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Wacey D, Urosevic L, Saunders M, George AD. Mineralisation of filamentous cyanobacteria in Lake Thetis stromatolites, Western Australia. GEOBIOLOGY 2018; 16:203-215. [PMID: 29318763 DOI: 10.1111/gbi.12272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 11/29/2017] [Indexed: 06/07/2023]
Abstract
Stromatolites are cited as some of the earliest evidence for life on Earth, but problems remain in reconciling the paucity of microfossils in ancient carbonate examples with the abundance of microbes that help construct modern analogues. Here, we trace the mineralisation pathway of filamentous cyanobacteria within stromatolites from Lake Thetis, Western Australia, providing new insights into microfossil preservation in carbonate stromatolites. Lake Thetis cyanobacteria exhibit a spectrum of mineralisation processes that include early precipitation of Mg-silicates, largely controlled by the morphochemical features of the cyanobacteria, followed by aragonite formation that is inferred to be driven by heterotrophic activity. Fossilised cyanobacteria with high-quality morphological preservation are characterised by a significant volume of authigenic Mg-silicates, which have preferentially nucleated in/on extracellular organic material and on cell walls, and now replicate the region once occupied by the cyanobacterial sheath. In such specimens, aragonite is restricted to the outer sheath margin and parts of the cell interior. Cyanobacteria that display more significant degradation appear to possess a higher ratio of aragonite to Mg-silicate. In these specimens, aragonite forms micronodules in the sheath zone and is spatially associated with the inferred remains of heterotrophic bacteria. Aragonite also occurs as an advancing front from the outer margin of the sheath where it is commonly intergrown with Mg-silicates. Where there is no evidence of Mg-silicates within filaments, the fidelity of microfossil preservation is poor. In these cases, individual filaments may no longer be visible under light microscopy, and little organic material remains, but filament traces remain detectable using electron microscopy due to variations in aragonite texture. These data provide further evidence that authigenic silicate minerals play a crucial role in the fossilisation of micro-organisms; in their absence, carbonate crystal growth potentially mediated by heterotrophic microbial decay may largely obliterate morphological evidence for life within stromatolites, although mineralogical traces may still be detectable using electron microscopy.
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Affiliation(s)
- D Wacey
- Centre for Microscopy Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
- School of Earth Sciences, The University of Western Australia, Perth, WA, Australia
| | - L Urosevic
- School of Earth Sciences, The University of Western Australia, Perth, WA, Australia
| | - M Saunders
- Centre for Microscopy Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - A D George
- School of Earth Sciences, The University of Western Australia, Perth, WA, Australia
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Cam N, Benzerara K, Georgelin T, Jaber M, Lambert JF, Poinsot M, Skouri-Panet F, Moreira D, López-García P, Raimbault E, Cordier L, Jézéquel D. Cyanobacterial formation of intracellular Ca-carbonates in undersaturated solutions. GEOBIOLOGY 2018; 16:49-61. [PMID: 29076282 DOI: 10.1111/gbi.12261] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 09/01/2017] [Indexed: 06/07/2023]
Abstract
Cyanobacteria have long been thought to induce the formation of Ca-carbonates as secondary by-products of their metabolic activity, by shifting the chemical composition of their extracellular environment to conditions favoring mineral precipitation. Some cyanobacterial species forming Ca-carbonates intracellularly were recently discovered. However, the environmental conditions under which this intracellular biomineralization process can occur and the impact of cyanobacterial species forming Ca-carbonates intracellularly on extracellular carbonatogenesis are not known. Here, we show that these cyanobacteria can form Ca-carbonates intracellularly while growing in extracellular solutions undersaturated with respect to all Ca-carbonate phases, that is, conditions thermodynamically unfavorable to mineral precipitation. This shows that intracellular Ca-carbonate biomineralization is an active process; that is, it costs energy provided by the cells. The cost of energy may be due to the active accumulation of Ca intracellularly. Moreover, unlike cyanobacterial strains that have been usually considered before by studies on Ca-carbonate biomineralization, cyanobacteria forming intracellular carbonates may slow down or hamper extracellular carbonatogenesis, by decreasing the saturation index of their extracellular solution following the buffering of the concentration of extracellular calcium to low levels.
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Affiliation(s)
- N Cam
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC), UMR CNRS 7590, Muséum National d'Histoire Naturelle, IRD UMR 206, Sorbonne Universités, UPMC Univ Paris 6, Paris, France
- Laboratoire de Réactivité de Surface (LRS), UMR CNRS 7197, Sorbonne Universités, UPMC Univ Paris 6, Paris, France
| | - K Benzerara
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC), UMR CNRS 7590, Muséum National d'Histoire Naturelle, IRD UMR 206, Sorbonne Universités, UPMC Univ Paris 6, Paris, France
| | - T Georgelin
- Laboratoire de Réactivité de Surface (LRS), UMR CNRS 7197, Sorbonne Universités, UPMC Univ Paris 6, Paris, France
| | - M Jaber
- Laboratoire d'Archéologie Moléculaire et Structurale (LAMS), Sorbonne Universités, UMR CNRS 8220, UPMC Univ Paris 6, Paris, France
| | - J-F Lambert
- Laboratoire de Réactivité de Surface (LRS), UMR CNRS 7197, Sorbonne Universités, UPMC Univ Paris 6, Paris, France
| | - M Poinsot
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC), UMR CNRS 7590, Muséum National d'Histoire Naturelle, IRD UMR 206, Sorbonne Universités, UPMC Univ Paris 6, Paris, France
| | - F Skouri-Panet
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC), UMR CNRS 7590, Muséum National d'Histoire Naturelle, IRD UMR 206, Sorbonne Universités, UPMC Univ Paris 6, Paris, France
| | - D Moreira
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, AgroParisTech, Université Paris-Sud/Paris-Saclay, Orsay, France
| | - P López-García
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, AgroParisTech, Université Paris-Sud/Paris-Saclay, Orsay, France
| | - E Raimbault
- Institut de Physique du Globe de Paris (IPGP), Sorbonne Paris Cité-Université Paris Diderot, UMR CNRS 7154, Paris Cedex 05, France
| | - L Cordier
- Institut de Physique du Globe de Paris (IPGP), Sorbonne Paris Cité-Université Paris Diderot, UMR CNRS 7154, Paris Cedex 05, France
| | - D Jézéquel
- Institut de Physique du Globe de Paris (IPGP), Sorbonne Paris Cité-Université Paris Diderot, UMR CNRS 7154, Paris Cedex 05, France
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53
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Whittaker ML, Smeets PJM, Asayesh-Ardakani H, Shahbazian-Yassar R, Joester D. Multi-Step Crystallization of Barium Carbonate: Rapid Interconversion of Amorphous and Crystalline Precursors. Angew Chem Int Ed Engl 2017; 56:16028-16031. [PMID: 29049848 DOI: 10.1002/anie.201709526] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/06/2016] [Indexed: 11/08/2022]
Abstract
The direct observation of amorphous barium carbonate (ABC), which transforms into a previously unknown barium carbonate hydrate (herewith named gortatowskite) within a few hundred milliseconds of formation, is described. In situ X-ray scattering, cryo-, and low-dose electron microscopy were used to capture the transformation of nanoparticulate ABC into gortatowskite crystals, highly anisotropic sheets that are up to 1 μm in width, yet only about 10 nm in thickness. Recrystallization of gortatowskite to witherite starts within 30 seconds. We describe a bulk synthesis and report a first assessment of the composition, vibrational spectra, and structure of gortatowskite. Our findings indicate that transient amorphous and crystalline precursors can play a role in aqueous precipitation pathways that may often be overlooked owing to their extremely short lifetimes and small dimensions. However, such transient precursors may be integral to the formation of more stable phases.
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Affiliation(s)
- Michael L Whittaker
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL, 60208, USA
| | - Paul J M Smeets
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL, 60208, USA
| | - Hasti Asayesh-Ardakani
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, 842 W. Taylor Street, Chicago, IL, 60607, USA
| | - Reza Shahbazian-Yassar
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, 842 W. Taylor Street, Chicago, IL, 60607, USA
| | - Derk Joester
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL, 60208, USA
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Sauze J, Ogée J, Maron PA, Crouzet O, Nowak V, Wohl S, Kaisermann A, Jones SP, Wingate L. The interaction of soil phototrophs and fungi with pH and their impact on soil CO 2, CO 18O and OCS exchange. SOIL BIOLOGY & BIOCHEMISTRY 2017; 115:371-382. [PMID: 29200510 PMCID: PMC5666291 DOI: 10.1016/j.soilbio.2017.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/06/2017] [Accepted: 09/10/2017] [Indexed: 06/07/2023]
Abstract
The stable oxygen isotope composition of atmospheric CO2 and the mixing ratio of carbonyl sulphide (OCS) are potential tracers of biospheric CO2 fluxes at large scales. However, the use of these tracers hinges on our ability to understand and better predict the activity of the enzyme carbonic anhydrase (CA) in different soil microbial groups, including phototrophs. Because different classes of the CA family (α, β and γ) may have different affinities to CO2 and OCS and their expression should also vary between different microbial groups, differences in the community structure could impact the 'community-integrated' CA activity differently for CO2 and OCS. Four soils of different pH were incubated in the dark or with a diurnal cycle for forty days to vary the abundance of native phototrophs. Fluxes of CO2, CO18O and OCS were measured to estimate CA activity alongside the abundance of bacteria, fungi and phototrophs. The abundance of soil phototrophs increased most at higher soil pH. In the light, the strength of the soil CO2 sink and the CA-driven CO2-H2O isotopic exchange rates correlated with phototrophs abundance. OCS uptake rates were attributed to fungi whose abundance was positively enhanced in alkaline soils but only in the presence of increased phototrophs. Our findings demonstrate that soil-atmosphere CO2, OCS and CO18O fluxes are strongly regulated by the microbial community structure in response to changes in soil pH and light availability and supports the idea that different members of the microbial community express different classes of CA, with different affinities to CO2 and OCS.
