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Next-generation sequencing revealed specific microbial symbionts in Porites lutea with pigment abnormalities in North Sulawesi, Indonesia
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Danyun OU1, Bin CHEN1, *, Tri Aryono HADI2, SUHARSONO2, Wentao NIU1, Yustian Rovi ALFIANSAH2
Acta Oceanologica Sinica | 2018, 37(12) : 78 - 84
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Acta Oceanologica Sinica | 2018, 37(12): 78-84
Coastal Environment and Biodiversity in North Sulawesi, Indonesia
Next-generation sequencing revealed specific microbial symbionts in Porites lutea with pigment abnormalities in North Sulawesi, Indonesia
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Danyun OU1, Bin CHEN1, *, Tri Aryono HADI2, SUHARSONO2, Wentao NIU1, Yustian Rovi ALFIANSAH2
Affiliations
  • 1 Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
  • 2 Research Center for Oceanography, Indonesian Institute of Sciences, Jakarta 14430, Indonesia
Published: 2018-12-25 doi: 10.1007/s13131-018-1291-4
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Bacterial diseases affecting corals pose an enormous threat to the health of coral reefs. The relationship between certain bacterial species and coral diseases remain largely unknown. Pigment abnormalities are common in Porites lutea. Here we used Illumina 16S rRNA gene sequencing to analyze the bacterial communities associated with healthy P. lutea and P. lutea with pigment abnormalities. We observed an increase of alpha diversity of the bacterial community of P. lutea with pigment abnormalities, relative to healthy corals. We then identified changes in the abundance of individual operational taxonomic units (OTUs) between pigmented and healthy corals. We were able to identify eight OTUs associated with pigment abnormalities, which are possibly the causative agents of pigment abnormalities.

Porites lutea  /  pigment abnormalities  /  next-generation sequencing  /  16S rRNA  /  bacterial diversity
Danyun OU, Bin CHEN, Tri Aryono HADI, SUHARSONO, Wentao NIU, Yustian Rovi ALFIANSAH. Next-generation sequencing revealed specific microbial symbionts in Porites lutea with pigment abnormalities in North Sulawesi, Indonesia[J]. Acta Oceanologica Sinica, 2018 , 37 (12) : 78 -84 . DOI: 10.1007/s13131-018-1291-4
Microbial symbionts are versatile organisms aiding in the development and health of their host (Neish, 2009; Webster and Taylor, 2012). The interaction of corals and microbes is a fundamental aspect in the dynamics on reefs (Bourne et al., 2009). Corals continuously face changing environmental conditions, both on local and global scales (Bourne et al., 2009; Wegley et al., 2007).
Some bacterial species are reportedly responsible for coral diseases (Ben-Haim et al., 2003; Cervino et al., 2004; Kushmaro et al., 2001). The identification of bacterial pathogens associated with specific coral diseases is not easy, because the causing pathogens should be isolated and confirmed to fulfill Kohl’s law (Sussman, 2009). Six pathogens have been identified as causative agents for five kinds of coral diseases.
Culture-independent techniques, based on the characterization of symbiotic microorganisms associated with corals, have been used to gain a better understanding of symbiotic interactions (Morrow et al., 2012), and of the health conditions of coral systems (De Castro et al., 2010; Salipante et al., 2013).
Porites is a stony coral genus that is an accurate recorder of past marine surface conditions (Lough, 2010; Suzuki et al., 2000). Porites is thought to be the holobiont of bacterial pathogens, and to be easily affected by environmental stressors (Raymundo et al., 2005; Thurber et al., 2008). Pigment abnormalities are considered an inflammatory response of corals; however, the relationship between pigment abnormalities and bacterial communities remain unclear (Benzoni et al., 2010).
To illustrate the relationship between specific microbial communities and the pigment abnormalities in P. lutea, we analyzed the symbiotic microbial community of P. lutea with pigment abnormalities, and compared it with the microbial communities of healthy P. lutea.
