Trophic strategies of intertidal foraminifera explored with single-cell microbiome metabarcoding and morphological methods: What is on the menu?

Type Article
Date 2022-11
Language English
Author(s) Schweizer Magali1, Jauffrais ThierryORCID1, 2, Choquel Constance1, 3, Méléder Vona4, Quinchard Sophie1, Geslin Emmanuelle1
Affiliation(s) 1 : UMR 6112 LPG, Laboratoire de Planétologie et Géosciences, Univ Angers, Nantes Université, Le Mans Université, CNRS, Angers, France
2 : UMR 9220 ENTROPIE, Ifremer, IRD, Univ Nouvelle-Calédonie, Univ La Réunion, CNRS, Noumea, New Caledonia
3 : Department of Geology, Lund University, Lund, Sweden
4 : UR 2160, ISOMer, Institut des Substances et Organismes de la Mer, Nantes Université, Nantes, France
Source Ecology And Evolution (2045-7758) (Wiley Open Access), 2022-11 , Vol. 12 , N. 11 , P. e9437 (28p.)
WOS© Times Cited 1
Keyword(s) kleptoplasty, microbiome, mudflat, protist, SSU rDNA, trophic behavior

In mudflats, interactions and transfers of nutrients and secondary metabolites may drive ecosystems and biodiversity. Foraminifera have complex trophic strategies as they often rely on bacteria and eukaryotes or on potential symbionts for carbon and nitrogen resources. The capacity of these protists to use a wide range of adaptive mechanisms requires clarifying the relationships between them and their microbial associates. Here, we investigate the interactions of three foraminiferal species with nearby organisms in situ, by coupling molecular (cloning/Sanger and high-throughput sequencing) and direct counting and morphological identification with microscopy. This coupling allows the identification of the organisms found in or around three foraminiferal species through molecular tools combined with a direct counting of foraminifera and diatoms present in situ through microscopy methods. Depending on foraminiferal species, and in addition to diatom biomass, diatom frustule shape, size and species are key factors driving the abundance and diversity of foraminifera in mudflat habitats. Three different trophic strategies were deduced for the foraminifera investigated in this study: Ammonia sp. T6 has an opportunistic strategy and is feeding on bacteria, nematoda, fungi, and diatoms when abundant; Elphidium oceanense is feeding mainly on diatoms, mixed with other preys when they are less abundant; and Haynesina germanica is feeding almost solely on medium-large pennate diatoms. Although there are limitations due to the lack of species coverage in DNA sequence databases and to the difficulty to compare morphological and molecular data, this study highlights the relevance of combining molecular with morphological tools to study trophic interactions and microbiome communities of protists at the single-cell scale.

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Schweizer Magali, Jauffrais Thierry, Choquel Constance, Méléder Vona, Quinchard Sophie, Geslin Emmanuelle (2022). Trophic strategies of intertidal foraminifera explored with single-cell microbiome metabarcoding and morphological methods: What is on the menu? Ecology And Evolution, 12(11), e9437 (28p.). Open Access version :