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Zhou J, Zhang CJ, Li M. Desulfovibrio mangrovi sp. nov., a sulfate-reducing bacterium isolated from mangrove sediments: a member of the proposed genus "Psychrodesulfovibrio". Antonie Van Leeuwenhoek 2023; 116:499-510. [PMID: 36917346 DOI: 10.1007/s10482-023-01820-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
"Psychrodesulfovibrio", a proposed genus within the family Desulfovibrionaceae, is a group of sulfate-reducing bacteria with biogeochemical significance but restricted child taxa availability. In this study, a strictly anaerobic bacterium, designed strain FT415T, was isolated from mangrove sediments in Futian Mangrove Nature Reserve in Shenzhen, China. The strain was Gram-stain-negative, motile, and vibrio-shaped with a single polar flagellum, which grew at the temperature range of 15-42 °C (optimum 37 °C), pH range of 6.0-7.5 (optimum 6.8), and in the presence of 0-36 g l-1 NaCl (optimum 6 g l-1 NaCl). In the presence of sulfate, electron donors including lactate, ethanol, pyruvate, malate, fumarate, succinate, cysteine, and glycerol were incompletely oxidized to acetate, and H2 and formate were used as electron donors with acetate as the carbon source by strain FT415T. Sulfate, thiosulfate, sulfide, and anthraquinone-2,6-disulfonate were reduced in the presence of lactate. Fe(III) oxide was reduced without cell growth. Fermentative growth was observed with pyruvate and cysteine. Vitamins were not required for growth. The major cellular fatty acids (> 10%) were C16:0, summed feature 10 (C18:1 c11/t9/t6 and/or unknown ECL 17.834), C16:1 cis 9, and C18:0. The major polar lipids were phosphatidylethanolamine, phospholipids, and aminolipids. The predominant menaquinone was MK-6(H2). The genomic DNA G+C content was 56.7%. Phylogenetic analysis showed that strain FT415T shared a 98.1% similarity in 16S rRNA gene sequence, an average nucleotide identity value of 84.0%, an average amino-acid identity value of 85.4%, and a digital DNA-DNA hybridization value of 25.7% with its closest relative Desulfovibrio subterraneus HN2T, which has been proposed to be transferred to the genus "Psychrodesulfovibrio". Based on phenotypic, phylogenetic, and genotypic evidence, a new species of the family Desulfovibrionaceae, Desulfovibrio mangrovi sp. nov. was proposed with the type strain FT415T (=GDMCC 1.3410T=KCTC 25525T).
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Affiliation(s)
- Jinjie Zhou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Cui-Jing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China.
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Razia S, Hadibarata T, Lau SY. Acidophilic microorganisms in remediation of contaminants present in extremely acidic conditions. Bioprocess Biosyst Eng 2023; 46:341-358. [PMID: 36602611 DOI: 10.1007/s00449-022-02844-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023]
Abstract
Acidophiles are a group of microorganisms that thrive in acidic environments where pH level is far below the neutral value 7.0. They belong to a larger family called extremophiles, which is a group that thrives in various extreme environmental conditions which are normally inhospitable to other organisms. Several human activities such as mining, construction and other industrial processes release highly acidic effluents and wastes into the environment. Those acidic wastes and wastewaters contain different types of pollutants such as heavy metals, radioactive, and organic, whose have adverse effects on human being as well as on other living organisms. To protect the whole ecosystem, those pollutants containing effluents or wastes must be clean properly before releasing into environment. Physicochemical cleanup processes under extremely acidic conditions are not always successful due to high cost and release of toxic byproducts. While in case of biological methods, except acidophiles, no other microorganisms cannot survive in highly acidic conditions. Therefore, acidophiles can be a good choice for remediation of different types of contaminants present in acidic conditions. In this review article, various roles of acidophilic microorganisms responsible for removing heavy metals and radioactive pollutants from acidic environments were discussed. Bioremediation of various acidic organic pollutants by using acidophiles was also studied. Overall, this review could be helpful to extend our knowledge as well as to do further relevant novel studies in the field of acidic pollutants remediation by applying acidophilic microorganisms.
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Affiliation(s)
- Sultana Razia
- Environmental Engineering Program, Faculty of Engineering and Science, Curtin University, Miri, Malaysia
| | - Tony Hadibarata
- Environmental Engineering Program, Faculty of Engineering and Science, Curtin University, Miri, Malaysia.
| | - Sie Yon Lau
- Department of Chemical and Energy Engineering, Faculty of Engineering and Science, Curtin University, Miri, Malaysia
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3
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Kaviani Rad A, Balasundram SK, Azizi S, Afsharyzad Y, Zarei M, Etesami H, Shamshiri RR. An Overview of Antibiotic Resistance and Abiotic Stresses Affecting Antimicrobial Resistance in Agricultural Soils. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:4666. [PMID: 35457533 PMCID: PMC9025980 DOI: 10.3390/ijerph19084666] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 01/29/2023]
Abstract
Excessive use of antibiotics in the healthcare sector and livestock farming has amplified antimicrobial resistance (AMR) as a major environmental threat in recent years. Abiotic stresses, including soil salinity and water pollutants, can affect AMR in soils, which in turn reduces the yield and quality of agricultural products. The objective of this study was to investigate the effects of antibiotic resistance and abiotic stresses on antimicrobial resistance in agricultural soils. A systematic review of the peer-reviewed published literature showed that soil contaminants derived from organic and chemical fertilizers, heavy metals, hydrocarbons, and untreated sewage sludge can significantly develop AMR through increasing the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in agricultural soils. Among effective technologies developed to minimize AMR's negative effects, salinity and heat were found to be more influential in lowering ARGs and subsequently AMR. Several strategies to mitigate AMR in agricultural soils and future directions for research on AMR have been discussed, including integrated control of antibiotic usage and primary sources of ARGs. Knowledge of the factors affecting AMR has the potential to develop effective policies and technologies to minimize its adverse impacts.
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Affiliation(s)
- Abdullah Kaviani Rad
- Department of Soil Science, School of Agriculture, Shiraz University, Shiraz 71946-85111, Iran;
| | - Siva K. Balasundram
- Department of Agriculture Technology, Faculty of Agriculture, University Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Shohreh Azizi
- UNESCO-UNISA Africa Chair in Nanosciences and Nanotechnology, College of Graduate Studies, University of South Africa, Pretoria 0003, South Africa;
- Nanosciences African Network (NANOAFNET), iThemba LABS-National Research Foundation, Cape Town 7129, South Africa
| | - Yeganeh Afsharyzad
- Department of Microbiology, Faculty of Modern Sciences, The Islamic Azad University of Tehran Medical Sciences, Tehran 19496-35881, Iran;
| | - Mehdi Zarei
- Department of Soil Science, School of Agriculture, Shiraz University, Shiraz 71946-85111, Iran;
- Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid 73819-43885, Iran
| | - Hassan Etesami
- Department of Soil Science, University of Tehran, Tehran 14179-35840, Iran;
| | - Redmond R. Shamshiri
- Leibniz Institute for Agricultural Engineering and Bioeconomy, 14469 Potsdam-Bornim, Germany;
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De La Fuente MJ, Gallardo-Bustos C, De la Iglesia R, Vargas IT. Microbial Electrochemical Technologies for Sustainable Nitrogen Removal in Marine and Coastal Environments. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:2411. [PMID: 35206599 PMCID: PMC8875524 DOI: 10.3390/ijerph19042411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 02/01/2023]
Abstract
For many years, the world's coastal marine ecosystems have received industrial waste with high nitrogen concentrations, generating the eutrophication of these ecosystems. Different physicochemical-biological technologies have been developed to remove the nitrogen present in wastewater. However, conventional technologies have high operating costs and excessive production of brines or sludge which compromise the sustainability of the treatment. Microbial electrochemical technologies (METs) have begun to gain attention due to their cost-efficiency in removing nitrogen and organic matter using the metabolic capacity of microorganisms. This article combines a critical review of the environmental problems associated with the discharge of the excess nitrogen and the biological processes involved in its biogeochemical cycle; with a comparative analysis of conventional treatment technologies and METs especially designed for nitrogen removal. Finally, current METs limitations and perspectives as a sustainable nitrogen treatment alternative and efficient microbial enrichment techniques are included.
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Affiliation(s)
- María José De La Fuente
- Departamento de Ingeniería Hidráulica y Ambiental, Facultad de Ingeniería, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (M.J.D.L.F.); (C.G.B.)
- Marine Energy Research & Innovation Center (MERIC), Santiago 7550268, Chile;
| | - Carlos Gallardo-Bustos
- Departamento de Ingeniería Hidráulica y Ambiental, Facultad de Ingeniería, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (M.J.D.L.F.); (C.G.B.)
