Taxonomic profiling of Symbiodiniaceae and bacterial communities associated with Indo-Pacific corals in the Gulf of Thailand using PacBio sequencing of full-length ITS and 16S rRNA genes

Pootakham, Wirulda; Mhuantong, Wuttichai; Yoocha, Thippawan; Sangsrakru, Duangjai; Kongkachana, Wasitthee; Sonthirod, Chutima; Naktang, Chaiwat; Jomchai, Nukoon; U‐thoomporn, Sonicha; Yeemin, Thammasak; Pengsakun, Sittiporn; Sutthacheep, Makamas; Tangphatsornruang, Sithichoke

doi:10.1016/j.ygeno.2021.06.001

Cited by 19 publications

(15 citation statements)

References 92 publications

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“…The high-quality libraries were sequenced on the PacBio Sequel platform. The quality filter, cluster, and analysis for 16S rRNA and internally transcribed spacer (ITS) sequencing data were performed as described by Chen et al (2020b) and Pootakham et al (2021) . The data were analyzed on Novogene Magic Platform.…”

Section: Methodsmentioning

confidence: 99%

Effects of Phenyllactic Acid, Lactic Acid Bacteria, and Their Mixture on Fermentation Characteristics and Microbial Community Composition of Timothy Silage

Zhao

et al. 2021

Front. Microbiol.

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This study investigated the effects of phenyllactic acid (PL), lactic acid bacteria (LAB), and their mixture on fermentation characteristics and microbial community composition of timothy silage. Timothy silages were treated without (CK) or with PL [10 mg/kg fresh matter (FM) basis], LAB inoculant (IN; a mixture of Lactobacillus plantarum and L.buchneri, 105 cfu/g FM), and their mixture (PI) and stored at ambient temperature (5°C∼15°C) in a dark room for 60 days. Compared with CK, all treated silages showed lower (P < 0.05) levels of butyric acid and ammonia-N. Treatment with PL enhanced (P < 0.05) the crude protein preservation of silage by favoring the growth of L. curvatus and Saccharomyces cerevisiae and inhibition of lactic acid–assimilating yeast belonging to Issatchenkia during ensiling. In particular, treatment with PL advanced (P < 0.05) the productions of lactic acid and volatile fatty acid in IN-treated silage. Therefore, PL used as a new additive exhibited potential for improving silage fermentation when it is combined with LAB IN during ensiling.

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Section: Methodsmentioning

confidence: 99%

Effects of Phenyllactic Acid, Lactic Acid Bacteria, and Their Mixture on Fermentation Characteristics and Microbial Community Composition of Timothy Silage

Zhao

et al. 2021

Front. Microbiol.

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“…The specific primers itsintfor2 (5′-GAATTGCAGAACTCCGTG-3′) and ITS2 reverse (5′-GGGATCCATATGCTAAGTTCAGCGGGT-3′) were used to for amplifying the ITS variable region of Symbiodiniaceae rRNA gene ( Grottoli et al, 2004 ). The bacterial full-length 16S rRNA gene was amplified using primers 27 f (5′-AGGRGTTYGATYMTGGCTCAG-3′) and 1492 R (5′-RGYTACCTTGTTACGACTT-3′; Pootakham et al, 2021 ). PCR amplification was performed using GeneAmp® 9700 thermal cycle controller (Thermo Fisher Scientific, United States) under the following conditions: 95°C for 30 s, followed by 35 cycles of 95°C for 10 s, 60°C for 30 s, 72°C for 45 s, and a final extension at 72°C for 10 min.…”

Section: Methodsmentioning

confidence: 99%

Adaptive changes of coral Galaxea fascicularis holobiont in response to nearshore stress

Zhu

Liu

et al. 2022

Front. Microbiol.

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Global change and local stressors are simultaneously affecting the nearshore corals, and microbiome flexibility may assist corals in thriving under such multiple stressors. Here, we investigated the effects of various environmental variables on Galaxea fascicularis holobiont from nearshore and offshore reefs. These nearshore reefs were more turbid, eutrophic, and warm than offshore reefs. However, coral physiological parameters did not differ significantly. Corals under stressful nearshore environments had low symbiont diversity and selected more tolerant Symbiodiniaceae. The bacterial diversity of offshore corals was significantly higher, and their community composition varied obviously. Diffusion limitations and environmental heterogeneity were essential in structuring microbial communities. Functional annotation analysis demonstrated significant differences between nearshore and offshore corals in bacterial functional groups. Environmental stress significantly reduced the complexity and connectivity of bacterial networks, and the abundances of keystone taxa altered considerably. These results indicated that corals could thrive nearshore through holobiont plasticity to cope with multiple environmental stresses.

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“…The effective reads were clustered into operational taxonomic units (OTUs) at 97% similarity level according to Tindall et al (2010) and Pootakham et al (2021) by USEARCH ( Edgar, 2010 ). The RDP Classifier ( Wang et al, 2007 ) was used to classify representative sequences of each OTU into different taxonomic groups based on the Silva database (release 138) ( Quast et al, 2012 ).…”

Section: Methodsmentioning

confidence: 99%

Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts

Hui

Wang

Cheng

et al. 2022

PeerJ

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Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R2 = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization.

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Taxonomic profiling of Symbiodiniaceae and bacterial communities associated with Indo-Pacific corals in the Gulf of Thailand using PacBio sequencing of full-length ITS and 16S rRNA genes

Cited by 19 publications

References 92 publications

Effects of Phenyllactic Acid, Lactic Acid Bacteria, and Their Mixture on Fermentation Characteristics and Microbial Community Composition of Timothy Silage

Effects of Phenyllactic Acid, Lactic Acid Bacteria, and Their Mixture on Fermentation Characteristics and Microbial Community Composition of Timothy Silage

Adaptive changes of coral Galaxea fascicularis holobiont in response to nearshore stress

Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts

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