Hydraulic Performance of the Denitrification Bioreactor

Denitrification bioreactors, also known as woodchip bioreactors, are a new strategy for improving drainage water quality before these flows arrive at local streams, rivers, and lakes. A bioreactor is an excavated, woodchip-filled pit that is capable of supporting native microbes that convert nitrate in the drainage water to nitrogen gas. The idea of these edgeof-field treatment systems is still relatively new, meaning it is important for investigations to be made into how to design these “pits” and to determine how drainage water moves through the woodchips. Because the bioreactor at the ISU Northeast Research Farm (NERF) is one of the best monitored bioreactor sites in the state, it provided an ideal location to not only monitor bioreactor nitrate-reduction performance, but also to investigate design hydraulics.

Sediment metabolism in samples off Northwest Africa

Sediments off northwest Africa were assayed for activities of the respiratory electron transport system (ETS) and for primary amino nitrogen. ETS activities were used to compute respiratory oxygen consuption, carbon oxidation, and nitrate reduction rates. Activities were correlated with depth of the water column, and their longshore distribution resembled that of euphotic zone phytoplankton productivity. Protein concentrations were closely correlated with ETS activities. Carbon biomass was calculated from protein and compared with other computed values. The carbon oxidation rate accounted for 13 % of the region's primary production.

Stable isotope analysis of Porites coral core from the Andaman Islands

North Atlantic climate variations are reflected in sedimentary records from the northern Indian Ocean in which two basins, the Arabian Sea and the Bay of Bengal, are strongly affected by the monsoon. Contrary to the Bay of Bengal the Arabian Sea plays an important role in the global marine nitrogen cycle. In its mid-water oxygen minimum zone (OMZ) bioavailable fixed nitrogen is reduced to nitrogen gas (NO3- - > N2), whereas oxygen concentrations are slightly above the threshold of nitrate reduction in the OMZ of the Bay of Bengal. A coral colony (Porites lutea) growing south of Port Blair on the Andaman Islands in the Bay of Bengal was studied for its response to changes in the monsoon system and its link to temperature changes in the North Atlantic Ocean, between 1975 and 2006. Its linear extension rates, d13C and d18O values measured within the coral skeleton reveal a strong seasonality, which seems to be caused by the monsoon-driven reversal of the surface ocean circulation. The sampling site appears to be influenced by low salinity Bay of Bengal Water during the NE monsoon (boreal winter) and by the high salinity Arabian Sea Water during the SW monsoon in summer. The high salinity Arabian Sea Water circulates along with the Summer Monsoon Current (S-MC) from the Arabia Sea into the Bay of Bengal. Decreasing d18O and reconstructed salinity values correlate to the increasing SSTs in the North Atlantic Ocean indicating a reduced influence of the S-MC at the sampling site in the course of northern hemispheric warming. During such periods oxygen-depletion became stronger in the OMZ of the Arabian Sea as indicated by the sedimentary records. A reduced propagation of oxygen-depleted high salinity Arabian Sea Water into the Bay of Bengal could be a mechanism maintaining oxygen concentration above the threshold of nitrate reduction in the OMZ of the Bay of Bengal in times of global warming.

Nitrogen cycling driven by organic matter export in the South Pacific oxygen minimum zone

Oxygen minimum zones are expanding globally, and at present account for around 20-40% of oceanic nitrogen loss. Heterotrophic denitrification and anammox-anaerobic ammonium oxidation with nitrite-are responsible for most nitrogen loss in these low-oxygen waters. Anammox is particularly significant in the eastern tropical South Pacific, one of the largest oxygen minimum zones globally. However, the factors that regulate anammox-driven nitrogen loss have remained unclear. Here, we present a comprehensive nitrogen budget for the eastern tropical South Pacific oxygen minimum zone, using measurements of nutrient concentrations, experimentally determined rates of nitrogen transformation and a numerical model of export production. Anammox was the dominant mode of nitrogen loss at the time of sampling. Rates of anammox, and related nitrogen transformations, were greatest in the productive shelf waters, and tailed off with distance from the coast. Within the shelf region, anammox activity peaked in both upper and bottom waters. Overall, rates of nitrogen transformation, including anammox, were strongly correlated with the export of organic matter. We suggest that the sinking of organic matter, and thus the release of ammonium into the water column, together with benthic ammonium release, fuel nitrogen loss from oxygen minimum zones.

CooA, a CO-sensing transcription factor from Rhodospirillum rubrum, is a CO-binding heme protein

Biological sensing of small molecules such as NO, O2, and CO is an important area of research; however, little is know about how CO is sensed biologically. The photosynthetic bacterium Rhodospirillum rubrum responds to CO by activating transcription of two operons that encode a CO-oxidizing system. A protein, CooA, has been identified as necessary for this response. CooA is a member of a family of transcriptional regulators similar to the cAMP receptor protein and fumavate nitrate reduction from Escherichia coli. In this study we report the purification of wild-type CooA from its native organism, R. rubrum, to greater than 95% purity. The purified protein is active in sequence-specific DNA binding in the presence of CO, but not in the absence of CO. Gel filtration experiments reveal the protein to be a dimer in the absence of CO. Purified CooA contains 1.6 mol heme per mol of dimer. Upon interacting with CO, the electronic spectrum of CooA is perturbed, indicating the direct binding of CO to the heme of CooA. A hypothesis for the mechanism of the protein’s response to CO is proposed.

