The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei

PLoS One. 2018 Nov 14;13(11):e0200437. doi: 10.1371/journal.pone.0200437. eCollection 2018.

Abstract

Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition of cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within the gills. In the present work we applied metagenomics to characterize microbiomes of the gills and digestive tract of Neoteredo reynei, a mangrove-adapted shipworm species found over a large range of the Brazilian coast. Comparative metagenomics grouped the gill symbiont community of different N. reynei specimens, indicating closely related bacterial types are shared. Similarly, the intestine and digestive gland communities were related, yet were more diverse than and showed no overlap with the gill community. Annotation of assembled metagenomic contigs revealed that the gill symbiotic community of N. reynei encodes a plethora of plant cell wall polysaccharides degrading glycoside hydrolase encoding genes, and Biosynthetic Gene Clusters (BGCs). In contrast, the digestive tract microbiomes seem to play little role in wood digestion and secondary metabolites biosynthesis. Metagenome binning recovered the nearly complete genome sequences of two symbiotic Teredinibacter strains from the gills, a representative of Teredinibacter turnerae "clade I" strain, and a yet to be cultivated Teredinibacter sp. type. These Teredinibacter genomes, as well as un-binned gill-derived gammaproteobacteria contigs, also include an endo-β-1,4-xylanase/acetylxylan esterase multi-catalytic carbohydrate-active enzyme, and a trans-acyltransferase polyketide synthase (trans-AT PKS) gene cluster with the gene cassette for generating β-branching on complex polyketides. Finally, we use multivariate analyses to show that the secondary metabolome from the genomes of Teredinibacter representatives, including genomes binned from N. reynei gills' metagenomes presented herein, stands out within the Cellvibrionaceae family by size, and enrichments for polyketide, nonribosomal peptide and hybrid BGCs. Results presented here add to the growing characterization of shipworm symbiotic microbiomes and indicate that the N. reynei gill gammaproteobacterial community is a prolific source of biotechnologically relevant enzymes for wood-digestion and bioactive compounds production.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bivalvia / microbiology*
  • Bivalvia / physiology
  • Gammaproteobacteria / enzymology*
  • Gammaproteobacteria / genetics
  • Gammaproteobacteria / physiology*
  • Genomics
  • Gills / microbiology
  • Glycoside Hydrolases / genetics
  • Glycoside Hydrolases / metabolism*
  • Metagenome
  • Microbiota
  • Multigene Family
  • Phylogeny
  • Polysaccharides / metabolism*
  • Secondary Metabolism
  • Symbiosis*
  • Wood / metabolism
  • Wood / parasitology

Substances

  • Polysaccharides
  • Glycoside Hydrolases

Grant support

This work was supported by the National Counsel of Technological and Scientific Development (CNPq) (http://cnpq.br) and by the Coordination for the Improvement of Higher Education Personnel (CAPES) (http://www.capes.gov.br) under the grant numbers 473030/2013-6 and 400764/2014-8 to AETS. BED is supported by Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.