Measurements of nitrite production in and around the primary nitrite maximum in the central California Current

Santoro, Alyson E.; Sakamoto, Carole M.; Smith, Jay W.; Plant, Joshua N.; Gehman, Alyssa‐Lois M.; Worden, Alexandra Z.; Johnson, Kenneth S.; Francis, Christopher A.; Casciotti, Karen L.

doi:10.5194/bg-10-7395-2013

Cited by 94 publications

(138 citation statements)

References 88 publications

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“…3B). NH 4 ϩ and NO 2 Ϫ concentrations were also positively associated, likely reflecting ammonia oxidation by bacteria and/or archaea (31 Among the picoprasinophytes we quantified, only Bathycoccus was present at all stations. This lack of biogeographical pattern might reflect the presence of multiple Bathycoccus ecotypes (which would both be amplified by our qPCR primer-probe set).…”

Section: Resultsmentioning

confidence: 86%

Abundance and Biogeography of Picoprasinophyte Ecotypes and Other Phytoplankton in the Eastern North Pacific Ocean

Simmons

Sudek

Monier

et al. 2016

Appl Environ Microbiol

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Eukaryotic algae within the picoplankton size class (<2 m in diameter) are important marine primary producers, but their spatial and ecological distributions are not well characterized. Here, we studied three picoeukaryotic prasinophyte genera and their cyanobacterial counterparts, Prochlorococcus and Synechococcus, during two cruises along a North Pacific transect characterized by different ecological regimes. Picoeukaryotes and Synechococcus reached maximum abundances of 1.44 ؋ 10 5 and 3.37 ؋ 10 5 cells · ml ؊1 , respectively, in mesotrophic waters, while Prochlorococcus reached 1.95 ؋ 10 5 cells · ml ؊1 in the oligotrophic ocean. Of the picoeukaryotes, Bathycoccus was present at all stations in both cruises, reaching 21,368 ؎ 327 18S rRNA gene copies · ml ؊1 . Micromonas and Ostreococcus clade OI were detected only in mesotrophic and coastal waters and Ostreococcus clade OII only in the oligotrophic ocean. To resolve proposed Bathycoccus ecotypes, we established genetic distances for 1,104 marker genes using targeted metagenomes and the Bathycoccus prasinos genome. The analysis was anchored in comparative genome analysis of three Ostreococcus species for which physiological and environmental data are available to facilitate data interpretation. We established that two Bathycoccus ecotypes exist, named here BI (represented by coastal isolate Bathycoccus prasinos) and BII. These share 82% ؎ 6% nucleotide identity across homologs, while the Ostreococcus spp. share 75% ؎ 8%. We developed and applied an analysis of ecomarkers to metatranscriptomes sequenced here and published -omics data from the same region. The results indicated that the Bathycoccus ecotypes cooccur more often than Ostreococcus clades OI and OII do. Exploratory analyses of relative transcript abundances suggest that Bathycoccus NRT2.1 and AMT2.2 are high-affinity NO 3 ؊ and low-affinity NH 4 ؉ transporters, respectively, with close homologs in multiple picoprasinophytes. Additionally, in the open ocean, where dissolved iron concentrations were low (0.08 nM), there appeared to be a shift to the use of nickel superoxide dismutases (SODs) from Mn/Fe/Cu SODs closer inshore. Our study documents the distribution of picophytoplankton along a North Pacific ecological gradient and offers new concepts and techniques for investigating their biogeography.

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Section: Resultsmentioning

confidence: 86%

Abundance and Biogeography of Picoprasinophyte Ecotypes and Other Phytoplankton in the Eastern North Pacific Ocean

Simmons

Sudek

Monier

et al. 2016

Appl Environ Microbiol

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“…Dissolved urea concentration was determined colorimetrically using the diacetyl monoxime method (Price and Harrison 1987) with previously frozen samples from the initial timepoints of the 15 N-urea addition experiments (see below) using 10 mL sample volumes with a detection limit of 100 nM. Nitrification rates were calculated using the model described previously (Santoro et al 2013 ) were calculated using a non-linear least squares curve fitting routine, implemented in MATLAB R2011b with the Optimization Toolbox. The fractionation factor for NO x assimilation (a) was taken to be 1.005.…”