- Centro de Desarrollo Urbano Sustentable (CEDEUS), Santiago 7820436, Chile
| | - Rodrigo De la Iglesia
- Marine Energy Research & Innovation Center (MERIC), Santiago 7550268, Chile;
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Ignacio T. Vargas
- Departamento de Ingeniería Hidráulica y Ambiental, Facultad de Ingeniería, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (M.J.D.L.F.); (C.G.B.)
- Marine Energy Research & Innovation Center (MERIC), Santiago 7550268, Chile;
- Centro de Desarrollo Urbano Sustentable (CEDEUS), Santiago 7820436, Chile
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5
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Distribution of Sulfate-Reducing Bacteria in the Environment: Cryopreservation Techniques and Their Potential Storage Application. Processes (Basel) 2021. [DOI: 10.3390/pr9101843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) are a heterogeneous group of anaerobic microorganisms that play an important role in producing hydrogen sulfide not only in the natural environment, but also in the gastrointestinal tract and oral cavity of animals and humans. The present review was written with the inclusion of 110 references including the time period from 1951 to 2021. The following databases were evaluated: Web of Science, Scopus and Google Scholar. The articles chosen to be included in the review were written mainly in the English and Czech languages. The molecular mechanisms of microbial cryoprotection differ depending on the environment where microorganisms were initially isolated. It was observed that the viability of microorganisms after cryopreservation is dependent on a number of factors, primarily colony age, amount of inoculum, cell size or rate of cooling, and their molecular inventory. Therefore, this paper is devoted to assessing the performance and suitability of various cryopreservation methods of intestinal bacteria, including molecular mechanisms of their protection. In order to successfully complete the cryopreservation process, selecting the correct laboratory equipment and cryopreservation methodology is important. Our analysis revealed that SRB should be stored in glass vials to help mitigate the corrosive nature of hydrogen sulfide, which can affect their physiology on a molecular level. Furthermore, it is recommended that their storage be performed in distilled water or in a suspension with a low salt concentration. From a molecular biological and bioengineering perspective, this contribution emphasizes the need to consider the potential impact associated with SRB in the medical, construction, and environmental sectors.
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Effects of Cattails and Hydraulic Loading on Heavy Metal Removal from Closed Mine Drainage by Pilot-Scale Constructed Wetlands. WATER 2021. [DOI: 10.3390/w13141937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This study demonstrated heavy metal removal from neutral mine drainage of a closed mine in Kyoto prefecture in pilot-scale constructed wetlands (CWs). The CWs filled with loamy soil and limestone were unplanted or planted with cattails. The hydraulic retention time (HRT) in the CWs was shortened gradually from 3.8 days to 1.2 days during 3.5 months of operation. A short HRT of 1.2 days in the CWs was sufficient to achieve the effluent standard for Cd (0.03 mg/L). The unplanted and the cattail-planted CWs reduced the average concentrations of Cd from 0.031 to 0.01 and 0.005 mg/L, Zn from 0.52 to 0.14 and 0.08 mg/L, Cu from 0.07 to 0.04 and 0.03 mg/L, and As from 0.011 to 0.006 and 0.006 mg/L, respectively. Heavy metals were removed mainly by adsorption to the soil in both CWs. The biological concentration factors in cattails were over 2 for Cd, Zn, and Cu. The translocation factors of cattails for all metals were 0.5–0.81. Sulfate-reducing bacteria (SRB) belonging to Deltaproteobacteria were detected only from soil in the planted CW. Although cattails were a minor sink, the plants contributed to metal removal by rhizofiltration and incubation of SRB, possibly producing sulfide precipitates in the rhizosphere.
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Goff JL, Schaefer JK, Yee N. Extracellular sulfite is protective against reactive oxygen species and antibiotic stress in Shewanella oneidensis MR-1. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:394-400. [PMID: 33870629 DOI: 10.1111/1758-2229.12947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/04/2021] [Indexed: 06/12/2023]
Abstract
In this study, we investigated the extracellular reactive sulfur species produced by Shewanella oneidensis MR-1 during growth. The results showed that sulfite is the major extracellular sulfur metabolite released to the growth medium under both aerobic and anaerobic growth conditions. Exogenous sulfite at physiological concentrations protected S. oneidensis MR-1 from hydrogen peroxide toxicity and enhanced tolerance to the beta-lactam antibiotics cefazolin, meropenem, doripenem and ertapenem. These findings suggest that the release of extracellular sulfite is a bacterial defence mechanism that plays a role in the mitigation of environmental stress.
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Affiliation(s)
- Jennifer L Goff
- Department of Earth and Planetary Sciences, Rutgers University, Piscataway, NJ, USA
| | - Jeffra K Schaefer
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Nathan Yee
- Department of Earth and Planetary Sciences, Rutgers University, Piscataway, NJ, USA
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, USA
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8
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Kushkevych I, Hýžová B, Vítězová M, Rittmann SKMR. Microscopic Methods for Identification of Sulfate-Reducing Bacteria from Various Habitats. Int J Mol Sci 2021; 22:4007. [PMID: 33924516 PMCID: PMC8069399 DOI: 10.3390/ijms22084007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 12/01/2022] Open
Abstract
This paper is devoted to microscopic methods for the identification of sulfate-reducing bacteria (SRB). In this context, it describes various habitats, morphology and techniques used for the detection and identification of this very heterogeneous group of anaerobic microorganisms. SRB are present in almost every habitat on Earth, including freshwater and marine water, soils, sediments or animals. In the oil, water and gas industries, they can cause considerable economic losses due to their hydrogen sulfide production; in periodontal lesions and the colon of humans, they can cause health complications. Although the role of these bacteria in inflammatory bowel diseases is not entirely known yet, their presence is increased in patients and produced hydrogen sulfide has a cytotoxic effect. For these reasons, methods for the detection of these microorganisms were described. Apart from selected molecular techniques, including metagenomics, fluorescence microscopy was one of the applied methods. Especially fluorescence in situ hybridization (FISH) in various modifications was described. This method enables visual identification of SRB, determining their abundance and spatial distribution in environmental biofilms and gut samples.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Blanka Hýžová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Wien, Austria
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Campeciño J, Lagishetty S, Wawrzak Z, Sosa Alfaro V, Lehnert N, Reguera G, Hu J, Hegg EL. Cytochrome c nitrite reductase from the bacterium Geobacter lovleyi represents a new NrfA subclass. J Biol Chem 2020; 295:11455-11465. [PMID: 32518164 PMCID: PMC7450111 DOI: 10.1074/jbc.ra120.013981] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/07/2020] [Indexed: 01/07/2023] Open
Abstract
Cytochrome c nitrite reductase (NrfA) catalyzes the reduction of nitrite to ammonium in the dissimilatory nitrate reduction to ammonium (DNRA) pathway, a process that competes with denitrification, conserves nitrogen, and minimizes nutrient loss in soils. The environmental bacterium Geobacter lovleyi has recently been recognized as a key driver of DNRA in nature, but its enzymatic pathway is still uncharacterized. To address this limitation, here we overexpressed, purified, and characterized G. lovleyi NrfA. We observed that the enzyme crystallizes as a dimer but remains monomeric in solution. Importantly, its crystal structure at 2.55-Å resolution revealed the presence of an arginine residue in the region otherwise occupied by calcium in canonical NrfA enzymes. The presence of EDTA did not affect the activity of G. lovleyi NrfA, and site-directed mutagenesis of this arginine reduced enzymatic activity to <3% of the WT levels. Phylogenetic analysis revealed four separate emergences of Arg-containing NrfA enzymes. Thus, the Ca2+-independent, Arg-containing NrfA from G. lovleyi represents a new subclass of cytochrome c nitrite reductase. Most genera from the exclusive clades of Arg-containing NrfA proteins are also represented in clades containing Ca2+-dependent enzymes, suggesting convergent evolution.
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Affiliation(s)
- Julius Campeciño
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Satyanarayana Lagishetty
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - Victor Sosa Alfaro
- Department of Chemistry and Biophysics, The University of Michigan, Ann Arbor, Michigan, USA
| | - Nicolai Lehnert
- Department of Chemistry and Biophysics, The University of Michigan, Ann Arbor, Michigan, USA
| | - Gemma Reguera
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Jian Hu
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA,Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Eric L. Hegg
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA,For correspondence: Eric L. Hegg,
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Kushkevych I, Coufalová M, Vítězová M, Rittmann SKMR. Sulfate-Reducing Bacteria of the Oral Cavity and Their Relation with Periodontitis-Recent Advances. J Clin Med 2020; 9:E2347. [PMID: 32717883 PMCID: PMC7464432 DOI: 10.3390/jcm9082347] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/13/2020] [Accepted: 07/18/2020] [Indexed: 01/14/2023] Open
Abstract
The number of cases of oral cavity inflammation in the population has been recently increasing, with periodontitis being the most common disease. It is caused by a change in the microbial composition of the biofilm in the periodontal pockets. In this context, an increased incidence of sulfate-reducing bacteria (SRB) in the oral cavity has been found, which are a part of the common microbiome of the mouth. This work is devoted to the description of the diversity of SRB isolated from the oral cavity. It also deals with the general description of periodontitis in terms of manifestations and origin. It describes the ability of SRB to participate in its development, although their effect on periodontal inflammation is not fully understood. The production of hydrogen sulfide as a cytochrome oxidase inhibitor may play a role in the etiology. A meta-analysis was conducted based on studies of the occurrence of SRB in humans.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic; (M.C.); (M.V.)
- Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Palackého tř. 1946/1, 61242 Brno, Czech Republic
| | - Martina Coufalová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic; (M.C.); (M.V.)
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic; (M.C.); (M.V.)
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Althanstraße 14, 1090 Vienna, Austria
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11
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Donertas Ayaz B, Zubcevic J. Gut microbiota and neuroinflammation in pathogenesis of hypertension: A potential role for hydrogen sulfide. Pharmacol Res 2020; 153:104677. [PMID: 32023431 PMCID: PMC7056572 DOI: 10.1016/j.phrs.2020.104677] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/27/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023]
Abstract
Inflammation and gut dysbiosis are hallmarks of hypertension (HTN). Hydrogen sulfide (H2S) is an important freely diffusing molecule that modulates the function of neural, cardiovascular and immune systems, and circulating levels of H2S are reduced in animals and humans with HTN. While most research to date has focused on H₂S produced endogenously by the host, H2S is also produced by the gut bacteria and may affect the host homeostasis. Here, we review an association between neuroinflammation and gut dysbiosis in HTN, with special emphasis on a potential role of H2S in this interplay.
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Affiliation(s)
- Basak Donertas Ayaz
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States; Department of Pharmacology, College of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - Jasenka Zubcevic
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States.
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Bojović K, Ignjatović ÐDI, Soković Bajić S, Vojnović Milutinović D, Tomić M, Golić N, Tolinački M. Gut Microbiota Dysbiosis Associated With Altered Production of Short Chain Fatty Acids in Children With Neurodevelopmental Disorders. Front Cell Infect Microbiol 2020; 10:223. [PMID: 32509596 PMCID: PMC7248180 DOI: 10.3389/fcimb.2020.00223] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/22/2020] [Indexed: 12/20/2022] Open
Abstract
While gut microbiota dysbiosis has been linked with autism, its role in the etiology of other neurodevelopmental disorders (NDD) is largely underexplored. To our knowledge this is the first study to evaluate gut microbiota diversity and composition in 36 children from the Republic of Serbia diagnosed with NDD and 28 healthy children. The results revealed an increased incidence of potentially harmful bacteria, closely related to Clostridium species, in the NDD patient group compared to the Control group: Desulfotomaculum guttoideum (P < 0.01), Intestinibacter bartlettii (P < 0.05), and Romboutsia ilealis (P < 0.001). On the other hand, significantly lower diversity of common commensal bacteria in the NDD group of patients was noticed. Enterococcus faecalis (P < 0.05), Enterococcus gallinarum (P < 0.01), Streptococcus pasteurianus (P < 0.05), Lactobacillus rhamnosus (P < 0.01) and Bifidobacteria sp. were detected in lower numbers of patients or were even absent in some NDD patients. In addition, butyrate-producing bacteria Faecalibacterium prausnitzii (P < 0.01), Butyricicoccus pullicaecorum (P < 0.05), and Eubacterium rectale (P = 0.07) were less frequent in the NDD patient group. In line with that, the levels of fecal short chain fatty acids (SCFAs) were determined. Although significant differences in SCFA levels were not detected between NDD patients and the Control group, a positive correlation was noted between number of rDNA amplicons obtained with universal primers and level of propionic acid, as well as a trend for levels of total SCFAs and butyric acid in the Control group. This correlation is lost in the NDD patient group, indicating that NDD patients' microbiota differs from the microbiota of healthy children in the presence or number of strong SCFA-producing bacteria. According to a range-weighted richness index it was observed that microbial diversity was significantly lower in the NDD patient group. Our study reveals that the intestinal microbiota from NDD patients differs from the microbiota of healthy children. It is hypothesized that early life microbiome might have an impact on GI disturbances and accompanied behavioral problems frequently observed in patients with a broad spectrum of NDD.
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Affiliation(s)
| | - Ður -d ica Ignjatović
- Department of Biochemistry, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
- *Correspondence: Ðurđica Ignjatović
| | - Svetlana Soković Bajić
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Danijela Vojnović Milutinović
- Department of Biochemistry, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Mirko Tomić
- Department of Biochemistry, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Nataša Golić
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Maja Tolinački
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- Maja Tolinački
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Microbial community structure of soils in Bamenwan mangrove wetland. Sci Rep 2019; 9:8406. [PMID: 31182804 PMCID: PMC6557889 DOI: 10.1038/s41598-019-44788-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 05/23/2019] [Indexed: 11/30/2022] Open
Abstract
Microbial community diversity and composition are important for the maintenance of mangrove ecosystem. Bacterial and archaeal community composition of the Bamenwan Mangrove Wetland soil in Hainan, China, was determined using pyrosequencing technique. Bacterial community composition presented differences among the five soil samples. Rhizobiales with higher abundance were observed in inner mangrove forest samples, while Desulfobacterales were in the seaward edge samples, and Frankiales, Gaiellales and Rhodospirillales in the landedge sample. For archaea, Crenarchaeota and Euryarchaeota dominated in five samples, but the proportion in each samples were different. Dominant archaeal community composition at the order level was similar in the seaward edge samples. The dominant archaeal clusters in the two inner mangrove forest samples were different, with Soil Crenarchaeotic Group (SCG) and Halobacteriales in sample inside of Bruguiera sexangula forest and SCG, Methanosarcinales and Marine Benthic Group B (MBGB) in sample inside of Xylocarpus mekongensis forest. The dominant archaeal clusters in land sample were unique, with Terrestrial Group and South African Gold Mine Group 1. The metabolic pathways including metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems and human diseases were all detected for bacterial and archaeal functional profiles, but metabolic potentials among five samples were different.
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14
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Ran S, Mu C, Zhu W. Diversity and community pattern of sulfate-reducing bacteria in piglet gut. J Anim Sci Biotechnol 2019; 10:40. [PMID: 31110701 PMCID: PMC6513522 DOI: 10.1186/s40104-019-0346-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 03/21/2019] [Indexed: 11/17/2022] Open
Abstract
Background Among the gut microbiota, sulfate-reducing bacteria (SRB) is a kind of hydrogen-utilizing functional bacteria that plays an important role in intestinal hydrogen and sulfur metabolism. However, information is lacking regarding diversity and community structure of SRB in the gut of piglets. Middle cecum contents were collected from 6 Yorkshire and 6 Meishan piglets at postnatal days (PND) 14, 28 and 49. Piglets were weaned at PND28. Real-time quantitative PCR was performed to detect the number of SRB in the cecum based on dissimilatory sulfite reductase subunit A (dsrA) gene. Prior to real-time PCR, plasmid containing the dsrA gene was constructed and used as external standard to create a standard curve, from which the gene copies of dsrA were calculated. H2S concentration in the cecal contents was measured. Illumina PE250 sequencing of dsrA gene was used to investigate SRB diversity in cecum contents. Results The qPCR results showed that the number of SRB at PND49 was significantly higher than that at PND28 in Meishan piglets. The concentration of H2S has no significant difference between piglet breeds and between different ages. The Illumina sequencing analysis revealed that the Chao1 richness index was significantly higher at PND49 than that at PND14 and PND28 in Yorkshire piglets. Based on dsrA gene similarities, Proteobacteria, Actinobacteria, and Firmicutes were identified at the phylum level, and most sequences were classified as Proteobacteria. At the genus level, most of sequences were classified as Desulfovibrio. At the species level, Desulfovibrio intestinalis was the predominant SRB in the piglet cecum. The relative abundance and the inferred absolute abundance of Faecalibacterium prausnitzii at PND49 were significantly higher than that at PND14 in Yorkshire piglets. Pig breeds did not affect the dsrA gene copies of SRB, diversity index and community pattern of SRB. Conclusions Sulfate-reducing bacteria are widely colonized in the cecum of piglets and D. intestinalis is the dominant SRB. The age of piglets, but not the pig breeds affects the diversity and community pattern of SRB. Electronic supplementary material The online version of this article (10.1186/s40104-019-0346-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuwen Ran
- 1Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, No. 6, Tongwei Road, Nanjing, 210095 Jiangsu China.,2National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095 China
| | - Chunlong Mu
- 1Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, No. 6, Tongwei Road, Nanjing, 210095 Jiangsu China.,2National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095 China
| | - Weiyun Zhu
- 1Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, No. 6, Tongwei Road, Nanjing, 210095 Jiangsu China.,2National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095 China
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15
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Vuillemin A, Horn F, Friese A, Winkel M, Alawi M, Wagner D, Henny C, Orsi WD, Crowe SA, Kallmeyer J. Metabolic potential of microbial communities from ferruginous sediments. Environ Microbiol 2018; 20:4297-4313. [PMID: 29968357 DOI: 10.1111/1462-2920.14343] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/22/2018] [Accepted: 06/25/2018] [Indexed: 01/22/2023]
Abstract
Ferruginous (Fe-rich, SO4 -poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.
