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Djebaili R, Mignini A, Vaccarelli I, Pellegrini M, Spera DM, Del Gallo M, D’Alessandro AM. Polyhydroxybutyrate-producing cyanobacteria from lampenflora: The case study of the “Stiffe” caves in Italy. Front Microbiol 2022; 13:933398. [PMID: 35966678 PMCID: PMC9366245 DOI: 10.3389/fmicb.2022.933398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
This study aimed to estimate the green formation lampenflora of “Stiffe” caves in order to evaluate their suitability as an isolation source of cyanobacteria useful for the production of polyhydroxyalkanoates (PHAs). The cave system was chosen as the sampling site due to its touristic use and the presence of high-impact illuminations. The biofilms and the mats of the illuminated walls were sampled. Samples were investigated by 16S rRNA gene analysis and culturable cyanobacteria isolation. The isolated strains were then screened for the production of PHAs under typical culturing and nutritional starvation. Cultures were checked for PHA accumulation, poly-β-hydroxybutyrate (PHB) presence (infrared spectroscopy), and pigment production. The 16S rRNA gene metabarcoding. Highlighted a considerable extent of the pressure exerted by anthropogenic activities. However, the isolation yielded eleven cyanobacteria isolates with good PHA (mainly PHB)-producing abilities and interesting pigment production rates (chlorophyll a and carotenoids). Under normal conditions (BG110), the accumulation abilities ranged from 266 to 1,152 ng mg dry biomass–1. The optimization of bioprocesses through nutritional starvation resulted in a 2.5-fold increase. Fourier transform infrared (FTIR) studies established the occurrence of PHB within PHAs extracted by cyanobacteria isolates. The comparison of results with standard strains underlined good production rates. For C2 and C8 strains, PHA accumulation rates under starvation were higher than Azospirillum brasilense and similar to Synechocystis cf. salina 192. This study broadened the knowledge of the microbial communities of mats and biofilms on the lightened walls of the caves. These findings suggested that these structures, which are common in tourist caves, could be used to isolate valuable strains before remediation measures are adopted.
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Affiliation(s)
- Rihab Djebaili
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Amedeo Mignini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Ilaria Vaccarelli
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Marika Pellegrini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- *Correspondence: Marika Pellegrini,
| | | | - Maddalena Del Gallo
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Anna Maria D’Alessandro
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- Anna Maria D’Alessandro,
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AlDhafiri S, Chiang YR, El Nayal AM, Abed RMM, Abotalib N, Ismail W. Temporal compositional shifts in an activated sludge microbiome during estrone biodegradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:32702-32716. [PMID: 35015225 DOI: 10.1007/s11356-021-18185-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Microbial biodegradation is a key process for the removal of estrogens during wastewater treatment. At least four degradation pathways for natural estrogens have been proposed. However, major estrogen degraders and the occurrence of different estrogen biodegradation pathways in wastewater treatment plants have been rarely investigated. This study was conducted to elucidate estrone biodegradation pathway and to identify key estrone-degrading bacteria in activated sludge from a major wastewater treatment plant in Bahrain. The biodegradation experiments were performed in activated sludge microcosms supplemented with estrone. Sludge samples were retrieved at time intervals to analyze the biodegradation metabolites and the temporal shifts in the bacterial community composition. Chemical analysis revealed the biodegradation of more than 90% of the added estrone within 6 days, and the compounds 4-hydroxyestrone and pyridinestrone acid, which are typical markers of the 4,5-seco pathway of aerobic estrone biodegradation, were detected. Temporal shifts in the relative abundance of bacteria were most prominent among members of Proteobacteria and Bacteroidetes. While the alphaproteobacterial genera Novosphingobium and Sphingoaurantiacus were significantly enriched (from ≤ 6% to an average of 31%) in the estrone-amended activated sludge after 2 days of incubation, the bacteroidete Pedobacter was uniquely detected in these microcosms at day 10. The relative abundance of Polyangia (Nannocyctis) increased to an average of 10 ± 0.4% in the estrone-amended activated sludge after 4 days of incubation. Enrichment cultivation of bacteria from the activated sludge on estrone resulted in a mixed culture that was capable of degrading estrone. An estrone-degrading strain was isolated from this mixed culture and was affiliated with the known estrogen-degrading Alphaproteobacteria Sphingobium estrogenivorans. We conclude that estrone degradation in the activated sludge from the studied wastewater treatment plant proceeds via the 4,5-seco pathway and is most likely mediated by alphaproteobacterial taxa.
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Affiliation(s)
- Sarah AlDhafiri
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Yin-Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ashraf M El Nayal
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Nasser Abotalib
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Wael Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Kingdom of Bahrain.
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Abed RMM, Al-Fori M, Al-Sabahi J, Prigent S, Headley T. Impacts of partially hydrolyzed polyacrylamide (HPAM) on microbial mats from a constructed wetland treating oilfield produced water. CHEMOSPHERE 2021; 285:131421. [PMID: 34242985 DOI: 10.1016/j.chemosphere.2021.131421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/01/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Constructed wetlands have been successfully used in the treatment of produced water brought to the surface in large quantities during oil extraction activities. However, with the increasing use of partially hydrolyzed polyacrylamide (HPAM) in enhancing oil recovery, the impacts of HPAM on the biological processes of wetlands is still unknown. Microbial mats in wetlands play a key role in hydrocarbon degradation. Here, we compared the bacterial communities of four wetland microbial mats after flooding with different concentrations of HPAM. Two mats (i.e. the HPAM-free and the 500 ppm HPAM pre-exposed mats) were selected to further investigate the effect of HPAM on respiration and biodegradation activities. The field mats exhibited clear differences in their bacterial community structure, where Cyanobacteria and Alphaproteobacteria became dominant in the presence of HPAM. In the laboratory experiments, the generated CO2 by the HPAM-free and the 500 ppm HPAM pre-exposed mats did not vary significantly when HPAM was added, although CO2 values were slightly higher in the presence of oil. Both mats were still able to degrade between 15 ± 14.4 to 50 ± 13.0% of C10 to C30 alkanes in 28 days, and this degradation was not affected by HPAM addition. The HPAM concentration decreased by 22-34% of the initial amount after 28 days of incubation in the HPAM-free mat, versus only 7-18.4% decrease in the 500 ppm HPAM pre-exposed mat. We conclude that the wetland microbial mats seem to have become well adapted to HPAM and could maintain their respiration and hydrocarbon degradation activities.
