Challenges in using allylthiourea and chlorate as specific nitrification inhibitors.

Allylthiourea (ATU) and chlorate (ClO3-) are often used to selectively inhibit nitritation and nitratation. In this work we identified challenges with use of these compounds in inhibitory assays with filter material from a biological rapid sand filter for groundwater treatment. Inhibition was investigated in continuous-flow lab-scale columns, packed with filter material from a full-scale filter and supplied with NH4+ or NO2-. ATU concentrations of 0.1-0.5 mM interfered with the indophenol blue method for NH4+ quantification leading to underestimation of the measured NH4+ concentration. Interference was stronger at higher ATU levels and resulted in no NH4+ detection at 0.5 mM ATU. ClO3- at typical concentrations for inhibition assays (1-10 mM) inhibited nitratation by less than 6%, while nitritation was instead inhibited by 91% when NH4+ was supplied. On the other hand, nitratation was inhibited by 67-71% at 10-20 mM ClO3- when NO2- was supplied, suggesting significant nitratation inhibition at higher NO2- concentrations. No chlorite (ClO2-) was detected in the effluent, and thus we could not confirm that nitritation inhibition was caused by ClO3- reduction to ClO2-. In conclusion, ATU and ClO3- should be used with caution in inhibition assays, because analytical interference and poor selectivity for the targeted process may affect the experimental outcome and compromise result interpretation.

Nitrogen losses in anoxic marine sediments driven by Thioploca-anammox bacterial consortia.

Ninety per cent of marine organic matter burial occurs in continental margin sediments, where a substantial fraction of organic carbon escapes oxidation and enters long-term geologic storage within sedimentary rocks. In such environments, microbial metabolism is limited by the diffusive supply of electron acceptors. One strategy to optimize energy yields in a resource-limited habitat is symbiotic metabolite exchange among microbial associations. Thermodynamic and geochemical considerations indicate that microbial co-metabolisms are likely to play a critical part in sedimentary organic carbon cycling. Yet only one association, between methanotrophic archaea and sulphate-reducing bacteria, has been demonstrated in marine sediments in situ, and little is known of the role of microbial symbiotic interactions in other sedimentary biogeochemical cycles. Here we report in situ molecular and incubation-based evidence for a novel symbiotic consortium between two chemolithotrophic bacteria--anaerobic ammonium-oxidizing (anammox) bacteria and the nitrate-sequestering sulphur-oxidizing Thioploca species--in anoxic sediments of the Soledad basin at the Mexican Pacific margin. A mass balance of benthic solute fluxes and the corresponding nitrogen isotope composition of nitrate and ammonium fluxes indicate that anammox bacteria rely on Thioploca species for the supply of metabolic substrates and account for about 57 ± 21 per cent of the total benthic N2 production. We show that Thioploca-anammox symbiosis intensifies benthic fixed nitrogen losses in anoxic sediments, bypassing diffusion-imposed limitations by efficiently coupling the carbon, nitrogen and sulphur cycles.

Towards a consistent classification scheme for geochemical environments, or, why we wish the term 'suboxic' would go away.

It is our opinion that the nomenclature used to define geochemical environments is inconsistent and confusing, and in particular the use and meaning of the term 'suboxic', which is widely applied in the geochemical and ecological literature. Our purpose here is to review the redox zonation of natural systems and the nomenclature used to designate this. Finally, we will outline what we feel is a straightforward and non-contradictory scheme for classifying metabolic zones and geochemical environments.

Mathematical simulation of the diel O, S, and C biogeochemistry of a hypersaline microbial mat.

