The zetaproteobacteria: ecology and metabolic functions of a model neutrophilic Fe-oxidizing clade
| Author(s) | McAllister, Sean M. | |
| Date Accessioned | 2022-09-23T11:31:57Z | |
| Date Available | 2022-09-23T11:31:57Z | |
| Publication Date | 2019 | |
| SWORD Update | 2022-08-11T19:09:49Z | |
| Abstract | Microbially-mediated Fe oxidation has been recognized in the environment since the work of Ehrenberg, Kützing, and Winogradsky in the mid 1800s. However, difficulty in culturing these organisms has led our understanding of the mechanisms of Fe oxidation to fall behind other environmentally-relevant microbial processes. This is particularly true for the marine environment, where the first conclusive evidence for microbially-mediated Fe oxidation was not shown until 2002 in isolates of the Zetaproteobacteria. Our knowledge of Zetaproteobacteria ecological distribution and taxonomy make them one of the best understood clades of neutrophilic Fe oxidizers. Combined with their high abundance in hydrothermal environments and apparent widespread capacity for Fe oxidation, the Zetaproteobacteria are a useful model for determining the mechanism and significance of neutrophilic Fe oxidation in the environment. However, to develop the Zetaproteobacteria as a model we need a better understanding of their taxonomic diversity, genome potential, and gene expression, which will help us to understand the variation in their Fe oxidation-driven metabolism. To this end, we focus on a synthesis of Zetaproteobacteria ecology, genome content, and patterns in gene expression in this dissertation. ☐ To understand the ecology of the Zetaproteobacteria, previous research focused primarily on surveys of the small subunit ribosomal RNA (SSU rRNA or 16S rRNA) gene and on physiological inferences from isolates. By synthesizing this disconnected information, we show that diverse Zetaproteobacteria operational taxonomic units (ZOTUs) are enriched in particular habitats and co-exist with each other. From Zetaproteobacteria genomes, we infer that O2, H2, and nitrate source are likely to correspond with Zetaproteobacteria niches, and review the current understanding of the neutrophilic Fe oxidation pathway. A better understanding of this Fe oxidation pathway is key to testing whether all Zetaproteobacteria are Fe oxidizers, which would make them a remarkably metabolically cohesive group. ☐ Most information on the Zetaproteobacteria comes from deep sea hydrothermal vent ecosystems, though they are also found in coastal habitats. Near-shore circumneutral Fe cycling can have a large impact on coastal water quality, particularly through the dissolution and formation of Fe oxides within beach aquifers. These processes can affect the discharge of heavy metals and toxins into estuaries through submarine groundwater discharge. However, few studies have looked at the microbial influences on these significant processes. In this environment, analysis of Zetaproteobacteria distribution suggests they play a significant role in Fe oxidation in oxic surface sediments, particularly where worm burrows circulate seawater into the subsurface. However, we found the Zetaproteobacteria only at very low abundance within the intertidal mixing zone. Instead, the location and composition of the Fe-mineralized zone was affected by a combination of abiotic processes and Fe- and S-cycling microbes, all influenced by solute fluxes within the system. Thus, microbial Fe oxidation plays a partial role in influencing the fate of Fe-mineralization in intertidal aquifers, ultimately affecting the transport of solutes bound for export into coastal waters. ☐ Developing a standardized taxonomy of the Zetaproteobacteria is critical for understanding their significance and variable impacts on geochemical cycling in the environment. For this reason, we developed tools for classifying Zetaproteobacteria using the 16S rRNA gene (ZetaHunter) and whole genome analyses (ribosomal protein tree, average amino acid identity, and average nucleotide identity). In total, we classified the Zetaproteobacteria into 1 order, 2 families, 11 genera, 59 ZOTUs, and 20 species. This work will allow us to better track and understand the activity and influence of the diverse Zetaproteobacteria. ☐ In order to understand the significance