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Junier P, Molina V, Dorador C, Hadas O, Kim OS, Junier T, Witzel JP, Imhoff JF. Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment. Appl Microbiol Biotechnol 2010; 85:425-40. [PMID: 19830422 PMCID: PMC2802487 DOI: 10.1007/s00253-009-2228-9] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 08/28/2009] [Accepted: 08/28/2009] [Indexed: 12/17/2022]
Abstract
The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments.
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Affiliation(s)
- Pilar Junier
- Laboratory of Microbial Ecology, University of Neuchatel, Neuchatel, Switzerland.
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Source of nitrous oxide emissions during the cow manure composting process as revealed by isotopomer analysis of and amoA abundance in betaproteobacterial ammonia-oxidizing bacteria. Appl Environ Microbiol 2010. [PMID: 20048060 DOI: 10.1128/aem.01394‐09] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A molecular analysis of betaproteobacterial ammonia oxidizers and a N(2)O isotopomer analysis were conducted to study the sources of N(2)O emissions during the cow manure composting process. Much NO(2)(-)-N and NO(3)(-)-N and the Nitrosomonas europaea-like amoA gene were detected at the surface, especially at the top of the composting pile, suggesting that these ammonia-oxidizing bacteria (AOB) significantly contribute to the nitrification which occurs at the surface layer of compost piles. However, the (15)N site preference within the asymmetric N(2)O molecule (SP = delta(15)N(alpha) - delta(15)N(beta), where (15)N(alpha) and (15)N(beta) represent the (15)N/(14)N ratios at the center and end sites of the nitrogen atoms, respectively) indicated that the source of N(2)O emissions just after the compost was turned originated mainly from the denitrification process. Based on these results, the reduction of accumulated NO(2)(-)-N or NO(3)(-)-N after turning was identified as the main source of N(2)O emissions. The site preference and bulk delta(15)N results also indicate that the rate of N(2)O reduction was relatively low, and an increased value for the site preference indicates that the nitrification which occurred mainly in the surface layer of the pile partially contributed to N(2)O emissions between the turnings.
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Source of nitrous oxide emissions during the cow manure composting process as revealed by isotopomer analysis of and amoA abundance in betaproteobacterial ammonia-oxidizing bacteria. Appl Environ Microbiol 2010; 76:1555-62. [PMID: 20048060 DOI: 10.1128/aem.01394-09] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A molecular analysis of betaproteobacterial ammonia oxidizers and a N(2)O isotopomer analysis were conducted to study the sources of N(2)O emissions during the cow manure composting process. Much NO(2)(-)-N and NO(3)(-)-N and the Nitrosomonas europaea-like amoA gene were detected at the surface, especially at the top of the composting pile, suggesting that these ammonia-oxidizing bacteria (AOB) significantly contribute to the nitrification which occurs at the surface layer of compost piles. However, the (15)N site preference within the asymmetric N(2)O molecule (SP = delta(15)N(alpha) - delta(15)N(beta), where (15)N(alpha) and (15)N(beta) represent the (15)N/(14)N ratios at the center and end sites of the nitrogen atoms, respectively) indicated that the source of N(2)O emissions just after the compost was turned originated mainly from the denitrification process. Based on these results, the reduction of accumulated NO(2)(-)-N or NO(3)(-)-N after turning was identified as the main source of N(2)O emissions. The site preference and bulk delta(15)N results also indicate that the rate of N(2)O reduction was relatively low, and an increased value for the site preference indicates that the nitrification which occurred mainly in the surface layer of the pile partially contributed to N(2)O emissions between the turnings.
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Alawi M, Off S, Kaya M, Spieck E. Temperature influences the population structure of nitrite-oxidizing bacteria in activated sludge. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:184-190. [PMID: 23765792 DOI: 10.1111/j.1758-2229.2009.00029.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Activated sludge from the municipal waste water treatment plant in Hamburg was seeded with mineral nitrite medium and incubated at 10°C, 17°C and 28°C. Dominant lithoautotrophic nitrite-oxidizing bacteria have been identified by electron microscopy, denaturing and temperature gradient gel electrophoresis and PCR with genus-specific primer pairs. The results have revealed the existence of three different genera of nitrite-oxidizing bacteria, namely Nitrospira, Nitrobacter and a novel cold-adapted nitrite oxidizer. As shown by electron microscopy members of the novel genus coexisted in activated sludge together with Nitrospira. A temperature-dependent shift in the population structure was demonstrated by cultivation-based approaches. The novel nitrite oxidizer was enriched at temperatures of 10°C and 17°C. Representatives of Nitrospira were able to grow in a broad temperature range between 10°C and 28°C and members of Nitrobacter were enriched during incubations at 17°C and 28°C. By subsequent 16S rDNA sequencing, the cold-adapted nitrite oxidizer was shown to be closely related to the betaproteobacterium 'Candidatus Nitrotoga arctica'. These findings demonstrated that the population structure of nitrite-oxidizing bacteria in activated sludge is more complex than previously thought and responds strongly to long-term temperature changes.
