Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen.

IF 5.1 Q1 ECOLOGY ISME communications Pub Date : 2024-06-04 eCollection Date: 2024-01-01 DOI:10.1093/ismeco/ycae076
Lina Ratinskaia, Stas Malavin, Tal Zvi-Kedem, Simina Vintila, Manuel Kleiner, Maxim Rubin-Blum
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Abstract

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 Lucinoma kazani 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 in situ gene expression, metabolism and physiology of the symbionts. We found genes needed for N2 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.

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代谢易变的 Ca.深海琉璃蛤(Lucinoma kazani)的硫代滋养菌共生体具有固氮的遗传潜力。
琉璃蛤是浅海和深海化合栖息地中种类最多、分布最广的共生动物群之一。琉球蛤类含有 Ca.Thiodiazotropha共生藻可以氧化硫化氢和甲酸盐等无机和有机底物以获得能量。Ca.Thiodiazotropha的这些关键代谢功能、养分吸收和生物相互作用之间的相互影响还不清楚。Thiodiazotropha中这些关键代谢功能之间的相互作用还不完全清楚。我们在地中海东部 1150 米深处的深海盐池旁采集了 Lucinoma kazani 个体,并使用 Oxford Nanopore 和 Illumina 测序技术获得了它们的 Ca.Thiodiazotropha gloverae 共生藻的高质量基因组。这些基因组是转录组和蛋白质组分析的基础,用于描述共生体的原位基因表达、新陈代谢和生理学特征。我们在深海共生体的基因组中发现了固定 N2 所需的基因,而这些基因迄今为止只在浅水的 Ca.Thiodiazotropha。但是,我们没有检测到这些基因的表达,因此,固氮作用在这种共生关系中的潜在作用仍有待确定。我们还发现碳固定和硫氧化基因的高表达,这表明化学溶解自养是 Ca.Thiodiazotropha。不过,我们也检测到利用甲醇和甲酸盐作为能量来源的途径的表达。我们的发现突显了这些微生物为支持宿主的营养和与宿主相互作用而保持的关键特性。
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