Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery

Microplastic contamination alters microbial community in commercially important bivalves, Geloina expansa, Anadara cornea, and Meretrix meretrix from tropical waters

Microplastics pose serious risks for aquatic organisms such as fishes, shrimps and bivalves. Bivalves are particularly vulnerable due to their filter-feeding strategy and sedentary life. While the microplastic bioaccumulation in bivalves has been well documented, the effects of microplastics accumulation on bivalve's gut microbiome in tropical sea waters remains poorly understood. To fill this knowledge gap, a 10-day feeding experiment with 13 mg L-1 polyethylene terephthalate particles was conducted using three commercially important bivalve species: Anadara cornea, Geloina expansa, and Meretrix meretrix taken from two contrasting locations (brackish water in protected Setiu Wetlands compared to open water in Kertih River) to investigate the effect of microplastic pollution on diversity and composition of gut prokaryotes using 16S rRNA amplicon sequencing. The results showed that alpha diversity of gut prokaryotes differed among species after microplastic exposure. For example, microplastic exposure increased operational taxonomic units (OTUs) richness of gut prokaryotes in G. expansa compared to A. cornea and M. meretrix during 10-day treatment. Community structure of prokaryotic community in bivalves gut showed strong divergence between Setiu Wetlands and Kertih River. Significant effects of microplastic exposure on relative abundance of prokaryotic phyla were also observed. Gut microbiome of G. expansa showed increase of relative abundance of Archaea and Firmicutes after microplastic exposure. The results suggest that microplastic treatment promotes dominance of certain bacterial species, likely those with plastic-metabolizing capabilities, potentially boosting bivalve resilience to microplastic contamination.

Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

BACKGROUND

The innovations of the "Omics Era" have ushered in significant advancements in genetic improvement of agriculturally important animal species through transforming genetics, genomics and breeding strategies. These advancements were often coordinated, in part, by support provided over 30 years through the 1993-2023 National Research Support Project 8 (NRSP8, National Animal Genome Research Program, NAGRP) and affiliate projects focused on enabling genomic discoveries in livestock, poultry, and aquaculture species. These significant and parallel advances demand strategic planning of future research priorities. This paper, as an output from the May 2023 Aquaculture Genomics, Genetics, and Breeding Workshop, provides an updated status of genomic resources for United States aquaculture species, highlighting major achievements and emerging priorities.

MAIN TEXT

Finfish and shellfish genome and omics resources enhance our understanding of genetic architecture and heritability of performance and production traits. The 2023 Workshop identified present aims for aquaculture genomics/omics research to build on this progress: (1) advancing reference genome assembly quality; (2) integrating multi-omics data to enhance analysis of production and performance traits; (3) developing resources for the collection and integration of phenomics data; (4) creating pathways for applying and integrating genomics information across animal industries; and (5) providing training, extension, and outreach to support the application of genome to phenome. Research focuses should emphasize phenomics data collection, artificial intelligence, identifying causative relationships between genotypes and phenotypes, establishing pathways to apply genomic information and tools across aquaculture industries, and an expansion of training programs for the next-generation workforce to facilitate integration of genomic sciences into aquaculture operations to enhance productivity, competitiveness, and sustainability.

CONCLUSION

This collective vision of applying genomics to aquaculture breeding with focus on the highlighted priorities is intended to facilitate the continued advancement of the United States aquaculture genomics, genetics and breeding research community and industries. Critical challenges ahead include the practical application of genomic tools and analytical frameworks beyond academic and research communities that require collaborative partnerships between academia, government, and industry. The scope of this review encompasses the use of omics tools and applications in the study of aquatic animals cultivated for human consumption in aquaculture settings throughout their life-cycle.

Polyester Microfibers Exposure Modulates Mytilus galloprovincialis Hemolymph Microbiome

Microplastic (MP) contamination in the aquatic environment is a cause of concern worldwide since MP can be taken up by different organisms, altering different biological functions. In particular, evidence is accumulating that MP can affect the relationship between the host and its associated microbial communities (the microbiome), with potentially negative health consequences. Synthetic microfibers (MFs) represent one of the main MPs in the marine environment, which can be accumulated by filter-feeding invertebrates, such as bivalves, with consequent negative effects and transfer through the food chain. In the mussel Mytilus galloprovincialis, polyethylene terephthalate (PET) MFs, with a size distribution resembling that of an MF released from textile washing, have been previously shown to induce multiple stress responses. In this work, in the same experimental conditions, the effects of exposure to PET-MF (96 h, 10, and 100 μg/L) on mussel hemolymph microbiome were evaluated by 16S rRNA gene amplification and sequencing. The results show that PET-MF affects the composition of bacterial communities at the phylum, family and genus level, with stronger effects at the lowest concentration tested. The relationship between MF-induced changes in hemolymph microbial communities and responses observed at the whole organism level are discussed.

Recent advances in bivalve-microbiota interactions for disease prevention in aquaculture

In bivalves, no clear-cut functional role of microbiota has yet been identified, although many publications suggest that they could be involved in nutrition or immunity of their host. In the context of climate change, integrative approaches at the crossroads of disciplines have been developed to explore the environment-host-pathogen-microbiota system. Here, we attempt to synthesize work on (1) the current methodologies to analyse bivalve microbiota, (2) the comparison of microbiota between species, between host compartments and their surrounding habitat, (3) how the bivalve microbiota are governed by environmental factors and host genetics and (4) how host-associated microorganisms act as a buffer against pathogens and/or promote recovery, and could thereby play a role in the prevention of disease or mortalities.