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Rhodolith metagenome diversity shifts across the Great Amazon System.

Carolina Salvador Duque Estrada1, Odara Araujo de Oliveira1, Thiago Augusto Calixto Lopes1

  • 1Laboratory of Microbiology, Graduate Program in Biological Sciences (Genetics), Health Sciences Center, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.

The Science of the Total Environment
|March 24, 2026
PubMed
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The microbial communities of rhodoliths in the Great Amazon Reef System adapt to environmental changes. These resilient microbiomes reorganize functions across different sectors, ensuring the algae

Area of Science:

  • Marine microbiology
  • Algal symbiosis
  • Biogeochemistry

Background:

  • Rhodolith-forming coralline algae inhabit the Great Amazon Reef System (GARS), facing environmental gradients from the Amazon River plume.
  • Understanding the microbial communities associated with these algae is crucial for reef health and stability.

Purpose of the Study:

  • To investigate the persistence of a core microbial community and the reorganization of metabolic functions in rhodolith holobionts across different sectors of the GARS.
  • To correlate microbial functions with local environmental conditions, such as light and redox gradients.

Main Methods:

  • Shotgun metagenomics was performed on rhodolith holobionts from South, Central, and North sectors of the GARS.
  • Taxonomic composition and functional pathway markers (KEGG/SEED; METABOLIC) were profiled to assess microbial diversity and function.
Keywords:
Amazon River plumeFunctional redundancyGreat Amazon Reef System (GARS)MetagenomicsPhototrophyRedox pathwaysRhodolith holobiont

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Main Results:

  • Bacteria, particularly Proteobacteria, Chloroflexi, and Bacteroidetes, dominated the holobiont, with Thaumarchaeota as the main archaeal lineage.
  • Functional profiles varied significantly across sectors, showing sector-specific adaptations in phototrophy, carbon fixation, respiration, nitrogen cycling, and sulfur metabolism.
  • The South sector exhibited oxygenic phototrophy, the Central sector showed combined phototrophy and nitrogen cycling, and the North sector was enriched in sulfur redox pathways.

Conclusions:

  • Rhodolith-associated microbiomes display resilience and functional redundancy, allowing persistence in mesophotic environments despite environmental gradients.
  • The study reveals a sector-specific reorganization of microbial functions along plume-driven gradients in the GARS.
  • These findings have implications for understanding biogenic calcification and biogeochemical stability under changing climate and ocean acidification scenarios.