Isolation and Genomic Characterization of Desulfuromonas soudanensis WTL, a Metal- and Electrode-Reducing Bacterium from Anoxic Deep Subsurface Brine

ABSTRACTReaching a depth of 713 m below the surface, the Soudan Underground Iron Mine (Soudan, Minnesota, USA) transects a massive Archaean (2.7 Ga) banded iron formation, providing a remarkably accessible window into the terrestrial deep biosphere. Despite carbon limitation, metal-reducing microbial communities are present in potentially ancient anoxic brines continuously emanating from exploratory boreholes on Level 27. Using graphite electrodes deposited in situ as bait, we enriched and isolated a novel halophilic iron-reducing Deltaproteobacterium, Desul-furomonas soudanensis strain WTL, from an acetate-fed three-electrode bioreactor poised at +0.24 V (vs. standard hydrogen electrode). Cyclic voltammetry revealed that D. soudanensis releases electrons at redox potentials approximately 100 mV more positive than the model freshwater surface isolate Geobacter sulfurreducens, suggesting that its extracellular respiration is tuned for higher potential electron acceptors. D. soudanensis contains a 3,958,620-bp circular genome, assembled to completion using single-molecule real-time (SMRT) sequencing reads, which encodes a complete TCA cycle, 38 putative multiheme c-type cytochromes, one of which contains 69 heme-binding motifs, and a LuxI/LuxR quorum sensing cassette that produces an unidentified N-acyl homoserine lactone. Another cytochrome is predicted to lie within a putative prophage, suggesting that horizontal transfer of respiratory proteins plays a role in respiratory flexibility among metal reducers. Isolation of D. soudanensis underscores the utility of electrode-based approaches for enriching rare metal reducers from a wide range of habitats.

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Redox potential as a master variable controlling pathways of metal reduction byGeobacter sulfurreducens

10.1101/043059 ◽

2016 ◽

Cited By ~ 1

Author(s):

Caleb E. Levar ◽

Colleen L. Hoffman ◽

Aubrey J. Dunshee ◽

Brandy M. Toner ◽

Daniel R. Bond

Keyword(s):

Redox Potential ◽

Geobacter Sulfurreducens ◽

High Potential ◽

Growth Yields ◽

Redox Potentials ◽

Hydrogen Electrode ◽

Additional Energy ◽

Single Organism ◽

Wide Range ◽

Dependent Pathway

AbstractGeobacter sulfurreducensuses at least two different pathways to transport electrons out of the inner membrane quinone pool before reducing acceptors beyond the outer membrane. When growing on electrodes poised at oxidizing potentials, the CbcL-dependent pathway operates at or below redox potentials of −0.10 V vs. the Standard Hydrogen Electrode (SHE), while the ImcH-dependent pathway operates only above this value. Here, we provide evidence thatG. sulfurreducensalso requires different electron transfer proteins for reduction of a wide range of Fe(III)- and Mn(IV)- (oxyhydr)oxides, and must transition from a high- to low-potential pathway during reduction of commonly studied soluble and insoluble metal electron acceptors. Freshly precipitated Fe(III)-(oxyhydr)oxides could not be reduced by mutants lacking the high potential pathway. Aging these minerals by autoclaving did not change their powder X-ray diffraction pattern, but restored reduction by mutants lacking the high-potential pathway. Mutants lacking the low-potential, CbcL-dependent pathway had higher growth yields with both soluble and insoluble Fe(III). Together, these data suggest that the ImcH-dependent pathway exists to harvest additional energy when conditions permit, and CbcL switches on to allow respiration closer to thermodynamic equilibrium conditions. With evidence of multiple pathways within a single organism, the study of extracellular respiration should consider not only the crystal structure or solubility of a mineral electron acceptor, but rather the redox potential, as this variable determines the energetic reward affecting reduction rates, extents, and final microbial growth yields in the environment.

