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Osman JR, Castillo J, Sanhueza V, Miller AZ, Novoselov A, Cotoras D, Morales D. Key energy metabolisms in modern living microbialites from hypersaline Andean lagoons of the Salar de Atacama, Chile. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 937:173469. [PMID: 38788953 DOI: 10.1016/j.scitotenv.2024.173469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/28/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Microbialites are organosedimentary structures formed mainly due to the precipitation of carbonate minerals, although they can also incorporate siliceous, phosphate, ferric, and sulfate minerals. The minerals' precipitation occurs because of local chemical changes triggered by changes in pH and redox transformations catalyzed by the microbial energy metabolisms. Here, geochemistry, metagenomics, and bioinformatics tools reveal the key energy metabolisms of microbial mats, stromatolites and an endoevaporite distributed across four hypersaline lagoons from the Salar de Atacama. Chemoautotrophic and chemoheterotrophic microorganisms seem to coexist and influence microbialite formation. The microbialite types of each lagoon host unique microbial communities and metabolisms that influence their geochemistry. Among them, photosynthetic, carbon- and nitrogen- fixing and sulfate-reducing microorganisms appear to control the main biogeochemical cycles. Genes associated with non-conventional energy pathways identified in MAGs, such as hydrogen production/consumption, arsenic oxidation/reduction, manganese oxidation and selenium reduction, also contribute to support life in microbialites. The presence of genes encoding for enzymes associated with ureolytic processes in the Cyanobacteria phylum and Gammaproteobacteria class might induce carbonate precipitation in hypersaline environments, contributing to the microbialites formation. To the best of our knowledge, this is the first study characterizing metagenomically microbialites enriched in manganese and identifying metabolic pathways associated with manganese oxidation, selenium reduction, and ureolysis in this ecosystem, which suggests that the geochemistry and bioavailability of energy sources (As, Mn and Se) shapes the microbial metabolisms in the microbialites.
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Affiliation(s)
- Jorge R Osman
- Instituto de Geología Económica Aplicada (GEA), Universidad de Concepción, Concepción, Chile.
| | - Julio Castillo
- University of the Free State, Department of Microbiology and Biochemistry, Bloemfontein, South Africa
| | - Vilma Sanhueza
- Instituto de Geología Económica Aplicada (GEA), Universidad de Concepción, Concepción, Chile
| | - Ana Z Miller
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Av. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Alexey Novoselov
- Instituto de Geología Económica Aplicada (GEA), Universidad de Concepción, Concepción, Chile
| | - Davor Cotoras
- Laboratorio de Microbiología y Biotecnología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont #964, Independencia, Santiago, Chile
| | - Daniela Morales
- Instituto de Geología Económica Aplicada (GEA), Universidad de Concepción, Concepción, Chile
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2
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Potvin M, Gauthier J, Langevin C, Mohit V, da Costa NB, Deschênes T, Pomerleau M, Kukavica-Ibrulj I, Verreault D, Comte J, Levesque RC. Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing. Front Microbiol 2023; 14:1267652. [PMID: 38029199 PMCID: PMC10646836 DOI: 10.3389/fmicb.2023.1267652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
With the increasing occurrence and severity of cyanobacterial harmful algal blooms (cHAB) at the global scale, there is an urgent need for rapid, accurate, accessible, and cost-effective detection tools. Here, we detail the RosHAB workflow, an innovative, in-the-field applicable genomics approach for real-time, early detection of cHAB outbreaks. We present how the proposed workflow offers consistent taxonomic identification of water samples in comparison to traditional microscopic analyses in a few hours and discuss how the generated data can be used to deepen our understanding on cyanobacteria ecology and forecast HABs events. In parallel, processed water samples will be used to iteratively build the International cyanobacterial toxin database (ICYATOX; http://icyatox.ibis.ulaval.ca) containing the analysis of novel cyanobacterial genomes, including phenomics and genomics metadata. Ultimately, RosHAB will (1) improve the accuracy of on-site rapid diagnostics, (2) standardize genomic procedures in the field, (3) facilitate these genomics procedures for non-scientific personnel, and (4) identify prognostic markers for evidence-based decisions in HABs surveillance.
