Anoxic Samples Research Articles

Measurement of proton light yield of water-based liquid scintillator

The proton light yield of liquid scintillators is an important property in the context of their use in large-scale neutrino experiments, with direct implications for neutrino-proton scattering measurements and the discrimination of fast neutrons from inverse beta -decay coincidence signals. This work presents the first measurement of the proton light yield of a water-based liquid scintillator (WbLS) formulated from 5% linear alkyl benzene (LAB), at energies below 20 MeV, as well as a measurement of the proton light yield of a pure LAB + 2 g/L 2,5-diphenyloxazole (PPO) mixture (LABPPO). The measurements were performed using a double time-of-flight method and a pulsed neutron beam from the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory. The proton light yields were measured relative to that of a 477 keV electron. The relative proton light yield of WbLS was approximately 3.8% lower than that of LABPPO, itself exhibiting a relative proton light yield 15–20% higher than previous measurements of an analogous anoxic sample. The observed quenching is not compatible with the Birks model for either material, but is well described with the addition of Chou’s bimolecular quenching term.

Estimation of phosphate extractability in flooded soils: Effect of solid-solution ratio and bicarbonate concentration

The Olsen method is widely used to determine bioavailable phosphate (P) in upland soils. It is also used in flooded soils, although different estimates of extractable-P are obtained under anoxic and oxic conditions. In this study, variations in extractable-P in three soils under different redox conditions were evaluated as a function of solid to solution ratio (SSR) (1:5–1:200) and bicarbonate concentration (0.1–1 M). The parameterized CD-MUSIC model was used to describe the data, with optimization of reactive surface area (RSA) and reversibly adsorbed-P (R–PO4). The RSA may vary due to the reductive dissolution of iron minerals and/or the formation of new reactive surfaces upon the establishment of reducing conditions. Changes in SSR and bicarbonate concentration significantly affected extractable-P under both oxic and anoxic conditions; more P was extracted under anoxic than under oxic conditions. The difference was 1.5–2 times greater for the highest SSR considered. In the soil samples with higher organic carbon content, the effect of bicarbonate concentration on extractable-P was remarkable. The large differences in extractable-P under oxic and anoxic conditions were probably due to differences in iron (hydr)oxide content. The CD-MUSIC model successfully predicted the effect of SSR on extractable-P under both conditions. R–PO4 data were fitted for oxic conditions and assumed unchanged for anoxic samples, while RSA data were fitted for both conditions. The RSA values were lower in anoxic than in oxic samples. Overall, our data and model calculations indicate that using wet soil samples obtained in-situ for evaluation of Olsen-P in submerged soils lead to a higher estimation of extractable-P than estimated in oxic soils. If soil testing in the presence of target plants confirms the reliability of in-situ sampling for Olsen-P estimation, the P fertilizer dose applied to submerged soils could be reduced, which is very important from environmental and economic perspectives.

Copper transformation, speciation, and detoxification in anoxic and suboxic freshwater sediments

The complex chemistry of copper (Cu) in freshwater sediments at low concentrations is not well understood. We evaluated the transformation processes of Cu added to freshwater sediments under suboxic and anoxic conditions. Freshwater sediments from three sources in Michigan with different characteristics (Spring Creek, River Raisin, and Maple Lake) were spiked with 30 or 60 mg kg−1 Cu and incubated under a nitrogen atmosphere. After 28-d, each treatment subset was amended with organic matter (OM) to promote anoxic conditions and evaluate its effects on Cu speciation. OM addition triggered a shift from suboxic to anoxic conditions, and sequential extractions showed that Cu accordingly shifted from acid-soluble to oxidizable fractions. Extended X-ray absorption fine-structure (EXAFS) spectroscopy revealed that Cu sulfides dominated all anoxic samples except for Spring Creek 30 mg kg−1, where Cu(I) was predominantly complexed to thiol groups of OM. Covellite and chalcopyrite (CuFeS2) were the predominant Cu species in nearly all anoxic samples, as determined by Raman spectroscopy, scanning electron microscopy, and X-ray absorption near-edge structure (XANES) spectroscopy. Copper reduction also occurred under suboxic conditions: for two of three sediments, around 80% had been reduced to Cu(I), while the remaining 20% persisted as Cu(II) complexed to OM. However, in the third coarsest (i.e., Spring Creek), around 50% of the Cu had been reduced, forming Cu(I)-OM complexes, while the remainder was Cu(II)-OM complexes. Toxicity tests showed that survival of H. azteca and D. magna were significantly lower in suboxic treatments. Anoxic sediments triggered a near-complete transformation of Cu to sulfide minerals, reducing its toxicity.