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Affiliation(s)
- Joana Sauze
- ISPA, Bordeaux Science Agro, INRA, 33140 Villenave d’Ornon, France
| | - Jérôme Ogée
- ISPA, Bordeaux Science Agro, INRA, 33140 Villenave d’Ornon, France
| | - Pierre-Alain Maron
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Olivier Crouzet
- INRA, UR 251 PESSAC, Centre Versailles-Grignon, RD 10, 78026 Versailles Cedex, France
| | - Virginie Nowak
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Steven Wohl
- ISPA, Bordeaux Science Agro, INRA, 33140 Villenave d’Ornon, France
| | | | - Sam P. Jones
- ISPA, Bordeaux Science Agro, INRA, 33140 Villenave d’Ornon, France
| | - Lisa Wingate
- ISPA, Bordeaux Science Agro, INRA, 33140 Villenave d’Ornon, France
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55
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Bradley JA, Daille LK, Trivedi CB, Bojanowski CL, Stamps BW, Stevenson BS, Nunn HS, Johnson HA, Loyd SJ, Berelson WM, Corsetti FA, Spear JR. Carbonate-rich dendrolitic cones: insights into a modern analog for incipient microbialite formation, Little Hot Creek, Long Valley Caldera, California. NPJ Biofilms Microbiomes 2017; 3:32. [PMID: 29177068 PMCID: PMC5698408 DOI: 10.1038/s41522-017-0041-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/24/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023] Open
Abstract
Ancient putative microbial structures that appear in the rock record commonly serve as evidence of early life on Earth, but the details of their formation remain unclear. The study of modern microbial mat structures can help inform the properties of their ancient counterparts, but modern mineralizing mat systems with morphological similarity to ancient structures are rare. Here, we characterize partially lithified microbial mats containing cm-scale dendrolitic coniform structures from a geothermal pool ("Cone Pool") at Little Hot Creek, California, that if fully lithified, would resemble ancient dendrolitic structures known from the rock record. Light and electron microscopy revealed that the cm-scale 'dendrolitic cones' were comprised of intertwined microbial filaments and grains of calcium carbonate. The degree of mineralization (carbonate content) increased with depth in the dendrolitic cones. Sequencing of 16S rRNA gene libraries revealed that the dendrolitic cone tips were enriched in OTUs most closely related to the genera Phormidium, Leptolyngbya, and Leptospira, whereas mats at the base and adjacent to the dendrolitic cones were enriched in Synechococcus. We hypothesize that the consumption of nutrients during autotrophic and heterotrophic growth may promote movement of microbes along diffusive nutrient gradients, and thus microbialite growth. Hour-glass shaped filamentous structures present in the dendrolitic cones may have formed around photosynthetically-produced oxygen bubbles-suggesting that mineralization occurs rapidly and on timescales of the lifetime of a bubble. The dendrolitic-conical structures in Cone Pool constitute a modern analog of incipient microbialite formation by filamentous microbiota that are morphologically distinct from any structure described previously. Thus, we provide a new model system to address how microbial mats may be preserved over geological timescales.
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Affiliation(s)
- James A. Bradley
- Department of Earth Sciences, University of Southern California, Los Angeles, CA USA
| | - Leslie K. Daille
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christopher B. Trivedi
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO USA
| | - Caitlin L. Bojanowski
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, OH 45433 USA
| | - Blake W. Stamps
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO USA
| | - Bradley S. Stevenson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK USA
| | - Heather S. Nunn
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK USA
| | - Hope A. Johnson
- Department of Biological Science, California State University, Fullerton, Fullerton, CA USA
| | - Sean J. Loyd
- Department of Geological Sciences, California State University, Fullerton, Fullerton, CA USA
| | - William M. Berelson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA USA
| | - Frank A. Corsetti
- Department of Earth Sciences, University of Southern California, Los Angeles, CA USA
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO USA
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56
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Whittaker ML, Smeets PJM, Asayesh‐Ardakani H, Shahbazian‐Yassar R, Joester D. Multi‐Step Crystallization of Barium Carbonate: Rapid Interconversion of Amorphous and Crystalline Precursors. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Michael L. Whittaker
- Department of Materials Science and Engineering Northwestern University 2220 Campus Drive Evanston IL 60208 USA
| | - Paul J. M. Smeets
- Department of Materials Science and Engineering Northwestern University 2220 Campus Drive Evanston IL 60208 USA
| | - Hasti Asayesh‐Ardakani
- Department of Mechanical and Industrial Engineering University of Illinois at Chicago 842 W. Taylor Street Chicago IL 60607 USA
| | - Reza Shahbazian‐Yassar
- Department of Mechanical and Industrial Engineering University of Illinois at Chicago 842 W. Taylor Street Chicago IL 60607 USA
| | - Derk Joester
- Department of Materials Science and Engineering Northwestern University 2220 Campus Drive Evanston IL 60208 USA
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Koo H, Mojib N, Hakim JA, Hawes I, Tanabe Y, Andersen DT, Bej AK. Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica. Front Microbiol 2017; 8:1347. [PMID: 28824553 PMCID: PMC5543034 DOI: 10.3389/fmicb.2017.01347] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/03/2017] [Indexed: 01/15/2023] Open
Abstract
In this study, we report the distribution of microbial taxa and their predicted metabolic functions observed in the top (U1), middle (U2), and inner (U3) decadal growth laminae of a unique large conical microbial mat from perennially ice-covered Lake Untersee of East Antarctica, using NextGen sequencing of the 16S rRNA gene and bioinformatics tools. The results showed that the U1 lamina was dominated by cyanobacteria, specifically Phormidium sp., Leptolyngbya sp., and Pseudanabaena sp. The U2 and U3 laminae had high abundances of Actinobacteria, Verrucomicrobia, Proteobacteria, and Bacteroidetes. Closely related taxa within each abundant bacterial taxon found in each lamina were further differentiated at the highest taxonomic resolution using the oligotyping method. PICRUSt analysis, which determines predicted KEGG functional categories from the gene contents and abundances among microbial communities, revealed a high number of sequences belonging to carbon fixation, energy metabolism, cyanophycin, chlorophyll, and photosynthesis proteins in the U1 lamina. The functional predictions of the microbial communities in U2 and U3 represented signal transduction, membrane transport, zinc transport and amino acid-, carbohydrate-, and arsenic- metabolisms. The Nearest Sequenced Taxon Index (NSTI) values processed through PICRUSt were 0.10, 0.13, and 0.11 for U1, U2, and U3 laminae, respectively. These values indicated a close correspondence with the reference microbial genome database, implying high confidence in the predicted metabolic functions of the microbial communities in each lamina. The distribution of microbial taxa observed in each lamina and their predicted metabolic functions provides additional insight into the complex microbial ecosystem at Lake Untersee, and lays the foundation for studies that will enhance our understanding of the mechanisms responsible for the formation of these unique mat structures and their evolutionary significance.
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Affiliation(s)
- Hyunmin Koo
- Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States
| | - Nazia Mojib
- Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States
| | - Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States
| | - Ian Hawes
- Gateway Antarctica, University of CanterburyChristchurch, New Zealand
| | - Yukiko Tanabe
- National Institute of Polar ResearchTachikawa, Japan
| | - Dale T Andersen
- Carl Sagan Center, SETI Institute, Mountain ViewCA, United States
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States
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58
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Modulation of calcium carbonate precipitation by exopolysaccharide in Bacillus sp. JH7. Appl Microbiol Biotechnol 2017. [DOI: 10.1007/s00253-017-8372-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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59
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Novoselov AA, Silva D, Schneider J, Abrevaya XC, Chaffin MS, Serrano P, Navarro MS, Conti MJ, Souza Filho CRD. Geochemical constraints on the Hadean environment from mineral fingerprints of prokaryotes. Sci Rep 2017; 7:4008. [PMID: 28638074 PMCID: PMC5479841 DOI: 10.1038/s41598-017-04161-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/22/2017] [Indexed: 11/21/2022] Open
Abstract
The environmental conditions on the Earth before 4 billion years ago are highly uncertain, largely because of the lack of a substantial rock record from this period. During this time interval, known as the Hadean, the young planet transformed from an uninhabited world to the one capable of supporting, and inhabited by the first living cells. These cells formed in a fluid environment they could not at first control, with homeostatic mechanisms developing only later. It is therefore possible that present-day organisms retain some record of the primordial fluid in which the first cells formed. Here we present new data on the elemental compositions and mineral fingerprints of both Bacteria and Archaea, using these data to constrain the environment in which life formed. The cradle solution that produced this elemental signature was saturated in barite, sphene, chalcedony, apatite, and clay minerals. The presence of these minerals, as well as other chemical features, suggests that the cradle environment of life may have been a weathering fluid interacting with dry-land silicate rocks. The specific mineral assemblage provides evidence for a moderate Hadean climate with dry and wet seasons and a lower atmospheric abundance of CO2 than is present today.
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Affiliation(s)
- Alexey A Novoselov
- University of Campinas, Institute of Geosciences, Campinas, 13083-970, Brazil.
- University of Concepción, Institute of Applied Economic Geology, Concepción, Casilla 160-C, Chile.
| | - Dailto Silva
- University of Campinas, Institute of Geosciences, Campinas, 13083-970, Brazil
| | - Jerusa Schneider
- University of Campinas, School of Civil Engineering, Architecture and Urban Design, Campinas, 13083-889, Brazil
| | - Ximena Celeste Abrevaya
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, C1428EHA, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Astronomía y Física del Espacio (IAFE), Buenos Aires, C1428ZAA, Argentina
| | | | - Paloma Serrano
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, 14473, Germany
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60
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Alleon J, Bernard S, Le Guillou C, Daval D, Skouri-Panet F, Kuga M, Robert F. Organic molecular heterogeneities can withstand diagenesis. Sci Rep 2017; 7:1508. [PMID: 28473702 PMCID: PMC5431453 DOI: 10.1038/s41598-017-01612-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 03/30/2017] [Indexed: 11/09/2022] Open
Abstract
Reconstructing the original biogeochemistry of organic fossils requires quantifying the extent of the chemical transformations that they underwent during burial-induced maturation processes. Here, we performed laboratory experiments on chemically different organic materials in order to simulate the thermal maturation processes that occur during diagenesis. Starting organic materials were microorganisms and organic aerosols. Scanning transmission X-ray microscopy (STXM) was used to collect X-ray absorption near edge spectroscopy (XANES) data of the organic residues. Results indicate that even after having been submitted to 250 °C and 250 bars for 100 days, the molecular signatures of microorganisms and aerosols remain different in terms of nitrogen-to-carbon atomic ratio and carbon and nitrogen speciation. These observations suggest that burial-induced thermal degradation processes may not completely obliterate the chemical and molecular signatures of organic molecules. In other words, the present study suggests that organic molecular heterogeneities can withstand diagenesis and be recognized in the fossil record.
