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Farias ME, Rasuk MC, Gallagher KL, Contreras M, Kurth D, Fernandez AB, Poiré D, Novoa F, Visscher PT. Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems at La Brava, a hypersaline lake at Salar de Atacama, Chile. PLoS One 2017; 12:e0186867. [PMID: 29140980 PMCID: PMC5687714 DOI: 10.1371/journal.pone.0186867] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/09/2017] [Indexed: 11/19/2022] Open
Abstract
Benthic microbial ecosystems of Laguna La Brava, Salar de Atacama, a high altitude hypersaline lake, were characterized in terms of bacterial and archaeal diversity, biogeochemistry, (including O2 and sulfide depth profiles and mineralogy), and physicochemical characteristics. La Brava is one of several lakes in the Salar de Atacama where microbial communities are growing in extreme conditions, including high salinity, high solar insolation, and high levels of metals such as lithium, arsenic, magnesium, and calcium. Evaporation creates hypersaline conditions in these lakes and mineral precipitation is a characteristic geomicrobiological feature of these benthic ecosystems. In this study, the La Brava non-lithifying microbial mats, microbialites, and rhizome-associated concretions were compared to each other and their diversity was related to their environmental conditions. All the ecosystems revealed an unusual community where Euryarchaeota, Crenarchaeota, Acetothermia, Firmicutes and Planctomycetes were the most abundant groups, and cyanobacteria, typically an important primary producer in microbial mats, were relatively insignificant or absent. This suggests that other microorganisms, and possibly novel pathways unique to this system, are responsible for carbon fixation. Depth profiles of O2 and sulfide showed active production and respiration. The mineralogy composition was calcium carbonate (as aragonite) and increased from mats to microbialites and rhizome-associated concretions. Halite was also present. Further analyses were performed on representative microbial mats and microbialites by layer. Different taxonomic compositions were observed in the upper layers, with Archaea dominating the non-lithifying mat, and Planctomycetes the microbialite. The bottom layers were similar, with Euryarchaeota, Crenarchaeota and Planctomycetes as dominant phyla. Sequences related to Cyanobacteria were very scarce. These systems may contain previously uncharacterized community metabolisms, some of which may be contributing to net mineral precipitation. Further work on these sites might reveal novel organisms and metabolisms of biotechnological interest.
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Affiliation(s)
- Maria Eugenia Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-Tucumán, CONICET, Tucumán, Argentina
- * E-mail:
| | - Maria Cecilia Rasuk
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-Tucumán, CONICET, Tucumán, Argentina
| | - Kimberley L. Gallagher
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | | | - Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-Tucumán, CONICET, Tucumán, Argentina
| | - Ana Beatriz Fernandez
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-Tucumán, CONICET, Tucumán, Argentina
| | - Daniel Poiré
- Centro de Investigaciones Geológicas, Universidad Nacional de La Plata-Conicet, La Plata, Argentina
| | - Fernando Novoa
- Centro de Ecología Aplicada (CEA), Ñuñoa, Santiago, Chile
| | - Pieter T. Visscher
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
- Australian Centre for Astrobiology, University of New South Wales, Sydney, New South Wales, Australia
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102
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Siahi M, Hofmann A, Master S, Mueller CW, Gerdes A. Carbonate ooids of the Mesoarchaean Pongola Supergroup, South Africa. GEOBIOLOGY 2017; 15:750-766. [PMID: 28737010 DOI: 10.1111/gbi.12249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
Ooids from the Mesoarchaean Chobeni Formation, Pongola Supergroup, KwaZulu-Natal, South Africa are older than any ooids reported to date. They are made of dolomite and ankerite and show concentric, radial-concentric, micritic, and radial fabrics. Radial ooids are interpreted to have originated from high-Mg-calcite and probably formed by microbial activity in a low-energy regime, while concentric ooids had an aragonite precursor and formed biotically under agitated/high-energy environmental conditions. Micritic ooids formed via the recrystallization of concentric ooids. Ooids and other allochems, such as intraclasts and peloids, contain carbonaceous matter. The close association of carbonaceous matter within ooid cortices with metabolically important elements, such as N, S and P, as identified by nano-scale secondary ion mass spectrometry analysis, allows us to propose a biologically induced origin for some ooids. By analogy with modern examples, a variety of microbial communities probably played a role in carbonate precipitation and ooid formation. Shale-normalized rare earth element (REE) distribution patterns of ooids and other allochems show positive LaSN , GdSN and YSN anomalies, superchondritic Y/Ho ratios and depleted light rare earth elements (LREEs) relative to the heavy rare earth elements (HREEs), which resemble those of seawater. These anomalies are less pronounced than expected for an open marine setting, which is interpreted as evidence for deposition in restricted shallow marine environments. Non-seawater REE patterns in recrystallized matrix and pore- and vein-filling carbonate likely reflect redistribution of rare earth elements during post-depositional alteration and/or reflect differences in the elemental and REE compositions of diagenetic fluids.
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Affiliation(s)
- M Siahi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-University, Munich, Germany
- Economic Geology Research Institute, School of Geosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A Hofmann
- Department of Geology, University of Johannesburg, Johannesburg, South Africa
| | - S Master
- Economic Geology Research Institute, School of Geosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - C W Mueller
- Department of Ecology and Ecosystem Management, Soil Science, Technical University, Munich, Germany
| | - A Gerdes
- Institute of Geosciences, Goethe-University Frankfurt, Frankfurt, Germany
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103
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Van Den Hende S, Rodrigues A, Hamaekers H, Sonnenholzner S, Vervaeren H, Boon N. Microalgal bacterial flocs treating paper mill effluent: A sunlight-based approach for removing carbon, nitrogen, phosphorus, and calcium. N Biotechnol 2017; 39:1-10. [PMID: 28385669 DOI: 10.1016/j.nbt.2017.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 01/19/2017] [Accepted: 03/28/2017] [Indexed: 10/19/2022]
Abstract
Treatment of upflow anaerobic sludge blanket (UASB) effluent from a paper mill in aerated activated sludge reactors involves high aeration costs. Moreover, this calcium-rich effluent leads to problematic scale formation. Therefore, a novel strategy for the aerobic treatment of paper mill UASB effluent in microalgal bacterial floc sequencing batch reactors (MaB-floc SBRs) is proposed, in which oxygen is provided via photosynthesis, and calcium is removed via bio-mineralization. Based on the results of batch experiments in the course of this study, a MaB-floc SBR was operated at an initial neutral pH. This SBR removed 58±21% organic carbon, 27±8% inorganic carbon, 77±5% nitrogen, 73±2% phosphorus, and 27±11% calcium. MaB-flocs contained 10±3% calcium, including biologically-influenced calcite crystals. The removal of calcium and inorganic carbon by MaB-flocs significantly decreased when inhibiting extracellular carbonic anhydrase (CA), an enzyme that catalyses the hydration and dehydration of CO2. This study demonstrates the potential of MaB-floc SBRs for the alternative treatment of calcium-rich paper mill effluent, and highlights the importance of extracellular CA in this treatment process.
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Affiliation(s)
- Sofie Van Den Hende
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Gent, Belgium(2); Laboratory of Industrial Water and Eco-Technology (LIWET), Faculty of Bioscience Engineering, Ghent University, Graaf Karel de Goedelaan 5, B-8500 Kortrijk, Belgium(3); ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Centro Nacional de Acuicultura e Investigaciones Marinas (CENAIM), Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador(4); ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Facultad de Ciencias de la Vida, Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador(5).
| | - André Rodrigues
- Laboratory of Industrial Water and Eco-Technology (LIWET), Faculty of Bioscience Engineering, Ghent University, Graaf Karel de Goedelaan 5, B-8500 Kortrijk, Belgium(3); Centre for the Study of Education, Technologies and Health (CSETH), Polytechnic Institute of Viseu, Av. J. M. Vale de Andrade, 3504-510 Viseu, Portugal(6).
| | - Helen Hamaekers
- Earth and Environmental Sciences, KU Leuven, Celestijnenlaan 200E, B-3001 Heverlee, Belgium(7).
| | - Stanislaus Sonnenholzner
- ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Centro Nacional de Acuicultura e Investigaciones Marinas (CENAIM), Campus Gustavo Galindo, Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador(4).
| | - Han Vervaeren
- Laboratory of Industrial Water and Eco-Technology (LIWET), Faculty of Bioscience Engineering, Ghent University, Graaf Karel de Goedelaan 5, B-8500 Kortrijk, Belgium(3); Centre for Advanced Process Technology for Urban Resources (CAPTURE), Ghent University, Coupure Links 653, B-9000 Gent, Belgium(8).
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Gent, Belgium(2).
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104
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Experimental Deployment of Microbial Mineral Carbonation at an Asbestos Mine: Potential Applications to Carbon Storage and Tailings Stabilization. MINERALS 2017. [DOI: 10.3390/min7100191] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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105
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Alegbeleye OO, Opeolu BO, Jackson VA. Polycyclic Aromatic Hydrocarbons: A Critical Review of Environmental Occurrence and Bioremediation. ENVIRONMENTAL MANAGEMENT 2017; 60:758-783. [PMID: 28573478 DOI: 10.1007/s00267-017-0896-2] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 05/23/2017] [Indexed: 05/21/2023]
Abstract
The degree of polycyclic aromatic hydrocarbon contamination of environmental matrices has increased over the last several years due to increase in industrial activities. Interest has surrounded the occurrence and distribution of polycyclic aromatic hydrocarbons for many decades because they pose a serious threat to the health of humans and ecosystems. The importance of the need for sustainable abatement strategies to alleviate contamination therefore cannot be overemphasised, as daily human activities continue to create pollution from polycyclic aromatic hydrocarbons and impact the natural environment. Globally, attempts have been made to design treatment schemes for the remediation and restoration of contaminated sites. Several techniques and technologies have been proposed and tested over time, the majority of which have significant limitations. This has necessitated research into environmentally friendly and cost-effective clean-up techniques. Bioremediation is an appealing option that has been extensively researched and adopted as it has been proven to be relatively cost-effective, environmentally friendly and is publicly accepted. In this review, the physicochemical properties of some priority polycyclic aromatic hydrocarbons, as well as the pathways and mechanisms through which they enter the soil, river systems, drinking water, groundwater and food are succinctly examined. Their effects on human health, other living organisms, the aquatic ecosystem, as well as soil microbiota are also elucidated. The persistence and bioavailability of polycyclic aromatic hydrocarbons are discussed as well, as they are important factors that influence the rate, efficiency and overall success of remediation. Bioremediation (aerobic and anaerobic), use of biosurfactants and bioreactors, as well as the roles of biofilms in the biological treatment of polycyclic aromatic hydrocarbons are also explored.
