scholarly journals Respiratory Heme A-Containing Oxidases Originated in the Ancestors of Iron-Oxidizing Bacteria

2021 ◽  
Vol 12 ◽  
Author(s):  
Mauro Degli Esposti ◽  
Ana Moya-Beltrán ◽  
Raquel Quatrini ◽  
Lars Hederstedt

Respiration is a major trait shaping the biology of many environments. Cytochrome oxidase containing heme A (COX) is a common terminal oxidase in aerobic bacteria and is the only one in mammalian mitochondria. The synthesis of heme A is catalyzed by heme A synthase (CtaA/Cox15), an enzyme that most likely coevolved with COX. The evolutionary origin of COX in bacteria has remained unknown. Using extensive sequence and phylogenetic analysis, we show that the ancestral type of heme A synthases is present in iron-oxidizing Proteobacteria such as Acidithiobacillus spp. These bacteria also contain a deep branching form of the major COX subunit (COX1) and an ancestral variant of CtaG, a protein that is specifically required for COX biogenesis. Our work thus suggests that the ancestors of extant iron-oxidizers were the first to evolve COX. Consistent with this conclusion, acidophilic iron-oxidizing prokaryotes lived on emerged land around the time for which there is the earliest geochemical evidence of aerobic respiration on earth. Hence, ecological niches of iron oxidation have apparently promoted the evolution of aerobic respiration.

2012 ◽  
Vol 40 (6) ◽  
pp. 1211-1216 ◽  
Author(s):  
David Emerson

Today high Fe(II) environments are relegated to oxic–anoxic habitats with opposing gradients of O2 and Fe(II); however, during the late Archaean and early Proterozoic eons, atmospheric O2 concentrations were much lower and aqueous Fe(II) concentrations were significantly higher. In current Fe(II)-rich environments, such as hydrothermal vents, mudflats, freshwater wetlands or the rhizosphere, rusty mat-like deposits are common. The presence of abundant biogenic microtubular or filamentous iron oxyhydroxides readily reveals the role of FeOB (iron-oxidizing bacteria) in iron mat formation. Cultivation and cultivation-independent techniques, confirm that FeOB are abundant in these mats. Despite remarkable similarities in morphological characteristics between marine and freshwater FeOB communities, the resident populations of FeOB are phylogenetically distinct, with marine populations related to the class Zetaproteobacteria, whereas freshwater populations are dominated by members of the Gallionallaceae, a family within the Betaproteobacteria. Little is known about the mechanism of how FeOB acquire electrons from Fe(II), although it is assumed that it involves electron transfer from the site of iron oxidation at the cell surface to the cytoplasmic membrane. Comparative genomics between freshwater and marine strains reveals few shared genes, except for a suite of genes that include a class of molybdopterin oxidoreductase that could be involved in iron oxidation via extracellular electron transport. Other genes are implicated as well, and the overall genomic analysis reveals a group of organisms exquisitely adapted for growth on iron.


Geosciences ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 480 ◽  
Author(s):  
Jeremiah Shuster ◽  
Maria Rea ◽  
Barbara Etschmann ◽  
Joël Brugger ◽  
Frank Reith

Terraced iron formations (TIFs) are laminated structures that cover square meter-size areas on the surface of weathered bench faces and tailings piles at the Mount Morgan mine, which is a non-operational open pit mine located in Queensland, Australia. Sampled TIFs were analyzed using molecular and microanalytical techniques to assess the bacterial communities that likely contributed to the development of these structures. The bacterial community from the TIFs was more diverse compared to the tailings on which the TIFs had formed. The detection of both chemolithotrophic iron-oxidizing bacteria, i.e., Acidithiobacillus ferrooxidans and Mariprofundus ferrooxydans, and iron-reducing bacteria, i.e., Acidobacterium capsulatum, suggests that iron oxidation/reduction are continuous processes occurring within the TIFs. Acidophilic, iron-oxidizing bacteria were enriched from the TIFs. High-resolution electron microscopy was used to characterize iron biomineralization, i.e., the association of cells with iron oxyhydroxide mineral precipitates, which served as an analog for identifying the structural microfossils of individual cells as well as biofilms within iron oxyhydroxide laminations—i.e., alternating layers containing schwertmannite (Fe16O16(OH)12(SO4)2) and goethite (FeO(OH)). Kinetic modeling estimated that it would take between 0.25–2.28 years to form approximately one gram of schwertmannite as a lamination over a one-m2 surface, thereby contributing to TIF development. This length of time could correspond with seasonable rainfall or greater than average annual rainfall. In either case, the presence of water is critical for sustaining microbial activity, and subsequently iron oxyhydroxide mineral precipitation. The TIFs from the Mount Morgan mine also contain laminations of gypsum (CaSO·2H2O) alternating with iron oxyhydroxide laminations. These gypsum laminations likely represented drier periods of the year, in which millimeter-size gypsum crystals presumably precipitated as water gradually evaporated. Interestingly, gypsum acted as a substrate for the attachment of cells and the growth of biofilms that eventually became mineralized within schwertmannite and goethite. The dissolution and reprecipitation of gypsum suggest that microenvironments with circumneutral pH conditions could exist within TIFs, thereby supporting iron oxidation under circumneutral pH conditions. In conclusion, this study highlights the relationship between microbes for the development of TIFs and also provides interpretations of biogeochemical processes contributing to the preservation of bacterial cells and entire biofilms under acidic conditions.