Anomalies of upper critical field in the spinel superconductor LiTi2O4−δ

High-field electrical transport and point-contact tunneling spectroscopy were used to investigate superconducting properties of the unique spinel oxide, LiTi$_2$O$_{4-\delta}$ films with various oxygen content. We find that the upper critical field $B_\mathrm{c2}$ gradually increases as more oxygen impurities are brought into the samples by carefully tuning the deposition atmosphere. It is striking that although the superconducting transition temperature and energy gap are almost unchanged, an astonishing isotropic $B_\mathrm{c2}$ up to $\sim$ 26 Tesla is observed in oxygen-rich sample, which is doubled compared to the anoxic sample and breaks the Pauli limit. Such anomalies of $B_\mathrm{c2}$ were rarely reported in other three dimensional superconductors. Combined with all the anomalies, three dimensional spin-orbit interaction induced by tiny oxygen impurities is naturally proposed to account for the remarkable enhancement of $B_\mathrm{c2}$ in oxygen-rich LiTi$_2$O$_{4-\delta}$ films. Such mechanism could be general and therefore provides ideas for optimizing practical superconductors with higher $B_\mathrm{c2}$.

Sulfate-Reducing Bacteria That Produce Exopolymers Thrive in the Calcifying Zone of a Hypersaline Cyanobacterial Mat.

Calcifying microbial mats in hypersaline environments are important model systems for the study of the earliest ecosystems on Earth that started to appear more than three billion years ago and have been preserved in the fossil record as laminated lithified structures known as stromatolites. It is believed that sulfate-reducing bacteria play a pivotal role in the lithification process by increasing the saturation index of calcium minerals within the mat. Strain L21-Syr-ABT was isolated from anoxic samples of a several centimeters-thick microbialite-forming cyanobacterial mat of a hypersaline lake on the Kiritimati Atoll (Kiribati, Central Pacific). The novel isolate was assigned to the family Desulfovibrionaceae within the Deltaproteobacteria. Available 16S rRNA-based population surveys obtained from discrete layers of the mat indicate that the occurrence of a species-level clade represented by strain L21-Syr-ABT is restricted to a specific layer of the suboxic zone, which is characterized by the presence of aragonitic spherulites. To elucidate a possible function of this sulfate-reducing bacterium in the mineral formation within the mat a comprehensive phenotypic characterization was combined with the results of a comparative genome analysis. Among the determined traits of strain L21-Syr-ABT, several features were identified that could play a role in the precipitation of calcium carbonate: (i) the potential deacetylation of polysaccharides and consumption of substrates such as lactate and sulfate could mobilize free calcium; (ii) under conditions that favor the utilization of formate and hydrogen, the alkalinity engine within the mat is stimulated, thereby increasing the availability of carbonate; (iii) the production of extracellular polysaccharides could provide nucleation sites for calcium mineralization. In addition, our data suggest the proposal of the novel species and genus Desulfohalovibrio reitneri represented by the type strain L21-Syr-ABT (=DSM 26903T = JCM 18662T).

Rat astrocytes during anoxia: Secretome profile of cytokines and chemokines.

