Occurrence of Priming in the Degradation of Lignocellulose in Marine Sediments

More than 50% of terrestrially-derived organic carbon (terrOC) flux from the continents to the ocean is remineralised in the coastal zone despite its perceived high refractivity. The efficient degradation of terrOC in the marine environment could be fuelled by labile marine-derived material, a phenomenon known as “priming effect”, but experimental data to confirm this mechanism are lacking. We tested this hypothesis by treating coastal sediments with ¹³C-lignocellulose, as a proxy for terrOC, with and without addition of unlabelled diatom detritus that served as the priming inducer. The occurrence of priming was assessed by the difference in lignocellulose mineralisation between diatom-amended treatments and controls in aerobic sediment slurries. Priming of lignocellulose degradation was observed only at the initial stages of the experiment (day 7) and coincided with overall high microbial activity as exemplified by total CO₂ production. Lignocellulose mineralisation did not differ consistently between diatom treatments and control for the remaining experimental time (days 14–28). Based on this pattern, we hypothesize that the faster initiation of lignocellulose mineralisation in diatom-amended treatments is attributed to the decomposition of accessible polysaccharide components within the lignocellulose complex by activated diatom degraders. The fact that diatom-degraders contributed to lignocellulose degradation was also supported by the different patterns in ¹³C-enrichment of phospholipid fatty acids between treatments. Although we did not observe differences between treatments in the total quantity of respired lignocellulose at the end of the experiment, differences in timing could be important in natural ecosystems where the amount of time that a certain compound is subject to aerobic degradation before burial to deeper anoxic sediments may be limited.     

Light and dissolved nutrients mediate recalcitrant organic matter decomposition via microbial priming in experimental streams

1. Environmental factors such as nutrient and light availability may play important roles in determining the magnitude and direction of microbial priming and detrital decomposition and, therefore, the relative importance of microbial priming in carbon (C) dynamics in freshwater ecosystems.
2. We integrated light availability with an existing conceptual model predicting the magnitude of the priming effect (PE) along a dissolved nutrient gradient (i.e. nutrient PE model). Our modified light-nutrient PE model hypothesises how light may mediate priming at any given nutrient concentration and provides a calculation method for quantitative PE values (i.e. light effect size at a given nutrient concentration).
3. We used recirculating stream mesocosms with Quercus stellata (post oak) leaf litter as an organic matter (OM) substrate in a 150-day experiment to test our model predictions. We manipulated light levels [ambient (full light), shaded (c. 19% of ambient)] and phosphorus (P) concentration (10, 100, 500 µg PO₄-P/L) in a fully factorial design. We also supplied all mesocosms with 500 µg/L dissolved inorganic nitrogen. Microbial biomass, water column dissolved organic C, and leaf litter dry mass and recalcitrant OM [i.e. the fibre (cellulose + lignin) component of post oak substrate] were measured. Recalcitrant OM (ROM) k-rates (day⁻¹) were used to calculate the light effect size within P treatments as a log response ratio (ln[ambient k-rate/shade k-rate]) to ascertain PE magnitude and direction (positive or negative).
4. Light was an important driver of dissolved organic C, a potential source of additional labile organic matter essential for priming heterotrophic microbes. There were weak PEs in total leaf litter dry mass remaining, but PEs were more pronounced in leaf litter ROM remaining. The strongest positive PEs (specific to litter ROM pools) occur in the highest P treatment, presumably due to a change in which nutrient, nitrogen versus P, was a limiting factor for microbes based on nutrient ratios rather than P concentration alone. These results illustrate the importance of considering light levels, nutrient ratios (rather than individual nutrients), and detrital ROM components in further PE model development.

