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1. Metazoan diversity and seasonality through eDNA metabarcoding at a Mediterranean long-term ecological research site

   https://doi.org/10.1093/icesjms/fsab059  

   Di Capua, Iole; Piredda, Roberta; Mazzocchi, Maria Grazia; Zingone, Adriana (April 2021, ICES Journal of Marine Science)

   Fields, David (Ed.)

   Abstract Metabarcoding of environmental DNA has provided striking insights into marine microbial diversity. With this approach, we assessed the diversity of metazoan assemblages and their temporal variations at the Long-Term Ecological Research site MareChiara (LTER-MC) in the Gulf of Naples (Mediterranean Sea). The Illumina sequencing of the V4-18S rRNA fragment from 48 surface samples collected from 2011 to 2013 produced a total of 5 011 047 marine metazoan reads. The normalized dataset was generally dominated by copepods (60.3%), followed by annelids (34.7%) mostly represented by the invasive benthic polychaete Hydroides elegans. Non-copepod holoplankton was mainly represented by siphonophores, rotifers, and appendicularians, with occasional mass occurrences of jellyfish. The rest of meroplankton (mainly molluscs, annelids, and anthozoans) showed a high diversity, covering all 11 zooplankton phyla, from Porifera to Craniata. A high number of copepod genera were identified, with seasonal recurrence matching patterns observed in 30 years of studies in the Gulf of Naples. Despite limitations related to the molecular marker resolution and reference dataset, the study provided valuable insights into diversity and seasonal patterns of the whole metazoan assemblage, expanding the knowledge on rare or hardly identifiable taxa and confirming DNA metabarcoding as a powerful approach to be integrated at LTER sites. 

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2. Co-occurrence and successional patterns among diatoms, dinoflagellates, and potential parasites in a coastal upwelling experiment

   Vineis, J H; Burger, J M; Fawcett, S E; Ward, B B (April 2025, Limnology and oceanography)

   Diatom-dominated blooms in coastal upwelling systems contribute disproportionately to global primary production. The fate of carbon captured during a diatom bloom is often influenced by species-specific ecological differences. However, successional patterns that take place during a diatom bloom are often oversimplified, and the diversity of diatom adaptations to different stages of a bloom remains poorly characterized. To improve our understanding of diatom specificity to certain conditions within a bloom, we employed microscopy, 18S rRNA amplicons, and biogeochemical analysis within a simulated upwelling mesocosm experiment. We successfully simulated a diatom bloom and found that diatoms bloomed during early and late phases of the bloom. Surprisingly, the relative abundance of congeneric diatoms with the Thalassiosira, Chaetoceros, and Pseudonitzschia displayed opposing patterns that were consistent among experimental mesocosms. The late stage of the bloom was especially interesting because some diatoms continued to bloom among mixotrophic dinoflagellate genera Akashiwo, Heterocapsa, and Prorocentrum. Additionally, Syndiniales putative parasites were correlated with several diatoms, especially in the initial phase of the bloom. The novel observations of consistent rapid successional changes within our mesocosms reflect the ability of diatom and dinoflagellate genera to occupy bloom conditions that fall outside traditional expectations. Syndiniales parasite co-occurrence with blooming diatoms may be important to successional trends of coastal diatom populations, and this parasitic interaction deserves further study in coastal upwelling systems. This study indicates there are underlying diatom traits and biotic interactions that should be considered when estimating their contribution to productivity and carbon cycling within upwelling systems. 

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3. Oligotrophic waters of the Northwest Atlantic support taxonomically diverse diatom communities that are distinct from coastal waters

   https://doi.org/10.1111/jpy.13388  

   Setta, Samantha P.; Lerch, Sarah; Jenkins, Bethany D.; Dyhrman, Sonya T.; Rynearson, Tatiana A. (September 2023, Journal of Phycology)

