Metagenomic insights into zooplankton-associated bacterial communities

Daniele De Corte*, Abhishek Srivastava, Marja Koski, Juan Antonio L Garcia, Yoshihiro Takaki, Taichi Yokokawa, Takuro Nunoura, Nathalie H. Elisabeth, Eva Sintes, Gerhard J. Herndl

*Corresponding author for this work

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Abstract

Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton-associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton-associated bacterial community is able to colonize the zooplankton's internal and external surfaces by using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton-associated microbiome suggests that this zooplankton-associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters. This article is protected by copyright. All rights reserved.
Original languageEnglish
JournalEnvironmental Microbiology
Volume20
Issue number2
Pages (from-to)492-405
ISSN1462-2912
DOIs
Publication statusPublished - 2018

Keywords

  • Atlantic Ocean
  • Illumina sequencing
  • Metagenome
  • Microbes
  • Oligotypes
  • Zooplankton

Cite this

De Corte, D., Srivastava, A., Koski, M., Garcia, J. A. L., Takaki, Y., Yokokawa, T., ... Herndl, G. J. (2018). Metagenomic insights into zooplankton-associated bacterial communities. Environmental Microbiology, 20(2), 492-405. https://doi.org/10.1111/1462-2920.13944
De Corte, Daniele ; Srivastava, Abhishek ; Koski, Marja ; Garcia, Juan Antonio L ; Takaki, Yoshihiro ; Yokokawa, Taichi ; Nunoura, Takuro ; Elisabeth, Nathalie H. ; Sintes, Eva ; Herndl, Gerhard J. / Metagenomic insights into zooplankton-associated bacterial communities. In: Environmental Microbiology. 2018 ; Vol. 20, No. 2. pp. 492-405.
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abstract = "Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton-associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton-associated bacterial community is able to colonize the zooplankton's internal and external surfaces by using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton-associated microbiome suggests that this zooplankton-associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters. This article is protected by copyright. All rights reserved.",
keywords = "Atlantic Ocean, Illumina sequencing, Metagenome, Microbes, Oligotypes, Zooplankton",
author = "{De Corte}, Daniele and Abhishek Srivastava and Marja Koski and Garcia, {Juan Antonio L} and Yoshihiro Takaki and Taichi Yokokawa and Takuro Nunoura and Elisabeth, {Nathalie H.} and Eva Sintes and Herndl, {Gerhard J.}",
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De Corte, D, Srivastava, A, Koski, M, Garcia, JAL, Takaki, Y, Yokokawa, T, Nunoura, T, Elisabeth, NH, Sintes, E & Herndl, GJ 2018, 'Metagenomic insights into zooplankton-associated bacterial communities', Environmental Microbiology, vol. 20, no. 2, pp. 492-405. https://doi.org/10.1111/1462-2920.13944

Metagenomic insights into zooplankton-associated bacterial communities. / De Corte, Daniele; Srivastava, Abhishek; Koski, Marja; Garcia, Juan Antonio L; Takaki, Yoshihiro; Yokokawa, Taichi; Nunoura, Takuro; Elisabeth, Nathalie H.; Sintes, Eva; Herndl, Gerhard J.

In: Environmental Microbiology, Vol. 20, No. 2, 2018, p. 492-405.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Metagenomic insights into zooplankton-associated bacterial communities

AU - De Corte, Daniele

AU - Srivastava, Abhishek

AU - Koski, Marja

AU - Garcia, Juan Antonio L

AU - Takaki, Yoshihiro

AU - Yokokawa, Taichi

AU - Nunoura, Takuro

AU - Elisabeth, Nathalie H.

AU - Sintes, Eva

AU - Herndl, Gerhard J.

PY - 2018

Y1 - 2018

N2 - Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton-associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton-associated bacterial community is able to colonize the zooplankton's internal and external surfaces by using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton-associated microbiome suggests that this zooplankton-associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters. This article is protected by copyright. All rights reserved.

AB - Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton-associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton-associated bacterial community is able to colonize the zooplankton's internal and external surfaces by using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton-associated microbiome suggests that this zooplankton-associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters. This article is protected by copyright. All rights reserved.

KW - Atlantic Ocean

KW - Illumina sequencing

KW - Metagenome

KW - Microbes

KW - Oligotypes

KW - Zooplankton

U2 - 10.1111/1462-2920.13944

DO - 10.1111/1462-2920.13944

M3 - Journal article

C2 - 28967193

VL - 20

SP - 492

EP - 405

JO - Environmental Microbiology

JF - Environmental Microbiology

SN - 1462-2912

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ER -