     

A laboratory study on biochemical degradation and microbial utilization of organic matter comprising a marine diatom,land grass,and salt marsh plant in estuarine ecosystems

We studied the biochemical degradation of organic matter comprising marine diatom, land grass, and salt marsh plant in estuarine ecosystems in two laboratory microcosms consisting of estuarine sediments and coastal seawater. The materials were incubated separately and together under controlled oxic and anoxic conditions to test effects of co-metabolism and redox on overall degradation of organic matter. We followed variations of bulk parameters [total organic carbon (TOC), total nitrogen (TN), C/N ratio, δ¹³C_TOC, and δ¹⁵N_TN], fatty acid concentrations, and compound-specific δ¹³C values over 3 months. Coexistence of marine diatom (relatively labile) with land grass/salt marsh plant (relatively refractory) in the microcosms yielded a negative co-metabolism effect (retardation rather than acceleration) on the overall degradation of organic matter. The ratios of oxic to anoxic degradation rate constants (k _ox/k _an) of TOC and most fatty acids were in a range of 1.1–1.7, implying that redox conditions per se had a limited influence on degradation of fresh organic materials in estuarine ecosystems. Variations of two bacteria-specific fatty acids (iso- and anteiso-15:0) and their δ¹³C values indicated that bacterial metabolism could use organic carbon (OC) from any available material when only one single-source material was dominant in the ecosystems. However, bacteria probably utilized OC preferentially from labile marine diatom when multiple-source materials were almost equally present in the ecosystems.     

Enzymatic Activity, Bacterial Distribution, and Organic Matter Composition in Sediments of the Ross Sea (Antarctica)

Enzymatic activities of aminopeptidase and β-glucosidase were investigated in Antarctic Ross Sea sediments at two sites (sites B and C, 567 and 439 m deep, respectively). The sites differed in trophic conditions related to organic matter (OM) composition and bacterial distribution. Carbohydrate concentrations at site B were about double those at site C, while protein and lipid levels were 10 times higher. Proteins were mainly found in a soluble fraction (>90%). Chloropigment content was generally low and phaeopigments were almost absent, indicating the presence of reduced inputs of primary organic matter. ATP concentrations (as a measure of the living microbial biomass) were significantly higher at site B. By contrast, benthic bacterial densities at site C were about double those at site B. Bacterial parameters do not appear to be “bottom-up controlled” by the amount of available food but rather “top-down controlled” by meiofauna predatory pressure, which was significantly higher at site B. Aminopeptidase and β-glucosidase extracellular enzyme activities (EEA) in Antarctic sediments appear to be high and comparable to those reported for temperate or Arctic sediments and characterized by low aminopeptidase/β-glucosidase ratios (about 10). Activity profiles showed decreasing patterns with increasing sediment depth, indicating vertical shifts in both availability and nutritional quality of degradable OM. Vertical profiles of aminopeptidase activity were related to a decrease in protein concentration and/or to an increase in the insoluble refractory proteinaceous fraction. The highest aminopeptidase activity rates were observed at site C, characterized by much lower protein concentrations. Differences in EEA between sites do not seem to be explained by differences in the in situ temperature (−1.6 and −0.8°C at sites B and C, respectively). Aminopeptidase activity profiles are consistent with the bacterial biomass and frequency of dividing cells. Enzyme substrate affinity was generally dependent upon substrate concentrations. EEA, normalized to bacterial numbers, indicated specific activities comparable to those reported for equally deep sediments at temperate latitudes. Vertical patterns of specific enzymatic activity appeared to be controlled by chloroplastic pigment concentrations that accumulate in the deeper sediment layers. The overall conclusion from the analysis of EEA in Antarctic sediments is that enzyme-dependent transformations of OM proceed at rates similar to those measured in temperate environments. Protein carbon potentially liberated by aminopeptidase activities (12.597 to 26.190 mg of C m⁻² day⁻¹) indicates that the whole protein pool could be mobilized within 1.3 to 17 h. Carbohydrate carbon mobilization (773 to 2,552 mg of C m⁻² day⁻¹) is sufficient to turn over the carbohydrate pool within 16 to 20 h. Such rates are 6 to 45 times higher than fluxes of particulate organic proteins and carbohydrates, indicating an “uncoupled hydrolysis” by the Antarctic benthic assemblages, in which bacteria appear to be able to rapidly exploit episodic OM pulses.     

