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Geosciences
Special Issues
Current and Future Perspectives in Microbial Carbonate Precipitation
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Current and Future Perspectives in Microbial Carbonate Precipitation

A special issue of Geosciences (ISSN 2076-3263).

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 13684

Special Issue Editors

Dr. Christophe Dupraz

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Guest Editor
Department of Geological Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
Interests: geomicrobiology; carbonate sedimentology; biogeosciences
Prof. Dr. Pieter T. Visscher

E-Mail Website
Guest Editor
Departments of Marine Sciences and Geosciences, University of Connecticut, Storrs, CT 06269, USA
Interests: geomicrobiology; biogeochemistry; geobiochemistry; element cycling; microbial ecophysiology
Special Issues, Collections and Topics in MDPI journals
Dr. Kimberley L Gallagher

E-Mail Website
Guest Editor
Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
Interests: geomicrobiology; biogeochemistry; chemistry; element cycling
Prof. Dr. Brendan Paul Burns

E-Mail Website
Guest Editor
School of Biotechnology and Biomolecular, University of New South Wales, Sydney, NSW 2052, Australia
Interests: metagenomics; stromatolites; archaea; extremophiles
Prof. Dr. Michael Rogerson

E-Mail Website
Guest Editor
Department of Geography and Environmental Sciences, Northumbria University, Newcastle-upon-Tyne NE7 7XA, Newcastle, UK
Interests: palaeoclimate; speleothems and tufa; geochemistry; environmental engineering

Special Issue Information

Dear Colleagues,

Microbe–mineral interactions, especially those including carbonate minerals, are at the center of current geomicrobiological research. Through metabolic activities, microbial communities modify saturation conditions in their immediate microenvironment and produce a wide array of organic compounds that may affect the nucleation and growth of those carbonate minerals. In the last two decades, the rapid advance of new technologies has pushed analytical limits involved in the characterization of mineral phases, community diversities, and metabolic processes, unveiling exciting new aspects (and modes) of forming microbial carbonates. Our more profound understanding of organomineralization processes is, for example, starting to rekindle the discussion of what a biosignature is.

Therefore, we invite contributions related to the five main topics that will frame this Special Issue on microbial carbonates (each topic will start with a “mini-review” or “introductory” invited papers setting the stage for that particular section):

(1) The physicochemical component: To understand how microbes and organic matter can mediate or interfere with carbonate mineral precipitation, it is important to have a fundamental mechanistic understanding of the nucleation and growth of carbonate minerals. Papers in this section shall discuss thermodynamic and kinetic controls on carbonate precipitation. We will also consider contributions addressing the precipitation associated with different mineralogical phases (e.g., Mg-Si phase) and other polymorphs. 

(2) Carbonate–organic interactions: This section will describe how mineralization processes can be affected by the “presence” of organic matter (biotic or abiotic in origin) in laboratory experiments or modeling efforts. It will deal with processes of organomineralization and biomineralization and the notion of an organosignature vs. a biosignature (seminal for origin of life and the search for life on other planets (Mars missions)). 

(3) Ecophysiological and molecular approaches (case studies): This section will deal with entire communities/ecosystems and their effect on carbonate precipitation. It includes the minute interaction of biogeochemical element cycles leading to specific conditions promoting the precipitation or the dissolution of carbonates.

(4) The future of carbonate precipitation research: This section will discuss state-of-the-art and ground-breaking novel approaches to characterize organic matter, microbial communities, and mineral products. Two examples come to mind: (1) the nanoscale characterization of phases and oxidation states of the main components of mineral products (e.g., synchrotron approaches), and (2) the various omics approaches with their qualities, issues, and novel analyses (e.g., machine learning). Papers in this section should propose opinions and visions that could shape the future direction of the field.

(5) Technological applications: the Special Issue will end with examples of applications from an engineering perspective including but not limited to carbon sequestration technology for climate change mitigation, or bioconcrete for restoration.

Dr. Christophe Dupraz
Prof. Dr. Pieter T. Visscher
Dr. Kimberley L Gallagher
Prof. Dr. Brendan Paul Burns
Prof. Dr. Michael Rogerson
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

  • Geomicrobiology
  • Biogeochemistry
  • Microbialite
  • Organomineralization
  • Carbonate mineral
  • Mineral nucleation
  • Microbe–mineral interactions
  • Amorphous calcium carbonate (ACC)
  • Extracellular organic matter (EOM)
  • “Alkalinity engine”
  • Organosignature
  • Biosignature

Published Papers (5 papers)

