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Dutta S, Kothari S, Singh D, Ghosh S, Narayan Sarangi A, Sanjita Behera S, Prajapati S, Kumar Sinha P, Prusty A, Tripathy S. Novel oceanic cyanobacterium isolated from Bangaram island with profound acid neutralizing ability is proposed as Leptolyngbya iicbica sp. nov. strain LK. Mol Phylogenet Evol 2024; 197:108092. [PMID: 38723790 DOI: 10.1016/j.ympev.2024.108092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/16/2024] [Accepted: 05/04/2024] [Indexed: 05/19/2024]
Abstract
An acid-neutralizing, filamentous, non-heterocytous, marine cyanobacterium named 'LK' has been isolated from the seashore of Bangaram Island, an atoll of Lakshadweep, India, and is described here as a novel species. LK has been characterized using morphological, ecological, and genomic features. Based on 16S rRNA, whole-genome sequencing, and marker gene-based analysis, LK has been identified as a new species. LK clustered with Leptolyngbya-like strains belonging to the LPP group but diverged from Leptolyngbya sensu stricto, indicating the polyphyletic nature of the Leptolyngbya genus. Leptolyngbya sp. SIOISBB and Halomicronema sp. CCY15110 were identified as LK's two closest phylogenetic neighbors in various phylogenetic studies. The analysis of 16S rRNA, ITS secondary structures, and genome relatedness indices such as AAI, ANI, and gANI strongly support LK as a novel species of the Leptolyngbya genus. The mechanism behind acid neutralization in LK has been delineated, attributing it to a surface phenomenon most likely due to the presence of salts of calcium, magnesium, sodium, and potassium. We name LK as Leptolyngbya iicbica strain LK which is a novel species with prominent acidic pH-neutralizing properties.
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Affiliation(s)
- Subhajeet Dutta
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shreya Kothari
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Deeksha Singh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Samrat Ghosh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aditya Narayan Sarangi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Smruti Sanjita Behera
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Molecular Genetics Division, CSIR Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Satish Prajapati
- Advanced Materials and Chemical Characterisation Division (AMCCD), CSIR-Central Glass & Ceramic Research Institute (CGCRI), Kolkata 700 032, West Bengal, India
| | - Prasanta Kumar Sinha
- Advanced Materials and Chemical Characterisation Division (AMCCD), CSIR-Central Glass & Ceramic Research Institute (CGCRI), Kolkata 700 032, West Bengal, India
| | - Asharani Prusty
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Kim M, Lopez-Canfin C, Lázaro R, Sánchez-Cañete EP, Weber B. Unravelling the main mechanism responsible for nocturnal CO 2 uptake by dryland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171751. [PMID: 38503391 DOI: 10.1016/j.scitotenv.2024.171751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/21/2024] [Accepted: 03/14/2024] [Indexed: 03/21/2024]
Abstract
Soil respiration, or CO2 efflux from soil, is a crucial component of the terrestrial carbon cycle in climate models. Contrastingly, many dryland soils absorb atmospheric CO2 at night, but the exact mechanisms driving this uptake are actively debated. Here we used a mechanistic model with heuristic approaches to unravel the underlying processes of the observed patterns of soil-atmosphere CO2 fluxes. We show that the temperature drop during nighttime is the main driver of CO2 uptake by increasing CO2 solubility and local water pH of a thin water film on soil particle surfaces, providing favourable conditions for carbonate precipitation. Our data demonstrate that the nocturnal inorganic carbon absorption is a common soil process, but often offset by biological CO2 production. The uptake rates can be impacted by different successional stages of biocrusts that consume or produce CO2 and modify the pH of the soil water film, which can be maintained by non-rainfall water inputs, such as pore space condensation. Annual estimates of nocturnal carbon uptake, based on in situ continuous measurements at the soil level in drylands are still very scarce, but fluxes of up to several tens of g C m-2 y-1 have been reported, potentially accounting for a considerable fraction of the global residual terrestrial carbon sink.
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Affiliation(s)
- Minsu Kim
- Institute of Biology, University of Graz, Graz, Austria.
| | - Clément Lopez-Canfin
- Department of Applied Physics, University of Granada (UGR), Granada, Spain; Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
| | - Roberto Lázaro
- Department of Desertification and Geo-Ecology, Experimental Station of Arid Zones (EEZA-CSIC), Almería, Spain
| | - Enrique P Sánchez-Cañete
- Department of Applied Physics, University of Granada (UGR), Granada, Spain; Inter-University Institute for Earth System Research (IISTA-CEAMA), Granada, Spain
| | - Bettina Weber
- Institute of Biology, University of Graz, Graz, Austria; Multiphase Chemistry, Max Planck Institute for Chemistry, Mainz, Germany
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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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4
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Garuglieri E, Marasco R, Odobel C, Chandra V, Teillet T, Areias C, Sánchez-Román M, Vahrenkamp V, Daffonchio D. Searching for microbial contribution to micritization of shallow marine sediments. Environ Microbiol 2024; 26:e16573. [PMID: 38217094 DOI: 10.1111/1462-2920.16573] [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: 07/25/2023] [Accepted: 12/21/2023] [Indexed: 01/15/2024]
Abstract
Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state-of-the-art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ 'fishing' strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process.
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Affiliation(s)
- Elisa Garuglieri
- Red Sea Research Center, Division of Biological Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ramona Marasco
- Red Sea Research Center, Division of Biological Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Charlene Odobel
- Red Sea Research Center, Division of Biological Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Viswasanthi Chandra
- Ali I. Al-Naimi Petroleum Engineering Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Thomas Teillet
- Ali I. Al-Naimi Petroleum Engineering Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Camila Areias
- Department of Earth Sciences, Faculty of Science, Vrije Universiteit, Amsterdam, the Netherlands
| | - Mónica Sánchez-Román
- Department of Earth Sciences, Faculty of Science, Vrije Universiteit, Amsterdam, the Netherlands
| | - Volker Vahrenkamp
- Ali I. Al-Naimi Petroleum Engineering Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Red Sea Research Center, Division of Biological Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Reid RP, Suosaari EP, Oehlert AM, Pollier CGL, Dupraz C. Microbialite Accretion and Growth: Lessons from Shark Bay and the Bahamas. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:487-511. [PMID: 38231736 DOI: 10.1146/annurev-marine-021423-124637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Microbialites provide geological evidence of one of Earth's oldest ecosystems, potentially recording long-standing interactions between coevolving life and the environment. Here, we focus on microbialite accretion and growth and consider how environmental and microbial forces that characterize living ecosystems in Shark Bay and the Bahamas interact to form an initial microbialite architecture, which in turn establishes distinct evolutionary pathways. A conceptual three-dimensional model is developed for microbialite accretion that emphasizes the importance of a dynamic balance between extrinsic and intrinsic factors in determining the initial architecture. We then explore how early taphonomic and diagenetic processes modify the initial architecture, culminating in various styles of preservation in the rock record. The timing of lithification of microbial products is critical in determining growth patterns and preservation potential. Study results have shown that all microbialites are not created equal; the unique evolutionary history of an individual microbialite matters.
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Affiliation(s)
- R Pamela Reid
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA; , ,
- Bahamas Marine EcoCentre, Miami, Florida, USA;
| | - Erica P Suosaari
- Bahamas Marine EcoCentre, Miami, Florida, USA;
- Department of Mineral Sciences, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Bush Heritage Australia, Melbourne, Victoria, Australia
| | - Amanda M Oehlert
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA; , ,
| | - Clément G L Pollier
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA; , ,
| | - Christophe Dupraz
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden;
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Krings S, Chen Y, Keddie JL, Hingley-Wilson S. Oxygen evolution from extremophilic cyanobacteria confined in hard biocoatings. Microbiol Spectr 2023; 11:e0187023. [PMID: 37747195 PMCID: PMC10580922 DOI: 10.1128/spectrum.01870-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/26/2023] Open
Abstract
Biocoatings, in which viable bacteria are immobilized within a waterborne polymer coating for a wide range of potential applications, have garnered greater interest in recent years. In bioreactors, biocoatings can be ready-to-use alternatives for carbon capture or biofuel production that could be reused multiple times. Here, we have immobilized cyanobacteria in mechanically hard biocoatings, which were deposited from polymer colloids in water (i.e., latex). The biocoatings are formed upon heating to 37°C and fully dried before rehydrating. The viability and oxygen evolution of three cyanobacterial species within the biocoatings were compared. Synechococcus sp. PCC 7002 was non-viable inside the biocoatings immediately after drying, whereas Synechocystis sp. PCC 6803 survived the coating formation, as shown by an adenosine triphosphate (ATP) assay. Synechocystis sp. PCC 6803 consumed oxygen (by cell respiration) for up to 5 days, but was unable to perform photosynthesis, as indicated by a lack of oxygen evolution. However, Chroococcidiopsis cubana PCC 7433, a strain of desiccation-resistant extremophilic cyanobacteria, survived and performed photosynthesis and carbon capture within the biocoating, with specific rates of oxygen evolution up to 0.4 g of oxygen/g of biomass per day. Continuous measurements of dissolved oxygen were carried out over a month and showed no sign of decreasing activity. Extremophilic cyanobacteria are viable in a variety of environments, making them ideal candidates for use in biocoatings and other biotechnology. IMPORTANCE As water has become a precious resource, there is a growing need for less water-intensive use of microorganisms, while avoiding desiccation stress. Mechanically robust, ready-to-use biocoatings or "living paints" (a type of artificial biofilm consisting of a synthetic matrix containing functional bacteria) represent a novel way to address these issues. Here, we describe the revolutionary, first-ever use of an extremophilic cyanobacterium (Chroococcidiopsis cubana PCC 7433) in biocoatings, which were able to produce high levels of oxygen and carbon capture for at least 1 month despite complete desiccation and subsequent rehydration. Beyond culturing viable bacteria with reduced water resources, this pioneering use of extremophiles in biocoatings could be further developed for a variety of applications, including carbon capture, wastewater treatment and biofuel production.
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Affiliation(s)
- Simone Krings
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Yuxiu Chen
- School of Mathematics and Physics, University of Surrey, Guildford, Surrey, United Kingdom
| | - Joseph L. Keddie
- School of Mathematics and Physics, University of Surrey, Guildford, Surrey, United Kingdom
| | - Suzanne Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
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7
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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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Elizabeth George S, Wan Y. Microbial functionalities and immobilization of environmental lead: Biogeochemical and molecular mechanisms and implications for bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131738. [PMID: 37285788 DOI: 10.1016/j.jhazmat.2023.131738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/09/2023]
Abstract
The increasing environmental and human health concerns about lead in the environment have stimulated scientists to search for microbial processes as innovative bioremediation strategies for a suite of different contaminated media. In this paper, we provide a compressive synthesis of existing research on microbial mediated biogeochemical processes that transform lead into recalcitrant precipitates of phosphate, sulfide, and carbonate, in a genetic, metabolic, and systematics context as they relate to application in both laboratory and field immobilization of environmental lead. Specifically, we focus on microbial functionalities of phosphate solubilization, sulfate reduction, and carbonate synthesis related to their respective mechanisms that immobilize lead through biomineralization and biosorption. The contributions of specific microbes, both single isolates or consortia, to actual or potential applications in environmental remediation are discussed. While many of the approaches are successful under carefully controlled laboratory conditions, field application requires optimization for a host of variables, including microbial competitiveness, soil physical and chemical parameters, metal concentrations, and co-contaminants. This review challenges the reader to consider bioremediation approaches that maximize microbial competitiveness, metabolism, and the associated molecular mechanisms for future engineering applications. Ultimately, we outline important research directions to bridge future scientific research activities with practical applications for bioremediation of lead and other toxic metals in environmental systems.