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Affiliation(s)
- Julien Alleon
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ. Paris 06, IRD UMR 206, 61 rue Buffon, 75005, Paris, France.,Department of Earth Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sylvain Bernard
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ. Paris 06, IRD UMR 206, 61 rue Buffon, 75005, Paris, France.
| | | | - Damien Daval
- Laboratoire d'Hydrologie et de Géochimie de Strasbourg, Université de Strasbourg/EOST - CNRS UMR 7517, 1 Rue Blessig, 67084, Strasbourg, France
| | - Feriel Skouri-Panet
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ. Paris 06, IRD UMR 206, 61 rue Buffon, 75005, Paris, France
| | - Maïa Kuga
- Department of Earth Sciences, ETH Zürich, 8092, Zürich, Switzerland
| | - François Robert
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ. Paris 06, IRD UMR 206, 61 rue Buffon, 75005, Paris, France
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61
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Recent developments and trends in the application of strontium and its isotopes in biological related fields. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.02.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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62
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Moreira D, Tavera R, Benzerara K, Skouri-Panet F, Couradeau E, Gérard E, Fonta CL, Novelo E, Zivanovic Y, López-García P. Description of Gloeomargarita lithophora gen. nov., sp. nov., a thylakoid-bearing, basal-branching cyanobacterium with intracellular carbonates, and proposal for Gloeomargaritales ord. nov. Int J Syst Evol Microbiol 2017; 67:653-658. [PMID: 27902306 DOI: 10.1099/ijsem.0.001679] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A unicellular cyanobacterium, strain Alchichica-D10, was isolated from microbialites of the alkaline Lake Alchichica, Mexico. The cells were short rods (3.9±0.6 µm in length and 1.1±0.1 µm in width) forming biofilms of intense emerald green colour. They exhibited red autofluorescence under UV light excitation. UV-visible absorption spectra revealed that they contain chlorophyll a and phycocyanin, and electron microscopy showed the presence of thylakoids. The strain grew within a temperature range of 15-30 °C. Genomic DNA G+C content was 52.2 mol%. The most remarkable feature of this species was its granular cytoplasm, due to the presence of numerous intracellular spherical granules (16-26 per cell) with an average diameter of 270 nm. These granules, easily visible under scanning electron microscopy, were composed of amorphous carbonate containing Ca, Mg, Ba and Sr. A multi-gene phylogeny based on the analysis of 59 conserved protein markers supported robustly that this strain occupies a deep position in the cyanobacterial tree. Based on its phenotypic characters and phylogenetic position, strain Alchichica-D10 is considered to represent a new genus and novel species of cyanobacteria for which the name Gloeomargarita lithophora gen. nov., sp. nov. is proposed. The type strain is Alchichica-D10 (Culture Collection of Algae and Protozoa CCAP strain 1437/1; Collections de Cyanobactéries et Microalgues Vivantes of the Museum National d'Histoire Naturelle in Paris strain PMC 919.15). Furthermore, a new family, Gloeomargaritaceae, and a new order, Gloeoemargaritales, are proposed to accommodate this species under the International Code of Nomenclature for algae, fungi and plants.
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Affiliation(s)
- David Moreira
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud/Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Rosaluz Tavera
- Facultad de Ciencias, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie, Sorbonne Universités-UPMC Univ Paris 06, CNRS UMR 7590, MNHN, IRD UMR 206, Paris, France
| | - Fériel Skouri-Panet
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie, Sorbonne Universités-UPMC Univ Paris 06, CNRS UMR 7590, MNHN, IRD UMR 206, Paris, France
| | - Estelle Couradeau
- Present address: School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.,Facultad de Ciencias, Universidad Nacional Autónoma de México, CDMX, Mexico.,Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud/Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Emmanuelle Gérard
- Géobiosphère Actuelle et Primitive, Institut de Physique du Globe de Paris, CNRS UMR 7154, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Céline Loussert Fonta
- Nestlé Research Center, Minerals and Imaging Group, P.O Box 44, Ch-1000 Lausanne 26, VD, Switzerland
| | - Eberto Novelo
- Facultad de Ciencias, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Yvan Zivanovic
- Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud/Paris-Saclay, 91405 Orsay, France
| | - Purificación López-García
- Nestlé Research Center, Minerals and Imaging Group, P.O Box 44, Ch-1000 Lausanne 26, VD, Switzerland
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63
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Endosymbiotic calcifying bacteria across sponge species and oceans. Sci Rep 2017; 7:43674. [PMID: 28262822 PMCID: PMC5337934 DOI: 10.1038/srep43674] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/27/2017] [Indexed: 11/17/2022] Open
Abstract
From an evolutionary point of view, sponges are ideal targets to study marine symbioses as they are the most ancient living metazoans and harbour highly diverse microbial communities. A recently discovered association between the sponge Hemimycale columella and an intracellular bacterium that generates large amounts of calcite spherules has prompted speculation on the possible role of intracellular bacteria in the evolution of the skeleton in early animals. To gain insight into this purportedly ancestral symbiosis, we investigated the presence of symbiotic bacteria in Mediterranean and Caribbean sponges. We found four new calcibacteria OTUs belonging to the SAR116 in two orders (Poecilosclerida and Clionaida) and three families of Demospongiae, two additional OTUs in cnidarians and one more in seawater (at 98.5% similarity). Using a calcibacteria targeted probe and CARD-FISH, we also found calcibacteria in Spirophorida and Suberitida and proved that the calcifying bacteria accumulated at the sponge periphery, forming a skeletal cortex, analogous to that of siliceous microscleres in other demosponges. Bacteria-mediated skeletonization is spread in a range of phylogenetically distant species and thus the purported implication of bacteria in skeleton formation and evolution of early animals gains relevance.
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Martignier A, Pacton M, Filella M, Jaquet JM, Barja F, Pollok K, Langenhorst F, Lavigne S, Guagliardo P, Kilburn MR, Thomas C, Martini R, Ariztegui D. Intracellular amorphous carbonates uncover a new biomineralization process in eukaryotes. GEOBIOLOGY 2017; 15:240-253. [PMID: 27696636 DOI: 10.1111/gbi.12213] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/25/2016] [Indexed: 06/06/2023]
Abstract
Until now, descriptions of intracellular biomineralization of amorphous inclusions involving alkaline-earth metal (AEM) carbonates other than calcium have been confined exclusively to cyanobacteria (Couradeau et al., 2012). Here, we report the first evidence of the presence of intracellular amorphous granules of AEM carbonates (calcium, strontium, and barium) in unicellular eukaryotes. These inclusions, which we have named micropearls, show concentric and oscillatory zoning on a nanometric scale. They are widespread in certain eukaryote phytoplankters of Lake Geneva (Switzerland) and represent a previously unknown type of non-skeletal biomineralization, revealing an unexpected pathway in the geochemical cycle of AEMs. We have identified Tetraselmis cf. cordiformis (Chlorophyta, Prasinophyceae) as being responsible for the formation of one micropearl type containing strontium ([Ca,Sr]CO3 ), which we also found in a cultured strain of Tetraselmis cordiformis. A different flagellated eukaryotic cell forms barium-rich micropearls [(Ca,Ba)CO3 ]. The strontium and barium concentrations of both micropearl types are extremely high compared with the undersaturated water of Lake Geneva (the Ba/Ca ratio of the micropearls is up to 800,000 times higher than in the water). This can only be explained by a high biological pre-concentration of these elements. The particular characteristics of the micropearls, along with the presence of organic sulfur-containing compounds-associated with and surrounding the micropearls-strongly suggest the existence of a yet-unreported intracellular biomineralization pathway in eukaryotic micro-organisms.
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Affiliation(s)
- A Martignier
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - M Pacton
- Laboratoire de Géologie de Lyon, Lyon 1 University, Villeurbanne, France
| | - M Filella
- Institute F.-A. Forel, University of Geneva, Geneva, Switzerland
| | - J-M Jaquet
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - F Barja
- Microbiology unit, University of Geneva, Geneva, Switzerland
| | - K Pollok
- Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - F Langenhorst
- Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - S Lavigne
- Service de l'Ecologie de l'Eau (SECOE), Geneva, Switzerland
| | - P Guagliardo
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - M R Kilburn
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - C Thomas
- CARRTEL of Thonon-les-Bains, INRA, Thonon-les-Bains, France
| | - R Martini
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - D Ariztegui
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
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65
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Ponce-Toledo RI, Deschamps P, López-García P, Zivanovic Y, Benzerara K, Moreira D. An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids. Curr Biol 2017; 27:386-391. [PMID: 28132810 DOI: 10.1016/j.cub.2016.11.056] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/04/2016] [Accepted: 11/29/2016] [Indexed: 01/29/2023]
Abstract
Photosynthesis evolved in eukaryotes by the endosymbiosis of a cyanobacterium, the future plastid, within a heterotrophic host. This primary endosymbiosis occurred in the ancestor of Archaeplastida, a eukaryotic supergroup that includes glaucophytes, red algae, green algae, and land plants [1-4]. However, although the endosymbiotic origin of plastids from a single cyanobacterial ancestor is firmly established, the nature of that ancestor remains controversial: plastids have been proposed to derive from either early- or late-branching cyanobacterial lineages [5-11]. To solve this issue, we carried out phylogenomic and supernetwork analyses of the most comprehensive dataset analyzed so far including plastid-encoded proteins and nucleus-encoded proteins of plastid origin resulting from endosymbiotic gene transfer (EGT) of primary photosynthetic eukaryotes, as well as wide-ranging genome data from cyanobacteria, including novel lineages. Our analyses strongly support that plastids evolved from deep-branching cyanobacteria and that the present-day closest cultured relative of primary plastids is Gloeomargarita lithophora. This species belongs to a recently discovered cyanobacterial lineage widespread in freshwater microbialites and microbial mats [12, 13]. The ecological distribution of this lineage sheds new light on the environmental conditions where the emergence of photosynthetic eukaryotes occurred, most likely in a terrestrial-freshwater setting. The fact that glaucophytes, the first archaeplastid lineage to diverge, are exclusively found in freshwater ecosystems reinforces this hypothesis. Therefore, not only did plastids emerge early within cyanobacteria, but the first photosynthetic eukaryotes most likely evolved in terrestrial-freshwater settings, not in oceans as commonly thought.
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Affiliation(s)
- Rafael I Ponce-Toledo
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud/Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Philippe Deschamps
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud/Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud/Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Yvan Zivanovic
- Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud/Paris-Saclay, 91405 Orsay, France
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie, Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7590, Muséum National d'Histoire Naturelle, IRD UMR 206, 75005 Paris, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud/Paris-Saclay, AgroParisTech, 91400 Orsay, France.
