Microbiome community and complexity indicate environmental gradient acclimatisation and potential microbial interaction of endemic coral holobionts in the South China Sea

Chen, Biao; Yu, Kefu; Liao, Zhiheng; Yu, Xiaopeng; Qin, Zhenjun; Liang, Jiayuan; Wang, Guanghua; Wu, Qian; Jiang, Leilei

doi:10.1016/j.scitotenv.2020.142690

Cited by 36 publications

(20 citation statements)

References 105 publications

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“…Only two operational taxonomic units (OTUs) (GU319135 and MT858037) were retrieved from the standard nucleotide database. SRA datasets for seawater and algae (Mei et al, 2019), sediment (Zhang et al, 2017;Ghate et al, 2021), coral and coral reefs (Liang et al, 2017;Pearman et al, 2019;Chen et al, 2021), and sponge (Baquiran and Conaco, 2018;Wu et al, 2018) were blasted, and the results indicated that strain M133 T allied reads were occasionally detected in the datasets of the Red Sea coral reef (PRJNA479721) and the Weizhou Island coral P. lutea (PRJNA786650). This occasional appearance of strain M133 T allied reads in high throughput sequencing datasets indicated that these bacteria do exist in related environments, but are usually not detected.…”

Section: Acidobacteria-animal Interactionmentioning

confidence: 99%

Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov.

Wang

Liu

et al. 2022

Front. Microbiol.

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Members of the phylum Acidobacteria are ubiquitous in various environments. Soil acidobacteria have been reported to present a variety of strategies for their success in terrestrial environments. However, owing to lack of pure culture, information on animal-associated acidobacteria are limited, except for those obtained from 16S rRNA genes. To date, only two acidobacteria have been isolated from animals, namely strain M133T obtained from coral Porites lutea and Acanthopleuribacter pedis KCTC 12899T isolated from chiton. Genomics and physiological characteristics of strain M133T and A. pedis KCTC 12899T were compared with 19 other isolates (one strain from each genus) in the phylum Acidobacteria. The results revealed that strain M133T represents a new species in a new genus in the family Acanthopleuribacteraceae. To date, these two Acanthopleuribacteraceae isolates have the largest genomes (10.85–11.79 Mb) in the phylum Acidobacteria. Horizontal gene transfer and gene duplication influenced the structure and plasticity of these large genomes. Dissimilatory nitrate reduction and abundant secondary metabolite biosynthetic gene clusters (including eicosapentaenoic acid de novo biosynthesis) are two distinct features of the Acanthopleuribacteraceae bacteria in the phylum Acidobacteria. The absence of glycoside hydrolases involved in plant polysaccharide degradation and presence of animal disease-related peptidases indicate that these bacteria have evolved to adapt to the animal hosts. In addition to low- and high-affinity respiratory oxygen reductases, enzymes for nitrate to nitrogen, and sulfhydrogenase were also detected in strain M133T, suggesting the capacity and flexibility to grow in aerobic and anaerobic environments. This study highlighted the differences in genome structure, carbohydrate and protein utilization, respiration, and secondary metabolism between animal-associated acidobacteria and other acidobacteria, especially the soil acidobacteria, displaying flexibility and versatility of the animal-associated acidobacteria in environmental adaption.

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Section: Acidobacteria-animal Interactionmentioning

confidence: 99%

Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov.

Wang

Liu

et al. 2022

Front. Microbiol.

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“…The Symbiodiniaceae community composition analysis was performed according to the following steps (Chen et al, 2020): Sterile surgical scissors were used to cut the coral samples (about 90 mg) containing the coral tissue, skeleton, and mucus, with five parallel samples at each pH gradient; (2) the Marine Animal Genomic DNA Extraction Kit (TIANGEN, DP324) and Plant Genomic DNA Kit (OMEGA, D3485-2) were used to extract the DNA of coral, and coral-associated bacteria and Symbiodiniaceae, respectively. Mixed animal DNA samples and plant DNA samples, and screened for quality and purity; (3) using forward ITS2 (5'-GAATTGCAGAACTCCGTG-3') and reverse ITS2 (5'-GGGATCCATATGCTTAAGTTCAGCGG GT-3') as primers, PCR amplification was performed on the rDNA Symbiodiniaceae ITS2 region.…”

Section: Symbiodiniaceae Density and Community Composition Analysismentioning

confidence: 99%

Regulation of the Coral-Associated Bacteria and Symbiodiniaceae in Acropora valida Under Ocean Acidification

Liang

et al. 2021

Front. Microbiol.

