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A Newly Designed Primer Revealed High Phylogenetic Diversity of Endozoicomonas in Coral Reefs.
- Source :
-
Microbes and environments [Microbes Environ] 2018 Jul 04; Vol. 33 (2), pp. 172-185. Date of Electronic Publication: 2018 May 12. - Publication Year :
- 2018
-
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.
- Subjects :
- Animals
Anthozoa classification
Anthozoa genetics
DNA, Bacterial genetics
Gammaproteobacteria genetics
Gammaproteobacteria physiology
Japan
RNA, Ribosomal, 16S genetics
Sequence Analysis, DNA
Species Specificity
Symbiosis
Taiwan
Anthozoa microbiology
Biodiversity
Coral Reefs
Gammaproteobacteria classification
Phylogeny
Seawater microbiology
Subjects
Details
- Language :
- English
- ISSN :
- 1347-4405
- Volume :
- 33
- Issue :
- 2
- Database :
- MEDLINE
- Journal :
- Microbes and environments
- Publication Type :
- Academic Journal
- Accession number :
- 29760298
- Full Text :
- https://doi.org/10.1264/jsme2.ME18054