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66
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Saghaï A, Zivanovic Y, Moreira D, Benzerara K, Bertolino P, Ragon M, Tavera R, López-Archilla AI, López-García P. Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient. Environ Microbiol 2016; 18:4990-5004. [PMID: 27422734 PMCID: PMC5477898 DOI: 10.1111/1462-2920.13456] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/13/2016] [Indexed: 12/15/2022]
Abstract
Modern microbialites are often used as analogs of Precambrian stromatolites; therefore, studying the metabolic interplay within their associated microbial communities can help formulating hypotheses on their formation and long-term preservation within the fossil record. We performed a comparative metagenomic analysis of microbialite samples collected at two sites and along a depth gradient in Lake Alchichica (Mexico). The community structure inferred from single-copy gene family identification and long-contig (>10 kb) assignation, consistently with previous rRNA gene surveys, showed a wide prokaryotic diversity dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Bacteroidetes, while eukaryotes were largely dominated by green algae or diatoms. Functional analyses based on RefSeq, COG and SEED assignations revealed the importance of housekeeping functions, with an overrepresentation of genes involved in carbohydrate metabolism, as compared with other metabolic capacities. The search for genes diagnostic of specific metabolic functions revealed the important involvement of Alphaproteobacteria in anoxygenic photosynthesis and sulfide oxidation, and Cyanobacteria in oxygenic photosynthesis and nitrogen fixation. Surprisingly, sulfate reduction appeared negligible. Comparative analyses suggested functional similarities among various microbial mat and microbialite metagenomes as compared with soil or oceans, but showed differences in microbial processes among microbialite types linked to local environmental conditions.
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Affiliation(s)
- Aurélien Saghaï
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Yvan Zivanovic
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Sud Orsay, Université Paris-Saclay, France
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Karim Benzerara
- Institut de Minéralogie et de Physique des Matériaux et de Cosmochimie, CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | - Paola Bertolino
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Marie Ragon
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de México, DF Mexico, Mexico
| | | | - Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
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67
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Reguer S, Mocuta C, Thiaudière D, Daudon M, Bazin D. Combination of X-ray synchrotron radiation techniques to gather information for clinicians. CR CHIM 2016. [DOI: 10.1016/j.crci.2015.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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68
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Cam N, Benzerara K, Georgelin T, Jaber M, Lambert JF, Poinsot M, Skouri-Panet F, Cordier L. Selective Uptake of Alkaline Earth Metals by Cyanobacteria Forming Intracellular Carbonates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:11654-11662. [PMID: 27712057 DOI: 10.1021/acs.est.6b02872] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The uptakes of calcium (Ca), strontium (Sr), and barium (Ba) by two cyanobacterial strains, Cyanothece sp. PCC7425 and Gloeomargarita lithophora, both forming intracellular carbonates, were investigated in laboratory cultures. In the culture medium BG-11 amended with 250 μM Ca and 50 or 250 μM Sr and Ba, G. lithophora accumulated first Ba, then Sr, and finally Ca. Sr and Ba were completely accumulated by G. lithophora cells at rates between 0.02 and 0.10 fmol h-1 cell-1 and down to extracellular concentrations below the detection limits of inductively coupled plasma atomic emission spectroscopy. Accumulation of Sr and Ba did not affect the growth rate of the strain. This sequential accumulation occurred mostly intracellularly within polyphosphate and carbonate granules and resulted in the formation of core-shell structures in carbonates. In contrast, Cyanothece sp. PCC7425 showed neither a preferential accumulation of heavier alkaline earth metals nor core-shell structures in the carbonates. This indicated that fractionation between alkaline earth metals was not inherent to intracellularly calcifying cyanobacteria but was likely a genetically based trait of G. lithophora. Overall, the capability of G. lithophora to sequester preferentially Sr and Ba at high rates may be of considerable interest for designing new remediation strategies and better understanding the geochemical cycles of these elements.
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Affiliation(s)
- Nithavong Cam
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Institut de Recherche pour le Développement (IRD) Unité Mixte de Recherche (UMR) 206, Muséum National d'Histoire Naturelle, UMR Centre National de la Recherche Scientifique (CNRS) 7590, Université Pierre et Marie Curie (UPMC) Université Paris 06, Sorbonne Universités , 4 Place Jussieu, 75005 Paris, France
- Laboratoire de Réactivité de Surface (LRS), Unité Mixte de Recherche (UMR) Centre National de la Recherche Scientifique (CNRS) 7197, Université Pierre et Marie Curie (UPMC) Université Paris 06, Sorbonne Universités , 4 Place Jussieu, 75005 Paris, France
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Institut de Recherche pour le Développement (IRD) Unité Mixte de Recherche (UMR) 206, Muséum National d'Histoire Naturelle, UMR Centre National de la Recherche Scientifique (CNRS) 7590, Université Pierre et Marie Curie (UPMC) Université Paris 06, Sorbonne Universités , 4 Place Jussieu, 75005 Paris, France
| | - Thomas Georgelin
- Laboratoire de Réactivité de Surface (LRS), Unité Mixte de Recherche (UMR) Centre National de la Recherche Scientifique (CNRS) 7197, Université Pierre et Marie Curie (UPMC) Université Paris 06, Sorbonne Universités , 4 Place Jussieu, 75005 Paris, France
| | - Maguy Jaber
- Laboratoire d'Archéologie Moléculaire et Structurale (LAMS), Unité Mixte de Recherche (UMR) Centre National de la Recherche Scientifique (CNRS) 8220, Université Pierre et Marie Curie (UPMC) Université Paris 06, Sorbonne Universités , 4 Place Jussieu, 75005 Paris, France
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface (LRS), Unité Mixte de Recherche (UMR) Centre National de la Recherche Scientifique (CNRS) 7197, Université Pierre et Marie Curie (UPMC) Université Paris 06, Sorbonne Universités , 4 Place Jussieu, 75005 Paris, France
| | - Mélanie Poinsot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Institut de Recherche pour le Développement (IRD) Unité Mixte de Recherche (UMR) 206, Muséum National d'Histoire Naturelle, UMR Centre National de la Recherche Scientifique (CNRS) 7590, Université Pierre et Marie Curie (UPMC) Université Paris 06, Sorbonne Universités , 4 Place Jussieu, 75005 Paris, France
- Laboratoire de Réactivité de Surface (LRS), Unité Mixte de Recherche (UMR) Centre National de la Recherche Scientifique (CNRS) 7197, Université Pierre et Marie Curie (UPMC) Université Paris 06, Sorbonne Universités , 4 Place Jussieu, 75005 Paris, France
| | - Fériel Skouri-Panet
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Institut de Recherche pour le Développement (IRD) Unité Mixte de Recherche (UMR) 206, Muséum National d'Histoire Naturelle, UMR Centre National de la Recherche Scientifique (CNRS) 7590, Université Pierre et Marie Curie (UPMC) Université Paris 06, Sorbonne Universités , 4 Place Jussieu, 75005 Paris, France
| | - Laure Cordier
- Institut de Physique du Globe de Paris (IPGP), Unité Mixte de Recherche (UMR) Centre National de la Recherche Scientifique (CNRS) 7154, Université Paris Diderot, Sorbonne Paris Cité , 1 Rue Jussieu, 75238 Paris Cedex 05, France
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69
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Calcium transport into the cells of the sea urchin larva in relation to spicule formation. Proc Natl Acad Sci U S A 2016; 113:12637-12642. [PMID: 27791140 DOI: 10.1073/pnas.1612017113] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigated the manner in which the sea urchin larva takes up calcium from its body cavity into the primary mesenchymal cells (PMCs) that are responsible for spicule formation. We used the membrane-impermeable fluorescent dye calcein and alexa-dextran, with or without a calcium channel inhibitor, and imaged the larvae in vivo with selective-plane illumination microscopy. Both fluorescent molecules are taken up from the body cavity into the PMCs and ectoderm cells, where the two labels are predominantly colocalized in particles, whereas the calcium-binding calcein label is mainly excluded from the endoderm and is concentrated in the spicules. The presence of vesicles and vacuoles inside the PMCs that have openings through the plasma membrane directly to the body cavity was documented using high-resolution cryo-focused ion beam-SEM serial imaging. Some of the vesicles and vacuoles are interconnected to form large networks. We suggest that these vacuolar networks are involved in direct sea water uptake. We conclude that the calcium pathway from the body cavity into cells involves nonspecific endocytosis of sea water with its calcium.
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70
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Lu H, Feng Y, Wang J, Wu Y, Shao H, Yang L. Responses of periphyton morphology, structure, and function to extreme nutrient loading. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 214:878-884. [PMID: 27173591 DOI: 10.1016/j.envpol.2016.03.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/03/2016] [Accepted: 03/27/2016] [Indexed: 06/05/2023]
Abstract
Periphyton have been widely applied in aquaculture systems, however, little information is available on how periphyton respond to such high nutrient levels in water. Thus, changes in the morphological characteristics, community structure, and metabolic function of periphyton under high eutrophic waters were evaluated. The results indicated that the morphology of periphyton was affected by increasing the nutrient concentration of water, which shifted the micromorphology of periphyton from spheriform to filamentous. The periphyton under higher water nutrient levels were able to utilize more carbon source types. Additionally, higher water nutrient levels increased the bacterial and protozoal proportions in periphyton. This study fills the gap in knowledge about the responses of periphytic communities to extremely eutrophic waters. It provides valuable information on the full understanding of the periphyton-nutrient relationship in aquaculture systems, which is beneficial for regulating the microbial species or communities in periphyton by manipulating the nutrient levels in water.
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Affiliation(s)
- Haiying Lu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agriculture Sciences, No. 50, Zhongling Rd, Nanjing 210014, PR China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.71, East Beijing Rd, Nanjing 210008, PR China; Institute of Agro-Biotechnology, Jiangsu Academy of Agriculture Sciences, No. 50, Zhongling Rd, Nanjing 210014, PR China
| | - Yanfang Feng
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agriculture Sciences, No. 50, Zhongling Rd, Nanjing 210014, PR China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.71, East Beijing Rd, Nanjing 210008, PR China
| | - Jinhua Wang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.71, East Beijing Rd, Nanjing 210008, PR China
| | - Hongbo Shao
- Institute of Agro-Biotechnology, Jiangsu Academy of Agriculture Sciences, No. 50, Zhongling Rd, Nanjing 210014, PR China.
| | - Linzhang Yang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agriculture Sciences, No. 50, Zhongling Rd, Nanjing 210014, PR China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.71, East Beijing Rd, Nanjing 210008, PR China.
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71
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Alleon J, Bernard S, Le Guillou C, Marin-Carbonne J, Pont S, Beyssac O, McKeegan KD, Robert F. Molecular preservation of 1.88 Ga Gunflint organic microfossils as a function of temperature and mineralogy. Nat Commun 2016; 7:11977. [PMID: 27312070 PMCID: PMC4915024 DOI: 10.1038/ncomms11977] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 05/18/2016] [Indexed: 01/06/2023] Open
Abstract
The significant degradation that fossilized biomolecules may experience during burial makes it challenging to assess the biogenicity of organic microstructures in ancient rocks. Here we investigate the molecular signatures of 1.88 Ga Gunflint organic microfossils as a function of their diagenetic history. Synchrotron-based XANES data collected in situ on individual microfossils, at the submicrometre scale, are compared with data collected on modern microorganisms. Despite diagenetic temperatures of ∼150–170 °C deduced from Raman data, the molecular signatures of some Gunflint organic microfossils have been exceptionally well preserved. Remarkably, amide groups derived from protein compounds can still be detected. We also demonstrate that an additional increase of diagenetic temperature of only 50 °C and the nanoscale association with carbonate minerals have significantly altered the molecular signatures of Gunflint organic microfossils from other localities. Altogether, the present study provides key insights for eventually decoding the earliest fossil record. Thermal diagenesis is generally seen as detrimental to the preservation of organic biosignatures. Using synchrotron-based XANES data, Alleon et al. find preservation of the molecular signatures of organic microfossils from the 1.88 Ga Gunflint cherts.