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Affiliation(s)
- Marianne Potvin
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Jeff Gauthier
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Christophe Langevin
- Centre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, Canada
- Groupe de recherche interuniversitaire en limnologie (GRIL), Montréal, QC, Canada
| | - Vani Mohit
- Direction générale de la coordination scientifique et du Centre d’expertise en analyse environnementale du Québec (CEAEQ), Ministère de l’Environnement et de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP), Québec, QC, Canada
| | - Naíla Barbosa da Costa
- Centre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, Canada
- Groupe de recherche interuniversitaire en limnologie (GRIL), Montréal, QC, Canada
| | - Thomas Deschênes
- Centre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, Canada
| | - Maude Pomerleau
- Centre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, Canada
| | - Irena Kukavica-Ibrulj
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Daniel Verreault
- Direction générale de la coordination scientifique et du Centre d’expertise en analyse environnementale du Québec (CEAEQ), Ministère de l’Environnement et de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP), Québec, QC, Canada
| | - Jérôme Comte
- Centre Eau Terre Environnement, Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, Canada
- Groupe de recherche interuniversitaire en limnologie (GRIL), Montréal, QC, Canada
| | - Roger C. Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
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3
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Nguyen STT, Vardeh DP, Nelson TM, Pearson LA, Kinsela AS, Neilan BA. Bacterial community structure and metabolic potential in microbialite-forming mats from South Australian saline lakes. GEOBIOLOGY 2022; 20:546-559. [PMID: 35312212 PMCID: PMC9311741 DOI: 10.1111/gbi.12489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/28/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Microbialites are sedimentary rocks created in association with benthic microorganisms. While they harbour complex microbial communities, Cyanobacteria perform critical roles in sediment stabilisation and accretion. Microbialites have been described from permanent and ephemeral saline lakes in South Australia; however, the microbial communities that generate and inhabit these biogeological structures have not been studied in detail. To address this knowledge gap, we investigated the composition, diversity and metabolic potential of bacterial communities from different microbialite-forming mats and surrounding sediments in five South Australian saline coastal lakes using 16S rRNA gene sequencing and predictive metagenome analyses. While Proteobacteria and Bacteroidetes were the dominant phyla recovered from the mats and sediments, Cyanobacteria were significantly more abundant in the mat samples. Interestingly, at lower taxonomic levels, the mat communities were vastly different across the five lakes. Comparative analysis of putative mat and sediment metagenomes via PICRUSt2 revealed important metabolic pathways driving the process of carbonate precipitation, including cyanobacterial oxygenic photosynthesis, ureolysis and nitrogen fixation. These pathways were highly conserved across the five examined lakes, although they appeared to be performed by distinct groups of bacterial taxa found in each lake. Stress response, quorum sensing and circadian clock were other important pathways predicted by the in silico metagenome analysis. The enrichment of CRISPR/Cas and phage shock associated genes in these cyanobacteria-rich communities suggests that they may be under selective pressure from viral infection. Together, these results highlight that a very stable ecosystem function is maintained by distinctly different communities in microbialite-forming mats in the five South Australian lakes and reinforce the concept that 'who' is in the community is not as critical as their net metabolic capacity.
