1,721,045 research outputs found
Development of a DNA Microarray for the Study of Functional Gene Diversity in the Environment
No full textNo Nitrification, No NO-? Nitrification as a Source of Regenerated Primary Production in the Epipelagic North Atlantic
No full textPrimary Production by phytoplankton is the base of the marine food web.
Phytoplankton are often limited by nitrogen availability, which is usually supplied in the
form of nitrate in the open ocean. Nitrate can either be supplied by mixing or upwelling
from subsurface waters or from the process of nitrification within the surface layer. This
work investigated the possibility that nitrification occurs in the epipelagic North Atlantic
Ocean at rates appreciable enough to have an impact on primary production there. To
quantify the importance of nitrification relative to nitrogen uptake by phytoplankton,
experiments were performed on two cruises ¿ EN532 (Fall, 2013) and EN538 (Spring
2014) ¿ at two process stations per cruise. Experiments included measuring: 1)
ammonium, nitrate, and bicarbonate assimilation rates, 2) ammonium oxidation rates, and
3) nitrite oxidation rates.
Experiments were performed at multiple depths spanning the surface water
column at each process station, so that integrated biological rates over the relevant depth
interval (upper mixed layer or euphotic zone) could be calculated and compared between
experiments at each station. While nitrification rates were on average higher during the
spring, nitrate assimilation rates were higher as well, such that nitrification met less of the
nitrate-uptake demand in the spring than in the fall. In general, however, nitrification was
only able to provide between 0.7% and 0.8% of the nitrate demand in the spring and
between 3% and 100% of the nitrate demand in the autumn, with the latter percentage
likely being an anomaly due to relatively high concentrations of ammonium at this
process station. These results indicate that the principal influx of nitrate to the epipelagic
North Atlantic Ocean is not derivative of nitrification occurring within the epipelagic
layer itself
Nitrogen Isotopic Variation in the Global Ocean: A Potential Anthropogenic Impact Indicator
No full textChanges to marine food webs have large global impacts on the economic stability and nutritional well-being of people around the world. It is a priority for conservation to develop qualitative and quantitative frameworks to measure the collective ecological impact of many anthropogenic drivers on various marine environments. This paper proposes the use of a trophodynamic indicator, nitrogen isotope versus length relationships, as a broadly applicable measure of ecosystem health. This study compiled a database of nitrogen isotopes in fish to investigate the relationship between fish size and muscle tissue nitrogen isotopic composition (δ15N) across diverse environments in the global ocean. In an analysis of individual species within each ecosystem, there was a declining relationship between δ15N and size as environmental health declined. In lesser disturbed food webs, fish were more likely to exhibit ontogenetic increases in δ15N, suggesting that a more fully realized trophic structure is indicative of a less-impacted ecosystem. In contrast, highly altered ecosystems observed almost no increases in δ15N. Environmental impact based on trends between δ15N and length significantly matched the results of an ecosystem health model developed by Halpern et al. (2008) which is based on a full range of anthropogenic drivers. Lastly, a case study investigating temporal trends in the relationship between δ15N and length within a single fish population confirmed that δ15N and length relationships strengthened following implementation of a marine protected area. δ15N vs. size relationships may therefore provide a quantitative measure of anthropogenic impact that could support conservation and management decisions
Prochlorococcus & the Secondary Chlorophyll Maximum in the East Tropical North Pacific Oxygen Deficient Zone
No full textOxygen deficient zones are responsible for a major fraction of global ocean nitrogen loss, and these regions are predicted to expand with continued global warming. We investigate a classic feature of these regions, the secondary chlorophyll maximum, that is often dominated by Prochlorococcus. We hypothesize that Prochlorococcus finds a niche at a depth where it can utilize the abundant nitrate that accumulates with depth, beneath competing organisms in the euphotic zone. We find that Prochlorococcus abundance does not correlate with nitrate, and its fluorescence properties in the water column do not seem to match expected growth rates. Prochlorococcus abundance may additionally have a strong advective forcing behind its variability in the water column
Biogeochemistry of Nitrogen Cycling in Low O2 Waters from Oxygen Minimum Zones, Soda Lakes, to Cultures