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Affiliation(s)
- Julien Alleon
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ Paris 06, IRD UMR 206, 61 rue Buffon, 75005 Paris, France
| | - Sylvain Bernard
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ Paris 06, IRD UMR 206, 61 rue Buffon, 75005 Paris, France
| | - Corentin Le Guillou
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ Paris 06, IRD UMR 206, 61 rue Buffon, 75005 Paris, France
| | - Johanna Marin-Carbonne
- Univ Lyon, UJM Saint Etienne, Laboratoire Magma et Volcans, UBP, CNRS, IRD, 23 rue Dr Paul Michelon, 42100 St Etienne, France
| | - Sylvain Pont
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ Paris 06, IRD UMR 206, 61 rue Buffon, 75005 Paris, France
| | - Olivier Beyssac
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ Paris 06, IRD UMR 206, 61 rue Buffon, 75005 Paris, France
| | - Kevin D McKeegan
- Department of Earth, Planetary and Space Sciences, University of California-Los Angeles, 595 Charles Young Drive East, Los Angeles, California 90095-1567, USA
| | - François Robert
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ Paris 06, IRD UMR 206, 61 rue Buffon, 75005 Paris, France
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Mineralogical Diversity in Lake Pavin: Connections with Water Column Chemistry and Biomineralization Processes. MINERALS 2016. [DOI: 10.3390/min6020024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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73
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Cao C, Jiang J, Sun H, Huang Y, Tao F, Lian B. Carbonate Mineral Formation under the Influence of Limestone-Colonizing Actinobacteria: Morphology and Polymorphism. Front Microbiol 2016; 7:366. [PMID: 27148166 PMCID: PMC4834437 DOI: 10.3389/fmicb.2016.00366] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/07/2016] [Indexed: 11/23/2022] Open
Abstract
Microorganisms and their biomineralization processes are widespread in almost every environment on earth. In this work, Streptomyces luteogriseus DHS C014, a dominant lithophilous actinobacteria isolated from microbial mats on limestone rocks, was used to investigate its potential biomineralization to allow a better understanding of bacterial contributions to carbonate mineralization in nature. The ammonium carbonate free-drift method was used with mycelium pellets, culture supernatant, and spent culture of the strain. Mineralogical analyses showed that hexagonal prism calcite was only observed in the sub-surfaces of the mycelium pellets, which is a novel morphology mediated by microbes. Hemispheroidal vaterite appeared in the presence of spent culture, mainly because of the effects of soluble microbial products (SMP) during mineralization. When using the culture supernatant, doughnut-like vaterite was favored by actinobacterial mycelia, which has not yet been captured in previous studies. Our analyses suggested that the effects of mycelium pellets as a molecular template almost gained an advantage over SMP both in crystal nucleation and growth, having nothing to do with biological activity. It is thereby convinced that lithophilous actinobacteria, S. luteogriseus DHS C014, owing to its advantageous genetic metabolism and filamentous structure, showed good biomineralization abilities, maybe it would have geoactive potential for biogenic carbonate in local microenvironments.
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Affiliation(s)
- Chengliang Cao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of SciencesGuiyang, China; Institute of Geochemistry, University of Chinese Academy of SciencesBeijing, China; The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal UniversityXuzhou, China
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University Xuzhou, China
| | - Henry Sun
- Division of Earth and Ecosystem Sciences, Desert Research Institute Las Vegas, NV, USA
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Faxiang Tao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences Guiyang, China
| | - Bin Lian
- Department of Biotechnology, College of Life Science, Nanjing Normal University Nanjing, China
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74
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Biomineralization Patterns of Intracellular Carbonatogenesis in Cyanobacteria: Molecular Hypotheses. MINERALS 2016. [DOI: 10.3390/min6010010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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75
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Duda JP, Van Kranendonk MJ, Thiel V, Ionescu D, Strauss H, Schäfer N, Reitner J. A Rare Glimpse of Paleoarchean Life: Geobiology of an Exceptionally Preserved Microbial Mat Facies from the 3.4 Ga Strelley Pool Formation, Western Australia. PLoS One 2016; 11:e0147629. [PMID: 26807732 PMCID: PMC4726515 DOI: 10.1371/journal.pone.0147629] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/06/2016] [Indexed: 11/19/2022] Open
Abstract
Paleoarchean rocks from the Pilbara Craton of Western Australia provide a variety of clues to the existence of early life on Earth, such as stromatolites, putative microfossils and geochemical signatures of microbial activity. However, some of these features have also been explained by non-biological processes. Further lines of evidence are therefore required to convincingly argue for the presence of microbial life. Here we describe a new type of microbial mat facies from the 3.4 Ga Strelley Pool Formation, which directly overlies well known stromatolitic carbonates from the same formation. This microbial mat facies consists of laminated, very fine-grained black cherts with discontinuous white quartz layers and lenses, and contains small domical stromatolites and wind-blown crescentic ripples. Light- and cathodoluminescence microscopy, Raman spectroscopy, and time of flight—secondary ion mass spectrometry (ToF-SIMS) reveal a spatial association of carbonates, organic material, and highly abundant framboidal pyrite within the black cherts. Nano secondary ion mass spectrometry (NanoSIMS) confirmed the presence of distinct spheroidal carbonate bodies up to several tens of μm that are surrounded by organic material and pyrite. These aggregates are interpreted as biogenic. Comparison with Phanerozoic analogues indicates that the facies represents microbial mats formed in a shallow marine environment. Carbonate precipitation and silicification by hydrothermal fluids occurred during sedimentation and earliest diagenesis. The deciphered environment, as well as the δ13C signature of bulk organic matter (-35.3‰), are in accord with the presence of photoautotrophs. At the same time, highly abundant framboidal pyrite exhibits a sulfur isotopic signature (δ34S = +3.05‰; Δ33S = 0.268‰; and Δ36S = -0.282‰) that is consistent with microbial sulfate reduction. Taken together, our results strongly support a microbial mat origin of the black chert facies, thus providing another line of evidence for life in the 3.4 Ga Strelley Pool Formation.
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Affiliation(s)
- Jan-Peter Duda
- Department of Geobiology, Geoscience Centre, Georg-August-University Göttingen, Goldschmidtstr. 3, 37077, Göttingen, Germany
- ‘Origin of Life’ Group, Göttingen Academy of Sciences and Humanities, Theaterstraße 7, 37073, Göttingen, Germany
- * E-mail:
| | - Martin J. Van Kranendonk
- Australian Centre for Astrobiology and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Volker Thiel
- Department of Geobiology, Geoscience Centre, Georg-August-University Göttingen, Goldschmidtstr. 3, 37077, Göttingen, Germany
| | - Danny Ionescu
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhütte 2, 16775, Stechlin, Germany
| | - Harald Strauss
- Institut für Geologie und Paläontologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 24, 48149, Münster, Germany
| | - Nadine Schäfer
- Department of Geobiology, Geoscience Centre, Georg-August-University Göttingen, Goldschmidtstr. 3, 37077, Göttingen, Germany
| | - Joachim Reitner
- Department of Geobiology, Geoscience Centre, Georg-August-University Göttingen, Goldschmidtstr. 3, 37077, Göttingen, Germany
- ‘Origin of Life’ Group, Göttingen Academy of Sciences and Humanities, Theaterstraße 7, 37073, Göttingen, Germany
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76
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Papineau D, De Gregorio B, Fearn S, Kilcoyne D, McMahon G, Purohit R, Fogel M. Nanoscale petrographic and geochemical insights on the origin of the Palaeoproterozoic stromatolitic phosphorites from Aravalli Supergroup, India. GEOBIOLOGY 2016; 14:3-32. [PMID: 26490161 DOI: 10.1111/gbi.12164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/02/2015] [Indexed: 06/05/2023]
Abstract
Stromatolites composed of apatite occur in post-Lomagundi-Jatuli successions (late Palaeoproterozoic) and suggest the emergence of novel types of biomineralization at that time. The microscopic and nanoscopic petrology of organic matter in stromatolitic phosphorites might provide insights into the suite of diagenetic processes that formed these types of stromatolites. Correlated geochemical micro-analyses of the organic matter could also yield molecular, elemental and isotopic compositions and thus insights into the role of specific micro-organisms among these communities. Here, we report on the occurrence of nanoscopic disseminated organic matter in the Palaeoproterozoic stromatolitic phosphorite from the Aravalli Supergroup of north-west India. Organic petrography by micro-Raman and Transmission Electron Microscopy demonstrates syngeneity of the organic matter. Total organic carbon contents of these stromatolitic phosphorite columns are between 0.05 and 3.0 wt% and have a large range of δ(13) Corg values with an average of -18.5‰ (1σ = 4.5‰). δ(15) N values of decarbonated rock powders are between -1.2 and +2.7‰. These isotopic compositions point to the important role of biological N2 -fixation and CO2 -fixation by the pentose phosphate pathway consistent with a population of cyanobacteria. Microscopic spheroidal grains of apatite (MSGA) occur in association with calcite microspar in microbial mats from stromatolite columns and with chert in the core of diagenetic apatite rosettes. Organic matter extracted from the stromatolitic phosphorites contains a range of molecular functional group (e.g. carboxylic acid, alcohol, and aliphatic hydrocarbons) as well as nitrile and nitro groups as determined from C- and N-XANES spectra. The presence of organic nitrogen was independently confirmed by a CN(-) peak detected by ToF-SIMS. Nanoscale petrography and geochemistry allow for a refinement of the formation model for the accretion and phototrophic growth of stromatolites. The original microbial biomass is inferred to have been dominated by cyanobacteria, which might be an important contributor of organic matter in shallow-marine phosphorites.