Primary Events, Energy Transfer, and Reactions in Photosynthetic Units: A Connected Model of the Photosynthetic Unit

The concept of photosynthetic unit (PSU) is reviewed in the light of the authors' results in the fields of fluorescence and luminescence (delayed light). Models of PSU are mainly distinguished by the amount of exciton exchange which is allowed between units. The “separate” model, with its “first-order” character, is not consistent with fluorescence kinetic data. The sigmoidal rise of fluorescence under actinic light is best explained by “nonseparate” models; however, most of these models assume a delocalization of excitons or centers. The “connected” model introduced here is not subject to this criticism. It discloses a new effect (the “îlot” effect): a nonrandom grouping of fluorescent units the consequences of which are discussed. It is noted that a “two-quantum” model for the photochemical reaction gives results very similar to those of the connected model. A relation between luminescence intensity and fluorescence yield is seen as a necessary consequence of the PSU concept. Its meaning is different in separate and nonseparate models. This relation is discussed in connection with the true system II fluorescence emission.     

Loss-on-ignition estimates of organic matter and relationships to organic carbon in fluvial bed sediments

Fluvial bed sediments represent an important sink and source for a variety of organic and inorganic compounds. Their most important constituent is organic matter (OM) and its primary component organic carbon (OC). Few studies have been conducted in fluvial environments examining bed-associated OM or OC. This is surprising given the recent interest in global carbon cycling and the importance of bed-associated organics as ecosystem energy sources. The objective of this study was to examine the relationship between OM, determined by loss-on-ignition (LOI), and OC in fluvial bed sediments determined by a dry combustion analyzer. The wide adoption of the LOI method in soil science reflects its ease of use, it is inexpensive, it is rapid, requires no specialized training, and strong statistical relationships commonly exist between OM and OC estimated by standard dry combustion procedures. Regression models were developed between OC and OM for six bed sediment size fractions (≤2.0 mm) for 113 sample sites in a tropical stream on Oahu, Hawaii. All models were highly significant (p < 0.0001), with coefficients of determination ranging from 35 to 79%. Measurement of LOI explained 64% of the variation in OC for all grouped data. The black-box LOI approach may be useful for rapid reconnaissance surveys of drainage systems. Examination of OM to OC conversion factors for Manoa bed sediments indicates that values typically observed in the soils literature (1.7–2.2) are far too low. Values of OM/OC were found to increase with increasing grain size, and decrease with increasing LOI percentage. Conversion factors obtained for grouped data had a mean of 14.9, a coefficient of variation of 21%, and a range of values between 6.2 and 27.4. It is suggested that these high conversion factors reflect significant water loss by dehydration of Fe, Al, and Mn oxides at a muffle furnace temperature of 450 °C. Therefore, the blind application of conversion factors developed from soils should be avoided when converting from OM to OC for fluvial bed sediments. This revised version was published online in July 2006 with corrections to the Cover Date.     

Macrofauna regulate heterotrophic bacterial carbon and nitrogen incorporation in low-oxygen sediments