The creation of a mathematical simulation model of photosynthetic microbial mats is important to our understanding of key biogeochemical cycles that may have altered the atmospheres and lithospheres of early Earth. A model is presented here as a tool to integrate empirical results from research on hypersaline mats from Baja California Sur (BCS), Mexico into a computational system that can be used to simulate biospheric inputs of trace gases to the atmosphere. The first version of our model, presented here, calculates fluxes and cycling of O(2), sulfide, and dissolved inorganic carbon (DIC) via abiotic components and via four major microbial guilds: cyanobacteria (CYA), sulfate reducing bacteria (SRB), purple sulfur bacteria (PSB) and colorless sulfur bacteria (CSB). We used generalized Monod-type equations that incorporate substrate and energy limits upon maximum rates of metabolic processes such as photosynthesis and sulfate reduction. We ran a simulation using temperature and irradiance inputs from data collected from a microbial mat in Guerrero Negro in BCS (Mexico). Model O(2), sulfide, and DIC concentration profiles and fluxes compared well with data collected in the field mats. There were some model-predicted features of biogeochemical cycling not observed in our actual measurements. For instance, large influxes and effluxes of DIC across the MBGC mat boundary may reveal previously unrecognized, but real, in situ limits on rates of biogeochemical processes. Some of the short-term variation in field-collected mat O(2) was not predicted by MBGC. This suggests a need both for more model sensitivity to small environmental fluctuations for the incorporation of a photorespiration function into the model.

Anaerobic ammonium oxidation by marine and freshwater planctomycete-like bacteria.

Recently, two fresh water species, " Candidatus Brocadia anammoxidans" and " Candidatus Kuenenia stuttgartiensis", and one marine species, " Candidatus Scalindua sorokinii", of planctomycete anammox bacteria have been identified. " Candidatus Scalindua sorokinii" was discovered in the Black Sea, and contributed substantially to the loss of fixed nitrogen. All three species contain a unique organelle--the anammoxosome--in their cytoplasm. The anammoxosome contains the hydrazine/hydroxylamine oxidoreductase enzyme, and is thus the site of anammox catabolism. The anammoxosome is surrounded by a very dense membrane composed almost exclusively of linearly concatenated cyclobutane-containing lipids. These so-called 'ladderanes' are connected to the glycerol moiety via both ester and ether bonds. In natural and man-made ecosystems, anammox bacteria can cooperate with aerobic ammonium-oxidising bacteria, which protect them from harmful oxygen, and provide the necessary nitrite. The cooperation of these two groups of ammonium-oxidising bacteria is the microbial basis for a sustainable one reactor system, CANON (completely autotrophic nitrogen-removal over nitrite) to remove ammonia from high strength wastewater.

Microbial manganese and sulfate reduction in Black Sea shelf sediments.

The microbial ecology of anaerobic carbon oxidation processes was investigated in Black Sea shelf sediments from mid-shelf with well-oxygenated bottom water to the oxic-anoxic chemocline at the shelf-break. At all stations, organic carbon (C(org)) oxidation rates were rapidly attenuated with depth in anoxically incubated sediment. Dissimilatory Mn reduction was the most important terminal electron-accepting process in the active surface layer to a depth of approximately 1 cm, while SO(4)(2-) reduction accounted for the entire C(org) oxidation below. Manganese reduction was supported by moderately high Mn oxide concentrations. A contribution from microbial Fe reduction could not be discerned, and the process was not stimulated by addition of ferrihydrite. Manganese reduction resulted in carbonate precipitation, which complicated the quantification of C(org) oxidation rates. The relative contribution of Mn reduction to C(org) oxidation in the anaerobic incubations was 25 to 73% at the stations with oxic bottom water. In situ, where Mn reduction must compete with oxygen respiration, the contribution of the process will vary in response to fluctuations in bottom water oxygen concentrations. Total bacterial numbers as well as the detection frequency of bacteria with fluorescent in situ hybridization scaled to the mineralization rates. Most-probable-number enumerations yielded up to 10(5) cells of acetate-oxidizing Mn-reducing bacteria (MnRB) cm(-3), while counts of Fe reducers were <10(2) cm(-3). At two stations, organisms affiliated with Arcobacter were the only types identified from 16S rRNA clone libraries from the highest positive MPN dilutions for MnRB. At the third station, a clone type affiliated with Pelobacter was also observed. Our results delineate a niche for dissimilatory Mn-reducing bacteria in sediments with Mn oxide concentrations greater than approximately 10 micromol cm(-3) and indicate that bacteria that are specialized in Mn reduction, rather than known Mn and Fe reducers, are important in this niche.

The Archean sulfur cycle and the early history of atmospheric oxygen.

