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Pavloudi C, Zafeiropoulos H. Deciphering the community structure and the functional potential of a hypersaline marsh microbial mat community. FEMS Microbiol Ecol 2022; 98:6843573. [PMID: 36416806 DOI: 10.1093/femsec/fiac141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/31/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Microbial mats are vertically stratified communities of microorganisms characterized by pronounced physiochemical gradients allowing for high species diversity and a wide range of metabolic capabilities. High Throughput Sequencing has the potential to reveal the biodiversity and function of such ecosystems in the cycling of elements. The present study combines 16S rRNA amplicon sequencing and shotgun metagenomics on a hypersaline marsh in Tristomo bay (Karpathos, Greece). Samples were collected in July 2018 and November 2019 from microbial mats, deeper sediment, aggregates observed in the water overlying the sediment, as well as sediment samples with no apparent layering. Metagenomic samples' coassembly and binning revealed 250 bacterial and 39 archaeal metagenome-assembled genomes, with completeness estimates higher than 70% and contamination less than 5%. All MAGs had KEGG Orthology terms related to osmoadaptation, with the 'salt in' strategy ones being prominent. Halobacteria and Bacteroidetes were the most abundant taxa in the mats. Photosynthesis was most likely performed by purple sulphur and nonsulphur bacteria. All samples had the capacity for sulphate reduction, dissimilatory arsenic reduction, and conversion of pyruvate to oxaloacetate. Overall, both sequencing methodologies resulted in similar taxonomic compositions and revealed that the formation of the microbial mat in this marsh exhibits seasonal variation.
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Affiliation(s)
- Christina Pavloudi
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), P.O. Box 2214, 71003, Heraklion, Crete, Greece.,Department of Biological Sciences, The George Washington University, 2029 G St NW, Bell Hall 302, Washington DC 20052, United States
| | - Haris Zafeiropoulos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), P.O. Box 2214, 71003, Heraklion, Crete, Greece.,Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013, Heraklion, Crete, Greece.,Laboratory of Molecular Bacteriology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, box 1028, 3000 Leuven, Belgium
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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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Oxidation of Molecular Hydrogen by a Chemolithoautotrophic Beggiatoa Strain. Appl Environ Microbiol 2016; 82:2527-36. [PMID: 26896131 PMCID: PMC4959497 DOI: 10.1128/aem.03818-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/10/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A chemolithoautotrophic strain of the family Beggiatoaceae, Beggiatoa sp. strain 35Flor, was found to oxidize molecular hydrogen when grown in a medium with diffusional gradients of oxygen, sulfide, and hydrogen. Microsensor profiles and rate measurements suggested that the strain oxidized hydrogen aerobically when oxygen was available, while hydrogen consumption under anoxic conditions was presumably driven by sulfur respiration.Beggiatoa sp. 35Flor reached significantly higher biomass in hydrogen-supplemented oxygen-sulfide gradient media, but hydrogen did not support growth of the strain in the absence of reduced sulfur compounds. Nevertheless, hydrogen oxidation can provide Beggiatoa sp. 35Flor with energy for maintenance and assimilatory purposes and may support the disposal of internally stored sulfur to prevent physical damage resulting from excessive sulfur accumulation. Our knowledge about the exposure of natural populations of Beggiatoa ceae to hydrogen is very limited, but significant amounts of hydrogen could be provided by nitrogen fixation, fermentation, and geochemical processes in several of their typical habitats such as photosynthetic microbial mats and submarine sites of hydrothermal fluid flow. IMPORTANCE Reduced sulfur compounds are certainly the main electron donors for chemolithoautotrophic Beggiatoa ceae, but the traditional focus on this topic has left other possible inorganic electron donors largely unexplored. In this paper, we provide evidence that hydrogen oxidation has the potential to strengthen the ecophysiological plasticity of Beggiatoa ceaein several ways. Moreover, we show that hydrogen oxidation by members of this family can significantly influence biogeochemical gradients and therefore should be considered in environmental studies.
