Unraveling regulatory networks in biological nutrient removal (BNR) microbiomes

解开生物营养去除（BNR）微生物组中的调控网络

• 批准号: 1803055
• 负责人: Daniel Noguera
• 金额: $ 33万
• 依托单位: University of Wisconsin-Madison
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2023-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1803055&HistoricalAwards=false
• 关键词: Unraveling; regulatory; networks; biological; nutrient; Unraveling; regulatory; networks; biological; nutrient

A large fraction of the energy cost in operating a wastewater treatment plant is supplying oxygen to the microorganisms performing the treatment process. These costs would decrease if treatment plants could be operated under low-oxygen conditions. It remains unknown how microorganisms adapt to low-oxygen conditions and whether treatment plants can be effectively operated with minimal oxygen aeration. This project will reveal how key microorganisms in wastewater treatment systems regulate their internal gene networks in response to plant operations with minimal aeration. Other impacts of the project include educational activities related to mentoring high school, undergraduate, and graduate students, and advancing the understanding of gene regulation in natural and engineered environments. If successful, this project will provide transformative information that can help protect the Nation's water security through advanced treatment processes to remove both reactive nitrogen and phosphorus.This proposal seeks to develop and test a framework to study transcriptional regulation in complex microbiomes. Specifically, the framework will be used to investigate transcriptional regulatory networks (TRNs) in an ammonia-oxidizing bacterium and a polyphosphate accumulating organism identified as major contributors to a biological nutrient removal (BNR) microbiome. This microbiome is maintained in a high-rate BNR bioreactor operated using cycles of anaerobic and micro-aerobic conditions. The proposed framework involves: (i) the use of metagenomic data to assemble genomes of key organisms; time-series metatranscriptomic data to identify gene expression patterns in the organisms of interest; (ii) chromatin immunoprecipitation (ChIP) followed by genome-scale DNA sequencing (ChIP-seq) to identify genes directly targeted by a specific transcription factor (TF); and (iii) an in silico phylogenomic approach to predict sets of co-regulated genes in assembled genomes. The project consists of four Tasks. Task 1 focuses on improving genome assembly by using novel tools, obtaining long DNA sequence reads with an emerging sequencing technology, and creating enrichments of the organisms of interest. Task 2 relates to the use ChIP-seq to experimentally identify genes in Nitrosomonas strain UW-LDO-1 targeted by ANR. Task 3 will use ChIP-seq to target RegA, ANR, and DNR - three TFs hypothesized to control aerobic and anoxic respiration in Accumulibacter strain UW-TNR-IC. Task 4 consists of an in silico reconstruction of large-scale TRNs of Nitrosomonas UW-LDO-1 and Accumulibacter UW-TNR-IC. The effective use of this integrative systems biology methodology is transformational because it is the first attempt at assembling a TRN in uncultured microbes using a combination of experimental and computational approaches. This project will provide the first analysis of how respiration is regulated at the transcription level in two key organisms.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.

在运营的废水处理厂中，很大一部分能源成本正在为执行治疗过程的微生物提供氧气。如果可以在低氧条件下运营治疗厂，这些成本将降低。微生物如何适应低氧条件以及是否可以使用最小的氧气曝气有效运行处理植物仍然未知。该项目将揭示废水处理系统中的关键微生物如何调节其内部基因网络，以响应植物的运营，并以最小的充气量调节其内部基因网络。该项目的其他影响包括与指导高中，本科生和研究生有关的教育活动，以及在自然和工程环境中促进对基因调节的理解。如果成功的话，该项目将提供变革性的信息，可以通过先进的治疗过程来消除反应性氮和磷。该提案旨在开发和测试一个框架，以研究复杂微生物中的转录调节框架。具体而言，该框架将用于研究氨氧化细菌中的转录调节网络（TRN）和鉴定为生物营养清除（BNR）微生物组的主要因素的多磷酸盐积累的生物。该微生物组维持在使用厌氧和微氧化物条件的循环进行的高速BNR生物反应器中。提出的框架涉及：（i）使用元基因组数据来组装关键生物的基因组；时间序列的元转录数据，以识别感兴趣的生物中的基因表达模式； （ii）染色质免疫沉淀（CHIP），然后是基因组尺度DNA测序（CHIP-SEQ），以识别由特定转录因子（TF）直接靶向的基因； （iii）一种用于预测组装基因组中共同调节基因集的硅系统基因方法。该项目由四个任务组成。任务1专注于通过使用新颖的工具来改善基因组组装，通过新兴的测序技术获得长的DNA序列读取，并创造出感兴趣的生物的丰富。任务2与使用CHIP-SEQ相关的，以实验性地识别ANR靶向的硝基瘤菌株UW-LDO-1中的基因。任务3将使用CHIP-SEQ靶向Rega，ANR和DNR-三个TFS，假设在累积的菌株UW-TNR-IC中控制有氧和缺氧呼吸。任务4由硝基诺氏菌UW-LDO-1和累积UW-TNR-IC的大规模TRN的硅重建组成。这种综合系统生物学方法的有效使用是转化的，因为它是使用实验和计算方法组合在未培养的微生物中组装TRN的尝试。该项目将对如何在两个关键有机体的转录级别进行呼吸进行首次分析。该奖项反映了NSF的法定任务，并被认为值得通过基金会的知识分子优点和更广泛的影响评估标准通过评估来提供支持。