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Affiliation(s)
- Aurèle Vuillemin
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany.,Department of Earth & Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - André Friese
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - Matthias Winkel
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany.,University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute of Earth and Environmental Sciences, Potsdam, Germany
| | - Cynthia Henny
- Research Center for Limnology (LIPI), Indonesian Institute of Sciences, Division of Inland Waterways Dynamics, Cibinong-Bogor, Indonesia
| | - William D Orsi
- Department of Earth & Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,Geobio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.,Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
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16
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Wu YT, Yang CY, Chiang PW, Tseng CH, Chiu HH, Saeed I, Baatar B, Rogozin D, Halgamuge S, Degermendzhi A, Tang SL. Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia. Front Microbiol 2018; 9:1763. [PMID: 30177915 PMCID: PMC6109700 DOI: 10.3389/fmicb.2018.01763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/16/2018] [Indexed: 11/20/2022] Open
Abstract
Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2–5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.
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Affiliation(s)
- Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Neipu, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Yu Yang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ching-Hung Tseng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Germark Biotechnology Co., Ltd., Taichung, Taiwan
| | - Hsiu-Hui Chiu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Isaam Saeed
- Optimisation and Pattern Recognition Group, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia
| | - Bayanmunkh Baatar
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Life Sciences, Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Denis Rogozin
- Institute of Biophysics, Siberian Division of Russian Academy of Sciences, Krasnoyarsk, Russia.,Siberian Federal University, Krasnoyarsk, Russia
| | - Saman Halgamuge
- Optimisation and Pattern Recognition Group, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia
| | - Andrei Degermendzhi
- Institute of Biophysics, Siberian Division of Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Life Sciences, Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
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17
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Gérard E, De Goeyse S, Hugoni M, Agogué H, Richard L, Milesi V, Guyot F, Lecourt L, Borensztajn S, Joseph MB, Leclerc T, Sarazin G, Jézéquel D, Leboulanger C, Ader M. Key Role of Alphaproteobacteria and Cyanobacteria in the Formation of Stromatolites of Lake Dziani Dzaha (Mayotte, Western Indian Ocean). Front Microbiol 2018; 9:796. [PMID: 29872424 PMCID: PMC5972316 DOI: 10.3389/fmicb.2018.00796] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 04/09/2018] [Indexed: 01/09/2023] Open
Abstract
Lake Dziani Dzaha is a thalassohaline tropical crater lake located on the "Petite Terre" Island of Mayotte (Comoros archipelago, Western Indian Ocean). Stromatolites are actively growing in the shallow waters of the lake shores. These stromatolites are mainly composed of aragonite with lesser proportions of hydromagnesite, calcite, dolomite, and phyllosilicates. They are morphologically and texturally diverse ranging from tabular covered by a cauliflower-like crust to columnar ones with a smooth surface. High-throughput sequencing of bacterial and archaeal 16S rRNA genes combined with confocal laser scanning microscopy (CLSM) analysis revealed that the microbial composition of the mats associated with the stromatolites was clearly distinct from that of the Arthrospira-dominated lake water. Unicellular-colonial Cyanobacteria belonging to the Xenococcus genus of the Pleurocapsales order were detected in the cauliflower crust mats, whereas filamentous Cyanobacteria belonging to the Leptolyngbya genus were found in the smooth surface mats. Observations using CLSM, scanning electron microscopy (SEM) and Raman spectroscopy indicated that the cauliflower texture consists of laminations of aragonite, magnesium-silicate phase and hydromagnesite. The associated microbial mat, as confirmed by laser microdissection and whole-genome amplification (WGA), is composed of Pleurocapsales coated by abundant filamentous and coccoid Alphaproteobacteria. These phototrophic Alphaproteobacteria promote the precipitation of aragonite in which they become incrusted. In contrast, the Pleurocapsales are not calcifying but instead accumulate silicon and magnesium in their sheaths, which may be responsible for the formation of the Mg-silicate phase found in the cauliflower crust. We therefore propose that Pleurocapsales and Alphaproteobacteria are involved in the formation of two distinct mineral phases present in the cauliflower texture: Mg-silicate and aragonite, respectively. These results point out the role of phototrophic Alphaproteobacteria in the formation of stromatolites, which may open new perspective for the analysis of the fossil record.
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Affiliation(s)
- Emmanuelle Gérard
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Siham De Goeyse
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Mylène Hugoni
- Université Lyon 1, UMR CNRS 5557 / INRA 1418, Ecologie Microbienne, Villeurbanne, France
| | - Hélène Agogué
- UMR 7266 CNRS-Université de la Rochelle, LIttoral ENvironnement Et Sociétés, La Rochelle, France
| | - Laurent Richard
- School of Mining and Geosciences, Nazarbayev University, Astana, Kazakhstan
| | - Vincent Milesi
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - François Guyot
- Museum National d’Histoire Naturelle, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS Sorbonne Universités, Université Pierre et Marie Curie, Institut de Recherche pour le Développement UMR 206, Paris, France
| | - Léna Lecourt
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Stephan Borensztajn
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Marie-Béatrice Joseph
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Thomas Leclerc
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Gérard Sarazin
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Didier Jézéquel
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | | | - Magali Ader
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
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18
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Zanacic E, McMartin DW, Stavrinides J. From source to filter: changes in bacterial community composition during potable water treatment. Can J Microbiol 2017; 63:546-558. [PMID: 28264165 DOI: 10.1139/cjm-2017-0077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rural communities rely on surface water reservoirs for potable water. Effective removal of chemical contaminants and bacterial pathogens from these reservoirs requires an understanding of the bacterial community diversity that is present. In this study, we carried out a 16S rRNA-based profiling approach to describe the bacterial consortia in the raw surface water entering the water treatment plants of 2 rural communities. Our results show that source water is dominated by the Proteobacteria, Bacteroidetes, and Cyanobacteria, with some evidence of seasonal effects altering the predominant groups at each location. A subsequent community analysis of transects of a biological carbon filter in the water treatment plant revealed a significant increase in the proportion of Proteobacteria, Acidobacteria, Planctomycetes, and Nitrospirae relative to raw water. Also, very few enteric coliforms were identified in either the source water or within the filter, although Mycobacterium was of high abundance and was found throughout the filter along with Aeromonas, Legionella, and Pseudomonas. This study provides valuable insight into bacterial community composition within drinking water treatment facilities, and the importance of implementing appropriate disinfection practices to ensure safe potable water for rural communities.
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Affiliation(s)
- Enisa Zanacic
- a Engineering Support & Research, SaskWater, Moose Jaw, Regina, SK S6H 1C8, Canada
| | - Dena W McMartin
- b Faculty of Engineering and Applied Science, University of Regina, Regina, SK S4S 0A2, Canada
| | - John Stavrinides
- c Department of Biology, University of Regina, Regina, SK S4S 0A2, Canada
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19
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Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions. mBio 2015; 6:e00066-15. [PMID: 25991679 PMCID: PMC4442139 DOI: 10.1128/mbio.00066-15] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. IMPORTANCE Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities that mediate carbon cycling in wetlands is critical to accurately predicting their responses to changes in land management and climate. Here, we studied a restored wetland and revealed substantial spatial heterogeneity in biogeochemistry, methane production, and microbial communities, largely associated with the wetland hydraulic design. We observed patterns in microbial community composition and functions correlated with biogeochemistry and methane production, including diverse microorganisms involved in methane production and consumption. We found that methanogenesis gene abundance is inversely correlated with genes from pathways exploiting other electron acceptors, yet the ubiquitous presence of genes from all these pathways suggests that diverse electron acceptors contribute to the energetic balance of the ecosystem. These investigations represent an important step toward effective management of wetlands to reduce methane flux to the atmosphere and enhance belowground carbon storage.
