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

Schweizer, Magali ; Jauffrais, Thierry LU ; Choquel, Constance LU ; Méléder, Vona ; Quinchard, Sophie and Geslin, Emmanuelle (2022) In Ecology and Evolution 12(11).
Abstract

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... (More)

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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author
; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
kleptoplasty, microbiome, mudflat, protist, SSU rDNA, trophic behavior
in
Ecology and Evolution
volume
12
issue
11
article number
e9437
publisher
Wiley-Blackwell
external identifiers
  • scopus:85142879072
  • pmid:36407902
ISSN
2045-7758
DOI
10.1002/ece3.9437
language
English
LU publication?
yes
id
3ec2a289-67a0-48ad-a1ad-61b7f2c0635b
date added to LUP
2022-12-23 11:45:00
date last changed
2024-03-03 23:38:21
@article{3ec2a289-67a0-48ad-a1ad-61b7f2c0635b,
  abstract     = {{<p>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.</p>}},
  author       = {{Schweizer, Magali and Jauffrais, Thierry and Choquel, Constance and Méléder, Vona and Quinchard, Sophie and Geslin, Emmanuelle}},
  issn         = {{2045-7758}},
  keywords     = {{kleptoplasty; microbiome; mudflat; protist; SSU rDNA; trophic behavior}},
  language     = {{eng}},
  number       = {{11}},
  publisher    = {{Wiley-Blackwell}},
  series       = {{Ecology and Evolution}},
  title        = {{Trophic strategies of intertidal foraminifera explored with single-cell microbiome metabarcoding and morphological methods : What is on the menu?}},
  url          = {{http://dx.doi.org/10.1002/ece3.9437}},
  doi          = {{10.1002/ece3.9437}},
  volume       = {{12}},
  year         = {{2022}},
}