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Nielsen M, Revsbech NP, Kühl M. Microsensor measurements of hydrogen gas dynamics in cyanobacterial microbial mats. Front Microbiol 2015; 6:726. [PMID: 26257714 PMCID: PMC4508582 DOI: 10.3389/fmicb.2015.00726] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/02/2015] [Indexed: 11/16/2022] Open
Abstract
We used a novel amperometric microsensor for measuring hydrogen gas production and consumption at high spatio-temporal resolution in cyanobacterial biofilms and mats dominated by non-heterocystous filamentous cyanobacteria (Microcoleus chtonoplastes and Oscillatoria sp.). The new microsensor is based on the use of an organic electrolyte and a stable internal reference system and can be equipped with a chemical sulfide trap in the measuring tip; it exhibits very stable and sulfide-insensitive measuring signals and a high sensitivity (1.5–5 pA per μmol L-1 H2). Hydrogen gas measurements were done in combination with microsensor measurements of scalar irradiance, O2, pH, and H2S and showed a pronounced H2 accumulation (of up to 8–10% H2 saturation) within the upper mm of cyanobacterial mats after onset of darkness and O2 depletion. The peak concentration of H2 increased with the irradiance level prior to darkening. After an initial build-up over the first 1–2 h in darkness, H2 was depleted over several hours due to efflux to the overlaying water, and due to biogeochemical processes in the uppermost oxic layers and the anoxic layers of the mats. Depletion could be prevented by addition of molybdate pointing to sulfate reduction as a major sink for H2. Immediately after onset of illumination, a short burst of presumably photo-produced H2 due to direct biophotolysis was observed in the illuminated but anoxic mat layers. As soon as O2 from photosynthesis started to accumulate, the H2 was consumed rapidly and production ceased. Our data give detailed insights into the microscale distribution and dynamics of H2 in cyanobacterial biofilms and mats, and further support that cyanobacterial H2 production can play a significant role in fueling anaerobic processes like e.g., sulfate reduction or anoxygenic photosynthesis in microbial mats.
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Affiliation(s)
- Michael Nielsen
- Section of Microbiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Niels P Revsbech
- Section of Microbiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen Helsingør, Denmark ; Plant Functional Biology and Climate Change Cluster, University of Technology, Sydney, Ultimo NSW, Australia
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Consortia of cyanobacteria/microalgae and bacteria: Biotechnological potential. Biotechnol Adv 2011; 29:896-907. [DOI: 10.1016/j.biotechadv.2011.07.009] [Citation(s) in RCA: 303] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 06/14/2011] [Accepted: 07/03/2011] [Indexed: 12/21/2022]
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Decho AW, Frey RL, Ferry JL. Chemical challenges to bacterial AHL signaling in the environment. Chem Rev 2010; 111:86-99. [PMID: 21142012 DOI: 10.1021/cr100311q] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alan W Decho
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, South Carolina 29208, USA.
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Visscher PT, Dupraz C, Braissant O, Gallagher KL, Glunk C, Casillas L, Reed RES. Biogeochemistry of Carbon Cycling in Hypersaline Mats: Linking the Present to the Past through Biosignatures. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2010. [DOI: 10.1007/978-90-481-3799-2_23] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Rios-Velazquez C, Casillas-Martinez L, Visscher PT. Learning geomicrobiology as a team using microbial mats, a multidisciplinary approach. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2009; 8:28-35. [PMID: 23653817 PMCID: PMC3577146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Microbial mats are one of the best suited laminar organo-sedimentary ecosystems for students from different educational backgrounds to visualize the direct relationship between microbes and minerals. We have used tropical hypersaline microbial mats from Puerto Rico as educational tools to promote active learning of geomicrobiology introductory concepts for undergraduate students organized in multidisciplinary teams with biological and geological backgrounds. Besides field trips and independent research projects focused on microbial mats, four intensive workshops and one capstone activity were designed to expose students to the different geomicrobiology subdisciplines (microbiology, molecular biology, geology, and geochemistry). The teaching-learning process was assessed using pre- and posttests, group discussions, activities including Gallery Walks and exquisite cadaver's, case studies, and focal interviews. While the posttest showed a significant difference in conceptual understanding, the Gallery Walk and the capstone activities demonstrated increase in the depth, coherence, and thoughtfulness in answering questions, including a clear integration of the different subdisciplines during their presentations. Finally, the main themes described by the students as important outcomes of their participation in the Research at Undergraduate Institutions: Microbial Observatory (RUI-MO) program were: (i) the opportunity to study and learn new and different science disciplines, (ii) the microbial mats were excellent tools to learn from and integrate different science disciplines, and (iii) working in multidisciplinary teams gave them the opportunity to learn from their peers' discipline backgrounds. To our knowledge this is the first educational initiative that uses tropical hypersaline microbial mats to teach geomicrobiology in a multidisciplinary fashion.