The isotope record of sedimentary sulfides can help resolve the history of oxygen accumulation into the atmosphere. We measured sulfur isotopic fractionation during microbial sulfate reduction up to 88 degrees C and show how sulfate reduction rate influences the preservation of biological fractionations in sediments. The sedimentary sulfur isotope record suggests low concentrations of seawater sulfate and atmospheric oxygen in the early Archean (3.4 to 2.8 billion years ago). The accumulation of oxygen and sulfate began later, in the early Proterozoic (2.5 to 0.54 billion years ago).

The response of the microbial community of marine sediments to organic carbon input under anaerobic conditions.

Cyanobacterial biomass was added to anaerobic sediment to simulate the natural input of complex organic substrate that occurs in nature after algae blooms. Sediments were incubated at 0 degree C, 8 degrees C and 24 degrees C for 13 days. Community dynamics were measured by fluorescence in situ hybridisation (FISH), denaturing gradient gel electrophoresis (DGGE), and sequencing of 16S rDNA PCR products. Metabolic changes were followed by the analysis of total carbon mineralisation, sulfate reduction, and ammonium production rates. The addition of organic material resulted in significant changes in the composition of the microbial community at all temperatures tested. Sulfate reduction was the main mineralisation process detected. However, not sulfate-reducers but rather members of the Cytophaga-Flavobacterium phylogenetic cluster showed the highest increase in the bacterial cells as detected by FISH. We conclude that these organisms play an important role in the anaerobic decomposition of complex organic material perhaps because they are the main catalysts of macromolecule hydrolysis and fermentation. The molecular methods also indicated a stimulation of ribosome synthesis. The detection of a large number of rRNA-rich cells belonging to the Cytophaga-Flavobacterium phylogenetic cluster further supports the importance of their role in the degradation of complex organic material in anaerobic marine sediments. Their detection in high numbers in the field may indicate recent deposition events.

Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment.

A mesophilic, anaerobic, gram-negative bacterium, strain SB164P1, was enriched and isolated from oxidized marine surface sediment with elemental sulfur as the sole energy substrate in the presence of ferrihydrite. Elemental sulfur was disproportionated to hydrogen sulfide and sulfate. Growth was observed exclusively in the presence of a hydrogen sulfide scavenger, e.g., ferrihydrite. In the absence of a scavenger, sulfide and sulfate production were observed but no growth occurred. Strain SB164P1 grew also by disproportionation of thiosulfate and sulfite. With thiosulfate, the growth efficiency was higher in ferrihydrite-supplemented media than in media without ferrihydrite. Growth coupled to sulfate reduction was not observed. However, a slight sulfide production occurred in cultures incubated with formate and sulfate. Strain SB164P1 is the first bacterium described that grows chemolithoautotrophically exclusively by the disproportionation of inorganic sulfur compounds. Comparative 16S rDNA sequencing analysis placed strain SB164P1 into the delta subclass of the class Proteobacteria. Its closest relative is Desulfocapsa thiozymogenes, and slightly more distantly related are Desulfofustis glycolicus and Desulforhopalus vacuolatus. This phylogenetic cluster of organisms, together with members of the genus Desulfobulbus, forms one of the main lines of descent within the delta subclass of the Proteobacteria. Due to the common phenotypic characteristics and the phylogenetic relatedness to Desulfocapsa thiozymogenes, we propose that strain SB164P1 be designated the type strain of Desulfocapsa sulfoexigens sp. nov.

Pathways of carbon oxidation in continental margin sediments off central Chile.