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Affiliation(s)
- Oluwadara Oluwaseun Alegbeleye
- Department of Environmental and Occupational Studies, Cape Peninsula University of Technology, Cape Town, Western Cape, South Africa.
| | - Beatrice Oluwatoyin Opeolu
- Extended Curriculum Programmes, Faculty of Applied Sciences, Cape Peninsula University of Technology, Cape Town, Western Cape, South Africa
| | - Vanessa Angela Jackson
- Department of Biotechnology and Consumer Science, Cape Peninsula University of Technology, Cape Town, Western Cape, South Africa
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106
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Lanier KA, Petrov AS, Williams LD. The Central Symbiosis of Molecular Biology: Molecules in Mutualism. J Mol Evol 2017; 85:8-13. [PMID: 28785970 PMCID: PMC5579163 DOI: 10.1007/s00239-017-9804-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/28/2017] [Indexed: 11/05/2022]
Abstract
As illustrated by the mitochondrion and the eukaryotic cell, little in biology makes sense except in light of mutualism. Mutualisms are persistent, intimate, and reciprocal exchanges; an organism proficient in obtaining certain benefits confers those on a partner, which reciprocates by conferring different benefits. Mutualisms (i) increase fitness, (ii) inspire robustness, (iii) are resilient and resistant to change, (iv) sponsor co-evolution, (v) foster innovation, and (vi) involve partners that are distantly related with contrasting yet complementary proficiencies. Previous to this work, mutualisms were understood to operate on levels of cells, organisms, ecosystems, and even societies and economies. Here, the concepts of mutualism are extended to molecules and are seen to apply to the relationship between RNA and protein. Polynucleotide and polypeptide are Molecules in Mutualism. RNA synthesizes protein in the ribosome and protein synthesizes RNA in polymerases. RNA and protein are codependent, and trade proficiencies. Protein has proficiency in folding into complex three-dimensional states, contributing enzymes, fibers, adhesives, pumps, pores, switches, and receptors. RNA has proficiency in direct molecular recognition, achieved by complementary base pairing interactions, which allow it to maintain, record, and transduce information. The large phylogenetic distance that characterizes partnerships in organismal mutualism has close analogy with large distance in chemical space between RNA and protein. The RNA backbone is anionic and self-repulsive and cannot form hydrophobic structural cores. The protein backbone is neutral and cohesive and commonly forms hydrophobic cores. Molecules in Mutualism extends beyond RNA and protein. A cell is a consortium of molecules in which nucleic acids, proteins, polysaccharides, phospholipids, and other molecules form a mutualism consortium that drives metabolism and replication. Analogies are found in systems such as stromatolites, which are large consortia of symbiotic organisms. It seems reasonable to suggest that 'polymers in mutualism relationships' is a useful and predictive definition of life.
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Affiliation(s)
- Kathryn A. Lanier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400 USA
| | - Anton S. Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400 USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400 USA
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107
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Ecological interactions in Cloudina from the Ediacaran of Brazil: implications for the rise of animal biomineralization. Sci Rep 2017; 7:5482. [PMID: 28710440 PMCID: PMC5511220 DOI: 10.1038/s41598-017-05753-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 06/05/2017] [Indexed: 11/23/2022] Open
Abstract
At the Ediacaran/Cambrian boundary, ecosystems witnessed an unparalleled biological innovation: the appearance of shelled animals. Here, we report new paleoecological and paleobiological data on Cloudina, which was one of the most abundant shelled animals at the end of the Ediacaran. We report the close association of Cloudina tubes with microbial mat textures as well as organic-rich material, syndepositional calcite and goethite cement between their flanges, thus reinforcing the awareness of metazoan/microorganism interactions at the end of the Ediacaran. The preservation of in situ tubes suggests a great plasticity of substrate utilization, with evidence of different life modes and avoidance behavior. Geochemical analysis revealed walls composed of two secondary laminae and organic sheets. Some walls presented boreholes that are here described as predation marks. Taken together, these data add further information regarding the structuring of shelled animal communities in marine ecosystems.
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108
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Decho AW, Gutierrez T. Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems. Front Microbiol 2017; 8:922. [PMID: 28603518 PMCID: PMC5445292 DOI: 10.3389/fmicb.2017.00922] [Citation(s) in RCA: 256] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/08/2017] [Indexed: 12/13/2022] Open
Abstract
Microbial cells (i.e., bacteria, archaea, microeukaryotes) in oceans secrete a diverse array of large molecules, collectively called extracellular polymeric substances (EPSs) or simply exopolymers. These secretions facilitate attachment to surfaces that lead to the formation of structured 'biofilm' communities. In open-water environments, they also lead to formation of organic colloids, and larger aggregations of cells, called 'marine snow.' Secretion of EPS is now recognized as a fundamental microbial adaptation, occurring under many environmental conditions, and one that influences many ocean processes. This relatively recent realization has revolutionized our understanding of microbial impacts on ocean systems. EPS occur in a range of molecular sizes, conformations and physical/chemical properties, and polysaccharides, proteins, lipids, and even nucleic acids are actively secreted components. Interestingly, however, the physical ultrastructure of how individual EPS interact with each other is poorly understood. Together, the EPS matrix molecules form a three-dimensional architecture from which cells may localize extracellular activities and conduct cooperative/antagonistic interactions that cannot be accomplished efficiently by free-living cells. EPS alter optical signatures of sediments and seawater, and are involved in biogeomineral precipitation and the construction of microbial macrostructures, and horizontal-transfers of genetic information. In the water-column, they contribute to the formation of marine snow, transparent exopolymer particles (TEPs), sea-surface microlayer biofilm, and marine oil snow. Excessive production of EPS occurs during later-stages of phytoplankton blooms as an excess metabolic by product and releases a carbon pool that transitions among dissolved-, colloidal-, and gel-states. Some EPS are highly labile carbon forms, while other forms appear quite refractory to degradation. Emerging studies suggest that EPS contribute to efficient trophic-transfer of environmental contaminants, and may provide a protective refugia for pathogenic cells within marine systems; one that enhances their survival/persistence. Finally, these secretions are prominent in 'extreme' environments ranging from sea-ice communities to hypersaline systems to the high-temperatures/pressures of hydrothermal-vent systems. This overview summarizes some of the roles of exopolymer in oceans.
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Affiliation(s)
- Alan W. Decho
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, ColumbiaSC, United States
| | - Tony Gutierrez
- School of Engineering and Physical Sciences, Heriot-Watt UniversityEdinburgh, United Kingdom
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109
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Saghaï A, Gutiérrez-Preciado A, Deschamps P, Moreira D, Bertolino P, Ragon M, López-García P. Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond. Environ Microbiol 2017; 19:2405-2421. [PMID: 28489281 DOI: 10.1111/1462-2920.13754] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 04/02/2017] [Accepted: 04/03/2017] [Indexed: 01/09/2023]
Abstract
Modern phototrophic microbial mats are complex communities often used as analogs of major Precambrian ecosystems. Characterizing biotic, notably metabolic, interactions among different microbial mat members is essential to gain insights into the ecology and biogeochemistry of these systems. We applied 16S/18S rRNA metabarcoding approaches to characterize the structure of archaea, bacteria and protist communities from microbial mats collected along strong physicochemical (oxygen, salinity, temperature, depth) gradients in a shallow pond at the salar de Llamara (Chile). All mats were highly diverse, including members of virtually all known high-rank eukaryotic and prokaryotic taxa but also many novel lineages. Bacterial candidate divisions accounted for almost 50% of sequences in deeper mats, while Archaea represented up to 40% of sequences in some mat layers. Molecular phylogenetic analyses revealed six novel deeply divergent archaeal groups, along abundant and diverse Pacearchaeota and Woesearchaeota. Multivariate statistical analyses showed that local environmental conditions strongly influenced community composition. Co-occurrence network structure was markedly different between surface mats located in the oxygenated zone and mats located in transition and anoxic water layers. We identified potential biotic interactions between various high- and low-rank taxa. Notably, a strong positive correlation was observed between Lokiarchaeota and the poorly known candidate bacterial division TA06.
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Affiliation(s)
- Aurélien Saghaï
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Ana Gutiérrez-Preciado
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Philippe Deschamps
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Paola Bertolino
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Marie Ragon
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
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110
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Louyakis AS, Mobberley JM, Vitek BE, Visscher PT, Hagan PD, Reid RP, Kozdon R, Orland IJ, Valley JW, Planavsky NJ, Casaburi G, Foster JS. A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses. ASTROBIOLOGY 2017; 17:413-430. [PMID: 28520472 PMCID: PMC5767104 DOI: 10.1089/ast.2016.1563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thrombolites are buildups of carbonate that exhibit a clotted internal structure formed through the interactions of microbial mats and their environment. Despite recent advances, we are only beginning to understand the microbial and molecular processes associated with their formation. In this study, a spatial profile of the microbial and metabolic diversity of thrombolite-forming mats of Highborne Cay, The Bahamas, was generated by using 16S rRNA gene sequencing and predictive metagenomic analyses. These molecular-based approaches were complemented with microelectrode profiling and in situ stable isotope analysis to examine the dominant taxa and metabolic activities within the thrombolite-forming communities. Analyses revealed three distinctive zones within the thrombolite-forming mats that exhibited stratified populations of bacteria and archaea. Predictive metagenomics also revealed vertical profiles of metabolic capabilities, such as photosynthesis and carboxylic and fatty acid synthesis within the mats that had not been previously observed. The carbonate precipitates within the thrombolite-forming mats exhibited isotopic geochemical signatures suggesting that the precipitation within the Bahamian thrombolites is photosynthetically induced. Together, this study provides the first look at the spatial organization of the microbial populations within Bahamian thrombolites and enables the distribution of microbes to be correlated with their activities within modern thrombolite systems. Key Words: Thrombolites-Microbial diversity-Metagenome-Stable isotopes-Microbialites. Astrobiology 17, 413-430.
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Affiliation(s)
- Artemis S. Louyakis
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
| | - Jennifer M. Mobberley
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
| | - Brooke E. Vitek
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Pieter T. Visscher
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut
| | - Paul D. Hagan
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - R. Pamela Reid
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Reinhard Kozdon
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin
| | - Ian J. Orland
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin
| | - John W. Valley
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin
| | - Noah J. Planavsky
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut
| | - Giorgio Casaburi
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
| | - Jamie S. Foster
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
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111
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Kurth D, Amadio A, Ordoñez OF, Albarracín VH, Gärtner W, Farías ME. Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis. Sci Rep 2017; 7:1024. [PMID: 28432307 PMCID: PMC5430908 DOI: 10.1038/s41598-017-00896-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/16/2017] [Indexed: 11/09/2022] Open
Abstract
Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa's stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences. A functional analysis indicated that carbon fixation might occur not only by the Calvin-Benson cycle, but also through alternative pathways such as the reverse TCA cycle, and the reductive acetyl-CoA pathway. Deltaproteobacteria were involved both in sulfate reduction and nitrogen fixation. Significant differences were found when comparing the Socompa stromatolite metagenome to the Shark Bay (Australia) smooth mat metagenome: namely, those involving stress related processes, particularly, arsenic resistance. An in-depth analysis revealed a surprisingly diverse metabolism comprising all known types of As resistance and energy generating pathways. While the ars operon was the main mechanism, an important abundance of arsM genes was observed in selected phyla. The data resulting from this work will prove a cornerstone for further studies on this rare microbial community.
