Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere.,The ISME Journal

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Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere.
The ISME Journal ( IF 10.8 ) Pub Date : 2019-11-21 , DOI: 10.1038/s41396-019-0557-y
Devin F R Doud ₁ , Robert M Bowers ₁ , Frederik Schulz ₁ , Markus De Raad ₂ , Kai Deng _{3,

4} , Angela Tarver ₁ , Evan Glasgow _{5,

6} , Kirk Vander Meulen _{5,

6} , Brian Fox _{5,

6} , Sam Deutsch ₁ , Yasuo Yoshikuni _{1,

2,

7} , Trent Northen _{1,

2} , Brian P Hedlund ₈ , Steven W Singer _{3,

7} , Natalia Ivanova _{1,

2} , Tanja Woyke _{1,

2,

9}

Affiliation

Assigning a functional role to a microorganism has historically relied on cultivation of isolates or detection of environmental genome-based biomarkers using a posteriori knowledge of function. However, the emerging field of function-driven single-cell genomics aims to expand this paradigm by identifying and capturing individual microbes based on their in situ functions or traits. To identify and characterize yet uncultivated microbial taxa involved in cellulose degradation, we developed and benchmarked a function-driven single-cell screen, which we applied to a microbial community inhabiting the Great Boiling Spring (GBS) Geothermal Field, northwest Nevada. Our approach involved recruiting microbes to fluorescently labeled cellulose particles, and then isolating single microbe-bound particles via fluorescence-activated cell sorting. The microbial community profiles prior to sorting were determined via bulk sample 16S rRNA gene amplicon sequencing. The flow-sorted cellulose-bound microbes were subjected to whole genome amplification and shotgun sequencing, followed by phylogenetic placement. Next, putative cellulase genes were identified, expressed and tested for activity against derivatives of cellulose and xylose. Alongside typical cellulose degraders, including members of the Actinobacteria, Bacteroidetes, and Chloroflexi, we found divergent cellulases encoded in the genome of a recently described candidate phylum from the rare biosphere, Goldbacteria, and validated their cellulase activity. As this genome represents a species-level organism with novel and phylogenetically distinct cellulolytic activity, we propose the name Candidatus 'Cellulosimonas argentiregionis'. We expect that this function-driven single-cell approach can be extended to a broad range of substrates, linking microbial taxonomy directly to in situ function.

中文翻译：

功能驱动的单细胞基因组学揭示了稀有生物圈中的纤维素降解细菌。

历史上，为微生物分配功能性角色依赖于培养分离物或使用后验功能知识检测基于环境基因组的生物标志物。然而，功能驱动的单细胞基因组学这一新兴领域旨在通过基于原位功能或特征识别和捕获单个微生物来扩展这一范式。为了识别和表征参与纤维素降解的尚未培养的微生物类群，我们开发并基准测试了功能驱动的单细胞筛选，我们将其应用于居住在内华达州西北部大沸泉 (GBS) 地热场的微生物群落。我们的方法包括将微生物招募到荧光标记的纤维素颗粒上，然后通过荧光激活细胞分选分离单个微生物结合的颗粒。通过批量样品 16S rRNA 基因扩增子测序确定分选前的微生物群落概况。对流分选的纤维素结合微生物进行全基因组扩增和鸟枪测序，然后进行系统发育定位。接下来，鉴定、表达并测试推定的纤维素酶基因对纤维素和木糖衍生物的活性。除了典型的纤维素降解剂，包括放线菌、拟杆菌和绿曲菌的成员，我们在最近描述的来自稀有生物圈的候选门金细菌的基因组中发现了不同的纤维素酶，并验证了它们的纤维素酶活性。由于这个基因组代表了一种具有新的和系统发育上不同的纤维素分解活性的物种水平的生物，我们建议命名 Candidatus ' 银纤维单胞菌'。我们期望这种功能驱动的单细胞方法可以扩展到广泛的底物，将微生物分类直接与原位功能联系起来。

更新日期：2020-01-17

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