of Zetaproteobacteria Fe oxidation in the environment, we need to better understand the mechanisms of the Fe oxidation pathway. Comparative isolate genomics has revealed a hypothetical pathway, featuring the putative Fe oxidase Cyc2. However the function of Cyc2 has not been verified, particularly in the environment. Using paired metagenomics and metatranscriptomics from three hydrothermal venting regions, we provide 53 new, high quality Zetaproteobacteria genomes representing the breadth of Zetaproteobacteria diversity. These genomes allow us to test the distribution and expression of this pathway. We found that all represented Zetaproteobacteria lineages possessed a complete aerobic Fe oxidation pathway. The cyc2 gene was highly expressed in situ, often as the highest expressed gene in a genome. Additionally, we found that all Zetaproteobacteria increased their cyc2 expression after Fe(II) amendment to an Fe mat sample, though some Zetaproteobacteria were already poised for Fe oxidation. Finally, we were able to use the Zetaproteobacteria core genome to identify genes characteristic of neutrophilic Fe oxidation that have been shared with the Gallionellaceae, suggesting an evolutionary history of horizontal gene transfer. Combined, these data validate the proposed Fe oxidation pathway, reinforce our assumptions of the capabilities of the Zetaproteobacteria as a group, will support efforts to detect Fe oxidation activity using genetic markers, and acted as a starting point for understanding the selective forces driving the evolution of neutrophilic Fe oxidation. ☐ Fe oxidation is a common feature of all Zetaproteobacteria, yet their taxonomic diversity suggests that other adaptations have driven diversification of the clade. For each Zetaproteobacteria lineage, these adaptations correspond with different effects on geochemical cycling. Thus far, we have found these adaptations primarily revolve around Fe, O2, N, H2, and As cycling. Most Zetaproteobacteria possess different and multiple options for genes at each step of the Fe oxidation pathway. Some of these genes may reflect environmental preferences, such as the preferential expression of terminal oxidases with varying O2 affinities. We also find genes for nitrate reduction primarily in the Mariprofundaceae while nitric oxide and nitrous oxide detoxification genes are primarily in Family 2. Dividing the denitrification pathway between Zetaproteobacteria families suggests that members from both clades can cooperate for detoxification. Two specific physiological traits for the Zetaproteobacteria were also explored, both found in limited subclades of their represented taxa. H2 oxidation, found in isolate Ghiorsea bivora, was limited to the marine ZOTU9 clade. Arsenite oxidase, a potential respiratory enzyme previously unexplored in the Zetaproteobacteria, was found in a subclade of ZOTU4. Together, these findings from the Zetaproteobacteria pangenome highlight the importance of differentiating Zetaproteobacteria lineages for understanding their significance and effects on geochemical cycling. Overall, through improving our understanding of their ecological distribution, validating the expression and importance of the putative Fe oxidation mechanism, and exploring the metabolic diversity of the Zetaproteobacteria, we are better able to understand their significance and geochemical influence in the environment. | en_US |
| Advisor | Chan, Clara S. | |
| Degree | Ph.D. | |
| Department | University of Delaware, School of Marine Science and Policy | |
| DOI | https://doi.org/10.58088/97k2-4c17 | |
| Unique Identifier | 1345517223 | |
| URL | https://udspace.udel.edu/handle/19716/31407 | |
| Language | en | |
| Publisher | University of Delaware | en_US |
| URI | https://login.udel.idm.oclc.org/login?url=https://www.proquest.com/dissertations-theses/zetaproteobacteria-ecology-metabolic-functions/docview/2704863516/se-2?accountid=10457 | |
| Keywords | Environmental gene expression | |
| Keywords | Fe oxidation | |
| Keywords | Marine Fe cycling | |
| Keywords | Microbial ecology | |
| Keywords | Microbial taxonomy | |
| Keywords | Zetaproteobacteria | |
| Title | The zetaproteobacteria: ecology and metabolic functions of a model neutrophilic Fe-oxidizing clade | en_US |
| Type | Thesis | en_US |