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Affiliation(s)
- Daniel Kurth
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT Tucumán, CONICET, San Miguel de Tucumán, Argentina
| | - Ariel Amadio
- E.E.A. Rafaela, Instituto Nacional de Tecnología Agropecuaria (INTA), CCT Santa Fe, CONICET, Rafaela, Argentina
| | - Omar F Ordoñez
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT Tucumán, CONICET, San Miguel de Tucumán, Argentina
| | - Virginia H Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT Tucumán, CONICET, San Miguel de Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Wolfgang Gärtner
- Max-Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - María E Farías
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT Tucumán, CONICET, San Miguel de Tucumán, Argentina.
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112
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Wong HL, Visscher PT, White RA, Smith DL, Patterson MM, Burns BP. Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes. Sci Rep 2017; 7:46160. [PMID: 28397816 PMCID: PMC5387419 DOI: 10.1038/srep46160] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/09/2017] [Indexed: 01/07/2023] Open
Abstract
The role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of putative niches in these systems. In the present study, high throughput amplicon sequencing was undertaken in conjunction with analysis of key biogeochemical properties of two mats (smooth and pustular) from Shark Bay, Australia. One-way analysis of similarity tests indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1%). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Pustular mats were enriched with Halobacteria and Parvarchaeota. Key metabolisms (bacterial and archaeal) were measured, and the rates of oxygen production/consumption and sulfate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic layers and was up to seven-fold higher in smooth than pustular mats. The finding of an abundance of anaerobic methanogens enriched at the surface where oxygen levels were highest, coupled with peak methane production in the oxic zone, suggests putative surface anoxic niches in these microbial mats.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Pieter T Visscher
- Department of Marine Sciences, University of Connecticut, USA.,Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Richard Allen White
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Daniela-Lee Smith
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | | | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
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113
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Zhu Y, Ma N, Jin W, Wu S, Sun C. Genomic and Transcriptomic Insights into Calcium Carbonate Biomineralization by Marine Actinobacterium Brevibacterium linens BS258. Front Microbiol 2017; 8:602. [PMID: 28428780 PMCID: PMC5382220 DOI: 10.3389/fmicb.2017.00602] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/23/2017] [Indexed: 01/31/2023] Open
Abstract
Calcium carbonate (CaCO3) biomineralization has been investigated due to its wide range of scientific and technological implications, however, the molecular mechanisms of this important geomicrobiological process are largely unknown. Here, a urease-positive marine actinobacterium Brevibacterium linens BS258 was demonstrated to effectively form CaCO3 precipitates. Surprisingly, this bacterium could also dissolve the formed CaCO3 with the increase of the Ca2+ concentration. To disclose the mechanisms of biomineralization, the genome of B. linens BS258 was further completely sequenced. Interestingly, the expression of three carbonic anhydrases was significantly up-regulated along with the increase of Ca2+ concentration and the extent of calcite dissolution. Moreover, transcriptome analyses revealed that increasing concentration of Ca2+ induced KEGG pathways including quorum sensing (QS) in B. linens BS258. Notably, most up-regulated genes related to QS were found to encode peptide/nickel ABC transporters, which suggested that nickel uptake and its associated urease stimulation were essential to boost CaCO3 biomineralization. Within the genome of B. linens BS258, there are both cadmium and lead resistance gene clusters. Therefore, the sequestration abilities of Cd2+ and Pb2+ by B. linens BS258 were checked. Consistently, Pb2+ and Cd2+ could be effectively sequestered with the precipitation of calcite by B. linens BS258. To our knowledge, this is the first study investigating the microbial CaCO3 biomineralization from both genomic and transcriptomic insights, which paves the way to disclose the relationships among bacterial metabolisms and the biomineralization.
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Affiliation(s)
- Yuying Zhu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of SciencesQingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
- College of Earth Science, University of Chinese Academy of SciencesBeijing, China
| | - Ning Ma
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of SciencesQingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
- College of Earth Science, University of Chinese Academy of SciencesBeijing, China
| | - Weihua Jin
- College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Shimei Wu
- College of Life Sciences, Qingdao UniversityQingdao, China
| | - Chaomin Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of SciencesQingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
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114
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The Effect Of microbial Mats In The Decay Of Anurans With Implications For Understanding Taphonomic Processes In The Fossil Record. Sci Rep 2017; 7:45160. [PMID: 28338095 PMCID: PMC5364532 DOI: 10.1038/srep45160] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/20/2017] [Indexed: 11/18/2022] Open
Abstract
The pattern and sequence of the decomposition of the Pipidae African dwarf frog (Hymenochirus boettgeri) is tracked in an experiment with microbial mats in order to explore soft tissue preservation over three years. Frog decay in microbial mats is preceded by rapid entombment (25–30 days) and mediated by the formation of a sarcophagus, which is built by a complex microbial community. The frog carcasses maintained a variety of soft tissues for years. Labile organic structures show greater durability within the mat, cells maintain their general shape (bone marrow cells and adipocytes), and muscles and connective tissues (adipose and fibrous tendons) exhibit their original organic structures. In addition, other soft tissues are promptly mineralized (day 540) in a Ca-rich carbonate phase (encephalic tectum) or enriched in sulphur residues (integumentary system). The result is coherent with a bias in soft-tissue preservation, as some tissues are more likely to be conserved than others. The outcomes support observations of exceptionally preserved fossil anurans (adults and tadpoles). Decomposition in mats shows singular conditions of pH and dissolved oxygen. Mineralization processes could be more diverse than in simple heterotrophic biofilms, opening new taphonomic processes that have yet to be explored.
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115
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Sforna MC, Daye M, Philippot P, Somogyi A, van Zuilen MA, Medjoubi K, Gérard E, Jamme F, Dupraz C, Braissant O, Glunk C, Visscher PT. Patterns of metal distribution in hypersaline microbialites during early diagenesis: Implications for the fossil record. GEOBIOLOGY 2017; 15:259-279. [PMID: 27935656 DOI: 10.1111/gbi.12218] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 09/28/2016] [Indexed: 06/06/2023]
Abstract
The use of metals as biosignatures in the fossil stromatolite record requires understanding of the processes controlling the initial metal(loid) incorporation and diagenetic preservation in living microbialites. Here, we report the distribution of metals and the organic fraction within the lithifying microbialite of the hypersaline Big Pond Lake (Bahamas). Using synchrotron-based X-ray microfluorescence, confocal, and biphoton microscopies at different scales (cm-μm) in combination with traditional geochemical analyses, we show that the initial cation sorption at the surface of an active microbialite is governed by passive binding to the organic matrix, resulting in a homogeneous metal distribution. During early diagenesis, the metabolic activity in deeper microbialite layers slows down and the distribution of the metals becomes progressively heterogeneous, resulting from remobilization and concentration as metal(loid)-enriched sulfides, which are aligned with the lamination of the microbialite. In addition, we were able to identify globules containing significant Mn, Cu, Zn, and As enrichments potentially produced through microbial activity. The similarity of the metal(loid) distributions observed in the Big Pond microbialite to those observed in the Archean stromatolites of Tumbiana provides the foundation for a conceptual model of the evolution of the metal distribution through initial growth, early diagenesis, and fossilization of a microbialite, with a potential application to the fossil record.
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Affiliation(s)
- M C Sforna
- Geobiosphère Actuelle & Primitive, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, CNRS, Paris, France
- Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia, Modena, Italy
| | - M Daye
- Geobiosphère Actuelle & Primitive, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, CNRS, Paris, France
- Synchrotron Soleil, Gif-sur-Yvette, France
| | - P Philippot
- Geobiosphère Actuelle & Primitive, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, CNRS, Paris, France
| | - A Somogyi
- Synchrotron Soleil, Gif-sur-Yvette, France
| | - M A van Zuilen
- Geomicrobiologie, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, CNRS, Paris, France
| | - K Medjoubi
- Synchrotron Soleil, Gif-sur-Yvette, France
| | - E Gérard
- Geomicrobiologie, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, CNRS, Paris, France
| | - F Jamme
- Synchrotron Soleil, Gif-sur-Yvette, France
| | - C Dupraz
- Department of Geological Sciences, Stockholms Universitet, Stockholm, Sweden
| | - O Braissant
- Center for Biomechanics and Biocalorimetry, University of Basel, Basel, Switzerland
| | - C Glunk
- Societe Suisse des Explosifs SA, Brig, Switzerland
| | - P T Visscher
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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116
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Ben Hania W, Joseph M, Bunk B, Spröer C, Klenk HP, Fardeau ML, Spring S. Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria. Environ Microbiol 2017; 19:1134-1148. [PMID: 27943642 DOI: 10.1111/1462-2920.13639] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/26/2016] [Accepted: 12/01/2016] [Indexed: 01/26/2023]
Abstract
The anaerobic, mesophilic and moderately halophilic strain L21-Spi-D4T was recently isolated from the suboxic zone of a hypersaline cyanobacterial mat using protein-rich extracts of Arthrospira (formerly Spirulina) platensis as substrate. Phylogenetic analyses based on 16S rRNA genes indicated an affiliation of the novel strain with the Bacteroidetes clade MgMjR-022, which is widely distributed and abundant in hypersaline microbial mats and heretofore comprised only sequences of uncultured bacteria. Analyses of the complete genome sequence of strain L21-Spi-D4T revealed a possible specialization on the degradation of cyanobacterial biomass. Besides genes for enzymes degrading specific cyanobacterial proteins a conspicuous transport complex for the polypeptide cyanophycin could be identified that is homologous to typical polysaccharide utilization loci of Bacteroidetes. A distinct and reproducible co-occurrence pattern of environmental 16S rRNA gene sequences of the MgMjR-022 clade and cyanobacteria in the suboxic zone of hypersaline mats points to a specific dependence of members of this clade on decaying cyanobacteria. Based on a comparative analysis of phenotypic, genomic and ecological characteristics we propose to establish the novel taxa Salinivirga cyanobacteriivorans gen. nov., sp. nov., represented by the type strain L21-Spi-D4T , and Salinivirgaceae fam. nov., comprising sequences of the MgMjR-022 clade.
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Affiliation(s)
- Wajdi Ben Hania
- Laboratoire de Microbiologie IRD, MIO, Aix Marseille Université, Marseille, France
| | - Manon Joseph
- Laboratoire de Microbiologie IRD, MIO, Aix Marseille Université, Marseille, France
| | - Boyke Bunk
- Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Marie-Laure Fardeau
- Laboratoire de Microbiologie IRD, MIO, Aix Marseille Université, Marseille, France
| | - Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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117
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Lindsay MR, Anderson C, Fox N, Scofield G, Allen J, Anderson E, Bueter L, Poudel S, Sutherland K, Munson-McGee JH, Van Nostrand JD, Zhou J, Spear JR, Baxter BK, Lageson DR, Boyd ES. Microbialite response to an anthropogenic salinity gradient in Great Salt Lake, Utah. GEOBIOLOGY 2017; 15:131-145. [PMID: 27418462 DOI: 10.1111/gbi.12201] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 06/10/2016] [Indexed: 06/06/2023]
Abstract
A railroad causeway across Great Salt Lake, Utah (GSL), has restricted water flow since its construction in 1959, resulting in a more saline North Arm (NA; 24%-31% salinity) and a less saline South Arm (SA; 11%-14% salinity). Here, we characterized microbial carbonates collected from the SA and the NA to evaluate the effect of increased salinity on community composition and abundance and to determine whether the communities present in the NA are still actively precipitating carbonate or if they are remnant features from prior to causeway construction. SSU rRNA gene abundances associated with the NA microbialite were three orders of magnitude lower than those associated with the SA microbialite, indicating that the latter community is more productive. SSU rRNA gene sequencing and functional gene microarray analyses indicated that SA and NA microbialite communities are distinct. In particular, abundant sequences affiliated with photoautotrophic taxa including cyanobacteria and diatoms that may drive carbonate precipitation and thus still actively form microbialites were identified in the SA microbialite; sequences affiliated with photoautotrophic taxa were in low abundance in the NA microbialite. SA and NA microbialites comprise smooth prismatic aragonite crystals. However, the SA microbialite also contained micritic aragonite, which can be formed as a result of biological activity. Collectively, these observations suggest that NA microbialites are likely to be remnant features from prior to causeway construction and indicate a strong decrease in the ability of NA microbialite communities to actively precipitate carbonate minerals. Moreover, the results suggest a role for cyanobacteria and diatoms in carbonate precipitation and microbialite formation in the SA of GSL.