IntroductionThe precise mechanisms of the inflammatory responses after cerebral ischemia in vivo are difficult to elucidate because of the complex nature of multiple series of interactions between cells and molecules. This study explored temporal patterns of secretion of 30 cytokines and chemokines from Sprague Dawley rat astrocytes in primary culture in order to elucidate signaling pathways that are triggered by astrocytes during anoxia.MethodsPrimary cultures of rat brain astrocytes were incubated for periods of 2–24 hr in the absence of oxygen (anoxia) or under normal partial pressure of oxygen (controls). Simultaneous detection of 29 cytokines and chemokines in the samples was performed using a rat cytokine array panel, while the temporal pattern of angiopoietin‐1 (Ang‐1) secretion was determined separately using ELISA. Wilcoxon–Mann–Whitney test was used to compare normoxic and anoxic samples and the Hodge–Lehman estimator with exact 95% confidence intervals was computed to assess the size of differences in cytokine secretion. The obtained data were imported into the Core Analysis tool of Ingenuity Pathways Analysis software in order to relate changes in secretion of cytokines and chemokines from astrocytes during anoxia to potential molecular signal networks.ResultsWith the exception of Ang‐1, concentrations of all cytokines/chemokines in samples collected after anoxia exposure were either the same, or higher, than in control groups. No clear pattern of changes could be established for groups of cytokines with similar effects (i.e., pro‐ or anti‐inflammatory cytokines). The pattern of changes in cytokine secretion during anoxia was associated with the HIF‐1α‐mediated response, as well as cytokines IL‐1β and cathepsin S pathways, which are related to initiation of inflammation and antigen presentation, respectively, and to ciliary neurotrophic factor.ConclusionsThese in vitro findings suggest that astrocytes may play a role in triggering inflammation during anoxia/ischemia of the brain.

Springtails (Collembola, Hexapoda) from Montebello Lakes, Chiapas, Mexico

ABSTRACTSpringtails are mostly terrestrial organisms, relatively rare in truly aquatic environments; a few are neustonic while others are found in humid caves, surfaces, and crevices of marine coastal zones. We have found them in the benthic zone of 4 deep lakes, Bosque Azul, Dos Lagos, Ensueño, and Tziscao of Lagunas de Montebello National Park in Chiapas. We recovered 43 specimens belonging to 13 species from the samples, all of which except Americabrya arida were first records for the state of Chiapas; the most abundant were A. arida and Lepidocyrtus lanuginosus. Species richness of each lake varied between 1 and 12; density varied between 15 ± 25 and 133 ± 118 org m−2, and biomass varied between 0.02 and 4.3 ± 4.4 and 0.02 μg m−2. Tziscao showed the highest abundance (35 individuals), species richness (12 species), and density (133 ± 118 org m−2), and Bosque Azul showed the highest average biomass (4.3 ± 4.4 μg). Together, 96% of the organisms were collected during summer when lakes were thermally stratified (warm monomixis); 44% of the organisms were recovered from deep anoxic samples (>20 m). Springtails were found living in warm waters in conditions varying from well oxygenated to anoxic, a slightly basic pH range (7.1–8.3), and a high range of electric conductivity (219.7–1716.0 μS cm−1) values. Sediments were mainly composed of sands and mud (silt and clay) with a wide organic matter range (15.4–51.2%) and sedimentary carbonates (6.0–98.3%). Of the 43 specimens, 17 were adults (12 males and 5 females) and 26 were immature, both with gut content composed mostly of Cladosporium hyphae and conidia. These are the first records of submerged Collembola inhabiting the deep benthic zones of Mexican lakes.

Differences in planktonic microbial communities associated with three types of macrophyte stands in a shallow lake.