Coral samples were collected during a Sino-Indonesia co-survey in late April to early May in 2013 at the Lembeh Strait. Samples of corals with pigment abnormalities, and of healthy corals, were collected at Site S5 located at the middle of the Lembeh Strait (1°27′13.6″N, 125°14′12.8″E, North Sulawesi, Indonesia) (Fig. 1). Coral samples were cut on site to collect separately pink segments and healthy segments (Fig. 2), and then fixed with 95% ethanol. Three parallels from pink segments and healthy segments respectively were subsampled for DNA analysis.
Total genomic DNA was extracted from samples using the MP FastDNA Spin kit for Soil (MP Biomedicals). DNA concentration and purity were monitored on 1% agarose gels. DNA was diluted to 1 ng/μL in sterile water. The regions V3–V4 from the 16S gene were amplified using the specific primer 515F-806R with the barcode designed for the following sequencing. PCR reactions were carried out in 30 μL containing 15 μL of Phusion® High-Fidelity PCR Master Mix (New England Biolabs), 0.2 μmol/L of forward and reverse primers, and approximately 10 ng template DNA. Thermal cycling consisted of an initial denaturation step at 98°C for 1 min, followed by 30 cycles of denaturation at 98°C or for 10 s, annealing at 50°C for 30 s, and elongation at 72°C for 60 s, plus a final elongation step at 72°C for 5 min. Mix same volume of 1× loading buffer (contained SYB green) with PCR products and operate electrophoresis on 2% agarose gel for detection, and samples containing a band of 400–450 bp were selected for further experiments. PCR products were mixed in equal ratios. Then, the PCR products were purified using the GeneJET Gel Extraction Kit (Thermo Scientific). Sequencing libraries were generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB), following the manufacturer’s recommendations. The library quality was assessed using the Qubit@2.0 Fluorometer (Thermo Scientific) and the Agilent Bioanalyzer 2100 system. Finally, the library was sequenced on an Illumina MiSeq platform, generating 250–300 bp paired-end reads.
High-throughput sequencing data were processed using the Mothur software, as described in the pipeline of “Costello stool analysis” (Costello et al., 2009). In order to obtain more accurate sequences, sequences that were shorter than 400 bp, or that contained more than six polymers, were eliminated. Sequencing errors corresponding to artifacts of the sequencing process were reduced through the “denoising” algorithm (Reeder and Knight, 2010). After screening, filtering, and pre-clustering, unique sequences were checked for chimeras using Vsearch (Rognes et al., 2016). The qualified sequences were aligned with the reference set in the SILVA SSURef database Release 123 (Pruesse et al., 2007). Sequencing data were subsampled to eliminate the deviation due to the difference of sequence numbers across samples. After achieving an even number of sequences across samples, optimized reads were taxonomically assigned using the RDP-classifier with a bootstrap cut-off of 97% (Wang et al., 2007).
Observed richness, Simpson diversity, and the Shannon–Wiener index were measured based on the frequency of operational taxonomic units (OTUs) and genera in the assigned sequence collections after rare sequences were removed (Hill et al., 2003). Rarefaction curves were computed after discarding singletons. Beta diversity was estimated by computing weighted and unweighted UniFrac distances between samples using QIIME (Caporaso et al., 2010). Correlation analysis between the symbiotic bacterial communities of the samples were carried out using the statistical R package commond cor.test (Liu et al., 2014).
A total of 439 734 sequences from six samples were recovered after Miseq sequencing. After sequence screening, filtering, pre-clustering and removal of chimeras, 425 182 qualified sequences were retained for alignment and OTU classification (these sequences accounted for 96.69% of the total raw sequences). In total 245 333 sequences representing bacterial taxons (16 951 to 98 768 sequences per sample) were recovered from these qualified sequences. As shown in the rarefaction curve based on the bacterial OTU number, the sequencing data can reflect the diversity and richness of the bacterial community of the coral samples, because all the curves reached the near plateau phase (Fig. 3). Additionally, the coverage value shown in Table 1 also indicated that pyro-sequencing data covered 89.39%–96.95% of the bacterial community in the coral samples.
