Structural and functional diversity of free-living microorganisms in reef surface, Kra island, Thailand

Abstract

BackgroundCoral reefs worldwide are being harmed through anthropogenic activities. Some coral reefs in Thailand remain well-preserved, including the shallow coral reefs along Kra island, Nakhon Si Thammarat province. Interestingly, the microbial community in this environment remains unknown. The present study identified biodiversity of prokaryotes and eukaryotes of 0.22-30 μm in sizes and their metabolic potentials in this coral reef surface in summer and winter seasons, using 16S and 18S rRNA genes pyrosequencing.ResultsThe marine microbial profiles in summer and winter seasons comprised mainly of bacteria, in phylum, particular the Proteobacteria. Yet, different bacterial and eukaryotic structures existed between summer and winter seasons, supported by low Lennon and Yue & Clayton theta similarity indices (8.48-10.43% for 16S rRNA, 0.32-7.81% for 18S rRNA ). The topmost prokaryotic phylum for the summer was Proteobacteria (99.68%), while for the winter Proteobacteria (62.49%) and Bacteroidetes (35.88%) were the most prevalent. Uncultured bacteria in phyla Cyanobacteria, Planctomycetes, SAR406 and SBR1093 were absent in the summer. For eukaryotic profiles, species belonging to animals predominated in the summer, correlating with high animal activities in the summer, whereas dormancy and sporulation predominated in the winter. For the winter, eukaryotic plant species predominated and several diverse species were detected. Moreover, comparison of our prokaryotic databases in summer and winter of Kra reef surface against worldwide marine culture-independent prokaryotic databases indicated our databases to most resemblance those of coastal Sichang island, Chonburi province, Thailand, and the 3 tropical GOS sites close to Galapagos island (GS039, GS040 and GS045), in orderly.ConclusionsThe study investigated and obtained culture-independent databases for marine prokaryotes and eukaryotes in summer and winter seasons of Kra reef surface. The data helped understand seasonal dynamics of microbial structures and metabolic potentials of this tropical ecosystem, supporting the knowledge of the world marine microbial biodiversity.

Bacterial community composition and distribution in different segments of the gastrointestinal tract of wild-caught adultPenaeus monodon

“…The results from the present experiment suggested that the large presence of Gram‐positive bacteria was in the middle intestine area of the GI tract. Since Firmicutes is not typically found in large abundance in aquaculture rearing water or natural marine environment (Johnson et al., ; Kawahara, Shigematsu, Miyadai & Kondo, ; Mills et al., ; Somboonna et al., ), it is possible that the host might exert selective pressure to attract these Firmicutes bacteria in the midgut. The examples in this area are rather scarce for shrimp.…”

Marine Bacterial Diversity in Coastal Sichang Island, the Upper Gulf of Thailand, in 2011 Wet Season

“…High water level in a wet season lowers concentration and availability of nutrients for marine microorganisms and organisms. Global ocean microbiome researches reported temperature and seasons as factors for changes of microbial structures, in open oceans and coral reefs (Gilbert et al, 2012;Somboonna et al, 2014;Campbell et al, 2015;Bulan et al, 2018); yet seasonal dynamics of microbial structures in coastal marine sites of the Gulf of Thailand remain limited. This study thereby described the Sichang coastal water microbiota in one period (July 2011) in a wet season of TW and TP (abbreviated TW-wet and TP-wet), and compared with our previous reports of dry season of TW and TP (abbreviated TW and TP) of the same corresponding year and analysis methods, metagenomics derived 16S rRNA gene sequencing (Somboonna et al, 2012).…”

Microbial and Small Eukaryotes Associated With Reefs in the Upper Gulf of Thailand

“…F-RISA measures a DNA length that is characteristic for fungal species, so different communities yield different combinations of lengths (Ranjard et al, 2001;Gillevet et al, 2009). The next generation sequencing (NGS) provides more power to detect and identify natural microbial diversity, without limitations due to media or other conditions associated with laboratory cultures (Riesenfeld et al, 2004;Rusch et al, 2007;Somboonna et al, 2014;Mahé et al, 2015;Khitmoh et al, 2017). Our study primarily characterized and compared the eukaryotic assemblages of the prevalent coral species at the three sites (Porites lutea, Platygyra sinensis, Acropora humilis and Acropora millepora), and the surrounding niches (sediment and seawater) during the wet and dry seasons in 1 year ( Figure 1A).…”