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Unveiling the Functional Microbiomes of the Ocean: From Genes to Ecosystem Services

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 20 June 2026 | Viewed by 855

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Guest Editor
1. Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud 123, Muscat P.O. Box 34, Oman
2. UNESCO Chair in Marine Biotechnology, Center of Excellence in Marine Biotechnology, Sultan Qaboos University, Al Khoud 123, Muscat P.O. Box 50, Oman
Interests: marine biotechnology; marine biofilms; prokaryote-eukaryote signaling; marine natural products; biofouling; antifouling; nanocoatings; quorum sensing; anticancer compound
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Special Issue Information

Dear Colleagues,

Marine microbiomes are emerging as drivers of ocean health, biogeochemical cycling, and ecosystem resilience. A functional microbiome includes specific microbiomes and frequently a microbiome host. Molecular biology techniques enable snapshots of the members of microbiomes, but not their function. This Special Issue aims to explore the functions of microbial communities across diverse marine environments—from biofilms in coastal zones and the deep sea to industrial and extreme habitats. In addition, this Special Issue will bring together original research and review articles on functional microbiomes and integrate diverse approaches to understand gene expression, enzyme production, communication, metabolic activities, and other contributions to ecosystem processes. We invite authors to submit articles that advance our understanding of functional microbiomes, their roles, and biotechnological applications.

Prof. Dr. Sergey Dobretsov
Prof. Dr. Daniel Rittschof
Guest Editors

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Keywords

  • microbiome
  • symbiosis
  • community organization
  • functional diversity
  • communication
  • microbial functions
  • metagenomics
  • metabolomics
  • transcriptomics
  • proteomics
  • biogeochemical cycling
  • biofouling
  • ocean health
  • marine biotechnology
  • microbial ecology

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Published Papers (1 paper)

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Research

11 pages, 1850 KB  
Article
Egg Hatching, Peptide Pheromones, and Endoproteinases in Barnacles
by Desa Bolger, Joshua Osterberg, Beatriz Orihuela, Arthur Moseley and Daniel Rittschof
Int. J. Mol. Sci. 2025, 26(23), 11393; https://doi.org/10.3390/ijms262311393 - 25 Nov 2025
Viewed by 555
Abstract
The striped barnacle, Amphibalanus amphitrite, is a simultaneous hermaphrodite crustacean that broods eggs. The eggs are physically and enzymatically cleaned in the mantle by the barnacle to manage biofouling during incubation. There is no physiological connection between the embryos and the adult. [...] Read more.
The striped barnacle, Amphibalanus amphitrite, is a simultaneous hermaphrodite crustacean that broods eggs. The eggs are physically and enzymatically cleaned in the mantle by the barnacle to manage biofouling during incubation. There is no physiological connection between the embryos and the adult. Instead, barnacles use enzyme products as pheromones to coordinate behavioral, physiological, and biochemical processes involved in egg hatching and larval release. Known larval release pheromones are peptides generated by exogenous trypsins that act on proteins. We characterized barnacle brooding endoproteinases using a proteomic analysis of peptides generated from the hydrolysis of pure proteins that were identified by high-resolution LC electrospray MS/MS. Utilizing pure proteins permitted us to completely identify sequences around proteolytic cleavage sites. Enzyme activity was 2.22 to 2.79 times greater in barnacle and barnacle microbiome samples compared to seawater samples. Distinct enzyme patterns emerged, with higher proline- and asparagine-cutting enzymes in barnacle samples and greater proportions of elastase in seawater. There are at least 13 endoproteinases based on the C-terminus amino acids of peptides, with major contributions from serine proteases. This approach has the potential to provide exceptionally detailed information on endoproteinases in any microbiome assemblage. With a little thought, this technique can be expanded to include exoproteinases as well. Full article
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