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Affiliation(s)
- Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, P. O. Box: 36, PC 123, Al Khoud, Oman.
| | - Marwan Al-Fori
- Biology Department, College of Science, Sultan Qaboos University, P. O. Box: 36, PC 123, Al Khoud, Oman
| | - Jamal Al-Sabahi
- Central Instrumentation Laboratory, College of Agricultural & Marine Sciences, Sultan Qaboos University, P. O. Box: 34, PC 123, Al Khoud, Oman
| | | | - Tom Headley
- BAUER Nimr LLC, P.O.Box 1186, P.C 114, Al Mina, Muscat, Oman
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Al-Yousef HM, Amina M. Phytoconstituents and pharmacological activities of cyanobacterium Fischerella ambigua. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Mourão MM, Gradíssimo DG, Santos AV, Schneider MPC, Faustino SMM, Vasconcelos V, Xavier LP. Optimization of Polyhydroxybutyrate Production by Amazonian Microalga Stigeoclonium sp. B23. Biomolecules 2020; 10:E1628. [PMID: 33287108 PMCID: PMC7761742 DOI: 10.3390/biom10121628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 01/22/2023] Open
Abstract
The present work established the optimization and production of biodegradable thermoplastic polyhydroxybutyrate (PHB) from Amazonian microalga Stigeoclonium sp. B23. The optimization was performed in eight different growth media conditions of Stigeoclonium sp. B23, supplemented with sodium acetate and sodium bicarbonate and total deprivation of sodium nitrate. B23 was stained with Nile Red, and PHB was extracted and quantified by correlating the amount of fluorescence and biopolymer concentration through spectrofluorimetry and spectrophotometry, respectively. Our results detected the production of PHB in Stigeoclonium sp. B23 and in all modified media. Treatment with increased acetate and bicarbonate and without nitrate gave the highest concentration of PHB, while the treatment with only acetate gave the lowest among supplemented media. Our results showed a great potential of Stigeoclonium sp. B23, the first Amazonian microalga reported on PHB production. The microalga was isolated from a poorly explored and investigated region and proved to be productive when compared to other cyanobacterial and bacterial species. Additionally, microalga biomass changes due to the nutritional conditions and, reversely, biopolymer is well-synthetized. This great potential could lead to the pursuit of new Amazonian microalgae species in the search for alternative polyesters.
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Affiliation(s)
- Murilo Moraes Mourão
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Federal University of Pará, 01 Augusto Corrêa Street, 66075-110 Belém, Pará, Brazil; (D.G.G.); (L.P.X.)
| | - Diana Gomes Gradíssimo
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Federal University of Pará, 01 Augusto Corrêa Street, 66075-110 Belém, Pará, Brazil; (D.G.G.); (L.P.X.)
| | - Agenor Valadares Santos
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Federal University of Pará, 01 Augusto Corrêa Street, 66075-110 Belém, Pará, Brazil; (D.G.G.); (L.P.X.)
| | - Maria Paula Cruz Schneider
- Genomics and Systems Biology Center, Federal University of Pará, 01 Augusto Corrêa Street, 66075-110 Belém, Pará, Brazil;
| | - Silvia Maria Mathes Faustino
- Laboratory of Algae Cultivation and Bioprospecting, Pharmacy Coordination, Federal University of Amapá, Marco Zero do Equador Campus, Juscelino Kubitschek Highway, Km 2, 68903-419 Macapá, Amapá, Brazil;
| | - Vitor Vasconcelos
- Interdisciplinary Center of Marine and Environmental Research, University of Porto, General Norton de Matos Av., 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Campo Alegre Street, 4069-007 Porto, Portugal
| | - Luciana Pereira Xavier
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Federal University of Pará, 01 Augusto Corrêa Street, 66075-110 Belém, Pará, Brazil; (D.G.G.); (L.P.X.)
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Swain SS, Paidesetty SK, Padhy RN. Antibacterial, antifungal and antimycobacterial compounds from cyanobacteria. Biomed Pharmacother 2017; 90:760-776. [PMID: 28419973 DOI: 10.1016/j.biopha.2017.04.030] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 04/02/2017] [Accepted: 04/10/2017] [Indexed: 11/18/2022] Open
Abstract
Infections from multidrug resistant (MDR) pathogenic bacteria, fungi and Mycobacterium tuberculosis remain progressively intractable. The search of effective antimicrobials from other possible non-conventional sources against MDR pathogenic bacteria, fungi and mycobacteria is call of the day. This review considers 121 cyanobacterial compounds or cyano-compounds with antimicrobial activities. Chemical structures of cyano-compounds were retrieved from ChemSpider and PubChem databases and were visualized by the software ChemDraw Ultra. Chemical information on cyano-compounds pertaining to Lipinski rules of five was assessed. The reviewed cyano-compounds belong to the following chemical classes (with examples): alkaloids (ambiguine isonitriles and 12-epi-hapalindole E isonitrile), aromatic compounds (benzoic acid and cyanobacterin), cyclic depsipeptides (cryptophycin 52 and lyngbyabellin A), cyclic peptides (calophycin and tenuecyclamides), cyclic undecapeptides (kawaguchipeptins and lyngbyazothrin A), cyclophane (carbamidocyclophane), extracellular pigment (nostocine A), fatty acids (alpha-dimorphecolic acid and majusculonic acid), linear peptides (muscoride A), lipopeptides (fischerellins and scytonemin A), nucleosides (tolytoxin and tubercidin), phenols (ambigols and 4-4'-hydroxybiphenyl), macrolides (scytophycin A and tolytoxin), polyketides (malyngolide and nostocyclyne), polyphenyl ethers (crossbyanol A), porphinoids (tolyporphin J) and terpenoids (noscomin and scytoscalarol). Cyanobacteria appear to be a diverse source of compounds with antimicrobial activity. Further attention is required to elucidate whether those could be applied as pharmaceuticals.