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Ocean acidification is one of many stressors that coral reef ecosystems are currently contending with. Thus, understanding the response of key symbiotic microbes to ocean acidification is of great significance for understanding the adaptation mechanism and development trend of coral holobionts. Here, high-throughput sequencing technology was employed to investigate the coral-associated bacteria and Symbiodiniaceae of the ecologically important coral Acropora valida exposed to different pH gradients. After 30 days of acclimatization, we set four acidification gradients (pH 8.2, 7.8, 7.4, and 7.2, respectively), and each pH condition was applied for 10 days, with the whole experiment lasting for 70 days. Although the Symbiodiniaceae density decreased significantly, the coral did not appear to be bleached, and the real-time photosynthetic rate did not change significantly, indicating that A. valida has strong tolerance to acidification. Moreover, the Symbiodiniaceae community composition was hardly affected by ocean acidification, with the C1 subclade (Cladocopium goreaui) being dominant among the Symbiodiniaceae dominant types. The relative abundance of the Symbiodiniaceae background types was significantly higher at pH 7.2, indicating that ocean acidification might increase the stability of the community composition by regulating the Symbiodiniaceae rare biosphere. Furthermore, the stable symbiosis between the C1 subclade and coral host may contribute to the stability of the real-time photosynthetic efficiency. Finally, concerning the coral-associated bacteria, the stable symbiosis between Endozoicomonas and coral host is likely to help them adapt to ocean acidification. The significant increase in the relative abundance of Cyanobacteria at pH 7.2 may also compensate for the photosynthesis efficiency of a coral holobiont. In summary, this study suggests that the combined response of key symbiotic microbes helps the whole coral host resist the threats of ocean acidification.

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“…However, all currently available sequences have been generated using short-read (50-300 bp) sequencing approaches, leaving incomplete information and sequence splicing errors [75][76][77]. Critically, although some high-quality sequences have been published for both corals themselves [23,24,[30][31][32][78][79][80][81][82][83][84][85][86][87][88][89][90][91][92][93] and their associated microorganisms [33,[94][95][96][97][98][99][100][101][102][103][104][105][106][107][108][109][110][111][112][113], the reliance on short reads has prevented the precise delimitation of the gene expression profiles of reef-building corals and their endosymbiotic Symbiodiniaceae.…”

Section: Introductionmentioning

confidence: 99%

Full-length transcriptome maps of reef-building coral illuminate the molecular basis of calcification, symbiosis, and circadian genes

Han¹,

Liao

Zhu³

et al. 2022

Preprint

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Background: Reef-building corals are critical species for sustaining coral reefs and are highly threatened by global climate change. However, relevant transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Results: We sequenced the full-length transcriptomes of four common and frequently dominant reef-building corals, including two Robusta clade species, Pocillopora damicornis and Pocillopora verrucosa, and two Complexa clade species, Acropora muricata and Montipora foliosa, using the PacBio Sequel II platform. We obtained information on gene functions, structures and expression profiles. Among them, a comparative analysis of biomineralization-related genes provided insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiote Symbiodiniaceae were also isolated and annotated from the holobiont sequence data; these profiles showed more highly convergent traits related to gene structure and expression level than those of coral hosts. Interestingly, we observed that intracellular algal cells share some evolutionary convergence between intracellular symbiosis in corals and intracellular digestion in amphioxus. Finally, a phylogenetic analysis of key circadian clock genes among 27 evolutionarily representative species indicated that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. Conclusions: Our work overcomes the incompleteness of short-read sequencing and illuminates the molecular basis of calcification, symbiosis, and circadian genes, thus providing a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.

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Microbiome community and complexity indicate environmental gradient acclimatisation and potential microbial interaction of endemic coral holobionts in the South China Sea

Cited by 36 publications

References 105 publications

Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov.

Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov.

Regulation of the Coral-Associated Bacteria and Symbiodiniaceae in Acropora valida Under Ocean Acidification

Full-length transcriptome maps of reef-building coral illuminate the molecular basis of calcification, symbiosis, and circadian genes

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