Rates and oxidative pathways of organic carbon mineralization were determined in sediments at six stations on the shelf and slope off Concepcion Bay at 36.5 degrees S. The depth distribution of C oxidation rates was determined to 10 cm from accumulation of dissolved inorganic C in 1-5-d incubations. Pathways of C oxidation were inferred from the depth distributions of the potential oxidants (O2, NO3-, and oxides of Mn and Fe) and from directly determined rates of SO4(2-) reduction. The study area is characterized by intense seasonal upwelling, and during sampling in late summer the bottom water over the shelf was rich in NO3- and depleted of O2. Sediments at the four shelf stations were covered by mats of filamentous bacteria of the genera Thioploca and Beggiatoa. Carbon oxidation rates at these sites were extremely high near the sediment surface (>3 micromol cm-3 d-1) and decreased exponentially with depth. The process was entirely coupled to SO4(2-) reduction. At the two slope stations where bottom-water O2 was > 100 microM, C oxidation rates were 10-fold lower and varied less with depth; C oxidation coupled to the reduction of O2, NO3-, and Mn oxides combined to yield an estimated 15% of the total C oxidation between 0 and 10 cm. Carbon oxidation through Fe reduction contributed a further 12-29% of the depth-integrated rate, while the remainder of C oxidation was through SO4(2-) reduction. The depth distribution of Fe reduction agreed well with the distribution of poorly crystalline Fe oxides, and as this pool decreased with depth, the importance of SO4(2-) reduction increased. The results point to a general importance of Fe reduction in C oxidation in continental margin sediments. At the shelf stations, Fe reduction was mainly coupled to oxidation of reduced S. These sediments were generally H2S-free despite high SO4(2-) reduction rates, and precipitation of Fe sulfides dominated H2S scavenging during the incubations. A large NO3- pool was associated with the Thioploca, and the shelf sediments were thus enriched in NO3- relative to the bottom water, with maximum concentrations of 3 micromol cm-3. The NO3- was consumed during our sediment incubations, but no effects on either C or S cycles could be discerned.

Distribution of bacterial populations in a stratified fjord (mariager fjord, denmark) quantified by in situ hybridization and related to chemical gradients in the water column.

Volumn 62, no. 4, p. 1392, lines 37 and 38: "Aluminum oxide filters (0.2 mm pore size; Anopore; Millipore GmbH, Eschborn, Germany)" should read "Aluminum oxide filters (0.2 (mu)m pore size; Anopore; Whatman, Inc., Clifton, N.J.)." Page 1403, reference 15: "Fenchel, T." should read "Fenchel, T., L. D. Kristensen, and L. Rasmussen." [This corrects the article on p. 1391 in vol. 62.].

Distribution of bacterial populations in a stratified fjord (mariager fjord, denmark) quantified by in situ hybridization and related to chemical gradients in the water column.

Volume 62, no. 4, p. 1391-1404: after publication of this article, it was brought to the attention of the authors that a more extensive treatment of the hydrodynamics of Mariager Fjord and the vertical distribution of bacteria and protozoa therein was published in a recent article by Fenchel et al. This work contains important information about the studied ecosystem, but unfortunately, the existence of this work was realized only after publication of our article. Thus, the following reference should have been cited in our article: [This corrects the article on p. 1391 in vol. 62.].

Distribution of bacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column.

The vertical distribution of major and intermediate electron acceptors and donors was measured in a shallow stratified fjord. Peaks of zero valence sulfur, Mn(IV), and Fe(III) were observed in the chemocline separating oxic surface waters from sulfidic and anoxic bottom waters. The vertical fluxes of electron acceptors and donors (principally O2 and H2S) balanced within 5%; however, the zones of oxygen reduction and sulfide oxidation were clearly separated. The pathway of electron transfer between O2 and H2S was not apparent from the distribution of sulfur, nitrogen, or metal compounds investigated. The chemical zonation was related to bacterial populations as detected by ethidium bromide (EtBr) staining and by in situ hybridization with fluorescent oligonucleotide probes of increasing specificity. About half of all EtBr-stained cells were detectable with a general oligonucleotide probe for all eubacteria when digital image analysis algorithms were used to improve sensitivity. Both EtBr staining and hybridization indicated a surprisingly uniform distribution of bacteria throughout the water column. However, the average cell size and staining intensity as well as the abundance of different morphotypes changed markedly within the chemocline. The constant overall cell counts thus concealed pronounced population shifts within the water column. Cells stained with a delta 385 probe (presumably sulfate-reducing bacteria) were detected at the chemocline at about 5 x 10(4) cells per ml, and this concentration increased to 2 x 10(5) cells per ml beneath the chemocline. A long slim rod-shaped bacterium was found in large numbers in the oxic part of the chemocline, whereas large ellipsoid cells dominated at greater depth. Application of selective probes for known genera of sulfate-reducing bacteria gave only low cell counts, and thus it was not possible to identify the dominant morphotypes of the sulfate-reducing community.

