Developing a functional marker gene for Fe oxidation

开发铁氧化功能标记基因

• 批准号: 1833525
• 负责人: Clara Chan
• 金额: $ 43.91万
• 依托单位: University of Delaware
• 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: 2018-08-15 至 2024-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1833525&HistoricalAwards=false
• 关键词: Developing; functional; marker; gene; Fe

Iron (Fe) is the 4th most abundant element in Earth's crust (5% by mass) - its abundance and chemical properties make it a critical element in biological and environmental processes. As a nutrient, Fe availability is a key determinant of ecological success. In soils and aquifers, Fe oxides (rust minerals) sequester many other nutrients and toxic metals, therefore controlling bioavailability and transport. Thus, the formation of Fe oxides affects water, food, and ecological resources. Fe oxides can be formed by iron-oxidizing bacteria (FeOB), which have been implicated in soil formation, corrosion, water purification, and bioremediation. However, since Fe can also oxidize abiotically, it is currently unclear to what extent microbes actually influence Fe oxidation in these and other environmental processes. Thus, the primary goal of this proposal is to develop a gene-based assay for microbial Fe oxidation, by determining the key gene(s) involved. A gene-based assay, coupled to systems-level understanding, would allow to determine controls on FeOB activity, and perhaps use these organisms for soil and water remediation. This project will train a range of students in interdisciplinary problem solving for geomicrobiology. Outreach will include an annual camp for 5th-8th grade girls, who are low-income minorities. Investigators will also develop new training modules on metatranscriptomic best practices and incorporate experiments into undergraduate classes. The team will present project findings to the general public through venues such as Science Cafe and Coast Day.Recent genomics, proteomics, and metatranscriptomics work strongly suggests that an outer membrane cytochrome, Cyc2, is a widespread Fe oxidase in FeOB, and also suggests a potential role for another outer membrane cytochrome MtoA, a homolog of the Fe reductase MtrA. When cyc2 or mtoA is found in genomes or transcriptomes, does this indicate microbial Fe oxidation capability/activity? To answer this, there is a need for evidence that cyc2/Cyc2 or mtoA/MtoA is specific to Fe oxidation. A challenge is that FeOB isolates typically grow exclusively on Fe(II), making it impossible to know which genes are specifically expressed for Fe oxidation. This study takes advantage of a group of FeOB isolates that also grow on other electron donors: Sideroxydans lithotrophicus and Thiomonas spp. Most of these strains are not well-characterized, so investigators will develop these as model, facultative FeOB to test which genes are specifically expressed during Fe oxidation, using transcriptomics and RT-qPCR. Beyond cyc2 and mtoA, they aim to determine additional key genes in the Fe oxidation pathway, so that they can propose a suite of markers, which they will test in environmental metatranscriptomes from an Fe-rich peatland and acid mine drainage sediments. The proposed work represents the next steps required to truly determine FeOB roles in the environment. A robust set of Fe oxidation genetic markers would allow biogeochemists to better understand the influence of FeOB on Fe cycling, and further, how they couple Fe oxidation to cycling of C, N, P, S, As, and other metals important to water and soil quality.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.