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Affiliation(s)
- M R Lindsay
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - C Anderson
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - N Fox
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - G Scofield
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - J Allen
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - E Anderson
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - L Bueter
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - S Poudel
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - K Sutherland
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - J H Munson-McGee
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - J D Van Nostrand
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - J Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J R Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
- NASA Astrobiology Institute, Mountain View, CA, USA
| | - B K Baxter
- Department of Biology, Westminster College, Salt Lake City, UT, USA
| | - D R Lageson
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - E S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
- NASA Astrobiology Institute, Mountain View, CA, USA
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118
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Pseudo-Second-Order Calcium-Mediated Cryptosporidium parvum Oocyst Attachment to Environmental Biofilms. Appl Environ Microbiol 2016; 83:AEM.02339-16. [PMID: 27793825 DOI: 10.1128/aem.02339-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/17/2016] [Indexed: 12/31/2022] Open
Abstract
Cryptosporidium parvum oocysts are able to infect a wide range of mammals, including humans, via fecal-oral transmission. The remobilization of biofilm-associated C. parvum oocysts back into the water column by biofilm sloughing or bulk erosion poses a threat to public health and may be responsible for waterborne outbreaks; thus, the investigation of C. parvum attachment mechanisms to biofilms, particularly the physical and chemical factors controlling oocyst attachment to biofilms, is essential to predict the behavior of oocysts in the environment. In our study, biofilms were grown in rotating annular bioreactors using prefiltered stream water (0.2-μm retention) and rock biofilms (6-μm retention) until the mean biofilm thickness reached steady state. Oocyst deposition followed a calcium-mediated pseudo-second-order kinetic model. Kinetic parameters (i.e., initial oocyst deposition rate constant and total number of oocysts adhered to biofilms at equilibrium) from the model were then used to evaluate the impact of water conductivity on the attachment of oocysts to biofilms. Oocyst deposition was independent of solution ionic strength; instead, the presence of calcium enhanced oocyst attachment, as demonstrated by deposition tests. Calcium was identified as the predominant factor that bridges the carboxylic functional groups on biofilm and oocyst surfaces to cause attachment. The pseudo-second-order kinetic profile fit all experimental conditions, regardless of water chemistry and/or lighting conditions. IMPORTANCE The cation bridging model in our study provides new insights into the impact of calcium on the attachment of C. parvum oocysts to environmental biofilms. The kinetic parameters derived from the model could be further analyzed to elucidate the behavior of oocysts in commonly encountered complex aquatic systems, which will enable future innovations in parasite detection and treatment technologies to protect public health.
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119
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Stolz JF. Gaia and her microbiome. FEMS Microbiol Ecol 2016; 93:fiw247. [DOI: 10.1093/femsec/fiw247] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/03/2016] [Accepted: 12/07/2016] [Indexed: 01/09/2023] Open
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120
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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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121
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Fernandez AB, Rasuk MC, Visscher PT, Contreras M, Novoa F, Poire DG, Patterson MM, Ventosa A, Farias ME. Microbial Diversity in Sediment Ecosystems (Evaporites Domes, Microbial Mats, and Crusts) of Hypersaline Laguna Tebenquiche, Salar de Atacama, Chile. Front Microbiol 2016; 7:1284. [PMID: 27597845 PMCID: PMC4992683 DOI: 10.3389/fmicb.2016.01284] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/04/2016] [Indexed: 02/01/2023] Open
Abstract
We combined nucleic acid-based molecular methods, biogeochemical measurements, and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity, and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions, and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea) in bulk samples, and in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity) in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB, and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum, and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems) than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity.
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Affiliation(s)
- Ana B Fernandez
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos, Centro Científico Tecnológico, CONICET Tucumán, Argentina
| | - Maria C Rasuk
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos, Centro Científico Tecnológico, CONICET Tucumán, Argentina
| | - Pieter T Visscher
- Department of Marine Sciences, University of ConnecticutGroton, CT, USA; Australian Centre for Astrobiology, University of New South WalesSydney, NSW, Australia
| | | | | | - Daniel G Poire
- Centro de Investigaciones Geológicas, Universidad Nacional de La Plata-Conicet La Plata, Argentina
| | - Molly M Patterson
- Department of Marine Sciences, University of Connecticut Groton, CT, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
| | - Maria E Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos, Centro Científico Tecnológico, CONICET Tucumán, Argentina
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122
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Warden JG, Casaburi G, Omelon CR, Bennett PC, Breecker DO, Foster JS. Characterization of Microbial Mat Microbiomes in the Modern Thrombolite Ecosystem of Lake Clifton, Western Australia Using Shotgun Metagenomics. Front Microbiol 2016; 7:1064. [PMID: 27458453 PMCID: PMC4933708 DOI: 10.3389/fmicb.2016.01064] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/24/2016] [Indexed: 12/02/2022] Open
Abstract
Microbialite-forming communities interact with the environment and influence the precipitation of calcium carbonate through their metabolic activity. The functional genes associated with these metabolic processes and their environmental interactions are therefore critical to microbialite formation. The microbiomes associated with microbialite-forming ecosystems are just now being elucidated and the extent of shared pathways and taxa across different environments is not fully known. In this study, we profiled the microbiome of microbial communities associated with lacustrine thrombolites located in Lake Clifton, Western Australia using metagenomic sequencing and compared it to the non-lithifying mats associated with surrounding sediments to determine whether differences in the mat microbiomes, particularly with respect to metabolic pathways and environmental interactions, may potentially contribute to thrombolite formation. Additionally, we used stable isotope biosignatures to delineate the dominant metabolism associated with calcium carbonate precipitation in the thrombolite build-ups. Results indicated that the microbial community associated with the Lake Clifton thrombolites was predominantly bacterial (98.4%) with Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria comprising the majority of annotated reads. Thrombolite-associated mats were enriched in photoautotrophic taxa and functional genes associated with photosynthesis. Observed δ13C values of thrombolite CaCO3 were enriched by at least 3.5‰ compared to theoretical values in equilibrium with lake water DIC, which is consistent with the occurrence of photoautotrophic activity in thrombolite-associated microbial mats. In contrast, the microbiomes of microbial communities found on the sandy non-lithifying sediments of Lake Clifton represented distinct microbial communities that varied in taxa and functional capability and were enriched in heterotrophic taxa compared to the thrombolite-associated mats. This study provides new insight into the taxa and functional capabilities that differentiate potentially lithifying mats from other non-lithifying types and suggests that thrombolites are actively accreting and growing in limited areas of Lake Clifton.
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Affiliation(s)
- John G Warden
- Department of Geological Sciences, University of Texas at Austin, AustinTX, USA; Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt IslandFL, USA
| | - Giorgio Casaburi
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt Island FL, USA
| | - Christopher R Omelon
- Department of Geological Sciences, University of Texas at Austin, Austin TX, USA
| | - Philip C Bennett
- Department of Geological Sciences, University of Texas at Austin, Austin TX, USA
| | - Daniel O Breecker
- Department of Geological Sciences, University of Texas at Austin, Austin TX, USA
| | - Jamie S Foster
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt Island FL, USA
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Cerqueda-García D, Falcón LI. Metabolic potential of microbial mats and microbialites: Autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources. J Bioinform Comput Biol 2016; 14:1650020. [PMID: 27324427 DOI: 10.1142/s0219720016500207] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Microbialites and microbial mats are complex communities with high phylogenetic diversity. These communities are mostly composed of bacteria and archaea, which are the earliest living forms on Earth and relevant to biogeochemical evolution. In this study, we identified the shared metabolic pathways for uptake of inorganic C and N in microbial mats and microbialites based on metagenomic data sets. An in silico analysis for autotrophic pathways was used to trace the paths of C and N to the system, following an elementary flux modes (EFM) approach, resulting in a stoichiometric model. The fragility was analyzed by the minimal cut sets method. We found four relevant pathways for the incorporation of CO2 (Calvin cycle, reverse tricarboxylic acid cycle, reductive acetyl-CoA pathway, and dicarboxylate/4-hydroxybutyrate cycle), some of them present only in archaea, while nitrogen fixation was the most important source of N to the system. The metabolic potential to incorporate nitrate to biomass was also relevant. The fragility of the network was low, suggesting a high redundancy of the autotrophic pathways due to their broad metabolic diversity, and highlighting the relevance of reducing power source. This analysis suggests that microbial mats and microbialites are "metabolic pumps" for the incorporation of inorganic gases and formation of organic matter.
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Affiliation(s)
- Daniel Cerqueda-García
- 1 Universidad Nacional Autónoma de México, Instituto de Ecología, Circuito Exterior, Ciudad Universitaria, Distrito Federal 04510, Mexico
| | - Luisa I Falcón
- 1 Universidad Nacional Autónoma de México, Instituto de Ecología, Circuito Exterior, Ciudad Universitaria, Distrito Federal 04510, Mexico
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Chan CS, McAllister SM, Leavitt AH, Glazer BT, Krepski ST, Emerson D. The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments. Front Microbiol 2016; 7:796. [PMID: 27313567 PMCID: PMC4888753 DOI: 10.3389/fmicb.2016.00796] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/11/2016] [Indexed: 11/13/2022] Open
Abstract
Microbes form mats with architectures that promote efficient metabolism within a particular physicochemical environment, thus studying mat structure helps us understand ecophysiology. Despite much research on chemolithotrophic Fe-oxidizing bacteria, Fe mat architecture has not been visualized because these delicate structures are easily disrupted. There are striking similarities between the biominerals that comprise freshwater and marine Fe mats, made by Beta- and Zetaproteobacteria, respectively. If these biominerals are assembled into mat structures with similar functional morphology, this would suggest that mat architecture is adapted to serve roles specific to Fe oxidation. To evaluate this, we combined light, confocal, and scanning electron microscopy of intact Fe microbial mats with experiments on sheath formation in culture, in order to understand mat developmental history and subsequently evaluate the connection between Fe oxidation and mat morphology. We sampled a freshwater sheath mat from Maine and marine stalk and sheath mats from Loihi Seamount hydrothermal vents, Hawaii. Mat morphology correlated to niche: stalks formed in steeper O2 gradients while sheaths were associated with low to undetectable O2 gradients. Fe-biomineralized filaments, twisted stalks or hollow sheaths, formed the highly porous framework of each mat. The mat-formers are keystone species, with nascent marine stalk-rich mats comprised of novel and uncommon Zetaproteobacteria. For all mats, filaments were locally highly parallel with similar morphologies, indicating that cells were synchronously tracking a chemical or physical cue. In the freshwater mat, cells inhabited sheath ends at the growing edge of the mat. Correspondingly, time lapse culture imaging showed that sheaths are made like stalks, with cells rapidly leaving behind an Fe oxide filament. The distinctive architecture common to all observed Fe mats appears to serve specific functions related to chemolithotrophic Fe oxidation, including (1) removing Fe oxyhydroxide waste without entombing cells or clogging flow paths through the mat and (2) colonizing niches where Fe(II) and O2 overlap. This work improves our understanding of Fe mat developmental history and how mat morphology links to metabolism. We can use these results to interpret biogenicity, metabolism, and paleoenvironmental conditions of Fe microfossil mats, which would give us insight into Earth's Fe and O2 history.