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Affiliation(s)
- Suong T. T. Nguyen
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - David P. Vardeh
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydneyNew South WalesAustralia
| | - Tiffanie M. Nelson
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Leanne A. Pearson
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Andrew S. Kinsela
- School of Civil and Environmental EngineeringThe University of New South WalesSydneyNew South WalesAustralia
| | - Brett A. Neilan
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydneyNew South WalesAustralia
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Abstract
Here we review the application of molecular biological approaches to mineral precipitation in modern marine microbialites. The review focuses on the nearly two decades of nucleotide sequencing studies of the microbialites of Shark Bay, Australia; and The Bahamas. Molecular methods have successfully characterized the overall community composition of mats, pinpointed microbes involved in key metabolisms, and revealed patterns in the distributions of microbial groups and functional genes. Molecular tools have become widely accessible, and we can now aim to establish firmer links between microbes and mineralization. Two promising future directions include “zooming in” to assess the roles of specific organisms, microbial groups, and surfaces in carbonate biomineralization and “zooming out” to consider broader spans of space and time. A middle ground between the two can include model systems that contain representatives of important microbial groups, processes, and metabolisms in mats and simplify hypothesis testing. These directions will benefit from expanding reference datasets of marine microbes and enzymes and enrichments of representative microbes from mats. Such applications of molecular tools should improve our ability to interpret ancient and modern microbialites and increase the utility of these rocks as long-term recorders of microbial processes and environmental chemistry.
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Campbell MA, Coolen MJL, Visscher PT, Morris T, Grice K. Structure and function of Shark Bay microbial communities following tropical cyclone Olwyn: A metatranscriptomic and organic geochemical perspective. GEOBIOLOGY 2021; 19:642-664. [PMID: 34180124 DOI: 10.1111/gbi.12461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/05/2021] [Indexed: 06/13/2023]
Abstract
Shark Bay, Western Australia, is episodically impacted by tropical cyclones. During 2015, the region was hit by a category 3 cyclone, "severe tropical cyclone Olywn," leading to the formation of a black sludge in an intertidal zone harboring microbial mats and microbialites. Upon returning to the impacted site 12 months later, the black sludge deposit was still recognizable between the microbialite columns and mucilaginous cobbles near the shoreline in the impacted area. Metatranscriptomic and organic geochemical analyses were carried out on the cyclone-derived materials and impacted microbial mat communities to unravel the structure, function, and potential preservation of these deposits following a tropical cyclone. It was found that samples derived from the black sludge contained low relative abundances of cyanobacteria but had higher proportions of heterotrophic and anaerobic microorganisms (e.g., methanogens and sulfate-reducing bacteria). Increased metabolic activity by these microorganisms (e.g., sulfate reduction and organic matter degradation) is thought to drive calcium carbonate precipitation and helps in mat preservation. Comparison of the aliphatic biomarker by gas chromatography-mass spectrometry (GC-MS) analyses showed that C25 highly branched isoprenoid (HBI) alkenes were significantly higher in the cyclone-derived materials attributed to the relocation of subtidal sediments containing HBI-producing diatom communities by the tropical cyclone. Raney nickel desulfurization of the polar fraction extracted from a mucilaginous cobble revealed sulfur-bound hopanoids and a series of benzohopanes. The presence of these compounds could be indicative of microbial matter that has been influenced by the tropical cyclone which may have caused elevated levels of water column anoxia promoting increased sulfurization of the organic matter to occur.
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Affiliation(s)
- Matthew A Campbell
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
| | - Marco J L Coolen
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
| | - Pieter T Visscher
- Departments of Marine Sciences and Geoscience, University of Connecticut, Storrs, CT, USA
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Therese Morris
- Applied Geology, Curtin University, Perth, WA, Australia
| | - Kliti Grice
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
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Osman JR, Viedma P, Mendoza J, Fernandes G, DuBow MS, Cotoras D. Prokaryotic diversity and biogeochemical characteristics of field living and laboratory cultured stromatolites from the hypersaline Laguna Interna, Salar de Atacama (Chile). Extremophiles 2021; 25:327-342. [PMID: 33993356 DOI: 10.1007/s00792-021-01232-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/02/2021] [Indexed: 10/21/2022]
Abstract
Stromatolites are organo-sedimentary structures found principally in seas and saline lakes that contain sheets of sediments and minerals formed by layers of microbial communities, which trap sediments and induce the precipitation of minerals.A living stromatolite from the alkaline Laguna Interna in the Salar de Atacama was collected and one of the fragments was deposited in an experimental aquarium for 18 months. We used Illumina sequencing of PCR-amplified V4 regions of 16S rRNA genes from total extracted DNA to identify the microbial populations. The chemical structure was studied using X-Ray Diffraction (XRD) and bench chemical methods. We found that members belonging to the Proteobacteria, Planctomycetes, Chloroflexi and Bacteroidetes phyla dominated the bacterial communities of the living and aquarium cultured samples. The potential metabolic functionality of the prokaryotic community reveals that sulfur, nitrogen, methane and carbon fixation metabolism functions are present in the samples. This study is the first to provide new insights into the prokaryotic community composition from this unusual aquatic desert site. Further studies will be helpful to obtain a better understanding of the biotic and abiotic mechanisms residing in stromatolites from Laguna Interna, as well as to have better knowledge about the formation of these biosignatures.