Oxygen minimum zones (OMZs) currently impinge upon >1 million km² of sea floor and are predicted to expand with climate change. We investigated how changes in oxygen availability, macrofaunal biomass and retention of labile organic matter (OM) regulate heterotrophic bacterial C and N incorporation in the sediments of the OMZ-impacted Indian continental margin (540–1100 m; [O₂]=0.35–15 μmol l⁻¹). In situ pulse-chase experiments traced ¹³C:¹⁵N-labelled phytodetritus into bulk sediment OM and hydrolysable amino acids, including the bacterial biomarker 𝒟-alanine. Where oxygen availability was lowest ([O₂]=0.35 μmol l⁻¹), metazoan macrofauna were absent and bacteria assimilated 30–90% of the labelled phytodetritus within the sediment. At higher oxygen levels ([O₂]=2–15 μmol l⁻¹) the macrofaunal presence and lower phytodetritus retention with the sediment occur concomitantly, and bacterial phytodetrital incorporation was reduced and retarded. Bacterial C and N incorporation exhibited a significant negative relationship with macrofaunal biomass across the OMZ. We hypothesise that fauna–bacterial interactions significantly influence OM recycling in low-oxygen sediments and need to be considered when assessing the consequences of global change on biogeochemical cycles.     

Identification of General Patterns of Nutrient and Labile Carbon Control on Soil Carbon Dynamics Across a Successional Gradient

Carbon (C) inputs and nutrient availability are known to affect soil organic carbon (SOC) stocks. However, general rules regarding the operation of these factors across a range of soil nutrient availabilities and substrate qualities are unidentified. “Priming” (stimulated decomposition by labile C inputs) and ‘preferential substrate utilization’ (retarded decomposition due to shifts in community composition towards microbes that do not mineralize SOC) are two hypotheses to explain effects of labile C additions on SOC dynamics. For effects of nutrient additions (nitrogen and phosphorus) on SOC dynamics, the stoichiometric (faster decomposition of materials of low carbon-to-nutrient ratios) and ‘microbial mining’ (that is, reduced breakdown of recalcitrant C forms for nutrients under fertile conditions) hypotheses have been proposed. Using the natural gradient of soil nutrient availability and substrate quality of a chronosequence, combined with labile C and nutrient amendments, we explored the support for these contrasting hypotheses. Additions of labile C, nitrogen (N), phosphorus (P), and combinations of C and N and C and P were applied to three sites: 2-year fallow grassland, mature grassland and forest, and the effects of site and nutrient additions on litter decomposition and soil C dynamics were assessed. The response to C addition supported the preferential substrate hypothesis for easily degradable litter C and the priming hypothesis for SOC, but only in nitrogen-enriched soils of the forest site. Responses to N addition supported the microbial mining hypothesis irrespective of C substrate (litter or SOC), but only in the forest site. Further, P addition effects on SOC support the stoichiometric hypothesis; P availability appeared key to soil C release (priming) in the forest site if labile C and N is available. These results clearly link previously contrasting hypotheses of the factors controlling SOC with the natural gradient in litter quality and nutrient availability that exists in ecosystems at different successional stages. A holistic theory that incorporates this variability of responses, due to different mechanisms, depending on nutrient availability and substrate quality is essential for devising management strategies to safeguard soil C stocks.     

Temperature response of permafrost soil carbon is attenuated by mineral protection

Climate change in Arctic ecosystems fosters permafrost thaw and makes massive amounts of ancient soil organic carbon (OC) available to microbial breakdown. However, fractions of the organic matter (OM) may be protected from rapid decomposition by their association with minerals. Little is known about the effects of mineral‐organic associations (MOA) on the microbial accessibility of OM in permafrost soils and it is not clear which factors control its temperature sensitivity. In order to investigate if and how permafrost soil OC turnover is affected by mineral controls, the heavy fraction (HF) representing mostly MOA was obtained by density fractionation from 27 permafrost soil profiles of the Siberian Arctic. In parallel laboratory incubations, the unfractionated soils (bulk) and their HF were comparatively incubated for 175 days at 5 and 15°C. The HF was equivalent to 70 ± 9% of the bulk CO₂ respiration as compared to a share of 63 ± 1% of bulk OC that was stored in the HF. Significant reduction of OC mineralization was found in all treatments with increasing OC content of the HF (HF‐OC), clay‐size minerals and Fe or Al oxyhydroxides. Temperature sensitivity (Q10) decreased with increasing soil depth from 2.4 to 1.4 in the bulk soil and from 2.9 to 1.5 in the HF. A concurrent increase in the metal‐to‐HF‐OC ratios with soil depth suggests a stronger bonding of OM to minerals in the subsoil. There, the younger ¹⁴C signature in CO₂ than that of the OC indicates a preferential decomposition of the more recent OM and the existence of a MOA fraction with limited access of OM to decomposers. These results indicate strong mineral controls on the decomposability of OM after permafrost thaw and on its temperature sensitivity. Thus, we here provide evidence that OM temperature sensitivity can be attenuated by MOA in permafrost soils.     

