1
|
Yu L, Adamson P, Lay Yap P, Tung T, Makar S, Turra M, Higgins G, Losic D. From Biowaste to Lab-Bench: Low-Cost Magnetic Iron Oxide Nanoparticles for RNA Extraction and SARS-CoV-2 Diagnostics. BIOSENSORS 2023; 13:196. [PMID: 36831962 PMCID: PMC9953475 DOI: 10.3390/bios13020196] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
The gold standard for diagnostics of SARS-CoV-2 (COVID-19) virus is based on real-time polymerase chain reaction (RT-PCR) using centralized PCR facilities and commercial viral RNA extraction kits. One of the key components of these kits are magnetic beads composed of silica coated magnetic iron oxide (Fe2O3 or Fe3O4) nanoparticles, needed for the selective extraction of RNA. At the beginning of the pandemic in 2019, due to a high demand across the world there were severe shortages of many reagents and consumables, including these magnetic beads required for testing for SARS-CoV-2. Laboratories needed to source these products elsewhere, preferably at a comparable or lower cost. Here, we describe the development of a simple, low-cost and scalable preparation of magnetic nanoparticles (MNPs) from biowaste and demonstrate their successful application in viral RNA extraction and the detection of COVID-19. These MNPs have a unique nanoplatelet shape with a high surface area, which are beneficial features, expected to provide improved RNA adsorption, better dispersion and processing ability compared with commercial spherical magnetic beads. Their performance in COVID-19 RNA extraction was evaluated in comparison with commercial magnetic beads and the results presented here showed comparable results for high throughput PCR analysis. The presented magnetic nanoplatelets generated from biomass waste are safe, low-cost, simple to produce in large scale and could provide a significantly reduced cost of nucleic acid extraction for SARS-CoV-2 and other DNA and RNA viruses.
Collapse
Affiliation(s)
- Le Yu
- School of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Hub for Graphene Enabled Industry Transformation, The University of Adelaide, Adelaide, SA 5005, Australia
| | | | - Pei Lay Yap
- School of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Hub for Graphene Enabled Industry Transformation, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Tran Tung
- School of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Hub for Graphene Enabled Industry Transformation, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Shaheer Makar
- School of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Hub for Graphene Enabled Industry Transformation, The University of Adelaide, Adelaide, SA 5005, Australia
- Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Mark Turra
- SA Pathology, Adelaide, SA 5000, Australia
| | | | - Dusan Losic
- School of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Hub for Graphene Enabled Industry Transformation, The University of Adelaide, Adelaide, SA 5005, Australia
| |
Collapse
|
2
|
Abstract
Iron (Fe) oxidation is one of Earth’s major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our understanding of microbial contribution is limited by incomplete knowledge of microbial iron oxidation mechanisms, particularly in neutrophilic iron oxidizers. The genomes of many diverse iron oxidizers encode a homolog to an outer membrane cytochrome (Cyc2) shown to oxidize iron in two acidophiles. Phylogenetic analyses show Cyc2 sequences from neutrophiles cluster together, suggesting a common function, though this function has not been verified in these organisms. Therefore, we investigated the iron oxidase function of heterologously expressed Cyc2 from a neutrophilic iron oxidizer Mariprofundus ferrooxydans PV-1. Cyc2PV-1 is capable of oxidizing iron, and its redox potential is 208 ± 20 mV, consistent with the ability to accept electrons from Fe2+ at neutral pH. These results support the hypothesis that Cyc2 functions as an iron oxidase in neutrophilic iron-oxidizing organisms. The results of sequence analysis and modeling reveal that the entire Cyc2 family shares a unique fused cytochrome-porin structure, with a defining consensus motif in the cytochrome region. On the basis of results from structural analyses, we predict that the monoheme cytochrome Cyc2 specifically oxidizes dissolved Fe2+, in contrast to multiheme iron oxidases, which may oxidize solid Fe(II). With our results, there is now functional validation for diverse representatives of Cyc2 sequences. We present a comprehensive Cyc2 phylogenetic tree and offer a roadmap for identifying cyc2/Cyc2 homologs and interpreting their function. The occurrence of cyc2 in many genomes beyond known iron oxidizers presents the possibility that microbial iron oxidation may be a widespread metabolism.