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Affiliation(s)
- Shasank S Swain
- Central Research Laboratory, Institute of Medical Sciences and Sum Hospital, Siksha 'O' Anusandhan University, Kalinga Nagar, Bhubaneswar 751003, Odisha, India
| | - Sudhir K Paidesetty
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan University, Kalinga Nagar, Bhubaneswar 751003, Odisha, India
| | - Rabindra N Padhy
- Central Research Laboratory, Institute of Medical Sciences and Sum Hospital, Siksha 'O' Anusandhan University, Kalinga Nagar, Bhubaneswar 751003, Odisha, India.
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Masuda LSM, Enrich-Prast A. Benthic microalgae community response to flooding in a tropical salt flat. BRAZ J BIOL 2017; 76:577-82. [PMID: 27097089 DOI: 10.1590/1519-6984.18314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/29/2015] [Indexed: 11/22/2022] Open
Abstract
This research evaluated the effect of flooding on the microphytobenthos community structure in a microbial mat from a tropical salt flat. Field samples were collected during four consecutive days: on the first three days the salt flat was dry, on the fourth day it was flooded by rain. In order to evaluate the community maintained in flood conditions, samples from this area were collected and kept in the laboratory for 10 days with sea water. The results of total abundance of microphytobenthos varied from 4.2 × 108 to 2.9 × 109 organisms L-1, total density increased one order of magnitude under the effect of water for both situations of precipitation in the salt flat and in experimental conditions, an increase due to the high abundance of Microcoleus spp. Shannon index (H') was higher during the desiccation period. Our data suggest that changes in the abundance of organisms were due to the effect of water. The dominance of the most abundant taxa remained the same under conditions of desiccation and influence of water, and there is probably a consortium of microorganisms in the microbial mat that helps to maintain these dominances.
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Affiliation(s)
- L S M Masuda
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ , Brazil, Programa de Pós-graduação em Ciências Biológicas (Microbiologia), Departamento Microbiologia Ambiental, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro - UFRJ, Av. Carlos Chagas Filho, 373, Bloco I, Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brazil.,Instituto de Biologia, Universidade Federal do Rio de Janeiro, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ , Brazil, Laboratório de Biogeoquímica, Instituto de Biologia, Universidade Federal do Rio de Janeiro - UFRJ, Av. Carlos Chagas Filho, 373, Bloco A, Ilha do Fundão, CEP 21941-971, Rio de Janeiro, RJ, Brazil
| | - A Enrich-Prast
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ , Brazil, Programa de Pós-graduação em Ciências Biológicas (Microbiologia), Departamento Microbiologia Ambiental, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro - UFRJ, Av. Carlos Chagas Filho, 373, Bloco I, Ilha do Fundão, CEP 21941-590, Rio de Janeiro, RJ, Brazil.,Instituto de Biologia, Universidade Federal do Rio de Janeiro, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ , Brazil, Laboratório de Biogeoquímica, Instituto de Biologia, Universidade Federal do Rio de Janeiro - UFRJ, Av. Carlos Chagas Filho, 373, Bloco A, Ilha do Fundão, CEP 21941-971, Rio de Janeiro, RJ, Brazil.,Department of Environmental Change, Linköping University, Linköpings Universitet, Linköping , Sweden, Department of Environmental Change, Linköping University, 581 83, Linköping, Sweden
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Kaushik MS, Singh P, Tiwari B, Mishra AK. Ferric Uptake Regulator (FUR) protein: properties and implications in cyanobacteria. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1134-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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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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Janatková K, Reháková K, Doležal J, Simek M, Chlumská Z, Dvorský M, Kopecký M. Community structure of soil phototrophs along environmental gradients in arid Himalaya. Environ Microbiol 2013; 15:2505-16. [PMID: 23647963 DOI: 10.1111/1462-2920.12132] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 03/24/2013] [Indexed: 11/29/2022]
Abstract
The well-developed biological soil crusts cover up to 40% of the soil surface in the alpine and subnival zones of the Tibetan Plateau, accounting for a vast area of Asia. We investigated the diversity and biomass of the phototrophic part (Cyanobacteria) of the microbial community inhabiting biological soil crusts and uncrusted soils in their surroundings on the elevation gradient of 5200-5900 m a.s.l. The influence of soil physico-chemical properties on phototrophs was studied. The ability of high-altitude phototrophs to fix molecular nitrogen was also determined under laboratory conditions. The biological soil crust phototroph community did not differ from that living in uncrusted soil in terms of the species composition, but the biomass is three-to-five times higher. An increasing trend in the cyanobacterial biomass from the biological soil crusts with elevation was observed, with the genera Nostoc spp., Microcoleus vaginatus and Phormidium spp. contributing to this increase. Based on the laboratory experiments, the highest nitrogenase activity was recorded in the middle elevations, and the rate of nitrogen fixation was not correlated with the cyanobacterial biomass.