Ecdysteroids in spinach (Spinacia oleracea L.): biosynthesis, transport and regulation of levels

Many plant species produce phytoecdysteroids (PEs: i.e. analogues of insect steroid hormones). There is increasing evidence that PEs are used as a chemical defence by plants against non-adapted insects and nematodes. PEs are good candidates for the development of an environmentally safe approach to crop protection. Most crop species do not accumulate PEs. However, many arguments support the idea that most, if not all, plant species have the genetic ability to produce PEs, but the biosynthetic pathway is not active. A better understanding of the PE biosynthetic pathway and its regulation is consequently necessary. Spinach is one of the very few crop plants which produce large amounts of PEs, of which 20-hydroxyecdysone is the major component. Labeling experiments with radiolabeled precursor (mevalonic acid), putative ecdysteroid intermediates and 20-hydroxyecdysone itself have allowed investigation of PE biosynthesis and transport during spinach development. Biosynthesis takes place in older leaf sets ("sources"), but not in the young developing ones, which in contrast accumulate (acting as "sinks") the PEs produced by the older leaves. PEs are thus continuously redistributed within the developing plant, as its leaf set number increases. The biosynthetic pathway has been analyzed using excised leaves and various labeled precursors, and a preferential sequence of the last steps has been established. Although they do not produce PEs, apical leaf sets are nevertheless able to perform several putative terminal steps of PE biosynthesis. The regulatory mechanisms of PE synthesis appear to involve a direct negative feedback of 20-hydroxyecdysone (the major PE in spinach) on its own synthesis; thus, a sustained synthesis in older leaves requires that they can export the PE they produce.     

Effects of Acute Cortisol Administration on Perceptual Priming of Trauma-Related Material

Intrusive memories are a hallmark symptom of posttraumatic stress disorder (PTSD). They reflect excessive and uncontrolled retrieval of the traumatic memory. Acute elevations of cortisol are known to impair the retrieval of already stored memory information. Thus, continuous cortisol administration might help in reducing intrusive memories in PTSD. Strong perceptual priming for neutral stimuli associated with a “traumatic” context has been shown to be one important learning mechanism that leads to intrusive memories. However, the memory modulating effects of cortisol have only been shown for explicit declarative memory processes. Thus, in our double blind, placebo controlled study we aimed to investigate whether cortisol influences perceptual priming of neutral stimuli that appeared in a “traumatic” context. Two groups of healthy volunteers (N = 160) watched either neutral or “traumatic” picture stories on a computer screen. Neutral objects were presented in between the pictures. Memory for these neutral objects was tested after 24 hours with a perceptual priming task and an explicit memory task. Prior to memory testing half of the participants in each group received 25 mg of cortisol, the other half received placebo. In the placebo group participants in the “traumatic” stories condition showed more perceptual priming for the neutral objects than participants in the neutral stories condition, indicating a strong perceptual priming effect for neutral stimuli presented in a “traumatic” context. In the cortisol group this effect was not present: Participants in the neutral stories and participants in the “traumatic” stories condition in the cortisol group showed comparable priming effects for the neutral objects. Our findings show that cortisol inhibits perceptual priming for neutral stimuli that appeared in a “traumatic” context. These findings indicate that cortisol influences PTSD-relevant memory processes and thus further support the idea that administration of cortisol might be an effective treatment strategy in reducing intrusive reexperiencing.     