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Affiliation(s)
- S Elizabeth George
- US EPA Office of Research and Development, Center for Environmental Measurement and Modeling, Gulf Ecosystem Measurement and Modeling Division, One Sabine Island Drive, Gulf Breeze, FL 32561, USA
| | - Yongshan Wan
- US EPA Office of Research and Development, Center for Environmental Measurement and Modeling, Gulf Ecosystem Measurement and Modeling Division, One Sabine Island Drive, Gulf Breeze, FL 32561, USA.
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Escoffier N, Perolo P, Many G, Pasche NT, Perga ME. Fine-scale dynamics of calcite precipitation in a large hardwater lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:160699. [PMID: 36528097 DOI: 10.1016/j.scitotenv.2022.160699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
In hardwater lakes, calcite precipitation is an important yet poorly understood process in the lacustrine carbon cycle, in which catchment-derived alkalinity (Alk) is both transformed and translocated. While the physico-chemical conditions supporting the supersaturation of water with respect to calcite are theoretically well described, the magnitude and conditions underlying calcite precipitation at fine temporal and spatial scales are poorly constrained. In this study, we used high frequency, depth-resolved (0-30 m) data collected over 18 months (June 2019 - November 2020) in the deeper basin of Lake Geneva to describe the dynamics of calcite precipitation fluxes at a fine temporal resolution (day to season) and to scale them to carbon fixation by primary production. Calcite precipitation occurred during the warm stratified periods when surface water CO2 concentrations were below atmospheric equilibrium. Seasonally, the extent of Alk loss due to calcite precipitation (i.e., [30-42] g C m-2) depended upon the level of Alk in surface waters. Moreover, interannual variability in seasonal calcite precipitation depended on the duration of stratification, which determined the volume of the water layer susceptible to calcite precipitation. At finer timescales, calcite precipitation was characterized by marked daily variability with dynamics strongly related to that of planktonic autotrophic metabolism. Increasing daily calcite precipitation rates (i.e., maximum values 9 mmol C m-3 d-1) coincided with increasing net ecosystem production (NEP) during periods of enhanced water column stability. In these conditions, calcite precipitation could remove as much inorganic carbon from the productive layers as NEP. This study provides mechanistic insights into the conditions driving pelagic calcite precipitation, and quantifies its essential contribution to the coupling of organic and inorganic carbon cycling in lakes.
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Affiliation(s)
- Nicolas Escoffier
- Institute of Earth Surface Dynamics, University of Lausanne, Switzerland.
| | - Pascal Perolo
- Institute of Earth Surface Dynamics, University of Lausanne, Switzerland
| | - Gaël Many
- Institute of Earth Surface Dynamics, University of Lausanne, Switzerland
| | | | - Marie-Elodie Perga
- Institute of Earth Surface Dynamics, University of Lausanne, Switzerland
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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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11
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Stanton C, Barnes BD, Kump LR, Cosmidis J. A re-examination of the mechanism of whiting events: A new role for diatoms in Fayetteville Green Lake (New York, USA). GEOBIOLOGY 2023; 21:210-228. [PMID: 36326137 PMCID: PMC10092686 DOI: 10.1111/gbi.12534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/24/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Whiting events-the episodic precipitation of fine-grained suspended calcium carbonates in the water column-have been documented across a variety of marine and lacustrine environments. Whitings likely are a major source of carbonate muds, a constituent of limestones, and important archives for geochemical proxies of Earth history. While several biological and physical mechanisms have been proposed to explain the onset of these precipitation events, no consensus has been reached thus far. Fayetteville Green Lake (New York, USA) is a meromictic lake that experiences annual whitings. Materials suspended in the water column collected through the whiting season were characterized using scanning electron microscopy and scanning transmission X-ray microscopy. Whitings in Fayetteville Green Lake are initiated in the spring within the top few meters of the water column, by precipitation of fine amorphous calcium carbonate (ACC) phases nucleating on microbial cells, as well as on abundant extracellular polymeric substances (EPS) frequently associated with centric diatoms. Whiting particles found in the summer consist of 5-7 μm calcite grains forming aggregates with diatoms and EPS. Simple calculations demonstrate that calcite particles continuously grow over several days, then sink quickly through the water column. In the late summer, partial calcium carbonate dissolution is observed deeper in the water column. Settling whiting particles, however, reach the bottom of the lake, where they form a major constituent of the sediment, along with diatom frustules. The role of diatoms and associated EPS acting as nucleation surfaces for calcium carbonates is described for the first time here as a potential mechanism participating in whitings at Fayetteville Green Lake. This mechanism may have been largely overlooked in other whiting events in modern and ancient environments.
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Affiliation(s)
- Chloe Stanton
- Department of GeosciencesThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Ben Davis Barnes
- Department of GeosciencesThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Lee R. Kump
- Department of GeosciencesThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- Earth and Environmental Systems InstituteThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Julie Cosmidis
- Department of GeosciencesThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- Earth and Environmental Systems InstituteThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
- Present address:
Department of Earth SciencesUniversity of OxfordOxfordUK
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12
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Liu Y, Ali A, Su JF, Li K, Hu RZ, Wang Z. Microbial-induced calcium carbonate precipitation: Influencing factors, nucleation pathways, and application in waste water remediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160439. [PMID: 36574549 DOI: 10.1016/j.scitotenv.2022.160439] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/19/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
Microbial-induced calcium carbonate precipitation (MICP) is a technique that uses the metabolic action of microorganisms to produce CO32- which combines with free Ca2+ to form CaCO3 precipitation. It has gained widespread attention in water treatment, aimed with the advantages of simultaneous removal of multiple pollutants, environmental protection, and ecological sustainability. This article reviewed the mechanism of MICP at both intra- and extra-cellular levels. It summarized the parameters affecting the MICP process in terms of bacterial concentration, ambient temperature, etc. The current status of MICP application in practical engineering is discussed. Based on this, the current technical difficulties faced in the use of MICP technology were outlined, and future research directions for MICP technology were highlighted. This review helps to improve the design of existing water treatment facilities for the simultaneous removal of multiple pollutants using the MICP and provides theoretical reference and innovative thinking for related research.
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Affiliation(s)
- Yu Liu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Amjad Ali
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Jun-Feng Su
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Kai Li
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Rui-Zhu Hu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Zhao Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
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13
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Gold DA, Vermeij GJ. Deep resilience: An evolutionary perspective on calcification in an age of ocean acidification. Front Physiol 2023; 14:1092321. [PMID: 36818444 PMCID: PMC9935589 DOI: 10.3389/fphys.2023.1092321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The success of today's calcifying organisms in tomorrow's oceans depends, in part, on the resilience of their skeletons to ocean acidification. To the extent this statement is true there is reason to have hope. Many marine calcifiers demonstrate resilience when exposed to environments that mimic near-term ocean acidification. The fossil record similarly suggests that resilience in skeletons has increased dramatically over geologic time. This "deep resilience" is seen in the long-term stability of skeletal chemistry, as well as a decreasing correlation between skeletal mineralogy and extinction risk over time. Such resilience over geologic timescales is often attributed to genetic canalization-the hardening of genetic pathways due to the evolution of increasingly complex regulatory systems. But paradoxically, our current knowledge on biomineralization genetics suggests an opposing trend, where genes are co-opted and shuffled at an evolutionarily rapid pace. In this paper we consider two possible mechanisms driving deep resilience in skeletons that fall outside of genetic canalization: microbial co-regulation and macroevolutionary trends in skeleton structure. The mechanisms driving deep resilience should be considered when creating risk assessments for marine organisms facing ocean acidification and provide a wealth of research avenues to explore.
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14
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Segovia‐Campos I, Filella M, Perron K, Ariztegui D. High calcium and strontium uptake by the green microalga Tetraselmis chui is related to micropearl formation and cell growth. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:38-50. [PMID: 36151741 PMCID: PMC10103758 DOI: 10.1111/1758-2229.13124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 09/01/2022] [Indexed: 05/20/2023]
Abstract
Strontium-rich micropearls (intracellular inclusions of amorphous calcium carbonate) have been observed in several species of green microalgae within the class Chlorodendrophyceae, suggesting the potential use of these organisms for 90 Sr bioremediation purposes. However, very little is known about the micropearl formation process and the Ca and Sr uptake dynamics of these microalgae. To better understand this phenomenon, we investigated, through laboratory cultures, the behaviour of two species within the class Chorodendrophyceae: Tetraselmis chui, forming micropearls, and T. marina, not forming micropearls. We show that T. chui growth and micropearl formation requires available Ca in the culture medium, and that the addition of dissolved Sr can partially replace the function of Ca in cells. On the other hand, T. marina can grow without added Ca and Sr, probably due to its inability to form micropearls. T. chui cells show a high Ca and Sr uptake, significantly decreasing the concentration of both elements in the culture medium. Strontium is incorporated in micropearls in a short period of time, suggesting that micropearl formation is, most likely, a fast process that only takes a few hours. In addition, we show that micropearls equally distribute between daughter cells during cell division.
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Affiliation(s)
| | | | - Karl Perron
- Microbiology UnitUniversity of GenevaGenevaSwitzerland
| | - Daniel Ariztegui
- Department of Earth SciencesUniversity of GenevaGenevaSwitzerland
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15
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Soria R, Rodríguez-Berbel N, Sánchez-Cañete EP, Villafuerte AB, Ortega R, Miralles I. Organic amendments from recycled waste promote short-term carbon sequestration of restored soils in drylands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 327:116873. [PMID: 36470184 DOI: 10.1016/j.jenvman.2022.116873] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Soils are considered as a major reservoir for terrestrial carbon and it can act as a source or sink depending upon the land management activities. In semi-arid areas, the natural recovery of soils degraded by mining activities is complicated. A possible solution to recover soil quality and functionality, plant cover and carbon sequestration capacity could be the application of organic amendments. This work focuses on a restoration carried out in 2018 by applying with different composted organic amendments (stabilized sludge, gardening and greenhouse waste) in a limestone quarry under semi-arid climate (SE Spain). The objective was to evaluate the effects of different organic amendments on net CO2 exchange in two microcosms: soil-Stipa tenacissima and soil-spontaneous vegetation. Soil physical and chemical properties, environmental and ecological variables and their interrelationship were studied in amended and unamended soils. The results obtained under soil-forming factors in the study area showed an increase in soil organic carbon and nitrogen content, improved moisture and plant growth, and plant canopy development in amended soils. Soil moisture, soil temperature and plant cover significantly influenced net CO2 exchange. In general, microcosms with S. tenacissima showed higher carbon sequestration rates than soils with only spontaneous plant cover. Soils treated with a vegetable-only amendments showed higher plant cover and CO2 fixation rates after significant rainfall. On the other hand, the plots treated with sludge compost presented more soil respiration than photosynthesis, especially in the wet seasons. Soils with sludge and greenhouse compost mixed had higher CO2 fixation rates than soils restored with a mixture of sludge and garden compost. Soils with greenhouse waste compost showed CO2 fixation in the microcosm with plants in all campaigns, being the best treatment to promote atmospheric CO2 sequestration in soil restoration.
