title: PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology.
abstract: Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease.
authors.affiliation: U.S. Geological Survey, 600 4th Street S., St. Petersburg, FL 33701, USA. ckellogg@usgs.gov
authors.forename: Christina A
authors.initials: CA
authors.lastname: Kellogg
authors.forename: Yvette M
authors.initials: YM
authors.lastname: Piceno
authors.forename: Lauren M
authors.initials: LM
authors.lastname: Tom
authors.forename: Todd Z
authors.initials: TZ
authors.lastname: DeSantis
authors.forename: David G
authors.initials: DG
authors.lastname: Zawada
authors.forename: Gary L
authors.initials: GL
authors.lastname: Andersen
mesh_terms: D053000:Analytic Sample Preparation Methods / Q000379:methods*; D000818:Animals; D037421:Anthozoa / Q000382:microbiology*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D044822:Biodiversity; D004269:DNA, Bacterial / Q000235:genetics; D017753:Ecosystem; D020411:Oligonucleotide Array Sequence Analysis; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S