2021 ◽  
Vol 6 (01) ◽  
pp. 74-82
Author(s):  
Tomi Apra Santosa ◽  
Winda Ayu Fietri ◽  
Abdul Razak ◽  
Ramadhan Sumarmin

Grouper fish (Serranidae) is a type of fish found in Indonesian waters. However, not many people have conducted further research on phylogenetics based on COI (Cytochrome Oxidase I). This study aims to explain the phylogeny of grouper fish from the Serranidae family based on COI (Cytochrome Oxidase I). This research is a literature study. The research samples were grouper fish from Lombok, Karimunjawa, Lampung, Kendari, Madura, Tanakeke, and Numfor. The research instrument was a grouper-type observation sheet and an observation sheet for the results of the MEGA 7 application test. The data were analyzed using qualitative descriptive analysis. The results showed that the level of kinship between the species tested was very close, including Epinephelus areolatus, E. merra, E. fasciatus, E. longispinis, E. coioides, E. ongus, and E. coeruleopunctatus with all genetic distance averages type. 0.02. The conclusion of this study is that in general the species relationships found are several species found in the same location with similar morphology and diet.


2016 ◽  
Vol 283 (1833) ◽  
pp. 20153026 ◽  
Author(s):  
Thomas John Dixon Halliday ◽  
Paul Upchurch ◽  
Anjali Goswami

The effect of the Cretaceous–Palaeogene (K–Pg) mass extinction on the evolution of many groups, including placental mammals, has been hotly debated. The fossil record suggests a sudden adaptive radiation of placentals immediately after the event, but several recent quantitative analyses have reconstructed no significant increase in either clade origination rates or rates of character evolution in the Palaeocene. Here we use stochastic methods to date a recent phylogenetic analysis of Cretaceous and Palaeocene mammals and show that Placentalia likely originated in the Late Cretaceous, but that most intraordinal diversification occurred during the earliest Palaeocene. This analysis reconstructs fewer than 10 placental mammal lineages crossing the K–Pg boundary. Moreover, we show that rates of morphological evolution in the 5 Myr interval immediately after the K–Pg mass extinction are three times higher than background rates during the Cretaceous. These results suggest that the K–Pg mass extinction had a marked impact on placental mammal diversification, supporting the view that an evolutionary radiation occurred as placental lineages invaded new ecological niches during the Early Palaeocene.


2014 ◽  
Vol 81 (2) ◽  
pp. 699-712 ◽  
Author(s):  
Zheng Wang ◽  
Dagmar H. Leary ◽  
Anthony P. Malanoski ◽  
Robert W. Li ◽  
W. Judson Hervey ◽  
...  

ABSTRACTBiocathode extracellular electron transfer (EET) may be exploited for biotechnology applications, including microbially mediated O2reduction in microbial fuel cells and microbial electrosynthesis. However, biocathode mechanistic studies needed to improve or engineer functionality have been limited to a few select species that form sparse, homogeneous biofilms characterized by little or no growth. Attempts to cultivate isolates from biocathode environmental enrichments often fail due to a lack of some advantage provided by life in a consortium, highlighting the need to study and understand biocathode consortiain situ. Here, we present metagenomic and metaproteomic characterization of a previously described biocathode biofilm (+310 mV versus a standard hydrogen electrode [SHE]) enriched from seawater, reducing O2, and presumably fixing CO2for biomass generation. Metagenomics identified 16 distinct cluster genomes, 15 of which could be assigned at the family or genus level and whose abundance was roughly divided betweenAlpha- andGammaproteobacteria. A total of 644 proteins were identified from shotgun metaproteomics and have been deposited in the the ProteomeXchange with identifier PXD001045. Cluster genomes were used to assign the taxonomic identities of 599 proteins, withMarinobacter,Chromatiaceae, andLabrenziathe most represented. RubisCO and phosphoribulokinase, along with 9 other Calvin-Benson-Bassham cycle proteins, were identified fromChromatiaceae. In addition, proteins similar to those predicted for iron oxidation pathways of known iron-oxidizing bacteria were observed forChromatiaceae. These findings represent the first description of putative EET and CO2fixation mechanisms for a self-regenerating, self-sustaining multispecies biocathode, providing potential targets for functional engineering, as well as new insights into biocathode EET pathways using proteomics.