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Affiliation(s)
- Jorge R Osman
- Laboratorio de Microbiología y Biotecnología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont #964, Independencia, Santiago, Chile. .,Instituto de Geología Económica Aplicada (GEA), Universidad de Concepción, Concepción, Chile.
| | - Pabla Viedma
- Laboratorio de Microbiología y Biotecnología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont #964, Independencia, Santiago, Chile
| | - Jorge Mendoza
- Laboratorio de Química de Suelos, Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago, Chile
| | - Gustavo Fernandes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Michael S DuBow
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay Campus CNRS, Bâtiment 21, Avenue de la Terasse, 91190, Gif-sur-Yvette, France
| | - Davor Cotoras
- Laboratorio de Microbiología y Biotecnología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont #964, Independencia, Santiago, Chile
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7
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Petryshyn VA, Junkins EN, Stamps BW, Bailey JV, Stevenson BS, Spear JR, Corsetti FA. Builders, tenants, and squatters: the origins of genetic material in modern stromatolites. GEOBIOLOGY 2021; 19:261-277. [PMID: 33524239 DOI: 10.1111/gbi.12429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/08/2020] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Micro-organisms have long been implicated in the construction of stromatolites. Yet, establishing a microbial role in modern stromatolite growth via molecular analysis is not always straightforward because DNA in stromatolites can have multiple origins. For example, the genomic material could represent the microbes responsible for the construction of the stromatolite (i.e., "builders"), microbes that inhabited the structure after it was built (i.e., "tenants"), or microbes/organic matter that were passively incorporated after construction from the water column or later diagenetic fluids (i.e., "squatters"). Disentangling the role of micro-organisms in stromatolite construction, already difficult in modern systems, becomes more difficult as organic signatures degrade, and their context is obscured. To evaluate our ability to accurately decipher the role of micro-organisms in stromatolite formation in geologically recent settings, 16/18S SSU rRNA gene sequences were analyzed from three systems where the context of growth was well understood: (a) an actively growing stromatolite from a silicic hot spring in Yellowstone National Park, Wyoming, where the construction of the structure is controlled by cyanobacteria; (b) a mixed carbonate and silica precipitate from Little Hot Creek, a hot spring in the Long Valley Caldera of California that has both abiogenic and biogenic components to accretion; and (c) a near-modern lacustrine carbonate stromatolite from Walker Lake, Nevada that is likely abiogenic. In all cases, the largest percentage of recovered DNA sequences, especially when focused on the deeper portions of the structures, belonged to either the tenant or squatter communities, not the actual builders. Once removed from their environmental context, correct interpretation of biology's role in stromatolite morphogenesis was difficult. Because high-throughput genomic analysis may easily lead to incorrect assumptions even in these modern and near-modern structures, caution must be exercised when interpreting micro-organismal involvement in the construction of accretionary structures throughout the rock record.
