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Schroedl P, Silverstein M, DiGregorio D, Blättler CL, Loyd S, Bradbury HJ, Edwards RL, Marlow J. Carbonate chimneys at the highly productive point Dume methane seep: Fine-scale mineralogical, geochemical, and microbiological heterogeneity reflects dynamic and long-lived methane-metabolizing habitats. GEOBIOLOGY 2024; 22:e12608. [PMID: 38946067 DOI: 10.1111/gbi.12608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/24/2024] [Accepted: 06/12/2024] [Indexed: 07/02/2024]
Abstract
Methane is a potent greenhouse gas that enters the marine system in large quantities at seafloor methane seeps. At a newly discovered seep site off the coast of Point Dume, CA, ~ meter-scale carbonate chimneys host microbial communities that exhibit the highest methane-oxidizing potential recorded to date. Here, we provide a detailed assessment of chimney geobiology through correlative mineralogical, geochemical, and microbiological studies of seven chimney samples in order to clarify the longevity and heterogeneity of these highly productive systems. U-Th dating indicated that a methane-driven carbonate precipitating system at Point Dume has existed for ~20 Kyr, while millimeter-scale variations in carbon and calcium isotopic values, elemental abundances, and carbonate polymorphs revealed changes in carbon source, precipitation rates, and diagenetic processes throughout the chimneys' lifespan. Microbial community analyses revealed diverse modern communities with prominent anaerobic methanotrophs, sulfate-reducing bacteria, and Anaerolineaceae; communities were more similar within a given chimney wall transect than in similar horizons of distinct structures. The chimneys represent long-lived repositories of methane-oxidizing communities and provide a window into how carbon can be transformed, sequestered, and altered over millennia at the Point Dume methane seep.
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Affiliation(s)
- Peter Schroedl
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | | | - Daisy DiGregorio
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Clara L Blättler
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Sean Loyd
- Department of Geological Sciences, California State University Fullerton, Fullerton, California, USA
| | - Harold J Bradbury
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - R Lawrence Edwards
- Department of Earth and Environmental Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jeffrey Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
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Cuaxinque-Flores G, Talavera-Mendoza O, Aguirre-Noyola JL, Hernández-Flores G, Martínez-Miranda V, Rosas-Guerrero V, Martínez-Romero E. Molecular and geochemical basis of microbially induced carbonate precipitation for treating acid mine drainage: The case of a novel Sporosarcina genomospecies from mine tailings. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135005. [PMID: 38996684 DOI: 10.1016/j.jhazmat.2024.135005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/12/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
Microbially induced carbonate precipitation (MICP) immobilizes toxic metals and reduces their bioavailability in aqueous systems. However, its application in the treatment of acid mine drainage (AMD) is poorly understood. In this study, the genomes of Sporosarcina sp. UB5 and UB10 were sequenced. Urease, carbonic anhydrases, and metal resistance genes were identified and enzymatic assays were performed for their validation. The geochemical mechanism of precipitation in AMD was elucidated through geo-mineralogical analysis. Sporosarcina sp. UB5 was shown to be a new genomospecies, with an average nucleotide identity < 95 % (ANI) and DNA-DNA hybridization < 70 % (DDH) whereas UB10 is close to S. pasteurii. UB5 contained two urease operons, whereas only one was identified in UB10. The ureolytic activities of UB5 and UB10 were 122.67 ± 15.74 and 131.70 ± 14.35 mM NH4+ min-1, respectively. Both strains feature several carbonic anhydrases of the α, β, or γ families, which catalyzed the precipitation of CaCO3. Only Sporosarcina sp. UB5 was able to immobilize metals and neutralize AMD. Geo-mineralogical analyses revealed that UB5 directly immobilized Fe (1-23 %), Mn (0.65-1.33 %) and Zn (0.8-3 %) in AMD via MICP and indirectly through adsorption to calcite and binding to bacterial cell walls. The MICP-treated AMD exhibited high removal rates (>67 %) for Ag, Al, As, Ca, Cd, Co, Cu, Fe, Mn, Pb, and Zn, and a removal rate of 15 % for Mg. This study provides new insights into the MICP process and its applications to AMD treatment using autochthonous strains.
