CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
mBio. 2022 Apr 26;13(2):e0028722. doi: 10.1128/mbio.00287-22. Epub 2022 Mar 1.
" Thermofonsia" represents a novel class within the phylum . Metagenomic analysis reveals " Thermofonsia" harbors phototrophs outside the classically phototrophic class. Unfortunately, the paucity of pure cultures limits further insights into their potential phototrophy. Here, we report the successful isolation of a " Thermofonsia" representative ( ZRK33) from a deep-sea cold seep. Using combined physiological, genomic, and transcriptomic methods, we further show the long-wavelength light (e.g., red and infrared light) could promote the growth of strain ZRK33 and upregulate the expression of genes associated with phototrophy. In particular, strain ZRK33 has a typical phototrophic lifestyle under both laboratory and deep-sea conditions. Strain ZRK33 also possesses the ability to fix inorganic carbon through the 3-hydroxypropionate bicycle in both laboratory and deep-sea environments, and the combined autotrophic, phototrophic, and heterotrophic capabilities endow strain ZRK33 with a photomixotrophic lifestyle. Notably, the predicted genes associated with phototrophy broadly exist in the metagenomes of 27 deep-sea members, strongly suggesting diverse phototrophic members are distributed in various unexplored deep biospheres. The deep ocean microbiota represents the unexplored majority of global ocean waters. The phylum is abundant and broadly distributed in various deep-sea ecosystems. It was reported that some members of " Thermofonsia" clade 2 might possess phototrophs; however, the absence of cultured representatives is a significant bottleneck toward understanding their phototrophic characteristics. In the present study, we successfully isolated a representative of the novel class " Thermofonsia" from a deep-sea cold seep by using an enrichment medium constantly supplemented with rifampicin, allowing researchers to isolate more members in the future. Importantly, outside the classically phototrophic class, we discover a novel phototrophic clade within the phylum and demonstrate the existence of phototrophic lifestyles in the deep sea. Thus, this study expands the range of phototrophic and provides a good model to study the mechanism of phototrophy performed in the deep biosphere.
“Thermofonsia”代表一门新的门。宏基因组分析表明，“Thermofonsia”在经典的光养类群之外拥有光养生物。不幸的是，纯培养物的缺乏限制了对其潜在光养能力的进一步了解。在这里，我们报告了一种深海冷渗流中“Thermofonsia”代表（ZRK33）的成功分离。使用组合生理、基因组和转录组学方法，我们进一步表明长波长光（例如，红光和红外线）可以促进菌株 ZRK33 的生长，并上调与光养相关的基因表达。特别是，在实验室和深海条件下，菌株 ZRK33 都具有典型的光养生活方式。菌株 ZRK33 还具有在实验室和深海环境中通过 3-羟基丙酸循环固定无机碳的能力，并且组合的自养、光养和异养能力赋予菌株 ZRK33 一种光混合营养生活方式。值得注意的是，与光养相关的预测基因广泛存在于 27 个深海成员的宏基因组中，强烈表明各种光养成员分布在各种未探索的深海生物圈中。深海微生物群代表了全球海洋水域中未被探索的大部分。门在各种深海生态系统中丰富且广泛分布。据报道，“Thermofonsia”类群 2 的一些成员可能具有光养生物；然而，缺乏培养代表是理解其光养特性的一个重大瓶颈。在本研究中，我们通过使用不断补充利福平的富集培养基，从深海冷渗流中成功分离到一种新型“Thermofonsia”类群的代表，这使得研究人员将来能够分离到更多的成员。重要的是，在经典的光养类群之外，我们在门内发现了一个新的光养类群，并证明了深海中存在光养生活方式。因此，这项研究扩展了光养的范围，并提供了一个很好的模型来研究在深海生物圈中进行的光养机制。
