College of Science and Engineering, James Cook University, Townsville, Queensland, Australia.
Australian Institute of Marine Science, Townsville, Queensland, Australia.
Environ Microbiol. 2023 Dec;25(12):3207-3224. doi: 10.1111/1462-2920.16509. Epub 2023 Sep 21.
The sponge microbiome underpins host function through provision and recycling of essential nutrients in a nutrient poor environment. Genomic data suggest that carbohydrate degradation, carbon fixation, nitrogen metabolism, sulphur metabolism and supplementation of B-vitamins are central microbial functions. However, validation beyond the genomic potential of sponge symbiont pathways is rarely explored. To evaluate metagenomic predictions, we sequenced the metagenomes and metatranscriptomes of three common coral reef sponges: Ircinia ramosa, Ircinia microconulosa and Phyllospongia foliascens. Multiple carbohydrate active enzymes were expressed by Poribacteria, Bacteroidota and Cyanobacteria symbionts, suggesting these lineages have a central role in assimilating dissolved organic matter. Expression of entire pathways for carbon fixation and multiple sulphur compound transformations were observed in all sponges. Gene expression for anaerobic nitrogen metabolism (denitrification and nitrate reduction) were more common than aerobic metabolism (nitrification), where only the I. ramosa microbiome expressed the nitrification pathway. Finally, while expression of the biosynthetic pathways for B-vitamins was common, the expression of additional transporter genes was far more limited. Overall, we highlight consistencies and disparities between metagenomic and metatranscriptomic results when inferring microbial activity, while uncovering new microbial taxa that contribute to the health of their sponge host via nutrient exchange.
海绵微生物组通过在营养贫瘠的环境中提供和回收必需营养物质来支持宿主功能。基因组数据表明，碳水化合物降解、碳固定、氮代谢、硫代谢和 B 族维生素的补充是微生物的核心功能。然而，很少有研究探索超出海绵共生体途径基因组潜力的验证方法。为了评估宏基因组预测，我们对三种常见珊瑚礁海绵：Ircinia ramosa、Ircinia microconulosa 和 Phyllospongia foliascens 的宏基因组和宏转录组进行了测序。Poribacteria、Bacteroidota 和 Cyanobacteria 共生体表达了多种碳水化合物活性酶，表明这些谱系在同化溶解有机物方面具有核心作用。在所有海绵中都观察到了碳固定和多种硫化合物转化的完整途径的表达。在所有海绵中都观察到了厌氧氮代谢（反硝化和硝酸盐还原）的基因表达比好氧代谢（硝化）更为常见，只有 I. ramosa 微生物组表达了硝化途径。最后，尽管 B 族维生素生物合成途径的表达很常见，但其他转运蛋白基因的表达则要有限得多。总的来说，我们在推断微生物活性时强调了宏基因组和宏转录组结果之间的一致性和差异，同时发现了新的微生物类群，它们通过营养物质交换为其海绵宿主的健康做出贡献。