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Research

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24 pages, 6505 KiB  
Article
Effect of Culture pH on Properties of Exopolymeric Substances from Synechococcus PCC7942: Implications for Carbonate Precipitation
by Marlisa Martinho de Brito, Irina Bundeleva, Frédéric Marin, Emmanuelle Vennin, Annick Wilmotte, Laurent Plasseraud and Pieter T. Visscher
Geosciences 2022, 12(5), 210; https://0-doi-org.brum.beds.ac.uk/10.3390/geosciences12050210 - 16 May 2022
Cited by 4 | Viewed by 2613
Abstract
The role of culture conditions on the production of exopolymeric substances (EPS) by Synechococcus strain PCC7942 was investigated. Carbonate mineral precipitation in these EPS was assessed in forced precipitation experiments. Cultures were grown in HEPES-buffered medium and non-buffered medium. The pH of buffered [...] Read more.
The role of culture conditions on the production of exopolymeric substances (EPS) by Synechococcus strain PCC7942 was investigated. Carbonate mineral precipitation in these EPS was assessed in forced precipitation experiments. Cultures were grown in HEPES-buffered medium and non-buffered medium. The pH of buffered medium remained constant at 7.5, but in non-buffered medium it increased to 9.5 within a day and leveled off at 10.5. The cell yield at harvest was twice as high in non-buffered medium than in buffered medium. High molecular weight (>10 kDa) and low molecular weight (3–10 kDa) fractions of EPS were obtained from both cultures. The cell-specific EPS production in buffered medium was twice as high as in non-buffered medium. EPS from non-buffered cultures contained more negatively charged macromolecules and more proteins than EPS from buffered cultures. The higher protein content at elevated pH may be due to the induction of carbon-concentrating mechanisms, necessary to perform photosynthetic carbon fixation in these conditions. Forced precipitation showed smaller calcite carbonate crystals in EPS from non-buffered medium and larger minerals in polymers from buffered medium. Vaterite formed only at low EPS concentrations. Experimental results are used to conceptually model the impact of pH on the potential of cyanobacterial blooms to produce minerals. We hypothesize that in freshwater systems, small crystal production may benefit the picoplankton by minimizing the mineral ballast, and thus prolonging the residence time in the photic zone, which might result in slow sinking rates. Full article
(This article belongs to the Special Issue Current and Future Perspectives in Microbial Carbonate Precipitation)
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9 pages, 1620 KiB  
Article
Methanogenesis from Mineral Carbonates, a Potential Indicator for Life on Mars
by Richard M. Wormald, Jeremy Hopwood, Paul N. Humphreys, William Mayes, Helena I. Gomes and Simon P. Rout
Geosciences 2022, 12(3), 138; https://0-doi-org.brum.beds.ac.uk/10.3390/geosciences12030138 - 16 Mar 2022
Cited by 2 | Viewed by 3065
Abstract
Priorities for the exploration of Mars involve the identification and observation of biosignatures that indicate the existence of life on the planet. The atmosphere and composition of the sediments on Mars suggest suitability for anaerobic chemolithotrophic metabolism. Carbonates are often considered as morphological [...] Read more.
Priorities for the exploration of Mars involve the identification and observation of biosignatures that indicate the existence of life on the planet. The atmosphere and composition of the sediments on Mars suggest suitability for anaerobic chemolithotrophic metabolism. Carbonates are often considered as morphological biosignatures, such as stromatolites, but have not been considered as potential electron acceptors. Within the present study, hydrogenotrophic methanogen enrichments were generated from sediments that had received significant quantities of lime from industrial processes (lime kiln/steel production). These enrichments were then supplemented with calcium carbonate powder or marble chips as a sole source of carbon. These microcosms saw a release of inorganic carbon into the liquid phase, which was subsequently removed, resulting in the generation of methane, with 0.37 ± 0.09 mmoles of methane observed in the steel sediment enrichments supplemented with calcium carbonate powder. The steel sediment microcosms and lime sediments with carbonate powder enrichments were dominated by Methanobacterium sp., whilst the lime/marble enrichments were more diverse, containing varying proportions of Methanomassiliicoccus, Methanoculleus and Methanosarcina sp. In all microcosm experiments, acetic acid was detected in the liquid phase. Our results indicate that chemolithotrophic methanogenesis should be considered when determining biosignatures for life on Mars. Full article
(This article belongs to the Special Issue Current and Future Perspectives in Microbial Carbonate Precipitation)
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29 pages, 115725 KiB  
Article
Successive Modes of Carbonate Precipitation in Microbialites along the Hydrothermal Spring of La Salsa in Laguna Pastos Grandes (Bolivian Altiplano)
by Elodie Muller, Magali Ader, Giovanni Aloisi, Cédric Bougeault, Christophe Durlet, Emmanuelle Vennin, Karim Benzerara, Eric C. Gaucher, Aurélien Virgone, Marco Chavez, Pierre Souquet and Emmanuelle Gérard
Geosciences 2022, 12(2), 88; https://0-doi-org.brum.beds.ac.uk/10.3390/geosciences12020088 - 16 Feb 2022
Cited by 3 | Viewed by 2543
Abstract
Interpreting the paleoecosystems of ancient microbialites relies on our understanding of how modern microbialites form in relation with the bio-physico-chemical conditions of their environment. In this study, we investigated the formation of modern carbonate microbialites in the hydrothermal system of La Salsa in [...] Read more.
Interpreting the paleoecosystems of ancient microbialites relies on our understanding of how modern microbialites form in relation with the bio-physico-chemical conditions of their environment. In this study, we investigated the formation of modern carbonate microbialites in the hydrothermal system of La Salsa in Laguna Pastos Grandes (Bolivia), which spans a wide range of physicochemical conditions and associated microbial communities. By combining dissolved inorganic carbon (DIC) isotope mass balance modeling, analysis of carbonates solubility diagram, and imaging of the microorganisms–mineral assemblages within microbial mats, we found that several modes of carbonate precipitation dominate in distinct portions of the hydrothermal system. (1) In high-[DIC] waters, undersaturated to slightly saturated with respect to calcite, cyanobacterial calcification is promoted by CO2 degassing and photosynthetic activity within the microbial mats. (2) In alkaline waters undergoing sustained evaporation, the precipitation of an amorphous calcium carbonate phase seems to control the water a(Ca2+)/a(CO32−) ratio and to serve as a precursor to micritic calcite formation in microbial mats. (3) In saline ephemeral ponds, where the carbonate precipitation is the highest, calcite precipitation probably occurs through a different pathway, leading to a different calcite texture, i.e., aggregates of rhombohedral crystals. Full article
(This article belongs to the Special Issue Current and Future Perspectives in Microbial Carbonate Precipitation)
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17 pages, 3200 KiB  
Article
First Observation of Unicellular Organisms Concentrating Arsenic in ACC Intracellular Inclusions in Lake Waters
by Agathe Martignier, Montserrat Filella, Jean-Michel Jaquet, Mathieu Coster and Daniel Ariztegui
Geosciences 2022, 12(1), 32; https://0-doi-org.brum.beds.ac.uk/10.3390/geosciences12010032 - 08 Jan 2022
Viewed by 1493
Abstract
In unicellular organisms, intracellular inclusions of amorphous calcium carbonate (ACC) were initially described in cyanobacteria and, later, in unicellular eukaryotes from Lake Geneva (Switzerland/France). Inclusions in unicellular eukaryotes, named micropearls, consist of hydrated ACCs, frequently enriched in Sr or Ba, and displaying internal [...] Read more.
In unicellular organisms, intracellular inclusions of amorphous calcium carbonate (ACC) were initially described in cyanobacteria and, later, in unicellular eukaryotes from Lake Geneva (Switzerland/France). Inclusions in unicellular eukaryotes, named micropearls, consist of hydrated ACCs, frequently enriched in Sr or Ba, and displaying internal oscillatory zonations, due to variations in the Ba:Ca or Sr:Ca ratios. An analysis of our database, consisting of 1597 micropearl analyses from Lake Geneva and 34 from Lake Titicaca (Bolivia/Peru), showed that a certain number of Sr- and Ba-enriched micropearls from these lakes contain As in amounts measurable by EDXS. A Q-mode statistical analysis confirmed the existence of five chemically distinct morpho-chemical groups of As-bearing micropearls, among which was a new category identified in Lake Geneva, where As is often associated with Mg. This new type of micropearl is possibly produced in a small (7–12 μm size) bi-flagellated organism. Micropearls from Lake Titicaca, which contain Sr, were found in an organism very similar to Tetraselmis cordiformis, which was observed earlier in Lake Geneva. Lake Titicaca micropearls contain larger As amounts, which can be explained by the high As concentration in the water of this lake. The ubiquity of this observed biomineralization process points to the need for a better understanding of the role of amorphous or crystalline calcium carbonates in As cycling in surface waters. Full article
(This article belongs to the Special Issue Current and Future Perspectives in Microbial Carbonate Precipitation)
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Review

