Long‐lasting effects of chronic exposure to chemical pollution on the hologenome of the Manila clam

Abstract

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Contaminants from dredged sediments alter the transcriptome of Manila clam and induce shifts in microbiota composition

“…The concomitant upregulation of genes involved in protein degradation and mTORC1 signalling can be explained in two possible ways, not necessarily mutually exclusive. First, increased degradation of damaged proteins following chemical exposure [ 38 – 40 ] may increase the availability of amino acids, a key signal to mTORC1 that the cell has sufficient nutrients for protein synthesis and cell growth. Upregulation of the Rag GTPases RAGD and FNIP , which are known to play a critical role in regulating mTORC1 activity by sensing amino acid availability, supports this hypothesis [ 41 – 44 ].…”

“…Clams exposed to sediments with the highest chemical contamination of industrial origin showed additional stress responses, mainly at an early stage. Among them, the upregulation of genes putatively involved in xenobiotic metabolism, such as SULT2 and NRF6, have already been widely described in clams populating sites close to Porto Marghera [ 27 , 38 , 40 , 67 ]. While SULT2 belongs to a family of phase II detoxification enzymes involved in protection against xenobiotics [ 68 – 70 ], NRF6 was found to be positively correlated with increased concentrations of PCDD/Fs and PCB-DL in Manila clams inhabiting different contaminated sites within the Venice lagoon [ 40 ].…”

“…The input reads quality was assessed with FastQC/v0.11.9 [ 102 ] in order to determine and remove low-quality reads and residual adaptors by using the BBDuk program contained in the BBTools suite (program-specific options were taken from the Lexogen’s website). High-quality reads and a reference transcriptome from the digestive gland [ 38 ] were employed to perform the mapping and the count table was obtained through Kallisto/v0.46.1 [ 103 ] with default settings and finally the “abundance_estimates_to_matrix.pl” script from the Trinity suite [ 104 ]. Raw reads count were then imported into R/v3.6.0 (R Core Team 2014) and filtered: contigs with less than 5 reads in at least 20% of total libraries (out of 130 for the first) were removed to limit the background noise [ 105 , 106 ].…”

“…Functional annotation of the reference transcriptome was performed by Blastx similarity search on Swissprot (Uniprot), Homo sapiens protein Ensembl database, Danio rerio protein Ensembl database and Crassostrea gigas protein Ensembl database (Evalue < 0.0001). Details and the annotation of each contig are reported in Iannello et al [ 38 ]. Gene expression profiles were explored through the PCA as an unsupervised method performed considering all samples within each sampling time, pairwise comparisons and enrichment analyses of differentially expressed genes.…”

Tracking the hologenome dynamics in aquatic invertebrates by the holo-2bRAD approach

“…There is now considerable evidence supporting this concept 15 – 17 , which has broadened our perspectives for studying host-microbe coevolution. Facilitated by the advances in high-throughput sequencing technologies, studies of the hologenome have progressively increased in number, extending to a diverse range of organisms through the use of different samples (e.g., intestinal contents in chicken 18 and salmonid 19 , feces and anal swab samples in vampire bat 20 and digestive gland in clams 21 ). However, few hologenome studies have been performed in marine organisms, and these studies mainly focused on static hologenome data (e.g., at a specific point in time).…”