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Affiliation(s)
- Kateřina Janatková
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, 37982, Třeboň, Czech Republic
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Lin XY, Yang YY, Zhao YH, Fu QL. Biodegradation of bensulfuron-methyl and its effect on bacterial community in paddy soils. ECOTOXICOLOGY (LONDON, ENGLAND) 2012; 21:1281-1290. [PMID: 22430059 DOI: 10.1007/s10646-012-0882-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/05/2012] [Indexed: 05/31/2023]
Abstract
Bensulfuron-methyl (BSM) is a new kind of sulfonylurea herbicide widely used to control broad-leaf weeds in rice paddies. The aim of this work was to study BSM biodegradation in paddy soils with BSM-degrading bacteria Bacillus megaterium L1 and Brevibacterium sp. BH and its effect on the structures of soil bacterial community. More than 90 % of BSM could be degraded in paddy soils with 0.0355 mg kg⁻¹ BSM concentration. Addition of BSM-degrading bacterial strains Bacillus megaterium L1 into BSM contaminated paddy soil could have the half-life time of BSM compared to treatment without Bacillus megaterium L1 inoculation. Denaturing gradient gel electrophoresis and principle component analysis indicated that the diversity of the soil microbial community structure changed along with the addition of BSM, which recovered at the end of the experiment (5 weeks). Addition of BSM-degrading bacteria Bacillus megaterium L1 enriched the diversity of soil microbial community structure in paddy soils. This study provides information on the biodegradation of BSM and BSM's influences on the soil bacteria microbial community structures.
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Affiliation(s)
- Xiao-Yan Lin
- Rice Product Quality Inspection and Supervision Testing Center, China National Rice Research Institute, Hangzhou 310006, People's Republic of China.
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Abed RMM, Al Kharusi S, Schramm A, Robinson MD. Bacterial diversity, pigments and nitrogen fixation of biological desert crusts from the Sultanate of Oman. FEMS Microbiol Ecol 2010; 72:418-28. [PMID: 20298501 DOI: 10.1111/j.1574-6941.2010.00854.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, Muscat, Sultanate of Oman.
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Comparative characterization of the microbial diversities of an artificial microbialite model and a natural stromatolite. Appl Environ Microbiol 2008; 74:7410-21. [PMID: 18836014 DOI: 10.1128/aem.01710-08] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Microbialites are organosedimentary structures that result from the trapping, binding, and lithification of sediments by microbial mat communities. In this study we developed a model artificial microbialite system derived from natural stromatolites, a type of microbialite, collected from Exuma Sound, Bahamas. We demonstrated that the morphology of the artificial microbialite was consistent with that of the natural system in that there was a multilayer community with a pronounced biofilm on the surface, a concentrated layer of filamentous cyanobacteria in the top 5 mm, and a lithified layer of fused oolitic sand grains in the subsurface. The fused grain layer was comprised predominantly of the calcium carbonate polymorph aragonite, which corresponded to the composition of the Bahamian stromatolites. The microbial diversity of the artificial microbialites and that of natural stromatolites were also compared using automated ribosomal intergenic spacer analysis (ARISA) and 16S rRNA gene sequencing. The ARISA profiling indicated that the Shannon indices of the two communities were comparable and that the overall diversity was not significantly lower in the artificial microbialite model. Bacterial clone libraries generated from each of the three artificial microbialite layers and natural stromatolites indicated that the cyanobacterial and crust layers most closely resembled the ecotypes detected in the natural stromatolites and were dominated by Proteobacteria and Cyanobacteria. We propose that such model artificial microbialites can serve as experimental analogues for natural stromatolites.
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Abed RM, Kohls K, Schoon R, Scherf AK, Schacht M, Palinska KA, Al-Hassani H, Hamza W, Rullkötter JÃ, Golubic S. Lipid biomarkers, pigments and cyanobacterial diversity of microbial mats across intertidal flats of the arid coast of the Arabian Gulf (Abu Dhabi, UAE). FEMS Microbiol Ecol 2008; 65:449-62. [DOI: 10.1111/j.1574-6941.2008.00537.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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16
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A salinity and sulfate manipulation of hypersaline microbial mats reveals stasis in the cyanobacterial community structure. ISME JOURNAL 2008; 2:457-70. [DOI: 10.1038/ismej.2008.6] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Lin X, Zhao Y, Fu Q, Umashankara ML, Feng Z. Analysis of culturable and unculturable microbial community in bensulfuron-methyl contaminated paddy soils. J Environ Sci (China) 2008; 20:1494-1500. [PMID: 19209638 DOI: 10.1016/s1001-0742(08)62555-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To investigate the influence of bensulfuron-methyl (BSM) on culturable microbial quantities and unculturable microbial community structures, conventional and molecular biological methods were employed in five BSM treated soils with three replications, respectively. The results obtained with traditional culture-dependent methods showed that a low-level of BSM had slight and transient effects on culturable microorganisms; nevertheless, high concentration of BSM resulted in a dramatic decrease in bacterial colony forming units (cfus). The result obtained using denaturing gradient gel electrophoresis (DGGE) revealed that more than 17 bands were observed in low BSM contaminated soil samples and only 10 bands were detected in samples with high BSM contamination. In other words, the diversity of soil community structure is related to the concentration of BSM. Cluster analysis showed that the community structure under low level of contamination was more similar to that of the control, while heavy contaminated amendments were far away from the above group. In a sense, the cooperation of the traditional method and the molecular biological method is more powerful to study the soil microbial information in contaminated ecosystem.