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Affiliation(s)
- D Papineau
- London Centre for Nanotechnology, University College London, London, UK
- Department of Earth Sciences, University College London, London, UK
| | - B De Gregorio
- Material Science and Technology Division, Naval Research Laboratory, Washington, DC, USA
| | - S Fearn
- Department of Material Sciences, Imperial College, London, UK
| | - D Kilcoyne
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - G McMahon
- School of Materials, The University of Manchester, Manchester, UK
| | - R Purohit
- Department of Geology, Government College Sirohi, Sirohi, Rajasthan, India
| | - M Fogel
- University of California at Merced, Merced, CA, USA
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77
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Yang ZN, Li XM, Umar A, Fan WH, Wang Y. Insight into calcification of Synechocystis sp. enhanced by extracellular carbonic anhydrase. RSC Adv 2016. [DOI: 10.1039/c5ra26159g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The mechanism of cyanobacterial calcification was proved to be related to extracellular carbonic anhydrase, which enhanced CaCO3 precipitation through facilitating proton consumption during transformation of bicarbonate to carbon dioxide.
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Affiliation(s)
- Zhen-Ni Yang
- Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education
- School of Chemistry and Environment
- Beihang University
- Beijing
- P. R. China
| | - Xiao-Min Li
- Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education
- School of Chemistry and Environment
- Beihang University
- Beijing
- P. R. China
| | - Ahmad Umar
- Department of Chemistry
- College of Science and Arts and Promising Centre for Sensors and Electronic Devices (PCSED)
- Najran University
- Najran 11001
- Kingdom of Saudi Arabia
| | - Wen-Hong Fan
- Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education
- School of Chemistry and Environment
- Beihang University
- Beijing
- P. R. China
| | - Yao Wang
- Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education
- School of Chemistry and Environment
- Beihang University
- Beijing
- P. R. China
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78
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Salman V, Yang T, Berben T, Klein F, Angert E, Teske A. Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh. THE ISME JOURNAL 2015; 9:2503-14. [PMID: 25909974 PMCID: PMC4611513 DOI: 10.1038/ismej.2015.62] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 03/17/2015] [Accepted: 03/20/2015] [Indexed: 11/08/2022]
Abstract
Large sulfur bacteria of the genus Achromatium are exceptional among Bacteria and Archaea as they can accumulate high amounts of internal calcite. Although known for more than 100 years, they remain uncultured, and only freshwater populations have been studied so far. Here we investigate a marine population of calcite-accumulating bacteria that is primarily found at the sediment surface of tide pools in a salt marsh, where high sulfide concentrations meet oversaturated oxygen concentrations during the day. Dynamic sulfur cycling by phototrophic sulfide-oxidizing and heterotrophic sulfate-reducing bacteria co-occurring in these sediments creates a highly sulfidic environment that we propose induces behavioral differences in the Achromatium population compared with reported migration patterns in a low-sulfide environment. Fluctuating intracellular calcium/sulfur ratios at different depths and times of day indicate a biochemical reaction of the salt marsh Achromatium to diurnal changes in sedimentary redox conditions. We correlate this calcite dynamic with new evidence regarding its formation/mobilization and suggest general implications as well as a possible biological function of calcite accumulation in large bacteria in the sediment environment that is governed by gradients. Finally, we propose a new taxonomic classification of the salt marsh Achromatium based on their adaptation to a significantly different habitat than their freshwater relatives, as indicated by their differential behavior as well as phylogenetic distance on 16S ribosomal RNA gene level. In future studies, whole-genome characterization and additional ecophysiological factors could further support the distinctive position of salt marsh Achromatium.
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Affiliation(s)
- Verena Salman
- Department of Microbiology, Cornell University, Ithaca, NY, USA
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tingting Yang
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tom Berben
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Frieder Klein
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Esther Angert
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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79
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DeVol RT, Sun CY, Marcus MA, Coppersmith SN, Myneni SCB, Gilbert PU. Nanoscale Transforming Mineral Phases in Fresh Nacre. J Am Chem Soc 2015; 137:13325-33. [DOI: 10.1021/jacs.5b07931] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ross T. DeVol
- Department
of Physics, University of Wisconsin−Madison, 1150 University Avenue, Madison, Wisconsin 53706, United States
| | - Chang-Yu Sun
- Department
of Physics, University of Wisconsin−Madison, 1150 University Avenue, Madison, Wisconsin 53706, United States
| | - Matthew A. Marcus
- Advanced
Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Susan N. Coppersmith
- Department
of Physics, University of Wisconsin−Madison, 1150 University Avenue, Madison, Wisconsin 53706, United States
| | - Satish C. B. Myneni
- Department
of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
| | - Pupa U.P.A. Gilbert
- Department
of Physics, University of Wisconsin−Madison, 1150 University Avenue, Madison, Wisconsin 53706, United States
- Department
of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Radcliffe
Institute for Advanced Study, Harvard University, 8 Garden Street, Cambridge, Massachusetts 02138, United States
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80
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Miot J, Remusat L, Duprat E, Gonzalez A, Pont S, Poinsot M. Fe biomineralization mirrors individual metabolic activity in a nitrate-dependent Fe(II)-oxidizer. Front Microbiol 2015; 6:879. [PMID: 26441847 PMCID: PMC4562303 DOI: 10.3389/fmicb.2015.00879] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/10/2015] [Indexed: 12/15/2022] Open
Abstract
Microbial biomineralization sometimes leads to periplasmic encrustation, which is predicted to enhance microorganism preservation in the fossil record. Mineral precipitation within the periplasm is, however, thought to induce death, as a result of permeability loss preventing nutrient and waste transit across the cell wall. This hypothesis had, however, never been investigated down to the single cell level. Here, we cultured the nitrate reducing Fe(II) oxidizing bacteria Acidovorax sp. strain BoFeN1 that have been previously shown to promote the precipitation of a diversity of Fe minerals (lepidocrocite, goethite, Fe phosphate) encrusting the periplasm. We investigated the connection of Fe biomineralization with carbon assimilation at the single cell level, using a combination of electron microscopy and Nano-Secondary Ion Mass Spectrometry. Our analyses revealed strong individual heterogeneities of Fe biomineralization. Noteworthy, a small proportion of cells remaining free of any precipitate persisted even at advanced stages of biomineralization. Using pulse chase experiments with (13)C-acetate, we provide evidence of individual phenotypic heterogeneities of carbon assimilation, correlated with the level of Fe biomineralization. Whereas non- and moderately encrusted cells were able to assimilate acetate, higher levels of periplasmic encrustation prevented any carbon incorporation. Carbon assimilation only depended on the level of Fe encrustation and not on the nature of Fe minerals precipitated in the cell wall. Carbon assimilation decreased exponentially with increasing cell-associated Fe content. Persistence of a small proportion of non-mineralized and metabolically active cells might constitute a survival strategy in highly ferruginous environments. Eventually, our results suggest that periplasmic Fe biomineralization may provide a signature of individual metabolic status, which could be looked for in the fossil record and in modern environmental samples.
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Affiliation(s)
- Jennyfer Miot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Laurent Remusat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Elodie Duprat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Adriana Gonzalez
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Sylvain Pont
- Département des Collections, Muséum National d’Histoire NaturelleParis, France
| | - Mélanie Poinsot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
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81
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Mansor M, Hamilton TL, Fantle MS, Macalady JL. Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing. Front Microbiol 2015; 6:822. [PMID: 26322031 PMCID: PMC4530308 DOI: 10.3389/fmicb.2015.00822] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/27/2015] [Indexed: 11/13/2022] Open
Abstract
Large, sulfur-cycling, calcite-precipitating bacteria in the genus Achromatium represent a significant proportion of bacterial communities near sediment-water interfaces at sites throughout the world. Our understanding of their potentially crucial roles in calcium, carbon, sulfur, nitrogen, and iron cycling is limited because they have not been cultured or sequenced using environmental genomics approaches to date. We utilized single-cell genomic sequencing to obtain one incomplete and two nearly complete draft genomes for Achromatium collected at Warm Mineral Springs (WMS), FL. Based on 16S rRNA gene sequences, the three cells represent distinct and relatively distant Achromatium populations (91-92% identity). The draft genomes encode key genes involved in sulfur and hydrogen oxidation; oxygen, nitrogen and polysulfide respiration; carbon and nitrogen fixation; organic carbon assimilation and storage; chemotaxis; twitching motility; antibiotic resistance; and membrane transport. Known genes for iron and manganese energy metabolism were not detected. The presence of pyrophosphatase and vacuolar (V)-type ATPases, which are generally rare in bacterial genomes, suggests a role for these enzymes in calcium transport, proton pumping, and/or energy generation in the membranes of calcite-containing inclusions.
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Affiliation(s)
- Muammar Mansor
- Geosciences Department, Pennsylvania State University University Park, PA, USA
| | - Trinity L Hamilton
- Department of Biological Sciences, University of Cincinnati Cincinnati, OH, USA
| | - Matthew S Fantle
- Geosciences Department, Pennsylvania State University University Park, PA, USA
| | - Jennifer L Macalady
- Geosciences Department, Pennsylvania State University University Park, PA, USA
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82
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Saghaï A, Zivanovic Y, Zeyen N, Moreira D, Benzerara K, Deschamps P, Bertolino P, Ragon M, Tavera R, López-Archilla AI, López-García P. Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites. Front Microbiol 2015; 6:797. [PMID: 26300865 PMCID: PMC4525015 DOI: 10.3389/fmicb.2015.00797] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 07/22/2015] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at macroscale, and suggest a potential causal link. Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.
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Affiliation(s)
- Aurélien Saghaï
- Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-SudOrsay, France
| | - Yvan Zivanovic
- Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-SudOrsay, France
| | - Nina Zeyen
- Institut de Minéralogie et de Physique des Matériaux et de Cosmochimie, CNRS UMR 7590, Université Pierre et Marie CurieParis, France
| | - David Moreira
- Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-SudOrsay, France
| | - Karim Benzerara
- Institut de Minéralogie et de Physique des Matériaux et de Cosmochimie, CNRS UMR 7590, Université Pierre et Marie CurieParis, France
| | - Philippe Deschamps
- Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-SudOrsay, France
| | - Paola Bertolino
- Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-SudOrsay, France
| | - Marie Ragon
- Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-SudOrsay, France
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
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83
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84
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Ruvindy R, White RA, Neilan BA, Burns BP. Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics. ISME JOURNAL 2015; 10:183-96. [PMID: 26023869 DOI: 10.1038/ismej.2015.87] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 12/31/2022]
Abstract
Modern microbial mats are potential analogues of some of Earth's earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic next-generation sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.
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Affiliation(s)
- Rendy Ruvindy
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Brett Anthony Neilan
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, New South Wales, Australia
| | - Brendan Paul Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, New South Wales, Australia
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85
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Liu HC, Xia JL, Nie ZY, Zhen XJ, Zhang LJ. Differential expression of extracellular thiol groups of moderately thermophilic Sulfobacillus thermosulfidooxidans and extremely thermophilic Acidianus manzaensis grown on S0 and Fe2+. Arch Microbiol 2015; 197:823-31. [DOI: 10.1007/s00203-015-1111-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 03/23/2015] [Accepted: 04/08/2015] [Indexed: 01/17/2023]
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86
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Abstract
The profound influence of microorganisms on human life and global biogeochemical cycles underlines the value of studying the biogeography of microorganisms, exploring microbial genomes and expanding our understanding of most microbial species on Earth: that is, those present at low relative abundance. The detection and subsequent analysis of low-abundance microbial populations—the 'rare biosphere'—have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. We discuss the ecology of rare microbial populations, and highlight molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities.
