Discovery of a Katablepharis sp. in the Columbia River estuary that is abundant during the spring and bears a unique large ribosomal subunit sequence element

Peter Kahn, Lydie Herfort, Tawnya Peterson, Peter Zuber

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Heterotrophic protists play significant roles in pelagic food webs as bacterivorous and herbivorous consumers. However, heterotrophic protists-unlike autotrophic ones-are often difficult to track since they tend to lack features such as photosynthetic pigments that allow for remote sensing or for bulk characterization. Difficulty in the identification of heterotrophic protists has often resulted in lumping them into broad groups, but there is a strong need to develop methods that increase the spatial and temporal resolution of observations applied to particular organisms in order to discover the drivers of population structure and ecological function. In surveys of small subunit rRNA, gene (SSU) sequences of microbial eukaryotes from the Columbia River to the Pacific Ocean, the heterotrophic flagellate Katablepharis sp. were found to dominate protist assemblages (including autotrophic and heterotrophic fractions) in the spring, prior to the freshet. We discovered a 332 base pair unique sequence element (USE) insertion in the large subunit rRNA gene (28S) that is not present in other katablepharids or in any other eukaryote. Using this USE, we were able to detect Katablepharis within mixed assemblages in river, estuarine, and oceanic samples and determine spatial and temporal patterns in absolute abundance through quantitative PCR and fluorescence in situ hybridization. Given their high abundance and repeatable temporal patterns of occurrence, we hypothesize that the Columbia River Estuary Katablepharis (Katablepharis CRE) plays an important role in estuarine biogeochemical and ecosystem function.

Original languageEnglish (US)
Pages (from-to)764-776
Number of pages13
JournalMicrobiologyOpen
Volume3
Issue number5
DOIs
StatePublished - Oct 1 2014

Fingerprint

Large Ribosome Subunits
Estuaries
Rivers
Eukaryota
rRNA Genes
Pacific Ocean
DNA Transposable Elements
Food Chain
Fluorescence In Situ Hybridization
Base Pairing
Ecosystem
Polymerase Chain Reaction
Population

Keywords

  • Columbia River coastal margin
  • Heterotrophic protist diversity
  • Katablepharis CRE
  • Unique sequence element

ASJC Scopus subject areas

  • Microbiology

Cite this

@article{6efd73d14bc34caab08b2e701b66c150,
title = "Discovery of a Katablepharis sp. in the Columbia River estuary that is abundant during the spring and bears a unique large ribosomal subunit sequence element",
abstract = "Heterotrophic protists play significant roles in pelagic food webs as bacterivorous and herbivorous consumers. However, heterotrophic protists-unlike autotrophic ones-are often difficult to track since they tend to lack features such as photosynthetic pigments that allow for remote sensing or for bulk characterization. Difficulty in the identification of heterotrophic protists has often resulted in lumping them into broad groups, but there is a strong need to develop methods that increase the spatial and temporal resolution of observations applied to particular organisms in order to discover the drivers of population structure and ecological function. In surveys of small subunit rRNA, gene (SSU) sequences of microbial eukaryotes from the Columbia River to the Pacific Ocean, the heterotrophic flagellate Katablepharis sp. were found to dominate protist assemblages (including autotrophic and heterotrophic fractions) in the spring, prior to the freshet. We discovered a 332 base pair unique sequence element (USE) insertion in the large subunit rRNA gene (28S) that is not present in other katablepharids or in any other eukaryote. Using this USE, we were able to detect Katablepharis within mixed assemblages in river, estuarine, and oceanic samples and determine spatial and temporal patterns in absolute abundance through quantitative PCR and fluorescence in situ hybridization. Given their high abundance and repeatable temporal patterns of occurrence, we hypothesize that the Columbia River Estuary Katablepharis (Katablepharis CRE) plays an important role in estuarine biogeochemical and ecosystem function.",
keywords = "Columbia River coastal margin, Heterotrophic protist diversity, Katablepharis CRE, Unique sequence element",
author = "Peter Kahn and Lydie Herfort and Tawnya Peterson and Peter Zuber",
year = "2014",
month = "10",
day = "1",
doi = "10.1002/mbo3.206",
language = "English (US)",
volume = "3",
pages = "764--776",
journal = "MicrobiologyOpen",
issn = "2045-8827",
publisher = "John Wiley and Sons Inc.",
number = "5",

