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

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

Research output: Contribution to journalArticleScientificpeer-review

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.
Original languageEnglish
Article number1169
JournalFrontiers in Microbiology
Volume10
Issue number1169
Number of pages16
ISSN1664-302X
DOIs
Publication statusPublished - 28 May 2019
MoE publication typeA1 Journal article-refereed

Fields of Science

  • AMMONIA
  • CHLOROPLASTS
  • DIVERSITY
  • MARINE FUNGI
  • MICROBIAL PLANKTON
  • MOLECULAR-IDENTIFICATION
  • OXYGEN
  • RIBOSOMAL DNA
  • SEA
  • VERTICAL-DISTRIBUTION
  • benthic food web
  • benthic foraminifera
  • benthic microbial ecology
  • metabarcoding
  • molecular phylogeny
  • trophic strategy
  • 1183 Plant biology, microbiology, virology

Cite this

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title = "Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera",
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.",
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author = "Myrsini Chronopoulou and Iines Salonen and Clare Bird and Gert-Jan Reichart and Karoliina Koho",
year = "2019",
month = "5",
day = "28",
doi = "10.3389/fmicb.2019.01169",
language = "English",
volume = "10",
journal = "Frontiers in Microbiology",
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Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera. / Chronopoulou, Myrsini; Salonen, Iines; Bird, Clare; Reichart, Gert-Jan; Koho, Karoliina.

In: Frontiers in Microbiology, Vol. 10, No. 1169, 1169, 28.05.2019.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera

AU - Chronopoulou, Myrsini

AU - Salonen, Iines

AU - Bird, Clare

AU - Reichart, Gert-Jan

AU - Koho, Karoliina

PY - 2019/5/28

Y1 - 2019/5/28

N2 - 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.

AB - 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.

KW - AMMONIA

KW - CHLOROPLASTS

KW - DIVERSITY

KW - MARINE FUNGI

KW - MICROBIAL PLANKTON

KW - MOLECULAR-IDENTIFICATION

KW - OXYGEN

KW - RIBOSOMAL DNA

KW - SEA

KW - VERTICAL-DISTRIBUTION

KW - benthic food web

KW - benthic foraminifera

KW - benthic microbial ecology

KW - metabarcoding

KW - molecular phylogeny

KW - trophic strategy

KW - 1183 Plant biology, microbiology, virology

U2 - 10.3389/fmicb.2019.01169

DO - 10.3389/fmicb.2019.01169

M3 - Article

VL - 10

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

IS - 1169

M1 - 1169

ER -