Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic.

Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (Royal NIOZ), PO Box 59, 1790 AB Den Burg, Texel, The Netherlands.
Nature (Impact Factor: 38.6). 12/2008; 456(7223):788-91. DOI: 10.1038/nature07535
Source: PubMed

ABSTRACT Aerobic nitrification of ammonia to nitrite and nitrate is a key process in the oceanic nitrogen cycling mediated by prokaryotes. Apart from Bacteria belonging to the beta- and gamma-Proteobacteria involved in the first nitrification step, Crenarchaeota have recently been recognized as main drivers of the oxidation of ammonia to nitrite in soil as well as in the ocean, as indicated by the dominance of archaeal ammonia monooxygenase (amoA) genes over bacterial amoA. Evidence is accumulating that archaeal amoA genes are common in a wide range of marine systems. Essentially, all these reports focused on surface and mesopelagic (200-1,000 m depth) waters, where ammonia concentrations are higher than in waters below 1,000 m depth. However, Crenarchaeota are also abundant in the water column below 1,000 m, where ammonia concentrations are extremely low. Here we show that, throughout the North Atlantic Ocean, the abundance of archaeal amoA genes decreases markedly from subsurface waters to 4,000 m depth, and from subpolar to equatorial deep waters, leading to pronounced vertical and latitudinal gradients in the ratio of archaeal amoA to crenarchaeal 16S ribosomal RNA (rRNA) genes. The lack of significant copy numbers of amoA genes and the very low fixation rates of dark carbon dioxide in the bathypelagic North Atlantic suggest that most bathypelagic Crenarchaeota are not autotrophic ammonia oxidizers: most likely, they utilize organic matter and hence live heterotrophically.

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    ABSTRACT: Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments, such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature (higher in the Arabian Sea than in the ETSP) was the main factor that correlated with the differences between the AOA communities. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role, than did geography, in shaping the AOA community composition.
    Frontiers in Microbiology 01/2013; 4:177. · 3.90 Impact Factor
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    ABSTRACT: Aims Nitrification inhibitors (NI) formulated on granulated ammonium sulphate nitrate (ASN) are an option to minimize nitrate leaching into ground waters and emissions of the greenhouse gas N2O. This paper focuses (a) on the development of an analytic enabling to extract and quantify the NI 3,4-dimethylpyrazolephosphate (DMPP), marketed since 1999. The efficiency of DMPP has been studied in laboratory and field soils. Here the DMPP analytic and the behaviour of a nitrifying bacterial consortium enriched from a field soil and exposed to zero, field applied and a 10 fold higher DMPP concentration than the recommended one for field application are in the focus. Methods For extracting DMPP quantitatively from soils a method connected to a HPLC analytic has been developed by us and was standardized in laboratory experiment with a silt clay field soil (allochtone Vega). The method is detailed described here. Its reliability has been tested in a 3 years field trial under varying cropping systems and climatic conditions asides the influence of DMPP on CO2−, CH4− and N2O- emissions, measured by the closed chamber method. Parallel a nitrifying bacterial consortium of the silty clay field soil was enriched and subjected to 0, the recommended DMPP concentration for field applications and a 10 times higher one. In incubation experiments the conversion of ammonium to nitrite and nitrate in presence and absence of DMPP was spectrophotometer determined and pH-shifts with a scaled litmus paper. In sacrificed flasks at the end of incubation morphological changes of the bacteria involved were studied by transmission electron microscope (TEM). Results The ammonium, nitrite and nitrate determinations and the TEM pictures show that in presence of the field applied DMPP concentration the nitrifying activity returned around 30 days later than in the control and the cells were slightly enlarged. In presence of a 10 times higher DMPP concentration a recovery was prevented. DMPP prolongs, compared with dicyandiamide (DCD), the period of nitrifiers’ inhibition and reduced N2O− and CO2− the emissions (Weiske et al., Biol Fertil Soils 34:109–117, 2001a, Nutr Cycl Agroecosys 60:57–64, b). Conclusions With the method developed by us the stability of DMPP in agricultural soils can be satisfyingly and reproducible studied down to a detection limit of 0.01 μg DMPP g−1 dry soil. The morphological changes in the nitrifying consortium due to DMPP concentrations are in agreement with the recovery rate found by nitrite and nitrate formation.
    Plant and Soil 10/2013; · 3.24 Impact Factor
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    ABSTRACT: Purpose Acidic red soils account for 21% of land area in China and contain low ammonia concentration due to ionization to ammonium. The unusual high affinity for ammonia of marine Nitrosopumilus maritimus and acidophilic soil Nitrosotalea devanaterra has suggested that ammonia-oxidizing archaea (AOA) may have greater selective advantage over ammonia-oxidizing bacteria (AOB) in ammonia-limited environment because ammonia rather than ammonium is thought to be the actual substrate for oxidation. The aim of this study was to assess whether nitrification activity can be attributed to AOA and/or AOB by relating community structures of AOA and AOB to nitrification activity in acidic red soils in southern China. Materials and methods In this study, the composition and abundance of AOA community were investigated in acidic red soils of coniferous Pinus forest, broad-leaf Cinnamomum forest, bush forest (BF), and a 30-year agricultural field converted from bush forest (BFA). The composition of AOA based on archaeal amoA genes were analyzed by denaturant gradient gel electrophoresis, and the abundances of AOA communities were determined by real-time quantitative polymerase chain reaction, while soil nitrification activity was measured using 15N pool enrichment technique. Results and discussion 15N pool enrichment technique indicated nitrification activity in acidic red soils, but AOB were not detected. The absence of AOB in acidic red soils could be well explained by the low ammonia concentration ranging from 17.8 to 34.3 nM, which is far below the known threshold values required to support the growth of AOB in culture. Nitrification activity change coupled well with abundance and composition changes of archaeal amoA genes, particularly for acidic BF and BFA soils. Phylogenetic analysis demonstrated that the putatively active AOA were related to amoA transcripts in a hot spring within the soil Crenarchaeota group 1.1b lineage. Conclusions These results suggest that AOA play important roles in ammonia oxidation in acidic red soils tested in this study.
    Journal of Soils and Sediments 12(3). · 1.97 Impact Factor