Collapse
|
3
|
Vigliaturo R, Marengo A, Bittarello E, Pérez-Rodríguez I, Dražić G, Gieré R. Micro- and nano-scale mineralogical characterization of Fe(II)-oxidizing bacterial stalks. GEOBIOLOGY 2020; 18:606-618. [PMID: 32459887 PMCID: PMC7442631 DOI: 10.1111/gbi.12398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Neutrophilic, microaerobic Fe(II)-oxidizing bacteria (FeOB) from marine and freshwater environments are known to generate twisted ribbon-like organo-mineral stalks. These structures, which are extracellularly precipitated, are susceptible to chemical influences in the environment once synthesized. In this paper, we characterize the minerals associated with freshwater FeOB stalks in order to evaluate key organo-mineral mechanisms involved in biomineral formation. Micro-Raman spectroscopy and Field Emission Scanning Electron Microscopy revealed that FeOB isolated from drinking water wells in Sweden produced stalks with ferrihydrite, lepidocrocite and goethite as main mineral components. Based on our observations made by micro-Raman Spectroscopy, field emission scanning electron microscopy and scanning transmission electron microscope combined with electron energy-loss spectroscopy, we propose a model that describes the crystal-growth mechanism, the Fe-oxidation state, and the mineralogical state of the stalks, as well as the biogenic contribution to these features. Our study suggests that the main crystal-growth mechanism in stalks includes nanoparticle aggregation and dissolution/re-precipitation reactions, which are dominant near the organic exopolymeric material produced by the microorganism and in the peripheral region of the stalk, respectively.
Collapse
Affiliation(s)
- Ruggero Vigliaturo
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Erica Bittarello
- Department of Earth Science, University of Torino, Torino, Italy
| | - Ileana Pérez-Rodríguez
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Goran Dražić
- Department for Materials Chemistry, National Institute of Chemistry, Ljubljana, Slovenia
| | - Reto Gieré
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
4
|
Johannessen KC, McLoughlin N, Vullum PE, Thorseth IH. On the biogenicity of Fe-oxyhydroxide filaments in silicified low-temperature hydrothermal deposits: Implications for the identification of Fe-oxidizing bacteria in the rock record. GEOBIOLOGY 2020; 18:31-53. [PMID: 31532578 DOI: 10.1111/gbi.12363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 08/02/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
Microaerophilic Fe(II)-oxidizing bacteria produce biomineralized twisted and branched stalks, which are promising biosignatures of microbial Fe oxidation in ancient jaspers and iron formations. Extracellular Fe stalks retain their morphological characteristics under experimentally elevated temperatures, but the extent to which natural post-depositional processes affect fossil integrity remains to be resolved. We examined siliceous Fe deposits from laminated mounds and chimney structures from an extinct part of the Jan Mayen Vent Fields on the Arctic Mid-Ocean Ridge. Our aims were to determine how early seafloor diagenesis affects morphological and chemical signatures of Fe-oxyhydroxide biomineralization and how extracellular stalks differ from abiogenic features. Optical and scanning electron microscopy in combination with focused ion beam-transmission electron microscopy (FIB-TEM) was used to study the filamentous textures and cross sections of individual stalks. Our results revealed directional, dendritic, and radial arrangements of biogenic twisted stalks and randomly organized networks of hollow tubes. Stalks were encrusted by concentric Fe-oxyhydroxide laminae and silica casings. Element maps produced by energy dispersive X-ray spectroscopy (EDS) in TEM showed variations in the content of Si, P, and S within filaments, demonstrating that successive hydrothermal fluid pulses mediate early diagenetic alteration and modify the chemical composition and surface features of stalks through Fe-oxyhydroxide mineralization. The carbon content of the stalks was generally indistinguishable from background levels, suggesting that organic compounds were either scarce initially or lost due to percolating hydrothermal fluids. Dendrites and thicker abiotic filaments from a nearby chimney were composed of nanometer-sized microcrystalline iron particles and silica and showed Fe growth bands indicative of inorganic precipitation. Our study suggests that the identification of fossil stalks and sheaths of Fe-oxidizing bacteria in hydrothermal paleoenvironments may not rely on the detection of organic carbon and demonstrates that abiogenic filaments differ from stalks and sheaths of Fe-oxidizing bacteria with respect to width distribution, ultrastructure, and textural context.