Characterization of organic matter in cross-margin sediment transects of an upwelling region in the Campos Basin (SW Atlantic, Brazil) using lipid biomarkers

Lipid biomarkers [fatty acids (FAs), sterols and alcohols] and total organic carbon (TOC) were analyzed in 48 surface (0–2 cm) sediment samples collected twice (winter 2008/2009 and summer/2009) in two transects ranging from 25 to 3,000 m depths. This sampling array encompassed the major upwelling region in the southeastern Brazilian continental margin, where the river influence is probably minimal. The objectives were (1) to evaluate the sources, transport and major areas of organic matter (OM) accumulation in the continental margin and (2) to identify the fraction of OM that is potentially available to secondary benthic producers. As expected from the regional oceanographic characteristics, lipids derived from primary and secondary autochthonous producers (0.073–5.3 mg gTOC^?1) made the major fraction of the sedimentary OM, whereas lipids from allochthonous sources (0.043–0.40 mg gTOC^?1) and from bacteria (<0.01–0.43 mg gTOC^?1) were of relatively less importance. The accumulation of OM in the sediments was highly dependent on the coupling of physical (hydrodynamics) and biological (response to upwelling) factors. It was found that while some restricted areas in the shelf was a sink of labile OM, the export of this material to the upper and middle slope (400–1,000 m depths) can represent an important source of bioavailable OM to the deep sea benthic community.     

Recurring Seasonal Dynamics of Microbial Communities in Stream Habitats

Recurring seasonal patterns of microbial distribution and abundance in three third-order temperate streams within the southeast Pennsylvania Piedmont were observed over 4 years. Populations associated with streambed sediments and rocks (epilithon) were identified using terminal restriction length polymorphism (tRFLP) and sequencing of 16S rRNA genes selectively amplified with primers for the bacterial domain. Analyses of the relative magnitudes of tRFLP peak areas by using nonmetric multidimensional scaling resolved clear seasonal trends in epilithic and sediment populations. Oscillations between two dominant groups of epilithic genotypes, explaining 86% of the seasonal variation in the data set, were correlated with temperature and dissolved organic carbon. Sequences affiliated with epilithic phototrophs (cyanobacteria and diatom chloroplasts), a Rhodoferax sp., and a Bacillus species clustered in the summer, whereas sequences most closely related to “Betaproteobacteria” (putative Burkholderia sp.), and a putative cyanobacterium clustered in the fall/spring. The sediment genotypes also clustered into two groups, and these explained 85% of seasonal variation but correlated only with temperature. A summer tRFLP pattern was characterized by prevalence of “Betaproteobacteria,” “Gammaproteobacteria,” and a Bacillus sp., whereas the winter/spring pattern was characterized by phylotypes most closely related to “Firmicutes,” “Gammaproteobacteria,” and “Nitrospirae.” A close association between these headwater streams and their watersheds was suggested by the recovery of sequences related to microbial populations provisionally attributed to not only freshwaters but also terrestrial habitats.     

Docking of Yeast Vacuoles Is Catalyzed by the Ras-like GTPase Ypt7p after Symmetric Priming by Sec18p (NSF)

Vacuole inheritance in yeast involves the formation of tubular and vesicular “segregation structures” which migrate into the bud and fuse there to establish the daughter cell vacuole. Vacuole fusion has been reconstituted in vitro and may be used as a model for an NSF-dependent reaction of priming, docking, and fusion. We have developed biochemical and microscopic assays for the docking step of in vitro vacuole fusion and characterized its requirements. The vacuoles must be primed for docking by the action of Sec17p (α-SNAP) and Sec18p (NSF). Priming is necessary for both fusion partners. It produces a labile state which requires rapid docking in order to lead productively to fusion. In addition to Sec17p/Sec18p, docking requires the activity of the Ras-like GTPase Ypt7p. Unlike Sec17p/Sec18p, which must act before docking, Ypt7p is directly involved in the docking process itself.     