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Affiliation(s)
- Rocío Soria
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
| | - Natalia Rodríguez-Berbel
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
| | - Enrique P Sánchez-Cañete
- Department of Applied Physics, University of Granada (UGR), Granada, Spain; Inter-University Institute for Earth System Research (IISTA-CEAMA), Granada, Spain
| | - Ana B Villafuerte
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
| | - Raúl Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain.
| | - Isabel Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain.
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16
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Cobos M, Condori RC, Grandez MA, Estela SL, Del Aguila MT, Castro CG, Rodríguez HN, Vargas JA, Tresierra AB, Barriga LA, Marapara JL, Adrianzén PM, Ruiz R, Castro JC. Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin region. Front Genet 2022; 13:973324. [DOI: 10.3389/fgene.2022.973324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022] Open
Abstract
Cyanobacteria are diverse photosynthetic microorganisms able to produce a myriad of bioactive chemicals. To make possible the rational exploitation of these microorganisms, it is fundamental to know their metabolic capabilities and to have genomic resources. In this context, the main objective of this research was to determine the genome features and the biochemical profile of Synechococcus sp. UCP002. The cyanobacterium was isolated from the Peruvian Amazon Basin region and cultured in BG-11 medium. Growth parameters, genome features, and the biochemical profile of the cyanobacterium were determined using standardized methods. Synechococcus sp. UCP002 had a specific growth rate of 0.086 ± 0.008 μ and a doubling time of 8.08 ± 0.78 h. The complete genome of Synechococcus sp. UCP002 had a size of ∼3.53 Mb with a high coverage (∼200x), and its quality parameters were acceptable (completeness = 99.29%, complete and single-copy genes = 97.5%, and contamination = 0.35%). Additionally, the cyanobacterium had six plasmids ranging from 24 to 200 kbp. The annotated genome revealed ∼3,422 genes, ∼ 3,374 protein-coding genes (with ∼41.31% hypothetical protein-coding genes), two CRISPR Cas systems, and 61 non-coding RNAs. Both the genome and plasmids had the genes for prokaryotic defense systems. Additionally, the genome had genes coding the transcription factors of the metalloregulator ArsR/SmtB family, involved in sensing heavy metal pollution. The biochemical profile showed primary nutrients, essential amino acids, some essential fatty acids, pigments (e.g., all-trans-β-carotene, chlorophyll a, and phycocyanin), and phenolic compounds. In conclusion, Synechococcus sp. UCP002 shows biotechnological potential to produce human and animal nutrients and raw materials for biofuels and could be a new source of genes for synthetic biological applications.
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17
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Zafar AM, Javed MA, Aly Hassan A, Sahle-Demessie E, Harmon S. Biodesalination using halophytic cyanobacterium Phormidium keutzingianum from brackish to the hypersaline water. CHEMOSPHERE 2022; 307:136082. [PMID: 36028126 PMCID: PMC10875329 DOI: 10.1016/j.chemosphere.2022.136082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/05/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
The biodesalination potential at different levels of salinity of Phormidium keutzingianum (P. keutzingianum) was investigated. A wide range of salinity from brackish to hypersaline water was explored in this study to ensure the adaptability of P. keutzingianum in extreme stress conditions. Brackish to hypersaline salt solutions were tested at selected NaCl concentrations 10, 30, 50, and 70 g.L-1. Chloride, pH, nitrate, and phosphate were the main parameters measured throughout the duration of the experiment. Biomass growth estimation revealed that the studied strain is adaptable to all the salinities inoculated. During the first growth phase (till day 20), chloride ion was removed up to 43.52% and 45.69% in 10 and 30 g.L-1 of salinity, respectively. Fourier transform infrared spectrometry analysis performed on P. keutzingianum showed the presence of active functional groups at all salinity levels, which resulted in biosorption leading to the bioaccumulation process. Samples for scanning electron microscopy (SEM) analysis supported with electron dispersive X-ray spectroscopy analysis (EDS) showed NaCl on samples already on day 0. This ensures the occurrence of the biosorption process. SEM-EDS results on 10th d showed evidence of additional ions deposited on the outer surface of P. keutzingianum. Calcium, magnesium, potassium, sodium, chloride, phosphorus, and iron were indicated in SEM-EDS analysis proving the occurrence of the biomineralization process. These findings confirmed that P. keutzingianum showed biomass production, biosorption, bioaccumulation, and biomineralization in all salinities; hence, the strain affirms the biodesalination process.
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Affiliation(s)
- Abdul Mannan Zafar
- Civil and Environmental Engineering Department and National Water & Energy Center, United Arab Emirates University, Al-Ain, 15551, Abu Dhabi, United Arab Emirates.
| | - Muhammad Asad Javed
- Civil and Environmental Engineering Department and National Water & Energy Center, United Arab Emirates University, Al-Ain, 15551, Abu Dhabi, United Arab Emirates.
| | - Ashraf Aly Hassan
- Civil and Environmental Engineering Department and National Water & Energy Center, United Arab Emirates University, Al-Ain, 15551, Abu Dhabi, United Arab Emirates.
| | - Endalkachew Sahle-Demessie
- Center for Environmental Solutions and Emergency Responses, Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, 45268, USA.
| | - Stephen Harmon
- Center for Environmental Solutions and Emergency Responses, Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, 45268, USA.
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18
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Mehta N, Gaëtan J, Giura P, Azaïs T, Benzerara K. Detection of biogenic amorphous calcium carbonate (ACC) formed by bacteria using FTIR spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121262. [PMID: 35526437 DOI: 10.1016/j.saa.2022.121262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 06/14/2023]
Abstract
While the formation of intracellular amorphous calcium carbonate (ACC) by living organisms is widespread, its detection in prokaryotes remains difficult owing to its susceptibility to transform or dissolve upon sample preparation. Because of these challenges, a large number of ACC-forming prokaryotes may have been undetected and their abundance in the natural environment is possibly underestimated. This study identifies diagnostic spectral markers of ACC-forming prokaryotes that facilitate their detection in the environment. Accordingly, ACC formed by cyanobacteria was characterized using Fourier transform infrared (FTIR) spectroscopy in near-IR, mid-IR, and far-IR spectral regions. Two characteristic FTIR vibrations of ACC, at ∼ 860 cm-1and ∼ 306 cm-1, were identified as reliable spectral probes to rapidly detect prokaryotic ACC. Using these spectral probes, several Microcystis strains whose ACC-forming capability was unknown, were tested. Four out of eight Microcystis strains were identified as possessing ACC-forming capability and these findings were confirmed by scanning electron microscopy (SEM) observations. Overall, our findings provide a systematic characterization of prokaryotic ACC that facilitate rapid detection of ACC forming prokaryotes in the environment, a prerequisite to shed light on the role of ACC-forming prokaryotes in the geochemical cycle of Ca in the environment.
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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), 4 Place Jussieu, 75005 Paris, France
| | - Juliette Gaëtan
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Paola Giura
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Thierry Azaïs
- Sorbonne Université, CNRS, Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), 4 Place Jussieu, 75005 Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
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19
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Colboc H, Moguelet P, Letavernier E, Frochot V, Bernaudin JF, Weil R, Rouzière S, Senet P, Bachmeyer C, Laporte N, Lucas I, Descamps V, Amode R, Brunet-Possenti F, Kluger N, Deschamps L, Dubois A, Reguer S, Somogyi A, Medjoubi K, Refregiers M, Daudon M, Bazin D. Pathologies related to abnormal deposits in dermatology: a physico-chemical approach. CR CHIM 2022. [DOI: 10.5802/crchim.153] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Han Z, Li D, Zhao Y, Wang J, Guo N, Yan H, Han C, Li Q, Tucker ME. Mineralogy of Bioprecipitate Evolution over Induction Times Mediated by Halophilic Bacteria under Various Mg/Ca Molar Ratios. ACS OMEGA 2022; 7:29755-29772. [PMID: 36061657 PMCID: PMC9435042 DOI: 10.1021/acsomega.2c02443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
In microbial mineralization experiments, the induction time of mineral precipitation is ambiguous, and this may lead to difficulties in reproducing and confirming the test results. To explore the link between induction time and microbially mediated carbonate precipitation, we report here the mineralogy and morphology of carbonate precipitates induced by the halophilic Halomonas utahensis WMS2 bacterium in media with various Mg/Ca molar ratios over a range of induction times. The results show that the biominerals are formed in an alkaline environment affected by ammonia secreted by H. utahensis WMS2 bacteria. The content of dissolved inorganic carbon increased as a result of carbonic anhydrase catalyzing the hydration of carbon dioxide to release bicarbonate and carbonate ions. The X-ray diffraction (XRD) results show that the phase of mineral precipitated gradually changes from an unstable Mg-rich calcite to metastable monohydrocalcite and then to stable hydromagnesite with an increase in the Mg2+ ion concentration and induction time. The scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and Fourier transform infrared spectroscopy (FTIR) results show that minerals mostly change from single particles/crystallites to aggregations under the action of the microorganisms at different Mg2+ ion concentrations and induction times. Our experiments demonstrate that the carbonate minerals produced in the presence of microbes change significantly with the induction time, in addition to the influence of the hydrochemical factors; this indicates that the induction time is significant in determining the mineralogy of biominerals.
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Affiliation(s)
- Zuozhen Han
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
- Laboratory
for Marine Mineral Resources, Qingdao National
Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Dan Li
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Yanyang Zhao
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Jiajia Wang
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Na Guo
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Huaxiao Yan
- College
of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China
| | - Chao Han
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Qiang Li
- College
of Earth Science and Engineering, Shandong Provincial Key Laboratory
of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Maurice E. Tucker
- School
of Earth Sciences, University of Bristol, Bristol BS8 1RJ, U.K.
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21
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Li D, Zhao H, Li G, Yan H, Han Z, Chi X, Meng L, Wang J, Xu Y, Tucker ME. Calcium ion biorecovery from industrial wastewater by Bacillus amyloliquefaciens DMS6. CHEMOSPHERE 2022; 298:134328. [PMID: 35304210 DOI: 10.1016/j.chemosphere.2022.134328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/08/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
Calcium ions in industrial wastewater needs to be removed to prevent the production of limescale, which can have negative consequences. Biomineralization has become the focus due to its lower costs than traditional methods of remediation. In this study, calcium ions were bio-precipitated under the action of free and immobilized Bacillus amyloliquefaciens DMS6 bacteria, and the calcium ion removal efficiency was also compared. The results show that it only needed 3 days to decrease the calcium ion concentration to an ideal level of 76-116 mg/L under the action of DMS6 bacteria immobilized by activated carbon fiber, with calcium ion removal ratios reaching 99%-95% by the 7th day. DMS6 bacteria immobilized by activated carbon fiber were superior to free bacteria and bacteria immobilized by sodium alginate in calcium ion removal. Calcium ions are biomineralized into calcite, Mg-rich calcite, aragonite and monohydrocalcite with abundant organic functional groups, 4 types of secondary protein structures, amino acids, phospholipids, negative stable carbon isotope δ13CPDB values (-16.68‰ to-17.25‰) and negatively charged biomineral surface. Calcium ions were diffused into cells and took part in the intracellular biomineralization of monohydrocalcite, also facilitating calcium ion removal. The formation of intracellular monohydrocalcite has rarely been reported. This study demonstrates an economic and environmentally friendly method to remove calcium ions from industrial wastewater.
