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Geosciences
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Microbial Biomineralization
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Microbial Biomineralization

A special issue of Geosciences (ISSN 2076-3263). This special issue belongs to the section "Biogeosciences".

Deadline for manuscript submissions: closed (31 October 2018) | Viewed by 19261

Special Issue Editors

Dr. Julie Cosmidis

E-Mail Website
Guest Editor
Department of Geosciences, Pennsylvania State University, State College, PA 16801, USA
Interests: microbial biomineralization; organomineralization; biosignatures; sulfur biogeochemistry; phosphorites
Dr. Aude Picard

E-Mail
Guest Editor
School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89119, USA
Interests: iron biogechemical cycle; biomineralization; microbial metabolism; biosignatures; spectroscopy; microscopy

Special Issue Information

Dear Colleagues,

We are inviting manuscript submissions for rapid, open-access publication of high-quality peer-reviewed studies in the field of microbial biomineralization. Microorganisms have been shaping the surface of the Earth at least for the past 3.8 Ga. Their ability to precipitate solid phases from aqueous species in a variety of environments has led to the deposition of mineral deposits of various sizes in the rock record and in modern environments. For this special issue, we encourage contributions from the laboratory or the field investigating the molecular mechanisms of induced and controlled microbial biomineralization, the impact of microbial biomineralization processes on biogeochemical cycles (e.g., C, Fe, Ca, P, S, Si), and the biosignatures of microbial biomineralization in the geological record. Studies focusing on the role of microbially-derived organic compounds (e.g., extracellular polymeric substances) in biomineral deposition are also welcome. This Special Issue also aims to cover interdisciplinary studies addressing the interactions between minerals and cellular or extracellular organic compounds, the role of biominerals in the geological preservation of organic matter, and the potential industrial and bioremediation applications of biominerals.

Dr. Julie Cosmidis
Dr. Aude Picard
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Geosciences is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Biomineralization
  • Microbe-mineral interactions
  • Organic-mineral interactions
  • Biosignatures
  • Microfossils
  • Biogeochemical cycles
  • Biomaterials
  • Bioremediation

Published Papers (5 papers)