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MESH Headings
- Bacteria, Anaerobic/genetics
- Bacteria, Anaerobic/isolation & purification
- Colony Count, Microbial
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- Electrophoresis, Polyacrylamide Gel
- Herbicides/metabolism
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- Soil Microbiology
- Soil Pollutants/metabolism
- Sulfonylurea Compounds/metabolism
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Affiliation(s)
- Xiaoyan Lin
- Department of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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18
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Abed RMM, Kohls K, de Beer D. Effect of salinity changes on the bacterial diversity, photosynthesis and oxygen consumption of cyanobacterial mats from an intertidal flat of the Arabian Gulf. Environ Microbiol 2007; 9:1384-92. [PMID: 17504476 DOI: 10.1111/j.1462-2920.2007.01254.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effects of salinity fluctuation on bacterial diversity, rates of gross photosynthesis (GP) and oxygen consumption in the light (OCL) and in the dark (OCD) were investigated in three submerged cyanobacterial mats from a transect on an intertidal flat. The transect ran 1 km inland from the low water mark along an increasingly extreme habitat with respect to salinity. The response of GP, OCL and OCD in each sample to various salinities (65 per thousand, 100 per thousand, 150 per thousand and 200 per thousand) were compared. The obtained sequences and the number of unique operational taxonomic units showed clear differences in the mats' bacterial composition. While cyanobacteria decreased from the lower to the upper tidal mat, other bacterial groups such as Chloroflexus and Cytophaga/Flavobacteria/Bacteriodetes showed an opposite pattern with the highest dominance in the middle and upper tidal mats respectively. Gross photosynthesis and OCL at the ambient salinities of the mats decreased from the lower to the upper tidal zone. All mats, regardless of their tidal location, exhibited a decrease in areal GP, OCL and OCD rates at salinities > 100 per thousand. The extent of inhibition of these processes at higher salinities suggests an increase in salt adaptation of the mats microorganisms with distance from the low water line. We conclude that the resilience of microbial mats towards different salinity regimes on intertidal flats is accompanied by adjustment of the diversity and function of their microbial communities.
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Affiliation(s)
- Raeid M M Abed
- Max-Planck Institute for Marine Microbiology, Microsensor group, Bremen, Germany.
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19
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Abed RMM, Zein B, Al-Thukair A, de Beer D. Phylogenetic diversity and activity of aerobic heterotrophic bacteria from a hypersaline oil-polluted microbial mat. Syst Appl Microbiol 2007; 30:319-30. [PMID: 17056222 DOI: 10.1016/j.syapm.2006.09.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Accepted: 09/18/2006] [Indexed: 11/17/2022]
Abstract
The diversity and function of aerobic heterotrophic bacteria (AHB) in cyanobacterial mats have been largely overlooked. We used culture-dependent and molecular techniques to explore the species diversity, degradative capacities and functional guilds of AHB in the photic layer (2mm) of an oil-polluted microbial mat from Saudi Arabia. Enrichment isolation was carried out at different salinities (5% and 12%) and temperatures (28 and 45 degrees C) and on various substrates (acetate, glycolate, Spirulina extract and crude oils). Counts of most probable number showed a numerical abundance of AHB in the range of 1.15-8.13x10(6) cellsg(-1) and suggested the presence of halotolerant and thermotolerant populations. Most of the 16S rRNA sequences of the obtained clones and isolates were phylogenetically affiliated to the groups Gammaproteobacteria, Bacteriodetes and Alphaproteobacteria. Groups like Deltaproteobacteria, Verrucomicrobia, Planctomycetes, Spirochaetes, Acidobacteria and Deinococcus-Thermus were only detected by cloning. The strains isolated on acetate and glycolate belonged to the genera Marinobacter, Halomonas, Roseobacter and Rhodobacter whereas the strains enriched on crude oil belonged to Marinobacter and Alcanivorax. Members of the Bacteriodetes group were only enriched on Spirulina extract indicating their specialization in the degradation of cyanobacterial dead cells. The substrate spectra of representative strains showed the ability of all AHB to metabolize cyanobacterial photosynthetic and fermentation products. However, the unique in situ conditions of the mat apparently favored the enrichment of versatile strains that grew on both the cyanobacterial exudates and the hydrocarbons. We conclude that AHB in cyanobacterial mats represent a diverse community that plays an important role in carbon-cycling within microbial mats.
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Affiliation(s)
- Raeid M M Abed
- Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-8359 Bremen, Germany.
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20
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Bachar A, Omoregie E, de Wit R, Jonkers HM. Diversity and function of Chloroflexus-like bacteria in a hypersaline microbial mat: phylogenetic characterization and impact on aerobic respiration. Appl Environ Microbiol 2007; 73:3975-83. [PMID: 17449697 PMCID: PMC1932729 DOI: 10.1128/aem.02532-06] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 04/11/2007] [Indexed: 11/20/2022] Open
Abstract
We studied the diversity of Chloroflexus-like bacteria (CLB) in a hypersaline phototrophic microbial mat and assayed their near-infrared (NIR) light-dependent oxygen respiration rates. PCR with primers that were reported to specifically target the 16S rRNA gene from members of the phylum Chloroflexi resulted in the recovery of 49 sequences and 16 phylotypes (sequences of the same phylotype share more than 96% similarity), and 10 of the sequences (four phylotypes) appeared to be related to filamentous anoxygenic phototrophic members of the family Chloroflexaceae. Photopigment analysis revealed the presence of bacteriochlorophyll c (BChlc), BChld, and gamma-carotene, pigments known to be produced by phototrophic CLB. Oxygen microsensor measurements for intact mats revealed a NIR (710 to 770 nm) light-dependent decrease in aerobic respiration, a phenomenon that we also observed in an axenic culture of Chloroflexus aurantiacus. The metabolic ability of phototrophic CLB to switch from anoxygenic photosynthesis under NIR illumination to aerobic respiration under non-NIR illumination was further used to estimate the contribution of these organisms to mat community respiration. Steady-state oxygen profiles under dark conditions and in the presence of visible (VIS) light (400 to 700 nm), NIR light (710 to 770 nm), and VIS light plus NIR light were compared. NIR light illumination led to a substantial increase in the oxygen concentration in the mat. The observed impact on oxygen dynamics shows that CLB play a significant role in the cycling of carbon in this hypersaline microbial mat ecosystem. This study further demonstrates that the method applied, a combination of microsensor techniques and VIS and NIR illumination, allows rapid establishment of the presence and significance of CLB in environmental samples.
