Organic Carbon Metabolism Research Articles

Early diagenesis and trace element accumulation in North American Arctic margin sediments

Concentrations of redox-sensitive elements (S, Mn, Mo, U, Cd, Re) were analyzed in a set of 27 sediment cores collected along the North American Arctic margin (NAAM) from the North Bering Sea to Davis Strait via the Canadian Archipelago. Sedimentary distributions and accumulation rates of the elements were used to evaluate early diagenesis in sediments along this section and to estimate the importance of this margin as a sink for key elements in the polar and global oceans. Distributions of Mn, total S and reduced inorganic S demonstrated that diagenetic conditions and thus sedimentary carbon turnover in the NAAM is organized regionally: undetectable or very thin layers (<0.5cm) of surface Mn enrichment occurred in the Bering–Chukchi shelves; thin layers (1–5cm) of surface Mn enrichment occurred in Barrow Canyon and Lancaster Sound; and thick layers (5–20cm) of surface Mn enrichment occurred in the Beaufort Shelf, Canadian Archipelago, and Davis Strait. Inventories of authigenic S below the Mn-rich layer decreased about fivefold from Bering–Chukchi shelf and Barrow Canyon to Lancaster Sound and more than ten-fold from Bering–Chukchi shelf to Beaufort Shelf, Canadian Archipelago and Davis Strait. The Mn, total S and reduced inorganic S distributions imply strong organic carbon (OC) flux and metabolism in the Bering–Chukchi shelves, lower aerobic OC metabolism in Barrow Canyon and Lancaster Sound, and deep O2 penetration and much lower OC metabolism in the Beaufort Shelf, Canadian Archipelago, and Davis Strait. Accumulation rates of authigenic S, Mo, Cd, Re, and U displayed marked spatial variability along the NAAM reflecting the range in sedimentary redox conditions. Strong relationships between the accumulation rates and vertical carbon flux, estimated from regional primary production values and water depth at the coring sites, indicate that the primary driver in the regional patterns is the supply of labile carbon to the seabed. Thus, high primary production combined with a shallow water column (average 64m) leads to high rates of authigenic trace element accumulation in sediments from the Bering–Chukchi shelves. High to moderate primary production combined with deep water (average 610m) leads to moderate rates of authigenic trace element accumulation in sediments from Lancaster Sound. Low to very low primary production combined with moderate water depths (average 380m) leads to low rates of authigenic trace element accumulation in sediments in the Beaufort Shelf, Davis Strait and Canadian Archipelago. Authigenic Mo accumulation rates show a significant relationship with vascular plant input to the sediments, implying that terrestrial organic matter contributes significantly to metabolism in Arctic margin sediments. Our results suggest that the broad and shallow shelf of the Chukchi Sea, which has high productivity sustained by imported nutrients, contributes disproportionately to global biogeochemical cycles.

Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool.

The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation. These genes included various glycoside hydrolases, nitrate and sulfate reductases, putative bacterial microcompartment biosynthetic clusters (BMC), and F420H2 dehydrogenases. Phylogenetic analysis suggested that the acquisition of these genes probably occurred through horizontal gene transfer (HGT). Metatranscriptomics illustrated that glycoside hydrolases are among the most highly expressed genes. Our results suggest that the microbial inhabitants are well adapted to this brine environment, and anaerobic carbohydrate consumption mediated by glycoside hydrolases and electron transport systems (ETSs) is a dominant process performed by microorganisms from various phyla within this ecosystem.

Proteomic Analyses Reveal the Mechanism of Dunaliella salina Ds-26-16 Gene Enhancing Salt Tolerance in Escherichia coli.