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Affiliation(s)
- Clara S Chan
- School of Marine Science and Policy, University of DelawareNewark, DE, USA; Geological Sciences, University of DelawareNewark, DE, USA
| | - Sean M McAllister
- School of Marine Science and Policy, University of DelawareNewark, DE, USA; Geological Sciences, University of DelawareNewark, DE, USA
| | - Anna H Leavitt
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
| | - Brian T Glazer
- Department of Oceanography, University of Hawaii Honolulu, HI, USA
| | - Sean T Krepski
- Geological Sciences, University of Delaware Newark, DE, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
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Iniesto M, Buscalioni ÁD, Carmen Guerrero M, Benzerara K, Moreira D, López-Archilla AI. Involvement of microbial mats in early fossilization by decay delay and formation of impressions and replicas of vertebrates and invertebrates. Sci Rep 2016; 6:25716. [PMID: 27162204 PMCID: PMC4861970 DOI: 10.1038/srep25716] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 04/21/2016] [Indexed: 01/31/2023] Open
Abstract
Microbial mats have been hypothesized to improve the persistence and the preservation of organic remains during fossilization processes. We test this hypothesis with long-term experiments (up to 5.5 years) using invertebrate and vertebrate corpses. Once placed on mats, the microbial community coats the corpses and forms a three-dimensional sarcophagus composed of microbial cells and exopolymeric substances (EPS). This coverage provides a template for i) moulding superficial features, resulting in negative impressions, and ii) generating replicas. The impressions of fly setulae, fish scales and frog skin verrucae are shaped mainly by small cells in an EPS matrix. Microbes also replicate delicate structures such as the three successive layers that compose a fish eye. The sarcophagus protects the body integrity, allowing the persistence of inner organs such as the ovaries and digestive apparatus in flies, the swim bladder and muscles in fish, and the bone marrow in frog legs. This study brings strong experimental evidence to the idea that mats favour metazoan fossilization by moulding, replicating and delaying decay. Rapid burial has classically been invoked as a mechanism to explain exceptional preservation. However, mats may play a similar role during early fossilization as they can preserve complex features for a long time.
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Affiliation(s)
- Miguel Iniesto
- Department of Ecology, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | | | - M Carmen Guerrero
- Department of Ecology, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie, Sorbonne Universités, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7590, Université Pierre et Marie Curie Paris 06, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement Unité Mixte de Recherche 206, 75005 Paris, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8079, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
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Canfora L, Vendramin E, Vittori Antisari L, Lo Papa G, Dazzi C, Benedetti A, Iavazzo P, Adamo P, Jungblut AD, Pinzari F. Compartmentalization of gypsum and halite associated with cyanobacteria in saline soil crusts. FEMS Microbiol Ecol 2016; 92:fiw080. [PMID: 27090760 DOI: 10.1093/femsec/fiw080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2016] [Indexed: 11/14/2022] Open
Abstract
The interface between biological and geochemical components in the surface crust of a saline soil was investigated using X-ray diffraction, and variable pressure scanning electron microscopy in combination with energy dispersive X-ray spectrometry. Mineral compounds such as halite and gypsum were identified crystallized around filaments of cyanobacteria. A total of 92 genera were identified from the bacterial community based on 16S gene pyrosequencing analysis. The occurrence of the gypsum crystals, their shapes and compartmentalization suggested that they separated NaCl from the immediate microenvironment of the cyanobacteria, and that some cyanobacteria and communities of sulfur bacteria may had a physical control over the distinctive halite and gypsum structures produced. This suggests that cyanobacteria might directly or indirectly promote the formation of a protective envelope made of calcium and sulfur-based compounds.
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Affiliation(s)
- Loredana Canfora
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per lo studio delle relazioni tra Pianta e Suolo, Rome, Italy
| | - Elisa Vendramin
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Frutticoltura, Rome, Italy
| | | | - Giuseppe Lo Papa
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di Palermo, Italy
| | - Carmelo Dazzi
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di Palermo, Italy
| | - Anna Benedetti
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per lo studio delle relazioni tra Pianta e Suolo, Rome, Italy
| | - Pietro Iavazzo
- Dipartimento di Agraria, Università di Napoli Federico II, Portici, Italy
| | - Paola Adamo
- Dipartimento di Agraria, Università di Napoli Federico II, Portici, Italy
| | - Anne D Jungblut
- Natural History Museum, Life Sciences Department, London, UK
| | - Flavia Pinzari
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per lo studio delle relazioni tra Pianta e Suolo, Rome, Italy Natural History Museum, Life Sciences Department, London, UK
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128
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Paul VG, Wronkiewicz DJ, Mormile MR, Foster JS. Mineralogy and Microbial Diversity of the Microbialites in the Hypersaline Storr's Lake, the Bahamas. ASTROBIOLOGY 2016; 16:282-300. [PMID: 27082142 DOI: 10.1089/ast.2015.1326] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Microbialites found in the low-light-intensity, hypersaline waters of Storr's Lake (SL), San Salvador Island, the Bahamas, were investigated with respect to their morphology, mineralogy, and microbial diversity. Previously described microbialite morphologies, as well as a newly identified "multi-cuspate" morphology, were observed at various depths. Electron microscopy analysis revealed the presence of angular, blocky, and needle-shaped crystals with mineralized cyanobacterial filaments and remains of exopolymeric substances. X-ray diffraction studies confirmed the presence of both Mg-calcite and aragonite in the plateau-mushroom and pinnacle mound microbialites, whereas only Mg-calcite was identified in the other microbialite morphotypes. A comprehensive molecular analysis using barcoded pyrosequencing of five different microbial mat communities identified at least 12 dominant bacterial phyla. Cyanobacteria were generally low in abundance and ranged from ∼0.01% in the deeper pinnacle mounds to ∼3.2% in the shallow calcareous knobs. Other photosynthetic members included green nonsulfur bacteria of the phylum Chloroflexi and purple sulfur bacteria of the class Gammaproteobacteria. All mat types contained significant amounts of sulfate-reducing and dehalogenating bacteria. The low light intensity reaching the deeper microbialites, the lack of dominant cyanobacteria, and the abundance of sulfate reducers and Chloroflexi collectively suggest that sulfate reduction and anoxygenic photosynthetic processes influence the carbonate biomineralization process in these systems.
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Affiliation(s)
- Varun G Paul
- 1 Department of Geological Sciences, Missouri University of Science and Technology , Rolla, Missouri
| | - David J Wronkiewicz
- 1 Department of Geological Sciences, Missouri University of Science and Technology , Rolla, Missouri
| | - Melanie R Mormile
- 2 Department of Biological Sciences, Missouri University of Science and Technology , Rolla, Missouri
| | - Jamie S Foster
- 3 Department of Microbiology and Cell Science, University of Florida , Space Life Science Lab, Merritt Island, Florida
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129
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Ratzke C, Gore J. Self-organized patchiness facilitates survival in a cooperatively growing Bacillus subtilis population. Nat Microbiol 2016; 1:16022. [PMID: 27572641 DOI: 10.1038/nmicrobiol.2016.22] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/01/2016] [Indexed: 01/15/2023]
Abstract
Ecosystems are highly structured. Organisms are not randomly distributed but can be found in spatial aggregates at many scales, leading to spatial heterogeneity or even regular patterns(1). The widespread occurrence of these aggregates in many different ecosystems suggests that generic factors intrinsic to the populations-such as interactions between the organisms-play a major role in their emergence(1,2). Beyond the emergence of spatial patchiness, its functional consequences remain unclear. Here we show in Bacillus subtilis that cooperative interactions in a spatial environment are sufficient to form self-organized patches. These patches allow for survival even when the microbe density is too low to sustain growth in a well-mixed environment. Decreasing cell mobility leads to more compact patches that enhance this survival advantage but also reduce the overall growth. Our results highlight that even populations lacking specific group-forming mechanisms can nonetheless form spatial patterns that allow for group survival in challenging environments.
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Affiliation(s)
- Christoph Ratzke
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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130
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Corman JR, Poret-Peterson AT, Uchitel A, Elser JJ. Interaction between lithification and resource availability in the microbialites of Río Mesquites, Cuatro Ciénegas, México. GEOBIOLOGY 2016; 14:176-189. [PMID: 26663088 DOI: 10.1111/gbi.12168] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 10/20/2015] [Indexed: 06/05/2023]
Abstract
Lithified microbial structures (microbialites) have been present on Earth for billions of years. Lithification may impose unique constraints on microbes. For instance, when CaCO3 forms, phosphate may be captured via coprecipitation and/or adsorption and potentially rendered unavailable for biological uptake. Therefore, the growth of microbes associated with CaCO3 may be phosphorus-limited. In this study, we compared the effects of resource addition on biogeochemical functions of microbial communities associated with microbialites and photoautotrophic microbial communities not associated with CaCO3 deposition in Río Mesquites, Cuatro Ciénegas, México. We also manipulated rates of CaCO3 deposition in microbialites to determine whether lithification reduces the bioavailability of phosphorus (P). We found that P additions significantly increased rates of gross primary production (F2,13 = 103.9, P < 0.001), net primary production (F2,13 = 129.6, P < 0.0001) and ecosystem respiration (F2,13 = 6.44, P < 0.05) in the microbialites, while P addition had no effect on photoautotrophic production in the non-CaCO3 -associated microbial communities. Growth of the non-CaCO3-associated phototrophs was only marginally stimulated when nitrogen and P were added simultaneously (F1,36 = 3.98, P = 0.053). In the microbialites, resource additions led to some shifts in the abundance of Proteobacteria, Bacteroidetes and Cyanobacteria but mostly had little effect on bacterial community composition. Ca(2+) uptake rates increased significantly with organic carbon additions (F1,13 = 8.02, P < 0.05). Lowering of CaCO3 deposition by decreasing calcium concentrations in the water led to increased microbial biomass accumulation rates in terms of both organic carbon (F4,48 = 5.23, P < 0.01) and P (F6,48 = 13.91, P < 0.001). These results provide strong evidence in support of a role of lithification in controlling P limitation of microbialite communities.
