Collaborative Research: Microdiversity drives ecosystem function: SAR11 bacteria as models for oceanic nitrogen loss

合作研究：微多样性驱动生态系统功能：SAR11 细菌作为海洋氮流失的模型

• 批准号: 2129823
• 负责人: Konstantinos Konstantinidis
• 金额: $ 43.66万
• 依托单位: Georgia Tech Research Corporation
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-12-01 至 2024-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2129823&HistoricalAwards=false
• 关键词: Collaborative; Research; Microdiversity; drives; ecosystem

This project studies how low oxygen availability influences the biodiversity and ecological role of SAR11 bacteria, one of the most abundant microbial groups in the ocean. The work involves oceanographic sampling across a range of oxygen and nutrient levels in the Eastern Tropical North Pacific Ocean. Using a combination of genomic, microbiological, and biogeochemical methods, the study identifies the mechanisms by which SAR11 strains diversify into separate niches and species and contribute biochemically to the ecosystem, likely through removing nitrogen from seawater. The project equips the next generation of researchers and educators, notably those from underrepresented minority groups, to use oceanographic, genomic, and microbiological concepts to meet contemporary scientific challenges. This goal is met through a combination of bioinformatic workshops that target undergraduate students from the University System of Puerto Rico, middle school teacher-training workshops, and middle or high school teacher internships in the investigator’s labs. This multifaceted research and educational agenda fills a gap in our understanding of marine biological diversity, identifies the contribution of SAR11 bacteria to nutrient and carbon cycles in low oxygen oceans, and provides lessons and analytical tools to study microbial processes in other ecosystems.This project has two aims. Aim 1 employs comparative metagenomic and single-cell genomic analyses to identify metabolic properties that distinguish SAR11 clades from low oxygen regions and processes of selection or gene flow operating across the clades. Aim 2 combines microbial transcriptomics, incubation experiments with isotope tracers, and culturing to delimit the oxygen and nutrient conditions that define the niche space of each SAR11 clade and to correlate SAR11 gene transcription with community biochemical outcomes, including nitrogen loss through denitrification. The results of these aims and the informatic methods used to probe microbial microdiversity are disseminated through genomics-focused undergraduate workshops, and new teacher-training educational modules, including lab-based modules focused on the importance of microorganisms under environmental change in the oceans. Data, manuscripts, and informatics workflows from this project are made publicly available. The results are critical for resolving the processes that create and sustain microbial diversity in the oceans and informing biogeochemical models that predict how diversity influences ecosystem processes.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.

这个项目研究了低氧气供应如何影响SAR11细菌的生物多样性和生态作用，SAR11细菌是海洋中最丰富的微生物群体之一。这项工作涉及对东热带北太平洋的一系列氧气和营养水平进行海洋采样。利用基因组、微生物和生物地球化学方法相结合的方法，该研究确定了SAR11菌株多样化到不同的生态位和物种并对生态系统做出生化贡献的机制，可能是通过从海水中去除氮。该项目使下一代研究人员和教育工作者，特别是那些来自代表性不足的少数群体的研究人员和教育工作者，能够使用海洋学、基因组和微生物学的概念来应对当代的科学挑战。通过以波多黎各大学系统本科生为对象的生物信息学讲习班、中学教师培训讲习班和调查员实验室的初中或高中教师实习相结合的方式实现了这一目标。这一多方面的研究和教育议程填补了我们对海洋生物多样性理解的空白，确定了SAR11细菌对低氧海洋的营养和碳循环的贡献，并为研究其他生态系统中的微生物过程提供了经验教训和分析工具。目的1利用比较的后基因组和单细胞基因组分析来确定将SAR11分支与低氧区域和选择过程或跨分支的基因流动区分开来的代谢特性。目的2结合微生物转录学、孵化实验和同位素示踪剂，确定决定每个SAR11分支生态位空间的氧气和营养条件，并将SAR11基因转录与群落生化结果(包括通过反硝化作用损失的氮)相关联。这些目标的结果和用于探索微生物微生物多样性的信息学方法通过以基因组学为重点的本科讲习班和新的教师培训教育单元传播，包括侧重于海洋环境变化下微生物重要性的实验室单元。这个项目的数据、手稿和信息学工作流程都是公开的。这些结果对于解决在海洋中创造和维持微生物多样性的过程以及为预测多样性如何影响生态系统过程的生物地球化学模型提供信息是至关重要的。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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

Sequence‐discrete species for prokaryotes and other microbes: A historical perspective and pending issues

• DOI: 10.1002/mlf2.12088
• 发表时间: 2023-12
• 期刊: Mlife
• 作者: K. Konstantinidis

An ANI gap within bacterial species that advances the definitionsdefinitionsof intra-species units

细菌物种内的 ANI 差距推动了物种内单位的定义

• 发表时间: 2023
• 期刊: MBio
• 影响因子: 6.4
• 作者: Luis M. Rodriguez-R, 1 Roth

Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., S

两种培养和两种未培养的新盐杆菌属物种的描述，其中一种按照细菌学代码规则命名：Salinibactergrasmerensis sp。

• DOI: 10.1016/j.syapm.2023.126416
• 发表时间: 2023
• 期刊: Systematic and Applied Microbiology
• 影响因子: 3.4
• 作者: Viver, Tomeu;Conrad, Roth E.;Lucio, Marianna;Harir, Mourad;Urdiain, Mercedes;Gago, Juan F.;Suárez-Suárez, Ana;Bustos-Caparros, Esteban;Sanchez-Martinez, Rodrigo;Mayol, Eva
• 通讯作者: Mayol, Eva