We previously screened the novel gene Ds-26-16 from a 4 M salt-stressed Dunaliella salina cDNA library and discovered that this gene conferred salt tolerance to broad-spectrum organisms, including E. coli (Escherichia coli), Haematococcus pluvialis and tobacco. To determine the mechanism of this gene conferring salt tolerance, we studied the proteome of E. coli overexpressing the full-length cDNA of Ds-26-16 using the iTRAQ (isobaric tags for relative and absolute quantification) approach. A total of 1,610 proteins were identified, which comprised 39.4% of the whole proteome. Of the 559 differential proteins, 259 were up-regulated and 300 were down-regulated. GO (gene ontology) and KEGG (Kyoto encyclopedia of genes and genomes) enrichment analyses identified 202 major proteins, including those involved in amino acid and organic acid metabolism, energy metabolism, carbon metabolism, ROS (reactive oxygen species) scavenging, membrane proteins and ABC (ATP binding cassette) transporters, and peptidoglycan synthesis, as well as 5 up-regulated transcription factors. Our iTRAQ data suggest that Ds-26-16 up-regulates the transcription factors in E. coli to enhance salt resistance through osmotic balance, energy metabolism, and oxidative stress protection. Changes in the proteome were also observed in E. coli overexpressing the ORF (open reading frame) of Ds-26-16. Furthermore, pH, nitric oxide and glycerol content analyses indicated that Ds-26-16 overexpression increases nitric oxide content but has no effect on glycerol content, thus confirming that enhanced nitric oxide synthesis via lower intercellular pH was one of the mechanisms by which Ds-26-16 confers salt tolerance to E. coli.

Effects of different forms of plant-derived organic matter on nitrous oxide emissions.

To investigate the impact of different forms of plant-derived organic matter on nitrous oxide (N2O) emissions, an incubation experiment with the same rate of total nitrogen (N) application was carried out at 25 °C for 250 days. Soils were incorporated with maize-derived organic matter (i.e., maize residue-derived dissolved organic matter and maize residues with different C/N ratios) and an inorganic N fertilizer (urea). The pattern and magnitude of nitrous oxide (N2O) emissions were affected by the form of N applied. Single application of maize-derived organic matter resulted in a higher N2O emission than single application of the inorganic N fertilizer or combined application of the inorganic N fertilizer and maize-derived organic matter. The positive effect of maize residue-derived dissolved organic matter (DOM) addition on N2O emissions was relatively short-lived and mainly occurred at the early stage following DOM addition. In contrast, the positive effect induced by maize residue addition was more pronounced and lasted for a longer period. Single application of maize residues resulted in a substantial decrease in soil nitric nitrogen (NO3(-)-N), but it did not affect the production of N2O. No significant relationship between N2O emission and NO3(-)-N and ammonium nitrogen (NH4(+)-N) suggested that the availability of soil N was not limiting the production of N2O in our study. The key factors affecting soil N2O emission were the soil dissolved organic carbon (DOC) content and metabolism quotient (qCO2). Both of them could explain 87% of the variation in cumulative N2O emission. The C/N ratio of maize-derived organic matter was a poor predictor of N2O emission when the soil was not limited by easily available C and the available N content met the microbial N demands for nitrification and denitrification. The results suggested that the magnitude of N2O emission was determined by the impact of organic amendments on soil C availability and microbial activity rather than on soil N availability. In agricultural management practices, if the N inputs from organic and inorganic N fertilizers are equivalent, addition of organic N fertilizers that contain high amounts of available C will result in a higher N2O emission.

Effects of foraging leaf litter of Aegiceras corniculatum (Ericales, Myrsinaceae) by Parasesarma plicatum (Brachyura, Sesarmidae) crabs on properties of mangrove sediment: a laboratory experiment

Sesarmid crabs play important roles in mangrove ecosystems as they affect litter carbon pool, nutrient recycling, and retention by their burrowing and foraging activities. The present study reported the effects of decomposition of Aegiceras corniculatum (L.) Blanco leaf and foraging on leaf litter by Parasesarma plicatum (Latreille, 1803) crabs on sediment nutrient concentrations and enzyme activities. Results showed no significant effects on sediment organic carbon (OC) and total nitrogen (TKN) concentrations due to non-leaf foraging activities of P. plicatum crabs. Concentrations of OC, TKN, and humics in sediment were higher in leaf decomposition treatment than in the control, and crab foraging activity accelerated the increase in organic matter, compared to either leaf litter decomposition or crab non-leaf foraging activity. Foraging on mangrove leaf litter by crabs also increased the activities of protease, urease, and invertase which are important in the metabolism of organic carbon and nutrients in sediment. The results further demonstrated that sesarmid crabs play important roles in the carbon and nutrient cycling in mangrove ecosystem, but the crabs had higher accumulation efficiency of leaf nitrogen to sediment than carbon.

The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat.