Collapse
Affiliation(s)
- Karen C Johannessen
- K. G. Jebsen Centre for Deep Sea Research and Department of Earth Science, University of Bergen, Bergen, Norway
| | - Nicola McLoughlin
- Department of Geology and the Albany Museum, Rhodes University, Grahamstown, South Africa
| | - Per Erik Vullum
- Department of Materials and Nanotechnology, SINTEF Industry, Trondheim, Norway
- Department of Physics, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Ingunn H Thorseth
- K. G. Jebsen Centre for Deep Sea Research and Department of Earth Science, University of Bergen, Bergen, Norway
| |
Collapse
|
5
|
Briegel A, Jensen G. Progress and Potential of Electron Cryotomography as Illustrated by Its Application to Bacterial Chemoreceptor Arrays. Annu Rev Biophys 2017; 46:1-21. [PMID: 28301773 DOI: 10.1146/annurev-biophys-070816-033555] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Electron cryotomography (ECT) can produce three-dimensional images of biological samples such as intact cells in a near-native, frozen-hydrated state to macromolecular resolution (∼4 nm). Because one of its first and most common applications has been to bacterial chemoreceptor arrays, ECT's contributions to this field illustrate well its past, present, and future. While X-ray crystallography and nuclear magnetic resonance spectroscopy have revealed the structures of nearly all the individual components of chemoreceptor arrays, ECT has revealed the mesoscale information about how the components are arranged within cells. Receptors assemble into a universally conserved 12-nm hexagonal lattice linked by CheA/CheW rings. Membrane-bound arrays are single layered; cytoplasmic arrays are double layered. Images of in vitro reconstitutions have led to a model of how arrays assemble, and images of native arrays in different states have shown that the conformational changes associated with signal transduction are subtle, constraining models of activation and system cooperativity. Phase plates, better detectors, and more stable stages promise even higher resolution and broader application in the near future.
Collapse
Affiliation(s)
- Ariane Briegel
- Department of Biology, Leiden University, 2333 Leiden, Netherlands
| | - Grant Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; .,Howard Hughes Medical Institute, Pasadena, California 91125
| |
Collapse
|
6
|
Oikonomou CM, Chang YW, Jensen GJ. A new view into prokaryotic cell biology from electron cryotomography. Nat Rev Microbiol 2016; 14:205-20. [PMID: 26923112 PMCID: PMC5551487 DOI: 10.1038/nrmicro.2016.7] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Electron cryotomography (ECT) enables intact cells to be visualized in 3D in an essentially native state to 'macromolecular' (∼4 nm) resolution, revealing the basic architectures of complete nanomachines and their arrangements in situ. Since its inception, ECT has advanced our understanding of many aspects of prokaryotic cell biology, from morphogenesis to subcellular compartmentalization and from metabolism to complex interspecies interactions. In this Review, we highlight how ECT has provided structural and mechanistic insights into the physiology of bacteria and archaea and discuss prospects for the future.
Collapse
Affiliation(s)
- Catherine M Oikonomou
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Yi-Wei Chang
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Grant J Jensen
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| |
Collapse
|
7
|
Mineralogical Diversity in Lake Pavin: Connections with Water Column Chemistry and Biomineralization Processes. MINERALS 2016. [DOI: 10.3390/min6020024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
8
|
Miot J, Remusat L, Duprat E, Gonzalez A, Pont S, Poinsot M. Fe biomineralization mirrors individual metabolic activity in a nitrate-dependent Fe(II)-oxidizer. Front Microbiol 2015; 6:879. [PMID: 26441847 PMCID: PMC4562303 DOI: 10.3389/fmicb.2015.00879] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/10/2015] [Indexed: 12/15/2022] Open
Abstract
Microbial biomineralization sometimes leads to periplasmic encrustation, which is predicted to enhance microorganism preservation in the fossil record. Mineral precipitation within the periplasm is, however, thought to induce death, as a result of permeability loss preventing nutrient and waste transit across the cell wall. This hypothesis had, however, never been investigated down to the single cell level. Here, we cultured the nitrate reducing Fe(II) oxidizing bacteria Acidovorax sp. strain BoFeN1 that have been previously shown to promote the precipitation of a diversity of Fe minerals (lepidocrocite, goethite, Fe phosphate) encrusting the periplasm. We investigated the connection of Fe biomineralization with carbon assimilation at the single cell level, using a combination of electron microscopy and Nano-Secondary Ion Mass Spectrometry. Our analyses revealed strong individual heterogeneities of Fe biomineralization. Noteworthy, a small proportion of cells remaining free of any precipitate persisted even at advanced stages of biomineralization. Using pulse chase experiments with (13)C-acetate, we provide evidence of individual phenotypic heterogeneities of carbon assimilation, correlated with the level of Fe biomineralization. Whereas non- and moderately encrusted cells were able to assimilate acetate, higher levels of periplasmic encrustation prevented any carbon incorporation. Carbon assimilation only depended on the level of Fe encrustation and not on the nature of Fe minerals precipitated in the cell wall. Carbon assimilation decreased exponentially with increasing cell-associated Fe content. Persistence of a small proportion of non-mineralized and metabolically active cells might constitute a survival strategy in highly ferruginous environments. Eventually, our results suggest that periplasmic Fe biomineralization may provide a signature of individual metabolic status, which could be looked for in the fossil record and in modern environmental samples.