2005 ◽  
Vol 51 (6-7) ◽  
pp. 59-68 ◽  
Author(s):  
D. Park ◽  
D.S. Lee ◽  
J.M. Park

Microbial oxidation of ferrous iron may be available alternative method of producing ferric iron, which is a reagent used for removal of H2S from biogas. In this study, a submerged membrane bioreactor (MBR) system was employed to oxidize ferrous iron to ferric iron. In the submerged MBR system, we could keep high concentration of iron-oxidizing bacteria and high oxidation rate of ferrous iron. There was membrane fouling caused by chemical precipitates such as K-jarosite and ferric phosphate. However, a strong acidity (pH 1.75) of solution and low ferrous iron concentration (below 3000 mg/l) significantly reduced the fouling of membrane module during the bioreactor operation. A fouled membrane module could be easily regenerated with a 1 M of sulfuric acid solution. In conclusion, the submerged MBR could be used for high-density culture of iron-oxidizing bacteria and for continuous ferrous iron oxidation. As far as our knowledge concerns, this is the first study on the application of a submerged MBR to high acidic conditions (below pH 2).


Microbiology ◽  
2005 ◽  
Vol 151 (1) ◽  
pp. 35-43 ◽  
Author(s):  
Ulrike Kappler ◽  
Lindsay I. Sly ◽  
Alastair G. McEwan

Metallosphaera sedula is a thermoacidophilic Crenarchaeon which is capable of leaching metals from sulfidic ores. The authors have investigated the presence and expression of genes encoding respiratory complexes in this organism when grown heterotrophically or chemolithotrophically on either sulfur or pyrite. The presence of three gene clusters, encoding two terminal oxidase complexes, the quinol oxidase SoxABCD and the SoxM oxidase supercomplex, and a gene cluster encoding a high-potential cytochrome b and components of a bc 1 complex analogue (cbsBA–soxL2N gene cluster) was established. Expression studies showed that the soxM gene was expressed to high levels during heterotrophic growth of M. sedula on yeast extract, while the soxABCD mRNA was most abundant in cells grown on sulfur. Reduced-minus-oxidized difference spectra of cell membranes showed cytochrome-related peaks that correspond to published spectra of Sulfolobus-type terminal oxidase complexes. In pyrite-grown cells, expression levels of the two monitored oxidase gene clusters were reduced by a factor of 10–12 relative to maximal expression levels, although spectra of membranes clearly contained oxidase-associated haems, suggesting the presence of additional gene clusters encoding terminal oxidases in M. sedula. Pyrite- and sulfur-grown cells contained high levels of the cbsA transcript, which encodes a membrane-bound cytochrome b with a possible role in iron oxidation or chemolithotrophy. The cbsA gene is not co-transcribed with the soxL2N genes, and therefore does not appear to be an integral part of this bc 1 complex analogue. The data show for the first time the differential expression of the Sulfolobus-type terminal oxidase gene clusters in a Crenarchaeon in response to changing growth modes.


2021 ◽  
Author(s):  
Julie Cosmidis ◽  
Shane O'Reilly ◽  
Eric Ellison ◽  
Katherine Crispin ◽  
David Diercks ◽  
...  

Crystal Geyser (Utah, USA) is a CO2-rich low-temperature geyser that is studied as a natural analog for CO2 leakage from carbon capture and storage (CCS) sites. In order to better constrain the biogeochemical processes influencing CaCO3 precipitation at geological CO2 escape sites, we characterized fast-forming iron-rich calcium carbonate pisoids and travertines precipitating from the fluids expelled by the geyser. The pisoids, located within a few meters from the vent, are composed of concentric layers of aragonite and calcite. Calcite layers contain abundant ferrihydrite shrubs in which iron is encasing bacterial forms. The aragonite layers contain less abundant and finely dispersed iron, present either as iron-oxide microspherules or iron adsorbed to organic matter dispersed within the carbonate matrix. We propose that carbonate polymorphism in the pisoids is mostly controlled by local fluctuations of the iron redox state of the fluids from which they form, caused by episodic blooms of iron-oxidizing bacteria. Indeed, the waters expelled by Crystal Geyser contain >200 µM dissolved iron (Fe2+), a known inhibitor of calcite growth. The calcite layers of the pisoids may record episodes of intense microbial iron oxidation, consistent with observations of iron-oxide rich biofilms thriving in the rimstone pools around the geyser and previous metagenomic analyses showing abundant neutrophilic, microaerophilic iron-oxidizing bacteria in vent water. In turn, aragonite layers of the pisoids likely precipitate from Fe2+-rich waters, registering periods of less intense iron oxidation. Separately, CaCO3 polymorphism in the travertines, where calcite and aragonite precipitate concurrently, is not controlled by iron dynamics, but may be locally influenced by the presence of microbial biofilms. This study documents for the first time an influence of microbial iron oxidation on CaCO3 polymorphism in the environment, and informs our understanding of carbonate formation at CO2 leakage sites and in CCS contexts.


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