Genomes were obtained for three closely related strains of Synechococcus that are representative of putative ecotypes (PEs) that predominate at different depths in the 1 mm-thick, upper-green layer in the 60°C mat of Mushroom Spring, Yellowstone National Park, and exhibit different light adaptation and acclimation responses. The genomes were compared to the published genome of a previously obtained, closely related strain from a neighboring spring, and differences in both gene content and orthologous gene alleles between high-light-adapted and low-light-adapted strains were identified. Evidence of genetic differences that relate to adaptation to light intensity and/or quality, CO2uptake, nitrogen metabolism, organic carbon metabolism, and uptake of other nutrients were found between strains of the different putative ecotypes. In situ diel transcription patterns of genes, including genes unique to either low-light-adapted or high-light-adapted strains and different alleles of an orthologous photosystem gene, revealed that expression is fine-tuned to the different light environments experienced by ecotypes prevalent at various depths in the mat. This study suggests that strains of closely related PEs have different genomic adaptations that enable them to inhabit distinct ecological niches while living in close proximity within a microbial community.

Phaeodactylum tricornutum photorespiration takes part in glycerol metabolism and is important for nitrogen-limited response.

BackgroundMicroalgae are potential sources of biofuels and high-value compounds. Mixotrophic conditions usually promote growth of microalgae. The pennate diatom Phaeodactylum tricornutum, with its short life cycle, completely sequenced genome, and ease of transformation, can be used as a model for studying carbon metabolism in microalgae.ResultsWe compared the growth rate of P. tricornutum (IOCAS-001) under different conditions and labeled the cells using [13C]glycerol (GL). The results revealed GL promoted the growth of P. tricornutum. Ser and Gly were synthesized via photorespiration. The 13C enrichment of Ser and Gly under nitrogen-limited conditions was much higher compared to other amino acids, indicating the enhancement of photorespiration. Addition of sodium acetate decreased the growth rate of P. tricornutum under nitrogen-limited conditions. Our results indicated that the GL carbon backbone enters the Calvin cycle in the form of dihydroxyacetone phosphate (DHAP), producing xylulose 5-phosphate (X5P) with a GL2_3-generated carbon backbone distributed at X5P1_2 and ribose 5-phosphate (R5P) with GL1-derived carbon atoms at R5P1 and R5P2. Both R5P and X5P can be converted into ribulose-1,5-bisphosphate (RuBP). By oxygenation of RuBP carboxylase/oxygenase (Rubisco) and metabolism through photorespiration, these RuBPs generate Ser and Gly with GL1 or GL2-derived carbon atoms at position 1 and GL1 or GL3-derived carbon atoms at other positions, resulting in a low level of 13C enrichment of Gly1 and Ser1.ConclusionOur results indicated different strains of P. tricornutum have different mechanisms for organic carbon metabolism. Photorespiration is involved in GL metabolism and is important for the nitrogen-limited response in P. tricornutum.ClassificationMetabolic flux analysis, microalgaeElectronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0256-5) contains supplementary material, which is available to authorized users.

Net ecosystem production, calcification and CO2 fluxes on a reef flat in Northeastern Brazil

The carbon cycle in coral reefs is usually dominated by the organic carbon metabolism and precipitation-dissolution of CaCO3, processes that control the CO2 partial pressure (pCO2) in seawater and the CO2 fluxes through the air–sea interface. In order to characterize these processes and the carbonate system, four sampling surveys were conducted at the reef flat of Coroa Vermelha during low tide (exposed flat). Net ecosystem production (NEP), net precipitation-dissolution of CaCO3 (G) and CO2 fluxes across the air–water interface were calculated. The reef presented net autotrophy and calcification at daytime low tide. The NEP ranged from −8.7 to 31.6 mmol C m−2 h−1 and calcification from −13.1 to 26.0 mmol C m−2 h−1. The highest calcification rates occurred in August 2007, coinciding with the greater NEP rates. The daytime CO2 fluxes varied from −9.7 to 22.6 μmol CO2 m−2 h−1, but reached up to 13,900 μmol CO2 m−2 h−1 during nighttime. Carbon dioxide influx to seawater was predominant in the reef flat during low tide. The regions adjacent to the reef showed a supersaturation of CO2, acting as a source of CO2 to the atmosphere (from −22.8 to −2.6 mol CO2 m−2 h−1) in the reef flat during ebbing tide. Nighttime gas release to the atmosphere indicates a net CO2 release from the Coroa Vermelha reef flat within 24 h, and that these fluxes can be important to carbon budget in coral reefs.