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Affiliation(s)
- M Alawi
- Universität Hamburg, Biozentrum Klein Flottbek, Abteilung Mikrobiologie und Biotechnologie, Ohnhorststr. 18, D-22609 Hamburg, Germany
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Global occurrence of archaeal amoA genes in terrestrial hot springs. Appl Environ Microbiol 2008; 74:6417-26. [PMID: 18676703 DOI: 10.1128/aem.00843-08] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the ubiquity of ammonium in geothermal environments and the thermodynamic favorability of aerobic ammonia oxidation, thermophilic ammonia-oxidizing microorganisms belonging to the crenarchaeota kingdom have only recently been described. In this study, we analyzed microbial mats and surface sediments from 21 hot spring samples (pH 3.4 to 9.0; temperature, 41 to 86 degrees C) from the United States, China, and Russia and obtained 846 putative archaeal ammonia monooxygenase large-subunit (amoA) gene and transcript sequences, representing a total of 41 amoA operational taxonomic units (OTUs) at 2% identity. The amoA gene sequences were highly diverse, yet they clustered within two major clades of archaeal amoA sequences known from water columns, sediments, and soils: clusters A and B. Eighty-four percent (711/846) of the sequences belonged to cluster A, which is typically found in water columns and sediments, whereas 16% (135/846) belonged to cluster B, which is typically found in soils and sediments. Although a few amoA OTUs were present in several geothermal regions, most were specific to a single region. In addition, cluster A amoA genes formed geographic groups, while cluster B sequences did not group geographically. With the exception of only one hot spring, principal-component analysis and UPGMA (unweighted-pair group method using average linkages) based on the UniFrac metric derived from cluster A grouped the springs by location, regardless of temperature or bulk water pH, suggesting that geography may play a role in structuring communities of putative ammonia-oxidizing archaea (AOA). The amoA genes were distinct from those of low-temperature environments; in particular, pair-wise comparisons between hot spring amoA genes and those from sympatric soils showed less than 85% sequence identity, underscoring the distinctness of hot spring archaeal communities from those of the surrounding soil system. Reverse transcription-PCR showed that amoA genes were transcribed in situ in one spring and the transcripts were closely related to the amoA genes amplified from the same spring. Our study demonstrates the global occurrence of putative archaeal amoA genes in a wide variety of terrestrial hot springs and suggests that geography may play an important role in selecting different assemblages of AOA.
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Reigstad LJ, Richter A, Daims H, Urich T, Schwark L, Schleper C. Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiol Ecol 2008; 64:167-74. [PMID: 18355293 DOI: 10.1111/j.1574-6941.2008.00466.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Archaea have been detected recently as a major and often dominant component of the microbial communities performing ammonia oxidation in terrestrial and marine environments. In a molecular survey of archaeal ammonia monooxygenase (AMO) genes in terrestrial hot springs of Iceland and Kamchatka, the amoA gene encoding the alpha-subunit of AMO was detected in a total of 14 hot springs out of the 22 investigated. Most of these amoA-positive hot springs had temperatures between 82 and 97 degrees C and pH range between 2.5 and 7. In phylogenetic analyses, these amoA genes formed three independent lineages within the known sequence clusters of marine or soil origin. Furthermore, in situ gross nitrification rates in Icelandic hot springs were estimated by the pool dilution technique directly on site. At temperatures above 80 degrees C, between 56 and 159 mumol NO(3)(-) L(-1) mud per day was produced. Furthermore, addition of ammonium to the hot spring samples before incubation yielded a more than twofold higher potential nitrification rate, indicating that the process was limited by ammonia supply. Our data provide evidence for an active role of archaea in nitrification of hot springs in a wide range of pH values and at a high temperature.
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Affiliation(s)
- Laila J Reigstad
- Department of Biology, Center for Geobiology, University of Bergen, Bergen, Norway
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Isaka K, Sumino T, Tsuneda S. Novel nitritation process using heat-shocked nitrifying bacteria entrapped in gel carriers. Process Biochem 2008. [DOI: 10.1016/j.procbio.2007.12.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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58
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Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci U S A 2008; 105:2134-9. [PMID: 18250313 PMCID: PMC2538889 DOI: 10.1073/pnas.0708857105] [Citation(s) in RCA: 552] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Indexed: 02/07/2023] Open
Abstract
The recent discovery of ammonia-oxidizing archaea (AOA) dramatically changed our perception of the diversity and evolutionary history of microbes involved in nitrification. In this study, a moderately thermophilic (46 degrees C) ammonia-oxidizing enrichment culture, which had been seeded with biomass from a hot spring, was screened for ammonia oxidizers. Although gene sequences for crenarchaeotal 16S rRNA and two subunits of the ammonia monooxygenase (amoA and amoB) were detected via PCR, no hints for known ammonia-oxidizing bacteria were obtained. Comparative sequence analyses of these gene fragments demonstrated the presence of a single operational taxonomic unit and thus enabled the assignment of the amoA and amoB sequences to the respective 16S rRNA phylotype, which belongs to the widely distributed group I.1b (soil group) of the Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH combined with microautoradiography (MAR) demonstrated metabolic activity of this archaeon in the presence of ammonium. This finding was corroborated by the detection of amoA gene transcripts in the enrichment. CARD-FISH/MAR showed that the moderately thermophilic AOA is highly active at 0.14 and 0.79 mM ammonium and is partially inhibited by a concentration of 3.08 mM. The enriched AOA, which is provisionally classified as "Candidatus Nitrososphaera gargensis," is the first described thermophilic ammonia oxidizer and the first member of the crenarchaeotal group I.1b for which ammonium oxidation has been verified on a cellular level. Its preference for thermophilic conditions reinvigorates the debate on the thermophilic ancestry of AOA.
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Affiliation(s)
| | - Elena V. Lebedeva
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia; and
| | - Eva Spieck
- University of Hamburg, Biocenter Klein Flottbek, Microbiology, Ohnhorststrasse 18, D-22609 Hamburg, Germany
| | | | - Andreas Richter
- Chemical Ecology and Ecosystem Research, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
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de la Torre JR, Walker CB, Ingalls AE, Könneke M, Stahl DA. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 2008; 10:810-8. [PMID: 18205821 DOI: 10.1111/j.1462-2920.2007.01506.x] [Citation(s) in RCA: 383] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The widespread occurrence and diversity of ammonia oxidizing Archaea suggests their contribution to the nitrogen cycle is of global significance. Their distribution appeared limited to low- and moderate-temperature environments until the recent finding of a diagnostic membrane lipid, crenarchaeol, in terrestrial hot springs. We report here the cultivation of a thermophilic nitrifier ('Candidatus Nitrosocaldus yellowstonii'), an autotrophic crenarchaeote growing up to 74 degrees C by aerobic ammonia oxidation. The major core lipid of this archaeon growing at 72 degrees C is crenarchaeol, providing the first direct evidence for its synthesis by a thermophile. These findings greatly extend the upper temperature limit of nitrification and document that the capacity for ammonia oxidation is broadly distributed among the Crenarchaeota.
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Affiliation(s)
- José R de la Torre
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195-2700, USA
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60
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Alawi M, Lipski A, Sanders T, Eva-Maria-Pfeiffer, Spieck E. Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic. ISME JOURNAL 2007; 1:256-64. [DOI: 10.1038/ismej.2007.34] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Daims H, Wagner M. Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis. Appl Microbiol Biotechnol 2007; 75:237-48. [PMID: 17333172 DOI: 10.1007/s00253-007-0886-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 12/22/2006] [Accepted: 02/09/2007] [Indexed: 11/28/2022]
Abstract
Traditional cultivation-based methods to quantify microbial abundance are not suitable for analyses of microbial communities in environmental or medical samples, which consist mainly of uncultured microorganisms. Recently, different cultivation-independent quantification approaches have been developed to overcome this problem. Some of these techniques use specific fluorescence markers, for example ribosomal ribonucleic acid targeted oligonucleotide probes, to label the respective target organisms. Subsequently, the detected cells are visualized by fluorescence microscopy and are quantified by direct visual cell counting or by digital image analysis. This article provides an overview of these methods and some of their applications with emphasis on (semi-)automated image analysis solutions.
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Affiliation(s)
- Holger Daims
- Department für Mikrobielle Okologie, Universität Wien, Althanstrasse 14, 1090, Vienna, Austria.
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62
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Spieck E, Hartwig C, McCormack I, Maixner F, Wagner M, Lipski A, Daims H. Selective enrichment and molecular characterization of a previously uncultured Nitrospira-like bacterium from activated sludge. Environ Microbiol 2006; 8:405-15. [PMID: 16478447 DOI: 10.1111/j.1462-2920.2005.00905.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previously uncultured nitrite-oxidizing bacteria affiliated to the genus Nitrospira have for the first time been successfully enriched from activated sludge from a municipal wastewater treatment plant. During the enrichment procedure, the abundance of the Nitrospira-like bacteria increased to approximately 86% of the total bacterial population. This high degree of purification was achieved by a novel enrichment protocol, which exploits physiological features of Nitrospira-like bacteria and includes the selective repression of coexisting Nitrobacter cells and heterotrophic contaminants by application of ampicillin in a final concentration of 50 microg ml(-1). The enrichment process was monitored by electron microscopy, fluorescence in situ hybridization (FISH) with rRNA-targeted probes and fatty acid profiling. Phylogenetic analysis of 16S rRNA gene sequences revealed that the enriched bacteria represent a novel Nitrospira species closely related to uncultured Nitrospira-like bacteria previously found in wastewater treatment plants and nitrifying bioreactors. The enriched strain is provisionally classified as 'Candidatus Nitrospira defluvii'.
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MESH Headings
- Ampicillin/pharmacology
- Anti-Bacterial Agents/pharmacology
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacterial Physiological Phenomena
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Genes, rRNA
- In Situ Hybridization, Fluorescence
- Microscopy, Electron
- Nitrobacter/drug effects
- RNA, Bacterial/analysis
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sewage/microbiology
- Water Microbiology
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Affiliation(s)
- Eva Spieck
- Universität Hamburg, Biozentrum Klein Flottbek, Mikrobiologie, Ohnhorststr. 18, D-22609 Hamburg, Germany.
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