Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China.
College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, Sichuan, China.
mSystems. 2024 Sep 17;9(9):e0017624. doi: 10.1128/msystems.00176-24. Epub 2024 Aug 6.
Nitrogen (N)-fixing organisms, also known as diazotrophs, play a crucial role in N-limited ecosystems by controlling the production of bioavailable N. The carbon-dominated cold-seep ecosystems are inherently N-limited, making them hotspots of N fixation. However, the knowledge of diazotrophs in cold-seep ecosystems is limited compared to other marine ecosystems. In this study, we used multi-omics to investigate the diversity and catabolism of diazotrophs in deep-sea cold-seep bottom waters. Our findings showed that the relative abundance of diazotrophs in the bacterial community reached its highest level in the cold-seep bottom waters compared to the cold-seep upper waters and non-seep bottom waters. Remarkably, more than 98% of metatranscriptomic reads aligned on diazotrophs in cold-seep bottom waters belonged to the genus , an alphaproteobacterium. Its metagenome-assembled genome, named Seep-BW-D1, contained catalytic genes () for nitrogen fixation, and the gene was actively transcribed . Seep-BW-D1 also exhibited chemosynthetic capability to oxidize C1 compounds (methanol, formaldehyde, and formate) and thiosulfate (SO). In addition, we observed abundant transcripts mapped to genes involved in the transport systems for acetate, spermidine/putrescine, and pectin oligomers, suggesting that Seep-BW-D1 can utilize organics from the intermediates synthesized by methane-oxidizing microorganisms, decaying tissues from cold-seep benthic animals, and refractory pectin derived from upper photosynthetic ecosystems. Overall, our study corroborates that carbon-dominated cold-seep bottom waters select for diazotrophs and reveals the catabolism of a novel chemosynthetic alphaproteobacterial diazotroph in cold-seep bottom waters.
Bioavailable nitrogen (N) is a crucial element for cellular growth and division, and its production is controlled by diazotrophs. Marine diazotrophs contribute to nearly half of the global fixed N and perform N fixation in various marine ecosystems. While previous studies mainly focused on diazotrophs in the sunlit ocean and oxygen minimum zones, recent research has recognized cold-seep ecosystems as overlooked N-fixing hotspots because the seeping fluids in cold-seep ecosystems introduce abundant bioavailable carbon but little bioavailable N, making most cold seeps inherently N-limited. With thousands of cold-seep ecosystems detected at continental margins worldwide in the past decades, the significant role of cold seeps in marine N biogeochemical cycling is emphasized. However, the diazotrophs in cold-seep bottom waters remain poorly understood. Through multi-omics, this study identified a novel alphaproteobacterial chemoheterotroph belonging to as one of the most active diazotrophs residing in cold-seep bottom waters and revealed its catabolism.
固氮生物，也称为固氮菌，通过控制生物可利用氮的产生，在氮限制的生态系统中发挥着关键作用。以碳为主导的冷渗生态系统本质上是氮限制的，因此成为氮固定的热点。然而，与其他海洋生态系统相比，冷渗生态系统中固氮菌的知识有限。在这项研究中，我们使用多组学方法研究了深海冷渗底层水中固氮菌的多样性和分解代谢。我们的研究结果表明，与冷渗上层水和非渗底层水相比，细菌群落中固氮菌的相对丰度在冷渗底层水中达到最高水平。值得注意的是，冷渗底层水中超过 98%的转录组比对序列与属的固氮菌相对应，属是一种α变形菌。其宏基因组组装基因组，命名为 Seep-BW-D1，包含氮固定的催化基因（），并且基因被积极转录。Seep-BW-D1 还表现出氧化 C1 化合物（甲醇、甲醛和甲酸盐）和硫代硫酸盐（SO）的化能合成能力。此外，我们观察到大量转录本映射到参与乙酸、亚精胺/腐胺和果胶低聚物运输系统的基因，表明 Seep-BW-D1 可以利用甲烷氧化微生物合成的中间产物、冷渗底栖动物分解的组织以及来自上层光合作用生态系统的不可降解果胶中的有机物。总的来说，我们的研究证实了以碳为主导的冷渗底层水选择了固氮菌，并揭示了冷渗底层水中一种新型化学合成α变形菌固氮菌的分解代谢。
生物可利用氮（N）是细胞生长和分裂的关键元素，其产生受固氮菌控制。海洋固氮菌对全球近一半的固定氮做出了贡献，并在各种海洋生态系统中进行氮固定。虽然先前的研究主要集中在阳光充足的海洋和缺氧区的固氮菌上，但最近的研究已经认识到冷渗生态系统是被忽视的固氮热点，因为冷渗生态系统中的渗出液引入了丰富的生物可利用碳，但很少有生物可利用氮，这使得大多数冷渗都本质上是氮限制的。在过去几十年中，在世界大陆边缘发现了数千个冷渗生态系统，强调了冷渗在海洋氮生物地球化学循环中的重要作用。然而，冷渗底层水中的固氮菌仍知之甚少。通过多组学，本研究鉴定了一种新型的α变形菌化能异养菌，属于属，是栖息在冷渗底层水中最活跃的固氮菌之一，并揭示了其分解代谢。
