Co-expression GO results and genes to GO terms.

Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen (Serratia marcescens) and white band disease. We then characterized the coral’s transcriptomic and prokaryotic microbiomes’ (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes’ inferred metagenomic function revealed infected corals’ prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts’ transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools.造礁珊瑚拥有由多种生物构成的复杂共生联合体（holobiont），其对疾病的响应具有动态特征，这为病原体鉴定带来了极大挑战。此前虽已有针对珊瑚转录组学与原核微生物组（prokaryotic microbiome）的相关表征研究，但尚未有工作评估二者对不同病原来源的响应异同。本研究将已知珊瑚致病菌粘质沙雷氏菌（Serratia marcescens）与白带病分别接种至4株加勒比分枝型麋角珊瑚（Acropora palmata）无性系株中，随后表征了珊瑚转录组与原核微生物组（prokaryiome）对病害接种的响应，以及病害接种前的短期热胁迫如何影响这些响应。研究发现，无论接种何种病原，珊瑚的转录组与原核微生物组响应均存在显著共性；但在保持健康与出现活跃病害症状的接种珊瑚之间，仍可观测到明显差异。转录组共表达分析显示，接种病害的珊瑚会上调免疫、伤口愈合及脂肪酸代谢相关通路的基因表达。原核微生物组共丰度分析鉴定出了健康状态与病害状态下的特异性细菌类群；而对原核微生物组推断的宏基因组功能进行共表达分析则发现，受感染珊瑚的原核微生物组从自由生活状态转向生物膜状态，同时代谢通路活性显著提升。短期热胁迫并未提升4株无性系株对任意一种病害接种的易感性，仅在珊瑚宿主的转录组与原核微生物组响应中观测到微弱效应。但无性系株身份是转录组变异的主要驱动因素，这主要源于基线免疫基因表达的差异。尽管基线基因表达存在基因型差异，我们仍鉴定出了珊瑚共生体（holobiont）各组分针对不同病害接种的共性响应模式。本研究鉴定出的基因与原核微生物组类群可作为未来珊瑚病害研究的重点方向，具体包括潜在的病害诊断工具。