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Affiliation(s)
- Dan Li
- College of Earth Science and Engineering, College of Chemical and Biological Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, 266590, Qingdao, China
| | - Hui Zhao
- College of Earth Science and Engineering, College of Chemical and Biological Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, 266590, Qingdao, China
| | - Guijiang Li
- College of Earth Science and Engineering, College of Chemical and Biological Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, 266590, Qingdao, China
| | - Huaxiao Yan
- College of Earth Science and Engineering, College of Chemical and Biological Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, 266590, Qingdao, China.
| | - Zuozhen Han
- College of Earth Science and Engineering, College of Chemical and Biological Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, 266590, Qingdao, China; Laboratory for Marine Mineral Resources, Center for Isotope Geochemistry and Geochronology, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, China.
| | - Xiangqun Chi
- College of Earth Science and Engineering, College of Chemical and Biological Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, 266590, Qingdao, China
| | - Long Meng
- College of Earth Science and Engineering, College of Chemical and Biological Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, 266590, Qingdao, China
| | - Jihan Wang
- College of Earth Science and Engineering, College of Chemical and Biological Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, 266590, Qingdao, China
| | - Yudong Xu
- College of Earth Science and Engineering, College of Chemical and Biological Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, 266590, Qingdao, China
| | - Maurice E Tucker
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK
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22
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Keren-Paz A, Maan H, Karunker I, Olender T, Kapishnikov S, Dersch S, Kartvelishvily E, Wolf SG, Gal A, Graumann PL, Kolodkin-Gal I. The roles of intracellular and extracellular calcium in Bacillus subtilis biofilms. iScience 2022; 25:104308. [PMID: 35663026 PMCID: PMC9160756 DOI: 10.1016/j.isci.2022.104308] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/26/2022] [Accepted: 04/22/2022] [Indexed: 11/06/2022] Open
Abstract
In nature, bacteria reside in biofilms– multicellular differentiated communities held together by an extracellular matrix. This work identified a novel subpopulation—mineral-forming cells—that is essential for biofilm formation in Bacillus subtilis biofilms. This subpopulation contains an intracellular calcium-accumulating niche, in which the formation of a calcium carbonate mineral is initiated. As the biofilm colony develops, this mineral grows in a controlled manner, forming a functional macrostructure that serves the entire community. Consistently, biofilm development is prevented by the inhibition of calcium uptake. Our results provide a clear demonstration of the orchestrated production of calcite exoskeleton, critical to morphogenesis in simple prokaryotes. The orchestrated formation of calcite scaffolds supports the morphogenesis of microbial biofilms A novel subpopulation—mineral-forming cells—is essential for biofilm formation This subpopulation contains an intracellular calcium-accumulating niche, supporting the formation of calcium carbonate Intracellular calcium homeostasis and calcium export are associated with a functional biofilm macrostructure
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Affiliation(s)
- Alona Keren-Paz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Harsh Maan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Iris Karunker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Kapishnikov
- Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Simon Dersch
- Centre for Synthetic Microbiology (SYNMIKRO), Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | | | - Sharon G Wolf
- Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Gal
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Peter L Graumann
- Centre for Synthetic Microbiology (SYNMIKRO), Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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23
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Lopez-Canfin C, Lázaro R, Sánchez-Cañete EP. Water vapor adsorption by dry soils: A potential link between the water and carbon cycles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153746. [PMID: 35150687 DOI: 10.1016/j.scitotenv.2022.153746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Water vapor adsorption (WVA) by soil is a potential contributor to the water cycle in drylands. However, continuous in-situ estimates of WVA are still scarce and the understanding of its coupling with carbon cycle and ecosystem processes remains at an incipient stage. Here we aimed to (1) identify periods of WVA and improve the understanding of the underlying processes involved in its temporal patterns by using the gradient method; (2) characterize a potential coupling between water vapor and CO2 fluxes, and (3) explore the effect of soil properties and biocrusts ecological succession on fluxes. We assumed that the nocturnal soil CO2 uptake increasingly reported in those environments could come from WVA enhancing geochemical reactions involving calcite. We measured continuously during ca. 2 years the relative humidity and CO2 molar fraction in soil and atmosphere, in association with below- and aboveground variables, over the biocrusts ecological succession. We estimated water vapor and CO2 fluxes with the gradient method, and cumulative fluxes over the study. Then, we used statistical modelling to explore relationships between variables. Our main findings are (1) WVA fluxes during hot and dry periods, and new insights on their underlying mechanisms; (2) a diel coupling between water vapor and CO2 fluxes and between cumulative fluxes, well predicted by our models; and (3) cumulative CO2 influxes increasing with specific surface area in early succession stages, thus mitigating CO2 emissions. During summer drought, as WVA was the main water source, it probably maintained ecosystem processes such as microbial activity and mineral reactions in this dryland. We suggest that WVA could drive the nocturnal CO2 uptake in those moments and discuss biogeochemical mechanisms potentially involved. Additional research is needed to monitor soil water vapor and CO2 uptake and separate their biotic and abiotic components as those sinks could grow with climate change.
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Affiliation(s)
- Clément Lopez-Canfin
- Department of Applied Physics, University of Granada (UGR), Calle Dr Severo Ochoa s/n, Granada, Spain.
| | - Roberto Lázaro
- Department of Desertification and Geo-Ecology, Experimental Station of Arid Zones (EEZA-CSIC), Carretera Sacramento s/n, Almería, Spain
| | - Enrique P Sánchez-Cañete
- Department of Applied Physics, University of Granada (UGR), Calle Dr Severo Ochoa s/n, Granada, Spain; Inter-University Institute for Earth System Research (IISTA-CEAMA), Avenida del Mediterráneo s/n, Granada, Spain
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24
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Biomineralization of Carbonates Induced by Mucilaginibacter gossypii HFF1: Significant Role of Biochemical Parameters. MINERALS 2022. [DOI: 10.3390/min12050614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Although the precipitation of carbonate minerals induced by various bacteria is widely studied, the changes in the biochemical parameters, and their significant role in the biomineralization processes, still need further exploration. In this study, Mucilaginibacter gossypii HFF1 was isolated, identified, and used to induce carbonate minerals at various Mg/Ca ratios. The biochemical parameters were determined in order to explore the biomineralization mechanisms, including cell concentration, pH, ammonia, carbonic anhydrase activity, and alkaline phosphatase activity. The characteristics of extracellular minerals and intracellular inclusions were both analyzed. In addition, the amino acid composition of the extracellular polymeric substance was also tested. Results show that the biochemical parameters provide an alkaline environment for precipitation, due to the combined effect of ammonia, carbonic anhydrase, and alkaline phosphatase. Biotic minerals are characterized by preferred orientation, specific shape, and better crystalline and better thermal stability, indicating their biogenesis. Most of the amino acids in the extracellular polymeric substance are negatived charged, and facilitate the binding of magnesium and calcium ions. The particles with weak crystalline structure in the EPS prove that it acts as a nucleation site. Intracellular analyses prove the presence of the intracellular amorphous inclusions. Our results suggest that the changes in the biochemical parameters caused by bacteria are beneficial to biomineralization, and play a necessary role in its process. This offers new insight into understanding the biomineralization mechanism of the bacteria HFF1.
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25
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Pruss SB, Leeser L, Smith EF, Zhuravlev AY, Taylor PD. The oldest mineralized bryozoan? A possible palaeostomate in the lower Cambrian of Nevada, USA. SCIENCE ADVANCES 2022; 8:eabm8465. [PMID: 35442738 PMCID: PMC9020656 DOI: 10.1126/sciadv.abm8465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
All skeletal marine invertebrate phyla appeared during the Cambrian explosion, except for Bryozoa with mineralized skeletons, which first appear in the Early Ordovician. However, the skeletal diversity of Early Ordovician bryozoans suggests a preceding interval of diversification. We report a possible earliest occurrence of palaeostomate bryozoans in limestones of the Cambrian Age 4 Harkless Formation, western United States. Following recent interpretations of the early Cambrian Protomelission as a soft-bodied bryozoan, our findings add to the evidence of early Cambrian roots for the Bryozoa. The Harkless fossils resemble some esthonioporate and cystoporate bryozoans, showing a radiating pattern of densely packed tubes of the same diameter and cross-sectional shape. Further, they show partitioning of new individuals from parent tubes through the formation of a separate wall, a characteristic of interzooecial budding in bryozoans. If confirmed as bryozoans, these fossils would push back the appearance of mineralized skeletons in this phylum by ~30 million years and impact interpretations of their evolution.
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Affiliation(s)
- Sara B. Pruss
- Department of Geosciences, Smith College, Northampton, MA 01062, USA
| | - Lexie Leeser
- Department of Geosciences, Smith College, Northampton, MA 01062, USA
| | - Emily F. Smith
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrey Yu. Zhuravlev
- Division of Biological Evolution, Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Paul D. Taylor
- Department of Earth Sciences, London Natural History Museum, Cromwell Road, London SW7 5BD, UK
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26
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Amor M, Faivre D, Corvisier J, Tharaud M, Busigny V, Komeili A, Guyot F. Defining Local Chemical Conditions in Magnetosomes of Magnetotactic Bacteria. J Phys Chem B 2022; 126:2677-2687. [PMID: 35362974 PMCID: PMC9098202 DOI: 10.1021/acs.jpcb.2c00752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Defining chemical properties of intracellular organelles is necessary to determine their function(s) as well as understand and mimic the reactions they host. However, the small size of bacterial and archaeal microorganisms often prevents defining local intracellular chemical conditions in a similar way to what has been established for eukaryotic organelles. This work proposes to use magnetite (Fe3O4) nanocrystals contained in magnetosome organelles of magnetotactic bacteria as reporters of elemental composition, pH, and redox potential of a hypothetical environment at the site of formation of intracellular magnetite. This methodology requires combining recent single-cell mass spectrometry measurements together with elemental composition of magnetite in trace and minor elements. It enables a quantitative characterization of chemical disequilibria of 30 chemical elements between the intracellular and external media of magnetotactic bacteria, revealing strong transfers of elements with active influx or efflux processes that translate into elemental accumulation (Mo, Se, and Sn) or depletion (Sr and Bi) in the bacterial internal medium of up to seven orders of magnitude relative to the extracellular medium. Using this concept, we show that chemical conditions in magnetosomes are compatible with a pH of 7.5-9.5 and a redox potential of -0.25 to -0.6 V.