No full textNitrogen (N) is an essential component of proteins and nucleic acids and therefore, an essential element for life. N can take many forms in the environment, all with different biological availabilities. Microorganisms play an outsize role in determining the partitioning of N between these forms. Here we present four studies that investigated the genetic capabilities, biochemical intricacies, and environmental significance of N cycling microbes, with a focus on low O2 environments and anaerobic ammonium oxidizing (anammox) bacteria, a clade responsible for substantial fixed nitrogen loss in oxygen minimum zones (OMZs), large naturally occurring anoxic marine regions. In chapter 2, we report genetic and biochemical evidence that three anammox bacteria encode an encapsulin system, a novel type of protein based cellular compartment. Searches through metagenomic databases returned 25 additional new encapsulins. Chapter 3 reports experiments that tested two hypotheses for how the most common type of anammox encapsulin functions: (1) that anammox encapsulins protect against reactive compounds and (2) that anammox encapsulins reduce NO2- to NO for the central anammox metabolism. In experiments using aerobic and anaerobic E. coli cultures engineered to express a model anammox encapsulin, no evidence for either hypothesis was observed. As a result, the biochemical function and role of encapsulins in anammox bacteria remains unexplained. Chapter 4 examines the N cycle in the soda lake Mono Lake by delving into a metagenomic data series across major chemical changes in oxygen, salinity, and winter mixing. Members of the Nitriliruptorales order were observed to be abundant at all times, depths, and oxygen concentrations, a phenomenon possibly due to an ability to metabolize a great variety of carbohydrates. Chapter 5 presents a comprehensive suite of stable isotope incubations designed to estimate the rates of microbial N transformations in OMZs. The results provide support for several new views of the marine N cycle: (1) that a rapid cycle of NO3- reduction and NO2- oxidation is of greater magnitude than N loss rates in OMZs, (2) that this rapid cycle maintains the deep secondary nitrite maximum observed in all OMZs, and (3) that anaerobic NO2- oxidation occurs in OMZ regions
Copper’s Role in Marine Denitrification: Phylogeny, Bioavailability, and Particulate Chemistry
No full textThe marine nitrogen cycle is a series of microbially mediated processes that transform nitrogen and control nitrogen bioavailability for marine organisms. Fixed nitrogen is the limiting nutrient in most of the global ocean. Denitrification, a key process that removes fixed nitrogen from the water column, comprises a sequential series of reduction reactions that convert nitrate to dinitrogen gas. Nitrous oxide (N2O), a potent greenhouse gas and ozone-depleting agent, is an intermediate in the denitrification pathway. Denitrification is prevalent in oxygen minimum zones (OMZs), which contribute to water column nitrogen loss and are hotspots for N2O production. Copper (Cu) is essential for two steps in the denitrification pathway, the reduction of nitrite and N2O. However, the bioavailability of free copper in seawater is limited by organic complexation. Decreased copper availability can inhibit denitrification, leading to decreased growth rates and accumulation of the intermediates, nitrite and N2O. This dissertation investigates the role of copper in marine denitrification, focusing on exploring the diversity organisms that use copper-dependent enzymes, characterizing the chemistry of Cu in particles and understanding how copper bioavailability, influenced by natural ligands, affects nitrogen cycling. The diversity, phylogenetic affiliation, and environmental distribution of nirK and nosZ genes, which encode Cu-containing enzymes, were examined using thousands of sequences from published databases and newly sequenced metagenomes. Meta-analysis of sequences revealed high diversity of both genes, along with strong habitat and niche separation.
Trace metal clean culture experiments using denitrifying bacterial isolates from the Arabian Sea OMZ examined the impact of natural ligands on the bioavailability of Cu. Both methanobactin and cysteine significantly affected denitrification rates and the accumulation of intermediates through complete or partial, respectively, inhibition of Cu-requiring steps in the denitrification pathway.
Lastly, suspended particles are hotspots for denitrification in seawater. Synchrotron X-ray spectroscopy techniques were used to characterize the Cu chemistry of particles collected from OMZs. A graphical user interface was developed to analyze the distribution and chemical associations within the particles. Overall, this work provides insights into the complex role of copper in marine nitrogen cycling and its broader environmental implications
Biogeochemical Controls on Fixed Nitrogen Loss Processes in the Marine Environment
No full textFixed nitrogen availability can regulate atmospheric carbon dioxide concentrations and climate as a whole. Its loss via two anaerobic microbial processes - anammox and denitrification - only occurs in two types of marine environments where oxygen is sufficiently depleted: (1) benthic sediments, concentrated on coastal shelves, and (2) pelagic oxygen deficient zones (ODZs). The same factors were found to control fixed nitrogen loss in all three ecosystems investigated - Chesapeake Bay sediments and the ODZs of the Eastern Tropical North and South Pacific (ETNP and ETSP). Very low oxygen concentrations are required for fixed nitrogen loss by either anammox or denitrification, but organic matter (OM) quantity determines the magnitudes of these rates and OM quality controls the partitioning between the two pathways.