Collapse
Affiliation(s)
- Jennyfer Miot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Laurent Remusat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Elodie Duprat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Adriana Gonzalez
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Sylvain Pont
- Département des Collections, Muséum National d’Histoire NaturelleParis, France
| | - Mélanie Poinsot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| |
Collapse
|
9
|
Emerson JB, Thomas BC, Alvarez W, Banfield JF. Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla. Environ Microbiol 2015; 18:1686-703. [DOI: 10.1111/1462-2920.12817] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/31/2015] [Accepted: 02/12/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Joanne B. Emerson
- Department of Earth and Planetary Science; University of California, Berkeley; Berkeley CA 94720-4767 USA
| | - Brian C. Thomas
- Department of Earth and Planetary Science; University of California, Berkeley; Berkeley CA 94720-4767 USA
| | - Walter Alvarez
- Department of Earth and Planetary Science; University of California, Berkeley; Berkeley CA 94720-4767 USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science; University of California, Berkeley; Berkeley CA 94720-4767 USA
- Department of Environmental Science, Policy, and Management; University of California, Berkeley; Berkeley CA 94720-4767 USA
| |
Collapse
|
10
|
Luef B, Frischkorn KR, Wrighton KC, Holman HYN, Birarda G, Thomas BC, Singh A, Williams KH, Siegerist CE, Tringe SG, Downing KH, Comolli LR, Banfield JF. Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun 2015; 6:6372. [DOI: 10.1038/ncomms7372] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/23/2015] [Indexed: 02/04/2023] Open
|
11
|
Delgado L, Martínez G, López-Iglesias C, Mercadé E. Cryo-electron tomography of plunge-frozen whole bacteria and vitreous sections to analyze the recently described bacterial cytoplasmic structure, the Stack. J Struct Biol 2015; 189:220-9. [PMID: 25617813 DOI: 10.1016/j.jsb.2015.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/13/2015] [Indexed: 11/25/2022]
Abstract
Cryo-electron tomography (CET) of plunge-frozen whole bacteria and vitreous sections (CETOVIS) were used to revise and expand the structural knowledge of the "Stack", a recently described cytoplasmic structure in the Antarctic bacterium Pseudomonas deceptionensis M1(T). The advantages of both techniques can be complementarily combined to obtain more reliable insights into cells and their components with three-dimensional imaging at different resolutions. Cryo-electron microscopy (Cryo-EM) and CET of frozen-hydrated P. deceptionensis M1(T) cells confirmed that Stacks are found at different locations within the cell cytoplasm, in variable number, separately or grouped together, very close to the plasma membrane (PM) and oriented at different angles (from 35° to 90°) to the PM, thus establishing that they were not artifacts of the previous sample preparation methods. CET of plunge-frozen whole bacteria and vitreous sections verified that each Stack consisted of a pile of oval disc-like subunits, each disc being surrounded by a lipid bilayer membrane and separated from each other by a constant distance with a mean value of 5.2±1.3nm. FM4-64 staining and confocal microscopy corroborated the lipid nature of the membrane of the Stacked discs. Stacks did not appear to be invaginations of the PM because no continuity between both membranes was visible when whole bacteria were analyzed. We are still far from deciphering the function of these new structures, but a first experimental attempt links the Stacks with a given phase of the cell replication process.