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20
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Lau MCY, Cameron C, Magnabosco C, Brown CT, Schilkey F, Grim S, Hendrickson S, Pullin M, Sherwood Lollar B, van Heerden E, Kieft TL, Onstott TC. Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships. Front Microbiol 2014; 5:531. [PMID: 25400621 PMCID: PMC4215791 DOI: 10.3389/fmicb.2014.00531] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 09/24/2014] [Indexed: 11/30/2022] Open
Abstract
Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1) screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S, and N; (2) to characterize the biodiversity represented by the common functional genes; (3) to investigate the subsurface biogeography as revealed by this subset of genes; and (4) to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN genes. Although these eight common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with geographical or environmental parameters or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes.
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Affiliation(s)
- Maggie C Y Lau
- Department of Geosciences, Princeton University Princeton, NJ, USA
| | | | - Cara Magnabosco
- Department of Geosciences, Princeton University Princeton, NJ, USA
| | - C Titus Brown
- Department of Computer Science and Engineering and Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| | - Faye Schilkey
- National Center for Genome Resources Santa Fe, NM, USA
| | - Sharon Grim
- The Marine Biological Laboratory Woods Hole, MA, USA
| | | | - Michael Pullin
- Department of Chemistry, New Mexico Tech Socorro, NM, USA
| | | | - Esta van Heerden
- Department of Biotechnology, University of Free State Bloemfontein, South Africa
| | | | - Tullis C Onstott
- Department of Geosciences, Princeton University Princeton, NJ, USA
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21
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Cheng TW, Lin LH, Lin YT, Song SR, Wang PL. Temperature-dependent variations in sulfate-reducing communities associated with a terrestrial hydrocarbon seep. Microbes Environ 2014; 29:377-87. [PMID: 25273230 PMCID: PMC4262361 DOI: 10.1264/jsme2.me14086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Terrestrial hydrocarbon seeps are an important source of naturally emitted methane over geological time. The exact community compositions responsible for carbon cycling beneath these surface features remain obscure. As sulfate reduction represents an essential process for anoxic organic mineralization, this study collected muddy fluids from a high-temperature hydrocarbon seep in Taiwan and analyzed community structures of sulfate-supplemented sediment slurries incubated anoxically at elevated temperatures. The results obtained demonstrated that sulfate consumption occurred between 40°C and 80°C. Dominant potential sulfate reducers included Desulfovibrio spp., Desulfonatronum spp., Desulforhabdus spp., and Desulfotomaculum spp. at 40°C, Thermodesulfovibrio spp. at 50°C, Thermodesulfovibrio spp. and Thermacetogenium spp. at 60°C, Thermacetogenium spp. and Archaeoglobus spp. at 70°C, and Archaeoglobus spp. at 80°C. None of these potential sulfate reducers exceeded 7% of the community in the untreated sample. Since no exogenous electron donor was provided during incubation, these sulfate reducers appeared to rely on the degradation of organic matter inherited from porewater and sediments. Aqueous chemistry indicated that fluids discharged in the region represented a mixture of saline formation water and low-salinity surface water; therefore, these lines of evidence suggest that deeply-sourced, thermophilic and surface-input, mesophilic sulfate-reducing populations entrapped along the subsurface fluid transport could respond rapidly once the ambient temperature is adjusted to a range close to their individual optima.
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22
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Syntrophs dominate sequences associated with the mercury methylation-related gene hgcA in the water conservation areas of the Florida Everglades. Appl Environ Microbiol 2014; 80:6517-26. [PMID: 25107983 DOI: 10.1128/aem.01666-14] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The mechanisms and rates of mercury methylation in the Florida Everglades are of great concern because of potential adverse impacts on human and wildlife health through mercury accumulation in aquatic food webs. We developed a new PCR primer set targeting hgcA, a gene encoding a corrinoid protein essential for Hg methylation across broad phylogenetic boundaries, and used this primer set to study the distribution of hgcA sequences in soils collected from three sites along a gradient in sulfate and nutrient concentrations in the northern Everglades. The sequences obtained were distributed in diverse phyla, including Proteobacteria, Chloroflexi, Firmicutes, and Methanomicrobia; however, hgcA clone libraries from all sites were dominated by sequences clustering within the order Syntrophobacterales of the Deltaproteobacteria (49 to 65% of total sequences). dsrB mRNA sequences, representing active sulfate-reducing prokaryotes at the time of sampling, obtained from these sites were also dominated by Syntrophobacterales (75 to 89%). Laboratory incubations with soils taken from the site low in sulfate concentrations also suggested that Hg methylation activities were primarily mediated by members of the order Syntrophobacterales, with some contribution by methanogens, Chloroflexi, iron-reducing Geobacter, and non-sulfate-reducing Firmicutes inhabiting the sites. This suggests that prokaryotes distributed within clades defined by syntrophs are the predominant group controlling methylation of Hg in low-sulfate areas of the Everglades. Any strategy for managing mercury methylation in the Everglades should consider that net mercury methylation is not limited to the action of sulfate reduction.
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Engelbrektson A, Hubbard CG, Tom LM, Boussina A, Jin YT, Wong H, Piceno YM, Carlson HK, Conrad ME, Anderson G, Coates JD. Inhibition of microbial sulfate reduction in a flow-through column system by (per)chlorate treatment. Front Microbiol 2014; 5:315. [PMID: 25071731 PMCID: PMC4092371 DOI: 10.3389/fmicb.2014.00315] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/09/2014] [Indexed: 11/13/2022] Open
Abstract
Microbial sulfate reduction is a primary cause of oil reservoir souring. Here we show that amendment with chlorate or perchlorate [collectively (per)chlorate] potentially resolves this issue. Triplicate packed columns inoculated with marine sediment were flushed with coastal water amended with yeast extract and one of nitrate, chlorate, or perchlorate. Results showed that although sulfide production was dramatically reduced by all treatments, effluent sulfide was observed in the nitrate (10 mM) treatment after an initial inhibition period. In contrast, no effluent sulfide was observed with (per)chlorate (10 mM). Microbial community analyses indicated temporal community shifts and phylogenetic clustering by treatment. Nitrate addition stimulated Xanthomonadaceae and Rhizobiaceae growth, supporting their role in nitrate metabolism. (Per)chlorate showed distinct effects on microbial community structure compared with nitrate and resulted in a general suppression of the community relative to the untreated control combined with a significant decrease in sulfate reducing species abundance indicating specific toxicity. Furthermore, chlorate stimulated Pseudomonadaceae and Pseudoalteromonadaceae, members of which are known chlorate respirers, suggesting that chlorate may also control sulfidogenesis by biocompetitive exclusion of sulfate-reduction. Perchlorate addition stimulated Desulfobulbaceae and Desulfomonadaceae, which contain sulfide oxidizing and elemental sulfur-reducing species respectively, suggesting that effluent sulfide concentrations may be controlled through sulfur redox cycling in addition to toxicity and biocompetitive exclusion. Sulfur isotope analyses further support sulfur cycling in the columns, even when sulfide is not detected. This study indicates that (per)chlorate show great promise as inhibitors of sulfidogenesis in natural communities and provides insight into which organisms and respiratory processes are involved.
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Affiliation(s)
- Anna Engelbrektson
- Department of Plant and Microbial Biology, University of California, Berkeley Berkeley, CA, USA
| | | | - Lauren M Tom
- Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA
| | - Aaron Boussina
- Department of Plant and Microbial Biology, University of California, Berkeley Berkeley, CA, USA
| | - Yong T Jin
- Department of Plant and Microbial Biology, University of California, Berkeley Berkeley, CA, USA
| | - Hayden Wong
- Department of Plant and Microbial Biology, University of California, Berkeley Berkeley, CA, USA
| | - Yvette M Piceno
- Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA
| | - Hans K Carlson
- Department of Plant and Microbial Biology, University of California, Berkeley Berkeley, CA, USA
| | - Mark E Conrad
- Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA
| | - Gary Anderson
- Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA
| | - John D Coates
- Department of Plant and Microbial Biology, University of California, Berkeley Berkeley, CA, USA ; Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA
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Richness and diversity of bacteria in the Nansha carbonate platform (Core MD05-2896), South China Sea. World J Microbiol Biotechnol 2013; 29:1895-905. [PMID: 23700125 DOI: 10.1007/s11274-013-1354-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
Abstract
We explored the bacterial diversity and vertical distribution along a sediment core (MD05-2896) from the coral reefs of the Nansha carbonate platform in the South China Sea. Bacterial diversity is determined by 16S rRNA molecular survey from twelve subsamples A, obtained via cloning, sequencing and phylogenetic analyses. We estimated the species richness by parametric and nonparametric models, which identified 326 ± 40 (SE) bacteria species. The dominant bacterial groups included Planctomycetes, Deltaproteobacteria, and candidate division OP3, which constituting 23.7, 10.4, and 9.5 % of bacterial 16S rRNAclone libraries, respectively. The observed stratification of bacterial communities was correlated with C/N ratio. This study improves our understanding of the species-environment relationship in the sub-sea floor sediment.