Little is known about how various substances from living and decomposing aquatic macrophytes affect the horizontal patterns of planktonic bacterial communities. Study sites were located within Lake Kolon, which is a freshwater marsh and can be characterised by open-water sites and small ponds with different macrovegetation (Phragmites australis, Nymphea alba and Utricularia vulgaris). Our aim was to reveal the impact of these macrophytes on the composition of the planktonic microbial communities using comparative analysis of environmental parameters, microscopy and pyrosequencing data. Bacterial 16S rRNA gene sequences were dominated by members of phyla Proteobacteria (36%-72%), Bacteroidetes (12%-33%) and Actinobacteria (5%-26%), but in the anoxic sample the ratio of Chlorobi (54%) was also remarkable. In the phytoplankton community, Cryptomonas sp., Dinobryon divergens, Euglena acus and chrysoflagellates had the highest proportion. Despite the similarities in most of the measured environmental parameters, the inner ponds had different bacterial and algal communities, suggesting that the presence and quality of macrophytes directly and indirectly controlled the composition of microbial plankton.

Validation of reference genes for quantitative real-time PCR (qPCR) analysis of Actinobacillus suis.

BackgroundQuantitative real-time PCR is a valuable tool for evaluating bacterial gene expression. However, in order to make best use of this method, endogenous reference genes for expression data normalisation must first be identified by carefully validating the stability of expression under experimental conditions. Therefore, the objective of this study was to validate eight reference genes of the opportunistic swine pathogen, Actinobacillus suis, grown in aerobic cultures with (Epinephrine) or without (Aerobic) epinephrine in the growth medium and in anoxic static cultures (Anoxic), and sampled during exponential and stationary phases.ResultsUsing the RefFinder tool, expression data were analysed to determine whether comprehensive stability rankings of selected reference genes varied with experimental design. When comparing Aerobic and Epinephrine cultures by growth phase, pyk and rpoB were both among the most stably expressed genes, but when analysing both growth phases together, only pyk remained in the top three rankings. When comparing Aerobic and Anoxic samples, proS ranked among the most stable genes in exponential and stationary phase data sets as well as in combined rankings. When analysing the Aerobic, Epinephrine, and Anoxic samples together, only gyrA ranked consistently among the top three most stably expressed genes during exponential and stationary growth as well as in combined rankings; the rho gene ranked as least stably expressed gene in this data set.ConclusionsReference gene stability should be carefully assessed with the design of the experiment in mind. In this study, even the commonly used reference gene 16S rRNA demonstrated large variability in stability depending on the conditions studied and how the data were analysed. As previously suggested, the best approach may be to use a geometric mean of multiple genes to normalise qPCR results. As researchers continue to validate reference genes for various organisms in multiple growth conditions and sampling time points, it may be possible to make informed predictions as to which genes may be most suitable to validate for a given experimental design, but in the meantime, the reference genes used to normalise qPCR data should be selected with caution.

The Effects of Oxygen Transition on Community Respiration and Potential Chemoautotrophic Production in a Seasonally Stratified Anoxic Estuary

To assess the effects of seasonal oxygen transition on microbial metabolism, we measured spatiotemporal changes in total dissolved inorganic carbon, respiratory products, and geochemical constituents in the mesohaline region of Chesapeake Bay from May to October 2010. Vertical redox zonation was examined, and a spatial transect survey was also conducted from the southern to northern limit of the mesohaline region in July providing an alternative approach for assessing the temporal dynamics of oxygen transition. The transitions from oxic to hypoxic to anoxic and back to oxic were illustrated by the pattern of nitrogen redox species. Respiration, measured from changes in total dissolved inorganic carbon (∆DIC) and dissolved oxygen (∆DO) during incubations, had an average respiratory quotient (∆DIC/∆DO) of 1.04 ± 0.06 under oxic conditions and 1.58 ± 0.48 under hypoxic conditions. The difference in the respiratory quotients suggested that oxygen-based respiration measurements would underestimate community respiration rates in hypoxic conditions. In the present study, we observed within the surface-mixed layer three- to sevenfold differences in temporal and vertical variation of community respiration, while net respiration across oxyclines and anaerobic respiration in deep waters had lower rates and variability. In some anoxic samples, there was a net decrease in dissolved inorganic carbon that was exacerbated with experimental augmentation of terminal electron acceptors. Potential carbon fixation rates of chemoautotrophs within and below oxyclines were estimated and ranged from 0.63 to 116.9 mg C m−2 day−1 depending on growth conditions. These results indicate that anaerobic metabolism during the seasonal anoxic transition and at oxic/anoxic interface can play an important role in the estuarine carbon cycle.

