Ammonia-Oxidizing β-Proteobacteria from the Oxygen Minimum Zone off Northern Chile

Abstract

The composition of ammonia-oxidizing bacteria from the ␤-Proteobacteria subclass (␤AOB) was studied in the surface and upper-oxycline oxic waters (2-to 50-m depth, ϳ200 to 44 M O 2 ) and within the oxygen minimum zone (OMZ) suboxic waters (50-to 400-m depth, <10 M O 2 ) of the eastern South Pacific off northern Chile. This study was carried out through cloning and sequencing of genes coding for 16S rRNA and the ammonia monooxygenase enzyme active subunit (amoA). Sequences affiliated with Nitrosospiralike cluster 1 dominated the 16S rRNA gene clone libraries constructed from both oxic and suboxic waters. Cluster 1 consists exclusively of yet-uncultivated ␤AOB from marine environments. However, a single clone, out of 224 obtained from the OMZ, was found to belong to Nitrosospira lineage cluster 0. To our knowledge, cluster 0 sequences have been derived from ␤AOB isolated only from sand, soil, and freshwater environments. Sequences in clone libraries of the amoA gene from the surface and upper oxycline could be grouped in a marine subcluster, also containing no cultured representatives. In contrast, all 74 amoA sequences originating from the OMZ were either closely affiliated with cultured Nitrosospira spp. from clusters 0 and 2 or with other yet-uncultured ␤AOB from soil and an aerated-anoxic Orbal process waste treatment plant. Our results reveal the presence of Nitrosospira-like ␤AOB in both oxic and suboxic waters associated with the OMZ but with a clear community shift at the functional level (amoA) along the strong oxygen gradient.Oxygen minimum zones (OMZs) are permanent areas of the ocean with dissolved O 2 concentrations of Յ22 M at intermediate depths (15, 18) caused by low rates of ventilation and high biological O 2 demand. The main zones are found in the eastern tropical Pacific and Arabian Sea. Associated with a sharp decrease of dissolved O 2 concentration with depth is an intense nitrogen cycle that generates characteristic vertical distributions of nitrogen compounds within the OMZ: i.e., high NO 3 Ϫ deficit, a secondary nitrite maximum, and low NH 4 ϩ concentrations are found within the core, as well as N 2 O maxima towards the OMZ boundaries (8,26,30,41). Such strong chemical gradients produced by OMZs could be considered as gene flow barriers and their oxygen-deficient waters as suitable environments for innovation, where organisms develop specific adaptations to exploit these unique conditions (9, 30, 42). In fact, novel and yet-uncultivated groups of denitrifiers have been found in the OMZ of the Arabian Sea (17a) and the eastern South Pacific (6a) by cloning and sequencing of the nirS genes. However, the diversity of most of the OMZ microbial world remains unexplored. Ammonia-oxidizing bacteria (AOB) are considered to play a key role in the nitrogen cycling of these OMZs, contributing to NH 4 ϩ removal and NO 2 Ϫ and N 2 O production (26, 33, 52).AOB consist of a group of chemolithoautotrophic microorganisms able to oxidize aerobically NH 4 ϩ to NO 2 Ϫ , via NH 2 OH (hydroxylamine), a dissimi...

Structure of denitrifying communities reducing N2O at suboxic waters off northern Chile and Perú

“…In the same sense, our data suggests that the variety of micro niches at oxyclines could be determining the observed differences in the structure of nosZ-communities inhabiting the ULOMZ off Chile and Perú; because it was evident the presence and dominance of the T-RFs of 77-bp and 710-bp off Chile and not off Perú. Our results support the hypothesis of niche differentiation previously proposed for global data set of nirS and nirK communities (Jones & Hallin 2010), and for ammoniaoxidizing -proteobacteria (Molina et al 2007) and anammox bacteria (Galán et al 2009) in the ESPO, which, could be a strategy of nosZ-community to be metabolically versatile in the ULOMZ to participate in several biologically mediated transformations of nitrogen and other elemental cycles as it has been argued by other researchers ).…”

“…Also, from a functional point of view, metatranscriptomic findings report the metabolic versatility of nitrifiers, archaea, anammox and denitrifiers type nirS, nirK and nosZ (Stewart et al 2012) in the area; and other studies indicated the co-occurring and activity of ammonia-oxidizing -proteobacteria, Nitrosospira spp. principally (Molina et al 2007) and nirS-denitrifiers (Castro-González et al 2005). These reports (with 16S RNA and functional genes) along with our results suggest that diverse microbial groups inhabit the OMZ in the ESPO.…”

“…Indeed, the OMZ off northern Chile and Perú is one of the shallowest and intense OMZ in the ocean with O 2 levels < 3 nM (Revsbech et al 2009), which has been defined as functional anoxia sensu Thamdrup et al (2012). Along that extreme O 2 gradient, NO 3 -, NO 2 -and N 2 O gradients are observed as well, being N 2 O, a potent greenhouse gas that shows high vertical variability (Farías et al 2007). It is not clear yet which processes are responsible for huge N 2 O accumulation at the upper limit of the oxygen minimum zone (ULOMZ) but it is clear that N 2 O is depleted towards OMZ´s core, as O 2 declines and favors the N 2 O reduction to N 2 by denitrifying process (Farías et al 2009).…”

“…It is not clear yet which processes are responsible for huge N 2 O accumulation at the upper limit of the oxygen minimum zone (ULOMZ) but it is clear that N 2 O is depleted towards OMZ´s core, as O 2 declines and favors the N 2 O reduction to N 2 by denitrifying process (Farías et al 2009). For example, N 2 O concentrations as high as 172.7 nM off Peru (Codispoti et al 1992) and 124 nM off northern Chile (Farías et al 2007) were registered in subsurface water (below the mixed layer), constituting a large N 2 O source estimated in ~12.78 Gg (Cornejo & Farías 2012). N 2 O can be produced by nitrification and partial denitrification of bacteria and Archaea (Cabello et al 2004, Castro-González & Farías 2004, Santoro et al 2011, Loescher et al 2012 as well as nitrifier denitrification (Shaw et al 2006), processes which can co-occur at oxyclines and pycnoclines, while dissimilative N 2 O to N 2 reduction at suboxic or anoxic condition takes place only by complete denitrification (Bange et al 2010).…”

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

“…All but two of the 99% OTUs fell within the marine/estuarine Nitrosospira-like clade (for example, cluster B in Francis et al 2003) (Figure 1). This cluster consists of environmental amoA sequences from various marine environments (Francis et al, 2003;Bernhard et al, 2005;Molina et al, 2007;Kim et al, 2008;Mosier and Francis, 2008). The other two OTUs are closely related to cultured N. europea and environmental sequences from various environments such as the Baltic Sea water column and an ANAMMOX bioreactor (Kim et al, 2008;Bae H, Paul T and Jung JY, unpublished).…”