Revealing the impact of global mass bleaching on coral microbiome through 16S rRNA gene-based metagenomic analysis

Meenatchi, R.; Thinesh, Thangadurai; Brindangnanam, Pownraj; Hassan, Saqib; Kiran, George Seghal; Selvin, Joseph

doi:10.1016/j.micres.2019.126408

Cited by 8 publications

(5 citation statements)

References 32 publications

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“…Along with the large-scale application of high throughout sequences and metagenome techniques, literatures in characterization and variation of microbiota in ruminant animals increased explosively. [156][157][158][159][160] The rumen microbiota is very complex, and the diversity of ruminal microorganisms can be affected by diet composition, genetics and environmental factors. There are approximately 7000 bacterial species and 1500 archaeal species in the rumen.…”

Section: Introductionmentioning

confidence: 99%

Microbiota in viral infection and disease in humans and farm animals

Yuan

Hensley

Mahsoub

et al. 2020

Progress in Molecular Biology and Translational Science

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Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre -including this research content -immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

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Section: Introductionmentioning

confidence: 99%

Microbiota in viral infection and disease in humans and farm animals

Yuan

Hensley

Mahsoub

et al. 2020

Progress in Molecular Biology and Translational Science

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“…Each 16S rRNA gene sequence was classified using the RDP Classifier algorithm (https ://rdp.cme.msu.edu/) and compared to the SILVA ribosomal RNA gene database (version 132) using a confidence threshold of 70% 44 . Prokaryotic OTUs assigned to chloroplasts and mitochondria were removed, and the resulting sequences were used for final analysis 45 . Sequence data was deposited at the NCBI SRA archive (accession number PRJNA609530).…”

Section: Experimental Design the Experiments Were Conducted In The Ementioning

confidence: 99%

Regulating soil bacterial diversity, community structure and enzyme activity using residues from golden apple snails

Wang

Zhang

et al. 2020

Sci Rep

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It has been shown that the golden apple snail (GAS, Pomacea canaliculata), which is a serious agricultural pest in Southeast Asia, can provide a soil amendment for the reversal of soil acidification and degradation. However, the impact of GAS residue (i.e., crushed, whole GAS) on soil bacterial diversity and community structure remains largely unknown. Here, a greenhouse pot experiment was conducted and 16S rRNA gene sequencing was used to measure bacterial abundance and community structure in soils amended with GAS residue and lime. The results suggest that adding GAS residue resulted in a significant variation in soil pH and nutrients (all P < 0.05), and resulted in a slightly alkaline (pH = 7.28–7.75) and nutrient-enriched soil, with amendment of 2.5–100 g kg−1 GAS residue. Soil nutrients (i.e., NO3-N and TN) and TOC contents were increased (by 132–912%), and some soil exocellular enzyme activities were enhanced (by 2–98%) in GAS residue amended soil, with amendment of 1.0–100 g kg−1 GAS residue. Bacterial OTU richness was 19% greater at the 2.5 g kg−1 GAS residue treatment than the control, while it was 40% and 53% lower at 100 g kg−1 of GAS residue and 50 g kg−1 of lime amended soils, respectively. Firmicutes (15–35%) was the most abundant phylum while Bacterioidetes (1–6%) was the lowest abundant one in GAS residue amended soils. RDA results suggest that the contents of soil nutrients (i.e., NO3-N and TN) and soil TOC explained much more of the variations of bacterial community than pH in GAS residue amended soil. Overuse of GAS residue would induce an anaerobic soil environment and reduce bacterial OTU richness. Soil nutrients and TOC rather than pH might be the main factors that are responsible for the changes of bacterial OTU richness and bacterial community structure in GAS residue amended soil.

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“…Recently, the continuous development of metagenomics has provided a broader overview of microbial communities in the environment, particularly enabling the study of environment-independent microbial communities using 16S rRNA sequences (Pootakham et al, 2017). Next-generation sequencing technology (NGS) has been utilized to sequence and analyze the 16S rRNA gene of microbial communities in various coral species, aiming to assess microbial diversity and identify prevalent symbiotic taxa in different coral species (Meenatchi et al, 2020). Overall, while there is extensive research on bacteria, studies on archaea are relatively scarce.…”

Section: Introductionmentioning

confidence: 99%

Metagenomic characterization of archaeal and bacterial communities associated with coral, sediment, and seawater in a coral reef ecosystem of Phu Quoc island, Vietnam.

Phuong Thao,

Minh Ngoc,

Tra

et al. 2023

Vietnam J. Biotechnol.

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Recent advancements in metagenomics, particularly in the studies of conservative 16S rRNA sequences, have significantly accelerated our understanding of the relationship between corals and their associated microbial communities. While bacteria are known to be closely linked with corals, there is limited understanding of the connections between archaea and corals. Unlike previous 16S rRNA studies conducted in similar tropical coral reef ecosystems, we analyzed both the archaeal and bacterial communities associated with Acropora sp. and Lobophyllia sp. corals, as well as the surrounding sediment and water columns in Phu Quoc Island, Kien Giang Province, Vietnam. The data collected were sequenced using the 16S rRNA sequencing method and further analyzed using bioinformatics tools in the R programming language, employing DADA2 and phyloseq pipelines. We examined the compositions and diversity of bacteria and archaea in coral, sediment, and water column samples to establish potential connections between these two domains. The results revealed that archaea constituted a small percentage of all samples, averaging 3.18% in coral mucus and reaching an average of 7.49% in sediment samples. Among the most abundant archaeal taxa were Crenarchaeota and Nanoarchaeota, alongside bacterial taxa Gammabacteria, Cyanobacteria, and Desulfobacteria, which are associated with important metabolic processes within coral hosts. Alpha and beta diversity analyses confirmed the highest archaeal diversity in sediment samples and the distinct existence of microbial communities in each biotope. These findings complement our knowledge of archaea’s presence and potential roles in the coral-associated microbiome.

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Revealing the impact of global mass bleaching on coral microbiome through 16S rRNA gene-based metagenomic analysis

Cited by 8 publications

References 32 publications

Microbiota in viral infection and disease in humans and farm animals

Microbiota in viral infection and disease in humans and farm animals

Regulating soil bacterial diversity, community structure and enzyme activity using residues from golden apple snails

Metagenomic characterization of archaeal and bacterial communities associated with coral, sediment, and seawater in a coral reef ecosystem of Phu Quoc island, Vietnam.

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