Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm

Foesel, Bärbel U.; Gieseke, Armin; Schwermer, Carsten Ulrich; Stief, Peter; Koch, Liat; Cytryn, Eddie; Torre, José R. de la; Rijn, Jaap van; Minz, Dror; Drake, Harold L.; Schramm, Andreas

doi:10.1111/j.1574-6941.2007.00418.x

Cited by 134 publications

(101 citation statements)

References 76 publications

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“…These metabolisms uncouple the growth of NOB from the nitrification process and could contribute to the unexpected higher abundances of NOB compared with AOM observed in nitrifying activated sludge, biofilm, and freshwater sediment (10,20,47,48). Taken together, Nitrospira play diverse functional roles and even participate in N-cycle processes other than nitrification.…”

Section: Discussionmentioning

confidence: 99%

Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira

Koch

Lücker

Albertsen

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

436

472

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Nitrospira are a diverse group of nitrite-oxidizing bacteria and among the environmentally most widespread nitrifiers. However, they remain scarcely studied and mostly uncultured. Based on genomic and experimental data from Nitrospira moscoviensis representing the ubiquitous Nitrospira lineage II, we identified ecophysiological traits that contribute to the ecological success of Nitrospira. Unexpectedly, N. moscoviensis possesses genes coding for a urease and cleaves urea to ammonia and CO2. Ureolysis was not observed yet in nitrite oxidizers and enables N. moscoviensis to supply ammonia oxidizers lacking urease with ammonia from urea, which is fully nitrified by this consortium through reciprocal feeding. The presence of highly similar urease genes in Nitrospira lenta from activated sludge, in metagenomes from soils and freshwater habitats, and of other ureases in marine nitrite oxidizers, suggests a wide distribution of this extended interaction between ammonia and nitrite oxidizers, which enables nitrite-oxidizing bacteria to indirectly use urea as a source of energy. A soluble formate dehydrogenase lends additional ecophysiological flexibility and allows N. moscoviensis to use formate, with or without concomitant nitrite oxidation, using oxygen, nitrate, or both compounds as terminal electron acceptors. Compared with Nitrospira defluvii from lineage I, N. moscoviensis shares the Nitrospira core metabolism but shows substantial genomic dissimilarity including genes for adaptations to elevated oxygen concentrations. Reciprocal feeding and metabolic versatility, including the participation in different nitrogen cycling processes, likely are key factors for the niche partitioning, the ubiquity, and the high diversity of Nitrospira in natural and engineered ecosystems.

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Section: Discussionmentioning

confidence: 99%

Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira

Koch

Lücker

Albertsen

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

436

472

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“…The second largest assemblage was the Nitrosomonas sp. Nm143 lineage, which has been observed in environmental clone libraries from marine sediments (Urakawa et al 2006) and marine aquaculture systems (Foesel et al 2008) and likely is of primarily marine origin (Purkhold et al 2003).…”

Section: Discussionmentioning

confidence: 99%

Ammonia availability shapes the seasonal distribution and activity of archaeal and bacterial ammonia oxidizers in the Puget Sound Estuary

Urakawa

Martens‐Habbena

Huguet

et al. 2014

Limnology & Oceanography

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A combination of molecular and activity measures was used to explore seasonal patterns of distribution, activity, and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in relationship to ammonia availability in Hood Canal, a fjord within the Puget Sound, Washington State estuary system. A greater contribution of AOA to nitrification, relative to AOB, was supported by complementary quantification of transcripts of a gene (amoA) coding for one subunit of the ammonia monooxygenase, quantification of intact glycerol dialkyl glycerol tetraether lipids, and kinetic modeling. High AOA : AOB ratios and nitrification rates measured by 15 NH z 4 dilution technique were associated with low concentrations of ammonia, whereas transient increases in AOB were most closely associated with regionally and seasonally elevated concentrations of ammonia in the water column. Additionally, single cell nitrification rates and transcript numbers were calculated for AOA and AOB populations. Together these observations offer additional ecological support for the idea that niche separation of AOA and AOB is in part determined by ammonia concentrations in estuarine ecosystems.