}

TY - JOUR

T1 - Discovery of a Katablepharis sp. in the Columbia River estuary that is abundant during the spring and bears a unique large ribosomal subunit sequence element

AU - Kahn, Peter

AU - Herfort, Lydie

AU - Peterson, Tawnya

AU - Zuber, Peter

PY - 2014/10/1

Y1 - 2014/10/1

N2 - Heterotrophic protists play significant roles in pelagic food webs as bacterivorous and herbivorous consumers. However, heterotrophic protists-unlike autotrophic ones-are often difficult to track since they tend to lack features such as photosynthetic pigments that allow for remote sensing or for bulk characterization. Difficulty in the identification of heterotrophic protists has often resulted in lumping them into broad groups, but there is a strong need to develop methods that increase the spatial and temporal resolution of observations applied to particular organisms in order to discover the drivers of population structure and ecological function. In surveys of small subunit rRNA, gene (SSU) sequences of microbial eukaryotes from the Columbia River to the Pacific Ocean, the heterotrophic flagellate Katablepharis sp. were found to dominate protist assemblages (including autotrophic and heterotrophic fractions) in the spring, prior to the freshet. We discovered a 332 base pair unique sequence element (USE) insertion in the large subunit rRNA gene (28S) that is not present in other katablepharids or in any other eukaryote. Using this USE, we were able to detect Katablepharis within mixed assemblages in river, estuarine, and oceanic samples and determine spatial and temporal patterns in absolute abundance through quantitative PCR and fluorescence in situ hybridization. Given their high abundance and repeatable temporal patterns of occurrence, we hypothesize that the Columbia River Estuary Katablepharis (Katablepharis CRE) plays an important role in estuarine biogeochemical and ecosystem function.

AB - Heterotrophic protists play significant roles in pelagic food webs as bacterivorous and herbivorous consumers. However, heterotrophic protists-unlike autotrophic ones-are often difficult to track since they tend to lack features such as photosynthetic pigments that allow for remote sensing or for bulk characterization. Difficulty in the identification of heterotrophic protists has often resulted in lumping them into broad groups, but there is a strong need to develop methods that increase the spatial and temporal resolution of observations applied to particular organisms in order to discover the drivers of population structure and ecological function. In surveys of small subunit rRNA, gene (SSU) sequences of microbial eukaryotes from the Columbia River to the Pacific Ocean, the heterotrophic flagellate Katablepharis sp. were found to dominate protist assemblages (including autotrophic and heterotrophic fractions) in the spring, prior to the freshet. We discovered a 332 base pair unique sequence element (USE) insertion in the large subunit rRNA gene (28S) that is not present in other katablepharids or in any other eukaryote. Using this USE, we were able to detect Katablepharis within mixed assemblages in river, estuarine, and oceanic samples and determine spatial and temporal patterns in absolute abundance through quantitative PCR and fluorescence in situ hybridization. Given their high abundance and repeatable temporal patterns of occurrence, we hypothesize that the Columbia River Estuary Katablepharis (Katablepharis CRE) plays an important role in estuarine biogeochemical and ecosystem function.

KW - Columbia River coastal margin

KW - Heterotrophic protist diversity

KW - Katablepharis CRE

KW - Unique sequence element

UR - http://www.scopus.com/inward/record.url?scp=84907870576&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84907870576&partnerID=8YFLogxK

U2 - 10.1002/mbo3.206

DO - 10.1002/mbo3.206

M3 - Article

VL - 3

SP - 764

EP - 776

JO - MicrobiologyOpen

JF - MicrobiologyOpen

SN - 2045-8827

IS - 5

ER -