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

Bulan, Dewi Embong; Wilantho, Alisa; Tongsima, Sissades; Viyakarn, Voranop; Chavanich, Suchana; Somboonna, Naraporn

doi:10.3389/fmars.2018.00436

Cited by 9 publications

(6 citation statements)

References 22 publications

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“…Overall, our findings suggested that there are alterations of coral microbiome during bleached events, with the specific pattern of changes related to each coral examined. Increases of Vibrionales, Alteromonadales, and Rhizobiales were previously reported in stressed corals (Bulan et al, 2018b;Tout et al, 2015;McDevitt-Irwin et al, 2017). Vibrionales were previously reported to increase following a rise in seawater temperature, and some species of this bacterial order may act as coral pathogens (Kushmaro et al, 1998;Bulan et al, 2018a;Tout et al, 2015).…”

Section: Discussionmentioning

confidence: 81%

Microbiomes of Healthy and Bleached Corals During a 2016 Thermal Bleaching Event in the Upper Gulf of Thailand

et al. 2021

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Global warming has caused elevated seawater temperature and coral bleaching, including events on shallow reefs in the upper Gulf of Thailand (uGoT). Previous studies have reported an association between loss of zooxanthellae and coral bleaching. However, studies on the microbial diversity of prokaryotes and eukaryotes (microbiome) as coral holobionts are also important and this information is still limited in the uGoT. To address this shortcoming, this report provided baseline information on the prokaryotic (bacteria and archaea) and eukaryotic microbes of healthy and bleached colonies of four prevalent corals Acropora humilis, Acropora millepora, Platygyra sinensis, and Porites lutea and surrounding seawater and sediments, using 16S and 18S rRNA gene next-generation sequencing. Both prokaryotic and eukaryotic microbes showed isolated community profiles among sample types (corals, sediment, and seawater) (ANOSIM: P < 0.001, R = 0.51 for prokaryotic profiles and P < 0.001, R = 0.985 for eukaryotic microbe profiles). Among coral species, P. sinensis showed the most diverse prokaryotic community compared with the others (ANOSIM: P < 0.001, R = 0.636), and P. lutea showed the most diverse eukaryotic microbes (P = 0.014, R = 0.346). Healthy and bleached corals had some different microbiomes in species and their prevalences. For instance, the significant increase of Alphaproteobacteria in P. sinensis resulted in reduced prokaryotic community evenness and altered potential metabolic profiles (i.e., increased amino acid metabolism and genetic information processing and transcription, but decreased prokaryotic functions in cell motility, signaling, and transduction). For eukaryotic microbes, the loss of the algal Symbiodinium (colloquially known as zooxanthellae) in bleached corals such as P. lutea resulted in increased Chromista and Protista and, hence, clearly distinct eukaryotic microbe (including fungi) communities in healthy vs. bleached colonies of corals. Bleached corals were enriched in bacterial pathogens (e.g., Acinetobacter, Helicobacter, Malassesia, and Aspergillus) and decreased coral-beneficial prokaryotic and eukaryotic microbes (e.g., Rhizobiales and Symbiodinium). Additionally, this study identified microbiome species in bleached P. lutea that might help bleaching recovery (e.g., high abundance of Rhizobiales, Oceanospirillales, Flavobacteriales, and Alteromonadales). Overall, our coral-associated microbiome analyses identified altered diversity patterns of bacteria, archaea, fungi, and eukaryotic microbes between healthy and bleached coral species that are prevalent in the uGoT. This knowledge supports our ongoing efforts to manipulate microbial diversity as a means of reducing the negative impacts of thermal bleaching events in corals inhabiting the uGoT.

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Section: Discussionmentioning

confidence: 81%

Microbiomes of Healthy and Bleached Corals During a 2016 Thermal Bleaching Event in the Upper Gulf of Thailand

et al. 2021

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“…Tropical coral reefs are highly diverse ecosystems in which complex environments provide diverse habitats and niches over time and space [1,2]. Microbial communities, including bacteria, microbial eukaryotes (fungi), and small eukaryotes, play an important role in nutrient cycling in coral reef ecosystems, encompassing many pelagic and benthic processes [3][4][5][6][7][8]. Vertical community stratification caused by redox gradients enables highly diverse microbial communities in coral reef sediments [9].…”

Section: Introductionmentioning

confidence: 99%

Microbial Community Diversity of Coral Reef Sediments on Liuqiu Island, Southwestern Taiwan