River metabolism and carbon dynamics in response to flooding in a lowland river

Lowland riverine–floodplain systems often have significant but irregular inputs of allochthonous carbon. However, the importance of this carbon to riverine systems remains poorly understood. We assessed open water dissolved organic carbon (DOC) concentrations, metabolism and biofilm stable isotope (δ13C) signatures, upstream and downstream of an extensive floodplain forest on the Murray River, Australia, before and after a flood event. Prior to flooding, all sites had similar concentrations of DOC, rates of metabolism and biofilm δ13C signatures. During the flood DOC concentration increased up to three-fold downstream of the forest, gross primary production (GPP) increased at all sites, but community respiration (CR) increased only at the downstream sites, resulting in decreased in NPP downstream and a slight increase upstream. Biofilm δ13C signatures became depleted by between 4 and 7‰ downstream of the forest during the flood, reflecting a rapid incorporation of allochthonous carbon into the biofilm. These results indicate that flooding led to a substantial increase to the energy budget of the Murray River through the provisioning of large quantities of allochthonous carbon and that terrestrial carbon was processed within the river biofilms. Allochthonous carbon assimilation within biofilms during flooding provides a potential pathway for allochthonous carbon to be incorporated into the metazoan foodweb.

Sulfur, iron and carbon cycling following hydrological restoration of acidic freshwater wetlands

Freshwater re-flooding is a relatively novel approach to remediate drained acid sulfate soil (ASS) wetlands. This study documents the geochemical consequences of restoring freshwater re-flooding for contemporary reduced inorganic sulfur (RIS) and iron species in two coastal floodplain ASS wetlands. Re-flooding has established predominantly reducing/suboxic conditions and encouraged organic carbon accumulation in surface sediments (~20–30%). The pH of former sulfuric horizons has increased by ~2–3 units, partly in response to alkalinity generation from anaerobic metabolism of organic carbon coupled with Fe(III) and SO42− reduction. Despite considerable sulfidisation, reactive Fe (FeR; sum of 1M HCl and citrate–dithionite extracts) and non-sulfidic Fe(II) remain abundant in both wetlands. High concentrations of Fe2+ (up to ~5mM) in wetland porewaters represent a considerable pool of labile net acidity and is partly a result of insufficient S(−II) to sequester excess Fe2+. Accumulation of iron sulfides appears to be constrained more by SO42− and carbon availability rather than FeR. Reformation and accumulation of RIS species is greatest in organic-rich surface horizons (~40–500μmolg−1), where time integrated RIS accumulation rates approximate 10–100nmolg−1 d−1. While pyrite is the dominant RIS species to have formed since re-flooding, there is anomalous accumulation of S(0) (up to 80μmolg−1), accounting for ~50% of the RIS pool in some samples. Greigite (Fe3S4) has formed in near-surface sediments and while AVS-S is a minor component of the RIS pool overall, at some locations maximum concentrations exceed 300μmolg−1. Contemporary near-surface pyrite is characterised by abundant small (200–300nm) crystals, in contrast to relic sedimentary pyrite of estuarine origin that is dominated by larger crystals with diverse habit. Although Fe and SO42− reduction are partly responsible for wetland-scale recovery from acute acidification, the resultant accumulation of diverse RIS species in surficial sediments indicates an oxidative component to the S-cycle and represents a hysteresis in S-cycling that contrasts markedly with the drained conditions existing before remediation. Analysis of seasonal climate fluctuations suggests that near-surface sediments containing contemporary RIS are vulnerable to oxidation and possible temporary re-acidification during future drought episodes. This study underscores the long-term legacy of ASS wetland drainage and highlights the need for both considered hydrological management of re-flooded wetlands and further study to quantify possible re-acidification risks associated with seasonal drought.

Comparison of Trees and Grasses for Rhizoremediation of Petroleum Hydrocarbons

Rhizoremediation of petroleum contaminants is a phytoremediation process that depends on interactions among plants, microbes, and soils. Trees and grasses are commonly used for phytoremediation, with trees typically being chosen for remediation of BTEX while grasses are more commonly used for remediation of PAHs and total petroleum hydrocarbons. The objective of this review was to compare the effectiveness of trees and grasses for rhizoremediation of hydrocarbons and address the advantages of each vegetation type. Grasses were more heavily represented in the literature and therefore demonstrated a wider range of effectiveness. However, the greater biomass and depth of tree roots may have greater potential for promoting environmental conditions that can improve rhizoremediation, such as increased metabolizable organic carbon, oxygen, and water. Overall, we found little difference between grasses and trees with respect to average reduction of hydrocarbons for studies that compared planted treatments with a control. Additional detailed investigations into plant attributes that most influence hydrocarbon degradation rates should provide data needed to determine the potential for rhizoremediation with trees or grasses for a given site and identify which plant characteristics are most important.

