Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, occurs in a wide variety of environments and plays a central role in the global nitrogen cycle. Catalyzed by the enzyme ammonia monooxygenase, the ability to oxidize ammonia was previously thought to be restricted to a few groups within the ␤-and ␥-Proteobacteria. However, recent metagenomic studies have revealed the existence of unique ammonia monooxygenase ␣-subunit (amoA) genes derived from uncultivated, nonextremophilic Crenarchaeota. Here, we report molecular evidence for the widespread presence of ammonia-oxidizing archaea (AOA) in marine water columns and sediments. Using PCR primers designed to specifically target archaeal amoA, we find AOA to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments. Diverse and distinct AOA communities are associated with each of these habitats, with little overlap between water columns and sediments. Within marine sediments, most AOA sequences are unique to individual sampling locations, whereas a small number of sequences are evidently cosmopolitan in distribution. Considering the abundance of nonextremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle.Crenarchaeota ͉ nitrification ͉ ammonia monooxygenase

Corals are known to harbor diverse microbial communities of Bacteria and Archaea, yet the ecological role of these microorganisms remains largely unknown. Here we report putative ammonia monooxygenase subunit A (amoA) genes of archaeal origin associated with corals. Multiple DNA samples drawn from nine coral species and four different reef locations were PCR screened for archaeal and bacterial amoA genes, and archaeal amoA gene sequences were obtained from five different species of coral collected in Bocas del Toro, Panama. The 210 coral-associated archaeal amoA sequences recovered in this study were broadly distributed phylogenetically, with most only distantly related to previously reported sequences from coastal/estuarine sediments and oceanic water columns. In contrast, the bacterial amoA gene could not be amplified from any of these samples. These results offer further evidence for the widespread presence of the archaeal amoA gene in marine ecosystems, including coral reefs.

Chemical profiles of the Black Sea suboxic zone show a distribution of nitrogen species which is traditionally associated with denitrification, i.e. a secondary nitrite maximum associated with nitrate depletion and a N(2) gas peak. To better understand the distribution and diversity of the denitrifier community in the Black Sea suboxic zone, we combined a cultivation approach with cloning and sequencing of PCR-amplified nitrite reductase (nirS and nirK) genes. The Black Sea suboxic zone appears to harbour a homogeneous community of denitrifiers. For nirK, over 94% of the sequences fell into only three distinct phylogenetic clusters, and for nirS, a single closely related sequence type accounted for 91% of the sequences retrieved. Both nirS and nirK genes showed a dramatic shift in community composition at the bottom of the suboxic zone, but overall, nirK-based community composition showed much greater variation across depths compared with the highly uniform distribution of nirS sequences throughout the suboxic zone. The dominant nirK and nirS sequences differed at the amino acid level by at least 17% and 8%, respectively, from their nearest database matches. Denitrifying isolates recovered from the suboxic zone shared 97% 16S rRNA gene sequence similarity with Marinobacter maritimus. Analysis of the recently discovered nirS gene from the anammox bacterium Candidatus'Kuenenia stuttgartiensis' revealed that mismatches with commonly used primers may have prevented the previous detection of this divergent sequence.

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Phosphorus (P) availability declines during ecosystem development due in part to chemical transformations of P in the soil. Here we report changes in soil P pools and the oxygen isotopic signature of inorganic phosphate (δ 18 O p ) in these pools over a 6500-year soil coastal dune chronosequence in a temperate humid environment. Total P declined from 384 to 129 mg P kg −1 during the first few hundred years of pedogenesis, due mainly to the depletion of primary mineral P in the HCl-extractable pool. The δ 18O p of HCl-extractable inorganic P initially reflected the signature of the parent material, but shifted over time towards (but not reaching) isotopic equilibrium. In contrast, δ 18 O p signatures of inorganic P extracted in water and NaHCO 3 (approximately 9 and 39 mg P kg −1 , respectively) were variable but consistent with isotopic equilibrium with soil water. In the NaOH-extractable P pool, which doubled from 63 to 128 mg P kg −1 in the early stages of pedogenesis and then gradually declined, the δ 18O p of the extracted inorganic P changed from equilibrium values early in the chronosequence to more depleted signatures in older soils, indicating greater rates of hydrolysis of labile organic P compounds such as DNA and increase involvement in P cycling as overall P availability declines through the sequence. In summary, this application of δ 18O p to a long-term soil chronosequence provides novel insight into P dynamics, indicating the importance of efficient recycling through tight uptake and mineralization in maintaining a stable bioavailable P pool during long-term ecosystem development.

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The isotopic signature of oxygen in phosphate (δ(18)O(P)) of various soil fractions may shed light on P transformations, including phosphorus (P) recycling by soil microorganisms, uptake by plants and P adsorption, precipitation and release by oxides and minerals, thus increasing our understanding on P cycling and lability in soils. We developed and tested a protocol to extract and purify inorganic phosphate (Pi) from different soil fractions distinguished by binding strength and precipitate it as silver phosphate (Ag(3)PO(4)) for δ(18)O(P) analysis. Soil P is extracted sequentially using water, NaHCO(3), NaOH and HCl and Pi in each solution is purified and precipitated as Ag(3)PO(4). The unique characteristics and possible interferences of the soil solution extracts are addressed. Two agricultural soil samples receiving reclaimed wastewater or fresh water were analyzed, and results indicate that all soil fractions analyzed have been impacted to some degree by biologically enzyme mediated cycling of P in the soil.

Atmospheric P solubility affects the amount of P available for phytoplankton in the surface ocean, yet our understanding of the timing and extent of atmospheric P solubility is based on short-term leaching experiments where conditions may differ substantially from the surface ocean. We conducted longer- term dissolution experiments of atmospheric aerosols in filtered seawater, and found up to 9-fold greater dissolution of P after 72 h compared to instantaneous leaching. Samples rich in anthropogenic materials released dissolved inorganic P (DIP) faster than mineral dust. To gauge the effect of biota on the fate of atmospheric P, we conducted field incubations with aerosol samples collected in the Sargasso Sea and Red Sea. In the Sargasso Sea phytoplankton were not P limited, and biological activity enhanced DIP release from aerosols, and aerosols induced biological mineralization of dissolved organic P in seawater, leading to DIP accumulation. However, in the Red Sea where phytoplankton were colimited by P and N, soluble P was rapidly consumed by phytoplankton following aerosol enrichment. Our results suggest that atmospheric P dissolution could continue over multiple days once reaching the surface ocean, and that previous estimates of atmospheric P deposition may underestimate the contribution from this source.