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Affiliation(s)
- Matthieu Amor
- Aix-Marseille Université, CEA, CNRS, BIAM, 13108 Saint-Paul-lez-Durance, France.,Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, United States
| | - Damien Faivre
- Aix-Marseille Université, CEA, CNRS, BIAM, 13108 Saint-Paul-lez-Durance, France
| | - Jérôme Corvisier
- Mines ParisTech, PSL Research University, Centre de Géosciences, 35 rue Saint Honoré, Fontainebleau Cedex 77305, France
| | - Mickaël Tharaud
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris F-75005, France
| | - Vincent Busigny
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris F-75005, France.,Institut Universitaire de France, Paris 75005, France
| | - Arash Komeili
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200, United States
| | - François Guyot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d'Histoire Naturelle, Sorbonne Université, UMR 7590 CNRS, 61 rue Buffon, 75005 Paris, France
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27
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Benzerara K, Duprat E, Tristan BF, Géraldine C, Corinne CC, Franck C, Manuela D, Issa DS, Geoffroy G, Sigrid G, Muriel G, Purificación LG, Maxime M, Fériel SP, David M, Isabelle C. A new gene family diagnostic for intracellular biomineralization of amorphous Ca-carbonates by cyanobacteria. Genome Biol Evol 2022; 14:6526398. [PMID: 35143662 PMCID: PMC8890360 DOI: 10.1093/gbe/evac026] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Cyanobacteria have massively contributed to carbonate deposition over the geological history. They are traditionally thought to biomineralize CaCO3 extracellularly as an indirect byproduct of photosynthesis. However, the recent discovery of freshwater cyanobacteria forming intracellular amorphous calcium carbonates (iACC) challenges this view. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and evolutionary history remain elusive. Here, using comparative genomics, we identify a new gene (ccyA) and protein family (calcyanin) possibly associated with cyanobacterial iACC biomineralization. Proteins of the calcyanin family are composed of a conserved C-terminal domain, which likely adopts an original fold, and a variable N-terminal domain whose structure allows differentiating 4 major types among the 35 known calcyanin homologs. Calcyanin lacks detectable full-length homologs with known function. The overexpression of ccyA in iACC-lacking cyanobacteria resulted in an increased intracellular Ca content. Moreover, ccyA presence was correlated and/or co-localized with genes involved in Ca or HCO3- transport and homeostasis, supporting the hypothesis of a functional role of calcyanin in iACC biomineralization. Whatever its function, ccyA appears as diagnostic of intracellular calcification in cyanobacteria. By searching for ccyA in publicly available genomes, we identified 13 additional cyanobacterial strains forming iACC, as confirmed by microscopy. This extends our knowledge about the phylogenetic and environmental distribution of cyanobacterial iACC biomineralization, especially with the detection of multicellular genera as well as a marine species. Moreover, ccyA was probably present in ancient cyanobacteria, with independent losses in various lineages that resulted in a broad but patchy distribution across modern cyanobacteria.
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Affiliation(s)
- Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Bitard-Feildel Tristan
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Caumes Géraldine
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Cassier-Chauvat Corinne
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Chauvat Franck
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Dezi Manuela
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Diop Seydina Issa
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Gaschignard Geoffroy
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Görgen Sigrid
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Gugger Muriel
- Institut Pasteur, Université de Paris, Collection of Cyanobacteria, F-75015 Paris, France
| | - López-García Purificación
- Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Millet Maxime
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Skouri-Panet Fériel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Moreira David
- Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Callebaut Isabelle
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
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28
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Huang S, Liu R, Sun M, Li X, Guan Y, Lian B. Transcriptome expression analysis of the gene regulation mechanism of bacterial mineralization tolerance to high concentrations of Cd 2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150911. [PMID: 34653453 DOI: 10.1016/j.scitotenv.2021.150911] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/23/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) pollution is a pressing environmental issue that must be addressed. In recent years, microbial mineralization biotechnology has been developed into an effective and eco-friendly heavy metal bioremediation solution. In the present research, RNA-Seq technology was utilized to reveal the molecular mechanism through which Bacillus velezensis LB002 induced the mineralization and Cd2+ fixation under high-concentration Cd2+ stress. The metabolic pathways involved in the genes that were significant differentially expressed in the process of bacterial mineralization were also investigated. The results showed that the physiological response of bacteria to Cd2+ toxicity may include bacterial chemotaxis, siderophore complexation, and transport across cell membranes. Bacteria subjected to high-concentration Cd2+ stress can up-regulate genes of argH, argF, hutU, hutH, lpdA, and acnA related to arginine synthesis, histidine metabolism, and citric acid cycle metabolism pathways, inducing vaterite formation and Cd2+ fixation. Thus, the toxicity of Cd2+ was decreased and bacteria were allowed to grow. Real-time quantitative polymerase chain reaction (RT-qPCR) results confirmed the data obtained by RNA-Seq, indicating that bacteria can reduce Cd2+ toxicity by regulating the expression of related genes to induce mineralization. A basic bioremediation strategy to deal with high-concentration heavy-metal pollution was proposed from the perspective of gene regulation.
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Affiliation(s)
- Shanshan Huang
- School of Life Sciences, School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Renlu Liu
- School of Life Sciences, School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; School of Life Sciences, Key Laboratory of Agricultural Environmental Pollution Prevention and Control in Red Soil Hilly Region of Jiangxi Province, Jinggangshan University, Ji'an 343009, China
| | - Menglin Sun
- School of Life Sciences, School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xiaofang Li
- School of Life Sciences, School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Yong Guan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, China
| | - Bin Lian
- School of Life Sciences, School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China.
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29
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First Observation of Unicellular Organisms Concentrating Arsenic in ACC Intracellular Inclusions in Lake Waters. GEOSCIENCES 2022. [DOI: 10.3390/geosciences12010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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 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.
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30
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Medina Ferrer F, Rosen MR, Feyhl-Buska J, Russell VV, Sønderholm F, Loyd S, Shapiro R, Stamps BW, Petryshyn V, Demirel-Floyd C, Bailey JV, Johnson HA, Spear JR, Corsetti FA. Potential role for microbial ureolysis in the rapid formation of carbonate tufa mounds. GEOBIOLOGY 2022; 20:79-97. [PMID: 34337850 DOI: 10.1111/gbi.12467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Modern carbonate tufa towers in the alkaline (~pH 9.5) Big Soda Lake (BSL), Nevada, exhibit rapid precipitation rates (exceeding 3 cm/year) and host diverse microbial communities. Geochemical indicators reveal that carbonate precipitation is, in part, promoted by the mixing of calcium-rich groundwater and carbonate-rich lake water, such that a microbial role for carbonate precipitation is unknown. Here, we characterize the BSL microbial communities and evaluate their potential effects on carbonate precipitation that may influence fast carbonate precipitation rates of the active tufa mounds of BSL. Small subunit rRNA gene surveys indicate a diverse microbial community living endolithically, in interior voids, and on tufa surfaces. Metagenomic DNA sequencing shows that genes associated with metabolisms that are capable of increasing carbonate saturation (e.g., photosynthesis, ureolysis, and bicarbonate transport) are abundant. Enzyme activity assays revealed that urease and carbonic anhydrase, two microbial enzymes that promote carbonate precipitation, are active in situ in BSL tufa biofilms, and urease also increased calcium carbonate precipitation rates in laboratory incubation analyses. We propose that, although BSL tufas form partially as a result of water mixing, tufa-inhabiting microbiota promote rapid carbonate authigenesis via ureolysis, and potentially via bicarbonate dehydration and CO2 outgassing by carbonic anhydrase. Microbially induced calcium carbonate precipitation in BSL tufas may generate signatures preserved in the carbonate microfabric, such as stromatolitic layers, which could serve as models for developing potential biosignatures on Earth and elsewhere.
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Affiliation(s)
- Fernando Medina Ferrer
- Department of Earth & Environmental Sciences, University of Minnesota, Twin Cities, Minneapolis, Minnesota, USA
| | - Michael R Rosen
- US Geological Survey, California Water Science Center, Carson City, Nevada, USA
| | - Jayme Feyhl-Buska
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | - Virginia V Russell
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Fredrik Sønderholm
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Sean Loyd
- Department of Geological Sciences, California State University Fullerton, Fullerton, California, USA
| | | | - Blake W Stamps
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio, USA
- UES, Inc., Dayton, Ohio, USA
| | - Victoria Petryshyn
- Environmental Studies Program, University of Southern California, Los Angeles, California, USA
| | | | - Jake V Bailey
- Department of Earth & Environmental Sciences, University of Minnesota, Twin Cities, Minneapolis, Minnesota, USA
| | - Hope A Johnson
- Department of Biological Science, California State University Fullerton, Fullerton, California, USA
| | - John R Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Frank A Corsetti
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
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31
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Whittaker M, Pri-gal E, Schmidt A, Joester D. Superlattice ordering transitions driven by short-range structure in barium calcium carbonates. Faraday Discuss 2022; 235:416-432. [DOI: 10.1039/d1fd00086a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Balcite (BaxCa1-xCO3) is a synthetic analog of rhombohedral carbonate minerals like calcite and dolomite that is disordered on both the cation and anion sublattices. Here, we show that multiple exotic...
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32
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Moroz TN, Palchik NA, Zhmodik SM, Ponomarchuk VA, Goryainov SV. Crystal-Chemical Features of Apatite in Carbonatites of the Tomtor Deposit (The Republic of Sakha (Yakutia), Russia): X-Ray Diffraction and Vibrational Spectroscopy Data. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521060225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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A Novel Magnetotactic Alphaproteobacterium Producing Intracellular Magnetite and Calcium-Bearing Minerals. Appl Environ Microbiol 2021; 87:e0155621. [PMID: 34756060 DOI: 10.1128/aem.01556-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Magnetotactic bacteria (MTB) are prokaryotes that form intracellular magnetite (Fe3O4) or greigite (Fe3S4) nanocrystals with tailored sizes, often in chain configurations. Such magnetic particles are each surrounded by a lipid bilayer membrane, called a magnetosome, and provide a model system for studying the formation and function of specialized internal structures in prokaryotes. Using fluorescence-coupled scanning electron microscopy, we identified a novel magnetotactic spirillum, XQGS-1, from freshwater Xingqinggong Lake, Xi'an City, Shaanxi Province, China. Phylogenetic analyses based on 16S rRNA gene sequences indicate that strain XQGS-1 represents a novel genus of the Alphaproteobacteria class in the Proteobacteria phylum. Transmission electron microscopy analyses reveal that strain XQGS-1 forms on average 17 ± 3 magnetite magnetosome particles with an ideal truncated octahedral morphology, with an average length and width of 88.3 ± 11.7 nm and 83.3 ± 11.0 nm, respectively. They are tightly organized into a single chain along the cell long axis close to the concave side of the cell. Intrachain magnetic interactions likely result in these large equidimensional magnetite crystals behaving as magnetically stable single-domain particles that enable bacterial magnetotaxis. Combined structural and chemical analyses demonstrate that XQGS-1 cells also biomineralize intracellular amorphous calcium phosphate (2 to 3 granules per cell; 90.5- ± 19.3-nm average size) and weakly crystalline calcium carbonate (2 to 3 granules per cell; 100.4- ± 21.4-nm average size) in addition to magnetite. Our results expand the taxonomic diversity of MTB and provide evidence for intracellular calcium phosphate biomineralization in MTB. IMPORTANCE Biomineralization is a widespread process in eukaryotes that form shells, teeth, or bones. It also occurs commonly in prokaryotes, resulting in more than 60 known minerals formed by different bacteria under wide-ranging conditions. Among them, magnetotactic bacteria (MTB) are remarkable because they might represent the earliest organisms that biomineralize intracellular magnetic iron minerals (i.e., magnetite [Fe3O4] or greigite [Fe3S4]). Here, we report a novel magnetotactic spirillum (XQGS-1) that is phylogenetically affiliated with the Alphaproteobacteria class. In addition to magnetite crystals, XQGS-1 cells form intracellular submicrometer calcium carbonate and calcium phosphate granules. This finding supports the view that MTB are also an important microbial group for intracellular calcium carbonate and calcium phosphate biomineralization.