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Affiliation(s)
- Ami Bachar
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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21
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Ohkubo S, Miyashita H, Murakami A, Takeyama H, Tsuchiya T, Mimuro M. Molecular detection of epiphytic Acaryochloris spp. on marine macroalgae. Appl Environ Microbiol 2006; 72:7912-5. [PMID: 17028237 PMCID: PMC1694208 DOI: 10.1128/aem.01148-06] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A molecular method for detecting the epiphyte community on marine macroalgae was developed by using PCR-denaturing gradient gel electrophoresis. Selective amplification of 16S rRNA gene fragments from either cyanobacteria or algal plastids improved the detection of minor epiphytes. Two phylotypes of Acaryochloris, a chlorophyll d-containing cyanobacterium, were found not only on red macroalgae but also on green and brown macroalgae.
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Affiliation(s)
- Satoshi Ohkubo
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
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22
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Moisander PH, Shiue L, Steward GF, Jenkins BD, Bebout BM, Zehr JP. Application of a nifH oligonucleotide microarray for profiling diversity of N2-fixing microorganisms in marine microbial mats. Environ Microbiol 2006; 8:1721-35. [PMID: 16958753 DOI: 10.1111/j.1462-2920.2006.01108.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diazotrophic community structure in microbial mats from Guerrero Negro (GN), Baja California, Mexico, was studied using polymerase chain reaction amplification of the nifH gene and a newly developed nifH oligonucleotide microarray. Ninety-six oligonucleotide probes designed for nifH sequences from cultivated isolates and the environment were printed on glass microarrays. Phylogenetic analysis showed that the probes represented all of the main nifH clusters. Specificity was tested by (i) evaluation of cross hybridization using individual targets, and (ii) comparison of the observed hybridization signals and those predicted from the sequences cloned from microbial mats. Signal intensity had a positive relationship with target concentration and the percentage identity between probe and target. Under moderate stringency and high target concentration, specificity of the probes varied from 77% to 100% with the individual targets tested. At the end of a 7-month long nutrient manipulation experiment in GN microbial mats, no expression of nitrogen fixation under nitrogen loading was detected, although a diverse community of diazotrophs was detected. The diversity in diazotrophic population present was higher than in the population expressing the nifH gene, and there were taxa specific differences in response to nutrients. The nifH microarray is a powerful tool for diazotroph community analysis in the marine environment.
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Affiliation(s)
- Pia H Moisander
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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23
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Lau E, Nash CZ, Vogler DR, Cullings KW. Molecular diversity of cyanobacteria inhabiting coniform structures and surrounding mat in a Yellowstone hot spring. ASTROBIOLOGY 2005; 5:83-92. [PMID: 15711172 DOI: 10.1089/ast.2005.5.83] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Lithified coniform structures are common within cyanobacterial mats in Yellowstone National Park hot springs. It is unknown whether these structures and the mats from which they develop are inhabited by the same cyanobacterial populations. Denaturing gradient gel electrophoresis and sequencing and phylogenetic analysis of 16S rDNA was used to determine whether (1) three different morphological types of lithified coniform structures are inhabited by different cyanobacterial species, (2) these species are partitioned along a vertical gradient of these structures, and (3) lithified and non-lithified sections of mat are inhabited by different cyanobacterial species. Our results, based on multiple samplings, indicate that the cyanobacterial community compositions in the three lithified morphological types were identical and lacked any vertical differentiation. However, lithified and non-lithified portions of the same mat were inhabited by distinct and different populations of cyanobacteria. Cyanobacteria inhabiting lithified structures included at least one undefined Oscillatorialean taxon, which may represent the dominant cyanobacteria genus in lithified coniform stromatolites, Phormidium, three Synechococcus-like species, and two unknown cyanobacterial taxa. In contrast, the surrounding mats contained four closely related Synechococcus-like species. Our results indicate that the distribution of lithified coniform stromatolites may be dependent on the presence of one or more microorganisms, which are phylogenetically different from those inhabiting surrounding non-lithified mats.
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Affiliation(s)
- Evan Lau
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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24
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Smith SM, Abed RMM, Gercia-Pichel F. Biological soil crusts of sand dunes in Cape Cod National Seashore, Massachusetts, USA. MICROBIAL ECOLOGY 2004; 48:200-8. [PMID: 15546040 DOI: 10.1007/s00248-004-0254-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2003] [Accepted: 01/16/2004] [Indexed: 05/10/2023]
Abstract
Biological soil crusts cover hundreds of hectares of sand dunes at the northern tip of Cape Cod National Seashore (Massachusetts, USA). Although the presence of crusts in this habitat has long been recognized, neither the organisms nor their ecological roles have been described. In this study, we report on the microbial community composition of crusts from this region and describe several of their physical and chemical attributes that bear on their environmental role. Microscopic and molecular analyses revealed that eukaryotic green algae belonging to the genera Klebsormidium or Geminella formed the bulk of the material sampled. Phylogenetic reconstruction of partial 16S rDNA sequences obtained from denaturing gradient gel electrophoresis (DGGE) fingerprints also revealed the presence of bacterial populations related to the subclass of the Proteobacteria, the newly described phylum Geothrix/ Holophaga/ Acidobacterium, the Cytophaga/ Flavobacterium/ Bacteroides group, and spirochetes. The presence of these crusts had significant effects on the hydric properties and nutrient status of the natural substrate. Although biological soil crusts are known to occur in dune environments around the world, this study enhances our knowledge of their geographic distribution and suggests a potential ecological role for crust communities in this landscape.