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87
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Ronholm J, Schumann D, Sapers HM, Izawa M, Applin D, Berg B, Mann P, Vali H, Flemming RL, Cloutis EA, Whyte LG. A mineralogical characterization of biogenic calcium carbonates precipitated by heterotrophic bacteria isolated from cryophilic polar regions. GEOBIOLOGY 2014; 12:542-556. [PMID: 25256888 DOI: 10.1111/gbi.12102] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/13/2014] [Indexed: 06/03/2023]
Abstract
Precipitation of calcium carbonate (CaCO3(s) ) can be driven by microbial activity. Here, a systematic approach is used to identify the morphological and mineralogical characteristics of CaCO3(s) precipitated during the heterotrophic growth of micro-organisms isolated from polar environments. Focus was placed on establishing mineralogical features that are common in bioliths formed during heterotrophic activity, while in parallel identifying features that are specific to bioliths precipitated by certain microbial phylotypes. Twenty microbial isolates that precipitated macroscopic CaCO3(s) when grown on B4 media supplemented with calcium acetate or calcium citrate were identified. A multimethod approach, including scanning electron microscopy, high-resolution transmission electron microscopy, and micro-X-ray diffraction (μ-XRD), was used to characterize CaCO3(s) precipitates. Scanning and transmission electron microscopy showed that complete CaCO3(s) crystal encrustation of Arthrobacter sp. cells was common, while encrustation of Rhodococcus sp. cells did not occur. Several euhedral and anhedral mineral formations including disphenoid-like epitaxial plates, rhomboid-like aggregates with epitaxial rhombs, and spherulite aggregates were observed. While phylotype could not be linked to specific mineral formations, isolates tended to precipitate either euhedral or anhedral minerals, but not both. Three anhydrous CaCO3(s) polymorphs (calcite, aragonite, and vaterite) were identified by μ-XRD, and calcite and aragonite were also identified based on TEM lattice-fringe d value measurements. The presence of certain polymorphs was not indicative of biogenic origin, although several mineralogical features such as crystal-encrusted bacterial cells, or casts of bacterial cells embedded in mesocrystals are an indication of biogenic origin. In addition, some features such as the formation of vaterite and bacterial entombment appear to be linked to certain phylotypes. Identifying phylotypes consistent with certain mineralogical features is the first step toward discovering a link between these crystal features and the precise underlying molecular biology of the organism precipitating them.
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Affiliation(s)
- J Ronholm
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
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88
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Lepot K, Compère P, Gérard E, Namsaraev Z, Verleyen E, Tavernier I, Hodgson DA, Vyverman W, Gilbert B, Wilmotte A, Javaux EJ. Organic and mineral imprints in fossil photosynthetic mats of an East Antarctic lake. GEOBIOLOGY 2014; 12:424-450. [PMID: 25039968 DOI: 10.1111/gbi.12096] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 06/16/2014] [Indexed: 06/03/2023]
Abstract
Lacustrine microbial mats in Antarctic ice-free oases are considered modern analogues of early microbial ecosystems as their primary production is generally dominated by cyanobacteria, the heterotrophic food chain typically truncated due to extreme environmental conditions, and they are geographically isolated. To better understand early fossilization and mineralization processes in this context, we studied the microstructure and chemistry of organo-mineral associations in a suite of sediments 50-4530 cal. years old from a lake in Skarvsnes, Lützow Holm Bay, East Antarctica. First, we report an exceptional preservation of fossil autotrophs and their biomolecules on millennial timescales. The pigment scytonemin is preserved inside cyanobacterial sheaths. As non-pigmented sheaths are also preserved, scytonemin likely played little role in the preservation of sheath polysaccharides, which have been cross-linked by ether bonds. Coccoids preserved thylakoids and autofluorescence of pigments such as carotenoids. This exceptional preservation of autotrophs in the fossil mats argues for limited biodegradation during and after deposition. Moreover, cell-shaped aggregates preserved sulfur-rich nanoglobules, supporting fossilization of instable intracellular byproducts of chemotrophic or phototrophic S-oxidizers. Second, we report a diversity of micro- to nanostructured CaCO3 precipitates intimately associated with extracellular polymeric substances, cyanobacteria, and/or other prokaryotes. Micro-peloids Type 1 display features that distinguish them from known carbonates crystallized in inorganic conditions: (i) Type 1A are often filled with globular nanocarbonates and/or surrounded by a fibrous fringe, (ii) Type 1B are empty and display ovoid to wrinkled fringes of nanocrystallites that can be radially oriented (fibrous or triangular) or multilayered, and (iii) all show small-size variations. Type 2 rounded carbonates 1-2 μm in diameter occurring inside autofluorescent spheres interpreted as coccoidal bacteria may represent fossils of intracellular calcification. These organo-mineral associations support organically driven nanocarbonate crystallization and stabilization, hence providing potential markers for microbial calcification in ancient rocks.
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Affiliation(s)
- K Lepot
- Paléobiogéologie, Paléobotanique & Paléopalynologie, Département de Géologie, Université de Liège, 4000, Liège, Belgium; Géosystèmes, Université Lille 1, CNRS UMR 8217, SN5, 59655, Villeneuve d'Ascq, France
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89
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Morphological and phylogenetic diversity of thermophilic cyanobacteria in Algerian hot springs. Extremophiles 2014; 18:1035-47. [PMID: 25078728 DOI: 10.1007/s00792-014-0680-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/13/2014] [Indexed: 11/27/2022]
Abstract
Geothermal springs in Algeria have been known since the Roman Empire. They mainly locate in Eastern Algeria and are inhabited by thermophilic organisms, which include cyanobacteria forming mats and concretions. In this work, we have investigated the cyanobacterial diversity of these springs. Cyanobacteria were collected from water, concretions and mats in nine hot springs with water temperatures ranging from 39 to 93 °C. Samples were collected for isolation in culture, microscopic morphological examination, and molecular diversity analysis based on 16S rRNA gene sequences. Nineteen different cyanobacterial morphotypes were identified, the most abundant of which were three species of Leptolyngbya, accompanied by members of the genera Gloeocapsa, Gloeocapsopsis, Stigonema, Fischerella, Synechocystis, Microcoleus, Cyanobacterium, Chroococcus and Geitlerinema. Molecular diversity analyses were in good general agreement with classical identification and allowed the detection of additional species in three springs with temperatures higher than 50 °C. They corresponded to a Synechococcus clade and to relatives of the intracellularly calcifying Candidatus Gloeomargarita lithophora. The hottest springs were dominated by members of Leptolyngbya, Synechococcus-like cyanobacteria and Gloeomargarita, whereas Oscillatoriales other than Leptolyngbya, Chroococcales and Stigonematales dominated lower temperature springs. The isolation of some of these strains sets the ground for future studies on the biology of thermophilic cyanobacteria.
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90
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Intracellular Ca-carbonate biomineralization is widespread in cyanobacteria. Proc Natl Acad Sci U S A 2014; 111:10933-8. [PMID: 25009182 DOI: 10.1073/pnas.1403510111] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria have played a significant role in the formation of past and modern carbonate deposits at the surface of the Earth using a biomineralization process that has been almost systematically considered induced and extracellular. Recently, a deep-branching cyanobacterial species, Candidatus Gloeomargarita lithophora, was reported to form intracellular amorphous Ca-rich carbonates. However, the significance and diversity of the cyanobacteria in which intracellular biomineralization occurs remain unknown. Here, we searched for intracellular Ca-carbonate inclusions in 68 cyanobacterial strains distributed throughout the phylogenetic tree of cyanobacteria. We discovered that diverse unicellular cyanobacterial taxa form intracellular amorphous Ca-carbonates with at least two different distribution patterns, suggesting the existence of at least two distinct mechanisms of biomineralization: (i) one with Ca-carbonate inclusions scattered within the cell cytoplasm such as in Ca. G. lithophora, and (ii) another one observed in strains belonging to the Thermosynechococcus elongatus BP-1 lineage, in which Ca-carbonate inclusions lie at the cell poles. This pattern seems to be linked with the nucleation of the inclusions at the septum of the cells, showing an intricate and original connection between cell division and biomineralization. These findings indicate that intracellular Ca-carbonate biomineralization by cyanobacteria has been overlooked by past studies and open new perspectives on the mechanisms and the evolutionary history of intra- and extracellular Ca-carbonate biomineralization by cyanobacteria.
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91
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Ragon M, Benzerara K, Moreira D, Tavera R, López-García P. 16S rDNA-based analysis reveals cosmopolitan occurrence but limited diversity of two cyanobacterial lineages with contrasted patterns of intracellular carbonate mineralization. Front Microbiol 2014; 5:331. [PMID: 25071744 PMCID: PMC4085569 DOI: 10.3389/fmicb.2014.00331] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/16/2014] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are mainly thought to induce carbonate precipitation extracellularly via their photosynthetic activity combined with the nucleation potential of exopolymeric substances. The discovery in microbialites of the alkaline lake Alchichica (Mexico) of Candidatus Gloeomargarita lithophora, a cyanobacterium forming large amounts of intracellular Mg-Ca-Sr-Ba carbonate spherules, showed that intracellular biomineralization in cyanobacteria is also possible. A second cyanobacterium isolated from the same environment, Candidatus Synechococcus calcipolaris G9, has been recently shown to also form intracellular calcium carbonates at the cell poles, a capability shared by all cultured species of the Thermosynechococcus clade, to which it belongs. To explore the diversity of these two distant cyanobacterial lineages representing two different patterns of intracellular calcification, we designed specific primers against their 16S rRNA genes and looked for their occurrence in a wide variety of samples. We identified the presence of members of the Gloeomargarita and Thermosynechococcus/S. calcipolaris lineages in microbialites collected from Lake Alchichica and three other neighboring Mexican lakes. The two clades also occurred in karstic areas and in some thermophilic or hypersaline microbial mats collected in South America and/or Southern Europe. Surprisingly, the within-group diversity in the two clades was low, especially within the S. calcipolaris clade, with all 16S rRNA gene sequences retrieved sharing more than 97% identity. This suggests that these clades are composed of a limited number of operational taxonomic units (OTUs) with cosmopolitan distribution. Moreover, scanning electron microscopy coupled with energy dispersive x-ray spectrometry showed the presence of intracellularly calcifying Gloeomargarita-like cyanobacteria in fresh samples where this clade was relatively abundant, suggesting that these cyanobacteria do precipitate carbonates intracellularly under natural conditions.