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Geobacter sulfurreducens inner membrane cytochrome CbcBA controls electron transfer and growth yield near the energetic limit of respiration

10.1101/2021.04.15.440034 ◽

2021 ◽

Author(s):

Komal Joshi ◽

Chi Ho Chan ◽

Daniel R. Bond

Keyword(s):

Electron Transfer ◽

Redox Potential ◽

Growth Yield ◽

Growth Efficiency ◽

Geobacter Sulfurreducens ◽

Redox Potentials ◽

Hydrogen Electrode ◽

Highly Expressed Genes ◽

Reducing Bacteria ◽

Transfer Chain

AbstractGeobacter sulfurreducens utilizes extracellular electron acceptors such as Mn(IV), Fe(III), syntrophic partners, and electrodes that vary from +0.4 to −0.3 V vs. Standard Hydrogen Electrode (SHE), representing a potential energy span that should require a highly branched electron transfer chain. Here we describe CbcBA, a bc-type cytochrome essential near the thermodynamic limit of respiration when acetate is the electron donor. Mutants lacking cbcBA ceased Fe(III) reduction at −0.21 V vs. SHE, could not transfer electrons to electrodes between −0.21 and −0.28 V, and could not reduce the final 10% – 35% of Fe(III) minerals. As redox potential decreased during Fe(III) reduction, cbcBA was induced with the aid of the regulator BccR to become one of the most highly expressed genes in G. sulfurreducens. Growth yield (CFU/mM Fe(II)) was 112% of WT in ΔcbcBA, and deletion of cbcL (a different bc-cytochrome essential near −0.15 V) in ΔcbcBA increased yield to 220%. Together with ImcH, which is required at high redox potentials, CbcBA represents a third cytoplasmic membrane oxidoreductase in G. sulfurreducens. This expanding list shows how these important metal-reducing bacteria may constantly sense redox potential to adjust growth efficiency in changing environments.

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EBSD analysis of rhombohedral twinning in hematite crystals of naturally deformed iron formations

Journal of Applied Crystallography ◽

10.1107/s1600576714025928 ◽

2015 ◽

Vol 48 (1) ◽

pp. 212-219 ◽

Cited By ~ 11

Author(s):

Carlos Fernando Ávila ◽

Leonardo Lagoeiro ◽

Paola Ferreira Barbosa ◽

Leonardo Graça

Keyword(s):

Electron Backscatter Diffraction ◽

Crystallographic Analysis ◽

Iron Formation ◽

Banded Iron Formation ◽

Pole Figures ◽

Textural Characterization ◽

Wide Range ◽

Backscatter Diffraction ◽

Iron Formations

The rhombohedral twinning in hematite has an important role in the accommodation of the deformation of hematite single crystals and hematite aggregates. It is a contact twinning and occurs as lamellae parallel to the \{10{\overline 1}2\} planes of hematite as a result of twin gliding on such planes. On account of the recent applications of electron backscatter diffraction (EBSD) techniques in a wide range of microstructural studies, the determination of symmetry operations that relate crystals in a deformed crystalline aggregate is crucial for the full textural characterization. This study presents an EBSD-based crystallographic analysis of the rhombohedral twinning on hematite crystals of a naturally deformed banded iron formation. Manipulations of theoretical pole figures depicting the symmetry relation of the rhombohedral twinning and misorientation and crystallographic data obtained by EBSD are used to establish the rotational relationship between twin and parent crystals. A method for determining pairs of axes and angles of rotation was developed which can be extended to any other twin laws or misorientation patterns in any other crystal system. It was found that the hematite rhombohedral twins are related to the parent crystal by an approximately 85° rotation about the 〈02{\overline 2}1〉 directions. Hence it could be determined that this consists of a macroscopic twinning element which is an alternative to the conventional ones used to describe the symmetry of the twin. It also matches microscopic twinning elements for the rhomb twinning law. Additionally, this method allows the determination of the crystallographic orientation of the twin lamellae and which particular 〈02{\overline 2}1〉 axis satisfies the 85°〈02{\overline 2}1〉 pair of rotation. The use of an unambiguous angle–axis pair of rotation allows the identification of twin boundaries in complex and finely grained aggregates and the distinction of twinning laws in a particular crystal.