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Affiliation(s)
- Victoria A Petryshyn
- Environmental Studies Program, University of Southern California, Los Angeles, CA, USA
| | - Emily N Junkins
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Blake W Stamps
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH, USA
- UES, Inc., Dayton, OH, USA
| | - Jake V Bailey
- Department of Earth Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Bradley S Stevenson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - John R Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
| | - Frank A Corsetti
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
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Kurth D, Elias D, Rasuk MC, Contreras M, Farías ME. Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile. PLoS One 2021; 16:e0246656. [PMID: 33561170 PMCID: PMC7872239 DOI: 10.1371/journal.pone.0246656] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 01/25/2021] [Indexed: 01/08/2023] Open
Abstract
In this work, molecular diversity of two hypersaline microbial mats was compared by Whole Genome Shotgun (WGS) sequencing of environmental DNA from the mats. Brava and Tebenquiche are lakes in the Salar de Atacama, Chile, where microbial communities are growing in extreme conditions, including high salinity, high solar irradiance, and high levels of toxic metals and metaloids. Evaporation creates hypersaline conditions in these lakes and mineral precipitation is a characteristic geomicrobiological feature of these benthic ecosystems. The mat from Brava was more rich and diverse, with a higher number of different taxa and with species more evenly distributed. At the phylum level, Proteobacteria, Cyanobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the most abundant, including ~75% of total sequences. At the genus level, the most abundant sequences were affilitated to anoxygenic phototropic and cyanobacterial genera. In Tebenquiche mats, Proteobacteria and Bacteroidetes covered ~70% of the sequences, and 13% of the sequences were affiliated to Salinibacter genus, thus addressing the lower diversity. Regardless of the differences at the taxonomic level, functionally the two mats were similar. Thus, similar roles could be fulfilled by different organisms. Carbon fixation through the Wood-Ljungdahl pathway was well represented in these datasets, and also in other mats from Andean lakes. In spite of presenting less taxonomic diversity, Tebenquiche mats showed increased abundance and variety of rhodopsin genes. Comparison with other metagenomes allowed identifying xantorhodopsins as hallmark genes not only from Brava and Tebenquiche mats, but also for other mats developing at high altitudes in similar environmental conditions.
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Affiliation(s)
- Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| | - Dario Elias
- Facultad de Ingeniería, Universidad Nacional de Entre Ríos, Oro Verde, Entre Ríos, Argentina
| | - María Cecilia Rasuk
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| | | | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
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Campbell MA, Grice K, Visscher PT, Morris T, Wong HL, White RA, Burns BP, Coolen MJL. Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses. Front Microbiol 2020; 11:560336. [PMID: 33312167 PMCID: PMC7702295 DOI: 10.3389/fmicb.2020.560336] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/09/2020] [Indexed: 11/25/2022] Open
Abstract
Microbial mat communities possess extensive taxonomic and functional diversity, which drive high metabolic rates and rapid cycling of major elements. Modern microbial mats occurring in hypersaline environments are considered as analogs to extinct geobiological formations dating back to ∼ 3.5 Gyr ago. Despite efforts to understand the diversity and metabolic potential of hypersaline microbial mats in Shark Bay, Western Australia, there has yet to be molecular analyses at the transcriptional level in these microbial communities. In this study, we generated metatranscriptomes for the first time from actively growing mats comparing the type of mat, as well as the influence of diel and seasonal cycles. We observed that the overall gene transcription is strongly influenced by microbial community structure and seasonality. The most transcribed genes were associated with tackling the low nutrient conditions by the uptake of fatty acids, phosphorus, iron, and nickel from the environment as well as with protective mechanisms against elevated salinity conditions and to prevent build-up of ammonium produced by nitrate reducing microorganisms. A range of pathways involved in carbon, nitrogen, and sulfur cycles were identified in mat metatranscriptomes, with anoxygenic photosynthesis and chemoautotrophy using the Arnon–Buchanan cycle inferred as major pathways involved in the carbon cycle. Furthermore, enrichment of active anaerobic pathways (e.g., sulfate reduction, methanogenesis, Wood–Ljungdahl) in smooth mats corroborates previous metagenomic studies and further advocates the potential of these communities as modern analogs of ancient microbialites.
