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

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.

Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes

“…Merged FASTA files were assembled using IDBA_ud (version 2) with standard parameters in the Center for High Performance Computing at the University of Utah. For the metagenome samples from Brazil, all Neoteredo reynei gill metagenomic samples previously analyzed were resequenced here to improve coverage depth (27). Teredo sp.…”

“…Moreover, several findings indicate that the BGCs found in cultivated isolates might also be harbored by symbionts within shipworm gills. Previous obtained data include the detection of tartrolons and turnerbactins and their BGCs in shipworms (17,18) and results of an investigation of four isolate genomes and one metagenome (26); also, an exploratory investigation of the metagenome of N. reynei gills and digestive tract led to the detection of known T. turnerae BGCs as well as novel clusters (27). These findings left unaddressed many major issues concerning shipworm secondary metabolites, including which symbionts make them, how they are distributed, how they vary by host and symbiont species, and what their roles might be in nature.…”

Xylanolytic Extremozymes Retrieved From Environmental Metagenomes: Characteristics, Genetic Engineering, and Applications

“…The acetyl xylan esterases (AXEs) (EC 3.1.1.6) cleave the acetyl group from acetyl-xylose moieties and contribute to the complete degradation of the complex xylans. Recently, a few studies have uncovered a handful of AXEs using metagenomic approaches (Adesioye et al, 2018;Brito et al, 2018; Table 2). A metagenomic AXE (Axe1NaM1) was identified by using a hot desert hypolith metagenomic DNA sequence data set (Adesioye et al, 2018).…”

“…Interestingly, a point mutation (N65S) improved its thermostability as well as catalytic efficiency; the crystal structure of this enzyme has also been solved. In another report, the gut microbiome of a shipworm also identified several AXEs that shared 50-75% similarity with the available carbohydrate esterases (Brito et al, 2018). Zhu et al (2016) studied the association and relative abundance of Firmicutes along with lignocellulosedegrading enzymes.…”

Diversity and Bioprospecting of Filamentous Fungi Isolated From Nausitora Fusticulus (Bivalvia: Teredinidae) Digestive Organs for Lignocellulolytic Enzymes / Diversidade E Bioprospecção De Fungos Filamentosos Isolados Dos Órgãos Digestivos De Nausitora Fusticulus (Bivalvia:teredinidae) Para Obtenção De Enzimas Lignocelulolíticas

“…The Teredinidae family consists of bivalves that inhabit marine environments and brackish water, from temperate and tropical regions (Borges et al 2014). The organisms of this family are specialized in the drilling and digestion of wood (Turner 1966;Borges et al 2014;Brito et al 2018). Teredinids have a specialized and modified digestive system for wood digestion, the only bivalves that have digestive glands effective in this function, as well as specific glands to digest suspended particles (Lopes & Narchi 1998).…”