Absence of YhdP,TamB, and YdbH leads to defects in glycerophospholipid transport and cell morphology in Gram-negative bacteria

The outer membrane (OM) of Gram-negative bacteria provides the cell with a formidable barrier that excludes external threats. The two major constituents of this asymmetric barrier are lipopolysaccharide (LPS) found in the outer leaflet, and glycerophospholipids (GPLs) in the inner leaflet. Maintaining the asymmetric nature and balance of LPS to GPLs in the OM is critical for bacterial viability. The biosynthetic pathways of LPS and GPLs are well characterized, but unlike LPS transport, how GPLs are translocated to the OM remains enigmatic. Understanding this aspect of cell envelope biology could provide a foundation for new antibacterial therapies. Here, we report that YhdP and its homologues, TamB and YdbH, members of the “AsmA-like” family, are critical for OM integrity and necessary for proper GPL transport to the OM. The absence of the two largest AsmA-like proteins (YhdP and TamB) leads to cell lysis and antibiotic sensitivity, phenotypes that are rescued by reducing LPS synthesis. We also find that yhdP, tamB double mutants shed excess LPS through outer membrane vesicles, presumably to maintain OM homeostasis when normal anterograde GPL transport is disrupted. Moreover, a yhdP, tamB, ydbH triple mutant is synthetically lethal, but if GPL transport is partially restored by overexpression of YhdP, the cell shape adjusts to accommodate increased membrane content as the cell accumulates GPLs in the IM. Our results therefore suggest a model in which “AsmA-like” proteins transport GPLs to the OM, and when hindered, changes in cell shape and shedding of excess LPS aids in maintaining OM asymmetry.     

Denitrification and Nitrogen Fixation in Alaskan Continental Shelf Sediments

Rates of nitrogen fixation and denitrification were measured in Alaskan continental shelf sediments. In some regions, rates of nitrogen fixation and denitrification appeared to be equal; in other areas, rates were significantly different. Potential rates of denitrification were found to be limited primarily by the available nitrate substrate. Major regional differences in rates of denitrification were not statistically significant, but significant differences were found for nitrogen fixation rates in different regions of the Alaskan continental shelf. Estimated net losses of nitrogen from Bering Sea sediments were calculated as 1.8 × 10¹² g of N/yr. Experimental exposure of continental shelf sediments to petroleum hydrocarbons reduced rates of nitrogen fixation and denitrification in some cases but not others. Long-term exposure was necessary before a reduction in nitrogen fixation rates was observed; unamended rates of denitrification but not potential denitrification rates (NO₃⁻ added) were depressed after exposure to hydrocarbons.     

Isotope alteration caused by changes in biochemical composition of sedimentary organic matter

Stable carbon (C) and nitrogen (N) isotope ratios of sedimentary organic matter (OM) can reflect the biogeochemical history of aquatic ecosystems. However, diagenetic processes in sediments may alter isotope records of OM via microbial activity and preferential degradation of isotopically distinct organic components. This study investigated the isotope alteration caused by preferential degradation in surface sediments sampled from a eutrophic reservoir in Germany. Sediments were treated sequentially with hot water extraction, hydrochloric acid hydrolysis, hydrogen peroxide oxidation and di-sodium peroxodisulfate oxidation to chemically simulate preferential degradation pathways of sedimentary OM. Residue and extracts from each extraction step were analyzed using elemental analyzer-isotope ratio mass spectrometry and solid-state ¹³C nuclear magnetic resonance spectroscopy. Our results show that stable C and N isotope ratios reacted differently to changes in the biochemical composition of sedimentary OM. Preferential degradation of proteins and carbohydrates resulted in a 1.2‰ depletion of ¹³C, while the isotope composition of ¹⁵N remained nearly the same. Sedimentary δ¹⁵N values were notably altered when lignins and lipids were oxidized from residual sediments. Throughout the sequential fractionation procedure, δ¹³C was linearly correlated with the C:N of residual sediments. This finding demonstrates that changes in biochemical composition caused by preferential degradation altered δ¹³C values of sedimentary OM, while this trend was not observed for δ¹⁵N values. Our study identifies the influence of preferential degradation on stable C isotope ratios and provide additional insight into the isotope alteration caused by post-depositional processes.