   Abstract Diatoms are important components of the marine food web and one of the most species‐rich groups of phytoplankton. The diversity and composition of diatoms in eutrophic nearshore habitats have been well documented due to the outsized influence of diatoms on coastal ecosystem functioning. In contrast, patterns of both diatom diversity and community composition in offshore oligotrophic regions where diatom biomass is low have been poorly resolved. To compare the diatom diversity and community composition in oligotrophic and eutrophic waters, diatom communities were sampled along a 1,250 km transect from the oligotrophic Sargasso Sea to the coastal waters of the northeast US shelf. Diatom community composition was determined by amplifying and sequencing the 18S rDNA V4 region. Of the 301 amplicon sequence variants (ASVs) identified along the transect, the majority (70%) were sampled exclusively from oligotrophic waters of the Gulf Stream and Sargasso Sea and included the generaBacteriastrum,Haslea,Hemiaulus,Pseudo‐nitzschia, andNitzschia. Diatom ASV richness did not vary along the transect, indicating that the oligotrophic Sargasso Sea and Gulf Stream are occupied by a diverse diatom community. Although ASV richness was similar between oligotrophic and coastal waters, diatom community composition in these regions differed significantly and was correlated with temperature and phosphate, two environmental variables known to influence diatom metabolism and geographic distribution. In sum, oligotrophic waters of the western North Atlantic harbor diverse diatom assemblages that are distinct from coastal regions, and these open ocean diatoms warrant additional study, as they may play critical roles in oligotrophic ecosystems. 

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4. Towards quantitative microbiome community profiling using internal standards

   https://doi.org/http://dx.doi.org/10.1128/AEM.02634-18  

   Lin, Y. (January 2019, Applied and environmental microbiology)

   An inherent issue in high-throughput rRNA gene tag sequencing microbiome surveys is that they provide compositional data in relative abundances. This often leads to spurious correlations, making the interpretation of relationships to biogeochemical rates challenging. To overcome this issue, we quantitatively estimated the abundance of microorganisms by spiking in known amounts of internal DNA standards. Using a 3-year sample set of diverse microbial communities from the Western Antarctica Peninsula, we demonstrated that the internal standard method yielded community profiles and taxon cooccurrence patterns substantially different from those derived using relative abundances. We found that the method provided results consistent with the traditional CHEMTAX analysis of pigments and total bacterial counts by flow cytometry. Using the internal standard method, we also showed that chloroplast 16S rRNA gene data in microbial surveys can be used to estimate abundances of certain eukaryotic phototrophs such as cryptophytes and diatoms. In Phaeocystis, scatter in the 16S/18S rRNA gene ratio may be explained by physiological adaptation to environmental conditions. We conclude that the internal standard method, when applied to rRNA gene microbial community profiling, is quantitative and that its application will substantially improve our understanding of microbial ecosystems. 

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5. The respiratory microbiota of three cohabiting beluga whales (Delphinapterus leucas) under human care

   https://doi.org/10.3389/fmars.2023.1168623  

   Smith, Susan A.; Ropati, Destiny V.; Santoferrara, Luciana F.; Romano, Tracy A.; McManus, George B. (December 2023, Frontiers in Marine Science)

   We sampled the respiratory mucus from voluntary blowhole exhalations (“blow”) of three healthy beluga whales (Delphinapterus leucas) under professional human care. Blow samples were collected from three resident belugas, one adult male (M1) and two adult females (F1, F2), with voluntary behaviors via non-invasive methods over three days in July 2021 (four days for M1). Samples were weighed and examined microscopically for the enumeration of eukaryotic and prokaryotic microbes, and then were used to evaluate carbon substrate use and taxonomic diversity of prokaryotic communities in the host respiratory sytem. Microscopical observations and 18S rRNA gene sequencing indicated the presence of eukaryotic microbiota, the ciliate generaPlanilaminaandKyaroikeusin all three individuals. Exposure of samples to different metabolic carbon substrates indicated significant differences in the number of carbon sources usable by the prokaryotic communities of different whales (range: 11-25 sources), as well as a signficantly decreased diversity of carbon sources used by the community in the habitat water (5 sources). Sequencing of the hypervariable V4 region of the 16S rRNA gene revealed 19 amplicon sequence variants (ASVs) that were present in all whale samples. The oldest femaleD. leucas(F2) had the lowest overall diversity, and was significantly different from M1 and F1 in taxon composition, including an anomalously low ratio of Baccillota: Bacteroidota (0.01) compared to the other whales. In comparisons of microbial community composition, M1 had a significantly higher diversity than F1 and F2. These results suggest that attention should be given to regular microbiome sampling, and indicate a need for the pairing of microbiome and clinical data for animals in aquaria. Overall, these data contribute to the growing database on the core respiratory microbiota in cohabiting cetaceans under professional human care, indicate the utility of non-invasive sampling, and help characterize a baseline for healthyD. leucas. 

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