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Zhao Y, Han Z, Yan H, Zhao H, Tucker ME, Gao X, Guo N, Meng R, Owusu DC. Selective Adsorption of Amino Acids in Crystals of Monohydrocalcite Induced by the Facultative Anaerobic Enterobacter ludwigii SYB1. Front Microbiol 2021; 12:696557. [PMID: 34394038 PMCID: PMC8358455 DOI: 10.3389/fmicb.2021.696557] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/23/2021] [Indexed: 12/05/2022] Open
Abstract
The morphology, crystal structure, and elemental composition of biominerals are commonly different from chemically synthesized minerals, but the reasons for these are not fully understood. A facultative anaerobic bacterium, Enterobacter ludwigii SYB1, is used in experiments to document the hydrochemistry, mineral crystallization, and cell surface characteristics of biomineralization. It was found that carbonate anhydrase and ammonia production were major factors influencing the alkalinity and saturation of the closed biosystem. X-ray diffraction (XRD) spectra showed that calcite, monohydrocalcite (MHC), and dypingite formed in samples with bacterial cells. It was also found that the (222) plane of MHC was the preferred orientation compared to standard data. Scanning transmission electron microscopy (STEM) analysis of cell slices provides direct evidence of concentrated calcium and magnesium ions on the surface of extracellular polymeric substances (EPS). In addition, high-resolution transmission electron microscopy (HRTEM) showed that crystallized nanoparticles were formed within the EPS. Thus, the mechanism of the biomineralization induced by E. ludwigii SYB1 can be divided into three stages: (i) the production of carbonate anhydrase and ammonia increases the alkalinity and saturation state of the milieu, (ii) free calcium and magnesium ions are adsorbed and chelated onto EPS, and (iii) nanominerals crystallize and grow within the EPS. Seventeen kinds of amino acids were identified within both biotic MHC and the EPS of SYB1, while the percentages of glutamic and aspartic acid in MHC increased significantly (p < 0.05). Furthermore, the adsorption energy was calculated for various amino acids on seven diffracted crystal faces, with preferential adsorption demonstrated on (111) and (222) faces. At the same time, the lowest adsorption energy was always that of glutamic and aspartic acid for the same crystal plane. These results suggest that aspartic and glutamic acid always mix preferentially in the crystal lattice of MHC and that differential adsorption of amino acids on crystal planes can lead to their preferred orientation. Moreover, the mixing of amino acids in the mineral structure may also have a certain influence on the mineral lattice dislocations, thus enhancing the thermodynamic characteristics.
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Affiliation(s)
- Yanyang Zhao
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China.,Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zuozhen Han
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China.,Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Huaxiao Yan
- Department of Bioengineering, College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Hui Zhao
- Department of Bioengineering, College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Maurice E Tucker
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom.,Cabot Institute, University of Bristol, Bristol, United Kingdom
| | - Xiao Gao
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Na Guo
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Ruirui Meng
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Daniel Cosmos Owusu
- Department of Bioengineering, College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, China
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35
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Environmentally friendly antibiofilm strategy based on cationized phytoglycogen nanoparticles. Colloids Surf B Biointerfaces 2021; 207:111975. [PMID: 34371317 DOI: 10.1016/j.colsurfb.2021.111975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 11/23/2022]
Abstract
Biofilm tolerance to antibiotics has led to the search for new alternatives in treating biofilms. The use of metallic nanoparticles has been a suggested strategy against biofilms, but their potential environmental toxicity and high cost of synthesizing have limited their applications. In this study, we investigate the potential of polysaccharidic phytoglycogen nanoparticles extracted from corn, in treating cyanobacterial biofilms, which are the source of toxins and pollution in aquatic environments. Our results revealed that the surface of cyanobacterial cells was dominated by the negatively charged functional groups such as carboxylic and phosphoric groups. The native phytoglycogen (PhX) nanoparticles were dominated with non-charged groups, such as hydroxyl groups, and the cationized phytoglycogen (PhXC) nanoparticles showed positively charged surfaces due to the presence of quaternary ammonium cations. Our results indicated that, as opposed to PhX, PhXC strongly inhibited biofilm formation when dispersed in the culture medium. PhXC also eradicated the already grown cyanobacterial biofilms. The antibiofilm properties of PhXC were attributed to its strong electrostatic interactions with the cyanobacterial cells, which could inhibit cell/cell and cell/substrate interactions and nutrient exchange with the media. This class of antibacterial polysaccharide nanoparticles may provide a novel cost-effective and environment-friendly strategy for treating biofilm formation by a broad spectrum of bacteria.
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Picard A, Gartman A, Girguis PR. Interactions Between Iron Sulfide Minerals and Organic Carbon: Implications for Biosignature Preservation and Detection. ASTROBIOLOGY 2021; 21:587-604. [PMID: 33780638 DOI: 10.1089/ast.2020.2276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microbe-mineral interactions can produce unique composite materials, which can preserve biosignatures. Geological evidence suggests that iron sulfide (Fe-S) minerals are abundant in the subsurface of Mars. On Earth, the formation of Fe-S minerals is driven by sulfate-reducing microorganisms (SRM) that produce reactive sulfide. Moreover, SRM metabolites, as well as intact cells, can influence the morphology, particle size, aggregation, and composition of biogenic Fe-S minerals. In this work, we evaluated how simple and complex organic molecules-hexoses and amino acid/peptide mixtures, respectively-influence the formation of Fe-S minerals (simulated prebiotic conditions), and whether the observed patterns mimic the biological influence of SRM. To this end, organo-mineral aggregates were characterized with X-ray diffraction, scanning electron microscopy, and scanning transmission X-ray microscopy coupled to near-edge X-ray absorption fine structure spectroscopy. Overall, Fe-S minerals were found to have a strong affinity for proteinaceous organic matter. Fe-S minerals precipitated at simulated prebiotic conditions yielded organic carbon distributions that were more homogeneous than treatments with whole SRM cells. In prebiotic experiments, spectroscopy detected potential organic transformations during Fe-S mineral formation, including conversion of hexoses to sugar acids and polymerization of amino acids/peptides into larger peptides/proteins. In addition, prebiotic mineral-carbon assemblages produced nanometer-scaled filamentous aggregated morphologies. On the contrary, in biotic treatments with cells, organic carbon in minerals displayed a more heterogeneous distribution. Notably, "hot spots" of organic carbon and oxygen-containing functional groups, with the size, shape, and composition of microbial cells, were preserved in mineral aggregates. We propose a list of characteristics that could be used to help distinguish biogenic from prebiotic/abiotic Fe-S minerals and help refine the search of extant or extinct microbial life in the martian subsurface.
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Affiliation(s)
- Aude Picard
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Amy Gartman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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Moroz TN, Edwards HGM, Zhmodik SM. Detection of carbonate, phosphate minerals and cyanobacteria in rock from the Tomtor deposit, Russia, by Raman spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 250:119372. [PMID: 33422877 DOI: 10.1016/j.saa.2020.119372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 11/09/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Samples of rock from the Tomtor Nb - REE (rare-earth elements) deposit (Russia) have been investigated by Raman micro-spectroscopy using visible 532 nm wavelength excitation. Raman spectra of different samples of this rock confirm their composition as calcites and other carbonates such as rhodochrosite, and mixed solid solution phases (Ca, Mn, Fe, Mg, Ba, Sr, REE)(CO3). An association between cyanobacteria and the apatite crystals has been noted Cyanobacteria exhibited Raman modes at 1520-1517 cm-1 located in the double bonds of the central part of the polyene chain of carotenoids. A slight shift of this mode in the apatite-containing samples are dependent upon the compositions of carotenoids, the ratio of the rare earth elements adsorbed by cyanobacteria as well as their interaction with the environment. Laser-induced photoluminescence of REE and Mn+2, obtained as an analytical artifact in the Raman spectra, has been observed in most cases with significant spectral intensity. The luminescence emission of Mn 2+, Sm3+, Eu 3+, Pr3+, Ho3+, Er 3+ in the spectra of the apatite-containing samples obtained with 532 nm excitation can be attributed both to apatite and to other mineral phases with a low concentration which contain these elemental ions. The results obtained in this study allowed us to confirm that the biogenic presence of the cyanobacterial mat had a significant impact on the formation of the unique Nb-REE Tomtor deposit.
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Affiliation(s)
- T N Moroz
- Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia.
| | - H G M Edwards
- School of Chemistry and Biosciences, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, West Yorkshire, United Kingdom.
| | - S M Zhmodik
- Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia
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Segovia-Campos I, Martignier A, Filella M, Jaquet JM, Ariztegui D. Micropearls and other intracellular inclusions of amorphous calcium carbonate: an unsuspected biomineralization capacity shared by diverse microorganisms. Environ Microbiol 2021; 24:537-550. [PMID: 33817930 PMCID: PMC9292747 DOI: 10.1111/1462-2920.15498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/24/2021] [Accepted: 04/01/2021] [Indexed: 11/29/2022]
Abstract
An unsuspected biomineralization process, which produces intracellular inclusions of amorphous calcium carbonate (ACC), was recently discovered in unicellular eukaryotes. These mineral inclusions, called micropearls, can be highly enriched with other alkaline‐earth metals (AEM) such as Sr and Ba. Similar intracellular inclusions of ACC have also been observed in prokaryotic organisms. These comparable biomineralization processes involving phylogenetically distant microorganisms are not entirely understood yet. This review gives a broad vision of the topic in order to establish a basis for discussion on the possible molecular processes behind the formation of the inclusions, their physiological role, the impact of these microorganisms on the geochemical cycles of AEM and their evolutionary relationship. Finally, some insights are provided to guide future research.
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Affiliation(s)
- Inés Segovia-Campos
- Department of Earth Sciences, University of Geneva, Geneva, CH-1205, Switzerland
| | - Agathe Martignier
- Department of Earth Sciences, University of Geneva, Geneva, CH-1205, Switzerland
| | - Montserrat Filella
- Department F.-A. Forel, University of Geneva, Geneva, CH-1205, Switzerland
| | - Jean-Michel Jaquet
- Department of Earth Sciences, University of Geneva, Geneva, CH-1205, Switzerland
| | - Daniel Ariztegui
- Department of Earth Sciences, University of Geneva, Geneva, CH-1205, Switzerland
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Lopez‐Canfin C, Lázaro R, Sánchez‐Cañete EP. Development of a new low‐cost device to measure calcium carbonate content, reactive surface area in solid samples and dissolved inorganic carbon content in water samples. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Clément Lopez‐Canfin
- Department of Desertification and Geo‐Ecology Experimental Station of Arid Zones (EEZA‐CSIC) Almería Spain
| | - Roberto Lázaro
- Department of Desertification and Geo‐Ecology Experimental Station of Arid Zones (EEZA‐CSIC) Almería Spain
| | - Enrique P. Sánchez‐Cañete
- Inter‐University Institute for Earth System Research (IISTA‐CEAMA) Granada Spain
- Department of Applied Physics University of Granada (UGR) Granada Spain
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40
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Benzerara K, Bolzoni R, Monteil C, Beyssac O, Forni O, Alonso B, Asta MP, Lefevre C. The gammaproteobacterium Achromatium forms intracellular amorphous calcium carbonate and not (crystalline) calcite. GEOBIOLOGY 2021; 19:199-213. [PMID: 33347698 DOI: 10.1111/gbi.12424] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/21/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Achromatium is a long known uncultured giant gammaproteobacterium forming intracellular CaCO3 that impacts C and S geochemical cycles functioning in some anoxic sediments and at oxic-anoxic boundaries. While intracellular CaCO3 granules have first been described as Ca oxalate then colloidal CaCO3 more than one century ago, they have often been referred to as crystalline solids and more specifically calcite over the last 25 years. Such a crystallographic distinction is important since the respective chemical reactivities of amorphous calcium carbonate (ACC) and calcite, hence their potential physiological role and conditions of formation, are significantly different. Here, we analyzed the intracellular CaCO3 granules of Achromatium cells from Lake Pavin using a combination of Raman microspectroscopy and scanning electron microscopy. Granules in intact Achromatium cells were unequivocally composed of ACC. Moreover, ACC spontaneously transformed into calcite when irradiated at high laser irradiance during Raman analyses. Few ACC granules also transformed spontaneously into calcite in lysed cells upon cell death and/or sample preparation. Overall, the present study supports the original claims that intracellular Ca-carbonates in Achromatium are amorphous and not crystalline. In that sense, Achromatium is similar to a diverse group of Cyanobacteria and a recently discovered magnetotactic alphaproteobacterium, which all form intracellular ACC. The implications for the physiology and ecology of Achromatium are discussed. Whether the mechanisms responsible for the preservation of such unstable compounds in these bacteria are similar to those involved in numerous ACC-forming eukaryotes remains to be discovered. Last, we recommend to future studies addressing the crystallinity of CaCO3 granules in Achromatium cells recovered from diverse environments all over the world to take care of the potential pitfalls evidenced by the present study.