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Affiliation(s)
- S M Smith
- National Park Service Cape Cod National Seashore, 99 Marconi Site Road, Wellfleet, Massachusetts 02667, USA.
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25
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Janse I, Meima M, Kardinaal WEA, Zwart G. High-resolution differentiation of Cyanobacteria by using rRNA-internal transcribed spacer denaturing gradient gel electrophoresis. Appl Environ Microbiol 2004; 69:6634-43. [PMID: 14602623 PMCID: PMC262283 DOI: 10.1128/aem.69.11.6634-6643.2003] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For many ecological studies of cyanobacteria, it is essential that closely related species or strains can be discriminated. Since this is often not possible by using morphological features, cyanobacteria are frequently studied by using DNA-based methods. A powerful method for analysis of the diversity and dynamics of microbial populations and for checking the purity and affiliation of cultivated strains is denaturing gradient gel electrophoresis (DGGE). We realized high-resolution discrimination of a variety of cyanobacteria by means of DGGE analysis of sections of the internal transcribed spacer between the 16S and 23S rRNA genes (rRNA-ITS). A forward primer specific for cyanobacteria, targeted at the 3' end of the 16S rRNA gene, was designed. The combination of this primer and three different reverse primers targeted to the rRNA-ITS or to the 23S rRNA gene yielded PCR products of different sizes from cultures of all 16 cyanobacterial genera that were tested but not from other bacteria. DGGE profiles produced from the shortest section of rRNA-ITS consisted of one band for all but one cyanobacterial genera, and those generated from longer stretches of rRNA-ITS yielded DGGE profiles containing one to four bands. The suitability of DGGE for detecting intrageneric and intraspecific variation was tested by using strains of the genus Microcystis: Many strains could be discriminated by means of rRNA-ITS DGGE, and the resolution of this method was strikingly higher than that obtained with previously described methods. The applicability of the developed DGGE assays for analysis of cyanobacteria in field samples was demonstrated by using samples from freshwater lakes. The advantages and disadvantages associated with the use of each developed primer set are discussed.
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Affiliation(s)
- Ingmar Janse
- Department of Microbial Ecology, Centre for Limnology, Netherlands Institute for Ecology, 3631 AC Nieuwersluis, The Netherlands.
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26
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Grötzschel S, Abed RMM, de Beer D. Metabolic shifts in hypersaline microbial mats upon addition of organic substrates. Environ Microbiol 2002; 4:683-95. [PMID: 12460276 DOI: 10.1046/j.1462-2920.2002.00356.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The responses of hypersaline microbial mats to the addition of acetate, glycolate or glucose were investigated using oxygen, pH and sulphide microsensors. Changes in community structure were investigated with molecular techniques. Acetate addition inhibited respiration in the photic zone, stimulated respiration in the aphotic zone and had no effect on gross photosynthesis. Glycolate addition strongly increased both respiration and gross photosynthesis in the photic zone. Thus, glycolate and acetate were probably consumed in those regions of the mat where these substrates are usually formed. Moreover, photosynthesis was only stimulated by increased respiration and concomitant CO2 production in the photic zone which indicates that the photosynthetic and respiratory populations must be present in close proximity to each other. Glucose addition had an unexpected negative effect on the microbial population, strongly inhibiting both respiration and gross photosynthesis within hours. After four days, oxygen profiles in the light were equal to those measured in the dark. After replacing the water phase with unamended water, photosynthesis and respiration recovered within a week. None of the physiological changes were accompanied by detectable shifts in the cyanobacterial or the overall microbial community. The mechanism of inhibition of photosynthesis by glucose requires further investigation.
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Affiliation(s)
- Stefan Grötzschel
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany.
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27
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Abed RMM, Schönhuber W, Amann R, Garcia-Pichel F. Picobenthic cyanobacterial populations revealed by 16S rRNA-targeted in situ hybridization. Environ Microbiol 2002; 4:375-82. [PMID: 12123473 DOI: 10.1046/j.1462-2920.2002.00307.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report on the morphological identification of a population of benthic cyanobacteria from microbial mats, known previously only from molecular analyses of field samples, based on the retrieval of environmental 16S rRNA sequences. We used in situ hybridization with horseradish peroxidase-labelled oligonucleotide probes designed to target the 16S rRNA of our unidentified population. Two probes were designed and checked for target binding ability and specificity using membrane hybridization against electroblotted bands from a denaturant gradient gel electrophoresis (DGGE) fingerprint of 16S rDNA gene fragments from the original cyanobacterial community. Under in situ hybridization, these probes bound specifically to extremely small, unicellular, colony-forming cyanobacteria, 0.75-1 microm in diameter, which were embedded in abundant mucilaginous investments. We propose the term picobenthos, by analogy with picoplankton, to describe those unicellular benthic microbes around or less than 1 microm in diameter. Although picoplanktonic cyanobacteria are abundant in ocean and freshwaters, picobenthic (<1 microm) unicellular cyanobacteria are not typically recognized as a major component of microbial mats. The small size and low levels of photopigment autofluorescence from these cells probably rendered them cryptic or indistinguishable from heterotrophic bacteria in routine microscopic observations. It is not known how widespread picobenthic cyanobacteria may be in other environments.