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Geology, Mining, and Mineral Potential of Southern Venezuela

SEG Discovery ◽

10.5382/segnews.2005-62.fea ◽

2005 ◽

pp. 5-22

Author(s):

Dominic Channer ◽

Elsa Graffe ◽

Pedro Vielma

Keyword(s):

Gold Mineralization ◽

Mining Industry ◽

Development Planning ◽

Iron Formation ◽

Banded Iron Formation ◽

Private Companies ◽

Diamond Mining ◽

Wide Range ◽

Felsic Volcanic ◽

Artisanal Miners

ABSTRACT The highly prospective Precambrian Guyana shield south of the Orinoco River in Venezuela can be divided into five main provinces: Imataca, Pastora-Botanamo, Cuchivero, Amazonas, and Roraima. The combination of gold-rich granite-greenstone belts, felsic volcanic and granitic terrains, highly diamondiferous kimberlites, widespread gold and diamond placers, and large unexplored areas makes this region an exciting exploration province. Important mineralization events occurred at different times over a wide range of geologic time, from 3.2 Ga for banded iron formation in Imataca, 2.0 to 1.9 Ga for gold mineralization in Pastora-Botanamo, 0.71 Ga for diamondiferous kimberlite emplacement in Cuchivero, and the Tertiary for formation of enriched iron ores and bauxite ores in Imataca and Amazonas. Iron and aluminum mining is controlled by state mining corporations, with current annual ore production of 23 and 5.2 Mt, respectively. Gold mining is divided between state and private companies and artisanal operations. Total gold production is probably about 750,000 oz per year, including artisanal production. All diamond production is currently artisanal, with total estimated annual production of 500,000 ct. When current project go into production, Venezuela’s gold and diamond production will pass 1.3 Moz/yr and 1 Mct/yr, respectively. Artisanal mining is a key part of the gold and diamond-mining industry in Venezuela, and prospective exploration and mining companies must be aware of this; they should include projects with artisanal miners and local communities in their exploration and development planning.

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Earth’s Middle Ages: What Came after the GOE

10.23943/princeton/9780691145020.003.0009 ◽

2017 ◽

Author(s):

Donald Eugene Canfield

Keyword(s):

Organic Matter ◽

Organic Carbon ◽

Middle Ages ◽

Atmospheric Oxygen ◽

Iron Formation ◽

Banded Iron Formation ◽

Dissolved Iron ◽

Great Oxidation Event ◽

Low Levels ◽

Substantial Rise

This chapter considers the aftermath of the great oxidation event (GOE). It suggests that there was a substantial rise in oxygen defining the GOE, which may, in turn have led to the Lomagundi isotope excursion, which was associated with high rates of organic matter burial and perhaps even higher concentrations of oxygen. This excursion was soon followed by a crash in oxygen to very low levels and a return to banded iron formation deposition. When the massive amounts of organic carbon buried during the excursion were brought into the weathering environment, they would have represented a huge oxygen sink, drawing down levels of atmospheric oxygen. There appeared to be a veritable seesaw in oxygen concentrations, apparently triggered initially by the GOE. The GOE did not produce enough oxygen to oxygenate the oceans. Dissolved iron was removed from the oceans not by reaction with oxygen but rather by reaction with sulfide. Thus, the deep oceans remained anoxic and became rich in sulfide, instead of becoming well oxygenated.

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A new volcanic province: evidence from glacial erratics in western North Greenland

Geological Survey of Denmark and Greenland Bulletin ◽

10.34194/ggub.v186.5213 ◽

2000 ◽

pp. 35-41 ◽

Cited By ~ 1

Author(s):

Peter R. Dawes ◽

Bjørn Thomassen ◽

T.I. Hauge Andersson

Keyword(s):

Volcanic Rocks ◽

Iron Formation ◽

Banded Iron Formation ◽

Common Component ◽

Volcanic Province ◽

North West ◽

North East ◽

The North ◽

Surficial Deposits ◽

North Greenland

NOTE: This article was published in a former series of GEUS Bulletin. Please use the original series name when citing this article, for example: Dawes, P. R., Thomassen, B., & Andersson, T. H. (2000). A new volcanic province: evidence from glacial erratics in western North Greenland. Geology of Greenland Survey Bulletin, 186, 35-41. https://doi.org/10.34194/ggub.v186.5213 _______________ Mapping and regional geological studies in northern Greenland were carried out during the project Kane Basin 1999 (see Dawes et al. 2000, this volume). During ore geological studies in Washington Land by one of us (B.T.), finds of erratics of banded iron formation (BIF) directed special attention to the till, glaciofluvial and fluvial sediments. This led to the discovery that in certain parts of Daugaard-Jensen Land and Washington Land volcanic rocks form a common component of the surficial deposits, with particularly colourful, red porphyries catching the eye. The presence of BIF is interesting but not altogether unexpected since BIF erratics have been reported from southern Hall Land just to the north-east (Kelly & Bennike 1992) and such rocks crop out in the Precambrian shield of North-West Greenland to the south (Fig. 1; Dawes 1991). On the other hand, the presence of volcanic erratics was unexpected and stimulated the work reported on here.