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Affiliation(s)
- J R Corman
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - A T Poret-Peterson
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
| | - A Uchitel
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
| | - J J Elser
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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White RA, Chan AM, Gavelis GS, Leander BS, Brady AL, Slater GF, Lim DSS, Suttle CA. Metagenomic Analysis Suggests Modern Freshwater Microbialites Harbor a Distinct Core Microbial Community. Front Microbiol 2016; 6:1531. [PMID: 26903951 PMCID: PMC4729913 DOI: 10.3389/fmicb.2015.01531] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 12/21/2015] [Indexed: 11/13/2022] Open
Abstract
Modern microbialites are complex microbial communities that interface with abiotic factors to form carbonate-rich organosedimentary structures whose ancestors provide the earliest evidence of life. Past studies primarily on marine microbialites have inventoried diverse taxa and metabolic pathways, but it is unclear which of these are members of the microbialite community and which are introduced from adjacent environments. Here we control for these factors by sampling the surrounding water and nearby sediment, in addition to the microbialites and use a metagenomics approach to interrogate the microbial community. Our findings suggest that the Pavilion Lake microbialite community profile, metabolic potential and pathway distributions are distinct from those in the neighboring sediments and water. Based on RefSeq classification, members of the Proteobacteria (e.g., alpha and delta classes) were the dominant taxa in the microbialites, and possessed novel functional guilds associated with the metabolism of heavy metals, antibiotic resistance, primary alcohol biosynthesis and urea metabolism; the latter may help drive biomineralization. Urea metabolism within Pavilion Lake microbialites is a feature not previously associated in other microbialites. The microbialite communities were also significantly enriched for cyanobacteria and acidobacteria, which likely play an important role in biomineralization. Additional findings suggest that Pavilion Lake microbialites are under viral selection as genes associated with viral infection (e.g CRISPR-Cas, phage shock and phage excision) are abundant within the microbialite metagenomes. The morphology of Pavilion Lake microbialites changes dramatically with depth; yet, metagenomic data did not vary significantly by morphology or depth, indicating that microbialite morphology is altered by other factors, perhaps transcriptional differences or abiotic conditions. This work provides a comprehensive metagenomic perspective of the interactions and differences between microbialites and their surrounding environment, and reveals the distinct nature of these complex communities.
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Affiliation(s)
- Richard Allen White
- Department of Microbiology and Immunology, University of British Columbia, Vancouver BC, Canada
| | - Amy M Chan
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver BC, Canada
| | - Gregory S Gavelis
- Department of Zoology, University of British Columbia, Vancouver BC, Canada
| | - Brian S Leander
- Department of Zoology, University of British Columbia, VancouverBC, Canada; Department of Botany, University of British Columbia, VancouverBC, Canada
| | - Allyson L Brady
- School of Geography and Earth Sciences, McMaster University, Hamilton ON, Canada
| | - Gregory F Slater
- School of Geography and Earth Sciences, McMaster University, Hamilton ON, Canada
| | - Darlene S S Lim
- Bay Area Environmental Institute, PetalumaCA, USA; NASA Ames Research Center, Moffett FieldCA, USA
| | - Curtis A Suttle
- Department of Microbiology and Immunology, University of British Columbia, VancouverBC, Canada; Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, VancouverBC, Canada; Department of Botany, University of British Columbia, VancouverBC, Canada; Canadian Institute for Advanced Research, TorontoON, Canada
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132
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Zhu T, Dittrich M. Carbonate Precipitation through Microbial Activities in Natural Environment, and Their Potential in Biotechnology: A Review. Front Bioeng Biotechnol 2016; 4:4. [PMID: 26835451 PMCID: PMC4718973 DOI: 10.3389/fbioe.2016.00004] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/07/2016] [Indexed: 11/24/2022] Open
Abstract
Calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. Microbial carbonate precipitation, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. This natural process occurring in various geological settings can be mimicked and used for a number of biotechnologies, such as metal remediation, carbon sequestration, enhanced oil recovery, and construction restoration. In this study, different metabolic activities leading to calcium carbonate precipitation, their native environment, and potential applications and challenges are reviewed.
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Affiliation(s)
- Tingting Zhu
- Department of Physical and Environmental Sciences, University of Toronto Scarborough , Toronto, ON , Canada
| | - Maria Dittrich
- Department of Physical and Environmental Sciences, University of Toronto Scarborough , Toronto, ON , Canada
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133
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The Snotty and the Stringy: Energy for Subsurface Life in Caves. THEIR WORLD: A DIVERSITY OF MICROBIAL ENVIRONMENTS 2016. [DOI: 10.1007/978-3-319-28071-4_5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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134
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Tomescu AMF, Klymiuk AA, Matsunaga KKS, Bippus AC, Shelton GWK. Microbes and the Fossil Record: Selected Topics in Paleomicrobiology. THEIR WORLD: A DIVERSITY OF MICROBIAL ENVIRONMENTS 2016. [DOI: 10.1007/978-3-319-28071-4_3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Casaburi G, Duscher AA, Reid RP, Foster JS. Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis. Environ Microbiol 2015; 18:1452-69. [PMID: 26471001 DOI: 10.1111/1462-2920.13094] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 02/01/2023]
Abstract
Modern stromatolites represent ideal ecosystems to understand the biological processes required for the precipitation of carbonate due to their long evolutionary history and occurrence in a wide range of habitats. However, most of the prior molecular work on stromatolites has focused on understanding the taxonomic complexity and not fully elucidating the functional capabilities of these systems. Here, we begin to characterize the microbiome associated with stromatolites of Little Darby Island, The Bahamas using predictive metagenomics of the 16S rRNA gene coupled with direct whole shotgun sequencing. The metagenomic analysis of the Little Darby stromatolites revealed many shared taxa and core pathways associated with biologically induced carbonate precipitation, suggesting functional convergence within Bahamian stromatolites. A comparison of the Little Darby stromatolites with other lithifying microbial ecosystems also revealed that although factors, such as geographic location and salinity, do drive some differences within the population, there are extensive similarities within the microbial populations. These results suggest that for stromatolite formation, 'who' is in the community is not as critical as metabolic activities and environmental interactions. Together, these analyses help improve our understanding of the similarities among lithifying ecosystems and provide an important first step in characterizing the shared microbiome of modern stromatolites.
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Affiliation(s)
- Giorgio Casaburi
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab, Merritt Island, FL, USA
| | - Alexandrea A Duscher
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab, Merritt Island, FL, USA
| | - R Pamela Reid
- Rosenstiel School of Marine Sciences, University of Miami, Miami, FL, USA
| | - Jamie S Foster
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab, Merritt Island, FL, USA
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Gontharet S, Artigas LF, Mathieu O, Levêque J, Milloux MJ, Caillaud J, Philippe S, Lesourd S, Gardel A. Effect of emersion/immersion cycles on the elemental and isotopic compositions of the organic matter from surface sediments of an intertidal mud bank (French Guiana): a preliminary study. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:2147-2157. [PMID: 26467227 DOI: 10.1002/rcm.7377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/24/2015] [Accepted: 08/08/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE In various marine environments, the combination of elemental ratios and stable isotopic compositions is usually used to trace the sources of organic matter (OM) in sediments. However, in intertidal areas, the sediments might be temporarily exposed to air during a more or less prolonged duration and the impact of this exposure on the latter parameter is unknown. METHODS The spatial variations of atomic Total Organic Carbon (TOC) and Total Nitrogen (TN) ratios, and δ(13)C and δ(15)N values, were measured on surface sediments of French Guiana, at the beginning and the end of five consecutive days of emersion during equinoctial tides, as well as at the beginning of a new emersion phase after returning to a normal tidal cycle. The concentrations of chlorophyll a and phaeopigments in sediments were also measured, in order to estimate the influence of microphytobenthos (MPB), growing at surface sediments, on these geochemical parameters. RESULTS The results showed that the emersion/immersion cycles influenced the development of MPB at the surface sediments, which, in turn, significantly controlled the spatio-temporal changes in the atomic elemental ratios and the δ(13)C values. This variability seemed not to be significantly altered by OM degradation. On the contrary, sediments were always (15) N-enriched compared with OM sources, indicating that OM diagenetic processes mainly controlled their spatio-temporal fluctuations. CONCLUSIONS The [TOC/TN]atomic ratios and the δ(13)C values, indicating the primary signal of OM sources, represented the most reliable geochemical proxies for calculating the relative contribution of OM sources to sediments in environments characterized by variable air exposure duration. The use of δ(15)N values in such environments is limited by OM degradation processes but their variation might enable the nature and the degree of these processes to be identified.
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Affiliation(s)
- Swanne Gontharet
- CNRS UMR 8187, LOG, Laboratoire d'Océanologie et des Géosciences, Université du Littoral-Côte d'Opale, Université de Lille, 32 avenue Foch, 62930, Wimereux, France
| | - Luis Felipe Artigas
- CNRS UMR 8187, LOG, Laboratoire d'Océanologie et des Géosciences, Université du Littoral-Côte d'Opale, Université de Lille, 32 avenue Foch, 62930, Wimereux, France
| | - Olivier Mathieu
- CNRS UMR 6282, Laboratoire Biogéosciences, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Jean Levêque
- CNRS UMR 6282, Laboratoire Biogéosciences, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Marie-Jeanne Milloux
- CNRS UMR 6282, Laboratoire Biogéosciences, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Jacinthe Caillaud
- CNRS UMR 8187, LOG, Laboratoire d'Océanologie et des Géosciences, Université du Littoral-Côte d'Opale, Université de Lille, 32 avenue Foch, 62930, Wimereux, France
| | - Sylvie Philippe
- CNRS UMR 8187, LOG, Laboratoire d'Océanologie et des Géosciences, Université du Littoral-Côte d'Opale, Université de Lille, 32 avenue Foch, 62930, Wimereux, France
| | - Sandric Lesourd
- Normandie Université, UNICAEN M2C, Morphodynamique Continentale et Côtière, UMR CNRS 6143, 24 rue des Tilleuls, 14032, Caen, France
| | - Antoine Gardel
- CNRS UMR 8187, LOG, Laboratoire d'Océanologie et des Géosciences, Université du Littoral-Côte d'Opale, Université de Lille, 32 avenue Foch, 62930, Wimereux, France
- CNRS-Guyane, USR 3456, 2 avenue Gustave Charlery, 97300, Cayenne, French Guiana
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137
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Wong HL, Smith DL, Visscher PT, Burns BP. Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats. Sci Rep 2015; 5:15607. [PMID: 26499760 PMCID: PMC4620479 DOI: 10.1038/srep15607] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/28/2015] [Indexed: 02/01/2023] Open
Abstract
Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
- Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Daniela-Lee Smith
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
- Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Pieter T. Visscher
- Department of Marine Sciences, University of Connecticut, USA
- Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Brendan P. Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
- Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
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138
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Singh R, Yoon H, Sanford RA, Katz L, Fouke BW, Werth CJ. Metabolism-Induced CaCO3 Biomineralization During Reactive Transport in a Micromodel: Implications for Porosity Alteration. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:12094-12104. [PMID: 26348257 DOI: 10.1021/acs.est.5b00152] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The ability of Pseudomonas stutzeri strain DCP-Ps1 to drive CaCO3 biomineralization has been investigated in a microfluidic flowcell (i.e., micromodel) that simulates subsurface porous media. Results indicate that CaCO3 precipitation occurs during NO3(-) reduction with a maximum saturation index (SIcalcite) of ∼1.56, but not when NO3(-) was removed, inactive biomass remained, and pH and alkalinity were adjusted to SIcalcite ∼ 1.56. CaCO3 precipitation was promoted by metabolically active cultures of strain DCP-Ps1, which at similar values of SIcalcite, have a more negative surface charge than inactive strain DCP-Ps1. A two-stage NO3(-) reduction (NO3(-) → NO2(-) → N2) pore-scale reactive transport model was used to evaluate denitrification kinetics, which was observed in the micromodel as upper (NO3(-) reduction) and lower (NO2(-) reduction) horizontal zones of biomass growth with CaCO3 precipitation exclusively in the lower zone. Model results are consistent with two biomass growth regions and indicate that precipitation occurred in the lower zone because the largest increase in pH and alkalinity is associated with NO2(-) reduction. CaCO3 precipitates typically occupied the entire vertical depth of pores and impacted porosity, permeability, and flow. This study provides a framework for incorporating microbial activity in biogeochemistry models, which often base biomineralization only on SI (caused by biotic or abiotic reactions) and, thereby, underpredict the extent of this complex process. These results have wide-ranging implications for understanding reactive transport in relevance to groundwater remediation, CO2 sequestration, and enhanced oil recovery.
