[Paper Review] Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Caroline Belser, Julie Poulain+34 more|arXiv (Cornell University)|Jul 6, 2022

Coral and Marine Ecosystems Studies4 citations

TL;DR

This paper presents an integrative multi-omics framework developed during the Tara Pacific expedition to characterize coral reef holobionts across the Pacific Ocean. By combining high-throughput sequencing of host, algal, bacterial, archaeal, fungal, and viral communities with extensive metadata, the study establishes a comprehensive, standardized workflow for assessing coral reef biodiversity and biocomplexity, enabling new insights into holobiont dynamics and resilience in the Anthropocene.

ABSTRACT

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the host coral organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

Motivation & Objective

• To develop a standardized, multi-omics workflow for characterizing the complex microbial and eukaryotic communities within coral holobionts.
• To address the urgent need for improved understanding of coral resilience in the face of environmental stressors driving global reef decline.
• To generate a large-scale, high-resolution dataset of coral reef biodiversity, including microorganisms, across the Pacific Ocean.
• To integrate multi-omics data with extensive metadata to enable systems-level analysis of holobiont dynamics and ecosystem function.
• To support future research on coral reef fate in the Anthropocene by providing a foundational, open-access resource.

Proposed method

• Employed state-of-the-art sequencing technologies to generate multi-omics data from coral samples collected across 18 Pacific archipelagos.
• Applied a standardized workflow for sample collection, preservation, and nucleic acid extraction to ensure data consistency across sites.
• Conducted whole-genome shotgun sequencing and 16S/18S rRNA gene amplicon sequencing to profile bacterial, archaeal, fungal, and protist communities.
• Integrated host genomic data with microbial and viral metagenomic, metatranscriptomic, and metabolomic data to capture holobiont-level interactions.
• Collected and curated a comprehensive set of concomitant metadata, including environmental parameters, host species, and sampling conditions.
• Deposited all raw and processed data into public repositories to ensure reproducibility and broad accessibility for future research.

Experimental results

Research questions

• RQ1 How can a standardized, multi-omics framework be developed to comprehensively characterize the biodiversity and biocomplexity of coral reef holobionts?
• RQ2 What is the distribution and composition of microbial and eukaryotic communities across the Pacific Ocean’s coral reef systems?
• RQ3 How do host-symbiont-microbiome interactions vary across geographic and environmental gradients?
• RQ4 What role do viruses and archaea play in shaping coral holobiont function and resilience?
• RQ5 How can integrated multi-omics and metadata enable predictive modeling of coral reef ecosystem dynamics under climate change?

Key findings

• The study established a robust, scalable, and standardized multi-omics pipeline for coral holobiont analysis, enabling consistent data generation across diverse Pacific locations.
• A comprehensive dataset was generated from 18 Pacific archipelagos, capturing the genetic diversity of coral hosts, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses.
• Extensive metadata collection enabled high-resolution analysis of environmental and biological variables influencing holobiont composition and function.
• The integration of multi-omics layers revealed complex, multi-trophic interactions within the holobiont, highlighting the importance of including all domains of life in reef assessments.
• The framework provides a foundational resource for systems-level understanding of coral reef resilience and vulnerability in the Anthropocene.
• All data and protocols are publicly available, ensuring reproducibility and enabling future comparative studies across reef ecosystems.