title: Genome Analysis of TwoPseudonocardiaPhylotypes Associated withAcromyrmexLeafcutter Ants Reveals Their Biosynthetic Potential.
abstract: The attine ants of South and Central America are ancient farmers, having evolved a symbiosis with a fungal food crop >50 million years ago. The most evolutionarily derived attines are theAttaandAcromyrmexleafcutter ants, which harvest fresh leaves to feed their fungus.Acromyrmexand many other attines vertically transmit a mutualistic strain ofPseudonocardiaand use antifungal compounds made by these bacteria to protect their fungal partner against co-evolved fungal pathogens of the genusEscovopsis.Pseudonocardiamutualists associated with the attinesApterostigma dentigerumandTrachymyrmex cornetzimake novel cyclic depsipeptide compounds called gerumycins, while a mutualist strain isolated from derivedAcromyrmex octospinosusmakes an unusual polyene antifungal called nystatin P1. The novelty of these antimicrobials suggests there is merit in exploring secondary metabolites ofPseudonocardiaon a genome-wide scale. Here, we report a genomic analysis of thePseudonocardiaphylotypes Ps1 and Ps2 that are consistently associated withAcromyrmexants collected in Gamboa, Panama. These were previously distinguished solely on the basis of 16S rRNA gene sequencing but genome sequencing of five Ps1 and five Ps2 strains revealed that the phylotypes are distinct species and each encodes between 11 and 15 secondary metabolite biosynthetic gene clusters (BGCs). There are signature BGCs for Ps1 and Ps2 strains and some that are conserved in both. Ps1 strains all contain BGCs encoding nystatin P1-like antifungals, while the Ps2 strains encode novel nystatin-like molecules. Strains show variations in the arrangement of these BGCs that resemble those seen in gerumycin gene clusters. Genome analyses and invasion assays support our hypothesis that vertically transmitted Ps1 and Ps2 strains have antibacterial activity that could help shape the cuticular microbiome. Thus, our work defines thePseudonocardiaspecies associated withAcromyrmexants and supports the hypothesis thatPseudonocardiaspecies could provide a valuable source of new antimicrobials.
authors.affiliation: School of Biological Sciences, University of East Anglia (UEA) Norwich, UK.
authors.forename: Neil A
authors.initials: NA
authors.lastname: Holmes
authors.affiliation: Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark.
authors.forename: Tabitha M
authors.initials: TM
authors.lastname: Innocent
authors.affiliation: Department of Molecular Microbiology, John Innes Centre Norwich, UK.
authors.forename: Daniel
authors.initials: D
authors.lastname: Heine
authors.affiliation: School of Biological Sciences, University of East Anglia (UEA) Norwich, UK.
authors.forename: Mahmoud Al
authors.initials: MA
authors.lastname: Bassam
authors.affiliation: School of Biological Sciences, University of East Anglia (UEA) Norwich, UK.
authors.forename: Sarah F
authors.initials: SF
authors.lastname: Worsley
authors.affiliation: Department of Molecular Microbiology, John Innes Centre Norwich, UK.
authors.forename: Felix
authors.initials: F
authors.lastname: Trottmann
authors.affiliation: School of Biological Sciences, University of East Anglia (UEA) Norwich, UK.
authors.forename: Elaine H
authors.initials: EH
authors.lastname: Patrick
authors.affiliation: School of Biological Sciences, University of East Anglia (UEA)Norwich, UK; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyKunming, China.
authors.forename: Douglas W
authors.initials: DW
authors.lastname: Yu
authors.affiliation: School of Environmental Sciences, University of East Anglia (UEA) Norwich, UK.
authors.forename: J C
authors.initials: JC
authors.lastname: Murrell
authors.affiliation: Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark.
authors.forename: Morten
authors.initials: M
authors.lastname: Schiøtt
authors.affiliation: Department of Molecular Microbiology, John Innes Centre Norwich, UK.
authors.forename: Barrie
authors.initials: B
authors.lastname: Wilkinson
authors.affiliation: Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark.
authors.forename: Jacobus J
authors.initials: JJ
authors.lastname: Boomsma
authors.affiliation: School of Biological Sciences, University of East Anglia (UEA) Norwich, UK.
authors.forename: Matthew I
authors.initials: MI
authors.lastname: Hutchings
keywords: Acromyrmex; Pseudonocardia; actinomycetes; antibiotics; genome mining; leafcutter ants; nystatin; polyene