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Affiliation(s)
- Gustavo Cuaxinque-Flores
- Doctorado en Recursos Naturales y Ecologia, Facultad de Ecología Marina, Universidad Autónoma de Guerrero, Gran vía tropical 20, Fraccionamiento Las playas, Acapulco de Juárez, Guerrero, Mexico
| | - Oscar Talavera-Mendoza
- Doctorado en Recursos Naturales y Ecologia, Facultad de Ecología Marina, Universidad Autónoma de Guerrero, Gran vía tropical 20, Fraccionamiento Las playas, Acapulco de Juárez, Guerrero, Mexico; Escuela Superior de Ciencias de la Tierra, Universidad Autónoma de Guerrero, Ex-hacienda, San Juan Bautista s/n, CP 40323 Taxco el Viejo, Guerrero, Mexico.
| | - José Luis Aguirre-Noyola
- Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tepatitlán de Morelos 47600, Jalisco, Mexico
| | - Giovanni Hernández-Flores
- CONAHCyT-Escuela Superior de Ciencias de la Tierra, Universidad Autónoma de Guerrero, Ex Hacienda San Juan Bautista s/n, Taxco de Alarcón 40323, Mexico
| | - Verónica Martínez-Miranda
- Instituto Interamericano de Tecnología y Ciencias del Agua (IITCA), Universidad Autónoma del Estado de México, Unidad San Cayetano, Km. 14.5, Carretera, Toluca-Atlacomulco, C.P. 50200 Toluca, Estado de México, Mexico
| | - Víctor Rosas-Guerrero
- Escuela Superior en Desarrollo Sustentable, Universidad Autónoma de Guerrero, Tecpan de Galeana 40900, Mexico
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, UNAM, Av. Universidad s/n, Chamilpa, 62210 Cuernavaca, Morelos, Mexico.
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Mehta N, Bradbury H, Benzerara K. Calcium isotope fractionation by intracellular amorphous calcium carbonate (ACC) forming cyanobacteria. GEOBIOLOGY 2024; 22:e12596. [PMID: 38591761 DOI: 10.1111/gbi.12596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/26/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
The formation of intracellular amorphous calcium carbonate (ACC) by various cyanobacteria is a widespread biomineralization process, yet its mechanism and importance in past and modern environments remain to be fully comprehended. This study explores whether calcium (Ca) isotope fractionation, linked to ACC-forming cyanobacteria, can serve as a reliable tracer for detecting these microorganisms in modern and ancient settings. Accordingly, we measured stable Ca isotope fractionation during Ca uptake by the intracellular ACC-forming cyanobacterium Cyanothece sp. PCC 7425. Our results show that Cyanothece sp. PCC 7425 cells are enriched in lighter Ca isotopes relative to the solution. This finding is consistent with the kinetic isotope effects observed in the Ca isotope fractionation during biogenic carbonate formation by marine calcifying organisms. The Ca isotope composition of Cyanothece sp. PCC 7425 was accurately modeled using a Rayleigh fractionation model, resulting in a Ca isotope fractionation factor (Δ44Ca) equal to -0.72 ± 0.05‰. Numerical modeling suggests that Ca uptake by these cyanobacteria is primarily unidirectional, with minimal back reaction observed over the duration of the experiment. Finally, we compared our Δ44Ca values with those of other biotic and abiotic carbonates, revealing similarities with organisms that form biogenic calcite. These similarities raise questions about the effectiveness of using the Ca isotope fractionation factor as a univocal tracer of ACC-forming cyanobacteria in the environment. We propose that the use of Δ44Ca in combination with other proposed tracers of ACC-forming cyanobacteria such as Ba and Sr isotope fractionation factors and/or elevated Ba/Ca and Sr/Ca ratios may provide a more reliable approach.