Collapse
Affiliation(s)
- Lidia Delgado
- Cryo-Electron Microscopy, Scientific and Technological Centers, University of Barcelona, Barcelona, Spain; Department of Microbiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Gema Martínez
- Cryo-Electron Microscopy, Scientific and Technological Centers, University of Barcelona, Barcelona, Spain
| | - Carmen López-Iglesias
- Cryo-Electron Microscopy, Scientific and Technological Centers, University of Barcelona, Barcelona, Spain.
| | - Elena Mercadé
- Department of Microbiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain.
| |
Collapse
|
12
|
Kikuchi S, Makita H, Takai K, Yamaguchi N, Takahashi Y. Characterization of biogenic iron oxides collected by the newly designed liquid culture method using diffusion chambers. GEOBIOLOGY 2014; 12:133-145. [PMID: 24382149 DOI: 10.1111/gbi.12073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/04/2013] [Indexed: 06/03/2023]
Abstract
We designed a new culture method for neutrophilic iron-oxidizing bacteria using liquid medium (i) to study the formation and mineralogical characteristics of biogenic iron oxides (BIOS) and (ii) to apply BIOS to various scientific and engineering applications. An iron-oxidizing bacterium, Mariprofundus ferrooxydans PV-1(T) (ATCC, BAA-1020), was cultured using a set of diffusion chambers to prepare a broad anoxic-oxic interface, upon which BIOS formation is typically observed in natural environments. Iron oxide precipitates were generated in parallel with bacterial growth. A scanning electron microscopy analysis indicated that the morphological features of the iron oxide precipitates in the medium (in vitro BIOS) were similar to those of BIOS collected from natural deep-sea hydrothermal environments in the Northwest Eifuku Seamount field in the northern Mariana Arc (in situ BIOS). Further chemical speciation of both the in vitro and in situ BIOS was examined with X-ray absorption fine structure (XAFS). A bulk XAFS analysis showed that the minerals in both BIOS were mainly ferrihydrite and oligomeric stages of amorphous iron oxyhydroxides with edge-sharing octahedral linkages. The amount of in vitro BIOS produced with the diffusion-chamber method was greater than those produced previously with other culture methods, such as gel-stabilized gradient and batch liquid culture methods. The larger yields of BIOS produced with the new culture method will allow us to clarify in the future the mineralization mechanisms during bacterial growth and to examine the physicochemical properties of BIOS, such as their adsorption to and coprecipitation with various elements and substances.
Collapse
Affiliation(s)
- S Kikuchi
- Department of Earth and Planetary Systems Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | | | | | | | | |
Collapse
|
13
|
Potential role of nitrite for abiotic Fe(II) oxidation and cell encrustation during nitrate reduction by denitrifying bacteria. Appl Environ Microbiol 2013; 80:1051-61. [PMID: 24271182 DOI: 10.1128/aem.03277-13] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microorganisms have been observed to oxidize Fe(II) at neutral pH under anoxic and microoxic conditions. While most of the mixotrophic nitrate-reducing Fe(II)-oxidizing bacteria become encrusted with Fe(III)-rich minerals, photoautotrophic and microaerophilic Fe(II) oxidizers avoid cell encrustation. The Fe(II) oxidation mechanisms and the reasons for encrustation remain largely unresolved. Here we used cultivation-based methods and electron microscopy to compare two previously described nitrate-reducing Fe(II) oxidizers ( Acidovorax sp. strain BoFeN1 and Pseudogulbenkiania sp. strain 2002) and two heterotrophic nitrate reducers (Paracoccus denitrificans ATCC 19367 and P. denitrificans Pd 1222). All four strains oxidized ∼8 mM Fe(II) within 5 days in the presence of 5 mM acetate and accumulated nitrite (maximum concentrations of 0.8 to 1.0 mM) in the culture media. Iron(III) minerals, mainly goethite, formed and precipitated extracellularly in close proximity to the cell surface. Interestingly, mineral formation was also observed within the periplasm and cytoplasm; intracellular mineralization is expected to be physiologically disadvantageous, yet acetate consumption continued to be observed even at an advanced stage of Fe(II) oxidation. Extracellular polymeric substances (EPS) were detected by lectin staining with fluorescence microscopy, particularly in the presence of Fe(II), suggesting that EPS production is a response to Fe(II) toxicity or a strategy to decrease encrustation. Based on the data presented here, we propose a nitrite-driven, indirect mechanism of cell encrustation whereby nitrite forms during heterotrophic denitrification and abiotically oxidizes Fe(II). This work adds to the known assemblage of Fe(II)-oxidizing bacteria in nature and complicates our ability to delineate microbial Fe(II) oxidation in ancient microbes preserved as fossils in the geological record.