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Affiliation(s)
| | | | - Pieter T. Visscher
- Center for Integrative Geosciences, University of Connecticut, Storrs, Connecticut 06269
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Decho AW, Visscher PT, Ferry J, Kawaguchi T, He L, Przekop KM, Norman RS, Reid RP. Autoinducers extracted from microbial mats reveal a surprising diversity of N-acylhomoserine lactones (AHLs) and abundance changes that may relate to diel pH. Environ Microbiol 2009; 11:409-20. [PMID: 19196272 DOI: 10.1111/j.1462-2920.2008.01780.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbial mats are highly structured and diverse communities, and one of the earliest-known life assemblages. Mat bacteria interact within an environment marked by strong geochemical gradients and fluctuations. We examined natural mat systems for the presence of autoinducers involved in quorum sensing, a form of cell-cell communication. Our results revealed that a diverse array of N-acylhomoserine lactones (AHLs) including C(4)- to C(14)-AHLs, were identified from mat extracts using mass spectrometry (MS), with further confirmation by MS/MS-collision-induced dissociation (CID), and additions of external standards. Microelectrode measurements showed that mats exhibited diel pH fluctuations, ranging from alkaline (pH 9.4) during daytime (net photosynthesis) to acidic (pH 6.8) during darkness (net respiration/fermentation). Under laboratory conditions, AHLs having shorter acyl-chains were degraded within the time frame that daily alkaline pH (> 8.2) conditions exist in mats. Intensive sampling of mats after full day- or night-time incubations revealed that accumulations of extractable shorter-chain AHLs (e.g. C(8)- and C(10)-AHLs) were significantly (P < 0.001) diminished during daytime. Our study offers evidence that stabilities of AHLs under natural conditions may be influenced by the proximal extracellular environment. We further propose that the ancient periodicity of photosynthesis/respiration in mats may potentially drive a mechanism for diel differences in activities of certain autoinducers, and hence bacterial activities mediated through quorum sensing.
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Affiliation(s)
- Alan W Decho
- Department of Environmental Health Sciences, Arnold School of Public Health, Columbia, SC, USA.
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Baptista MS, Vasconcelos MT. Cyanobacteria Metal Interactions: Requirements, Toxicity, and Ecological Implications. Crit Rev Microbiol 2008; 32:127-37. [PMID: 16893750 DOI: 10.1080/10408410600822934] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The environmental health-related relevance of cyanobacteria is primarily related to their ability to produce a wide range of toxins, which are known to be hazardous to many organisms, including human beings. The occurrence of cyanobacterial blooms has been related to eutrophic surface water. In the bloom-forming process the levels of phosphorus and nitrogen have been well documented but information regarding concentrations of other chemicals (inorganic, organo-metallic, and organic) is still incipient. Several contaminants, like trace metals, elicit a variety of acute and chronic toxicity effects, but cyanobacteria also have the capability to accumulate, detoxify, or metabolize such substances, to some extent. The role of cyanobacterial exudates has been proved a means of both nutrient acquisition and detoxification. In addition, cyanobacteria are effective biological metal sorbents, representing an important sink for metals in aquatic environment. Understanding the fundamental physicochemical mechanisms of trace metal bio-uptake by cyanobacteria in natural systems is a step towards identifying under what conditions cyanobacterial growth is favored and to ascertain the mechanisms by which blooms (and toxin production) are triggered. In this review the cyanobacterial interactions with metals will be discussed, focusing on freshwater systems.
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Affiliation(s)
- Mafalda S Baptista
- Chemistry Department, Faculty of Sciences, University of Porto, Porto, Portugal.