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Affiliation(s)
- Neha Mehta
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique Des Matériaux et de Cosmochimie (IMPMC), Paris, France
- Department of Geosciences, Environment and Society, Université Libre de Bruxelles, Brussels, Belgium
| | - Harold Bradbury
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique Des Matériaux et de Cosmochimie (IMPMC), Paris, France
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Cosmidis J. Will tomorrow's mineral materials be grown? Microb Biotechnol 2023; 16:1713-1722. [PMID: 37522764 PMCID: PMC10443349 DOI: 10.1111/1751-7915.14298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 08/01/2023] Open
Abstract
Biomineralization, the capacity to form minerals, has evolved in a great diversity of bacterial lineages as an adaptation to different environmental conditions and biological functions. Microbial biominerals often display original properties (morphology, composition, structure, association with organics) that significantly differ from those of abiotically formed counterparts, altogether defining the 'mineral phenotype'. In principle, it should be possible to take advantage of microbial biomineralization processes to design and biomanufacture advanced mineral materials for a range of technological applications. In practice, this has rarely been done so far and only for a very limited number of biomineral types. This is mainly due to our poor understanding of the underlying molecular mechanisms controlling microbial biomineralization pathways, preventing us from developing bioengineering strategies aiming at improving biomineral properties for different applications. Another important challenge is the difficulty to upscale microbial biomineralization from the lab to industrial production. Addressing these challenges will require combining expertise from environmental microbiologists and geomicrobiologists, who have historically been working at the forefront of research on microbe-mineral interactions, alongside bioengineers and material scientists. Such interdisciplinary efforts may in the future allow the emergence of a mineral biomanufacturing industry, a critical tool towards the development more sustainable and circular bioeconomies.
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Affiliation(s)
- Julie Cosmidis
- Department of Earth SciencesUniversity of OxfordOxfordUK
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Gaëtan J, Halary S, Millet M, Bernard C, Duval C, Hamlaoui S, Hecquet A, Gugger M, Marie B, Mehta N, Moreira D, Skouri-Panet F, Travert C, Duprat E, Leloup J, Benzerara K. Widespread formation of intracellular calcium carbonates by the bloom-forming cyanobacterium Microcystis. Environ Microbiol 2023; 25:751-765. [PMID: 36550062 DOI: 10.1111/1462-2920.16322] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
The formation of intracellular amorphous calcium carbonates (iACC) has been recently observed in a few cultured strains of Microcystis, a potentially toxic bloom-forming cyanobacterium found worldwide in freshwater ecosystems. If iACC-forming Microcystis are abundant within blooms, they may represent a significant amount of particulate Ca. Here, we investigate the significance of iACC biomineralization by Microcystis. First, the presence of iACC-forming Microcystis cells has been detected in several eutrophic lakes, indicating that this phenomenon occurs under environmental conditions. Second, some genotypic (presence/absence of ccyA, a marker gene of iACC biomineralization) and phenotypic (presence/absence of iACC) diversity have been detected within a collection of strains isolated from one single lake. This illustrates that this trait is frequent but also variable within Microcystis even at a single locality. Finally, one-third of publicly available genomes of Microcystis were shown to contain the ccyA gene, revealing a wide geographic and phylogenetic distribution within the genus. Overall, the present work shows that the formation of iACC by Microcystis is common under environmental conditions. While its biological function remains undetermined, this process should be further considered regarding the biology of Microcystis and implications on the Ca geochemical cycle in freshwater environments.
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Affiliation(s)
- Juliette Gaëtan
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
- Sorbonne Université, UMR 7618 CNRS-INRA-IRD-Paris 7-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), Paris, France
| | - Sébastien Halary
- Muséum National d'Histoire Naturelle, UMR 7245 CNRS-MNHN, Molécules de Communication et Adaptation des Microorganismes, Paris, France
| | - Maxime Millet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Cécile Bernard
- Muséum National d'Histoire Naturelle, UMR 7245 CNRS-MNHN, Molécules de Communication et Adaptation des Microorganismes, Paris, France
| | - Charlotte Duval
- Muséum National d'Histoire Naturelle, UMR 7245 CNRS-MNHN, Molécules de Communication et Adaptation des Microorganismes, Paris, France
| | - Sahima Hamlaoui
- Muséum National d'Histoire Naturelle, UMR 7245 CNRS-MNHN, Molécules de Communication et Adaptation des Microorganismes, Paris, France
| | - Amandine Hecquet
- Sorbonne Université, UMR 7618 CNRS-INRA-IRD-Paris 7-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), Paris, France
| | - Muriel Gugger
- Institut Pasteur, Université Paris Cité, Collection of Cyanobacteria, Paris, France
| | - Benjamin Marie
- Muséum National d'Histoire Naturelle, UMR 7245 CNRS-MNHN, Molécules de Communication et Adaptation des Microorganismes, Paris, France
| | - Neha Mehta
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Fériel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Cynthia Travert
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Julie Leloup
- Sorbonne Université, UMR 7618 CNRS-INRA-IRD-Paris 7-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS-SU-MNHN 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
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