Table_1_Bacterial Metabolic Potential and Micro-Eukaryotes Enriched in Stony Coral Tissue Loss Disease Lesions.XLSX

The epizootic disease outbreak known as stony coral tissue loss disease (SCTLD) is arguably the most devastating coral disease in recorded history. SCTLD emerged off the coast of South Florida in 2014 and has since moved into the Caribbean, resulting in coral mortality rates that have changed reef structure and function. Currently, the cause of SCTLD is unknown, but there is evidence from 16S rRNA gene sequencing and bacterial culture studies that the microbial community plays a role in the progression of SCTLD lesions. In this study, we applied shotgun metagenomics to characterize the potential function of bacteria, as well as the composition of the micro-eukaryotic community, associated with SCTLD lesions. We re-examined samples that were previously analyzed using 16S rRNA gene high-throughput sequencing from four coral species: Stephanocoenia intersepta, Diploria labyrinthiformis, Dichocoenia stokesii, and Meandrina meandrites. For each species, tissue from apparently healthy (AH) corals, and unaffected tissue (DU) and lesion tissue (DL) on diseased corals, were collected from sites within the epidemic zone of SCTLD in the Florida Keys. Within the micro-eukaryotic community, the taxa most prominently enriched in DL compared to AH and DU tissue were members of Ciliophora. We also found that DL samples were relatively more abundant in less energy-efficient pathways like the pentose phosphate pathways. While less energy-efficient processes were identified, there were also relatively higher abundances of nucleotide biosynthesis and peptidoglycan maturation pathways in diseased corals compared to AH, which suggests there was more bacteria growth in diseased colonies. In addition, we generated 16 metagenome-assembled genomes (MAGs) belonging to the orders Pseudomonadales, Beggiatoales, Rhodobacterales, Rhizobiales, Rs-D84, Flavobacteriales, and Campylobacterales, and all MAGs were enriched in DL samples compared to AH samples. Across all MAGs there were antibiotic resistance genes that may have implications for the treatment of SCTLD with antibiotics. We also identified genes and pathways linked to virulence, such as nucleotide biosynthesis, succinate dehydrogenase, ureases, nickel/iron transporters, Type-1 secretion system, and metalloproteases. Some of these enzymes/pathways have been previously targeted in the treatment of other bacterial diseases and they may be of interest to mitigate SCTLD lesion progression.

被称为石珊瑚组织脱落病（stony coral tissue loss disease, SCTLD）的动物流行病暴发事件，堪称有记录以来破坏性最强的珊瑚病害。SCTLD于2014年在南佛罗里达近岸海域首次出现，随后扩散至加勒比海地区，造成的珊瑚死亡率已显著改变了珊瑚礁的结构与功能。目前，SCTLD的致病原因仍不明晰，但已有基于16S rRNA基因测序（16S rRNA gene sequencing）与细菌培养研究的证据表明，微生物群落参与了SCTLD病灶的发展进程。本研究采用鸟枪法宏基因组学（shotgun metagenomics）技术，对与SCTLD病灶相关的细菌潜在功能以及微型真核生物群落的组成特征进行解析。我们重新分析了此前采用16S rRNA基因高通量测序（16S rRNA gene high-throughput sequencing）的样本，这些样本采自4种珊瑚：Stephanocoenia intersepta、Diploria labyrinthiformis、Dichocoenia stokesii与Meandrina meandrites。针对每种珊瑚，我们从佛罗里达群岛SCTLD流行区域的采样点中，分别采集了表观健康（apparently healthy, AH）珊瑚的组织、患病珊瑚上未受感染的组织（unaffected tissue, DU）以及病灶组织（lesion tissue, DL）。在微型真核生物群落中，与表观健康组织和未受感染组织相比，病灶组织中富集程度最高的类群为纤毛虫门（Ciliophora）成员。我们还发现，相较于表观健康组织，病灶组织样本中能量效率较低的代谢通路（如磷酸戊糖途径（pentose phosphate pathways））的相对丰度更高。尽管检测到了能量效率较低的代谢通路，但患病珊瑚组织中核苷酸生物合成与肽聚糖成熟通路的相对丰度也显著高于表观健康组织，这表明患病珊瑚菌落中的细菌生长更为旺盛。此外，我们共获得了16个宏基因组组装基因组（metagenome-assembled genomes, MAGs），分属于假单胞菌目（Pseudomonadales）、贝氏硫菌目（Beggiatoales）、红杆菌目（Rhodobacterales）、根瘤菌目（Rhizobiales）、Rs-D84、黄杆菌目（Flavobacteriales）以及弯曲菌目（Campylobacterales）；且所有MAGs在病灶组织样本中的富集程度均高于表观健康组织样本。所有MAGs中均携带抗生素抗性基因，这或许可为采用抗生素治疗SCTLD提供参考依据。我们还鉴定出了与毒力相关的基因及通路，包括核苷酸生物合成、琥珀酸脱氢酶、脲酶、镍/铁转运蛋白、I型分泌系统（Type-1 secretion system）以及金属蛋白酶（metalloproteases）。其中部分酶类或通路此前已被用于其他细菌性病害的治疗，因此有望成为缓解SCTLD病灶发展的潜在靶点。