Section: Nutrient Analysesmentioning

confidence: 99%

Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

Santoro

Saito

Goepfert

et al. 2017

Limnology & Oceanography

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Thaumarchaea are among the most abundant microbial groups in the ocean, but controls on their abundance and the distribution and metabolic potential of different subpopulations are poorly constrained. Here, two ecotypes of ammonia-oxidizing thaumarchaea were quantified using ammonia monooxygenase (amoA) genes across the equatorial Pacific Ocean. The shallow, or water column "A" (WCA), ecotype was the most abundant ecotype at the depths of maximum nitrification rates, and its abundance correlated with other biogeochemical indicators of remineralization such as NO 3 : Si and total Hg. Metagenomes contained thaumarchaeal genes encoding for the catalytic subunit of the urease enzyme (ureC) at all depths, suggesting that members of both WCA and the deep, water column "B" (WCB) ecotypes may contain ureC. Coupled urea hydrolysisammonia oxidation rates were similar to ammonia oxidation rates alone, suggesting that urea could be an important source of ammonia for mesopelagic ammonia oxidizers. Potential inducement of metal limitation of both ammonia oxidation and urea hydrolysis was demonstrated via additions of a strong metal chelator. The water column inventory of WCA was correlated with the depth-integrated abundance of WCB, with both likely controlled by the flux of sinking particulate organic matter, providing strong evidence of vertical connectivity between the ecotypes. Further, depth-integrated amoA gene abundance and nitrification rates were correlated with particulate organic nitrogen flux measured by contemporaneously deployed sediment traps. Together, the results refine our understanding of the controls on thaumarchaeal distributions in the ocean, and provide new insights on the relationship between material flux and microbial communities in the mesopelagic.

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“…The method underestimates the total N uptake because the uptake of other forms of regenerated N such as DON (e.g., urea, amino acids, and proteins) is not quantified (McCarthy, 1972;Eppley and Peterson, 1979), and because some fraction of the 15 N label that is taken up by phytoplankton and then exuded as DON is not retained on the filter. Another important consideration is that nitrification within the euphotic zone can generate a significant fraction of the total euphotic zone NO − 3 inventory in many oceanic regions Diaz and Raimbault, 2000;Yool et al, 2007;Grundle et al, 2013;Santoro et al, 2013) including Monterey Bay (Ward, 2005;Smith et al, 2014a,b). In this study, we performed nitrification rate estimates to separate NO − 3 produced within the euphotic zone from NO − 3 produced below the euphotic zone, for the purpose of calculating new production (Yool et al, 2007).…”

Section: N Incubationsmentioning

confidence: 99%

Insight into chemical, biological, and physical processes in coastal waters from dissolved oxygen and inert gas tracers

Manning¹

2017

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In this thesis, I use coastal measurements of dissolved O 2 and inert gases to provide insight into the chemical, biological, and physical processes that impact the oceanic cycles of carbon and dissolved gases. Dissolved O 2 concentration and triple isotopic composition trace net and gross biological productivity. The saturation states of inert gases trace physical processes, such as air-water gas exchange, temperature change, and mixing, that affect all gases.First, I developed a field-deployable system that measures Ne, Ar, Kr, and Xe gas ratios in water. It has precision and accuracy of 1 % or better, enables near-continuous measurements, and has much lower cost compared to existing laboratory-based methods. The system will increase the scientific community's access to use dissolved noble gases as environmental tracers.Second, I measured O 2 and five noble gases during a cruise in Monterey Bay, California. I developed a vertical model and found that accurately parameterizing bubble-mediated gas exchange was necessary to accurately simulate the He and Ne measurements. I present the first comparison of multiple gas tracer, incubation, and sediment trap-based productivity estimates in the coastal ocean. Net community production estimated from 15 NO -3 uptake and O 2 /Ar gave equivalent results at steady state. Underway O 2 /Ar measurements revealed submesoscale variability that was not apparent from daily incubations.Third, I quantified productivity by O 2 mass balance and air-water gas exchange by dual tracer ( 3 He/SF 6 ) release during ice melt in the Bras d'Or Lakes, a Canadian estuary. The gas transfer velocity at >90 % ice cover was 6 % of the rate for nearly ice-free conditions. Rates of volumetric gross primary production were similar when the estuary was completely ice-covered and ice-free, and the ecosystem was on average net autotrophic during ice melt and net heterotrophic following ice melt. I present a method for incorporating the isotopic composition of H 2 O into the O 2 isotope-based productivity calculations, which increases the estimated gross primary production in this study by 46-97 %.In summary, I describe a new noble gas analysis system and apply O 2 and inert gas observations in new ways to study chemical, biological, and physical processes in coastal waters.

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Measurements of nitrite production in and around the primary nitrite maximum in the central California Current

Abstract: Abstract. Nitrite (NOwithin the PNM ranged from 18 to 470 days at the mesotrophic station and was 40 days at the oligotrophic station. Our results suggest the PNM is a dynamic, rather than relict, feature with a source term dominated by ammonia oxidation.

Cited by 94 publications

References 88 publications

Abundance and Biogeography of Picoprasinophyte Ecotypes and Other Phytoplankton in the Eastern North Pacific Ocean

Abundance and Biogeography of Picoprasinophyte Ecotypes and Other Phytoplankton in the Eastern North Pacific Ocean

Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

Insight into chemical, biological, and physical processes in coastal waters from dissolved oxygen and inert gas tracers

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