The bacterial community in P. lutea with pigment abnormalities had features differing from those of healthy P. lutea. The relative diversity of the bacterial community from P. lutea with pigment abnormalities was higher than that from healthy coral samples, as indicated by the Shannon index. The Shannon’s index showed different patterns; it increased as the sequence number increased in the samples of P. lutea with pigment abnormalities, while in healthy corals the Shannon’s index decreased as the sequence number increased. The Simpson’s index in the samples of P. lutea with pigment abnormalities was higher than that of healthy corals, which also indicates that the bacterial community in P. lutea with pigment abnormalities is more diverse than in healthy corals. The community richness represented by Chao’s index and sobs showed that the bacterial community in P. lutea with pigment abnormalities has higher richness than healthy corals (Table 1).
A total of 16 951 sequences from each sample were clustered into 8 007 OTUs at a similarity of 97%, using the furthest neighbor algorithm by Vsearch. Bray-Curtis distance matrix, based on the correlation analysis of the six samples, indicated that the symbiotic bacterial community structure in P. lutea with pigment abnormalities and in healthy corals were different from each other, while those in the three parallels of each group were quite similar (Fig. 4).
From the 8 007 OTUs clustered using Mothur, 7 943 OTUs were classified by blasting against NCBI microbial 16S rRNA database. After removing rare OTUs, 936 qualified OTUs accounted for the 15 335–16 049 sequences that were finally recovered. The most abundant bacteria phyla, as calculated by the size (number of sequences) of the phylum of each sample, were Proteobacteria (58.47% of the total), Actinobacteria (19.49% of the total) and Chlorobi (14.18% of the total). Proteobacteria was the most versatile phylum, accounting for 3 449–10 022 and 10 114–12 767 of the sequences in healthy corals, and in P. lutea with pigment abnormalities, respectively.
A total of 399 genera of symbiotic bacteria in healthy P. lutea and in P. lutea with pigment abnormalities were identified by OTU analysis. Bacteria belonging to the 20 most abundant genera constituted more than 77% of the total identified bacteria in P. lutea (77.30% of the total in healthy P. lutea, and 78.09% in P. lutea with pigment abnormalities). The five most abundant genera, Vibrio, Prosthecochloris, Blastococcus, Roseibium and Pseudoalteromonas accounted for 16.21%, 14.18%, 10.06%, 6.25% and 3.77% of the total sequences, respectively. Among these genera, the most abundant OTUs of symbiotic bacteria were Vibrio (0.97%–8.33% in healthy P. lutea and 16.89%–34.57% in P. lutea with pigment abnormalities), Prosthecochloris (0.20%–61.69% in healthy P. lutea and 0.45%–8.67% in P. lutea with pigment abnormalities), Blastococcus (4.66%–19.69% in healthy P. lutea and 4.17%–11.33% in P. lutea with pigment abnormalities), Roseibium (2.19%–8.77% in healthy P. lutea and 5.55%–9.73% in P. lutea with pigment abnormalities), and Pseudoalteromonas (0.90%–2.32% in healthy P. lutea and 4.89%–8.63% in P. lutea with pigment abnormalities) (Fig. 5). Vibrio species in P. lutea with pigment abnormalities (16.21%) were significantly more abundant than in healthy P. lutea (4.94%), which suggests that Vibrio might play an important role in the pigment development in P. lutea.
According to Silva 16S rRNA database, and after removing rare OTUs, a total of 936 bacterial OTUs belonging to 575 species were recovered from subsampled healthy P. lutea and P. lutea with pigment abnormalities. Vibrio, Photobacterium, Acinetobacter, Mesorhizobium and Desulfovibrio were most versatile bacteria genus with 24, 9, 7, 6, and 5 species, respectively (Appendix Table A1). After comparing the 22 most abundant bacterial OTUs (with abundance over 1% of the total OTUs) of healthy P. lutea and P. lutea with pigment abnormalities, we identified 2 OTUs consistently associated with P. lutea with pigment abnormalities, and 8 OTUs consistently associated with healthy P. lutea (Fig. 6). OTUs associated with healthy P. lutea were Prothecochloris vibrioformis and Prothecochloris aestuarii. OTUs associated with P. lutea with pigment abnormalities were Vibrio hyugaensis, Vibrio fortis, Roseibium aquae, Pseudoalteromonas arabiensis, Oscillochloris trichoides, Kofleria flava, Photobacterium gaetbulicola and Vibrio xuii, with 12.80%, 10.58%, 6.30%, 4.93%, 3.25%, 2.26%, 1.98% and 1.90% of the pigmented group versus 1.95%, 1.85%, 2.05 %, 1.34%, 0.66%, 0.67%, 0.27% and 0.31% of the healthy group (Fig. 6). Among these, six OTUs associated with P. lutea with pigment abnormalities were related to bacterial families that include known coral pathogens (Vibrionaceae), to symbiotic bacteria found in diseased marine invertebrates (Rhodobacteraceae), or to algicidal bacteria (Pseudoalteromonadaceae) (Sunagawa et al., 2009).