Wang¹,

Liu²

2023

JMSE

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Microbes in coral reef sediments are thought to play an important role in organic matter remineralization and nutrient recycling. Microbial communities also reflect the environmental conditions, such as nutrient status, of an ecosystem. This study investigates the relationship between microbial community diversity in the reef sediments and environmental conditions at Liuqiu Island. We sampled sediments seasonally from four sites around the island, Beauty Cave, Geban Bay, Houshi Fringing Reef, and Lobster Cave, from 2015–2020. The V5–V6 hypervariable region of 16S rRNA was amplified and sequenced using the Illumina MiSeq platform to identify the microbial communities. The results showed that the high abundance of Pseudomonadota, Planctomycetota, and Bacteroidota might reflect the eutrophic environments of the sediments on Liuqiu Island. Second, the identification of putative pathogens and human-related genera suggests that human activities have affected the marine environment of Liuqiu Island. Third, the insignificant spatial differences and the significant temporal differences in the microbial communities of Liuqiu Island indicate that annual or periodical events, such as the Kuroshio Branch Current and South China Sea Surface Current, could shape the microbial communities of Liuqiu Island. Furthermore, the abundance of human-related genera—Cutibacterium, Herbaspirillum, Corynebacterium 1, Escherichia-Shigella, and Kocuria—increased dramatically in the Lobster Cave site in September 2015 and may have been induced by a strong climate event, such as a typhoon or heavy rainfall. Our results revealed that the microbial communities of Liuqiu Island are dynamic and sensitive to adjacent environmental conditions. The sedimented microbial communities could monitor the bacteria and pathogens related to human activities and even reveal the putative events that could affect the ecological environments.

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“…Eukaryotes play critical roles in ecosystem processes by decomposing organic material (e.g., decomposition processes by fungi in soil) (Baldrian et al, 2012), predating on other microbes, or producing organic compounds from inorganic compounds (Bik et al, 2012;Bulan et al, 2018;Lind & Pollard, 2021;West, Probst, Grigoriev, Thomas, & Banfield, 2018). An estimated 8.7 million eukaryotic species inhabit our planet (Sweetlove, 2011), but as of 4 th January 2022, only slightly more than 54000 eukaryotic reference genomes exist in RefSeq (O'Leary et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Recovery of 447 Eukaryotic bins reveals major challenges for Eukaryote genome reconstruction from metagenomes

Saraiva

Bartholomäus

Toscan

et al. 2022

Preprint

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An estimated 8.7 million eukaryotic species exist on our planet. However, recent tools for taxonomic classification of eukaryotes only dispose of 734 reference genomes. As most Eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recover Prokaryotic genomes have become common in genome biology, few studies have tackled the recovery of Eukaryotic genomes from metagenomes. This study assessed the reconstruction of Eukaryotic genomes using 215 metagenomes from diverse environments using the EukRep pipeline. We obtained 447 eukaryotic bins from 15 classes (e.g., Saccharomycetes, Sordariomycetes, and Mamiellophyceae) and 16 orders (e.g., Mamiellales, Saccharomycetales, and Hypocreales). More than 73% of the obtained eukaryotic bins were recovered from samples whose biomes were classified as host-associated, aquatic and anthropogenic terrestrial. However, only 93 bins showed taxonomic classification to (9 unique) genera and 17 bins to (6 unique) species. A total of 193 bins contained completeness and contamination measures. Average completeness and contamination were 44.64% (σ=27.41%) and 3.97% (σ=6.53%), respectively. Micromonas commoda was the most frequent taxa found while Saccharomyces cerevisiae presented the highest completeness, possibly resulting from a more significant number of reference genomes. However, mapping eukaryotic bins to the chromosomes of the reference genomes suggests that completeness measures should consider both single-copy genes and chromosome coverage. Recovering eukaryotic genomes will benefit significantly from long-read sequencing, intron removal after assembly, and improved reference genomes databases.

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

Cited by 9 publications

References 22 publications

Microbiomes of Healthy and Bleached Corals During a 2016 Thermal Bleaching Event in the Upper Gulf of Thailand

Microbiomes of Healthy and Bleached Corals During a 2016 Thermal Bleaching Event in the Upper Gulf of Thailand

Microbial Community Diversity of Coral Reef Sediments on Liuqiu Island, Southwestern Taiwan

Recovery of 447 Eukaryotic bins reveals major challenges for Eukaryote genome reconstruction from metagenomes

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