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Affiliation(s)
- Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR CNRS 7590, Muséum National d'Histoire Naturelle, Sorbonne Université, Paris, France
| | - Romain Bolzoni
- CEA Cadarache, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA, CNRS, Aix-Marseille University, Saint-Paul-lez-Durance, France
| | - Caroline Monteil
- CEA Cadarache, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA, CNRS, Aix-Marseille University, Saint-Paul-lez-Durance, France
| | - Olivier Beyssac
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR CNRS 7590, Muséum National d'Histoire Naturelle, Sorbonne Université, Paris, France
| | - Olivier Forni
- Institut de Recherche en Astrophysique et Planétologie (CNRS, Univ. Toulouse, CNES), Toulouse, France
| | - Béatrice Alonso
- CEA Cadarache, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA, CNRS, Aix-Marseille University, Saint-Paul-lez-Durance, France
| | - Maria P Asta
- IFSTTAR, CNRS, University Grenoble Alpes, Grenoble, France
| | - Christopher Lefevre
- CEA Cadarache, UMR7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA, CNRS, Aix-Marseille University, Saint-Paul-lez-Durance, France
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Precipitation of Magnetic Iron Oxide Induced by Sporosarcina pasteurii Cells. Microorganisms 2021; 9:microorganisms9020331. [PMID: 33562239 PMCID: PMC7916055 DOI: 10.3390/microorganisms9020331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 11/17/2022] Open
Abstract
Sporosarcina pasteurii (S. pasteurii) is bacterium notable for its highly efficient urea degradation ability. Due to its high urease activity, S. pasteurii has been successfully utilized in applications including solidifying soil or sand, termed “bio-concrete”. In addition to calcium carbonate precipitation, urease isolated from the jack bean plant was recently demonstrated to induce the formation of magnetic iron oxide particles from soluble ferrous ion in a designed reaction. However, it remained unknown if a similar magnetic material could be formed using whole cells with high urease activity under biocompatible conditions. Here, we demonstrated that magnetic iron oxide with a highly ordered structure could be formed on the surface of S. pasteurii cells with a theoretical product of 1.17 mg in a 2-mL reaction. Moreover, the cells surrounded by the precipitated magnetic iron oxide maintained their viability. Due to the simple cultivation of S. pasteurii, the process developed in this study could be useful for the green synthesis of magnetic iron oxide, basic research on the mechanism of magnetic microbial-induced precipitation (MIP), and related engineering applications.
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Frochot V, Castiglione V, Lucas IT, Haymann JP, Letavernier E, Bazin D, Fogazzi GB, Daudon M. Advances in the identification of calcium carbonate urinary crystals. Clin Chim Acta 2021; 515:1-4. [PMID: 33387465 DOI: 10.1016/j.cca.2020.12.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/01/2020] [Accepted: 12/20/2020] [Indexed: 11/26/2022]
Abstract
The examination of the urinary sediment of a 64-year-old woman showed the presence of three different types of crystals, all with unusual morphology, which could not be identified with bright field microscopy, polarized light, and the knowledge of urine pH (7.5). The use of microscopic infrared spectroscopy, Raman spectroscopy and energy dispersive X-ray spectroscopy led to the identification of the three types of crystals as calcite, vaterite and aragonite, which are all variants of calcium carbonate crystals. This paper confirms the complex morphology and nature that urinary crystals may at times have and the utility of advanced infrared spectroscopy techniques for their identification.
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Affiliation(s)
- Vincent Frochot
- Sorbonne Universités, UPMC Université Paris-6, UMR S 1155, Paris, France; INSERM, UMR S 1155, Paris, France; AP-HP, Hôpital Tenon, Service d'explorations fonctionnelles multidisciplinaires, Paris-6, France.
| | | | - Ivan T Lucas
- Sorbonne Université, CNRS, Laboratoire Interfaces et Systèmes Electrochimiques, LISE, F-75005 Paris, France
| | - Jean-Philippe Haymann
- Sorbonne Universités, UPMC Université Paris-6, UMR S 1155, Paris, France; INSERM, UMR S 1155, Paris, France; AP-HP, Hôpital Tenon, Service d'explorations fonctionnelles multidisciplinaires, Paris-6, France
| | - Emmanuel Letavernier
- Sorbonne Universités, UPMC Université Paris-6, UMR S 1155, Paris, France; INSERM, UMR S 1155, Paris, France; AP-HP, Hôpital Tenon, Service d'explorations fonctionnelles multidisciplinaires, Paris-6, France
| | | | - Giovanni B Fogazzi
- Laboratorio Clinico e di Ricerca sul Sedimento Urinario, U.O.C. di Nefrologia, Dialisi e Trapianto di Rene, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano Italy
| | - Michel Daudon
- Sorbonne Universités, UPMC Université Paris-6, UMR S 1155, Paris, France; INSERM, UMR S 1155, Paris, France; AP-HP, Hôpital Tenon, Service d'explorations fonctionnelles multidisciplinaires, Paris-6, France
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43
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Song N, Li Q, Zhou Y, Sun G, Pan L, Zhao X, Dong P, Zhao Y, Yang L, Huang Y. Carbonate biomineralization differentially induced by two psychrophilic Pseudomonas psychrophila strains isolated from an alpine travertine landform. RSC Adv 2021; 11:12885-12892. [PMID: 35423815 PMCID: PMC8697359 DOI: 10.1039/d1ra00578b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/19/2021] [Indexed: 11/21/2022] Open
Abstract
Besides geography and climate, biological factors play an important role in shaping travertine landforms, but the biochemical mechanisms of microbial processes in travertine formation have been rarely studied. Two psychrophilic bacterial strains, A20-18 and B21-3 of Pseudomonas psychrophila, isolated from travertine pools of Huanglong, a typical alpine travertine landform, were investigated for their roles in calcium carbonate mineralization, including the deposition process and products. X-ray diffraction, Fourier-transform infrared spectroscopy, and scanning electron microscopy were used to characterize the crystal phase and morphology of CaCO3 precipitation. The results showed that there were no significant differences between the two strains in CaCO3 deposition rate. Extracellular polymeric substances (EPS)-free cells significantly inhibited calcification, compared with a control. Irregular crystals and polyhedral structures are common to all treatments using the two strains. These complex polycrystals were the result of the synergistic effect of homogeneous nucleation and heterogeneous nucleation. EPS and cells of strain B21-3 formed ring-like structures of calcium carbonate, which was possibly from the amphiphilic polymer forming a circular arrangement in water. These results are significant for understanding the microbial factor in Huanglong travertine deposition and providing new insights into the morphological control of the biomineralization mechanism at low temperatures. Calcium carbonate crystals induced by two Pseudomonas psychrophila strains and their organic compounds were studied.![]()
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Affiliation(s)
- Na Song
- Life Science and Engineering College
- Southwest University of Science and Technology
- Mianyang 621010
- China
| | - Qiongfang Li
- Life Science and Engineering College
- Southwest University of Science and Technology
- Mianyang 621010
- China
- Key Laboratory of Solid Waste Treatment and Resource Recycle
| | - Yi Zhou
- School of Agriculture, Food & Wine
- Waite Campus
- The University of Adelaide
- Urrbrae
- Australia
| | - Geng Sun
- Chengdu Institute of Biology
- Chinese Academy of Sciences
- Chengdu 610041
- China
| | - Ling Pan
- Life Science and Engineering College
- Southwest University of Science and Technology
- Mianyang 621010
- China
| | - Xiaoxia Zhao
- Life Science and Engineering College
- Southwest University of Science and Technology
- Mianyang 621010
- China
| | - Pengju Dong
- Life Science and Engineering College
- Southwest University of Science and Technology
- Mianyang 621010
- China
| | - Yulian Zhao
- Life Science and Engineering College
- Southwest University of Science and Technology
- Mianyang 621010
- China
| | - Lijun Yang
- School of Environment and Resource
- Southwest University of Science and Technology
- Mianyang 621010
- China
| | - Yunbi Huang
- School of Environment and Resource
- Southwest University of Science and Technology
- Mianyang 621010
- China
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44
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Büttner SH, Isemonger EW, Isaacs M, van Niekerk D, Sipler RE, Dorrington RA. Living phosphatic stromatolites in a low-phosphorus environment: Implications for the use of phosphorus as a proxy for phosphate levels in paleo-systems. GEOBIOLOGY 2021; 19:35-47. [PMID: 33067916 DOI: 10.1111/gbi.12415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 08/01/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
In the geological record, fossil phosphatic stromatolites date back to the Great Oxidation Event in the Paleoproterozoic, but living phosphatic stromatolites have not been described previously. Here, we report on cyanobacterial stromatolites in a supratidal freshwater environment at Cape Recife, South African southern coast, precipitating Ca carbonate alternating with episodes of Ca phosphate deposition. In their structure and composition, the living stromatolites from Cape Recife closely resemble their fossilized analogues, showing phosphatic zonation, microbial casts, tunnel structures and phosphatic crusts of biogenic origin. The microbial communities appear to be also similar to those proposed to have formed fossil phosphatic stromatolites. Phosphatic domains in the material from Cape Recife are spatially and texturally associated with carbonate precipitates, but form distinct entities separated by sharp boundaries. Electron Probe Micro-Analysis shows that Ca/P ratios and the overall chemical compositions of phosphatic precipitates are in the range of octacalcium phosphate, amorphous tricalcium phosphate and apatite. The coincidence in time of the emergence of phosphatic stromatolites in the fossil record with a major episode of atmospheric oxidation led to the assumption that at times of increased oxygen release the underlying increased biological production may have been linked to elevated phosphorus availability. The stromatolites at Cape Recife, however, form in an environment where ambient phosphorus concentrations do not exceed 0.28 μM, one to two orders of magnitude below the previously predicted minimum threshold of >5 μM for biogenic phosphate precipitation in paleo-systems. Accordingly, we contest the previously proposed suitability of phosphatic stromatolites as a proxy for high ambient phosphate concentrations in supratidal to shallow ocean settings in earth history.