铁 (Fe) 是地壳中第四丰富的元素（按质量计 5%） - 其丰度和化学性质使其成为生物和环境过程中的关键元素。作为一种营养素，铁的可用性是生态成功的关键决定因素。在土壤和含水层中，铁氧化物（铁锈矿物质）会隔离许多其他营养物质和有毒金属，从而控制生物利用度和运输。因此，铁氧化物的形成会影响水、食物和生态资源。铁氧化物可由铁氧化细菌 (FeOB) 形成，与土壤形成、腐蚀、水净化和生物修复有关。然而，由于铁也可以非生物氧化，目前尚不清楚微生物在这些和其他环境过程中实际上在多大程度上影响铁的氧化。因此，该提案的主要目标是通过确定所涉及的关键基因，开发一种基于基因的微生物铁氧化测定方法。基于基因的测定与系统级的理解相结合，将允许确定对 FeOB 活性的控制，并可能利用这些生物体进行土壤和水修复。该项目将培训一系列学生解决地球微生物学的跨学科问题。外展活动将包括为低收入少数族裔 5 至 8 年级女孩举办年度夏令营。研究人员还将开发有关元转录组最佳实践的新培训模块，并将实验纳入本科生课程。该团队将通过 Science Cafe 和 Coast Day 等场所向公众展示项目研究结果。最近的基因组学、蛋白质组学和宏转录组学工作强烈表明，外膜细胞色素 Cyc2 是 FeOB 中广泛存在的 Fe 氧化酶，并且还表明另一种外膜细胞色素 MtoA（Fe 还原酶 MtrA 的同源物）的潜在作用。当在基因组或转录组中发现 cyc2 或 mtoA 时，这是否表明微生物具有铁氧化能力/活性？为了回答这个问题，需要有证据表明 cyc2/Cyc2 或 mtoA/MtoA 对 Fe 氧化具有特异性。一个挑战是 FeOB 分离株通常只在 Fe(II) 上生长，因此不可能知道哪些基因专门表达 Fe 氧化。这项研究利用了一组也在其他电子供体上生长的 FeOB 分离株：Sideroxydans lithotropicus 和 Thiomonas spp。这些菌株中的大多数都没有得到很好的表征，因此研究人员将开发它们作为模型、兼性 FeOB，以使用转录组学和 RT-qPCR 来测试哪些基因在 Fe 氧化过程中特异性表达。除了 cyc2 和 mtoA 之外，他们的目标是确定 Fe 氧化途径中的其他关键基因，以便他们可以提出一套标记，他们将在来自富铁泥炭地和酸性矿山排水沉积物的环境宏转录组中测试这些标记。拟议的工作代表了真正确定 FeOB 在环境中的角色所需的后续步骤。一组强大的 Fe 氧化遗传标记将使生物地球化学家能够更好地了解 FeOB 对 Fe 循环的影响，以及它们如何将 Fe 氧化与 C、N、P、S、As 和其他对水和水重要的金属的循环结合起来。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力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

Ligand Effects on Biotic and Abiotic Fe(II) Oxidation by the Microaerophile Sideroxydans lithotrophicus

微需氧微生物氧化铁盐对生物和非生物 Fe(II) 氧化的配体效应

• DOI: 10.1021/acs.est.1c00497
• 发表时间: 2021-07
• 期刊: Environmental Science & Technology
• 影响因子: 11.4
• 作者: Zhou, Nanqing;Luther, George W.;Chan, Clara S.
• 通讯作者: Chan, Clara S.

Mixotrophic Iron-Oxidizing Thiomonas Isolates from an Acid Mine Drainage-Affected Creek

从受酸性矿井排水影响的小溪中分离出混合营养型铁氧化硫单胞菌

• DOI: 10.1128/aem.01424-20
• 发表时间: 2020-11
• 期刊: Applied and Environmental Microbiology
• 影响因子: 4.4
• 作者: Akob, Denise M.;Hallenbeck, Michelle;Beulig, Feli;Fabisch, Maria;Küsel, Kirsten;Keffer, Jessica L.;Woyke, Tanja;Shapiro, Nicole;Lapidus, Alla;Klenk, Hans;et al
• 通讯作者: et al

FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies

FeGenie：用于识别基因组和宏基因组组合中铁基因和铁基因邻域的综合工具

• DOI: 10.3389/fmicb.2020.00037
• 发表时间: 2020-01
• 期刊: Frontiers in Microbiology
• 影响因子: 5.2
• 作者: Garber, Arkadiy I.;Nealson, Kenneth H.;Okamoto, Akihiro;McAllister, Sean M.;Chan, Clara S.;Barco, Roman A.;Merino, Nancy
• 通讯作者: Merino, Nancy

Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms

Gallionellaceae 全基因组分析揭示了系统发育、代谢灵活性和铁氧化机制的见解

• DOI: 10.1128/msystems.00038-23
• 发表时间: 2023-12
• 期刊: mSystems
• 影响因子: 6.4
• 作者: Hoover, Rene L.;Keffer, Jessica L.;Polson, Shawn W.;Chan, Clara S.
• 通讯作者: Chan, Clara S.

Draft Genome Sequence of Sideroxydans sp. Strain CL21, an Fe(II)-Oxidizing Bacterium

Sideroxydans sp. 的基因组序列草案。

• DOI: 10.1128/mra.01444-19
• 发表时间: 2020-01
• 期刊: Microbiology Resource Announcements
• 影响因子: 0.8
• 作者: Cooper, Rebecca E.;Wegner, Carl;McAllister, Sean M.;Shevchenko, Olga;Chan, Clara S.;Küsel, Kirsten;Stewart, Frank J.
• 通讯作者: Stewart, Frank J.