Collapse
|
14
|
Abstract
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.
Collapse
|
15
|
Fleming EJ, Davis RE, McAllister SM, Chan CS, Moyer CL, Tebo BM, Emerson D. Hidden in plain sight: discovery of sheath-forming, iron-oxidizing Zetaproteobacteria at Loihi Seamount, Hawaii, USA. FEMS Microbiol Ecol 2013; 85:116-27. [PMID: 23480633 DOI: 10.1111/1574-6941.12104] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/28/2013] [Accepted: 02/28/2013] [Indexed: 12/01/2022] Open
Abstract
Lithotrophic iron-oxidizing bacteria (FeOB) form microbial mats at focused flow or diffuse flow vents in deep-sea hydrothermal systems where Fe(II) is a dominant electron donor. These mats composed of biogenically formed Fe(III)-oxyhydroxides include twisted stalks and tubular sheaths, with sheaths typically composing a minor component of bulk mats. The micron diameter Fe(III)-oxyhydroxide-containing tubular sheaths bear a strong resemblance to sheaths formed by the freshwater FeOB, Leptothrix ochracea. We discovered that veil-like surface layers present in iron-mats at the Loihi Seamount were dominated by sheaths (40-60% of total morphotypes present) compared with deeper (> 1 cm) mat samples (0-16% sheath). By light microscopy, these sheaths appeared nearly identical to those of L. ochracea. Clone libraries of the SSU rRNA gene from this top layer were dominated by Zetaproteobacteria, and lacked phylotypes related to L. ochracea. In mats with similar morphologies, terminal-restriction fragment length polymorphism (T-RFLP) data along with quantitative PCR (Q-PCR) analyses using a Zetaproteobacteria-specific primer confirmed the presence and abundance of Zetaproteobacteria. A Zetaproteobacteria fluorescence in situ hybridization (FISH) probe hybridized to ensheathed cells (4% of total cells), while a L. ochracea-specific probe and a Betaproteobacteria probe did not. Together, these results constitute the discovery of a novel group of marine sheath-forming FeOB bearing a striking morphological similarity to L. ochracea, but belonging to an entirely different class of Proteobacteria.
Collapse
Affiliation(s)
- Emily J Fleming
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | | | | | | | | | | |
Collapse
|
16
|
Saini G, Chan CS. Near-neutral surface charge and hydrophilicity prevent mineral encrustation of Fe-oxidizing micro-organisms. GEOBIOLOGY 2013; 11:191-200. [PMID: 23279435 DOI: 10.1111/gbi.12021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 11/13/2012] [Indexed: 06/01/2023]
Abstract
Microbial survival in mineralizing environments depends on the ability to evade surface encrustation by minerals, which could obstruct nutrient uptake and waste output. Some organisms localize mineral precipitation away from the cell; however, cell surface properties - charge and hydrophobicity - must also play a role in preventing surface mineralization. This is especially relevant for iron-oxidizing bacteria (FeOB), which face an encrustation threat from both biotic and abiotic mineralization. We used electron microscopy and surface characterization techniques to study the surfaces of two stalk-forming neutrophilic FeOB: the marine Zetaproteobacterium Mariprofundus ferrooxydans PV-1 and the recently isolated freshwater Betaproteobacterium Gallionellales strain R-1. Both organisms lack detectable iron on cell surfaces. Live and azide-inhibited M. ferrooxydans PV-1 cells had small negative zeta potentials (-0.34 to -2.73 mV), over the pH range 4.2-9.4; Gallionellales strain R-1 cells exhibited an even smaller zeta potential (-0.10 to -0.19 mV) over pH 4.2-8.8. Cells have hydrophilic surfaces, according to water contact angle measurements and microbial adhesion to hydrocarbons tests. Thermodynamic and extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) calculations showed that as low charge causes low electrostatic attraction, hydrophilic repulsion dominates cell-mineral interactions. Therefore, we conclude that surface properties help enable these FeOB to survive in highly mineralizing environments. Given both mineral-repelling surface properties and the ability to sequester Fe(III) biominerals in an organomineral stalk, these two FeOB have a well-coordinated system to localize both biotic and abiotic mineral distribution.