     

Novel Phycoerythrins in Marine Synechococcus spp. : Characterization and Evolutionary and Ecological Implications

Four clones of the marine, unicellular, cyanobacteria Synechococcus spp., were examined for the spectral and biochemical features of their phycoerythrins (PE) and their photosynthetic characteristics. Two spectral types of PE which are distinct from known PEs were found. One PE type possessed absorption maxima at 500 and 545 nm and a fluorescence emission at 560 nm. Upon denaturation in acid-urea, two chromophore absorption maxima were obtained, one corresponding to phycourobilin (A_max 500 nm) and one at 558 nm, ascribed to a phycoerythrobilin-like chromophore. The ratio of phycoerythrobilin-like to phycourobilin chromophores was 4.9:1.3. This PE possessed two subunits of M_rs of 17.0 and 19.5 kD for the α and β subunits, respectively. The other PE possessed a single symmetrical absorption at 551 nm and a fluorescence emission at 570 nm. This phycobiliprotein showed a single chromophore absorption band (A_max 558 nm) and yielded two polypeptides, an α of 17.5 kD and a β subunit of 20.8 kD. Both PEs showed a (α, β)_n structure. The presence of phycoerythrobilin-like chromophores (A_max 558 nm) appears to be diagnostic of this marine cyanobacterial group. The features of these PEs combined with additional biochemical data, suggest a possible evolutionary link between the PE-containing marine Synechococcus group and the red algal chloroplast. When the Synechococcus clones were grown under low light intensity the PE-containing clones showed higher photosynthetic performance, larger photosynthetic units sizes, reaction center I to II ratios near unity, and steeper initial slopes of photosynthesis versus irradiance curves than a non-PE-containing clone. These findings demonstrate the high photosynthetic efficiency of PE-containing clones in low light environments common to middepth neritic and oceanic habitats.     

CT Pulmonary Angiography: Increasingly Diagnosing Less Severe Pulmonary Emboli

Background

It is unknown whether the observed increase in computed tomography pulmonary angiography (CTPA) utilization has resulted in increased detection of pulmonary emboli (PEs) with a less severe disease spectrum.

Methods

Trends in utilization, diagnostic yield, and disease severity were evaluated for 4,048 consecutive initial CTPAs performed in adult patients in the emergency department of a large urban academic medical center between 1/1/2004 and 10/31/2009. Transthoracic echocardiography (TTE) findings and peak serum troponin levels were evaluated to assess for the presence of PE-associated right ventricular (RV) abnormalities (dysfunction or dilatation) and myocardial injury, respectively. Statistical analyses were performed using multivariate logistic regression.

Results

268 CTPAs (6.6%) were positive for acute PE, and 3,780 (93.4%) demonstrated either no PE or chronic PE. There was a significant increase in the likelihood of undergoing CTPA per year during the study period (odds ratio [OR] 1.05, 95% confidence interval [CI] 1.04–1.07, P<0.01). There was no significant change in the likelihood of having a CTPA diagnostic of an acute PE per year (OR 1.03, 95% CI 0.95–1.11, P = 0.49). The likelihood of diagnosing a less severe PE on CTPA with no associated RV abnormalities or myocardial injury increased per year during the study period (OR 1.39, 95% CI 1.10–1.75, P = 0.01).

Conclusions

CTPA utilization has risen with no corresponding change in diagnostic yield, resulting in an increase in PE detection. There is a concurrent rise in the likelihood of diagnosing a less clinically severe spectrum of PEs.