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Affiliation(s)
| | - Hongkyu Yoon
- Geoscience Research and Applications, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
| | | | - Lynn Katz
- Civil, Architectural and Environmental Engineering, University of Texas at Austin , Austin, Texas 78712, United States
| | | | - Charles J Werth
- Civil, Architectural and Environmental Engineering, University of Texas at Austin , Austin, Texas 78712, United States
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139
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White RA, Power IM, Dipple GM, Southam G, Suttle CA. Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential. Front Microbiol 2015; 6:966. [PMID: 26441900 PMCID: PMC4585152 DOI: 10.3389/fmicb.2015.00966] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 08/31/2015] [Indexed: 12/15/2022] Open
Abstract
Within the subarctic climate of Clinton Creek, Yukon, Canada, lies an abandoned and flooded open-pit asbestos mine that harbors rapidly growing microbialites. To understand their formation we completed a metagenomic community profile of the microbialites and their surrounding sediments. Assembled metagenomic data revealed that bacteria within the phylum Proteobacteria numerically dominated this system, although the relative abundances of taxa within the phylum varied among environments. Bacteria belonging to Alphaproteobacteria and Gammaproteobacteria were dominant in the microbialites and sediments, respectively. The microbialites were also home to many other groups associated with microbialite formation including filamentous cyanobacteria and dissimilatory sulfate-reducing Deltaproteobacteria, consistent with the idea of a shared global microbialite microbiome. Other members were present that are typically not associated with microbialites including Gemmatimonadetes and iron-oxidizing Betaproteobacteria, which participate in carbon metabolism and iron cycling. Compared to the sediments, the microbialite microbiome has significantly more genes associated with photosynthetic processes (e.g., photosystem II reaction centers, carotenoid, and chlorophyll biosynthesis) and carbon fixation (e.g., CO dehydrogenase). The Clinton Creek microbialite communities had strikingly similar functional potentials to non-lithifying microbial mats from the Canadian High Arctic and Antarctica, but are functionally distinct, from non-lithifying mats or biofilms from Yellowstone. Clinton Creek microbialites also share metabolic genes (R2 < 0.750) with freshwater microbial mats from Cuatro Ciénegas, Mexico, but are more similar to polar Arctic mats (R2 > 0.900). These metagenomic profiles from an anthropogenic microbialite-forming ecosystem provide context to microbialite formation on a human-relevant timescale.
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Affiliation(s)
- Richard Allen White
- Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada
| | - Ian M Power
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada
| | - Gregory M Dipple
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada
| | - Gordon Southam
- School of Earth Sciences, University of Queensland Brisbane, QLD, Australia
| | - Curtis A Suttle
- Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada ; Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada ; Department of Botany, University of British Columbia Vancouver, BC, Canada ; Canadian Institute for Advanced Research Toronto, ON, Canada
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140
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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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141
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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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142
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Pagès A, Grice K, Welsh DT, Teasdale PT, Van Kranendonk MJ, Greenwood P. Lipid Biomarker and Isotopic Study of Community Distribution and Biomarker Preservation in a Laminated Microbial Mat from Shark Bay, Western Australia. MICROBIAL ECOLOGY 2015; 70:459-472. [PMID: 25812998 DOI: 10.1007/s00248-015-0598-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 03/09/2015] [Indexed: 06/04/2023]
Abstract
Modern microbial mats from Shark Bay present some structural similarities with ancient stromatolites; thus, the functionality of microbial communities and processes of diagenetic preservation of modern mats may provide an insight into ancient microbial assemblages and preservation. In this study, the vertical distribution of microbial communities was investigated in a well-laminated smooth mat from Shark Bay. Biolipid and compound-specific isotopic analyses were performed to investigate the distribution of microbial communities in four distinct layers of the mat. Biomarkers indicative of cyanobacteria were more abundant in the uppermost oxic layer. Diatom markers (e.g. C25 HBI alkene, C20:4ω6 and C20:5ω3 polar lipid fatty acids (PLFAs)) were also detected in high abundance in the uppermost layer, but also in the deepest layer under conditions of permanent darkness and anoxia, where they probably used NO3 (-) for respiration. CycC19:0, an abundant PLFA of purple sulfur bacteria (PSB), was detected in all layers and presented the most (13)C-depleted values of all PLFAs, consistent with photoautotrophic PSB. Sulfur-bound aliphatic and aromatic biomarkers were detected in all layers, highlighting the occurrence of early sulfurisation which may be an important mechanism in the sedimentary preservation of functional biolipids in living and, thus, also ancient mats.
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Affiliation(s)
- Anais Pagès
- WA Organic and Isotope Geochemistry Centre, Department of Chemistry, The Institute for Geoscience Research, Curtin University, GPO Box U1987, Perth, Western Australia, 6845, Australia,
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143
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Mobberley JM, Khodadad CLM, Visscher PT, Reid RP, Hagan P, Foster JS. Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling. Sci Rep 2015. [PMID: 26213359 PMCID: PMC4515876 DOI: 10.1038/srep12601] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Microbialites are sedimentary deposits formed by the metabolic interactions of microbes and their environment. These lithifying microbial communities represent one of the oldest ecosystems on Earth, yet the molecular mechanisms underlying the function of these communities are poorly understood. In this study, we used comparative metagenomic and metatranscriptomic analyses to characterize the spatial organization of the thrombolites of Highborne Cay, The Bahamas, an actively forming microbialite system. At midday, there were differences in gene expression throughout the spatial profile of the thrombolitic mat with a high abundance of transcripts encoding genes required for photosynthesis, nitrogen fixation and exopolymeric substance production in the upper three mm of the mat. Transcripts associated with denitrification and sulfate reduction were in low abundance throughout the depth profile, suggesting these metabolisms were less active during midday. Comparative metagenomics of the Bahamian thrombolites with other known microbialite ecosystems from across the globe revealed that, despite many shared core pathways, the thrombolites represented genetically distinct communities. This study represents the first time the metatranscriptome of living microbialite has been characterized and offers a new molecular perspective on those microbial metabolisms, and their underlying genetic pathways, that influence the mechanisms of carbonate precipitation in lithifying microbial mat ecosystems.
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Affiliation(s)
- J M Mobberley
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab-Exploration Park, Merritt Island, FL 32953
| | - C L M Khodadad
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab-Exploration Park, Merritt Island, FL 32953
| | - P T Visscher
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340
| | - R P Reid
- Rosenstiel School of Marine Sciences, University of Miami, Miami, FL, 33149
| | - P Hagan
- Rosenstiel School of Marine Sciences, University of Miami, Miami, FL, 33149
| | - J S Foster
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab-Exploration Park, Merritt Island, FL 32953
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144
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Marlow J, Peckmann J, Orphan V. Autoendoliths: a distinct type of rock-hosted microbial life. GEOBIOLOGY 2015; 13:303-307. [PMID: 25879487 DOI: 10.1111/gbi.12131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 02/21/2015] [Indexed: 06/04/2023]
Affiliation(s)
- J Marlow
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - J Peckmann
- Department of Geodynamics and Sedimentology, University of Vienna, Vienna, Austria
| | - V Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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145
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Theisen CH, Sumner DY, Mackey TJ, Lim DSS, Brady AL, Slater GF. Carbonate fabrics in the modern microbialites of Pavilion Lake: two suites of microfabrics that reflect variation in microbial community morphology, growth habit, and lithification. GEOBIOLOGY 2015; 13:357-372. [PMID: 25809931 DOI: 10.1111/gbi.12134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 02/23/2015] [Indexed: 06/04/2023]
Abstract
Modern microbialites in Pavilion Lake, BC, provide an analog for ancient non-stromatolitic microbialites that formed from in situ mineralization. Because Pavilion microbialites are mineralizing under the influence of microbial communities, they provide insights into how biological processes influence microbialite microfabrics and mesostructures. Hemispherical nodules and micrite-microbial crusts are two mesostructures within Pavilion microbialites that are directly associated with photosynthetic communities. Both filamentous cyanobacteria in hemispherical nodules and branching filamentous green algae in micrite-microbial crusts were associated with calcite precipitation at microbialite surfaces and with characteristic microfabrics in the lithified microbialite. Hemispherical nodules formed at microbialite surfaces when calcite precipitated around filamentous cyanobacteria with a radial growth habit. The radial filament pattern was preserved within the microbialite to varying degrees. Some subsurface nodules contained well-defined filaments, whereas others contained only dispersed organic inclusions. Variation in filament preservation is interpreted to reflect differences in timing and amount of carbonate precipitation relative to heterotrophic decay, with more defined filaments reflecting greater lithification prior to degradation than more diffuse filaments. Micrite-microbial crusts produce the second suite of microfabrics and form in association with filamentous green algae oriented perpendicular to the microbialite surface. Some crusts include calcified filaments, whereas others contained voids that reflect the filamentous community in shape, size, and distribution. Pavilion microbialites demonstrate that microfabric variation can reflect differences in lithification processes and microbial metabolisms as well as microbial community morphology and organization. Even when the morphology of individual filaments or cells is not well preserved, the microbial growth habit can be captured in mesoscale microbialite structures. These results suggest that when petrographic preservation is extremely good, ancient microbialite growth structures and microfabrics can be interpreted in the context of variation in community organization, community composition, and lithification history. Even in the absence of distinct microbial microfabrics, mesostructures can capture microbial community morphology.
