ena-STUDY-SBCS-18-05-2018-14:41:06:912-514
Metabarcoding insights into the identity and trophic behaviour of foraminifera in intertidal sediments
Next Generation Sequencing (NGS) has proven to be a useful tool for ecological studies of marine organisms. An increasing number of studies use NGS approaches to gain insights into foraminiferal diversity. Nevertheless, information on the taxonomy and complex ecological interactions of benthic foraminifera is still scarce. Here, we aim to determine the taxonomic identity and elucidate the feeding patterns of foraminifera from intertidal mudflats using the v9 region of the 18S rRNA gene. Isolation of living foraminiferal cells was done from intact sediment cores, retrieved from two locations of the Wadden Sea. Foraminifera were picked from the top 10 cm, their vitality was confirmed based on their motility and they were morphologically identified to genus level (Ammonia sp., Elphidium sp. and Haynesina sp.). DNA was extracted from within single foraminiferal cells and from the surrounding sediments. Subsequently, the v9 region of the 18S rRNA gene was amplified and sequenced on the Illumina MiSeq platform. Paired-end reads were joined, quality filtered and assigned taxonomy based on the SILVA database. Additionally, the Protist Ribosomal Reference (PR2) database was used for the taxonomical identification of foraminiferal operational taxonomic units (OTUs) retrieved from single-cells. Ongoing phylogenetic analysis will enable the exact placement of these specimens among known groups and previously identified foraminiferal genotypes. OTUs found in the foraminiferal cells generally reflect the diversity of small eukaryotes in the surrounding sediments, with dominant groups those of diatoms, dinoflagellates, ciliates and metazoans (e.g. nematodes, maxillopoda). However, the intracellular eukaryotic community signal differs among foraminiferal species, suggesting differences in their trophic behaviour. This is confirmed by multivariate statistical analysis, which indicates that foraminiferal species and the sampling depth are significant factors for the observed intracellular community variance. Further analysis will reveal more details about specific eukaryotes that foraminifera potentially feed on.
Next Generation Sequencing (NGS) has proven to be a useful tool for ecological studies of marine organisms. An increasing number of studies use NGS approaches to gain insights into foraminiferal diversity. Nevertheless, information on the taxonomy and complex ecological interactions of benthic foraminifera is still scarce. Here, we aim to determine the taxonomic identity and elucidate the feeding patterns of foraminifera from intertidal mudflats using the v9 region of the 18S rRNA gene. Isolation of living foraminiferal cells was done from intact sediment cores, retrieved from two locations of the Wadden Sea. Foraminifera were picked from the top 10 cm, their vitality was confirmed based on their motility and they were morphologically identified to genus level (Ammonia sp., Elphidium sp. and Haynesina sp.). DNA was extracted from within single foraminiferal cells and from the surrounding sediments. Subsequently, the v9 region of the 18S rRNA gene was amplified and sequenced on the Illumina MiSeq platform. Paired-end reads were joined, quality filtered and assigned taxonomy based on the SILVA database. Additionally, the Protist Ribosomal Reference (PR2) database was used for the taxonomical identification of foraminiferal operational taxonomic units (OTUs) retrieved from single-cells. Ongoing phylogenetic analysis will enable the exact placement of these specimens among known groups and previously identified foraminiferal genotypes. OTUs found in the foraminiferal cells generally reflect the diversity of small eukaryotes in the surrounding sediments, with dominant groups those of diatoms, dinoflagellates, ciliates and metazoans (e.g. nematodes, maxillopoda). However, the intracellular eukaryotic community signal differs among foraminiferal species, suggesting differences in their trophic behaviour. This is confirmed by multivariate statistical analysis, which indicates that foraminiferal species and the sampling depth are significant factors for the observed intracellular community variance. Further analysis will reveal more details about specific eukaryotes that foraminifera potentially feed on.