Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents
Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents
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DOI：
10.1128/msystems.00553-19
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发表时间：
2020-02
期刊：
影响因子：
6.4
通讯作者：
S. McAllister;Shawn W. Polson;D. Butterfield;B. Glazer;J. Sylvan;C. Chan
中科院分区：
文献类型：
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作者：
S. McAllister;Shawn W. Polson;D. Butterfield;B. Glazer;J. Sylvan;C. Chan
氧化铁是土壤、水供应和生态系统的重要组成部分，因为它们隔离了养分、碳和金属。微生物可以形成铁氧化物，但目前还不清楚这是否是环境中的一个重要机制。与其他主要的微生物能量代谢不同，没有铁氧化的标记基因，阻碍了我们追踪这些微生物的能力。在这里，我们研究了一种可能的铁氧化基因，Cyc2，在富含铁的热液喷口，在那里铁氧化微生物占主导地位。我们拼凑了不同的泽塔变形杆菌基因组，比较了这些基因组，并分析了cyc2和其他假想的铁氧化基因的表达。我们发现，Cyc2在铁氧化剂中广泛存在，并且高度表达并受到潜在的调控，使其成为铁氧化能力的良好标记，并有可能成为活性的标记。这些发现将帮助我们理解和潜在地量化中性铁氧化剂在各种海洋和陆地环境中的影响。摘要Zeta变形杆菌在海洋热液喷口产生大量的氧化铁(Fe)垫，使其成为在近中性pH条件下微生物氧化铁的理想模型。中性铁氧化剂分离株的基因组比较揭示了一种假设的铁氧化途径，其特征是与氧化亚铁硫杆菌的铁氧化酶Cyc2同源。然而，Cyc2在中性铁氧化剂中的功能还没有得到很好的验证，特别是在铁氧化环境中。对此，我们使用了53个新的高质量元基因组组装的基因组，这些基因组是从中大西洋海脊、马里亚纳背弧岛和洛伊希海山(夏威夷)的热液喷口的铁垫上重建的，我们分析了泽塔蛋白细菌的基因组和转录本。系统发育分析表明，Cyc2序列在大多数嗜中性铁氧化剂中是保守的，这表明它们具有共同的功能。我们证实了Cyc2和其他模型铁氧化途径基因在所有代表ZetaProtecteria谱系的ZetaProducteria中的广泛分布。在多种环境条件下和培养条件下，这些基因在不同的Zeta蛋白细菌中都有高表达。推测的铁氧化酶基因cyc2在原位高表达，通常是最高表达的基因。在Fe(II)修饰的培养中，cyc2基因的表达增加，相应地，固碳和中枢代谢基因的表达也增加。这些结果证实了中性粒细胞中以Cyc2为基础的铁氧化途径，并证明了其在海洋铁矿化环境中的意义。重要性氧化铁是土壤、水供应和生态系统的重要组成部分，因为它们隔离养分、碳和金属。微生物可以形成铁氧化物，但目前还不清楚这是否是环境中的一个重要机制。与其他主要的微生物能量代谢不同，没有铁氧化的标记基因，阻碍了我们追踪这些微生物的能力。在这里，我们研究了一种可能的铁氧化基因，Cyc2，在富含铁的热液喷口，在那里铁氧化微生物占主导地位。我们拼凑了不同的泽塔变形杆菌基因组，比较了这些基因组，并分析了cyc2和其他假想的铁氧化基因的表达。我们发现，Cyc2在铁氧化剂中广泛存在，并且高度表达并受到潜在的调控，使其成为铁氧化能力的良好标记，并有可能成为活性的标记。这些发现将帮助我们理解和潜在地量化中性铁氧化剂在各种海洋和陆地环境中的影响。
Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse Zetaproteobacteria genomes, compared these genomes, and analyzed expression of cyc2 and other hypothetical iron oxidation genes. We show that cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments. ABSTRACT Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans. However, Cyc2 function is not well verified in neutrophilic Fe oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome-assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions and in incubations. The putative Fe oxidase gene cyc2 was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments. IMPORTANCE Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse Zetaproteobacteria genomes, compared these genomes, and analyzed expression of cyc2 and other hypothetical iron oxidation genes. We show that cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments.