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Keuter S, Koch H, Nowka B, Lipski A, Kruse M, Lücker S, Spieck E. A novel Nitrospira lineage isolated from activated sludge using elevated temperatures. FEMS Microbiol Lett 2023; 370:7134069. [PMID: 37081766 DOI: 10.1093/femsle/fnad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/07/2023] [Accepted: 04/19/2023] [Indexed: 04/22/2023] Open
Abstract
The genus Nitrospira represents the dominant nitrite-oxidizing clade in most wastewater treatment plants (WWTPs) globally, and several Nitrospira strains have been isolated from activated sludge. Using a pre-enrichment strategy with alternating nitrifying and denitrifying conditions, followed by incubation at elevated temperatures, we isolated a novel Nitrospira species, named Nitrospira tepida. This moderately thermophilic species with optimal growth between 37 and 45°C is only distantly related to other Nitrospira and forms a novel lineage VII within the genus, together with few environmental 16S rRNA gene sequences predominantly detected in thermal wastewater or oxygen-limited systems. Genomic and physiological analyses revealed remarkable differences between N. tepida and two other isolates previously obtained from the same WWTP, suggesting niche differentiation between these nitrite oxidizers. N. tepida grows in aggregates, and tolerates nitrite and nitrate concentrations of up to 20 mM and 40 mM, respectively. The Km value for nitrite of N. tepida is 77 ± 26 µM. In summary, this novel Nitrospira lineage seems to be well adapted for wastewater treatment processes at elevated temperatures and limited aeration, conditions that potentially reduce operational costs of such systems.
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Affiliation(s)
- Sabine Keuter
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Hanna Koch
- Department of Microbiology, RIBES, Radboud University, Nijmegen, the Netherlands
| | - Boris Nowka
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - André Lipski
- Department of Food Microbiology and Hygiene, University of Bonn, Bonn, Germany
| | - Myriam Kruse
- Department of Food Microbiology and Hygiene, University of Bonn, Bonn, Germany
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Nijmegen, the Netherlands
| | - Eva Spieck
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
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Sakoula D, Nowka B, Spieck E, Daims H, Lücker S. The draft genome sequence of " Nitrospira lenta" strain BS10, a nitrite oxidizing bacterium isolated from activated sludge. Stand Genomic Sci 2018; 13:32. [PMID: 30498561 PMCID: PMC6251164 DOI: 10.1186/s40793-018-0338-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/10/2018] [Indexed: 11/10/2022] Open
Abstract
The genus Nitrospira is considered to be the most widespread and abundant group of nitrite-oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed the high quality draft genome of "Nitrospira lenta" strain BS10, a sublineage II Nitrospira that was isolated from a municipal wastewater treatment plant in Hamburg, Germany. The genome of "N. lenta" has a size of 3,756,190 bp and contains 3968 genomic objects, of which 3907 are predicted protein-coding sequences. Thorough genome annotation allowed the reconstruction of the "N. lenta" core metabolism for energy conservation and carbon fixation. Comparative analyses indicated that most metabolic features are shared with N. moscoviensis and "N. defluvii", despite their ecological niche differentiation and phylogenetic distance. In conclusion, the genome of "N. lenta" provides important insights into the genomic diversity of the genus Nitrospira and provides a foundation for future comparative genomic studies that will generate a better understanding of the nitrification process.
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Affiliation(s)
- Dimitra Sakoula
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Boris Nowka
- Department of Microbiology & Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Eva Spieck
- Department of Microbiology & Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Holger Daims
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
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Füssel J, Lücker S, Yilmaz P, Nowka B, van Kessel MAHJ, Bourceau P, Hach PF, Littmann S, Berg J, Spieck E, Daims H, Kuypers MMM, Lam P. Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus. Sci Adv 2017; 3:e1700807. [PMID: 29109973 PMCID: PMC5665590 DOI: 10.1126/sciadv.1700807] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 10/13/2017] [Indexed: 05/22/2023]
Abstract
Nitrite-oxidizing bacteria (NOB) have conventionally been regarded as a highly specialized functional group responsible for the production of nitrate in the environment. However, recent culture-based studies suggest that they have the capacity to lead alternative lifestyles, but direct environmental evidence for the contribution of marine nitrite oxidizers to other processes has been lacking to date. We report on the alternative biogeochemical functions, worldwide distribution, and sometimes high abundance of the marine NOB Nitrococcus. These largely overlooked bacteria are capable of not only oxidizing nitrite but also reducing nitrate and producing nitrous oxide, an ozone-depleting agent and greenhouse gas. Furthermore, Nitrococcus can aerobically oxidize sulfide, thereby also engaging in the sulfur cycle. In the currently fast-changing global oceans, these findings highlight the potential functional switches these ubiquitous bacteria can perform in various biogeochemical cycles, each with distinct or even contrasting consequences.
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Affiliation(s)
- Jessika Füssel
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton SO14 3ZH, UK
| | - Sebastian Lücker
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, 6525 AJ Nijmegen, Netherlands
| | - Pelin Yilmaz
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Boris Nowka
- Section Microbiology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Maartje A. H. J. van Kessel
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, 6525 AJ Nijmegen, Netherlands
| | - Patric Bourceau
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, 6525 AJ Nijmegen, Netherlands
| | - Philipp F. Hach
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Jasmine Berg
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Eva Spieck
- Section Microbiology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Holger Daims
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | | | - Phyllis Lam
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton SO14 3ZH, UK
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Nowka B, Off S, Daims H, Spieck E. Improved isolation strategies allowed the phenotypic differentiation of two Nitrospira strains from widespread phylogenetic lineages. FEMS Microbiol Ecol 2014; 91:fiu031. [DOI: 10.1093/femsec/fiu031] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Pester M, Maixner F, Berry D, Rattei T, Koch H, Lücker S, Nowka B, Richter A, Spieck E, Lebedeva E, Loy A, Wagner M, Daims H. NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira. Environ Microbiol 2013; 16:3055-71. [PMID: 24118804 DOI: 10.1111/1462-2920.12300] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 09/26/2013] [Indexed: 12/01/2022]
Abstract
Nitrospira are the most widespread and diverse known nitrite-oxidizing bacteria and key nitrifiers in natural and engineered ecosystems. Nevertheless, their ecophysiology and environmental distribution are understudied because of the recalcitrance of Nitrospira to cultivation and the lack of a molecular functional marker, which would allow the detection of Nitrospira in the environment. Here we introduce nxrB, the gene encoding subunit beta of nitrite oxidoreductase, as a functional and phylogenetic marker for Nitrospira. Phylogenetic trees based on nxrB of Nitrospira were largely congruent to 16S ribosomal RNA-based phylogenies. By using new nxrB-selective polymerase chain reaction primers, we obtained almost full-length nxrB sequences from Nitrospira cultures, two activated sludge samples, and several geographically and climatically distinct soils. Amplicon pyrosequencing of nxrB fragments from 16 soils revealed a previously unrecognized diversity of terrestrial Nitrospira with 1801 detected species-level operational taxonomic units (OTUs) (using an inferred species threshold of 95% nxrB identity). Richness estimates ranged from 10 to 946 coexisting Nitrospira species per soil. Comparison with an archaeal amoA dataset obtained from the same soils [Environ. Microbiol. 14: 525-539 (2012)] uncovered that ammonia-oxidizing archaea and Nitrospira communities were highly correlated across the soil samples, possibly indicating shared habitat preferences or specific biological interactions among members of these nitrifier groups.
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Affiliation(s)
- Michael Pester
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Ecology Centre, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
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Lücker S, Nowka B, Rattei T, Spieck E, Daims H. The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer. Front Microbiol 2013; 4:27. [PMID: 23439773 PMCID: PMC3578206 DOI: 10.3389/fmicb.2013.00027] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 02/02/2013] [Indexed: 01/17/2023] Open
Abstract
In marine systems, nitrate is the major reservoir of inorganic fixed nitrogen. The only known biological nitrate-forming reaction is nitrite oxidation, but despite its importance, our knowledge of the organisms catalyzing this key process in the marine N-cycle is very limited. The most frequently encountered marine NOB are related to Nitrospina gracilis, an aerobic chemolithoautotrophic bacterium isolated from ocean surface waters. To date, limited physiological and genomic data for this organism were available and its phylogenetic affiliation was uncertain. In this study, the draft genome sequence of N. gracilis strain 3/211 was obtained. Unexpectedly for an aerobic organism, N. gracilis lacks classical reactive oxygen defense mechanisms and uses the reductive tricarboxylic acid cycle for carbon fixation. These features indicate microaerophilic ancestry and are consistent with the presence of Nitrospina in marine oxygen minimum zones. Fixed carbon is stored intracellularly as glycogen, but genes for utilizing external organic carbon sources were not identified. N. gracilis also contains a full gene set for oxidative phosphorylation with oxygen as terminal electron acceptor and for reverse electron transport from nitrite to NADH. A novel variation of complex I may catalyze the required reverse electron flow to low-potential ferredoxin. Interestingly, comparative genomics indicated a strong evolutionary link between Nitrospina, the nitrite-oxidizing genus Nitrospira, and anaerobic ammonium oxidizers, apparently including the horizontal transfer of a periplasmically oriented nitrite oxidoreductase and other key genes for nitrite oxidation at an early evolutionary stage. Further, detailed phylogenetic analyses using concatenated marker genes provided evidence that Nitrospina forms a novel bacterial phylum, for which we propose the name Nitrospinae.
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Affiliation(s)
- Sebastian Lücker
- Department of Microbial Ecology, Ecology Centre, University of Vienna Vienna, Austria
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Spang A, Poehlein A, Offre P, Zumbrägel S, Haider S, Rychlik N, Nowka B, Schmeisser C, Lebedeva EV, Rattei T, Böhm C, Schmid M, Galushko A, Hatzenpichler R, Weinmaier T, Daniel R, Schleper C, Spieck E, Streit W, Wagner M. The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 2012; 14:3122-45. [PMID: 23057602 DOI: 10.1111/j.1462-2920.2012.02893.x] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 09/01/2012] [Indexed: 01/21/2023]
Abstract
The cohort of the ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota is a diverse, widespread and functionally important group of microorganisms in many ecosystems. However, our understanding of their biology is still very rudimentary in part because all available genome sequences of this phylum are from members of the Nitrosopumilus cluster. Here we report on the complete genome sequence of Candidatus Nitrososphaera gargensis obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments. With its 2.83 Mb the genome is much larger than that of other AOA. The presence of a high number of (active) IS elements/transposases, genomic islands, gene duplications and a complete CRISPR/Cas defence system testifies to its dynamic evolution consistent with low degree of synteny with other thaumarchaeal genomes. As expected, the repertoire of conserved enzymes proposed to be required for archaeal ammonia oxidation is encoded by N. gargensis, but it can also use urea and possibly cyanate as alternative ammonia sources. Furthermore, its carbon metabolism is more flexible at the central pyruvate switch point, encompasses the ability to take up small organic compounds and might even include an oxidative pentose phosphate pathway. Furthermore, we show that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates. Lateral gene transfer from bacteria and euryarchaeota has contributed to the metabolic versatility of N. gargensis. This organisms is well adapted to its niche in a heavy metal-containing thermal spring by encoding a multitude of heavy metal resistance genes, chaperones and mannosylglycerate as compatible solute and has the genetic ability to respond to environmental changes by signal transduction via a large number of two-component systems, by chemotaxis and flagella-mediated motility and possibly even by gas vacuole formation. These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers.
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Affiliation(s)
- Anja Spang
- Department of Genetics in Ecology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
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Nacke H, Will C, Herzog S, Nowka B, Engelhaupt M, Daniel R. Identification of novel lipolytic genes and gene families by screening of metagenomic libraries derived from soil samples of the German Biodiversity Exploratories. FEMS Microbiol Ecol 2011; 78:188-201. [PMID: 21395625 DOI: 10.1111/j.1574-6941.2011.01088.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Microbial metagenomes derived from soils are rich sources for the discovery of novel genes and biocatalysts. Fourteen environmental plasmid and seven fosmid libraries obtained from 10 German forest soils (A horizons) and six grassland soils (A and B horizons) were screened for genes conferring lipolytic activity. The libraries comprised approximately 29.3 Gb of cloned soil DNA. Partial activity-based screening of the constructed libraries resulted in the identification of 37 unique lipolytic clones. The amino acid sequences of the 37 corresponding lipolytic gene products shared 29-90% identity to other lipolytic enzymes, which were mainly uncharacterized or derived from uncultured microorganisms. Multiple sequence alignments and phylogenetic tree analysis revealed that 35 of the predicted proteins were new members of known families of lipolytic enzymes. The remaining two gene products represent two putatively new families. In addition, sequence analysis indicated that two genes encode true lipases, whereas the other genes encode esterases. The determination of substrate specificity and chain-length selectivity using different triacylglycerides and p-nitrophenyl esters of fatty acids as substrates supported the classification of the esterases.
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Affiliation(s)
- Heiko Nacke
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
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