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Abstract
BACKGROUND Genome sequencing has revolutionized our view of the relationships among genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT). Phylogenomic techniques have been used to construct purported trees of microbial life. Although such trees are easily interpreted and allow the use of a subset of genomes as "proxies" for the full set, LGT and other phenomena impact the positioning of different groups in genome trees, confounding and potentially invalidating attempts to construct a phylogeny-based taxonomy of microorganisms. Network and graph approaches can reveal complex sets of relationships, but applying these techniques to large data sets is a significant challenge. Notwithstanding the question of what exactly it might represent, generating and interpreting a Tree or Network of All Genomes will only be feasible if current algorithms can be improved upon. RESULTS Complex relationships among even the most-similar genomes demonstrate that proxy-based approaches to simplifying large sets of genomes are not alone sufficient to solve the analysis problem. A phylogenomic analysis of 1173 sequenced bacterial and archaeal genomes generated phylogenetic trees for 159,905 distinct homologous gene sets. The relationships inferred from this set can be heavily dependent on the inclusion of other taxa: for example, phyla such as Spirochaetes, Proteobacteria and Firmicutes are recovered as cohesive groups or split depending on the presence of other specific lineages. Furthermore, named groups such as Acidithiobacillus, Coprothermobacter and Brachyspira show a multitude of affiliations that are more consistent with their ecology than with small subunit ribosomal DNA-based taxonomy. Network and graph representations can illustrate the multitude of conflicting affinities, but all methods impose constraints on the input data and create challenges of construction and interpretation. CONCLUSIONS These complex relationships highlight the need for an inclusive approach to genomic data, and current methods with minor alterations will likely scale to allow the analysis of data sets with 10,000 or more genomes. The main challenges lie in the visualization and interpretation of genomic relationships, and the redefinition of microbial taxonomy when subsets of genomic data are so evidently in conflict with one another, and with the "canonical" molecular taxonomy.
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Affiliation(s)
- Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 1W5 Canada.
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Overestimation of the abundance of sulfate-reducing bacteria in human feces by quantitative PCR targeting the Desulfovibrio 16S rRNA gene. Appl Environ Microbiol 2011; 77:3544-6. [PMID: 21460115 DOI: 10.1128/aem.02851-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The dominant genus of sulfate-reducing bacteria (SRB) in humans is Desulfovibrio, and quantitative PCR (QPCR) targeting the 16S rRNA gene is often used in assays. We show that the 16S rRNA gene assay overestimated SRB abundance in feces from 24 adults compared to QPCR assays using primers targeting two genes involved in SRB energy metabolism.
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Sitte J, Akob DM, Kaufmann C, Finster K, Banerjee D, Burkhardt EM, Kostka JE, Scheinost AC, Büchel G, Küsel K. Microbial links between sulfate reduction and metal retention in uranium- and heavy metal-contaminated soil. Appl Environ Microbiol 2010; 76:3143-52. [PMID: 20363796 PMCID: PMC2869125 DOI: 10.1128/aem.00051-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 03/23/2010] [Indexed: 11/20/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) can affect metal mobility either directly by reductive transformation of metal ions, e.g., uranium, into their insoluble forms or indirectly by formation of metal sulfides. This study evaluated in situ and biostimulated activity of SRB in groundwater-influenced soils from a creek bank contaminated with heavy metals and radionuclides within the former uranium mining district of Ronneburg, Germany. In situ activity of SRB, measured by the (35)SO(4)(2-) radiotracer method, was restricted to reduced soil horizons with rates of < or =142 +/- 20 nmol cm(-3) day(-1). Concentrations of heavy metals were enriched in the solid phase of the reduced horizons, whereas pore water concentrations were low. X-ray absorption near-edge structure (XANES) measurements demonstrated that approximately 80% of uranium was present as reduced uranium but appeared to occur as a sorbed complex. Soil-based dsrAB clone libraries were dominated by sequences affiliated with members of the Desulfobacterales but also the Desulfovibrionales, Syntrophobacteraceae, and Clostridiales. [(13)C]acetate- and [(13)C]lactate-biostimulated soil microcosms were dominated by sulfate and Fe(III) reduction. These processes were associated with enrichment of SRB and Geobacteraceae; enriched SRB were closely related to organisms detected in soils by using the dsrAB marker. Concentrations of soluble nickel, cobalt, and occasionally zinc declined < or =100% during anoxic soil incubations. In contrast to results in other studies, soluble uranium increased in carbon-amended treatments, reaching < or =1,407 nM in solution. Our results suggest that (i) ongoing sulfate reduction in contaminated soil resulted in in situ metal attenuation and (ii) the fate of uranium mobility is not predictable and may lead to downstream contamination of adjacent ecosystems.
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Affiliation(s)
- Jana Sitte
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Denise M. Akob
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Christian Kaufmann
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Kai Finster
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Dipanjan Banerjee
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Eva-Maria Burkhardt
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Joel E. Kostka
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Andreas C. Scheinost
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Georg Büchel
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
| | - Kirsten Küsel
- Institute of Ecology, Friedrich Schiller University Jena, D-07743 Jena, Germany, Department of Oceanography, Florida State University, Tallahassee, Florida 32306, Department of Microbial Ecology, Institute for Biological Sciences, DK-8000 Aarhus C, Denmark, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D-01314 Dresden, Germany, and The Rossendorf Beamline at ESRF, F-38043 Grenoble, France, Institute of Earth Science, Friedrich Schiller University, D-07749 Jena, Germany
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Pavissich JP, Silva M, González B. Sulfate reduction, molecular diversity, and copper amendment effects in bacterial communities enriched from sediments exposed to copper mining residues. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2010; 29:256-264. [PMID: 20821443 DOI: 10.1002/etc.43] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Sulfate-reducing bacterial communities from coastal sediments with a long-term exposure to copper (Cu)-mining residues were studied in lactate enrichments. The toxicity of excess copper may affect sulfate-reducing bacterial communities. Sulfate reduction was monitored by sulfate and organic acid measurements. Molecular diversity was analyzed by 16S rRNA, dissimilatory sulfate reduction dsrAB, and Cu translocating phospho-type adenosine triphosphatases (P-ATPases) cop-like gene sequence profiling. The influence of Cu amendment was tested in these enrichments. Results showed fast sulfate reduction mostly coupled to incomplete organic carbon oxidation and partial sulfate reduction inhibition due to copper amendment. The 16S rRNA clonal libraries analysis indicated that delta- and gamma-Proteobacteria and Cytophaga-Flexibacter-Bacteroides dominated the enrichments. The dsrAB libraries revealed the presence of Desulfobacteraceae and Desulfovibrionaceae families-related sequences. Copper produced significant shifts (i.e., a decrease in the relative abundance of sulfate-reducing microorganisms) in the enriched bacterial community structure as determined by terminal-restriction fragment length polymorphism (T-RFLP) profiling and multivariate analyses. Clonal libraries of cop-like sequences showed low richness in the enriched microbial communities, and a strong effect of copper on its relative abundance. Novel Cu-P(IB)-ATPase sequences encoding Cu resistance were detected. The present study indicates that Cu does not significantly affect sulfate reduction and genetic diversity of taxonomic and dissimilatory sulfate-reduction molecular markers. However, the diversity of Cu resistance genetic determinants was strongly modified by this toxic metal.