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“…For each replicate core, DNA was extracted in triplicate from 200 mg sediment by combining enzymatic and chemical cell lysis with a Fast DNA Spin kit for soil (Qbiogene Inc.) (13). Archaeal and bacterial amoA genes were amplified using a HotStar Taq Mastermix kit (Qiagen), previously described protocols, and primer sets Arch-AmoAF/ Arch-AmoAR (14) and AmoA-1F/AmoA-2R-TC (28).…”

mentioning

confidence: 99%

Archaea Dominate the Ammonia-Oxidizing Community in the Rhizosphere of the Freshwater Macrophyte Littorella uniflora

Herrmann

Saunders

Schramm

2008

Appl Environ Microbiol

Self Cite

169

125

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Archaeal and bacterial ammonia monooxygenase genes (amoA) had similar low relative abundances in freshwater sediment. In the rhizosphere of the submersed macrophyte Littorella uniflora, archaeal amoA was 500-to >8,000-fold enriched compared to bacterial amoA, suggesting that the enhanced nitrification activity observed in the rhizosphere was due to ammonia-oxidizing Archaea.In shallow aquatic ecosystems, rhizosphere-associated nitrogen transformations are central to understanding nutrient cycling (29). Oxygen release from the roots of freshwater macrophytes like Littorella uniflora, Lobelia dortmanna, and Glyceria maxima stimulates nitrification and coupled nitrificationdenitrification in freshwater sediments (4,29,34). However, the nitrifying community responsible for the increase in the rate has rarely been investigated (4, 21). The recent discovery of ammonia-oxidizing Archaea (AOA) (19, 41), the widespread distribution of these organisms (2,3,9,14,31,35), and their predominance in soils (24) and oceans (22,27,42) led to the hypothesis that AOA might also be important for nitrification in freshwater environments, including in the rhizosphere of freshwater macrophytes. The goals of this study were therefore (i) to test for the occurrence of AOA in freshwater sediment and in the rhizosphere of the macrophyte Littorella uniflora, (ii) to compare AOA diversity and abundance to the diversity and abundance of ammonia-oxidizing bacteria (AOB), and (iii) to compare the ammonia oxidizer communities in bulk and rhizosphere sediments.Sampling and chemical analysis. Sediment cores were obtained in triplicate from within monospecies stands of L. uniflora and from unvegetated sediment that was Ն5 m from the plant stands at a water depth of 20 to 30 cm in oligomesotrophic Lake Hampen, Jutland, Denmark (7). The distances between replicate cores were 2 to 70 m for vegetated sediment and 10 to 40 m for unvegetated sediment. For molecular (September 2005 and June 2006) and pore water (June 2006) analyses, the upper 1.5 cm of unvegetated sediment and L. uniflora rhizosphere sediment (depth, 1 to 6 cm) were transferred in the field to sterile 50-ml Falcon tubes and kept on ice during transport. In the laboratory, pore water was extracted within 24 h for analyses of pH, NO 2 Ϫ plus NO 3 Ϫ (6), NO 2 Ϫ (15), and NH 4 ϩ (5), and samples for DNA extraction were frozen at Ϫ80°C.To determine potential nitrification rates (June 2006), intact sediment cores were transported to the laboratory at ambient temperature (22 to 24°C). Rhizosphere and surface sediment samples were obtained and homogenized separately for each replicate core, and incubations at room temperature and 120 rpm were immediately set up with 20-g (fresh weight) subsamples in 40 ml of sterile lake water containing 100 M NH 4 ϩ . Apparent potential nitrification rates were calculated from the linear increase in concentrations of NO 2 Ϫ plus NO 3 Ϫ during the first 6 h, and the values were about eight times higher for the rhizosphere than for the unvegetated sediment.

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Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm

Cited by 134 publications

References 76 publications

Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira

Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira

Ammonia availability shapes the seasonal distribution and activity of archaeal and bacterial ammonia oxidizers in the Puget Sound Estuary

Archaea Dominate the Ammonia-Oxidizing Community in the Rhizosphere of the Freshwater Macrophyte Littorella uniflora

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