Amphibian skin-associated Pigmentiphaga: Genome sequence and occurrence across geography and hosts

English version

Autoři: Molly C. Bletz ^aff001; Boyke Bunk ^aff003; Cathrin Spröer ^aff003; Peter Biwer ^aff004; Silke Reiter ^aff005; Falitiana C. E. Rabemananjara ^aff006; Stefan Schulz ^aff004; Jörg Overmann ^aff003; Miguel Vences ^aff002
Působiště autorů: Department of Biology, University of Massachusetts Boston, Boston, MA, United States of America ^aff001; Zoological Institute, Technische Universitt Braunschweig, Braunschweig, Germany ^aff002; DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany ^aff003; Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany ^aff004; Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany ^aff005; Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar ^aff006; Microbiology Institute, Technische Universität Braunschweig, Braunschweig, Germany ^aff007
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0223747

Souhrn

The bacterial communities colonizing amphibian skin have been intensively studied due to their interactions with pathogenic chytrid fungi that are causing drastic amphibian population declines. Bacteria of the family Alcaligenaceae, and more specifically of the genus Pigmentiphaga, have been found to be associated specifically to arboreal frogs. Here we analyze their occurrence in a previously assembled global skin microbiome dataset from 205 amphibian species. Pigmentiphaga made up about 5% of the total number of reads in this global dataset. They were mostly found in unrelated arboreal frogs from Madagascar (Mantellidae and Hyperoliidae), but also occurred at low abundances on Neotropical frogs. Based on their 16S sequences, most of the sequences belong to a clade within Pigmentiphaga not assignable to any type strains of the five described species of the genus. One isolate from Madagascar clustered with Pigmentiphaga aceris (>99% sequence similarity on 16S rRNA gene level). Here, we report the full genome sequence of this bacterium which, based on 16S sequences of >97% similarity, has previously been found on human skin, floral nectar, tree sap, stream sediment and soil. Its genome consists of a single circular chromosome with 6,165,255 bp, 5,300 predicted coding sequences, 57 tRNA genes, and three rRNA operons. In comparison with other known Pigmentiphaga genomes it encodes a higher number of genes associated with environmental information processing and cellular processes. Furthermore, it has a biosynthetic gene cluster for a nonribosomal peptide syntethase, and bacteriocin biosynthetic genes can be found, but clusters for β-lactones present in other comparative Pigmentiphaga genomes are lacking.

Klíčová slova:

Amphibian genomics – Amphibians – Comparative genomics – Microbiome – Multiple alignment calculation – Phylogenetic analysis – Sequence alignment – Sequence analysis

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Amphibian skin-associated Pigmentiphaga: Genome sequence and occurrence across geography and hosts

Souhrn

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Zdroje

PLOS One

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