The production of 34S-depleted sulfide during bacterial disproportionation of elemental sulfur.

Bacteria that disproportionate elemental sulfur fractionate sulfur isotopes such that sulfate is enriched in sulfur-34 by 12.6 to 15.3 per mil and sulfide is depleted in sulfur-34 by 7.3 to 8.6 per mil. Through a repeated cycle of sulfide oxidation to S0 and subsequent disproportionation, these bacteria can deplete sedimentary sulfides in sulfur-34. A prediction, borne out by observation, is that more extensive sulfide oxidation will lead to sulfides that are more depleted in sulfur-34. Thus, the oxidative part of the sulfur cycle creates circumstances by which sulfides become more depleted in sulfur-34 than would be possible with sulfate-reducing bacteria alone.

The anaerobic degradation of organic matter in Danish coastal sediments: iron reduction, manganese reduction, and sulfate reduction.

We used a combination of porewater and solid phase analysis, as well as a series of sediment incubations, to quantify organic carbon oxidation by dissimilatory Fe reduction, Mn reduction, and sulfate reduction, in sediments from the Skagerrak (located off the northeast coast of Jutland, Denmark). In the deep portion of the basin, surface Mn enrichments reached 3.5 wt%, and Mn reduction was the only important anaerobic carbon oxidation process in the upper 10 cm of the sediment. In the less Mn-rich sediments from intermediate depths in the basin, Fe reduction ranged from somewhat less, to far more important than sulfate reduction. Most of the Mn reduction in these sediments may have been coupled to the oxidation of acid volatile sulfides (AVS), rather than to dissimilatory reduction. High rates of metal oxide reduction at all sites were driven by active recycling of both Fe and Mn, encouraged by bioturbation. Recycling was so rapid that the residence time of Fe and Mn oxides, with respect to reduction, ranged from 70-250 days. These results require that, on average, an atom of Fe or Mn is oxidized and reduced between 100-300 times before ultimate burial into the sediment. We observed that dissolved Mn2+ was completely removed onto fully oxidized Mn oxides until the oxidation level of the oxides was reduced to about 3.8, presumably reflecting the saturation by Mn2+ of highly reactive surface adsorption sites. Fully oxidized Mn oxides in sediments, then, may act as a cap preventing Mn2+ escape. We speculate that in shallow sediments of the Skagerrak, surface Mn oxides are present in a somewhat reduced oxidation level (< 3.8) allowing Mn2+ to escape, and perhaps providing the Mn2+ which enriches sediments of the deep basin.

Bacterial disproportionation of elemental sulfur coupled to chemical reduction of iron or manganese.

A new chemolithotrophic bacterial metabolism was discovered in anaerobic marine enrichment cultures. Cultures in defined medium with elemental sulfur (S) and amorphous ferric hydroxide (FeOOH) as sole substrates showed intense formation of sulfate. Furthermore, precipitation of ferrous sulfide and pyrite was observed. The transformations were accompanied by growth of slightly curved, rod-shaped bacteria. The quantification of the products revealed that S was microbially disproportionated to sulfate and sulfide, as follows: 4S + 4H(2)O --> SO(4) + 3H(2)S + 2H. Subsequent chemical reactions between the formed sulfide and the added FeOOH led to the observed precipitation of iron sulfides. Sulfate and iron sulfides were also produced when FeOOH was replaced by FeCO(3). Further enrichment with manganese oxide, MnO(2), instead of FeOOH yielded stable cultures which formed sulfate during concomitant reduction of MnO(2) to Mn. Growth of small rod-shaped bacteria was observed. When incubated without MnO(2), the culture did not grow but produced small amounts of SO(4) and H(2)S at a ratio of 1:3, indicating again a disproportionation of S. The observed microbial disproportionation of S only proceeds significantly in the presence of sulfide-scavenging agents such as iron and manganese compounds. The population density of bacteria capable of S disproportionation in the presence of FeOOH or MnO(2) was high, > 10 cm in coastal sediments. The metabolism offers an explanation for recent observations of anaerobic sulfide oxidation to sulfate in anoxic sediments.