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Affiliation(s)
- Matthew A Campbell
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
| | - Kliti Grice
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
| | - Pieter T Visscher
- Departments of Marine Sciences and Geoscience, University of Connecticut, Storrs, CT, United States.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Therese Morris
- Applied Geology, Curtin University, Perth, WA, Australia
| | - Hon Lun Wong
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Richard Allen White
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,Plant Pathology, Washington State University, Pullman, WA, United States.,RAW Molecular Systems (RMS) LLC, Spokane, WA, United States
| | - Brendan P Burns
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Marco J L Coolen
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
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10
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Digital Proxy of a Bio-Reactor (DIYBOT) combines sensor data and data analytics to improve greywater treatment and wastewater management systems. Sci Rep 2020; 10:8015. [PMID: 32415099 PMCID: PMC7229150 DOI: 10.1038/s41598-020-64789-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/14/2020] [Indexed: 02/01/2023] Open
Abstract
Technologies to treat wastewater in decentralized systems are critical for sustainable development. Bioreactors are suitable for low-energy removal of inorganic and organic compounds, particularly for non-potable applications where a small footprint is required. One of the main problems associated with bioreactor use is sporadic spikes of chemical toxins, including nanoparticles. Here, we describe the development of DIYBOT (Digital Proxy of a Bio-Reactor), which enables remote monitoring of bioreactors and uses the data to inform decisions related to systems management. To test DIYBOT, a household-scale membrane aerated bioreactor with real-time water quality sensors was used to treat household greywater simulant. After reaching steady-state, silver nanoparticles (AgNP) representative of the mixture found in laundry wastewater were injected into the system to represent a chemical contamination. Measurements of carbon metabolism, effluent water quality, biofilm sloughing rate, and microbial diversity were characterized after nanoparticle exposure. Real-time sensor data were analyzed to reconstruct phase-space dynamics and extrapolate a phenomenological digital proxy to evaluate system performance. The management implication of the stable-focus dynamics, reconstructed from observed data, is that the bioreactor self-corrects in response to contamination spikes at AgNP levels below 2.0 mg/L. DIYBOT may help reduce the frequency of human-in-the-loop corrective management actions for wastewater processing.
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11
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Valdespino-Castillo PM, Hu P, Merino-Ibarra M, López-Gómez LM, Cerqueda-García D, González-De Zayas R, Pi-Puig T, Lestayo JA, Holman HY, Falcón LI. Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba. Front Microbiol 2018; 9:510. [PMID: 29666607 PMCID: PMC5891642 DOI: 10.3389/fmicb.2018.00510] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/06/2018] [Indexed: 01/23/2023] Open
Abstract
Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (Corg), nitrogen and Corg:Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations.
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Affiliation(s)
- Patricia M Valdespino-Castillo
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States
| | - Ping Hu
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States
| | - Martín Merino-Ibarra
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luz M López-Gómez
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Daniel Cerqueda-García
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Teresa Pi-Puig
- Instituto de Geología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Laboratorio Nacional de Geoquímica y Mineralogía, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Julio A Lestayo
- Centro de Investigaciones de Ecosistemas Costeros, Cayo Coco, Cuba
| | - Hoi-Ying Holman
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States
| | - Luisa I Falcón
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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12
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Louyakis AS, Gourlé H, Casaburi G, Bonjawo RME, Duscher AA, Foster JS. A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles. Environ Microbiol 2017; 20:842-861. [DOI: 10.1111/1462-2920.14029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 12/12/2017] [Accepted: 12/12/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Artemis S. Louyakis
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Hadrien Gourlé
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
- Department of Animal Breeding and Genetics; Global Bioinformatics Centre, Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Giorgio Casaburi
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Rachelle M. E. Bonjawo
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Alexandrea A. Duscher
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Jamie S. Foster
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
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13
