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Downloaded from the NCBI Genome Database, Dehyde, and Post-Fixed in 1% Oso4 Yang et al. Microbiome (2019) 7:3 https://doi.org/10.1186/s40168-018-0616-z RESEARCH Open Access Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera Shan-Hua Yang1,2,3,4, Kshitij Tandon1,5,6, Chih-Ying Lu1, Naohisa Wada1, Chao-Jen Shih7, Silver Sung-Yun Hsiao8,9, Wann-Neng Jane10, Tzan-Chain Lee1, Chi-Ming Yang1, Chi-Te Liu11, Vianney Denis12, Yu-Ting Wu13, Li-Ting Wang7, Lina Huang7, Der-Chuen Lee8, Yu-Wei Wu14, Hideyuki Yamashiro2 and Sen-Lin Tang1* Abstract Background: Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a green layer beneath coral tissues, the anaerobic photoautotrophic green sulfur bacteria (GSB) Prosthecochloris is dominant in the skeleton of Isopora palifera. However, due to inherent challenges in studying anaerobic microbes in coral skeleton, the reason for its niche preference and function are largely unknown. Results: This study characterized a diverse and dynamic community of endolithic microbes shaped by the availability of light and oxygen. In addition, anaerobic bacteria isolated from the coral skeleton were cultured for the first time to experimentally clarify the role of these GSB. This characterization includes GSB’s abundance, genetic and genomic profiles, organelle structure, and specific metabolic functions and activity. Our results explain the advantages endolithic GSB receive from living in coral skeletons, the potential metabolic role of a clade of coral- associated Prosthecochloris (CAP) in the skeleton, and the nitrogen fixation ability of CAP. Conclusion: We suggest that the endolithic microbial community in coral skeletons is diverse and dynamic and that light and oxygen are two crucial factors for shaping it. This study is the first to demonstrate the ability of nitrogen uptake by specific coral-associated endolithic bacteria and shed light on the role of endolithic bacteria in coral skeletons. Keywords: Green sulfur bacteria, Endoliths, Isopora palifera, Anaerobic cultivation, Nitrogen fixation Background new nitrogen input and process nutrient regeneration in All biomes in marine environments, including coral reef coral reefs [6–8]. For example, diazotrophs process ni- ecosystems, are fundamentally dependent on their mi- trogen fixation in coral skeletons and carbonated sand, crobial constituents for biomass and metabolism [1]. adding new nitrogen to the reef at a rate about 5 − Endolithic communities are prevalent within corals, mg m2 day 1, which may be essential to the coral reef’s though our understanding of these communities is overall nitrogen budget [8]. poorly resolved [2–5]. For example, the endolithic algae Endolithic microorganisms are considered major food contribute more biomass than photosynthetic symbionts chain components [9, 10]. Nutrients generated by in the living corals, indicating that phototrophic endo- coral-associated endoliths may be alternative nutrient liths are one of the primary producers in coral reefs [3]. sources for the coral host [2, 11, 12]. Ferrer and Szmant In addition, endolithic microbes are able to contribute to [13] found that endolithic organisms can fix 55–60% of the nitrogen required by its coral host. In addition, when * Correspondence: [email protected] coral undergoes thermal bleaching, endolithic algae can 1Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan translocate photosynthetic carbon to their coral host [12]. Full list of author information is available at the end of the article © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Yang et al. Microbiome (2019) 7:3 Page 2 of 13 Endolithic microbes associated with coral skeletons in- temperature was 26–27 °C. Coral samples were immedi- clude algae, fungi, bacteria, archaea, and viruses [4, 5]. ately rinsed twice with sterilized water, then transported The green algae Ostreobium is the major component of to the laboratory (< 1 h) and placed in freezers (− 20 °C). the conspicuous green layers beneath coral tissue in the Slurries of green layers were collected from coral skeletons coral skeleton, which are found in many live corals and using the method described in Yang et al. [17] and pre- are considered a coral symbiont [14]. Recently, it has been pared for cell counting (Additional file 1: supplementary suggested that the distribution of Ostreobium clades materials and methods), 16S rDNA amplicon 454 pyrose- shares