Aqueous Carbon Monoxide Cycling in a Fjord-Like Estuary

Dissolved carbon monoxide, [CO], was measured in oxic surface waters and in the anoxic layer of the Pettaquamscutt River, Rhode Island, from March to August 2008. Samples were collected at near-shore locations to examine spatial and seasonal changes at solar noon. Each month, a set of diel samples was collected at the surface stations to evaluate photoproduction and biological processing. In July and August, anoxic samples from depths >6 m were collected to examine the presence of an active anaerobic CO metabolism. The surface [CO] decreased from 65 to 5 nmol kg−1 from spring to summer, which was attributed to a decline in dissolved organic matter. Diel [CO] showed a strong mid-afternoon maximum with a late evening and early morning minimum. Inferred first-order loss rates, attributed to biological processing, ranged from 0.1–0.6 h−1 without a clear seasonal pattern. [CO] saturation ratios were typically >200 at mid-day, >7 in morning/late evening, and never below 1, implying the river is always a net source of CO to the atmosphere. [CO] in the anoxic layer averaged 2 nmol kg−1.

CellTracker Green labelling vs. rose bengal staining: CTG wins by points in distinguishing living from dead anoxia-impacted copepods and nematodes

Abstract. Hypoxia and anoxia have become a key threat to shallow coastal seas. Much is known about their impact on macrofauna, less on meiofauna. In an attempt to shed more light on the latter group, in particular from a process-oriented view, we experimentally induced short-term anoxia (1 week) in the northern Adriatic Sea (Mediterranean) and examined the two most abundant meiofauna taxa – harpacticoid copepods and nematodes. Both taxa also represent different ends of the tolerance spectrum, with copepods being the most sensitive and nematodes among the most tolerant. We compared two methods: CellTracker Green (CTG) – new labelling approach for meiofauna – with the traditional rose bengal (RB) staining method. CTG binds to active enzymes and therefore colours live organisms only. The two methods show considerable differences in the number of living and dead individuals of both meiofauna taxa. Generally, RB will stain dead but not yet decomposed copepods and nematodes equally as it does live ones. Specifically, RB significantly overestimated the number of living copepods in all sediment layers in anoxic samples, but not in any normoxic samples. In contrast, for nematodes, the methods did not show such a clear difference between anoxia and normoxia. RB overestimated the number of living nematodes in the top sediment layer of normoxic samples, which implies an overestimation of the overall live nematofauna. For monitoring and biodiversity studies, the RB method might be sufficient, but for more precise quantification of community degradation, especially after an oxygen depletion event, CTG labelling is a better tool. Moreover, it clearly highlights the surviving species within the copepod or nematode community. As already accepted for foraminiferal research, we demonstrate that the CTG labelling is also valid for other meiofauna groups.

Structural and functional responses of harpacticoid copepods to anoxia in the Northern Adriatic: an experimental approach