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Affiliation(s)
- Juan P Pavissich
- Departamento de Genética Molecular y Microbiología, Millennium Nucleus on Microbial Ecology and Environmental Microbiology and Biotechnology (EMBA), Center for Advanced Studies in Ecology and Biodiversity (CASEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Facultad de Ingeniería y Ciencia, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Macarena Silva
- Departamento de Genética Molecular y Microbiología, Millennium Nucleus on Microbial Ecology and Environmental Microbiology and Biotechnology (EMBA), Center for Advanced Studies in Ecology and Biodiversity (CASEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Facultad de Ingeniería y Ciencia, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Bernardo González
- Departamento de Genética Molecular y Microbiología, Millennium Nucleus on Microbial Ecology and Environmental Microbiology and Biotechnology (EMBA), Center for Advanced Studies in Ecology and Biodiversity (CASEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Facultad de Ingeniería y Ciencia, Universidad Adolfo Ibáñez, Santiago, Chile
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29
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Boudaud N, Coton M, Coton E, Pineau S, Travert J, Amiel C. Biodiversity analysis by polyphasic study of marine bacteria associated with biocorrosion phenomena. J Appl Microbiol 2009; 109:166-79. [PMID: 20059620 DOI: 10.1111/j.1365-2672.2009.04643.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS A polyphasic approach was used to study the biodiversity bacteria associated with biocorrosion processes, in particular sulfate-reducing bacteria (SRB) and thiosulfate-reducing bacteria (TRB) which are described to be particularly aggressive towards metallic materials, notably via hydrogen sulfide release. METHODS AND RESULTS To study this particular flora, an infrared spectra library of 22 SRB and TRB collection strains were created using a Common Minimum Medium (CMM) developed during this study and standardized culture conditions. The CMM proved its ability to allow for growth of both SRB and TRB strains. These sulfurogen collection strains were clearly discriminated and differentiated at the genus level by fourier transform infrared (FT-IR) spectroscopy. In a second step, infrared spectra of isolates, recovered from biofilms formed on carbon steel coupons immersed for 1 year in three different French harbour areas, were compared to the infrared reference spectra library. In parallel, molecular methods (M13-PCR and 16S rRNA gene sequencing) were used to qualitatively evaluate the intra- and inter-species genetic diversity of biofilm isolates. The biodiversity study indicated that strains belonging to the Vibrio genus were the dominant population; strains belonging to the Desulfovibrio genus (SRB) and Peptostreptococcaceae were also identified. CONCLUSION Overall, the combination of the FT-IR spectroscopy and molecular approaches allowed for the taxonomic and ecological study of a bacterial flora, cultivated on CMM, associated with microbiology-induced corrosion (MIC) processes. SIGNIFICANCE AND IMPACT OF THE STUDY Via the use of the CMM medium, the culture of marine bacteria (including both SRB and TRB bacteria) was allowed, and the implication of nonsulforogen bacteria in MIC was observed. Their involvement in the biocorrosion phenomena will have to be studied and taken into account in the future.
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Affiliation(s)
- N Boudaud
- Equipe de Recherche en Physico-Chimie et Biotechnologies, Université Caen Basse Normandie, Caen Cedex, France
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Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersaline basin. Proc Natl Acad Sci U S A 2009; 106:9151-6. [PMID: 19470485 DOI: 10.1073/pnas.0811984106] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Urania basin in the deep Mediterranean Sea houses a lake that is >100 m deep, devoid of oxygen, 6 times more saline than seawater, and has very high levels of methane and particularly sulfide (up to 16 mM), making it among the most sulfidic water bodies on Earth. Along the depth profile there are 2 chemoclines, a steep one with the overlying oxic seawater, and another between anoxic brines of different density, where gradients of salinity, electron donors and acceptors occur. To identify and differentiate the microbes and processes contributing to the turnover of organic matter and sulfide along the water column, these chemoclines were sampled at a high resolution. Bacterial cell numbers increased up to a hundredfold in the chemoclines as a consequence of elevated nutrient availability, with higher numbers in the upper interface where redox gradient was steeper. Bacterial and archaeal communities, analyzed by DNA fingerprinting, 16S rRNA gene libraries, activity measurements, and cultivation, were highly stratified and metabolically more active along the chemoclines compared with seawater or the uniformly hypersaline brines. Detailed analysis of 16S rRNA gene sequences revealed that in both chemoclines delta- and epsilon-Proteobacteria, predominantly sulfate reducers and sulfur oxidizers, respectively, were the dominant bacteria. In the deepest layers of the basin MSBL1, putatively responsible for methanogenesis, dominated among archaea. The data suggest that the complex microbial community is adapted to the basin's extreme chemistry, and the elevated biomass is driven largely by sulfur cycling and methanogenesis.
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Identification of critical members in a sulfidogenic benzene-degrading consortium by DNA stable isotope probing. Appl Environ Microbiol 2008; 74:6476-80. [PMID: 18757571 DOI: 10.1128/aem.01082-08] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Stable isotope probing (SIP) was used to identify the active members in a benzene-degrading sulfidogenic consortium. SIP-terminal restriction fragment length polymorphism analysis indicated that a 270-bp peak incorporated the majority of the (13)C label and is a sequence closely related to that of clone SB-21 (GenBank accession no. AF029045). This target may be an important biomarker for anaerobic benzene degradation in the field.
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Thevenieau F, Fardeau ML, Ollivier B, Joulian C, Baena S. Desulfomicrobium thermophilum sp. nov., a novel thermophilic sulphate-reducing bacterium isolated from a terrestrial hot spring in Colombia. Extremophiles 2006; 11:295-303. [PMID: 17136317 DOI: 10.1007/s00792-006-0039-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 10/06/2006] [Indexed: 10/23/2022]
Abstract
A moderately thermophilic, sulphate-reducing bacterium, designated strain P6-2(T), was isolated from a terrestrial hot spring located at a height of 2,500 m in the Andean region, Colombia (5 degrees 43'69''N, 73 degrees 6'10''W). Cells of strain P6-2(T) were rod-shaped, stained Gram-negative and were motile by means of a single polar flagellum. The strain grew lithotrophically with H(2) as the electron donor and organotrophically on lactate, pyruvate, ethanol, malate, fumarate, n-propanol and succinate in the presence of sulphate as the terminal electron acceptor. Fumarate and pyruvate was fermented. Strain P6-2(T) grew optimally at 55 degrees C (range 37-60 degrees C), pH 6.6 (range 5.8-8.8) in the presence of 0.5% NaCl (range 0-4.5%) with lactate and sulphate and produced acetate, CO(2) and H(2)S as the major end-products. Sulphate, sulphite and thiosulphate could be used as electron acceptors but not elemental sulphur or nitrate. The G + C content of the genomic DNA was 58.7 mol%. The 16S rRNA sequence analysis indicated that strain P6-2(T) was a member of the class Deltaproteobacteria, domain Bacteria with Desulfomicrobium baculatum being the closest relative (similarity value of 94%). Phylogeny of genes encoding alpha- and beta-subunits of the dissimilatory sulphite reductase (dsrAB genes) supported its affiliation to members of the genus Desulfomicrobium. On the basis of this evidence, we propose to assign strain P6-2(T) as new species of the genus Desulfomicrobium, D. thermophilum sp. nov., with strain P6-2(T) as the type strain (= DSM 16697(T) = CCUG 49732(T)).
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Affiliation(s)
- France Thevenieau
- IRD, UMR 180 Microbiologie et Biotechnologie des Environnements Chauds, IFR-BAIM, ESIL, Universités de Provence et de la Mediterranée, Case 925, 13288, Marseille, France
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Olapade OA, Depas MM, Jensen ET, McLellan SL. Microbial communities and fecal indicator bacteria associated with Cladophora mats on beach sites along Lake Michigan shores. Appl Environ Microbiol 2006; 72:1932-8. [PMID: 16517640 PMCID: PMC1393218 DOI: 10.1128/aem.72.3.1932-1938.2006] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A high biomasses of Cladophora, a filamentous green alga, is found mainly during the summer along the shores of Lake Michigan. In this study, the abundance and persistence of the fecal indicator bacterium Escherichia coli and sulfate-reducing bacteria (SRB) on Cladophora mats collected at Lake Michigan beaches were evaluated using both culture-based and molecular analyses. Additionally, 16S rRNA gene cloning and sequencing were used to examine the bacterial community composition. Overall, E. coli was detected in all 63 samples obtained from 11 sites, and the average levels at most beaches ranged from 2,700 CFU/100 g (wet weight) of Cladophora to 7,500 CFU/100 g of Cladophora. However, three beaches were found to have site average E. coli densities of 12,800, 21,130, and 27,950 CFU/100 g of Cladophora. The E. coli levels in the lake water collected at the same time from these three sites were less than the recommended U.S. Environmental Protection Agency limit, 235 CFU/100 ml. E. coli also persisted on Cladophora mats in microcosms at room temperature for more than 7 days, and in some experiments it persisted for as long as 28 days. The SRB densities on Cladophora mats were relatively high, ranging from 4.4x10(6) cells/g (6.64 log CFU/g) to 5.73x10(6) cells/g (6.76 log CFU/g) and accounting for between 20% and 27% of the total bacterial counts. Partial sequences of the 16S rRNA gene clones revealed a phylogenetically diverse community, in which the Cytophaga-Flavobacterium-Bacteroides cluster and the low-G+C-content gram-positive bacteria were the dominant organisms, accounting for 40% and 12.8%, respectively, of the total clone library. These results further reveal the potential public health and ecological significance of Cladophora mats that are commonly found along the shoreline of Lake Michigan, especially with regard to the potential to harbor microorganisms associated with fecal pollution and odor-causing bacteria.
