Validating the Cyc2 neutrophilic Fe oxidation pathway using meta-omics of Zetaproteobacteria iron mats at marine hydrothermal vents

Abstract

27 Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making 28 them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic 29 Fe-oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a 30 homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans. However, Cyc2 function is 31 not well verified in neutrophilic Fe-oxidizers, particularly in Fe-oxidizing environments. Toward 32 this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-33 quality metagenome assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, 34 Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis 35 demonstrated conservation of Cyc2 sequences among most neutrophilic Fe-oxidizers, suggesting 36 a common function. We confirmed the widespread distribution of cyc2 and other model Fe 37 oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of 38

Microbial chemolithotrophy mediates oxidative weathering of granitic bedrock

“…This process, termed extracellular electron transfer (EET), was originally recognized in dissimilatory Fe(III)-reducing organisms (32), but has subsequently been shown to be utilized by FeOB (33,34). Homologs to the Cyc2-type EET system have been found to be present in a broad range of FeOB genomes, including those of aerobic neutrophilic FeOB (33,35), and recently validated via metaomics (36). Organisms of the genera Ralstonia and Rhodopseudomonas which are known to harbor FeOB (37,38) were among the top 10 genera in the enrichment culture based on read classification (SI Appendix, Fig.…”

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

“…FeGenie demonstrates the potential for iron oxidation and reduction in environments that are rich in reduced iron, including the Rifle Aquifer (Jewell et al, 2016), Jinata Hot Springs (Ward, 2017;Ward et al, 2019), and iron mats found at the Loihi Seamount, Mid-Atlantic Ridge, and Mariana Backarc hydrothermal vent (McAllister et al, 2019). FeGenie also demonstrates the potential for these metabolisms to occur in other environments, including the Amazon river plume (Satinsky et al, 2017) and in the open ocean (Tully et al, 2018) (Figure 5A).…”

“…For determination of iron oxidation potential, we included the candidate iron oxidase from acidophilic and neutrophilic iron-oxidizing bacteria, Cyc2 (Barco et al, 2015). As shown by McAllister et al (2019), Cyc2 is represented by three phylogenetically distinct clusters; thus, we constructed three different HMMs, specific to each cluster. Cluster 1 includes sequences from most known, well-established neutrophilic ironoxidizers but is yet to be genetically or biochemically verified as an iron oxidase.…”

“…Genes associated with dissimilatory iron reduction often coincide with those for iron oxidation. Exceptions to this include the upper centimeters (i.e., syringe samples) of iron mats from Loihi and the Mariana Backarc (McAllister et al, 2019); these samples encode many genes for iron oxidation but have no genes linked exclusively to iron reduction. This may indicate that (1) iron reducers form a non-detectable fraction of the community in those samples, (2) that the geochemical regimes present there do not favor dissimilatory iron reduction, or (3) that there are other, currently unknown, mechanisms for iron reduction occurring.…”

“…This may indicate that (1) iron reducers form a non-detectable fraction of the community in those samples, (2) that the geochemical regimes present there do not favor dissimilatory iron reduction, or (3) that there are other, currently unknown, mechanisms for iron reduction occurring. For example, the surficial iron mat sample from the Loihi Seamount appears to have the highest number of genes related to iron oxidation, and none related to iron reduction; it also happens to be the sample dominated by the iron-oxidizing Zetaproteobacteria at 96% relative abundance (McAllister et al, 2019). Nonetheless, the predicted occurrence of iron reduction in most (7 out of 10) FIGURE 5 | (A) Dot plot showing the distribution of iron genes on 27 metagenomes and (B) a scaled heatmap with accompanying dendrogram that represents hierarchical clustering of metagenome datasets based on identified iron genes.…”