Stability of temperate coral <em>Astrangia poculata</em> microbiome is reflected across different sequencing methodologies

Dawn B. Goldsmith; Zoe A. Pratte; Christina A. Kellogg; Sara E. Snader; Koty H. Sharp; Dawn B. Goldsmith; Zoe A. Pratte; Christina A. Kellogg; Sara E. Snader; Koty H. Sharp

doi:10.3934/microbiol.2019.1.62

AIMS Microbiology

2019, Volume 5, Issue 1: 62-76. doi: 10.3934/microbiol.2019.1.62

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Research article

Stability of temperate coral Astrangia poculata microbiome is reflected across different sequencing methodologies

1.
St. Petersburg Coastal and Marine Science Center, U.S. Geological Survey, St. Petersburg, FL 33701, USA
2.
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
3.
Cherokee Nation Technologies, contracted to U.S. Geological Survey, St. Petersburg, FL 33701, USA
4.
Department of Biology, Marine Biology and Environmental Science, Roger Williams University, Bristol, RI 02809, USA

Received: 28 November 2018 Accepted: 21 February 2019 Published: 01 March 2019

The microbiome of the temperate coral Astrangia poculata was first described in 2017 using next-generation Illumina sequencing to examine the coral’s bacterial and archaeal associates across seasons and among hosts of differing symbiotic status. To assess the impact of methodology on the detectable diversity of the coral’s microbiome, we obtained near full-length Sanger sequences from clone libraries constructed from a subset of the same A. poculata samples. Eight samples were analyzed: two sets of paired symbiotic (brown) and aposymbiotic (white) colonies collected in the fall (September) and two sets collected in the spring (April). Analysis of the Sanger sequences revealed that the microbiome of A. poculata exhibited a high level of richness; 806 OTUs were identified among 1390 bacterial sequences. While the Illumina study revealed that A. poculata’s microbial communities did not significantly vary according to symbiotic state, but did vary by season, Sanger sequencing did not expose seasonal or symbiotic differences in the microbiomes. Proteobacteria dominated the microbiome, forming the majority (55% to 80%) of classifiable bacteria in every sample, and the five bacterial classes with the highest mean relative portion (5% to 35%) were the same as those determined by prior Illumina sequencing. Sanger sequencing also captured the same core taxa previously identified by next-generation sequencing. Alignment of all sequences and construction of a phylogenetic tree revealed that both sequencing methods provided similar portrayals of the phylogenetic diversity within A. poculata’s bacterial associates. Consistent with previous findings, the results demonstrated that the Astrangia microbiome is stable notwithstanding the choice of sequencing method and the far fewer sequences generated by clone libraries (46 to 326 sequences per sample) compared to next-generation sequencing (3634 to 48481 sequences per sample). Moreover, the near-full length 16S rRNA sequences produced by this study are presented as a resource for the community studying this model system since they provide necessary information for designing primers and probes to further our understanding of this coral’s microbiome.
- Astrangia poculata,
- coral,
- microbiome,
- bacteria,
- archaea,
- microbes,
- clone library,
- Sanger sequencing,
- 16S rRNA
Citation: Dawn B. Goldsmith, Zoe A. Pratte, Christina A. Kellogg, Sara E. Snader, Koty H. Sharp. Stability of temperate coral Astrangia poculata microbiome is reflected across different sequencing methodologies[J]. AIMS Microbiology, 2019, 5(1): 62-76. doi: 10.3934/microbiol.2019.1.62

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Abstract

The microbiome of the temperate coral Astrangia poculata was first described in 2017 using next-generation Illumina sequencing to examine the coral’s bacterial and archaeal associates across seasons and among hosts of differing symbiotic status. To assess the impact of methodology on the detectable diversity of the coral’s microbiome, we obtained near full-length Sanger sequences from clone libraries constructed from a subset of the same A. poculata samples. Eight samples were analyzed: two sets of paired symbiotic (brown) and aposymbiotic (white) colonies collected in the fall (September) and two sets collected in the spring (April). Analysis of the Sanger sequences revealed that the microbiome of A. poculata exhibited a high level of richness; 806 OTUs were identified among 1390 bacterial sequences. While the Illumina study revealed that A. poculata’s microbial communities did not significantly vary according to symbiotic state, but did vary by season, Sanger sequencing did not expose seasonal or symbiotic differences in the microbiomes. Proteobacteria dominated the microbiome, forming the majority (55% to 80%) of classifiable bacteria in every sample, and the five bacterial classes with the highest mean relative portion (5% to 35%) were the same as those determined by prior Illumina sequencing. Sanger sequencing also captured the same core taxa previously identified by next-generation sequencing. Alignment of all sequences and construction of a phylogenetic tree revealed that both sequencing methods provided similar portrayals of the phylogenetic diversity within A. poculata’s bacterial associates. Consistent with previous findings, the results demonstrated that the Astrangia microbiome is stable notwithstanding the choice of sequencing method and the far fewer sequences generated by clone libraries (46 to 326 sequences per sample) compared to next-generation sequencing (3634 to 48481 sequences per sample). Moreover, the near-full length 16S rRNA sequences produced by this study are presented as a resource for the community studying this model system since they provide necessary information for designing primers and probes to further our understanding of this coral’s microbiome.

Acknowledgments

The annual Astrangia workshop at Roger Williams University, co-convened by K. Sharp, R. Rotjan, and S. Grace, was funded by RWU and Southern Connecticut State University. The workshop fostered creative conversations and collaborations leading to this work. The authors thank Sarah Schmid for lab assistance. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. government.

Conflict of interest

All authors declare no conflicts of interest in this paper.

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