Institutional Repository of Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences
|Place of Conferral||中国科学院海洋研究所|
放线菌是一大类广泛分布于包括海洋在内的多种环境中的重要原核生物，具有巨大的应用潜力。然而，与其陆源放线菌成员相比，人们分离的海洋放线菌相对较少，尤其是深海。本研究中我们通过使用以牛磺酸为唯一碳源的基础培养基培养了数株深海放线菌，选取其中一株属于诺卡氏菌科的Marmoricola sp. TYQ2进行深入研究，发现其与最近源菌株的16S rRNA基因相似度低于97%，基因组学分析其与近缘菌株基因组相似性均低于新菌临界值，表明其为潜在新种。基于生理生化实验和转录组学分析，牛磺酸的补充能显著促进菌株TYQ2的生长，添加牛磺酸能促使编码与牛磺酸代谢利用以及能量产生相关的基因表达量明显上调。宏基因组分析表明牛磺酸代谢相关基因在深海放线菌中广泛存在。此外，转录组分析表明菌株TYQ2能通过胞外醌酚的氧化还原反应及铁离子与亚铁离子相互转化过程降解聚乙烯醇（PVA），并利用其降解产物产生能量来促进菌体生长。通过16S rRNA扩增子测序分析及前人研究，我们发现放线菌广泛分布于深海中。总体而言，我们的研究结果表明，放线菌可能在深海生态系统的元素（碳、硫等）循环中发挥重要作用，主要归因于它们的广泛分布且具有突出的有机物（牛磺酸、聚乙烯醇等）降解能力。
The deep sea is the largest ecosystem in the world and contains abundant microbial resources. The microbes have abundant genetic diversity and metabolic characteristics here, which play extremely important roles in the decomposition of organic matters in deep-sea environments and drive global biogeochemical cycling processes. At present, due to the difficulty of sampling and the bottleneck of isolation and culture technology, people's understanding and research on deep-sea microorganisms are still very limited. Obtaining deep-sea microbial strain resources is the premise to further explore deep-sea microbial resources and study their special metabolic pathways.
In this study, we obtained 53 species of microorganisms (including 123 strains), belonging to 6 phyla, 7 classes, 14 orders, 23 families, and 39 genera from deep-sea cold seep and hydrothermal samples using different isolation strategies and various media. 52 species of bacteria and 1 species of fungi were included. We analyzed the physiological and biochemical traits and carried out genomic analysis of the Planctomycetes strain TYQ1 and Actinobacteria strain TYQ2 from deep-sea cold seep, revealing the relevant metabolic pathways mediated by them. Taking the actinomycete strain TYQ2 as an example, we conducted a more in-depth study on its ability to metabolize specific organic substances.
Planctomycetes is often considered to be a decomposer of sugars and can participate in the marine carbon cycle by metabolizing sugars. At present, there are many reports on freshwater and shallow sea Planctomycetes, but there are relatively few studies on deep-sea Planctomycetes, which is closely related to the difficulty in isolating and culturing the deep-sea Planctomycetes. In this study, we took N-acetyl-D-glucosamine (GlcNAc) as the main carbon source and used a combination of antibiotics to inhibit the growth of common strains, and finally obtained a Planctomycetes strain TYQ1 from deep-sea cold seep’s sediments. Combined with physiological experiments and genomic analysis, we preliminarily studied the metabolic capacity of strain TYQ1 on N-acetyl-D-glucosamine (GlcNAc), and found that strain TYQ1 could transport GlcNAc into the cytoplasm through the ABC-type sugar transporter, and then enter the glycolysis pathway and nitrogen metabolism through the processes of phosphorylation by sugar kinase, deacetylation by deacetylase, deaminase deamination, etc. Finally, GlcNAc was metabolized and utilized for its own growth.
Actinomycetes are a large group of important prokaryotes widely distributed in various environments including the ocean, and have great potential for application. However, compared with their terrestrial actinomycete members, there are relatively less available marine Actinobacteria isolates, especially deep-sea counterparts. In this study, we cultivated several deep-sea actinomycetes by using taurine as the only carbon source in the basal medium. We selected one of them, Marmoricola sp. TYQ2, belonging to the Nocardiaceae family, for further study. It was found that the similarity of 16S rRNA gene between it and the most recent strain was less than 97%. Genomic analysis showed that the genomic similarity between it and the closely related strains were lower than the critical value of novel bacteria, which indicated that it was a potential novel species. Based on physiological and biochemical experiments and transcriptomic analysis, supplementing taurine can significantly promote the growth of strain TYQ2, and the addition of taurine can significantly up-regulate the expression of genes encoding taurine metabolism and utilization and energy production. Metagenomic analysis indicated that taurine metabolism-related genes were widely present in deep-sea actinomycetes. In addition, transcriptome analysis showed that strain TYQ2 could degrade polyvinyl alcohol (PVA) through the redox reaction of extracellular quinol and quinone and the interconversion of iron ion and ferrous ion, and use its degradation products to generate energy to promote bacterial growth. Through 16S rRNA amplicon sequencing analysis and previous studies, we found that actinomycetes are widely distributed in the deep sea. Overall, our findings suggest that Actinobacteria may play a vital role in elemental cycling (carbon, sulfur, etc.) in the deep-sea ecosystem, mainly due to their widespread distribution and prominent organic substances (taurine, PVA, etc.) degradation capabilities.
In summary, we isolated and obtained microorganisms through the strategy of substance metabolism-driven isolation and culture of deep-sea microorganisms and carried out related research. It will help us to develop and utilize deep-sea microorganisms and understand the cycle process of substances and elements in the deep sea.
|MOST Discipline Catalogue||理学|
|Table of Contents|
|谭颖琪. 深海微生物分离培养及两株深海细菌物质代谢性质的研究[D]. 中国科学院海洋研究所. 中国科学院大学,2022.|
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