PDF(Sci-hub)
Abstract：
In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella.
Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host\'s immune system.
This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. Video Abstract.
Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host\'s immune system.
This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. Video Abstract.
摘要：
在八珊瑚（CnidariaOctocorallia）中，宿主健康与其共生联盟之间的功能关系尚未确定。这里,我们使用比较宏基因组学来揭示健康的欧洲风球菌的微生物组的独特功能和系统发育特征，疣状大肠杆菌,和纹状体组织，与在海水和沉积物中发现的微生物群相反。我们进一步探索了八珊瑚微生物组如何在E.gazella中转变为病理生物学状态。
基于16SrRNA基因的多变量分析，直系同源蛋白质群（COG），蛋白质家族(Pfams),和从20个Illumina测序的宏基因组中注释的次级代谢产物-生物合成基因簇，每个都揭示了三种八珊瑚物种的健康组织样本的原核群落与坏死的E.gazella组织和周围环境的聚集。虽然健康的八珊瑚微生物群是由迄今为止未培养的内生虫科区分的，海洋螺旋藻,和所有寄主物种中的Alteromonadales表型，黄杆菌科和α-变形杆菌的明显增加，源自海水，在坏死E.gazella组织中观察到。真核生物样蛋白的丰度增加，核酸外切酶,限制性核酸内切酶,CRISPR/Cas蛋白,和编码热休克蛋白的基因，无机离子传输，和铁的储存区分了健康的八珊瑚组织的原核群落，而与宿主物种无关。精氨酸酶和一氧化氮还原酶基因的增加，在坏死E.gazella组织中观察到，表明存在一种抑制亚硝酸盐氧化物产生的机制，通过这种机制，八珊瑚病原体可以克服宿主的免疫系统。
这是第一个采用无引物的研究，鸟枪宏基因组测序来揭示分类学，功能，八角珊瑚原核生物群落的次生代谢特征。我们的分析表明，八珊瑚的微生物组与周围环境不同，是宿主属(但不是种)特定的，并经历了巨大的，向生态失调状态过渡的复杂结构变化。宿主共生生物识别，非生物应激反应，微量营养素采集，和包含多种限制性内切酶的抗病毒防御武器库，CRISPR/Cas系统，噬菌体溶源调节因子是八角珊瑚中原核生物群落的特征。我们认为，这些特征共同促进了八珊瑚全体共生的稳定，并构成了有益的特征，可以指导未来对珊瑚礁保护和微生物组治疗的研究。视频摘要。
基于16SrRNA基因的多变量分析，直系同源蛋白质群（COG），蛋白质家族(Pfams),和从20个Illumina测序的宏基因组中注释的次级代谢产物-生物合成基因簇，每个都揭示了三种八珊瑚物种的健康组织样本的原核群落与坏死的E.gazella组织和周围环境的聚集。虽然健康的八珊瑚微生物群是由迄今为止未培养的内生虫科区分的，海洋螺旋藻,和所有寄主物种中的Alteromonadales表型，黄杆菌科和α-变形杆菌的明显增加，源自海水，在坏死E.gazella组织中观察到。真核生物样蛋白的丰度增加，核酸外切酶,限制性核酸内切酶,CRISPR/Cas蛋白,和编码热休克蛋白的基因，无机离子传输，和铁的储存区分了健康的八珊瑚组织的原核群落，而与宿主物种无关。精氨酸酶和一氧化氮还原酶基因的增加，在坏死E.gazella组织中观察到，表明存在一种抑制亚硝酸盐氧化物产生的机制，通过这种机制，八珊瑚病原体可以克服宿主的免疫系统。
这是第一个采用无引物的研究，鸟枪宏基因组测序来揭示分类学，功能，八角珊瑚原核生物群落的次生代谢特征。我们的分析表明，八珊瑚的微生物组与周围环境不同，是宿主属(但不是种)特定的，并经历了巨大的，向生态失调状态过渡的复杂结构变化。宿主共生生物识别，非生物应激反应，微量营养素采集，和包含多种限制性内切酶的抗病毒防御武器库，CRISPR/Cas系统，噬菌体溶源调节因子是八角珊瑚中原核生物群落的特征。我们认为，这些特征共同促进了八珊瑚全体共生的稳定，并构成了有益的特征，可以指导未来对珊瑚礁保护和微生物组治疗的研究。视频摘要。