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Koo H, Mojib N, Hakim JA, Hawes I, Tanabe Y, Andersen DT, Bej AK. Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica. Front Microbiol 2017; 8:1347. [PMID: 28824553 PMCID: PMC5543034 DOI: 10.3389/fmicb.2017.01347] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/03/2017] [Indexed: 01/15/2023] Open
Abstract
In this study, we report the distribution of microbial taxa and their predicted metabolic functions observed in the top (U1), middle (U2), and inner (U3) decadal growth laminae of a unique large conical microbial mat from perennially ice-covered Lake Untersee of East Antarctica, using NextGen sequencing of the 16S rRNA gene and bioinformatics tools. The results showed that the U1 lamina was dominated by cyanobacteria, specifically Phormidium sp., Leptolyngbya sp., and Pseudanabaena sp. The U2 and U3 laminae had high abundances of Actinobacteria, Verrucomicrobia, Proteobacteria, and Bacteroidetes. Closely related taxa within each abundant bacterial taxon found in each lamina were further differentiated at the highest taxonomic resolution using the oligotyping method. PICRUSt analysis, which determines predicted KEGG functional categories from the gene contents and abundances among microbial communities, revealed a high number of sequences belonging to carbon fixation, energy metabolism, cyanophycin, chlorophyll, and photosynthesis proteins in the U1 lamina. The functional predictions of the microbial communities in U2 and U3 represented signal transduction, membrane transport, zinc transport and amino acid-, carbohydrate-, and arsenic- metabolisms. The Nearest Sequenced Taxon Index (NSTI) values processed through PICRUSt were 0.10, 0.13, and 0.11 for U1, U2, and U3 laminae, respectively. These values indicated a close correspondence with the reference microbial genome database, implying high confidence in the predicted metabolic functions of the microbial communities in each lamina. The distribution of microbial taxa observed in each lamina and their predicted metabolic functions provides additional insight into the complex microbial ecosystem at Lake Untersee, and lays the foundation for studies that will enhance our understanding of the mechanisms responsible for the formation of these unique mat structures and their evolutionary significance.
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Affiliation(s)
- Hyunmin Koo
- Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States
| | - Nazia Mojib
- Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States
| | - Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States
| | - Ian Hawes
- Gateway Antarctica, University of CanterburyChristchurch, New Zealand
| | - Yukiko Tanabe
- National Institute of Polar ResearchTachikawa, Japan
| | - Dale T Andersen
- Carl Sagan Center, SETI Institute, Mountain ViewCA, United States
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States
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14
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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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15
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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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16
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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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17
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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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18
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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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19
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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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20
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Davison M, Hall E, Zare R, Bhaya D. Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity. PHOTOSYNTHESIS RESEARCH 2015; 126:135-146. [PMID: 25515769 DOI: 10.1007/s11120-014-0066-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 12/10/2014] [Indexed: 06/04/2023]
Abstract
Cyanobacteria have played a crucial role in the history of early earth and continue to be instrumental in shaping our planet, yet applications of cutting edge technology have not yet been widely used to explore cyanobacterial diversity. To provide adequate background, we briefly review current sequencing technologies and their innovative uses in genomics and metagenomics. Next, we focus on current cell capture technologies and the challenges of using them with cyanobacteria. We illustrate the utility in coupling breakthroughs in DNA amplification with cell capture platforms, with an example of microfluidic isolation and subsequent targeted amplicon sequencing from individual terrestrial thermophilic cyanobacteria. Single cells of thermophilic, unicellular Synechococcus sp. JA-2-3-B'a(2-13) (Syn OS-B') were sorted in a microfluidic device, lysed, and subjected to whole genome amplification by multiple displacement amplification. We amplified regions from specific CRISPR spacer arrays, which are known to be highly diverse, contain semi-palindromic repeats which form secondary structure, and can be difficult to amplify. Cell capture, lysis, and genome amplification on a microfluidic device have been optimized, setting a stage for further investigations of individual cyanobacterial cells isolated directly from natural populations.
