Denitrifier Community Composition along a Nitrate and Salinity Gradient in a Coastal Aquifer

Abstract

Nitrogen flux into the coastal environment via submarine groundwater discharge may be modulated by microbial processes such as denitrification, but the spatial scales at which microbial communities act and vary are not well understood. In this study, we examined the denitrifying community within the beach aquifer at Huntington Beach, California, where high-nitrate groundwater is a persistent feature. Nitrite reductaseencoding gene fragments (nirK and nirS), responsible for the key step in the denitrification pathway, were PCR amplified, cloned, and sequenced from DNAs extracted from aquifer sediments collected along a cross-shore transect, where groundwater ranged in salinity from 8 to 34 practical salinity units and in nitrate concentration from 0.5 to 330 M. We found taxonomically rich and novel communities, with all nirK clones exhibiting <85% identity and nirS clones exhibiting <92% identity at the amino acid level to those of cultivated denitrifiers and other environmental clones in the database. Unique communities were found at each site, despite being located within 40 m of each other, suggesting that the spatial scale at which denitrifier diversity and community composition vary is small. Statistical analyses of nir sequences using the Monte Carlo-based program ͐-Libshuff confirmed that some populations were indeed distinct, although further sequencing would be required to fully characterize the highly diverse denitrifying communities at this site.Denitrification, the microbial dissimilatory reduction of nitrate and nitrite to gaseous products (NO, N 2 O, and N 2 ) under suboxic conditions, has long been considered the main biological loss term for fixed nitrogen from ecosystems. In coastal and estuarine sediments, this process can remove more than half of the inorganic nitrogen inputs from terrestrial systems (27). One source of nitrogen for coastal environments is submarine groundwater discharge from unconfined aquifers, which is increasingly recognized as an important source of nutrients (7,16). Groundwater below the beach face at Huntington Beach (HB), California, is enriched in nitrate, with reported nitrate concentrations in excess of 400 M (3). The source of this nitrate is unknown, but potential sources include infiltration of fertilizercontaminated surface water, microbial nitrification, or leaking subsurface sewage lines. Nitrate concentrations in the groundwater pool decrease 2 orders of magnitude in the cross-shore direction as the nitrate-rich brackish groundwater mixes with saline, nitrate-depleted seawater (Fig. 1). This mixing establishes ideal gradients in both nitrate and salinity over which to examine the geochemical parameters that may be controlling microbial diversity, especially the diversity of denitrifying bacteria.Because denitrifying microorganisms span a wide range of taxonomic groups, including over 50 different genera (32), 16S rRNA-based approaches are not generally useful for investigating natural denitrifying communities. Nitrite reduction to nitric oxide is the rate-limi...

Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

“…nirS diversity is higher than nirK diversity in some aquifers, marsh and costal sediments, suggesting that (semi-)aquatic systems sustain diverse nirS-type denitrifiers (Braker et al, 2000;Prieme et al, 2002;Santoro et al, 2006). Such findings are in agreement with the high detected nirS diversity in acidic peat soils (Table 4).…”

Habitat partitioning of denitrifying bacterial communities carrying nirS or nirK genes in the stratified water column of Lake Kinneret, Israel

“…In Lake Kinneret, bacteria carrying nirK appear to be adapted to the specific environmental conditions in each layer of the stratified water column. A similar tendency was observed in a salinity gradient in a beach aquifer at Huntington Beach (California) where different clades of nirK sequences were associated to specific salinities, whereas nirS did not show any specific environmental adaptation (Santoro et al 2006). Also, a recent study in the suboxic zone of the Black Sea (Oakley et al 2007) showed much greater variation of nirK sequences at the bottom of the suboxic zone, while nirS sequences were more homogeneously distributed.…”

“…A similar tendency was observed in a salinity gradient in a beach aquifer at Huntington Beach (California) where different clades of nirK sequences were associated to specific salinities, whereas nirS did not show any specific environmental adaptation (Santoro et al 2006). Also, a recent study in the suboxic zone of the Black Sea (Oakley et al 2007) showed much greater variation of nirK sequences at the bottom of the suboxic zone, while nirS sequences were more homogeneously distributed.The nirS and nirK sequences from Lake Kinneret differed from those of marine habitats and coastal aquifers (Jayakumar et al 2004, Castro-Gonzalez et al 2005, Francis et al 2005, Santoro et al 2006). This suggests a differentiation of marine and purely freshwater denitrifying bacteria carrying nirS, but has to be substantiated by additional studies.…”

“…Aquat Microb Ecol 51: [129][130][131][132][133][134][135][136][137][138][139][140] 2008 ment (Nogales et al 2002), marine sediments (Braker et al 2000(Braker et al , 2001, aquifers (Santoro et al 2006), seawater (Jayakumar et al 2004, Castro-Gonzalez et al 2005) and the oxygen minimum zone of the Black Sea (Oakley et al 2007). In marine environments a shift in the community structure of nirS denitrifying bacteria occurs along the physical-chemical gradient in the stratified water column (Castro-Gonzalez et al 2005, Oakley et al 2007.…”

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

“…The nosZ-communities were separated between some characteristics of the upper oxycline (TRFs: 616,151,142,493,70,113,295,327,184,187) and the rest of TRFs into of core and/or the lower oxycline (TRF 77). Several studies have reported that the denitrifiers respond differently to environmental gradients of available nitrogen species and that the NH 4 + , NO 2 -, O 2 or NO 3 -could be determining the differences in its structure (Santoro et al 2006, Hones & Hallin 2010. However, our results show that although the composition of nosZ-TRFs was positively correlated with O 2 , N 2 O and NH 4 + and negatively with NO 2 -there is not a clear trend in this aspect, suggesting that probably other variables not measured in this study, could also impact the structure of nosZ-type denitrifiers.…”