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Research

18 pages, 2565 KiB  
Article
Biogeochemical Characterization of Metal Behavior from Novel Mussel Shell Bioreactor Sludge Residues
by Sara C. Butler, James Pope, Subba Rao Chaganti, Daniel D. Heath and Christopher G. Weisener
Geosciences 2019, 9(1), 50; https://doi.org/10.3390/geosciences9010050 - 18 Jan 2019
Cited by 1 | Viewed by 3038
Abstract
Acid mine drainage (AMD) remediation commonly produces byproducts which must be stored or utilized to reduce the risk of further contamination. A mussel shell bioreactor has been implemented at a coal mine in New Zealand, which is an effective remediation option, although an [...] Read more.
Acid mine drainage (AMD) remediation commonly produces byproducts which must be stored or utilized to reduce the risk of further contamination. A mussel shell bioreactor has been implemented at a coal mine in New Zealand, which is an effective remediation option, although an accumulated sludge layer decreased efficiency which was then removed and requires storage. To understand associated risks related to storage or use of the AMD sludge material, a laboratory mesocosm study investigated the physio-chemical and biological influence in two conditions: anoxic storage (burial deep within a waste rock dump) or exposure to oxic environments (use of sludge on the surface of the mine). Solid phase characterization by Scanning Electron Microscopy (SEM) and selective extraction was completed to compare two environmental conditions (oxic and anoxic) under biologically active and abiotic systems (achieved by gamma irradiation). Changes in microbial community structure were monitored using 16s rDNA amplification and next-generation sequencing. The results indicate that microbes in an oxic environment increase the formation of oxyhydroxides and acidic conditions increase metal mobility. In an oxic and circumneutral environment, the AMD sludge may be repurposed to act as an oxygen barrier for mine tailings or soil amendment. Anoxic conditions would likely promote the biomineralization of sulfide minerals in the AMD sludge by sulfate reducing bacteria (SRB), which were abundant in the system. The anoxic conditions reduced the risk of trace metals (Zn) associated with oxides, but increased Fe associated with organic material. In summary, fewer risks are associated with anoxic burial but repurposing in an oxic condition may be appropriate under favorable conditions. Full article
(This article belongs to the Special Issue Microbial Biomineralization)
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33 pages, 9921 KiB  
Article
Microbial Geochemistry Reflecting Sulfur, Iron, Manganese, and Calcium Sources in the San Diego River Watershed, Southern California USA
by Eleanora I. Robbins, Shannon Quigley-Raymond, Ming Lai and Janae Fried
Geosciences 2018, 8(12), 495; https://doi.org/10.3390/geosciences8120495 - 17 Dec 2018
Viewed by 4435
Abstract
Microbial populations involved in forming the distinctive precipitates of S, Fe, Mn, and Ca in the San Diego River watershed reflect an interplay between the mineralogy of the rocks in the watershed, sparse rainfall, ground- and surface-water anoxia, and runoff of high sulfate, [...] Read more.
Microbial populations involved in forming the distinctive precipitates of S, Fe, Mn, and Ca in the San Diego River watershed reflect an interplay between the mineralogy of the rocks in the watershed, sparse rainfall, ground- and surface-water anoxia, and runoff of high sulfate, treated imported water. In the sparsely developed headwaters, the Temescal Creek tributary emerges from pyrite-bearing metamorphic rocks, and thus exhibits both an oxidized Fe and reduced S. In the middle reaches, the river moves through developed land where treated, imported high sulfate Colorado River water enters from urban runoff. Mast Park surrounded by caliche-bearing sedimentary rocks is a site where marl is precipitating. Cobbles in riffles along the river are coated black with Mn oxide. When the river encounters deep-seated volcanic bedrock, it wells up to precipitate both Fe and Mn oxides at the Old Mission Dam. Then, directly flowing through caliche-laced sedimentary rocks, Birchcreek tributary precipitates tufa. Further downstream at a site under a bridge that blocks sunlight, a sulfuretum sets up when the river is deoxygenated. Such a rich geochemistry results in activity of iron and manganese oxidizing bacteria, sulfur oxidizers and reducers, and cyanobacteria precipitating calcareous marl and tufa. Full article
(This article belongs to the Special Issue Microbial Biomineralization)
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20 pages, 27989 KiB  
Article
Terraced Iron Formations: Biogeochemical Processes Contributing to Microbial Biomineralization and Microfossil Preservation
by Jeremiah Shuster, Maria Angelica Rea, Barbara Etschmann, Joël Brugger and Frank Reith
Geosciences 2018, 8(12), 480; https://doi.org/10.3390/geosciences8120480 - 13 Dec 2018
Cited by 5 | Viewed by 3832
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Microbial Biomineralization)
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20 pages, 5041 KiB  
Article
Effects of Phosphorus in Growth Media on Biomineralization and Cell Surface Properties of Marine Cyanobacteria Synechococcus
by Carlos Paulo, Janice P. L. Kenney, Per Persson and Maria Dittrich
Geosciences 2018, 8(12), 471; https://doi.org/10.3390/geosciences8120471 - 11 Dec 2018
Cited by 16 | Viewed by 4776
Abstract
Through geological time, cyanobacterial picoplankton have impacted the global carbon cycle by sequestrating CO2 and forming authigenic carbonate minerals. Various studies have emphasized the cyanobacterial cell envelopes as nucleation sites for calcium carbonate formation. Little is known, however, about how environmental conditions [...] Read more.
Through geological time, cyanobacterial picoplankton have impacted the global carbon cycle by sequestrating CO2 and forming authigenic carbonate minerals. Various studies have emphasized the cyanobacterial cell envelopes as nucleation sites for calcium carbonate formation. Little is known, however, about how environmental conditions (e.g., nutrient content) trigger a cell surface and its properties and, consequently, influence biomineralization. Our study aims to understand how phosphorus (P) concentration impacts the properties of cell surfaces and cell–mineral interactions. Changes to the surface properties of marine Synechococcus strains grown under various P conditions were characterized by potentiometric titrations, X-ray photoelectron spectroscopy (XPS), and tip-enhanced Raman spectroscopy (TERS). Biomineralization experiments were performed using cyanobacterial cells, which were grown under different P concentrations and exposed to solutions slightly oversaturated with respect to calcium carbonate. We observed the changes induced by different P conditions in the macromolecular composition of the cyanobacteria cell envelope and its consequences for biomineralization. The modified properties of cell surfaces were linked to carbonate precipitation rates and mineral morphology from biomineralization experiments. Our analysis shows that the increase of phosphoryl groups and surface charge, as well as the relative proportion of polysaccharides and proteins, can impact carbonate precipitation by picocyanobacteria. Full article
(This article belongs to the Special Issue Microbial Biomineralization)
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20 pages, 4083 KiB  
Article
Hydrodynamic Shear-Induced Densification of Bacteriogenic Iron Oxides: Mechanisms and Implications
by Brock A. Edwards and F. Grant Ferris
Geosciences 2018, 8(11), 423; https://doi.org/10.3390/geosciences8110423 - 16 Nov 2018
Cited by 1 | Viewed by 2724
Abstract
Bacterial–mineral aggregates are the products of a tight biogeochemical coupling between microbes and geological media and play an outsized role in governing the composition of natural waters through biogeochemical cycling and mineral formation and dissolution processes. The results of combined batch column settling [...] Read more.
Bacterial–mineral aggregates are the products of a tight biogeochemical coupling between microbes and geological media and play an outsized role in governing the composition of natural waters through biogeochemical cycling and mineral formation and dissolution processes. The results of combined batch column settling experiments, volumetric analyses, and microscopic investigations demonstrate that composite bacteriogenic iron oxide aggregates are sensitive to densification in response to hydrodynamic shear, a physical fluid phenomenon that introduces significant alterations to aggregate size and structure, permeability, and settling and transport behaviour. After exposing aggregate suspensions to varying degrees of shear stress, final solids volume fractions decreased by as much as 75% from initial data, while aggregate bulk density saw increases from 999 kg·m–3 to as much as 1010 kg·m–3. Inverse modelling of time course data yielded estimates for settling rate constants and initial settling velocities that increased with shear stress application. As well as having implications for aqueous contaminant transport and potential bacterial bioenergetic strategies, these results suggest the preservation potential of microfossils formed from bacterial–mineral aggregates may be significantly reduced with shear-induced alterations, leading to a possible underrepresentation of these microfossils in the sedimentary record and a gap in our understanding of early life on Earth. Full article
(This article belongs to the Special Issue Microbial Biomineralization)
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