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Affiliation(s)
- Marie Ragon
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 7590, MNHN, IRD UMR 206 Paris, France ; Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique CNRS UMR8079, Université Paris-Sud Orsay, France
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 7590, MNHN, IRD UMR 206 Paris, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique CNRS UMR8079, Université Paris-Sud Orsay, France
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de México DF Mexico, Mexico
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique CNRS UMR8079, Université Paris-Sud Orsay, France
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92
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93
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Ettensohn CA. Horizontal transfer of themsp130gene supported the evolution of metazoan biomineralization. Evol Dev 2014; 16:139-48. [DOI: 10.1111/ede.12074] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Charles A. Ettensohn
- Department of Biological Sciences; Carnegie Mellon University; 4400 Fifth Avenue Pittsburgh PA 15213 USA
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94
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Marin F, Le Roy N, Marie B, Ramos-Silva P, Bundeleva I, Guichard N, Immel F. Metazoan calcium carbonate biomineralizations: macroevolutionary trends – challenges for the coming decade. ACTA ACUST UNITED AC 2014. [DOI: 10.2113/gssgfbull.185.4.217] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Calcium carbonate-based biominerals, also referred as biocalcifications, are the most abundant biogenic mineralized products at the surface of the Earth. In this paper, we summarize general concepts on biocalcifications and we sketch macro-evolutionary trends throughout the history of the Earth, from Archean to Phanerozoic times. Then, we expose five fundamental issues that represent key-challenges in biocalcification researches for the coming decade: the first one concerns the comprehension of the micro- and nano-structure of calcium carbonate biominerals from a mineral viewpoint, while the second one deals with the understanding of the dynamic process of their fabrication. The third one treats the subtle interplay between organics and the mineral phase. The fourth issue focuses on an environmental challenge related to ocean acidification (OA); at last, the diagenetic processes that affect biogenic calcium carbonate mineral constitute the fifth issue.
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Affiliation(s)
- Frédéric Marin
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne, 6 boulevard Gabriel, 21000 Dijon, France
| | - Nathalie Le Roy
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne, 6 boulevard Gabriel, 21000 Dijon, France
- Centre Scientifique de Monaco (CSM), 8 Quai Antoine Ier, MC 98000 Monaco
| | - Benjamin Marie
- UMR CNRS 7245 MCAM, Muséum National d’Histoire Naturelle (MNHN), 75005 Paris, France
| | - Paula Ramos-Silva
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne, 6 boulevard Gabriel, 21000 Dijon, France
- Computational Science, Informatics Institute, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, Pays-Bas
- Computational Genomics Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Irina Bundeleva
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne, 6 boulevard Gabriel, 21000 Dijon, France
| | - Nathalie Guichard
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne, 6 boulevard Gabriel, 21000 Dijon, France
| | - Françoise Immel
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne, 6 boulevard Gabriel, 21000 Dijon, France
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95
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The quest for a unified view of bacterial land colonization. ISME JOURNAL 2014; 8:1358-69. [PMID: 24451209 PMCID: PMC4069389 DOI: 10.1038/ismej.2013.247] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 11/15/2013] [Accepted: 12/12/2013] [Indexed: 12/13/2022]
Abstract
Exploring molecular mechanisms underlying bacterial water-to-land transition represents a critical start toward a better understanding of the functioning and stability of the terrestrial ecosystems. Here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. We hypothesize that bacterial land colonization is dominated by a single-gene sweep, that is, the emergence of dnaE2 derived from an early duplication event of the primordial dnaE, followed by a series of niche-specific genomic adaptations, including GC content increase, intensive horizontal gene transfer and constant genome expansion. In addition, early bacterial radiation may be stimulated by an explosion of land-borne hosts (for example, plants and animals) after initial land colonization events.
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96
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Benzerara K, Couradeau E, Gérard E, Tavera R, Lopez-Archilla AI, Moreira D, Lopez-Garcia P. Geomicrobiological study of modern microbialites from Mexico: towards a better understanding of the ancient fossil record. BIO WEB OF CONFERENCES 2014. [DOI: 10.1051/bioconf/20140202002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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97
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Chalmin E, Reiche I. Synchrotron X-ray microanalysis and imaging of synthetic biological calcium carbonate in comparison with archaeological samples originating from the Large cave of Arcy-sur-Cure (28000-24500 BP, Yonne, France). MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2013; 19:1523-1534. [PMID: 24001921 DOI: 10.1017/s1431927613013342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Biosynthetic calcite samples were investigated using combined synchrotron X-ray microspectroscopy mapping. These samples were prepared with bacteria isolated from the Large cave of Arcy-sur-Cure in which prehistoric figures are masked by an opaque calcite layer. The biotic or abiotic origin of this layer is the issue of the present work. As previously known, a large community of bacteria may be involved in the CaCO3 formation in caves. A mixture of calcite/vaterite was obtained from bacteria isolated from the cave. Therefore, we can offer conclusions on their calcifying capability. The rare presence of vaterite in cave environments may be treated as a marker of biotic carbonate formations. Moreover, an amorphous calcium phosphate phase was present in the form of a calcite/vaterite mixture in the biotic model samples. This mixture of phases could be used as a tracer of the biotic process of CaCO3 formation. These biotic tracer phases were not identified using the applied analytical methods in the natural samples taken from the opaque calcite layers that covered the prehistoric figures of the Large cave. In this case, based on the obtained results, the biotic calcite formation process is likely to be considered as an undetectable effect at minimum.
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Affiliation(s)
- Emilie Chalmin
- European Synchrotron Radiation Facility, Polygone Scientifique Louis Neel -6, rue Jules Horowitz - 38000 Grenoble, France
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98
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Rahn-Lee L, Komeili A. The magnetosome model: insights into the mechanisms of bacterial biomineralization. Front Microbiol 2013; 4:352. [PMID: 24324464 PMCID: PMC3840617 DOI: 10.3389/fmicb.2013.00352] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/05/2013] [Indexed: 11/13/2022] Open
Abstract
Though the most ready example of biomineralization is the calcium phosphate of vertebrate bones and teeth, many bacteria are capable of creating biominerals inside their cells. Because of the diversity of these organisms and the minerals they produce, their study may reveal aspects of the fundamental mechanisms of biomineralization in more complex organisms. The best-studied case of intracellular biomineralization in bacteria is the magnetosome, an organelle produced by a diverse group of aquatic bacteria that contains single-domain crystals of the iron oxide magnetite (Fe3O4) or the iron sulfide greigite (Fe3S4). Here, recent advances in our understanding of the mechanisms of bacterial magnetite biomineralization are discussed and used as a framework for understanding less-well studied examples, including the bacterial intracellular biomineralization of cadmium, selenium, silver, nickel, uranium, and calcium carbonate. Understanding the molecular mechanisms underlying the biological formation of these minerals will have important implications for technologies such as the fabrication of nanomaterials and the bioremediation of toxic compounds.
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Affiliation(s)
- Lilah Rahn-Lee
- Plant and Microbial Biology, University of California Berkeley Berkeley, CA, USA
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99
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Saw JHW, Schatz M, Brown MV, Kunkel DD, Foster JS, Shick H, Christensen S, Hou S, Wan X, Donachie SP. Cultivation and complete genome sequencing of Gloeobacter kilaueensis sp. nov., from a lava cave in Kīlauea Caldera, Hawai'i. PLoS One 2013; 8:e76376. [PMID: 24194836 PMCID: PMC3806779 DOI: 10.1371/journal.pone.0076376] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 08/24/2013] [Indexed: 02/05/2023] Open
Abstract
The ancestor of Gloeobacter violaceus PCC 7421T is believed to have diverged from that of all known cyanobacteria before the evolution of thylakoid membranes and plant plastids. The long and largely independent evolutionary history of G. violaceus presents an organism retaining ancestral features of early oxygenic photoautotrophs, and in whom cyanobacteria evolution can be investigated. No other Gloeobacter species has been described since the genus was established in 1974 (Rippka et al., Arch Microbiol 100:435). Gloeobacter affiliated ribosomal gene sequences have been reported in environmental DNA libraries, but only the type strain's genome has been sequenced. However, we report here the cultivation of a new Gloeobacter species, G. kilaueensis JS1T, from an epilithic biofilm in a lava cave in Kīlauea Caldera, Hawai'i. The strain's genome was sequenced from an enriched culture resembling a low-complexity metagenomic sample, using 9 kb paired-end 454 pyrosequences and 400 bp paired-end Illumina reads. The JS1T and G. violaceus PCC 7421T genomes have little gene synteny despite sharing 2842 orthologous genes; comparing the genomes shows they do not belong to the same species. Our results support establishing a new species to accommodate JS1T, for which we propose the name Gloeobacter kilaueensis sp. nov. Strain JS1T has been deposited in the American Type Culture Collection (BAA-2537), the Scottish Marine Institute's Culture Collection of Algae and Protozoa (CCAP 1431/1), and the Belgian Coordinated Collections of Microorganisms (ULC0316). The G. kilaueensis holotype has been deposited in the Algal Collection of the US National Herbarium (US# 217948). The JS1T genome sequence has been deposited in GenBank under accession number CP003587. The G+C content of the genome is 60.54 mol%. The complete genome sequence of G. kilaueensis JS1T may further understanding of cyanobacteria evolution, and the shift from anoxygenic to oxygenic photosynthesis.
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Affiliation(s)
- Jimmy H. W. Saw
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
| | - Michael Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Mark V. Brown
- NASA Astrobiology Institute, University of Hawai'i, Honolulu, Hawai'i, United States of America
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Dennis D. Kunkel
- Dennis Kunkel Microscopy, Inc., Kailua, Hawai'i, United States of America
| | - Jamie S. Foster
- Department of Microbiology and Cell Science, University of Florida Space Life Science Laboratory, Kennedy Space Center, Kennedy, Florida, United States of America
| | | | - Stephanie Christensen
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'I, United States of America
| | - Shaobin Hou
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
- Advanced Studies of Genomics, Proteomics and Bioinformatics, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
| | - Xuehua Wan
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
- Advanced Studies of Genomics, Proteomics and Bioinformatics, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
| | - Stuart P. Donachie
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
- * E-mail:
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100
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Xia JL, Liu HC, Nie ZY, Peng AA, Zhen XJ, Yang Y, Zhang XL. Synchrotron radiation based STXM analysis and micro-XRF mapping of differential expression of extracellular thiol groups by Acidithiobacillus ferrooxidans grown on Fe2+ and S0. J Microbiol Methods 2013; 94:257-61. [DOI: 10.1016/j.mimet.2013.06.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 06/17/2013] [Accepted: 06/24/2013] [Indexed: 11/26/2022]
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