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Affiliation(s)
- C Harwood Theisen
- Department of Earth and Planetary Sciences, University of California, Davis, CA, USA
| | - D Y Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, CA, USA
| | - T J Mackey
- Department of Earth and Planetary Sciences, University of California, Davis, CA, USA
| | - D S S Lim
- Bay Area Environmental Research Institute, Petaluma, CA, USA
- NASA Ames Research Center, Moffett Field, CA, USA
| | - A L Brady
- School of Geography and Earth Sciences, McMaster University, Hamilton, ON, Canada
| | - G F Slater
- School of Geography and Earth Sciences, McMaster University, Hamilton, ON, Canada
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146
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Wei S, Cui H, Jiang Z, Liu H, He H, Fang N. Biomineralization processes of calcite induced by bacteria isolated from marine sediments. Braz J Microbiol 2015; 46:455-64. [PMID: 26273260 PMCID: PMC4507537 DOI: 10.1590/s1517-838246220140533] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 11/16/2014] [Indexed: 11/23/2022] Open
Abstract
Biomineralization is a known natural phenomenon associated with a wide range of
bacterial species. Bacterial-induced calcium carbonate precipitation by marine
isolates was investigated in this study. Three genera of ureolytic bacteria,
Sporosarcina sp., Bacillus sp. and
Brevundimonas sp. were observed to precipitate calcium
carbonate minerals. Of these species, Sporosarcina sp.
dominated the cultured isolates. B. lentus CP28 generated
higher urease activity and facilitated more efficient precipitation of calcium
carbonate at 3.24 ± 0.25 × 10−4 mg/cell. X-ray diffraction indicated
that the dominant calcium carbonate phase was calcite. Scanning electron
microscopy showed that morphologies of the minerals were dominated by cubic,
rhombic and polygonal plate-like crystals. The dynamic process of microbial
calcium carbonate precipitation revealed that B. lentus CP28
precipitated calcite crystals through the enzymatic hydrolysis of urea, and that
when ammonium ion concentrations reached 746 mM and the pH reached 9.6, that
favored calcite precipitation at a higher level of 96 mg/L. The results of this
research provide evidence that a variety of marine bacteria can induce calcium
carbonate precipitation, and may influence the marine carbonate cycle in natural
environments.
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Affiliation(s)
- Shiping Wei
- China University of Geosciences, School of Marine Sciences, China University of Geosciences, Beijing, China, School of Marine Sciences, China University of Geosciences, Beijing, China
| | - Hongpeng Cui
- China University of Geosciences, School of Marine Sciences, China University of Geosciences, Beijing, China, School of Marine Sciences, China University of Geosciences, Beijing, China
| | - Zhenglong Jiang
- China University of Geosciences, School of Marine Sciences, China University of Geosciences, Beijing, China, School of Marine Sciences, China University of Geosciences, Beijing, China
| | - Hao Liu
- China University of Geosciences, School of Marine Sciences, China University of Geosciences, Beijing, China, School of Marine Sciences, China University of Geosciences, Beijing, China
| | - Hao He
- China University of Geosciences, School of Marine Sciences, China University of Geosciences, Beijing, China, School of Marine Sciences, China University of Geosciences, Beijing, China
| | - Nianqiao Fang
- China University of Geosciences, School of Marine Sciences, China University of Geosciences, Beijing, China, School of Marine Sciences, China University of Geosciences, Beijing, China
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147
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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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148
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Coman C, Chiriac CM, Robeson MS, Ionescu C, Dragos N, Barbu-Tudoran L, Andrei AŞ, Banciu HL, Sicora C, Podar M. Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania. Front Microbiol 2015; 6:253. [PMID: 25870594 PMCID: PMC4378309 DOI: 10.3389/fmicb.2015.00253] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/14/2015] [Indexed: 02/01/2023] Open
Abstract
Modern mineral deposits play an important role in evolutionary studies by providing clues to the formation of ancient lithified microbial communities. Here we report the presence of microbialite-forming microbial mats in different microenvironments at 32°C, 49°C, and 65°C around the geothermal spring from an abandoned oil drill in Ciocaia, Romania. The mineralogy and the macro- and microstructure of the microbialites were investigated, together with their microbial diversity based on a 16S rRNA gene amplicon sequencing approach. The calcium carbonate is deposited mainly in the form of calcite. At 32°C and 49°C, the microbialites show a laminated structure with visible microbial mat-carbonate crystal interactions. At 65°C, the mineral deposit is clotted, without obvious organic residues. Partial 16S rRNA gene amplicon sequencing showed that the relative abundance of the phylum Archaea was low at 32°C (<0.5%) but increased significantly at 65°C (36%). The bacterial diversity was either similar to other microbialites described in literature (the 32°C sample) or displayed a specific combination of phyla and classes (the 49°C and 65°C samples). Bacterial taxa were distributed among 39 phyla, out of which 14 had inferred abundances >1%. The dominant bacterial groups at 32°C were Cyanobacteria, Gammaproteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Thermi, Actinobacteria, Planctomycetes, and Defferibacteres. At 49°C, there was a striking dominance of the Gammaproteobacteria, followed by Firmicutes, Bacteroidetes, and Armantimonadetes. The 65°C sample was dominated by Betaproteobacteria, Firmicutes, [OP1], Defferibacteres, Thermi, Thermotogae, [EM3], and Nitrospirae. Several groups from Proteobacteria and Firmicutes, together with Halobacteria and Melainabacteria were described for the first time in calcium carbonate deposits. Overall, the spring from Ciocaia emerges as a valuable site to probe microbes-minerals interrelationships along thermal and geochemical gradients.
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Affiliation(s)
- Cristian Coman
- Taxonomy and Ecology, Algology, National Institute of Research and Development for Biological Sciences, Institute of Biological Research Cluj-Napoca, Romania ; Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University Cluj-Napoca, Romania
| | - Cecilia M Chiriac
- Taxonomy and Ecology, Algology, National Institute of Research and Development for Biological Sciences, Institute of Biological Research Cluj-Napoca, Romania ; Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University Cluj-Napoca, Romania
| | - Michael S Robeson
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Fish, Wildlife, and Conservation Biology, Colorado State University Fort Collins, CO, USA
| | - Corina Ionescu
- Geology Department, Faculty of Biology and Geology, Babeş-Bolyai University Cluj-Napoca, Romania ; Kazan (Volga Region) Federal University Tatarstan, Russia
| | - Nicolae Dragos
- Taxonomy and Ecology, Algology, National Institute of Research and Development for Biological Sciences, Institute of Biological Research Cluj-Napoca, Romania ; Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University Cluj-Napoca, Romania
| | - Lucian Barbu-Tudoran
- Electron Microscopy Center, Faculty of Biology and Geology, Babeş-Bolyai University Cluj-Napoca, Romania
| | - Adrian-Ştefan Andrei
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University Cluj-Napoca, Romania ; Molecular Biology Center, Institute for Interdisciplinary Research on Bio-Nano-Sciences, Babeş-Bolyai University Cluj-Napoca, Romania
| | - Horia L Banciu
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University Cluj-Napoca, Romania ; Molecular Biology Center, Institute for Interdisciplinary Research on Bio-Nano-Sciences, Babeş-Bolyai University Cluj-Napoca, Romania
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
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149
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Kaźmierczak J, Fenchel T, Kühl M, Kempe S, Kremer B, Łącka B, Małkowski K. CaCO3 precipitation in multilayered cyanobacterial mats: clues to explain the alternation of micrite and sparite layers in calcareous stromatolites. Life (Basel) 2015; 5:744-69. [PMID: 25761263 PMCID: PMC4390877 DOI: 10.3390/life5010744] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/17/2015] [Accepted: 02/25/2015] [Indexed: 11/17/2022] Open
Abstract
Marine cyanobacterial mats were cultured on coastal sediments (Nivå Bay, Øresund, Denmark) for over three years in a closed system. Carbonate particles formed in two different modes in the mat: (i) through precipitation of submicrometer-sized grains of Mg calcite within the mucilage near the base of living cyanobacterial layers, and (ii) through precipitation of a variety of mixed Mg calcite/aragonite morphs in layers of degraded cyanobacteria dominated by purple sulfur bacteria. The d13C values were about 2‰ heavier in carbonates from the living cyanobacterial zones as compared to those generated in the purple bacterial zones. Saturation indices calculated with respect to calcite, aragonite, and dolomite inside the mats showed extremely high values across the mat profile. Such high values were caused by high pH and high carbonate alkalinity generated within the mats in conjunction with increased concentrations of calcium and magnesium that were presumably stored in sheaths and extracellular polymer substances (EPS) of the living cyanobacteria and liberated during their post-mortem degradation. The generated CaCO3 morphs were highly similar to morphs reported from heterotrophic bacterial cultures, and from bacterially decomposed cyanobacterial biomass emplaced in Ca-rich media. They are also similar to CaCO3 morphs precipitated from purely inorganic solutions. No metabolically (enzymatically) controlled formation of particular CaCO3 morphs by heterotrophic bacteria was observed in the studied mats. The apparent alternation of in vivo and post-mortem generated calcareous layers in the studied cyanobacterial mats may explain the alternation of fine-grained (micritic) and coarse-grained (sparitic) laminae observed in modern and fossil calcareous cyanobacterial microbialites as the result of a probably similar multilayered mat organization.
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Affiliation(s)
- Józef Kaźmierczak
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00-818 Warsaw, Poland.
| | - Tom Fenchel
- Marine Biological Laboratory, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark.
| | - Michael Kühl
- Marine Biological Laboratory, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark.
| | - Stephan Kempe
- Institute of Applied Geosciences, Technische Universität Darmstadt, Schnittspahnstr. 9, 64287 Darmstadt, Germany.
| | - Barbara Kremer
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00-818 Warsaw, Poland.
| | - Bożena Łącka
- Institute of Geological Sciences, Polish Academy of Sciences, Twarda 51/55, 00-818 Warsaw, Poland.
| | - Krzysztof Małkowski
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00-818 Warsaw, Poland.
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150
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Della Porta G. Carbonate build-ups in lacustrine, hydrothermal and fluvial settings: comparing depositional geometry, fabric types and geochemical signature. ACTA ACUST UNITED AC 2015. [DOI: 10.1144/sp418.4] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractCarbonate build-ups in lakes, hydrothermal and fluvial settings are characterized by distinctive geometry, spatial distribution, fabrics and geochemical signature but also by some comparable features. Lake margin bioherms form continuous belts for hundreds of metres to kilometres, subparallel to shorelines. Sublacustrine spring mounds are spaced at hundreds of metres to kilometres and aligned along faults. Hydrothermal travertine mounds and aprons with planar clinoforms or terraced slopes are controlled by faults, thermal water discharge and substrate topography. Fluvial tufa barrages, cascades and terraced slopes are controlled by climate, vegetation and substrate gradient. The wide spectrum of carbonate microfabrics ranges from clotted peloidal micrite and laminated boundstone to crystalline dendrite cementstone. Non-marine carbonate microfabrics cannot be linked to specific depositional environments, and are not deterministic proxies for the interpretation of build-up architecture. Microfabric associations can be indicative, but not exclusive, of specific depositional environments and geometry. Stable isotope geochemistry is a useful tool to distinguish between hydrothermal, karstic freshwater and evaporative lake carbonates. Carbonate precipitation results from a continuum of abiotic and biologically influenced/induced processes in settings where carbonate supersaturation is largely driven by physico-chemical mechanisms and microbial biofilms, even if acting as passive low-energy surface sites for nucleation, are widely present.
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