Ratinskaia Lina, Malavin Stas, Zvi-Kedem Tal, Vintila Simina, Kleiner Manuel, Rubin-Blum Maxim
Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa 3108000Israel.
Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838Israel.
ISME Commun. 2024 Jun 4;4(1):ycae076. doi: 10.1093/ismeco/ycae076. eCollection 2024 Jan.
Lucinid clams are one of the most diverse and widespread symbiont-bearing animal groups in both shallow and deep-sea chemosynthetic habitats. Lucinids harbor Ca. Thiodiazotropha symbionts that can oxidize inorganic and organic substrates such as hydrogen sulfide and formate to gain energy. The interplay between these key metabolic functions, nutrient uptake and biotic interactions in Ca. Thiodiazotropha is not fully understood. We collected individuals from next to a deep-sea brine pool in the eastern Mediterranean Sea, at a depth of 1150 m and used Oxford Nanopore and Illumina sequencing to obtain high-quality genomes of their Ca. Thiodiazotropha gloverae symbiont. The genomes served as the basis for transcriptomic and proteomic analyses to characterize the gene expression, metabolism and physiology of the symbionts. We found genes needed for N fixation in the deep-sea symbiont's genome, which, to date, were only found in shallow-water Ca. Thiodiazotropha. However, we did not detect the expression of these genes and thus the potential role of nitrogen fixation in this symbiosis remains to be determined. We also found the high expression of carbon fixation and sulfur oxidation genes, which indicate chemolithoautotrophy as the key physiology of Ca. Thiodiazotropha. However, we also detected the expression of pathways for using methanol and formate as energy sources. Our findings highlight the key traits these microbes maintain to support the nutrition of their hosts and interact with them.
发光蛤是浅海和深海化学合成栖息地中最多样化且分布最广泛的携带共生体的动物群体之一。发光蛤体内含有硫代重氮营养菌属（Candidatus Thiodiazotropha）共生体，这些共生体能够氧化无机和有机底物，如硫化氢和甲酸，以获取能量。硫代重氮营养菌属在这些关键代谢功能、营养吸收以及生物相互作用之间的相互关系尚未完全明确。我们从地中海东部一个深度为1150米的深海盐水池附近采集了个体，并使用牛津纳米孔测序和Illumina测序技术来获取其硫代重氮营养菌属格洛弗菌（Candidatus Thiodiazotropha gloverae）共生体的高质量基因组。这些基因组作为转录组学和蛋白质组学分析的基础，用于表征共生体的基因表达、代谢和生理学特性。我们在深海共生体的基因组中发现了固氮所需的基因，迄今为止，这些基因仅在浅水硫代重氮营养菌属中发现。然而，我们并未检测到这些基因的表达，因此固氮在这种共生关系中的潜在作用仍有待确定。我们还发现了碳固定和硫氧化基因的高表达，这表明化能无机自养是硫代重氮营养菌属的关键生理特性。然而，我们也检测到了利用甲醇和甲酸作为能源的途径的表达。我们的研究结果突出了这些微生物为支持宿主营养并与宿主相互作用而维持的关键特性。
