Biogeochemical processes in a small California estuary. 2. Nitrification activity, community structure and role in nitrogen budgets

Caffrey, Jane M.; Harrington, Neil; Solem, Icarus; Ward, Bess B.

doi:10.3354/meps248027

Cited by 83 publications

(74 citation statements)

References 55 publications

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“…The resulting nitrification rates (456 pmol g -1 sediment day -1 ) are comparable to those reported for estuarine sediments (400 to 9000 nmol m -2 day -1 or 11 pmol g -1 sediment day -1 to 257 pmol g -1 sediment day -1 ) (Henriksen et al 1981;Caffrey et al 2003). Compared to carbon rich environment like salt marsh sediment our nitrification rate estimates are 100 to 1000 times slower (Dollhopf et al 2005).…”

Section: Surface Metersupporting

confidence: 80%

Geomicrobiology of nitrogen in a coastal aquifer : isotopic and molecular methods to examine nitrification and denitrification in groundwater

Rogers¹

2010

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Excess nitrogen input is deleterious to coastal waters, resulting in deterioration of the water quality, increases in harmful algal blooms and disease in commercial fish stocks. A significant portion of this nitrogen enters coastal waters through groundwater systems. Here we use isotopic and molecular biological methods to identify the populations of nitrifiers and denitrifiers, where they occur, and what levels of activity are present through the upper four meters of a coastal groundwater system. This work shows two different populations of putative ammonia-oxidizing archaea (AOA) based on the ammonia monooxygenase gene (amoA), one shallow population most closely related to open ocean water column-like sequences and a deeper population that is more closely related to estuarine-like AOA. Interestingly, while the surface population has a potential nitrification rates (456 pmol g -1 sediment day -1 ) similar to marine sediments, the deeper population does not show detectable evidence of nitrification. Between these two archaeal populations resides an active population of ammonia-oxidizing bacteria with similar nitrification rates as the surface AOA population. The upper meter of the aquifer is also an active area of denitrification as evidenced by the coincident drop in nitrate concentration and increase in both δ 15 N (up to + 20.1‰) and δ 18 O (up to + 11.7‰), characteristic of groundwater affected by denitrification. 16S rRNA gene surveys of the organisms present in the upper meter also are similar to soil/sediment type environments including many potential denitrifiers. However, nitrite reductase, nirS and nirK, genes were also recovered from the sediments with nirK dominating in the surface sediments. This contrasts with the deep salt wedge, where the microbial community 16S rRNA genes appear more closely related to marine or reducing sediment/wastewater type organisms, and nirS genes become the dominant denitrification gene.

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Section: Surface Metersupporting

confidence: 80%

Geomicrobiology of nitrogen in a coastal aquifer : isotopic and molecular methods to examine nitrification and denitrification in groundwater

Rogers¹

2010

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“…1). Those results have been published separately in conjunction with nutrient and nitrification rate measurements from that site by Caffrey et al (2002Caffrey et al ( , 2003, who described sequence-analysis methods and results and their findings are related to the current study in 'Discussion' below.…”

Section: Methodsmentioning

confidence: 87%

Temporal variability in nitrification rates and related biogeochemical factors in Monterey Bay, California, USA

Ward

2005

Mar. Ecol. Prog. Ser.

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134

114

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The scales of temporal variability in the rate of ammonium oxidation and a suite of related biogeochemical parameters were investigated in the surface layer of the water column of Monterey Bay, California, on the west coast of the USA. Samples were collected on bimonthly (approx. every 2 mo) cruises during the course of 2 yr. The signal of El Niño was evident in the water column temperature and nitrate distributions during the initial cruise in February 1998. Throughout the 2 yr period, variation in temperature and salinity was small and consistent with seasonal upwelling. The biological parameters, however, varied much more than might have been predicted by the minimal variability in hydrographic signals. Ammonium assimilation rates, chlorophyll a concentrations and bacterial abundance varied by 41-, 65-and 147-fold, respectively. Ammonium oxidation rates often exhibited a subsurface maximum near the bottom of the euphotic zone, and varied by a factor of 4.5 over the 2 yr study. The presence of the rate maximum was not obviously related to the dominant seasonal signals of hydrography or to other biological variables. Nitrification rates were much less variable in the bay than in Elkhorn Slough, a small estuary that opens onto the bay. The small variability in ammonium oxidation rates may be related to more dynamic responses in the community composition of the ammonia-oxidizing bacteria. Different groups of ammonia-oxidizing bacteria were detected as dominants in clone libraries from the Monterey Bay and Elkhorn Slough. The time scale of bimonthly sampling was evidently inadequate to resolve the response of nitrification rates to direct physical forcing in the bay.

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“…Interestingly, the efflux of ammonium decreased by some 33% at this site under hypoxia, which would suggest that nitrification in the sediment was largely unaffected by the availability of oxygen and that some other factor regulated the exchange of ammonium at this site. The fact that the sediments were consistent sources of ammonium throughout the year under ambient oxygen at the OG site, even outside of summer, may be indicative of chronic hypoxia and a long-term negative effect on the nitrifying community in the sediment (Caffrey et al 2003;Weston et al 2008;Greenwood et al 2010).…”

Section: Discussionmentioning

confidence: 99%

Short‐term hypoxia alters the balance of the nitrogen cycle in coastal sediments

Neubacher

Parker

Trimmer

2011

Limnology & Oceanography

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We measured denitrification, anaerobic ammonium oxidation (anammox), oxygen uptake, nutrient exchange, and pore-water profiles of oxygen in intact sediments at three sites in the southern North Sea, which we experimentally exposed to different oxygen saturations (ambient and , 33% of air-saturation for oxygen [i.e., our hypoxic treatment]) over 14 months. Denitrification ranged from 1 mmol N m 22 h 21 to 21 mmol N m 22 h 21 , anammox 0.2 mmol N m 22 h 21 to 5.7 mmol N m 22 h 21 , and oxygen uptake 47 mmol O 2 m 22 h 21 to 631 mmol O 2 m 22 h 21 . The seasonal patterns under ambient oxygen were correlated with those in the hypoxic treatment; though, on the whole, the magnitude of flux was different. On average, under hypoxia, both the penetration and consumption of oxygen decreased by , 50%, denitrification increased by 32%, and anammox remained constant. Anammox accounted for between 10% and 20% of the total N 2 production, which agrees with expectations for waters of these depths (30-80 m). Under ambient oxygen the sediments were strong sources of nitrate to the overlying water, 12 mmol NO { 3 m 22 h 21 on average, but under hypoxia total N mineralization decreased by 46% and nitrate exchanged ceased. Short-term hypoxia alters the balance between available N returned to the overlying water, primarily as NO { 3 , and that removed from the ecosystem as N 2 gas.

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Biogeochemical processes in a small California estuary. 2. Nitrification activity, community structure and role in nitrogen budgets

Cited by 83 publications

References 55 publications

Geomicrobiology of nitrogen in a coastal aquifer : isotopic and molecular methods to examine nitrification and denitrification in groundwater

Geomicrobiology of nitrogen in a coastal aquifer : isotopic and molecular methods to examine nitrification and denitrification in groundwater

Temporal variability in nitrification rates and related biogeochemical factors in Monterey Bay, California, USA

Short‐term hypoxia alters the balance of the nitrogen cycle in coastal sediments

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