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Affiliation(s)
- Michelle Davison
- Department of Plant Biology, Carnegie Institution of Science, 260 Panama Street, Stanford, CA, 94305, USA.
| | - Eric Hall
- SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA
| | - Richard Zare
- Department of Chemistry, Stanford University, 333 Campus Drive Mudd Building, Room 121, Stanford, CA, 94305-4401, USA
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution of Science, 260 Panama Street, Stanford, CA, 94305, USA
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21
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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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22
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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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23
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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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24
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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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25
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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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26
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Foster JS, Lemus JD. Developing the critical thinking skills of astrobiology students through creative and scientific inquiry. ASTROBIOLOGY 2015; 15:89-99. [PMID: 25474292 PMCID: PMC4290794 DOI: 10.1089/ast.2014.1219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 10/17/2014] [Indexed: 06/04/2023]
Abstract
Scientific inquiry represents a multifaceted approach to explore and understand the natural world. Training students in the principles of scientific inquiry can help promote the scientific learning process as well as help students enhance their understanding of scientific research. Here, we report on the development and implementation of a learning module that introduces astrobiology students to the concepts of creative and scientific inquiry, as well as provide practical exercises to build critical thinking skills. The module contained three distinct components: (1) a creative inquiry activity designed to introduce concepts regarding the role of creativity in scientific inquiry; (2) guidelines to help astrobiology students formulate and self-assess questions regarding various scientific content and imagery; and (3) a practical exercise where students were allowed to watch a scientific presentation and practice their analytical skills. Pre- and post-course surveys were used to assess the students' perceptions regarding creative and scientific inquiry and whether this activity impacted their understanding of the scientific process. Survey results indicate that the exercise helped improve students' science skills by promoting awareness regarding the role of creativity in scientific inquiry and building their confidence in formulating and assessing scientific questions. Together, the module and survey results confirm the need to include such inquiry-based activities into the higher education classroom, thereby helping students hone their critical thinking and question asking skill set and facilitating their professional development in astrobiology.
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Affiliation(s)
- Jamie S. Foster
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab, Merritt Island, Florida
| | - Judith D. Lemus
- Hawai‘i Institute of Marine Biology, University of Hawai‘i, Kane‘ohe, Hawai‘i
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27
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Diaz MR, Van Norstrand JD, Eberli GP, Piggot AM, Zhou J, Klaus JS. Functional gene diversity of oolitic sands from Great Bahama Bank. GEOBIOLOGY 2014; 12:231-249. [PMID: 24612324 DOI: 10.1111/gbi.12079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 01/22/2014] [Indexed: 06/03/2023]
Abstract
Despite the importance of oolitic depositional systems as indicators of climate and reservoirs of inorganic C, little is known about the microbial functional diversity, structure, composition, and potential metabolic processes leading to precipitation of carbonates. To fill this gap, we assess the metabolic gene carriage and extracellular polymeric substance (EPS) development in microbial communities associated with oolitic carbonate sediments from the Bahamas Archipelago. Oolitic sediments ranging from high-energy 'active' to lower energy 'non-active' and 'microbially stabilized' environments were examined as they represent contrasting depositional settings, mostly influenced by tidal flows and wave-generated currents. Functional gene analysis, which employed a microarray-based gene technology, detected a total of 12,432 of 95,847 distinct gene probes, including a large number of metabolic processes previously linked to mineral precipitation. Among these, gene-encoding enzymes for denitrification, sulfate reduction, ammonification, and oxygenic/anoxygenic photosynthesis were abundant. In addition, a broad diversity of genes was related to organic carbon degradation, and N2 fixation implying these communities has metabolic plasticity that enables survival under oligotrophic conditions. Differences in functional genes were detected among the environments, with higher diversity associated with non-active and microbially stabilized environments in comparison with the active environment. EPS showed a gradient increase from active to microbially stabilized communities, and when combined with functional gene analysis, which revealed genes encoding EPS-degrading enzymes (chitinases, glucoamylase, amylases), supports a putative role of EPS-mediated microbial calcium carbonate precipitation. We propose that carbonate precipitation in marine oolitic biofilms is spatially and temporally controlled by a complex consortium of microbes with diverse physiologies, including photosynthesizers, heterotrophs, denitrifiers, sulfate reducers, and ammonifiers.
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Affiliation(s)
- M R Diaz
- Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA
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