Pathways of organic carbon oxidation in three continental margin sediments.

We have combined several different methodologies to quantify rates of organic carbon mineralization by the various electron acceptors in sediments from the coast of Denmark and Norway. Rates of NH4+ and Sigma CO2 liberation sediment incubations were used with O2 penetration depths to conclude that O2 respiration accounted for only between 3.6-17.4% of the total organic carbon oxidation. Dentrification was limited to a narrow zone just below the depth of O2 penetration, and was not a major carbon oxidation pathway. The processes of Fe reduction, Mn reduction and sulfate reduction dominated organic carbon mineralization, but their relative significance varied depending on the sediment. Where high concentrations of Mn-oxide were found (3-4 wt% Mn), only Mn reduction occurred. With lower Mn oxide concentrations more typical of coastal sediments, Fe reduction and sulfate reduction were most important and of a similar magnitude. Overall, most of the measured O2 flux into the sediment was used to oxidized reduced inorganic species and not organic carbon. We suspect that the importance of O2 respiration in many coastal sediments has been overestimated, whereas metal oxide reduction (both Fe and Mn reduction) has probably been well underestimated.

Plasma exchange in the treatment of propoxyphene intoxications.

Six patients heavily intoxicated by propoxyphene were treated with plasma exchange. Only one patient died because of cardiac dysrhythmia, the other five patients survived, probably because the plasma exchange removed the free plasma fraction of propoxyphene. Plasma exchange also proved to be effective in improving the consciousness of the patients.

Reliability of a 99mTc-DTPA gamma camera technique for determination of single kidney glomerular filtration rate. A comparison to plasma clearance of 51Cr-EDTA in one-kidney patients, using the renal clearance of inulin as a reference.

In a recent paper we described a method for calculation of single kidney glomerular filtration rate (SKGFR) from the 99mTc-DTPA renogram obtained by gamma camera. Determination of the injected dose and collection of urine or blood was not needed. In this paper the reliability of the method was compared to other methods for estimation of GFR in 20 unilaterally nephrectomized patients. The renal clearance of inulin served as reference measure of GFR. The values for SKGFR obtained from the renograms and from the estimated endogenous creatinine clearances according to serum creatinine concentration and a nomogram were both accurate. The reliability of the renography method was significantly better judged by less variance in the estimates. SKGFR calculated from the plasma clearance of 51Cr-EDTA overestimated the renal clearance of inulin on an average by 11.3%. No difference was found in the variance of the values obtained from the renograms and from the plasma clearances of 51Cr-EDTA compared to the renal clearance of inulin. Apart from the inaccuracy in the GFR values calculated from the plasma clearance of 51Cr-EDTA, the reliability of these two methods was equal. The day to day variation of SKGFR estimated from the renograms in 24 patients (48 kidneys) with SKGFR values from 5 to 76 ml/min was 8.8%. This equals the day to day variation in the plasma clearance of 51Cr-EDTA.

Reliability of single kidney glomerular filtration rate measured by a 99mTc-DTPA gamma camera technique.

The reliability of a previously published method for determination of single kidney glomerular filtration rate (SKGFR) by means of technetium-99m-diethylenetriaminepenta-acetate (99mTc-DTPA) gamma camera renography was evaluated. The day-to-day variation in the calculated SKGFR values was earlier found to be 8.8%. The technique was compared to the simultaneously measured renal clearance of inulin in 19 unilaterally nephrectomized patients with GFR varying from 11 to 76 ml/min. The regression line (y = 1.04 X -2.5) did not differ significantly from the line of identity. The standard error of estimate was 4.3 ml/min. In 17 patients the inter- and intraobserver variation of the calculated SKGFR values was 1.2 ml/min and 1.3 ml/min, respectively. In 21 of 25 healthy subjects studied (age range 27-29 years), total GFR calculated from the renograms was within an established age-dependent normal range of GFR.