In mesocosms containing Chesapeake Bay sediments, two magnitudes of OM stimulated anammox and denitrification proportionally. Higher amounts of OM also induced a shift in the denitrifying bacterial community. But, because the same quality OM (i.e., C/N ratio) was applied to both treatments, the proportions of nitrogen loss attributed to anammox and denitrification did not change.
Complementary water column experiments using isotope tracers in the ETNP showed the proportion of nitrogen loss attributed to anammox increased with OM nitrogen content and identically matched theoretical expectations. Moreover, the depth distribution of in situ nitrogen loss rates showed OM mass fluxes regulated the total rates of nitrogen loss. Dissolved oxygen concentrations also affected the production of N2: nitrogen loss was reduced to negligible rates with an oxygen amendment as low as 3 μmol L-1. OM and oxygen also controlled nitrous oxide production and consumption rates in the ETNP. Measured rates indicated extremely rapid turnover times (as low as 1 day) and a simple one-dimensional biogeochemistry model identified denitrification as a major N2O production pathway.
In the ETSP ODZ, OM drove nitrate reduction rates in the same way it controlled fixed nitrogen loss in the ETNP. Anammox rates positively correlated with the measured nitrate deficit, suggesting regulation by the supply of nitrite and ammonium from nitrate reduction. Meanwhile, rates of anaerobic nitrite oxidization were significant at the ODZ boundaries, with iodate shown to be a plausible oxidant. A one-dimensional model revealed that the measured rates of nitrate reduction provided anammox with sufficient nitrite but not ammonium. The model also reasonably reproduced the observed nutrient distributions from all directly measured rates in a time frame of 260 days, suggesting the residence time for nitrite in the ODZ to be of this scale
Nitrogen cycling in strong redox gradients of marine environments: Oceanic oxygen minimum zones and salt marsh sediments
No full textEssential for all known living organisms, nitrogen is often the limiting nutrient in most of the open ocean and other types of marine environments. Therefore it is important to understand the budget and cycling of nitrogen, which supports primary production. Nitrogen takes multiple forms with different reduction-oxidation (redox) states, and the transformation between them controls the biological availability of nitrogen. Strong redox gradients in the environment are hotspots of nitrogen cycling, which is largely mediated by microorganisms. This thesis reports investigations of microbial nitrogen cycling in two types of marine environments characterized by sharp oxygen gradients: oceanic oxygen minimum zones (OMZs) and salt marsh sediments.
Nitrification, the oxidation of ammonia to nitrite and then nitrate, links the most reduced and the most oxidized forms nitrogen. It was recently discovered that ammonia-oxidizing archaea (AOA) are one of the most abundant groups of picoplankton in the ocean. Although AOA are considered to be obligate aerobes, high abundances of AOA functional genes were reported at anoxic depths of OMZs. I analyzed the AOA community composition in OMZs using a DNA microarray, and found that the AOA assemblages at anoxic depths were not different from those at oxic depths. This suggests that AOA might possess some unknown metabolism that allows them to survive at anoxic conditions.
Nitrification produces substrates for denitrification, the sequential reduction of nitrate to dinitrogen gas, which is highly active in both OMZs and salt marsh sediments. The depth and spatial distribution of ammonia and nitrite oxidation rates were determined using incubations with 15N labeled substrates in two major OMZs: eastern tropical North and South Pacific. While organic matter flux exerts a first-order control on nitrification rates in OMZs, my study revealed that light, in situ concentrations of oxygen and ammonium are all strongly correlated with ammonia oxidation rates. High rates of nitrite oxidation were measured at anoxic depths, and this remains unexplained.
Situated between the land and the sea, salt marshes provide numerous valuable ecological services. Among them nitrogen removal alleviates nitrogen loading entering the coastal ocean and hence reduces the chance of eutrophication, which has increased due to high anthropogenic sources of nitrogen (¿fertilization¿). The effect of long-term fertilization on nitrogen cycling was examined in experimental plots established in a New England salt marsh. Using slurry incubations with 15N labeled substrates, I found that nitrification and denitrification rates have increased by more than ten-fold due to long-term fertilization. On the other hand, dissimilatory nitrate reduction to ammonium, which retains nitrogen in the system, was high in unfertilized plots but not detected in fertilized plots. These results suggest that long-term fertilization shifted nitrogen cycling in salt marsh sediments from predominantly retention to removal
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