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Comprehensive Multi-omics Approaches Provide Insights to Summer Mortality in the Clam Meretrix petechialis

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Abstract

Bivalve mass mortalities have been reported worldwide, which not only can be explained as a result of pathogen infection, but may reflect changes in environments. Although these episodes were often reported, there was limited information concerning the molecular responses to various stressors leading to summer mortality. In the present work, RNA sequencing (RNA-seq), tandem mass tagging (TMT)-based quantitative proteomics, and 16S rRNA sequencing were used to explore the natural outbreak of summer mortality in the clam Meretrix petechialis. We identified a total of 172 differentially expressed genes (DEGs) and 222 differentially expressed proteins (DEPs) in the diseased group compared to the normal group. The inconsistent expression profiles of immune DEGs/DEPs may be due to the immune dysregulation of the diseased clams. Notably, 11 solute carrier family genes were found among the top 20 down-regulated genes in the diseased group, indicating that weakened transmembrane transport ability might occur in the diseased clams. Integration analysis of transcriptomic and proteomic results showed that many metabolic processes such as “arginine and proline metabolism” and “tyrosine metabolism” were inhibited in the diseased group, suggesting metabolic inhibition. Moreover, 16S rRNA sequencing revealed that the microbial composition of clam hepatopancreas was disordered in the diseased group. The comparison of DEGs expression between the natural summer mortality event and an artificial challenge experiment involving both Vibrio infection and heat stress revealed 9/15 genes showing similar expression trends between the two conditions, suggesting that the summer mortality might be caused by a combination of high temperature and Vibrio infection. These results would deepen our understanding of summer mortality and provide candidate resistance markers for clam resistance breeding.

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Data Availability

The transcriptome datasets in this study have been submitted to the Sequence Read Archive (SRA) of the National Center for Biotechnology Information with the BioProject accession number PRJNA1025978. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the iProX partner repository with the dataset identifier PXD046074.

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Funding

This research was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA24030304), the Key Research and Development Program of Shandong (2021LZGC029), the earmarked fund for CARS-49, and the Taishan Industrial Leading Talents Project to Shandong Dehe Mingxing Biotechnology Co., Ltd. Chinese Academy of Sciences,XDA24030304,XDA24030304.

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Authors and Affiliations

  1. CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China

    Jing Tian, Hongxia Wang, Pin Huan, Xin Yue & Baozhong Liu

  2. Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266000, China

    Hongxia Wang, Pin Huan, Xin Yue & Baozhong Liu

  3. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao, 266071, China

    Pin Huan & Baozhong Liu

  4. University of Chinese Academy of Sciences, Beijing, 100049, China

    Jing Tian & Baozhong Liu

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  1. Jing Tian
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  4. Xin Yue
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Contributions

Jing Tian, Hongxia Wang, and Xin Yue performed the experiment. Jing Tian analyzed the data and drafted the manuscript. Pin Huan and Baozhong Liu revised the manuscript. Baozhong Liu conceived the study and obtained the funding. All authors reviewed and approved the manuscript.

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Correspondence to Baozhong Liu.

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The clams are neither an endangered nor protected species. All experiments in this study were conducted according to national and institutional guidelines.

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Tian, J., Wang, H., Huan, P. et al. Comprehensive Multi-omics Approaches Provide Insights to Summer Mortality in the Clam Meretrix petechialis. Mar Biotechnol 26, 389–403 (2024). https://doi.org/10.1007/s10126-024-10304-0

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