Abstract. Combined in situ and laboratory studies were conducted to document the effects of anoxia on the structure and functioning of meiobenthic communities, with special focus on harpacticoid copepods. In a first step, anoxia was created artificially by means of an underwater chamber at 24 m depth in the Northern Adriatic, Gulf of Trieste (Mediterranean). Nematodes were found as the most abundant taxon, followed by harpacticoid copepods. While nematode densities were not affected by treatment (anoxia/normoxia) or sediment depth, these factors had a significant impact on copepod abundances. Harpacticoid copepod family diversity, in contrast, was not affected by anoxic conditions, only by depth. Ectinosomatidae and Cletodidae were most abundant in both normoxic and anoxic samples. The functional response of harpacticoid copepods to anoxia was studied in a laboratory tracer experiment by adding 13C pre-labelled diatoms to sediment cores in order to test (1) if there is a difference in food uptake by copepods under normoxic and anoxic conditions and (2) whether initial (normoxia) feeding of harpacticoid copepods on diatoms results in a better survival of copepods in subsequent anoxic conditions. Independent of the addition of diatoms, there was a higher survival rate in normoxia than anoxia. The supply of additional food did not result in a higher survival rate of copepods in anoxia, which might be explained by the presence of a nutritionally better food source and/or a lack of starvation before adding the diatoms. However, there was a reduced grazing pressure by copepods on diatoms in anoxic conditions. This resulted in a modified fatty acid composition of the sediment. We concluded that anoxia not only impacts the survival of consumers (direct effect) but also of primary producers (indirect effect), with important implications for the recovery phase.

Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands

Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide (CO2) and methane (CH4) production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between natural, mined, and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and CH4 or CO2 production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought about by these land uses.

Abiotic oxidation of Fe(II) by reactive nitrogen species in cultures of the nitrate‐reducing Fe(II) oxidizer Acidovorax sp. BoFeN1 – questioning the existence of enzymatic Fe(II) oxidation

Nitrate-reducing, Fe(II)-oxidizing bacteria were suggested to couple with enzymatic Fe(II) oxidation to nitrate reduction. Denitrification proceeds via intermediates (NO2 -, NO) that can oxidize Fe(II) abiotically at neutral and particularly at acidic pH. Here, we present a revised Fe(II) quantification protocol preventing artifacts during acidic Fe extraction and evaluate the contribution of abiotic vs. enzymatic Fe(II) oxidation in cultures of the nitrate-reducing, Fe(II) oxidizer Acidovorax sp. BoFeN1. Sulfamic acid used instead of HCl reacts with nitrite and prevents abiotic Fe(II) oxidation during Fe extraction. Abiotic experiments without sulfamic acid showed that acidification of oxic Fe(II) nitrite samples leads to 5.6-fold more Fe(II) oxidation than in anoxic samples because the formed NO becomes rapidly reoxidized by O(2) , therefore leading to abiotic oxidation and underestimation of Fe(II). With our revised protocol using sulfamic acid, we quantified oxidation of approximately 7mm of Fe(II) by BoFeN1 within 4days. Without addition of sulfamic acid, the same oxidation was detected within only 2days. Additionally, abiotic incubation of Fe(II) with nitrite in the presence of goethite as surface catalyst led to similar abiotic Fe(II) oxidation rates as observed in growing BoFeN1 cultures. BoFeN1 growth was observed on acetate with N(2) O as electron acceptor. When adding Fe(II), no Fe(II) oxidation was observed, suggesting that the absence of reactive N intermediates (NO2 -, NO) precludes Fe(II) oxidation. The addition of ferrihydrite [Fe(OH)(3) ] to acetate/nitrate BoFeN1 cultures led to growth stimulation equivalent to previously described effects on growth by adding Fe(II). This suggests that elevated iron concentrations might provide a nutritional effect rather than energy-yielding Fe(II) oxidation. Our findings therefore suggest that although enzymatic Fe(II) oxidation by denitrifiers cannot be fully ruled out, its contribution to the observed Fe(II) oxidation in microbial cultures is probably lower than previously suggested and has to be questioned in general until the enzymatic machinery-mediating Fe(II) oxidation is identified.