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Affiliation(s)
- Raeid M M Abed
- Max-Planck Institute for Marine Microbiology, Celsiusstrasse1, D-28359 Bremen, Germany.
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28
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Abed RMM, Safi NMD, Köster J, de Beer D, El-Nahhal Y, Rullkötter J, Garcia-Pichel F. Microbial diversity of a heavily polluted microbial mat and its community changes following degradation of petroleum compounds. Appl Environ Microbiol 2002; 68:1674-83. [PMID: 11916684 PMCID: PMC123877 DOI: 10.1128/aem.68.4.1674-1683.2002] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the microbial diversity of benthic cyanobacterial mats inhabiting a heavily polluted site in a coastal stream (Wadi Gaza) and monitored the microbial community response induced by exposure to and degradation of four model petroleum compounds in the laboratory. Phormidium- and Oscillatoria-like cyanobacterial morphotypes were dominant in the field. Bacteria belonging to different groups, mainly the Cytophaga-Flavobacterium-Bacteriodes group, the gamma and beta subclasses of the class Proteobacteria, and the green nonsulfur bacteria, were also detected. In slurry experiments, these communities efficiently degraded phenanthrene and dibenzothiophene completely in 7 days both in the light and in the dark. n-Octadecane and pristane were degraded to 25 and 34% of their original levels, respectively, within 7 days, but there was no further degradation until 40 days. Both cyanobacterial and bacterial communities exhibited noticeable changes concomitant with degradation of the compounds. The populations enriched by exposure to petroleum compounds included a cyanobacterium affiliated phylogenetically with Halomicronema. Bacteria enriched both in the light and in the dark, but not bacteria enriched in any of the controls, belonged to the newly described Holophaga-Geothrix-Acidobacterium phylum. In addition, another bacterial population, found to be a member of green nonsulfur bacteria, was detected only in the bacteria treated in the light. All or some of the populations may play a significant role in metabolizing the petroleum compounds. We concluded that the microbial mats from Wadi Gaza are rich in microorganisms with high biodegradative potential.
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Affiliation(s)
- Raeid M M Abed
- Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
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29
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Bebout BM, Carpenter SP, Des Marais DJ, Discipulo M, Embaye T, Garcia-Pichel F, Hoehler TM, Hogan M, Jahnke LL, Keller RM, Miller SR, Prufert-Bebout LE, Raleigh C, Rothrock M, Turk K. Long-term manipulations of intact microbial mat communities in a greenhouse collaboratory: simulating earth's present and past field environments. ASTROBIOLOGY 2002; 2:383-402. [PMID: 12593778 DOI: 10.1089/153110702762470491] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Photosynthetic microbial mat communities were obtained from marine hypersaline saltern ponds, maintained in a greenhouse facility, and examined for the effects of salinity variations. Because these microbial mats are considered to be useful analogs of ancient marine communities, they offer insights about evolutionary events during the >3 billion year time interval wherein mats co-evolved with Earth's lithosphere and atmosphere. Although photosynthetic mats can be highly dynamic and exhibit extremely high activity, the mats in the present study have been maintained for >1 year with relatively minor changes. The major groups of microorganisms, as assayed using microscopic, genetic, and biomarker methodologies, are essentially the same as those in the original field samples. Field and greenhouse mats were similar with respect to rates of exchange of oxygen and dissolved inorganic carbon across the mat-water interface, both during the day and at night. Field and greenhouse mats exhibited similar rates of efflux of methane and hydrogen. Manipulations of salinity in the water overlying the mats produced changes in the community that strongly resemble those observed in the field. A collaboratory testbed and an array of automated features are being developed to support remote scientific experimentation with the assistance of intelligent software agents. This facility will permit teams of investigators the opportunity to explore ancient environmental conditions that are rare or absent today but that might have influenced the early evolution of these photosynthetic ecosystems.
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Affiliation(s)
- Brad M Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, California 94035, USA.
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30
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Neilan BA, Burns BP, Relman DA, Lowe DR. Molecular identification of cyanobacteria associated with stromatolites from distinct geographical locations. ASTROBIOLOGY 2002; 2:271-280. [PMID: 12530237 DOI: 10.1089/153110702762027853] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Modern stromatolites represent a significant resource for studying microbial ecology and evolution. A preliminary investigation was undertaken employing specific genetic probes to characterize the cyanobacteria responsible for stromatolite construction in a range of environments, including microbial mats found in Australia not previously examined with molecular methods. Isolates of cyanobacteria were collected from stromatolites in thermal springs, hypersaline lakes, and oceanic fringes on two continents. A polymerase chain reaction specific for DNA of cyanobacterial 16S rRNA was developed, the resulting products of the DNA amplification reaction were sequenced, and the data were used to infer relatedness between the isolates studied and other members of the cyanobacterial radiation. Complete sequence was generated for the region from position 27 to 408 for 13 strains of cyanobacteria associated with stromatolites. All stromatolite-derived sequences were most closely related to cyanobacteria, as indicated by local sequence alignment. It was possible to correlate genetic identity with morphological nomenclatures and to expand the phylogeny of benthic cyanobacteria. These inferences were also expanded to temporal variation in the dominant resident cyanobacterial species based on sampling of surface and core sinter laminations. Under the methods employed, only one cyanobacterial strain was detected in each sample, suggesting the possible dominance of a specific clonal population of cyanobacteria at any one time in the biota of the samples tested. The data indicate that internal core samples of a stromatolite at least 10 years old can be successfully analyzed by DNA-based methods to identify preserved cyanobacteria.
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Affiliation(s)
- Brett A Neilan
- Departments of Geological and Environmental Sciences and Microbiology and Immunology, Stanford University, Stanford, California, USA.
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