Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera.

Panagiota-Myrsini Chronopoulou,Clare Bird,Gert-Jan Reichart,Karoliina A Koho,Iines Salonen

doi:10.3389/fmicb.2019.01169

Abstract

Foraminifera are ubiquitous marine protists with an important role in the benthic carbon cycle. However, morphological observations often fail to resolve their exact taxonomic placement and there is a lack of field studies on their particular trophic preferences. Here, we propose the application of metabarcoding as a tool for the elucidation of the in situ feeding behavior of benthic foraminifera, while also allowing the correct taxonomic assignment of the feeder, using the V9 region of the 18S (small subunit; SSU) rRNA gene. Living foraminiferal specimens were collected from two intertidal mudflats of the Wadden Sea and DNA was extracted from foraminiferal individuals and from the surrounding sediments. Molecular analysis allowed us to confirm that our foraminiferal specimens belong to three genetic types: Ammonia sp. T6, Elphidium sp. S5 and Haynesina sp. S16. Foraminiferal intracellular eukaryote communities reflected to an extent those of the surrounding sediments but at different relative abundances. Unlike sediment eukaryote communities, which were largely determined by the sampling site, foraminiferal intracellular eukaryote communities were driven by foraminiferal species, followed by sediment depth. Our data suggests that Ammonia sp. T6 can predate on metazoan classes, whereas Elphidium sp. S5 and Haynesina sp. S16 are more likely to ingest diatoms. These observations, alongside the use of metabarcoding in similar ecological studies, significantly contribute to our overall understanding of the ecological roles of these protists in intertidal benthic environments and their position and function in the benthic food webs.

Highlights

Sediment samples obtained from the same depths as foraminiferal specimens (0–10 cm for site M, 0–4 cm for site C) were used for metabarcoding along with the foraminifera
After filtering out Operational Taxonomic Units (OTUs) with low number of reads and noneukaryote OTUs, 1,608 OTUs were obtained from the sediment and 510 OTUs from the foraminiferal dataset, of which 65 OTUs (TF) were assigned to phylum Retaria and all other 445 OTUs to their intracellular eukaryote content (TIFC)
We cannot preclude the possibility of foraminifera praying on other foraminifera (e.g., Lipps, 1983), on average 87% of the TF reads within our specimens were taxonomically assigned to the same foraminiferal species as the species assigned based on morphology

Summary

Introduction

Due to their opportunistic character (e.g., Moodley et al, 2000; Woulds et al, 2007), foraminifera can take advantage of their environment very efficiently and they are able to thrive in a wide variety of marine environments. Their ecology is complex, with some species harboring photosynthetically active symbionts or kleptoplasts (e.g., Hallock, 2000; LeKieffre et al, 2018; Schmidt et al, 2018) and other various. Understanding species-specific feeding behaviors is crucial to unraveling the adaptability strategies of benthic foraminifera in their habitats, understanding the benthic food webs structure and addressing implications for the global marine benthic biogeochemical cycles

Objectives

Methods

Results

Discussion

Conclusion