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Dupraz C, Visscher PT. Microbial lithification in marine stromatolites and hypersaline mats. Trends Microbiol 2005; 13:429-38. [PMID: 16087339 DOI: 10.1016/j.tim.2005.07.008] [Citation(s) in RCA: 247] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Revised: 06/27/2005] [Accepted: 07/21/2005] [Indexed: 11/16/2022]
Abstract
Lithification in microbial ecosystems occurs when precipitation of minerals outweighs dissolution. Although the formation of various minerals can result from microbial metabolism, carbonate precipitation is possibly the most important process that impacts global carbon cycling. Recent investigations have produced models for stromatolite formation in open marine environments and lithification in shallow hypersaline lakes, which could be highly relevant for interpreting the rock record and searching for extraterrestrial life. Two factors that are controlled by microbial processes and physicochemical characteristics determine precipitation: exopolymeric substances and the saturation index, the latter being determined by the pH, {Ca(2+)} and {CO(3)(2-)}. Here, we evaluate community metabolism in microbial mats and hypothesize why these organosedimentary biofilms sometimes lithify and sometimes do not.
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Affiliation(s)
- Christophe Dupraz
- Institut de Géologie, Université de Neuchâtel, Rue Emile-Argand 11, CP 2, CH-2007 Neuchâtel, Switzerland
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Visscher PT, Baumgartner LK, Buckley DH, Rogers DR, Hogan ME, Raleigh CD, Turk KA, Des Marais DJ. Dimethyl sulphide and methanethiol formation in microbial mats: potential pathways for biogenic signatures. Environ Microbiol 2003; 5:296-308. [PMID: 12662177 DOI: 10.1046/j.1462-2920.2003.00418.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mechanisms of dimethyl sulphide (DMS) and methanethiol (MT) production and consumption were determined in moderately hypersaline mats, Guerrero Negro, Mexico. Biological pathways regulated the net flux of DMS and MT as revealed by increases in flux resulting from decreased salinity, increased temperature and the removal of oxygen. Dimethylsulphoniopropionate (DMSP) was not present in these microbial mats and DMS and MT are probably formed by the reaction of photosynthetically produced low-molecular weight organic carbon and biogenic hydrogen sulphide derived from sulphate reduction. These observations provide an alternative to the notion that DMSP or S-containing amino acids are the dominant precursors of DMS in intertidal sediment systems. The major sink for DMS in the microbial mats was biological consumption, whereas photochemical oxidation to dimethylsulphoxide was the major sink for DMS in the overlying water column. Diel flux measurements demonstrated that significantly more DMS is released from the system during the night than during the day. The major consumers of DMS in the presence of oxygen were monooxygenase-utilizing bacteria, whereas under anoxic conditions, DMS was predominantly consumed by sulphate-reducing bacteria and methanethiol was consumed by methanogenic bacteria. Aerobic and anaerobic consumption rates of DMS were nearly identical. Mass balance estimates suggest that the consumption in the water column is likely to be smaller than net the flux from the mats. Volatile organic sulphur compounds are thus indicators of high rates of carbon fixation and sulphate reduction in these laminated sediment ecosystems, and atmospheric sulphur can be generated as a biogenic signature of the microbial mat community.
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Affiliation(s)
- Pieter T Visscher
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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Abstract
Metallocluster-containing enzymes catalyze some of the most basic redox transformations in the biosphere. The reactions catalyzed by these enzymes typically involve small molecules such as N2, CO, and H2 that are used to generate both chemical building blocks and energy for metabolic purposes. During the past decade, structures have been established for the iron-sulfur-based metalloclusters present in the molybdenum nitrogenase, the iron-only hydrogenase, and the nickel-carbon monoxide dehydrogenase, and for the copper-sulfide-based cluster in nitrous oxide reductase. Although these clusters are built from interactions observed in simpler metalloproteins, they contain novel features that may be relevant for their catalytic function. The mechanisms of metallocluster-containing enzymes are still poorly defined, and represent substantial and continuing challenges to biochemists, biophysicists, and synthetic chemists. These proteins also provide a window into the union of the biological and inorganic worlds that may have been relevant to the early evolution of biochemical catalysis.
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Affiliation(s)
- Douglas C Rees
- Division of Chemistry and Chemical Engineering 147-75CH, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA.
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