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Affiliation(s)
- Ola A Olapade
- Great Lakes WATER Institute, University of Wisconsin-Milwaukee, 600 E. Greenfield Avenue, Milwaukee, WI 53204, USA
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Achá D, Iñiguez V, Roulet M, Guimarães JRD, Luna R, Alanoca L, Sanchez S. Sulfate-reducing bacteria in floating macrophyte rhizospheres from an Amazonian floodplain lake in Bolivia and their association with Hg methylation. Appl Environ Microbiol 2005; 71:7531-5. [PMID: 16269796 PMCID: PMC1287671 DOI: 10.1128/aem.71.11.7531-7535.2005] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five subgroups of sulfate-reducing bacteria (SRB) were detected by PCR in three macrophyte rhizospheres (Polygonum densiflorum, Hymenachne donacifolia, and Ludwigia helminthorriza) and three subgroups in Eichhornia crassipes from La Granja, a floodplain lake from the upper Madeira basin. The SRB community varied according to the macrophyte species but with different degrees of association with their roots. The rhizosphere of the C4 plant Polygonum densiflorum had higher frequencies of SRB subgroups as well as higher mercury methylation potentials (27.5 to 36.1%) and carbon (16.06 +/- 5.40%), nitrogen (2.03 +/- 0.64%), Hg (94.50 +/- 6.86 ng Hg g(-1)), and methylmercury (8.25 +/- 1.45 ng Hg g(-1)) contents than the rhizosphere of the C3 plant Eichhornia crassipes. Mercury methylation in Polygonum densiflorum and Eichhornia crassipes was reduced when SRB metabolism was inhibited by sodium molybdate.
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Affiliation(s)
- Darío Achá
- Instituto de Biología Molecular y Biotecnología, Facultad de Ciencias Puras, Universidad Mayor de San Andrés, La Paz, Bolivia.
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Dhillon A, Teske A, Dillon J, Stahl DA, Sogin ML. Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl Environ Microbiol 2003; 69:2765-72. [PMID: 12732547 PMCID: PMC154542 DOI: 10.1128/aem.69.5.2765-2772.2003] [Citation(s) in RCA: 249] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse sulfate-reducing bacteria. We explored the phylogenetic and functional diversity of the sulfate-reducing bacteria by characterizing PCR-amplified dissimilatory sulfite reductase (dsrAB) and 16S rRNA genes from the upper 4 cm of the Guaymas sediment. The dsrAB sequences revealed that there was a major clade closely related to the acetate-oxidizing delta-proteobacterial genus Desulfobacter and a clade of novel, deeply branching dsr sequences related to environmental dsr sequences from marine sediments in Aarhus Bay and Kysing Fjord (Denmark). Other dsr clones were affiliated with gram-positive thermophilic sulfate reducers (genus Desulfotomaculum) and the delta-proteobacterial species Desulforhabdus amnigena and Thermodesulforhabdus norvegica. Phylogenetic analysis of 16S rRNAs from the same environmental samples resulted in identification of four clones affiliated with Desulfobacterium niacini, a member of the acetate-oxidizing, nutritionally versatile genus Desulfobacterium, and one clone related to Desulfobacula toluolica and Desulfotignum balticum. Other bacterial 16S rRNA bacterial phylotypes were represented by non-sulfate reducers and uncultured lineages with unknown physiology, like OP9, OP8, as well as a group with no clear affiliation. In summary, analyses of both 16S rRNA and dsrAB clone libraries resulted in identification of members of the Desulfobacteriales in the Guaymas sediments. In addition, the dsrAB sequencing approach revealed a novel group of sulfate-reducing prokaryotes that could not be identified by 16S rRNA sequencing.
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Affiliation(s)
- Ashita Dhillon
- Marine Biological Laboratory, The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, NASA AStrobiology Institute, 7 MBL Street, Woods Hole, MA 02543, USA
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Castro H, Reddy KR, Ogram A. Composition and function of sulfate-reducing prokaryotes in eutrophic and pristine areas of the Florida Everglades. Appl Environ Microbiol 2002; 68:6129-37. [PMID: 12450837 PMCID: PMC134442 DOI: 10.1128/aem.68.12.6129-6137.2002] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As a result of agricultural activities in regions adjacent to the northern boundary of the Florida Everglades, a nutrient gradient developed that resulted in physicochemical and ecological changes from the original system. Sulfate input from agricultural runoff and groundwater is present in soils of the Northern Everglades, and sulfate-reducing prokaryotes (SRP) may play an important role in biogeochemical processes such as carbon cycling. The goal of this project was to utilize culture-based and non-culture-based approaches to study differences between the composition of assemblages of SRP in eutrophic and pristine areas of the Everglades. Sulfate reduction rates and most-probable-number enumerations revealed SRP populations and activities to be greater in eutrophic zones than in more pristine soils. In eutrophic regions, methanogenesis rates were higher, the addition of acetate stimulated methanogenesis, and SRP able to utilize acetate competed to a limited degree with acetoclastic methanogens. A surprising amount of diversity within clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) genes was observed, and the majority of DSR sequences were associated with gram-positive spore-forming Desulfotomaculum and uncultured microorganisms. Sequences associated with Desulfotomaculum fall into two categories: in the eutrophic regions, 94.7% of the sequences related to Desulfotomaculum were associated with those able to completely oxidize substrates, and in samples from pristine regions, all Desulfotomaculum-like sequences were related to incomplete oxidizers. This metabolic selection may be linked to the types of substrates that Desulfotomaculum spp. utilize; it may be that complete oxidizers are more versatile and likelier to proliferate in nutrient-rich zones of the Everglades. Desulfotomaculum incomplete oxidizers may outcompete complete oxidizers for substrates such as hydrogen in pristine zones where diverse carbon sources are less available.
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Affiliation(s)
- Hector Castro
- Soil and Water Science Department, University of Florida, Gainesville 32611, USA
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Joulian C, Ramsing NB, Ingvorsen K. Congruent phylogenies of most common small-subunit rRNA and dissimilatory sulfite reductase gene sequences retrieved from estuarine sediments. Appl Environ Microbiol 2001; 67:3314-8. [PMID: 11425760 PMCID: PMC93019 DOI: 10.1128/aem.67.7.3314-3318.2001] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity of sulfate-reducing bacteria (SRB) in brackish sediment was investigated using small-subunit rRNA and dissimilatory sulfite reductase (DSR) gene clone libraries and cultivation. The phylogenetic affiliation of the most commonly retrieved clones for both genes was strikingly similar and produced Desulfosarcina variabilis-like sequences from the inoculum but Desulfomicrobium baculatum-like sequences from a high dilution in natural media. Related organisms were subsequently cultivated from the site. PCR bias appear to be limited (or very similar) for the two primersets and target genes. However, the DSR primers showed a much higher phylogenetic specificity. DSR gene analysis is thus a promising and specific approach for investigating SRB diversity in complex habitats.
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Affiliation(s)
- C Joulian
- Institute of Biological Sciences, Department of Microbial Ecology, Aarhus University, Ny Munkegade, DK-8000 Aarhus C, Denmark.
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Benoit JM, Gilmour CC, Mason RP. Aspects of bioavailability of mercury for methylation in pure cultures of Desulfobulbus propionicus (1pr3). Appl Environ Microbiol 2001; 67:51-8. [PMID: 11133427 PMCID: PMC92513 DOI: 10.1128/aem.67.1.51-58.2001] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have previously hypothesized that sulfide inhibits Hg methylation by decreasing its bioavailability to sulfate-reducing bacteria (SRB), the important methylators of Hg in natural sediments. With a view to designing a bioassay to test this hypothesis, we investigated a number of aspects of Hg methylation by the SRB Desulfobulbus propionicus, including (i) the relationship between cell density and methylmercury (MeHg) production, (ii) the time course of Hg methylation relative to growth stage, (iii) changes in the bioavailability of an added inorganic Hg (Hg(I)) spike over time, and (iv) the dependence of methylation on the concentration of dissolved Hg(I) present in the culture. We then tested the effect of sulfide on MeHg production by this microorganism. These experiments demonstrated that under conditions of equal bioavailability, per-cell MeHg production was constant through log-phase culture growth. However, the methylation rate of a new Hg spike dramatically decreased after the first 5 h. This result was seen whether methylation rate was expressed as a fraction of the total added Hg or the filtered Hg(I) concentration, which suggests that Hg bioavailability decreased through both changes in Hg complexation and formation of solid phases. At low sulfide concentration, MeHg production was linearly related to the concentration of filtered Hg(I). The methylation of filtered Hg(I) decreased about fourfold as sulfide concentration was increased from 10(-6) to 10(-3) M. This decline is consistent with a decrease in the bioavailability of Hg(I), possibly due to a decline in the dissolved neutral complex, HgS(0).
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Affiliation(s)
- J M Benoit
- Estuarine Research Center, Academy of Natural Sciences, St. Leonard, Maryland 20685, USA.
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