Molybdenum reduction in a sulfidic lake: Evidence from X-ray absorption fine-structure spectroscopy and implications for the Mo paleoproxy

Marine euxinic sediments, particularly organic-rich black shales, are important sinks for oceanic molybdenum (Mo), and the determination of Mo concentration and isotopic composition are used to constrain oxygenation state and specifically expansion of marine anoxic and sulfidic (euxinic) waters in ancient oceans. The use of Mo as a paleo-redox tracer is based on its distinct geochemical behavior in oxic and sulfidic environments. Mo removal from sulfidic waters starts with MoO42− reacting with aqueous H2S to form particle reactive thiomolybdates, MoO4−xSx2−, but the post-thiomolybdate steps and the ultimate Mo host in euxinic sediments are not well understood. We used X-ray absorption fine structure (XAFS) spectroscopy to determine the oxidation state and the molecular coordination environment of pristine, solid phase Mo in sediments from permanently euxinic Lake Cadagno, Switzerland. Samples were taken from a 9-meter piston core representing the last ten thousand years of deposition.The euxinic lake sediments provide unequivocal evidence that the post-thiomolybdate steps along the burial pathway involve Mo(VI) reduction to Mo(IV) before it is ultimately hosted in the sediments. Anoxic samples contain Mo(IV)–S compounds that, when oxidized upon air-exposure, are transformed into Mo(VI)–O, thus confirming our results. This observation is important to better understand the Mo burial pathway from oxic waters to euxinic sediments. Our results support a model where post-thiomolybdate MoVI reduction proceeds via reactions with zero-valent sulfur, S(0) (mainly S8, Vorlicek et al., 2004). In this model, Mo is scavenged from sulfidic waters as reactive Mo-polysulfide species, Mo(IV)O(S4)S2− or Mo(IV)S(S4)S2−, and not as thiomolybdate (MoOS32− or MoS42−) as has been previously assumed. This result can have important implications for how paleoenvironmental redox conditions are inferred from sedimentary Mo enrichments, Mo/TOC ratios, and δ98Mo, if the Mo accumulation rate is accelerated via the S8-assisted pathway in settings where partial oxidation of S is possible. For example, euxinic Mo/TOC ratios are predicted not only as a function of Mo concentration in overlying seawater. Instead, the ratio will be higher in sediments deposited under highly sulfidic waters where S8 is also abundant, such as in settings where the chemocline depth fluctuates considerably and/or oxygen intrusions occur to the overlying bottom waters. Partial oxidation of dissolved sulfide is an important step in polysulfide production. Finally, we conclude that XAFS measurements are a powerful way to study the Mo burial pathway in sediments and enhance our ability to infer past environmental conditions from the sedimentary record.

A Biogeochemical and Genetic Survey of Acetylene Fermentation by Environmental Samples and Bacterial Isolates

Anoxic samples (sediment and groundwater) from 13 chemically diverse field sites were assayed for their ability to consume acetylene (C2H2). Over incubation periods ranging from ∼ 10 to 80 days, selected samples from 7 of the 13 tested sites displayed significant C2H2 removal. No significant formation of ethylene was noted in these incubations; therefore, C2H2 consumption could be attributed to acetylene hydratase (AH) rather than nitrogenase activity. This putative AH (PAH) activity was observed in only 21% of the total of assayed samples, while amplification of AH genes from extracted DNA using degenerate primers derived from Pelobacter acetylenicus occurred in even fewer (9.8%) samples. Acetylene-fermenting bacteria were isolated as a pure culture from the sediments of a tidal mudflat in San Francisco Bay (SFB93) and as an enrichment culture from freshwater Searsville Lake (SV7). Comparison of 16S rDNA clone libraries revealed that SFB93 was closely related to P. carbolinicus, while SV7 consisted of several unrelated bacteria. AH gene was amplified from SFB93 but not SV7. The inability of the primers to generate amplicons in the SV7 enrichment, as well as from several of the environmental samples that displayed PAH activity, implied that either the primers were too highly constrained in their specificity or that there was a different type of AH gene in these environmental samples than occurs in P. acetylenicus. The significance of this work with regard to the search for life in the outer Solar System, where C2H2 is abundant, is discussed.

