DOI: 10.5061/dryad.5dv41nsbb
title: Wooden steps to shallow depths: A new bathymodiolin mussel, Vadumodiolus teredinicola, inhabits shipworm burrows in an ancient submarine forest

description: Large mussels of the mytilid subfamily Bathymodiolinae are common
 inhabitants of deep-sea hydrothermal vents and cold seeps, where
 gill-borne symbionts allow them to utilize energy-rich compounds such as
 hydrogen sulfide and methane to support abundant growth. This subfamily
 also includes smaller symbiont-bearing mussels found on deep-sea wood and
 organic deposits. Phylogenetic analyses suggest that wood association is
 ancestral to bathymodiolin evolution. This observation led to the “wooden
 steps” hypothesis, which proposed that wood and other large organic
 deposits have acted as evolutionary steppingstones, introducing the
 progenitors of the modern vent and seep Bathymodiolinae to their remote
 environments. Although this hypothesis implies an evolutionary trajectory
 from shallow to deep water, no bathymodiolin species that grows and
 reproduces at depths less than 100 m has yet been formally described. Here
 we describe a new bathymodiolin genus and species, Vadumodiolus
 teredinicola, found growing and reproducing at a depth of 18 m in
 uninhabited shipworm burrows in the remnants of an ancient submerged bald
 cypress forest off the coast of Alabama. These results demonstrate that
 the bathymodiolin radiation has not been limited to deep water and that
 specific association with wood has led to the successful invasion of both
 deep and shallow marine environments.
description: To search for evidence of bacterial symbionts in the tissues of
 <em>Vadumodiolus teredinicola</em>, we sequenced the gill
 metagenomes of three specimens, assembled contigs and sorted contigs of
 predicted bacterial origin into bins reflecting individual predicted
 bacterial MAGs using SPADES and metaBAT2. Reads of bacterial origin were
 sparsely represented in the three individual gill metagenome datasets.
 However, by combining reads from all three gill metagenome sequences
 during SPADES assembly, a single, though highly fragmented, bacterial MAG
 was assembled. MetaBAT2 uses tetranucleotide composition information to
 perform binning. MetaBAT2 takes a metagenome assembly and the reads that
 produced the assembly and organizes the contigs into putative genomes,
 called "bins". Because metaBAT2 only uses contigs longer than
 1.5 kbp during binning, we performed BLASTn searches using the 16S rRNA
 genes, 23S rRNA genes, and coding sequences (CDS) of
 <em>Bathymodiolus thermophilus</em> thioautotrophic gill
 symbiont strain EPR9N to recruit un-binned short bacterial contigs in the
 assembled metagenome. Because the metaBAT2 binned bacterial contigs and
 concatenated contigs obtained using BLAST searches are phylogenetically
 indistinguishable, it is reasonable to assume that they represent the same
 bacterial genome present in the gills, and thus can be combined to create
 a more complete assembly. The final draft genome of <em>Vadumodiolus
 teredinicola</em> gill bacterium was annotated using Prokka and is
 deposited in GenBank format (GBK extension).
description: # Wooden steps to shallow depths: a new bathymodiolin mussel, Vadumodiolus
 teredinicola, inhabits shipworm burrows in an ancient submarine forest ---
 Files included: * DRYAD :
 Vt_gill_bac_5288ABC_2023-05-05_NCBI_decontam.fsa.fasta * ZENODO: Altamia
 et al._2023-1212_supplement.1.reordered.final.pdf * ZENODO:
 Vadumodiolus_teredinicola_Supplementary_Video_SV1.MP4 * ZENODO:
 Vadumodiolus_teredinicola_Supplementary_Video_SV2.mp4 ## Description of
 the data and file structure *
 Vt_gill_bac_5288ABC_2023-05-05_NCBI_decontam.fsa.fasta Draft metagenome
 assembled genome of Vadumodiolus teredinicola gill bacterium in FASTA
 format Wooden steps to shallow depths: a new bathymodiolin mussel,
 Vadumodiolus teredinicola, inhabits shipworm burrows in an ancient
 submarine forest Marvin A. Altamia, Hannah J. Appiah-Madson, Rosalia Falco
 Poulin, Bruno Huettel, Maxim Rubin-Blum, Nicole Dubilier, Harald R.
 Gruber-Vodicka, Nikolaus Leisch, and Daniel L. Distel* ## Sharing/Access
 information GenBank accession numbers referred to in the manuscript will
 become active on August 30, 2023.