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18 pages, 2467 KiB  
Review
Using Molecular Tools to Understand Microbial Carbonates
by Elise M. Cutts, Matthew J. Baldes, Emilie J. Skoog, James Hall, Jian Gong, Kelsey R. Moore and Tanja Bosak
Geosciences 2022, 12(5), 185; https://doi.org/10.3390/geosciences12050185 - 25 Apr 2022
Cited by 6 | Viewed by 2649
Abstract
Here we review the application of molecular biological approaches to mineral precipitation in modern marine microbialites. The review focuses on the nearly two decades of nucleotide sequencing studies of the microbialites of Shark Bay, Australia; and The Bahamas. Molecular methods have successfully characterized [...] Read more.
Here we review the application of molecular biological approaches to mineral precipitation in modern marine microbialites. The review focuses on the nearly two decades of nucleotide sequencing studies of the microbialites of Shark Bay, Australia; and The Bahamas. Molecular methods have successfully characterized the overall community composition of mats, pinpointed microbes involved in key metabolisms, and revealed patterns in the distributions of microbial groups and functional genes. Molecular tools have become widely accessible, and we can now aim to establish firmer links between microbes and mineralization. Two promising future directions include “zooming in” to assess the roles of specific organisms, microbial groups, and surfaces in carbonate biomineralization and “zooming out” to consider broader spans of space and time. A middle ground between the two can include model systems that contain representatives of important microbial groups, processes, and metabolisms in mats and simplify hypothesis testing. These directions will benefit from expanding reference datasets of marine microbes and enzymes and enrichments of representative microbes from mats. Such applications of molecular tools should improve our ability to interpret ancient and modern microbialites and increase the utility of these rocks as long-term recorders of microbial processes and environmental chemistry. Full article
(This article belongs to the Special Issue Current and Future Perspectives in Microbial Carbonate Precipitation)
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