The symbiotic bacterial community changed drastically in P. lutea with pigment abnormalities, exhibiting an increase in hundreds of OTUs, relative to healthy P. lutea. This change was evidenced by increased bacterial diversity and richness, which is consistent with other coral diseases (Pantos et al., 2003; Séré et al., 2013; Sunagawa et al., 2009).
Proteobacteria was the most abundant phylum in the symbiotic bacterial OTUs, which is in keeping with previous 16S rDNA and metagenomic analysis of bacteria associated with Porites (Rohwer et al., 2002; Wegley et al., 2007). The other two most abundant phyla were Actinobacteria and Chlorobi, which were different to those reported in previous studies, in which Firmicutes and Actinobacteria were the second and third most abundant phyla (Rohwer et al., 2002; Wegley et al., 2007).
The five most abundant genera, Vibrio, Prosthecochloris, Blastococcus, Roseibium and Pseudoalteromonas accounted for more than 50% of the total sequences found in P. lutea. These results are similar to previous reports which suggested that Vibrio and Pseudoalteromonas were the most abundant bacterial genera in P. lutea from southern Hainan Island in China. It is thus likely that these genera form a part of the natural microbiota of P. lutea (Li et al., 2014). Furthermore, Vibrio were more abundant in P. lutea with pigment abnormalities than in healthy P. lutea, indicating that Vibrio might be involved in the etiology of the pigment abnormalities of P. lutea.
Several Vibrio species are well-known pathogens of marine shrimp, fish, invertebrates and coral (Austin et al., 2005; Ben-Haim and Rosenberg, 2002; Kushmaro et al., 1997). Vibrio Shiloi, the first coral pathogen to be identified, is an etiological agent of bleaching of the coral Oculina patagonica (Kushmaro et al., 1996; 2001). Vibrio coralliilyticus is an etiological agent of bleaching of the coral Pocillopora damicornis (Ben-Haim et al., 2003). Four Vibrio species are related to yellow blotch/band disease of the coral Montastrea spp. (Cervino et al., 2004). In our research, three Vibrio species, Vibrio hyugaensis, Vibrio fortis, and Vibrio xuii accounted more than 25% of the total microbial OTUs in P. lutea with pigment abnormalities, which suggested these Vibrio species may be involved in the development of pigment abnormalities.
The authors thank Bai Renao for contributing to DNA extraction, and Novogene Ltd. for helping with Illumina DNA sequencing.
  • The China-Indonesia Maritime Cooperation Fund Project “China-Indonesia Bitung Ecological Station Establishment”; the National Natural Science Foundation of China under contract No. 41506180; the Public Science and Technology Research Funds Projects of Ocean under contract No. 201505009.
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doi: 10.1007/s13131-018-1291-4
  • Receive Date:2017-06-15
  • Online Date:2026-04-14
  • Published:2018-12-25
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  • Received:2017-06-15
  • Accepted:2018-03-15
Funding
The China-Indonesia Maritime Cooperation Fund Project “China-Indonesia Bitung Ecological Station Establishment”; the National Natural Science Foundation of China under contract No. 41506180; the Public Science and Technology Research Funds Projects of Ocean under contract No. 201505009.
Affiliations
    1 Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
    2 Research Center for Oceanography, Indonesian Institute of Sciences, Jakarta 14430, Indonesia

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表12种不同金属材料的力学参数

Family
属数
Number of
genus
种数
Number of
species
占总种数比例
Percentage of
total species (%)

Genus
种数
Number of
species
占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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