Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics

Emerson, David; Field, Erin K.; Chertkov, Olga; Davenport, Karen W.; Goodwin, Lynne; Munk, Christine; Nolan, Matt; Woyke, Tanja

doi:10.3389/fmicb.2013.00254

Cited by 166 publications

(241 citation statements)

References 87 publications

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“…Acidophilic iron-oxidizing Leptospirillum spp. also show similarities at the amino-acid level to many of these genes (Emerson et al, 2013). Homologs to these genes were identified in 10 of the SAGs (Figure 6).…”

Section: Cytochromes and Electron Transportmentioning

confidence: 94%

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Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

et al. 2014

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The Zetaproteobacteria are a candidate class of marine iron-oxidizing bacteria that are typically found in high iron environments such as hydrothermal vent sites. As much remains unknown about these organisms due to difficulties in cultivation, single-cell genomics was used to learn more about this elusive group at Loihi Seamount. Comparative genomics of 23 phylogenetically diverse single amplified genomes (SAGs) and two isolates indicate niche specialization among the Zetaproteobacteria may be largely due to oxygen tolerance and nitrogen transformation capabilities. Only Form II ribulose 1,5-bisphosphate carboxylase (RubisCO) genes were found in the SAGs, suggesting that some of the uncultivated Zetaproteobacteria may be adapted to low oxygen and/or high carbon dioxide concentrations. There is also genomic evidence of oxygen-tolerant cytochrome c oxidases and oxidative stress-related genes, indicating that others may be exposed to higher oxygen conditions. The Zetaproteobacteria also have the genomic potential for acquiring nitrogen from numerous sources including ammonium, nitrate, organic compounds, and nitrogen gas. Two types of molybdopterin oxidoreductase genes were found in the SAGs, indicating that those found in the isolates, thought to be involved in iron oxidation, are not consistent among all the Zetaproteobacteria. However, a novel cluster of redox-related genes was found to be conserved in 10 SAGs as well as in the isolates warranting further investigation. These results were used to isolate a novel iron-oxidizing Zetaproteobacteria. Physiological studies and genomic analysis of this isolate were able to support many of the findings from SAG analyses demonstrating the value of these data for designing future enrichment strategies.

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Section: Cytochromes and Electron Transportmentioning

confidence: 94%

“…Emerson et al (2013) pointed out this large cluster, composed of two distinct subclusters, is conserved between strain PV-1 and S. lithotrophicus ES-1. Acidophilic iron-oxidizing Leptospirillum spp.…”

Section: Cytochromes and Electron Transportmentioning

confidence: 99%

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

et al. 2014

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“…constituted approximately 12% of a bacterial cDNA library from sediments beneath Robertson Glacier in the Canadian Rockies [78]. The only known cultured representative of the Sideroxydans are obligate chemoautotrophic iron and sulfur oxidizers [80], suggesting that these are important processes in subglacial ecosystems.…”

Section: (D) a Chemosynthetic Ecosystem Below Icementioning

confidence: 99%

Subglacial Lake Whillans microbial biogeochemistry: a synthesis of current knowledge

Mikucki

Lee

Ghosh

et al. 2016

Phil. Trans. R. Soc. A.

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Liquid water occurs below glaciers and ice sheets globally, enabling the existence of an array of aquatic microbial ecosystems. In Antarctica, large subglacial lakes are present beneath hundreds to thousands of metres of ice, and scientific interest in exploring these environments has escalated over the past decade. After years of planning, the first team of scientists and engineers cleanly accessed and retrieved pristine samples from a West Antarctic subglacial lake ecosystem in January 2013. This paper reviews the findings to date on Subglacial Lake Whillans and presents new supporting data on the carbon and energy metabolism of resident microbes. The analysis of water and sediments from the lake revealed a diverse microbial community composed of bacteria and archaea that are close relatives of species known to use reduced N, S or Fe and CH4 as energy sources. The water chemistry of Subglacial Lake Whillans was dominated by weathering products from silicate minerals with a minor influence from seawater. Contributions to water chemistry from microbial sulfide oxidation and carbonation reactions were supported by genomic data. Collectively, these results provide unequivocal evidence that subglacial environments in this region of West Antarctica host active microbial ecosystems that participate in subglacial biogeochemical cyclingauthorsversionPeer reviewe

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“…lithotrophicus' LD-1 (Weiss et al, 2007); 5, 'S. lithotrophicus' ES-1 (Emerson & Moyer, 1997;Emerson et al, 2013); 6, 'G. capsiferriformans' ES-2 (Emerson & Moyer, 1997;Emerson et al, 2013); 7, G. ferruginea (Hallbeck & Pedersen, 1990, 1991Hallbeck et al, 1993 *Components present at more than 10 % of the total fatty acids are given.…”

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confidence: 99%

Ferriphaselus amnicola gen. nov., sp. nov., a neutrophilic, stalk-forming, iron-oxidizing bacterium isolated from an iron-rich groundwater seep

Kato

Krepski

Chan

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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A neutrophilic, stalk-forming, iron-oxidizing bacterium, strain OYT1T, which was isolated from a groundwater seep in Ohyato Park, Tokyo, Japan, was subjected to taxonomic analysis. OYT1T was a motile, bean-shaped, Gram-negative bacterium that was able to grow at 8–30 °C (optimally at 25–30 °C) and at pH 5.6–7.3 (optimally at pH 6.1–6.5). The strain grew microaerobically and autotrophically. Major cellular fatty acids detected were C16 : 1ω7c/C16 : 1ω6c and C16 : 0. The total DNA G+C content was 57.6 mol%. 16S rRNA gene sequence analysis revealed that strain OYT1T was affiliated with the class Betaproteobacteria and clustered with iron-oxidizing bacteria isolated from groundwater seeps and wetlands and with uncultured clones detected in freshwater iron-rich environments. Based on the phenotypic and phylogenetic characteristics of strain OYT1T, we propose that the strain represents a novel species in a new genus, for which the name Ferriphaselus amnicola gen. nov., sp. nov. is proposed; the type strain of Ferriphaselus amnicola is OYT1T ( = JCM 18545T = DSM 26810T).

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Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics

Cited by 166 publications

References 87 publications

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

Subglacial Lake Whillans microbial biogeochemistry: a synthesis of current knowledge

Ferriphaselus amnicola gen. nov., sp. nov., a neutrophilic, stalk-forming, iron-oxidizing bacterium isolated from an iron-rich groundwater seep

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