在单细胞水平上将未培养的磁性氮螺虫的形态、基因组和代谢活动联系起来。

IF 13.8 1区 生物学 Q1 MICROBIOLOGY
Runjia Ji, Juan Wan, Jia Liu, Jinbo Zheng, Tian Xiao, Yongxin Pan, Wei Lin
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引用次数: 0

摘要

背景:磁力细菌(MTB)是一类独特的微生物,它们通过将磁性纳米颗粒生物矿化来感知地磁场并在地磁场中导航。来自硝螺菌门(以前称为硝螺菌)的 MTB 在各种水生生态系统中繁衍生息。它们每个细胞能产生数百个磁铁矿(Fe3O4)磁小体纳米颗粒,远远超过其他 MTB,因此备受关注。人们已对硝螺菌的形态、系统发育和基因组多样性进行了广泛研究。方法:在此,我们建立了一种方法,利用纳米级二次离子质谱(NanoSIMS)结合基于 rRNA 的原位杂交和靶标特异性微型基因组学,在单细胞水平上将未培养的硝螺菌 MTB 群体(命名为 LHC-1)的形态、基因组和代谢研究联系起来:我们用磁力分离了淡水湖中的 LHC-1,并利用基因组分辨微型基因组学重建了 LHC-1 的基因组草案。我们发现,以 10 个 LHC-1 细胞为模板足以获得高质量的基因组草案。基因组分析表明,LHC-1 具有固定 CO2 和还原 NO3 的潜力,通过结合稳定同位素孵育和 NanoSIMS 分析,我们进一步确定了单细胞水平的特征。此外,NanoSIMS 结果显示了 LHC-1 中特定元素的分布,而且不同 LHC-1 细胞间 CO2 和 NO3- 代谢的异质性随着培养时间的延长而增加:据我们所知,本研究首次对单个硝螺藻 MTB 细胞进行了代谢测量,以解读其生态生理特征。本研究中构建的程序为同时研究自然环境中未培养微生物的形态、基因组和生态生理学提供了一种有前途的策略。视频摘要。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Linking morphology, genome, and metabolic activity of uncultured magnetotactic Nitrospirota at the single-cell level.

Background: Magnetotactic bacteria (MTB) are a unique group of microorganisms that sense and navigate through the geomagnetic field by biomineralizing magnetic nanoparticles. MTB from the phylum Nitrospirota (previously known as Nitrospirae) thrive in diverse aquatic ecosystems. They are of great interest due to their production of hundreds of magnetite (Fe3O4) magnetosome nanoparticles per cell, which far exceeds that of other MTB. The morphological, phylogenetic, and genomic diversity of Nitrospirota MTB have been extensively studied. However, the metabolism and ecophysiology of Nitrospirota MTB are largely unknown due to the lack of cultivation techniques.

Methods: Here, we established a method to link the morphological, genomic, and metabolic investigations of an uncultured Nitrospirota MTB population (named LHC-1) at the single-cell level using nanoscale secondary-ion mass spectrometry (NanoSIMS) in combination with rRNA-based in situ hybridization and target-specific mini-metagenomics.

Results: We magnetically separated LHC-1 from a freshwater lake and reconstructed the draft genome of LHC-1 using genome-resolved mini-metagenomics. We found that 10 LHC-1 cells were sufficient as a template to obtain a high-quality draft genome. Genomic analysis revealed that LHC-1 has the potential for CO2 fixation and NO3- reduction, which was further characterized at the single-cell level by combining stable-isotope incubations and NanoSIMS analyses over time. Additionally, the NanoSIMS results revealed specific element distributions in LHC-1, and that the heterogeneity of CO2 and NO3- metabolisms among different LHC-1 cells increased with incubation time.

Conclusions: To our knowledge, this study provides the first metabolic measurements of individual Nitrospirota MTB cells to decipher their ecophysiological traits. The procedure constructed in this study provides a promising strategy to simultaneously investigate the morphology, genome, and ecophysiology of uncultured microbes in natural environments. Video Abstract.

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来源期刊
Microbiome
Microbiome MICROBIOLOGY-
CiteScore
21.90
自引率
2.60%
发文量
198
审稿时长
4 weeks
期刊介绍: Microbiome is a journal that focuses on studies of microbiomes in humans, animals, plants, and the environment. It covers both natural and manipulated microbiomes, such as those in agriculture. The journal is interested in research that uses meta-omics approaches or novel bioinformatics tools and emphasizes the community/host interaction and structure-function relationship within the microbiome. Studies that go beyond descriptive omics surveys and include experimental or theoretical approaches will be considered for publication. The journal also encourages research that establishes cause and effect relationships and supports proposed microbiome functions. However, studies of individual microbial isolates/species without exploring their impact on the host or the complex microbiome structures and functions will not be considered for publication. Microbiome is indexed in BIOSIS, Current Contents, DOAJ, Embase, MEDLINE, PubMed, PubMed Central, and Science Citations Index Expanded.
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