Collapse
Affiliation(s)
- G Saini
- Department of Geological Sciences, University of Delaware, Newark, DE, USA
| | | |
Collapse
|
17
|
Luef B, Fakra SC, Csencsits R, Wrighton KC, Williams KH, Wilkins MJ, Downing KH, Long PE, Comolli LR, Banfield JF. Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth. THE ISME JOURNAL 2013; 7:338-50. [PMID: 23038172 PMCID: PMC3554402 DOI: 10.1038/ismej.2012.103] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/30/2012] [Accepted: 07/30/2012] [Indexed: 11/09/2022]
Abstract
Iron-reducing bacteria (FeRB) play key roles in anaerobic metal and carbon cycling and carry out biogeochemical transformations that can be harnessed for environmental bioremediation. A subset of FeRB require direct contact with Fe(III)-bearing minerals for dissimilatory growth, yet these bacteria must move between mineral particles. Furthermore, they proliferate in planktonic consortia during biostimulation experiments. Thus, a key question is how such organisms can sustain growth under these conditions. Here we characterized planktonic microbial communities sampled from an aquifer in Rifle, Colorado, USA, close to the peak of iron reduction following in situ acetate amendment. Samples were cryo-plunged on site and subsequently examined using correlated two- and three-dimensional cryogenic transmission electron microscopy (cryo-TEM) and scanning transmission X-ray microscopy (STXM). The outer membranes of most cells were decorated with aggregates up to 150 nm in diameter composed of ∼3 nm wide amorphous, Fe-rich nanoparticles. Fluorescent in situ hybridization of lineage-specific probes applied to rRNA of cells subsequently imaged via cryo-TEM identified Geobacter spp., a well-studied group of FeRB. STXM results at the Fe L(2,3) absorption edges indicate that nanoparticle aggregates contain a variable mixture of Fe(II)-Fe(III), and are generally enriched in Fe(III). Geobacter bemidjiensis cultivated anaerobically in the laboratory on acetate and hydrous ferric oxyhydroxides also accumulated mixed-valence nanoparticle aggregates. In field-collected samples, FeRB with a wide variety of morphologies were associated with nano-aggregates, indicating that cell surface Fe(III) accumulation may be a general mechanism by which FeRB can grow while in planktonic suspension.
Collapse
Affiliation(s)
- Birgit Luef
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, USA
| | - Sirine C Fakra
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Advanced Light Source, Berkeley, CA, USA
| | - Roseann Csencsits
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, USA
| | - Kelly C Wrighton
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Kenneth H Williams
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Berkeley, CA, USA
| | - Michael J Wilkins
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, USA
| | - Kenneth H Downing
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, USA
| | - Philip E Long
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Berkeley, CA, USA
| | - Luis R Comolli
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| |
Collapse
|
18
|
Comolli LR, Duarte R, Baum D, Luef B, Downing KH, Larson DM, Csencsits R, Banfield JF. A portable cryo-plunger for on-site intact cryogenic microscopy sample preparation in natural environments. Microsc Res Tech 2012; 75:829-36. [PMID: 22213355 PMCID: PMC4677670 DOI: 10.1002/jemt.22001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 11/11/2011] [Indexed: 11/05/2022]
Abstract
We present a modern, light portable device specifically designed for environmental samples for cryogenic transmission-electron microscopy (cryo-TEM) by on-site cryo-plunging. The power of cryo-TEM comes from preparation of artifact-free samples. However, in many studies, the samples must be collected at remote field locations, and the time involved in transporting samples back to the laboratory for cryogenic preservation can lead to severe degradation artifacts. Thus, going back to the basics, we developed a simple mechanical device that is light and easy to transport on foot yet effective. With the system design presented here we are able to obtain cryo-samples of microbes and microbial communities not possible to culture, in their near-intact environmental conditions as well as in routine laboratory work, and in real time. This methodology thus enables us to bring the power of cryo-TEM to microbial ecology.
Collapse
Affiliation(s)
- Luis R Comolli
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
| | | | | | | | | | | | | | | |
Collapse
|