A newly designed primer revealed high phylogenetic diversity of endozoicomonas in coral reefs

Jia Ho Shiu, Jiun Yan Ding, Ching Hung Tseng, Shueh Ping Lou, Takuma Mezaki, Yu Ting Wu, Hsiang Iu Wang, Sen Lin Tang

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Endozoicomonas bacteria are commonly regarded as having a potentially symbiotic relationship with their coral hosts. However, their diversity and phylogeny in samples collected from various sources remain unclear. Therefore, we designed an Endozoicomonas-specific primer paired with a bacterial universal primer to detect the 16S ribosomal RNA (rRNA) genes of this taxon and conducted an in-depth investigation of the Endozoicomonas community structure in reef-building corals. The primer had high specificity in the V3–V4 region (95.6%) and its sensitivity was high, particularly when Endozoicomonas was rare in samples (e.g., in seawater, which had a higher alpha diversity of Endozoicomonas than corals). In coral samples, predominant V3–V4 ribotypes had greater divergence than predominant V1–V2 ribotypes, and were grouped into at least 9 novel clades in a phylogenetic tree, indicating Endozoicomonas had high phylogenetic diversity. Divergence within this genus was potentially higher than that among 7 outgroup genera based on the phylogenetic distances of partial 16S rDNA sequences, suggesting that the taxonomy of this genus needs to be revised. In conclusion, dominant Endozoicomonas populations had variable phylogenies; furthermore, the newly designed primers may be useful molecular tools for the reliable detection of the Endozoicomonas community in marine environments.

Original languageEnglish
Pages (from-to)172-185
Number of pages14
JournalMicrobes and Environments
Volume33
Issue number2
DOIs
Publication statusPublished - 2018 Jan 1

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coral reefs
coral reef
coral
corals
phylogenetics
phylogeny
ribotypes
divergence
marine environment
community structure
reef
sampling
seawater
reefs
bacterium
gene
taxonomy
bacteria
genes

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Soil Science
  • Plant Science

Cite this

Shiu, Jia Ho ; Ding, Jiun Yan ; Tseng, Ching Hung ; Lou, Shueh Ping ; Mezaki, Takuma ; Wu, Yu Ting ; Wang, Hsiang Iu ; Tang, Sen Lin. / A newly designed primer revealed high phylogenetic diversity of endozoicomonas in coral reefs. In: Microbes and Environments. 2018 ; Vol. 33, No. 2. pp. 172-185.
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Shiu, JH, Ding, JY, Tseng, CH, Lou, SP, Mezaki, T, Wu, YT, Wang, HI & Tang, SL 2018, 'A newly designed primer revealed high phylogenetic diversity of endozoicomonas in coral reefs', Microbes and Environments, vol. 33, no. 2, pp. 172-185. https://doi.org/10.1264/jsme2.ME18054

A newly designed primer revealed high phylogenetic diversity of endozoicomonas in coral reefs. / Shiu, Jia Ho; Ding, Jiun Yan; Tseng, Ching Hung; Lou, Shueh Ping; Mezaki, Takuma; Wu, Yu Ting; Wang, Hsiang Iu; Tang, Sen Lin.

In: Microbes and Environments, Vol. 33, No. 2, 01.01.2018, p. 172-185.

Research output: Contribution to journalArticle

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