Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic.
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: Thaumarchaeota and the gene encoding for a subunit of ammonia monooxygenase (amoA) are ubiquitous in Polar Seas, and some Thaumarchaeota also have a gene coding for ureC, diagnostic for urease. Using quantitative PCR we investigated the occurrence of genes and transcripts of ureC and amoA in Arctic samples from winter, spring and summer. AmoA genes, ureC genes and amoA transcripts were always present, but ureC transcripts were rarely detected. Over a 48 h light manipulation experiment amoA transcripts persisted under light and dark conditions, but not ureC transcripts. In addition, maxima for amoA transcript were nearer the surface compared to amoA genes. Clone libraries using DNA template recovered shallow and deep amoA clades but only the shallow clade was recovered from cDNA (from RNA). These results imply environmental control of amoA expression with direct or indirect light effects, and rare ureC expression despite its widespread occurrence in the Arctic Ocean.Scientific Reports 01/2014; 4:4661. · 2.93 Impact Factor
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ABSTRACT: The interest for microorganisms inhabiting the hypolimnion and for their role in biogeochemical cycles of lakes is considerable, but knowledge is far from complete. The presence of chemolithoautotrophic Bacteria and mesophilic Archaea ( e.g ., Thaumarchaeota) assimilating inorganic carbon in the deep hypolimnion of lakes has been ascertained. We measured, for the first time at 350 m in lake Maggiore (Northern Italy), the prokaryotic in situ dark [ 14 C]HCO 3 incorporation with a new custom-made apparatus, which takes samples and adds tracers in situ . Thereby stress factors affecting prokaryotes during sample recovery from the depth were avoided. We tested the new instrument at different depths and conditions, performing parallel conventional on board incubations. We found that in situ dark [ 14 C]HCO 3 incorporations had lower standard deviation in in situ incubations with respect to the on board ones, but their means were not statistically different. At 350 m we estimated an uptake of 187.7±15 µg C m -3 d –1 , which is in line with the published uptake rates in aquatic systems. By inhibiting the bacterial metabolism, we found that Archaea were responsible for 28% of the total CO 2 uptake. At the same depth, Thaumarchaeota, on average, constituted 11% of total DAPI counts. Dark [ 14 C]HCO 3 incorporation integrated along the aphotic water column was 65.8±5.2 mg C m –2 d –1 which corresponds to 87% of picophytoplanktonic autotrophic fixation in the euphotic layer. This study provides the first evidence of Bacteria and Archaea dark CO 2 fixation in the deep hypolimnion of a subalpine lake and indicates a potentially significant prokaryotic CO 2 sink.Journal of limnology 01/2014; 73. · 1.47 Impact Factor
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ABSTRACT: During the 2011 exploration season of the EV Nautilus in the Mediterranean Sea, we conducted a multidisciplinary study, aimed at exploring the microbial populations below the sediment-water interface (SWI) in the hydrocarbon rich environments of the Levantine basin. Two ~1000 m deep locations were sampled: sediments fueled by methane seepage at the toe of the Palmachim disturbance and a patch of euxinic sediment with high sulfide and methane content offshore Acre, enriched by hydrocarbon from an unknown source. We describe the composition of the microbial population in the top 5 cm of the sediment with 1 cm resolution, accompanied by measurements of methane and sulfate concentrations, and the isotopic composition of this methane and sulfate (δ(13) CCH 4 , δ(18) OSO 4 and δ(34) SSO 4 ). Our geochemical and microbiological results indicate the presence of the anaerobic methane oxidation (AOM) coupled to bacterial sulfate reduction (BSR). We show that complex methane and sulfur metabolizing microbial populations are present in both locations, although their community structure and metabolic preferences differ due to potential variation in the hydrocarbon source. This article is protected by copyright. All rights reserved.FEMS Microbiology Ecology 03/2014; 87(3):780–796. · 3.56 Impact Factor