Collaborative research: BEE: Discovery and characterization of novel microbial lineages in an early Earth analog sulfur-based ecosystem.

合作研究：BEE：早期地球模拟硫基生态系统中新型微生物谱系的发现和表征。

• 批准号: 2016423
• 负责人: Noha Youssef
• 金额: $ 57.78万
• 依托单位: Oklahoma State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2016423&HistoricalAwards=false
• 关键词: Collaborative; research; BEE; Discovery; characterization

Evolution of life on Earth is closely linked to geological changes occurring at its surface. Changes in early Earth’s geology and atmosphere drove the evolution of new microorganisms adapted to the prevailing new conditions. Consequently, growth of these newly-evolved microorganisms was associated with the production of new end products such as oxygen, carbon dioxide, and sulfides, that in turn greatly impacted the physical conditions on Earth in a never-ending feedback loop between biology and geology. So far, it is not clearly understood what types of microorganisms inhabited early Earth. Early unicellular lifeforms are fragile, boneless, and have not been preserved. Since direct sampling is impossible, an alternative approach based on the identification of current locations with conditions paralleling those prevailing in past eons is warranted. The researchers have identified a unique site in southwestern Oklahoma (Zodletone spring), where physical conditions at various locations in the spring remarkably correspond to conditions prevalent at various geological eons throughout Earth’s history. Therefore, spatial sampling in Zodletone spring can substitute for inaccessible temporal time scales. The project will utilize a range of cutting-edge laboratory methodologies to characterize the microbial community in this unique site. This knowledge will contribute to our understanding of how life evolved on Earth, and the prerequisites for its potential evolution on other planets and celestial objects within the solar system and beyond. The research will contribute to workforce training of multiple high-school, undergraduate, and graduate students in two states with special emphasis on students from groups that are underrepresented in science. The overall goal of this project is to identify and characterize novel bacterial lineages prevalent in Zodletone spring: a surficial, light-exposed, and euxinic (anoxic, sulfide-rich) habitat representing an early Earth analog. The researchers will characterize novel yet-uncultured bacterial lineages encountered in the spring using a combination of genome-resolved metagenomics, metabolic reconstruction, community transcriptomics, targeted isolation, and global diversity and pangenomic surveys. This will be achieved by: 1) Metabolic reconstruction to deduce the metabolic potential and physiological preferences of uncultured lineages recovered from various locations in the spring; 2) Validating the proposed metabolic capabilities and ecological roles using expression studies and reverse-genomics based isolation strategies, and; 3) Assessing the global distribution patterns and pangenomic diversity of the identified lineages using data mining approaches and comparative genomics strategies to trace the ecological success/retreat/extinction of these novel lineages.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

地球上生命的演化与其表面发生的地质变化密切相关。早期地球地质和大气的变化推动了新微生物的进化，以适应当时的新环境。因此，这些新进化的微生物的生长与氧气、二氧化碳和硫化物等新最终产物的产生有关，而这些最终产物反过来又在生物学和地质学之间永无止境的反馈循环中极大地影响了地球的物理条件。到目前为止，人们还不清楚什么类型的微生物居住在早期地球上。早期的单细胞生命形式是脆弱的，无骨的，并且没有被保存下来。由于直接采样是不可能的，一个替代的方法的基础上确定当前位置的条件平行的那些在过去的几年中普遍是有道理的。研究人员在俄克拉荷马州西南部确定了一个独特的地点（Zodletone spring），春季不同地点的物理条件与整个地球历史上各种地质时期的普遍条件非常一致。因此，Zodletone春天的空间采样可以替代无法访问的时间尺度。该项目将利用一系列尖端的实验室方法来表征这个独特地点的微生物群落。这些知识将有助于我们了解地球上的生命是如何进化的，以及它在太阳系内外的其他行星和天体上潜在进化的先决条件。该研究将有助于两个州的多所高中，本科和研究生的劳动力培训，特别强调来自科学代表性不足的群体的学生。 该项目的总体目标是识别和表征Zodletone泉中流行的新型细菌谱系：代表早期地球模拟物的表面活性剂，光照和缺氧（缺氧，富含硫化物）栖息地。研究人员将使用基因组解析宏基因组学，代谢重建，社区转录组学，靶向分离，全球多样性和泛基因组学调查的组合来表征春季遇到的新型尚未培养的细菌谱系。这将通过以下方式实现：1）代谢重建以推断春季从不同地点回收的未培养谱系的代谢潜力和生理偏好; 2）使用表达研究和基于反向基因组学的分离策略来验证所提出的代谢能力和生态作用，以及;第三章使用数据挖掘方法和比较基因组学策略评估已确定谱系的全球分布模式和泛基因组多样性追踪这些新的谱系的生态成功/撤退/灭绝。这个奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Spatiotemporal Analysis of the Water and Sediment Nile Microbial Community Along an Urban Metropolis

城市沿线水和沉积物尼罗河微生物群落的时空分析

• DOI: 10.1007/s00248-020-01674-8
• 发表时间: 2021
• 期刊: Microbial Ecology
• 影响因子: 3.6
• 作者: Eraqi, Walaa A.;ElRakaiby, Marwa T.;Megahed, Salwa A.;Yousef, Noha H.;Elshahed, Mostafa S.;Yassin, Aymen S.
• 通讯作者: Yassin, Aymen S.

Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the phylum

• DOI: 10.1111/1462-2920.15614
• 发表时间: 2021-06-05
• 期刊: ENVIRONMENTAL MICROBIOLOGY
• 影响因子: 5.1
• 作者: Murphy, Chelsea L.;Biggerstaff, James;Youssef, Noha H.
• 通讯作者: Youssef, Noha H.

Pectin in diet: Interactions with the human microbiome, role in gut homeostasis, and nutrient-drug interactions

• DOI: 10.1016/j.carbpol.2020.117388
• 发表时间: 2021-01-09
• 期刊: CARBOHYDRATE POLYMERS
• 影响因子: 11.2
• 作者: Elshahed, Mostafa S.;Miron, Anca;Farag, Mohamed A.
• 通讯作者: Farag, Mohamed A.

Genomes of Novel Myxococcota Reveal Severely Curtailed Machineries for Predation and Cellular Differentiation

• DOI: 10.1128/aem.01706-21
• 发表时间: 2021-12-01
• 期刊: APPLIED AND ENVIRONMENTAL MICROBIOLOGY
• 影响因子: 4.4
• 作者: Murphy, Chelsea L.;Yang, R.;Youssef, Noha H.
• 通讯作者: Youssef, Noha H.

Genomic analysis of family UBA6911 (Group 18 Acidobacteria) expands the metabolic capacities of the phylum and highlights adaptations to terrestrial habitats.

UBA6911 家族（酸杆菌第 18 组）的基因组分析扩大了该门的代谢能力，并强调了对陆地栖息地的适应。

• DOI: 10.1101/2021.04.09.439258
• 发表时间: 2021
• 期刊: bioRxiv
• 作者: Archana Yadav, Jenna Borrelli