Catalyzing progress in the blue economy through joint marine microbiome research across the Atlantic

International agreements recognize the importance of cooperative scientific research to conserve and promote sustainable development of a shared Atlantic Ocean. In 2022, the All-Atlantic Ocean Research and Innovation Alliance Declaration was signed. The All-Atlantic Declaration continues and extends relationships forged by the Galway Statement on Atlantic Ocean Cooperation and the Belém Statement on Atlantic Ocean Research and Innovation Cooperation. These efforts are consistent with programs, actions, and aims of the United Nations Decade of Ocean Science for Sustainable Development. In preparation for implementation of the All-Atlantic Declaration, members of the Marine Microbiome Working Group and the Marine Biotechnology Initiative for the Atlantic under the Galway and Belém Statements respectively, joined forces to call for cooperation across the Atlantic to increase marine microbiome and biotechnology research to promote ocean health and a sustainable bioeconomy. This article reviews the goals of the marine microbiome and biotechnology initiatives under the Galway and Belém Statements and outlines an approach to implement those goals under the All-Atlantic Declaration through a Blue Biotech and Marine Microbiome (BBAMM) collaboration

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs

Combined Operational Taxonomic Unit (OTU) Table

This operational taxonomic unit (OTU) table is the same as the final OTU (fOTU) table, EXCEPT the technical replicates have been combined into one sample. Therefore there are no A and B samples anymore and they are combined and treated as one sample

DNA Barcoding Significantly Improves Resolution of Invasive Lionfish Diet in the Northern Gulf of Mexico

Invasive Indo-Pacific red lionfish (Pterois volitans) have become well-established residents within reef communities across the western Atlantic Ocean where they pose substantial threats to native fish communities and reef ecosystems. Species-specific identification of prey is necessary to elucidate predator–prey interactions, but can be challenging with traditional visual identification methods given prey are often highly digested, thus not identifiable visually. To supplement visual diet analysis of lionfish (n = 934) sampled in the northern Gulf of Mexico, we applied DNA barcoding to identify otherwise unidentifiable fish prey (n = 696) via amplification of the cytochrome c oxidase subunit I (COI) of the mitochondrial genome. Barcoding nearly doubled the number of identifiable fish prey, thereby greatly enhancing our ability to describe lionfish diet. Thirty-three fish prey species were identified via barcoding, twenty-four of which were not previously detected by traditional methods. Some exploited reef fishes were newly reported (e.g., red snapper, Lutjanus campechanus) or found to constitute higher proportions of lionfish diet than previously reported (e.g., vermilion snapper, Rhomboplites aurorubens). Barcoding added a significant amount of new dietary information, and we observed the highest prey diversity reported to date for invasive lionfish. Potential cannibalism on juveniles also was identified via DNA barcoding, with the highest incidence corresponding to high lionfish densities, thus suggesting density-dependent prey demand may have driven this response. Overall, DNA barcoding greatly enhanced our ability to describe invasive lionfish diet in this study, suggesting that even studies with relatively large diet sample sizes could benefit from barcoding analysis

The Degree of Urbanization Across the Globe is not Reflected in the δ15N of Seagrass Leaves

Many studies show that seagrass δ15N ratios increase with the amount of urbanization in coastal watersheds. However, there is little information on the relationship between urbanization and seagrass δ15N ratios on a global scale. We performed a meta-analysis on seagrass samples from 79 independent locations to test if seagrass δ15N ratios correlate with patterns of population density and fertilizer use within a radius of 10–200 km around the sample locations. Our results show that seagrass δ15N ratios are more influenced by intergeneric and latitudinal differences than the degree of urbanization or the amount of fertilizer used in nearby watersheds. The positive correlation between seagrass δ15N ratios and latitude hints at an underlying pattern in discrimination or a latitudinal gradient in the 15N isotopic signature of nitrogen assimilated by the plants. The actual mechanisms responsible for the correlation between δ15N and latitude remain unknown

Data from: Metabarcoding reveals environmental factors influencing spatio-temporal variation in pelagic micro-eukaryotes

Marine environments harbour a vast diversity of micro-eukaryotic organisms (protists and other small eukaryotes) that play important roles in structuring marine ecosystems. However, micro-eukaryote diversity is not well understood. Likewise, knowledge is limited regarding micro-eukaryote spatial and seasonal distribution, especially over long temporal scales. Given the importance of this group for mobilizing energy from lower trophic levels near the base of the food chain to larger organisms, assessing community stability, diversity and resilience is important to understand ecosystem health. Herein, we use a metabarcoding approach to examine pelagic micro-eukaryote communities over a 2.5-year time series. Bimonthly surface sampling (July 2009 to December 2011) was conducted at four locations within Mobile Bay (Bay) and along the Alabama continental shelf (Shelf). Alpha-diversity only showed significant differences in Shelf sites, with the greatest differences observed between summer and winter. Beta-diversity showed significant differences in community composition in relation to season and the Bay was dominated by diatoms, while the Shelf was characterized by dinoflagellates and copepods. The northern Gulf of Mexico is heavily influenced by the Mobile River Basin, which brings low-salinity nutrient-rich water mostly during winter and spring. Community composition was correlated with salinity, temperature and dissolved silicate. However, species interactions (e.g. predation and parasitism) may also contribute to the observed variation, especially on the Shelf, which warrants further exploration. Metabarcoding revealed clear patterns in surface pelagic micro-eukaryote communities that were consistent over multiple years, demonstrating how these techniques could be greatly beneficial to ecological monitoring and management over temporal scales

The Architecture and Chemical Stability of the Archaeal Sulfolobus Turreted Icosahedral Virus ▿

Viruses utilize a diverse array of mechanisms to deliver their genomes into hosts. While great strides have been made in understanding the genome delivery of eukaryotic and prokaryotic viruses, little is known about archaeal virus genome delivery and the associated particle changes. The Sulfolobus turreted icosahedral virus (STIV) is a double-stranded DNA (dsDNA) archaeal virus that contains a host-derived membrane sandwiched between the genome and the proteinaceous capsid shell. Using cryo-electron microscopy (cryo-EM) and different biochemical treatments, we identified three viral morphologies that may correspond to biochemical disassembly states of STIV. One of these morphologies was subtly different from the previously published 27-Å-resolution electron density that was interpreted with the crystal structure of the major capsid protein (MCP). However, these particles could be analyzed at 12.5-Å resolution by cryo-EM. Comparing these two structures, we identified the location of multiple proteins forming the large turret-like appendages at the icosahedral vertices, observed heterogeneous glycosylation of the capsid shell, and identified mobile MCP C-terminal arms responsible for tethering and releasing the underlying viral membrane to and from the capsid shell. Collectively, our studies allow us to propose a fusogenic mechanism of genome delivery by STIV, in which the dismantled capsid shell allows for the fusion of the viral and host membranes and the internalization of the viral genome

Original Operational Taxonomic Unit (OTU) Table

This is the original operational taxonomic unit (OTU) table resulting from the sequences clustering prior to any filtering of OTUs

Final Operational Taxonomic Unit (fOTU) Table

The filtered operational taxonomic unit (OTU) table that excludes OTUs that failed to align with PyNAST or were classified as Archaea and Bacteria. This OTU table corresponds to the final OTU (fOTU) table listed in the manuscript