-8816-4680
authors.initials: Z
authors.lastname: Charlop-Powers
authors.affiliation: Natural Areas Conservancy, New York, NY 10029.
authors.forename: Clara C
authors.initials: CC
authors.lastname: Pregitzer
authors.affiliation: Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065.
authors.forename: Christophe
authors.initials: C
authors.lastname: Lemetre
authors.affiliation: Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065.
authors.forename: Melinda A
authors.initials: MA
authors.lastname: Ternei
authors.affiliation: Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Maniko
authors.affiliation: Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065.
authors.forename: Bradley M
authors.initials: BM
authors.lastname: Hover
authors.affiliation: Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065.
authors.forename: Paula Y
authors.initials: PY
authors.lastname: Calle
authors.affiliation: Department of Biology, Barnard College, Columbia University, New York, NY 10027.|Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027.
authors.forename: Krista L
authors.initials: KL
authors.lastname: McGuire
authors.affiliation: Science Outreach Program, The Rockefeller University, New York, NY 10065.
authors.forename: Jeanne
authors.initials: J
authors.lastname: Garbarino
authors.affiliation: Natural Areas Conservancy, New York, NY 10029.
authors.forename: Helen M
authors.initials: HM
authors.lastname: Forgione
authors.affiliation: Natural Areas Conservancy, New York, NY 10029.
authors.forename: Sarah
authors.initials: S
authors.lastname: Charlop-Powers
authors.affiliation: Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065; sbrady@rockefeller.edu.
authors.forename: Sean F
authors.initials: SF
authors.lastname: Brady
mesh_terms: D001419:Bacteria / Q000235:genetics*; D044822:Biodiversity; D001688:Biological Products; D015195:Drug Design; D054892:Metagenome; D064307:Microbiota; D009519:New York City; D000068316:Parks, Recreational; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012987:Soil / Q000737:chemistry*; D012988:Soil Microbiology
chemical_list: D001688:Biological Products; D012987:Soil
keywords: biosynthesis; metagenomics; natural products