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Synthesis and Biological Evaluation of Novel 4,5,6,7-Tetrahydrobenzo[D]-Thiazol-2- Yl Derivatives Derived from Dimedone with Anti-Tumor, C-Met, Tyrosine Kinase and Pim-1 Inhibitions

Anti-Cancer Agents in Medicinal Chemistry ◽

10.2174/1871520619666190416102144 ◽

2019 ◽

Vol 19 (12) ◽

pp. 1438-1453 ◽

Cited By ~ 1

Author(s):

Rafat M. Mohareb ◽

Amr S. Abouzied ◽

Nermeen S. Abbas

Keyword(s):

Tyrosine Kinase ◽

Tumor Cell ◽

Cell Lines ◽

Single Molecule ◽

Anticancer Agents ◽

Biological Evaluation ◽

New Drugs ◽

Tumor Cell Lines ◽

Thiazole Derivatives ◽

Wide Range

Background: Dimedone and thiazole moieties are privileged scaffolds (acting as primary pharmacophores) in many compounds that are useful to treat several diseases, mainly tropical infectious diseases. Thiazole derivatives are a very important class of compounds due to their wide range of pharmaceutical and therapeutic activities. On the other hand, dimedone is used to synthesize many therapeutically active compounds. Therefore, the combination of both moieties through a single molecule to produce heterocyclic compounds will produce excellent anticancer agents. Objective: The present work reports the synthesis of 47 new substances belonging to two classes of compounds: Dimedone and thiazoles, with the purpose of developing new drugs that present high specificity for tumor cells and low toxicity to the organism. To achieve this goal, our strategy was to synthesize a series of 4,5,6,7-tetrahydrobenzo[d]-thiazol-2-yl derivatives using the reaction of the 2-bromodimedone with cyanothioacetamide. Methods: The reaction of 2-bromodimedone with cyanothioacetamide gave the 4,5,6,7-tetrahydrobenzo[d]- thiazol-2-yl derivative 4. The reactivity of compound 4 towards some chemical reagents was observed to produce different heterocyclic derivatives. Results: A cytotoxic screening was performed to evaluate the performance of the new derivatives in six tumor cell lines. Thirteen compounds were shown to be promising toward the tumor cell lines which were further evaluated toward five tyrosine kinases. Conclusion: The results of antitumor screening showed that many of the tested compounds were of high inhibition towards the tested cell lines. Compounds 6c, 8c, 11b, 11d, 13b, 14b, 15c, 15g, 21b, 21c, 20d and 21d were the most potent compounds toward c-Met kinase and PC-3 cell line. The most promising compounds 6c, 8c, 11b, 11d, 13b, 14b, 15c, 15g, 20c, 20d, 21b, 21c and 21d were further investigated against tyrosine kinase (c-Kit, Flt-3, VEGFR-2, EGFR, and PDGFR). Compounds 6c, 11b, 11d, 14b, 15c, and 20d were selected to examine their Pim-1 kinase inhibition activity the results revealed that compounds 11b, 11d and 15c had high activities.

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The Fennoscandian Shield deep terrestrial virosphere suggests slow motion ‘boom and burst’ cycles

Communications Biology ◽

10.1038/s42003-021-01810-1 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Karin Holmfeldt ◽

Emelie Nilsson ◽

Domenico Simone ◽

Margarita Lopez-Fernandez ◽

Xiaofen Wu ◽

...

Keyword(s):

Antibiotic Production ◽

Nutrient Recycling ◽

Slow Motion ◽

Deep Biosphere ◽

Wide Range ◽

Domains Of Life ◽

Microbial Turnover ◽

Rna Transcript ◽

Viral Isolates ◽

Antagonistic Interactions

AbstractThe deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in ‘metabolic standby’. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of ‘kill-the-winner’ oscillations creating slow motion ‘boom and burst’ cycles.

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