similar biogeographical patterns as Symbiodinia- quencing, and metagenome analyses. ceae [15]. In addition, coral host specificity may also influ- Three additional coral colonies were collected from ence endolithic communities because tissue thickness and the same place on July 25, 2017, for pigment analysis skeleton structures may result in differences in microenvi- (Additional file1: supplementary materials and methods) ronments within the coral skeleton [16]. and ultra-thin sections and transmission electron micro- Instead of Ostreobium and other aerobic microorgan- scope observation. Three coral colonies were further col- isms, our previous study found that the anaerobic photo- lected on October 16, 2017, for anaerobic cultivation of autotrophic green sulfur bacteria (GSB) Prosthecochloris is endolithic bacteria. dominant and prevalent in the skeleton of the coral Isopora palifera [17]. Although GSB are one of the DNA extraction coral-associated bacteria, they are usually present in coral Total genomic DNA of slurry samples from the green tissue, mucus, and skeleton at relatively low abundances layer was extracted using an UltraClean Soil DNA Kit [18–22]. Therefore, the prevalence of Prosthecochloris in (MioBio, Solana Beach, CA, USA). The DNA extraction coral skeletons suggests that abiotic factors, such as oxy- followed the manufacture’s protocol with one exception: gen and light intensity, within coral skeletons might be de- bacterial cell pellets from the samples of endolithic cul- cisive and understudied factors for the composition of ture were collected by centrifugation at 7000×g at 20 °C endolithic microbes. In addition, GSB are potential nitro- for 10 min prior the DNA extraction. gen fixers and photoautotrophs that might act as nitrogen and carbon sources for the coral holobiont [17]. The dis- PCR amplification, 16S rRNA amplicon, metagenomic DNA covery of the green layers made of predominantly GSB sequencing and data analyses has lead us to reconsider the compositional heterogen- To prepare 16S rRNA amplicons, PCR amplification was eity and diverse functions of endoliths [16, 17]. This performed using two universal primers for bacteria— phenomenon also raises more in-depth questions about 968F (5′-AACGCGAAGAACCTTAC-3′) and 1391R ecological functioning, compositional dynamics, and (5′-ACGGGCGGTGWGTRC-3′)—both of which were evolutionary ecology of GSB in corals [16, 17, 22]. designed for the bacterial V6–V8 hypervariable regions However, to date, major gaps still persist in the know- of the 16S rDNA [23, 24]. The PCR condition and DNA ledge of the GSB. tagging PCR for pyrosequencing condition were the To comprehend GSB’s role within coral skeletons, we same as those in Yang et al. [17]. A library was prepared conducted multi-level approaches including metage- and sequenced using the Roche 454 Genome Sequencer nomics, biochemistry, physiology, histology, and morph- Junior system at Genomics Core Lab, Institute of ology. Using culture-independent and -dependent Molecular Biology, Academia Sinica. methods, we discovered putative functions of nitrogen, For metagenomic analysis, the total genomic DNA was sulfur, and carbon metabolisms in GSB and other endo- amplified using REPLI-g Mini Kit (QIAGEN) according lithic microbes; visualized the distribution of GSB in coral to the manufacturer’s protocol. All of WGA products skeletons; revealed microscopic cellular structures of GSB; were purified using the QIAamp DNA Mini Kit and detected nitrogenase activity in GSB. This study is the (QIAGEN). All amplified and purified DNAs of the nine first, to our knowledge, to use anaerobic cultivation and samples were sent to Yourgene Bioscience (Taipei, experiments to characterize the coral microbiota. Taiwan) for library preparation and sequencing by Illumina MiSeq system (USA). Materials and methods Methods for 16S amplicon, metagenome analyses, and Sample collection draft genome assembly were provided in supplementary Samples of I. palifera were collected from Ludao (Green material and methods. Summary of 16S amplicon reads Island), an offshore volcanic islet in the western Pacific and OTUs assigned across samples and metagenome Ocean (southeastern Taiwan). Nine healthy coral colonies reads and contigs are shown in Table 1. For metagenome located at 5–20 m depths were collected from Gongguan analysis, details for sequencing reads summary and gene (22° 40′
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