Mössbauer spectroscopy as a tool for the study of activation/inactivation of the transcription regulator FNR in whole cells of Escherichia coli

The global regulator FNR (for fumarate nitrate reduction) controls the transcription of >100 genes whose products facilitate adaptation of Escherichia coli to growth under O2-limiting conditions. Previous Mössbauer studies have shown that anaerobically purified FNR contains a [4Fe-4S]2+ cluster that, on exposure to oxygen, is converted into a [2Fe-2S]2+ cluster, a process that decreases DNA binding by FNR. Using 57Fe Mössbauer spectroscopy of E. coli cells containing overexpressed FNR, we show here that the same cluster conversion also occurs in vivo on exposure to O2. Furthermore, the data show that a significant amount of the [4Fe-4S]2+ cluster is regenerated when the cells are shifted back to an anaerobic environment. The present study also demonstrates that 57Fe Mössbauer spectroscopy can be employed to study the in vivo behavior of (overexpressed) proteins. The use of this technique to study other iron-containing cell components is discussed.

Altering the anaerobic transcription factor FNR confers a hemolytic phenotype on Escherichia coli K12

The recent outbreaks of Escherichia coli 0157-associated food poisoning have focused attention on the virulence determinants of E. coli. Here, it is reported that single base substitutions in the fnr gene encoding the oxygen-responsive transcription regulator FNR (fumarate and nitrate reduction regulator) are sufficient to confer a hemolytic phenotype on E. coli K12, the widely used laboratory strain. The mechanism involves enhancing the expression of a normally dormant hemolysin gene (hlyE) located in the E. coli chromosome. The mutations direct single amino acid substitutions in the activating regions (AR1 and AR3) of FNR that contact RNA polymerase. It is concluded that altering a resident transcription regulator, or acquisition of a competent heterologous regulator, could generate a pool of hemolytic, and therefore more virulent, strains of E. coli in nature.

Association of a polynuclear iron-sulfur center with a mutant FNR protein enhances DNA binding.

In the facultative anaerobe Escherichia coli, the transcription factor FNR (fumarate nitrate reduction) regulates gene expression in response to oxygen deprivation. To investigate how the activity of FNR is regulated by oxygen availability, two mutant proteins, DA154 and LH28-DA154, which have enhanced in vivo activity in the presence of oxygen, were purified and compared. Unlike other previously examined FNR preparations, the absorption spectrum of LH28-DA154 had two maxima at 324 nm and 419 nm, typical of iron-sulfur (Fe-S)-containing proteins. Consistent with these data, metal analysis showed that only the LH28-DA154 protein contained a significant amount of iron and acid-labile sulfide, and, by low temperature EPR spectroscopy, a signal typical of a [3Fe-4S]+ cluster was detected. The LH28-DA154 protein that contained the Fe-S cluster also contained a higher proportion of dimers and had a 3- to 4-fold higher apparent affinity for the target DNA than the DA154 protein. In agreement with this, we found that when the LH28-DA154 protein was treated with an iron chelator (alpha,alpha'-dipyridyl), it lost its characteristic absorption and the apparent affinity for DNA was reduced 6-fold. However, increased DNA binding and the characteristic absorption spectrum could be restored by in vitro reconstitution of the Fe-S center. DNA binding of the LH28-DA154 protein was also affected by the redox state of the Fe-S center, since protein exposed to oxygen bound 1/10th as much DNA as the protein reduced anaerobically with dithionite. The observation that DNA binding is enhanced when the Fe-S center is reduced indicates that the redox state of the Fe-S center affects the DNA-binding activity of this protein and suggests a possible mechanism for regulation of the wild-type protein.

Communities and microhabitats of living benthic foraminifera from the tropical East Atlantic

Living (Rose Bengal stained) benthic foraminifera were collected with a multicorer from six stations between 2°N and 12°S off West Africa. The foraminiferal communities in the investigated area reflect the direct influence of different productivity regimes, and are characterized by spatially and seasonally varying upwelling activity. At five stations, foraminiferal abundance coincides well with the gradient of surface productivity. However, at one station off the Congo River, the influence of strong fresh water discharge is documented. Although this station lies directly in the center of an upwelling area, foraminiferal standing stocks are surprisingly low. It is suggested that the Congo discharge may induce a fractionation of the organic matter into small and light particles of low nutritional content, by contrast to the relatively fast-sinking aggregates found in the centers of high productivity areas. Quality and quantity of the organic matter seem to influence the distribution of microhabitats as well. The flux of organic carbon to the sea-floor controls the sequence of degradation of organic matter in sediment and the position of different redox fronts. The vertical foraminiferal stratification within sediment closely parallels the distribution of oxygen and nitrate in porewater, and reflects different nutritive strategies and adaptation to different types of organic matter. The epifauna and shallow infauna colonize oxygenated sediments where labile organic matter is available. The intermediate infauna (M. barleeanum) is linked to the zone of nitrate reduction in sediments where epifaunal and shallow infaunal species are not competitive anymore, and must feed on bacterial biomass or on metabolizable nutritious particles produced by bacterial degradation of more refractory organic matter. The deep infauna shows its maximum distribution in anoxic sediments, where no easily metabolizable organic matter is available.