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Affiliation(s)
- Steffen H Büttner
- Department of Geology, Rhodes University, Makhanda (Grahamstown), South Africa
| | - Eric W Isemonger
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda (Grahamstown), South Africa
| | - Michelle Isaacs
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda (Grahamstown), South Africa
| | - Deon van Niekerk
- Department of Geology, Rhodes University, Makhanda (Grahamstown), South Africa
| | - Rachel E Sipler
- Department of Ocean Sciences, Memorial University of Newfoundland, St John's, NL, Canada
| | - Rosemary A Dorrington
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda (Grahamstown), South Africa
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Piñar G, Sclocchi MC, Pinzari F, Colaizzi P, Graf A, Sebastiani ML, Sterflinger K. The Microbiome of Leonardo da Vinci's Drawings: A Bio-Archive of Their History. Front Microbiol 2020; 11:593401. [PMID: 33329475 PMCID: PMC7718017 DOI: 10.3389/fmicb.2020.593401] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/26/2020] [Indexed: 12/04/2022] Open
Abstract
Seven emblematic Leonardo da Vinci’s drawings were investigated through third generation sequencing technology (Nanopore). In addition, SEM analyses were carried out to acquire photographic documentation and to infer the nature of the micro-objects removed from the surface of the drawings. The Nanopore generated microbiomes can be used as a “bio-archive” of the drawings, offering a kind of fingerprint for current and future biological comparisons. This information might help to create a biological catalog of the drawings (cataloging), a microbiome-fingerprint for each single analyzed drawing, as a reference dataset for future studies (monitoring) and last but not least a bio-archive of the history of each single object (added value). Results showed a relatively high contamination with human DNA and a surprising dominance of bacteria over fungi. However, it was possible to identify typical bacteria of the human microbiome, which are mere contaminants introduced by handling of the drawings as well as other microorganisms that seem to have been introduced through vectors, such as insects and their droppings, visible through the SEM analyses. All drawings showed very specific bio-archives, but a core microbiome of bacteria and fungi that are repeatedly found in this type of material as true degraders were identified, such as members of the phyla Proteobacteria, Actinobacteria, and Firmicutes among bacteria, and fungi belonging to the classes Sordariomycetes and Eurotiomycetes. In addition, some similarities were observed that could be influenced by their geographical location (Rome or Turin), indicating the influence of this factor and denoting the importance of environmental and storage conditions on the specific microbiomes.
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Affiliation(s)
- Guadalupe Piñar
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Maria Carla Sclocchi
- Laboratorio di Biologia, Istituto Centrale per la Patologia degli Archivi e del Libro (ICPAL), Rome, Italy
| | - Flavia Pinzari
- Institute for Biological Systems (ISB), Council of National Research of Italy (CNR), Monterotondo, Italy
| | - Piero Colaizzi
- Laboratorio di Biologia, Istituto Centrale per la Patologia degli Archivi e del Libro (ICPAL), Rome, Italy
| | - Alexandra Graf
- Applied Life Sciences/Bioengineering/Bioinformatics, FH Campus, Vienna, Austria
| | - Maria Letizia Sebastiani
- Laboratorio di Biologia, Istituto Centrale per la Patologia degli Archivi e del Libro (ICPAL), Rome, Italy
| | - Katja Sterflinger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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Martignier A, De Respinis S, Filella M, Segovia-Campos I, Marin B, Günther G, Barja F, Tonolla M, Jaquet JM, Melkonian M, Ariztegui D. Biomineralization Capacities of Chlorodendrophyceae: Correlation Between Chloroplast Morphology and the Distribution of Micropearls in the Cell. Protist 2020; 171:125760. [DOI: 10.1016/j.protis.2020.125760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/17/2020] [Accepted: 08/22/2020] [Indexed: 11/30/2022]
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Karabourniotis G, Horner HT, Bresta P, Nikolopoulos D, Liakopoulos G. New insights into the functions of carbon-calcium inclusions in plants. THE NEW PHYTOLOGIST 2020; 228:845-854. [PMID: 32583442 DOI: 10.1111/nph.16763] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
Carbon-calcium inclusions (CCaI) either as calcium oxalate crystals (CaOx) or amorphous calcium carbonate cystoliths are spread among most photosynthetic organisms. They represent dynamic structures with a significant construction cost and their appearance during evolution indicates an ancient origin. Both types of inclusions share some similar functional characteristics providing adaptive advantages such as the regulation of Ca levels, and the release of CO2 and water molecules upon decomposition. The latter seems to be essential under drought conditions and explains the intense occurrence of these structures in plants thriving in dry climates. It seems, however, that for plants CaOx may represent a more prevalent storage system compared with CaCO3 due to the multifunctionality of oxalate. This compound participates in a number of important soil biogeochemical processes, creates endosymbiosis with beneficial bacteria and provides tolerance against a combination of abiotic (nutrient deprivation, metal toxicity) and biotic (pathogens, herbivores) stress factors. We suggest a re-evaluation of the roles of these fascinating plant structures under a new and holistic approach that could enhance our understanding of carbon sequestration at the whole plant level and provide future perspectives.
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Affiliation(s)
- George Karabourniotis
- Laboratory of Plant Physiology and Morphology, Faculty of Crop Science, Agricultural University of Athens, Athens, 11855, Greece
| | - Harry T Horner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Panagiota Bresta
- Laboratory of Plant Physiology and Morphology, Faculty of Crop Science, Agricultural University of Athens, Athens, 11855, Greece
| | - Dimosthenis Nikolopoulos
- Laboratory of Plant Physiology and Morphology, Faculty of Crop Science, Agricultural University of Athens, Athens, 11855, Greece
| | - Georgios Liakopoulos
- Laboratory of Plant Physiology and Morphology, Faculty of Crop Science, Agricultural University of Athens, Athens, 11855, Greece
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Intracellular amorphous Ca-carbonate and magnetite biomineralization by a magnetotactic bacterium affiliated to the Alphaproteobacteria. ISME JOURNAL 2020; 15:1-18. [PMID: 32839547 DOI: 10.1038/s41396-020-00747-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/30/2020] [Accepted: 08/10/2020] [Indexed: 11/08/2022]
Abstract
Bacteria synthesize a wide range of intracellular submicrometer-sized inorganic precipitates of diverse chemical compositions and structures, called biominerals. Their occurrences, functions and ultrastructures are not yet fully described despite great advances in our knowledge of microbial diversity. Here, we report bacteria inhabiting the sediments and water column of the permanently stratified ferruginous Lake Pavin, that have the peculiarity to biomineralize both intracellular magnetic particles and calcium carbonate granules. Based on an ultrastructural characterization using transmission electron microscopy (TEM) and synchrotron-based scanning transmission X-ray microscopy (STXM), we showed that the calcium carbonate granules are amorphous and contained within membrane-delimited vesicles. Single-cell sorting, correlative fluorescent in situ hybridization (FISH), scanning electron microscopy (SEM) and molecular typing of populations inhabiting sediments affiliated these bacteria to a new genus of the Alphaproteobacteria. The partially assembled genome sequence of a representative isolate revealed an atypical structure of the magnetosome gene cluster while geochemical analyses indicate that calcium carbonate production is an active process that costs energy to the cell to maintain an environment suitable for their formation. This discovery further expands the diversity of organisms capable of intracellular Ca-carbonate biomineralization. If the role of such biomineralization is still unclear, cell behaviour suggests that it may participate to cell motility in aquatic habitats as magnetite biomineralization does.
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Mansor M, Xu J. Benefits at the nanoscale: a review of nanoparticle-enabled processes favouring microbial growth and functionality. Environ Microbiol 2020; 22:3633-3649. [PMID: 32705763 DOI: 10.1111/1462-2920.15174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 11/29/2022]
Abstract
Nanoparticles are ubiquitous and co-occur with microbial life in every environment on Earth. Interactions between microbes and nanoparticles impact the biogeochemical cycles via accelerating various reaction rates and enabling biological processes at the smallest scales. Distinct from microbe-mineral interactions at large, microbe-nanoparticle interactions may involve higher levels of active recognition and utilization of the reactive, changeable, and thereby 'moldable' nano-sized inorganic phases by microbes, which has been given minimal attention in previous reviews. Here we have compiled the various cases of microbe-nanoparticle interactions with clear and potential benefits to the microbial cells and communities. Specifically, we discussed (i) the high bioavailabilities of nanoparticles due to increased specific surface areas and size-dependent solubility, with a focus on environmentally-relevant iron(III) (oxyhydr)oxides and pyrite, (ii) microbial utilization of nanoparticles as 'nano-tools' for electron transfer, chemotaxis, and storage units, and (iii) speculated benefits of precipitating 'moldable' nanoparticles in extracellular biomineralization. We further discussed emergent questions concerning cellular level responses to nanoparticle-associated cues, and the factors that affect nanoparticles' bioavailabilities beyond size-dependent effects. We end the review by proposing a framework towards more quantitative approaches and by highlighting promising techniques to guide future research in this exciting field.
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Affiliation(s)
- Muammar Mansor
- Geomicrobiology, Center for Applied Geoscience, University of Tuebingen, Tuebingen, 72076, Germany
| | - Jie Xu
- Department of Geological Sciences, the University of Texas at El Paso, El Paso, Texas, 79968, USA
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Brito Â, Vieira J, Vieira CP, Zhu T, Leão PN, Ramos V, Lu X, Vasconcelos VM, Gugger M, Tamagnini P. Comparative Genomics Discloses the Uniqueness and the Biosynthetic Potential of the Marine Cyanobacterium Hyella patelloides. Front Microbiol 2020; 11:1527. [PMID: 32774329 PMCID: PMC7381351 DOI: 10.3389/fmicb.2020.01527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/12/2020] [Indexed: 11/16/2022] Open
Abstract
Baeocytous cyanobacteria (Pleurocapsales/Subsection II) can thrive in a wide range of habitats on Earth but, compared to other cyanobacterial lineages, they remain poorly studied at genomic level. In this study, we sequenced the first genome from a member of the Hyella genus - H. patelloides LEGE 07179, a recently described species isolated from the Portuguese foreshore. This genome is the largest of the thirteen baeocyte-forming cyanobacterial genomes sequenced so far, and diverges from the most closely related strains. Comparative analysis revealed strain-specific genes and horizontal gene transfer events between H. patelloides and its closest relatives. Moreover, H. patelloides genome is distinctive by the number and diversity of natural product biosynthetic gene clusters (BGCs). The majority of these clusters are strain-specific BGCs with a high probability of synthesizing novel natural products. One BGC was identified as being putatively involved in the production of terminal olefin. Our results showed that, H. patelloides produces hydrocarbon with C15 chain length, and synthesizes C14, C16, and C18 fatty acids exceeding 4% of the dry cell weight. Overall, our data contributed to increase the information on baeocytous cyanobacteria, and shed light on H. patelloides evolution, phylogeny and natural product biosynthetic potential.
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Affiliation(s)
- Ângela Brito
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Jorge Vieira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Cristina P Vieira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Tao Zhu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Pedro N Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Matosinhos, Portugal
| | - Vitor Ramos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Matosinhos, Portugal
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Vitor M Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Matosinhos, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, Paris, France
| | - Paula Tamagnini
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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