Keratinophilic fungi in activated sludge of wastewater treatment plants with MBR in Berlin, Germany

Seventy-two samples of aerobic and anoxic activated sludge were collected from two wastewater treatment plants (36 from each) with membrane bioreactors (MBR) in Berlin (Germany) to determine the presence of cycloheximide-resistant, keratinophilic fungi using the hair-baiting technique. This is the first study on the occurrence of these fungi in MBR sludges. Forty-six fungal species belonging to 21 genera were isolated and identified (41 species and 21 genera versus 36 species and 19 genera from aerobic and anoxic sludge samples, respectively). Twelve species were dermatophytes or closely related fungi: Chrysosporium asperatum, C. georgii, C. indicum, C. keratinophilum, C. tropicum, C. pannorum, Microsporum cookei, M. ferrugineum, M. gypseum, Trichophyton ajelloi, T. mentagrophytes and T. terrestre. The other 32 species, included membe rs of Acremonium, Alternaria, Aspergillus, Candida, Chaetomium, Cladosporium, Fusarium, Geotrichum, Gliocladium, Gymnoascus, Mucor, Paecilomyces, Penicillium, Scopulariopsis, Sporothrix, Trichoderma, Verticillium and unidentified yeasts. The fungi isolated are pathogenic or potentially pathogenic to humans and animals, and their occurrence in activated sludge poses a health risk to wastewater treatment workers and the environment.

Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: community spatial structure, rare members and nitrogen‐cycling guilds

Ribosomal tag libraries based on DNA and RNA in coral reef sediment from Hawaii show the microbial community to be dominated by the bacterial phyla Proteobacteria, Firmicutes and Actinobacteria, the archaeal order Nitrosopumilales and the uncultivated divisions Marine Group III (Euryarchaeota) and Marine Benthic Group C (Crenarchaeota). Operational taxonomic units (OTUs) number in the high thousands, and richness varies with site, presence or absence of porewater sulfide (sediment depth), and nucleotide pool. Rank abundance curves of DNA-based libraries, but not RNA-based libraries, possess a tail of low abundance taxa, supporting the existence of an inactive 'rare' biosphere. While bacterial libraries from two oxic samples differ markedly, those from two anoxic (sulfidic) samples are similar. The four dominant bacterial OTUs are members of genera that include pathogens, but are found in marine environments, and include facultative anaerobes, i.e. dissimilatory nitrate reducers and denitrifiers. This may explain their abundance in both oxic and anoxic samples. A numerous archaeon is closely related to the lithoautotrophic ammonia oxidizer Nitrosopumilus maritimus. Known bacterial ammonia oxidizers are essentially absent, but bacterial nitrite oxidizers are abundant. Although other studies of this reef found evidence for anaerobic ammonia oxidizers, primer bias rendered that clade invisible to this study.

Monitoring of redox state in a dechlorinating culture with immobilized redox indicators

During the dechlorination of tetrachloroethene (PCE) to ethene (ETH) in a microcosm bottle containing an enriched chlororespiring culture, redox conditions were spectrophotometrically monitored with the redox indicators thionine (THI) and cresyl violet (CV) immobilized on transparent films. Measurements were taken with a unique flow redox monitoring system based on circulating solution from the bottle through a specially constructed flow cell and returning it to the bottle. An enclosure for a peristaltic pump was constructed to minimize contamination of the solution with atmospheric O(2). The redox monitoring instrumentation was shown to be an excellent tool to evaluate the ability of an enclosure for anoxic samples to prevent diffusion of very small amounts of oxygen from the atmosphere into the sample. With careful design of the apparatus, the O(2) permeation rate into a solution of THI in a microcosm bottle during redox monitoring was reduced to less than 40 nmol h(-1). When monitoring a dechlorinating culture, dechlorination was not observed until immobilized THI was completely reduced and vinyl chloride was not produced until partial reduction of CV.