A huge biocatalytic filter in the centre of Barents Sea shelf?

A primary production model for the Barents Sea shows a hot spot of organic carbon settlement to the sea bed over 100km long, a shallow pile of highly permeable sediments (mainly large Balanus, Mya and Pecten shell fragments over 1cm in size) of glacial origin. Hydrodynamic flow models suggest an intensive, deep flow of near-bottom waters into the sediment. Depending on wave height, water in shallow (30m depth) places may percolate more than 5m into the sediment. During 10days of stormy weather as much as 4 to 8kg wet weight pelagic biomass can be processed per square metre through this extremely permeable sediment. Analogous processes known in coastal waters lead to intense biocatalytic phenomena and metabolism of organic carbon within the seabed, estimated here as more intense than surface consumption. Spitsbergenbanken may be acting as a huge sink for organic carbon and an important source of nutrients in one of the most productive areas of the North Atlantic.

Quantifying alkalinity generating processes in a tidally remediating acidic wetland

Abstract Lime-assisted tidal exchange (LATE) is a new remediation technique that is demonstrably effective at decreasing acidity in coastal acid sulfate soils (CASS). However, the relative magnitude of the major in situ alkalinity generating processes and external alkalinity inputs that dominate neutralization of acidity during LATE have not been quantified. Here, we combine investigations of porewater and solid-phase geochemistry from a remediating CASS wetland to derive first-order estimates of alkalinity generating processes and inputs after 6 years of LATE. Quantified inputs include: marine derived HCO3− from tidal exchange; hydrated lime additions; and in situ alkalinity from anaerobic metabolism of organic carbon coupled with reduction of iron and sulfate. A progressive increase in tidal inundation led to the development of significant relationships (α = 0.01) between topography and both non-sulfidic, solid-phase Fe(II) and solid-phase reduced inorganic sulfur species. These topographic relationships were conjoined with a digital elevation model, enabling up-scaling of alkalinity estimates to a sub-catchment level. Estimates indicate the relative order of importance of alkalinity generating processes and inputs is Fe reduction (50–64%) > tidal exchange (25–42%) > sulfate reduction (7–13%) >> hydrated lime addition ( 99%) of net alkalinity generation was due to either tides or microbial metabolism. This indicates that the LATE remediation technique is both a cost effective means of decreasing soil acidity and is readily transferable to similar CASS landscapes - provided there is adequate supply of suitable electron donors and sufficient regenerative capacity in the adjacent estuarine/marine tidal HCO3− pool.

Prokaryotic diversity in sediments beneath two polar glaciers with contrasting organic carbon substrates

Microbial ecosystems beneath glaciers and ice sheets are thought to play an active role in regional and global carbon cycling. Subglacial sediments are assumed to be largely anoxic, and thus various pathways of organic carbon metabolism may occur here. We examine the abundance and diversity of prokaryotes in sediment beneath two glaciers (Lower Wright Glacier in Antarctica and Russell Glacier in Greenland) with different glaciation histories and thus with different organic carbon substrates. The total microbial abundance in the Lower Wright Glacier sediment, originating from young lacustrine sediment, was an order of magnitude higher (~8 × 10(6) cells per gram of wet sediment) than in Russell Glacier sediment (~9 × 10(5) cells g(-1)) that is of Holocene-aged soil origin. 4% of the microbes from the Russell Glacier sediment and 0.04-0.35% from Lower Wright Glacier were culturable at 10°C. The Lower Wright Glacier subglacial community was dominated by Proteobacteria, followed by Firmicutes. The Russell Glacier library was much less diverse and also dominated by Proteobacteria. Low numbers and diversity of both Euryarchaeota and Crenarchaeota were found in both sediments. The identified clones were related to bacteria with both aerobic and anaerobic metabolisms, indicating the presence of both oxic and anoxic conditions in the sediments.

Synechococcus sp. Strain PCC 7002 Transcriptome: Acclimation to Temperature, Salinity, Oxidative Stress, and Mixotrophic Growth Conditions

Synechococcus sp. strain PCC 7002 is a unicellular, euryhaline cyanobacterium. It is a model organism for studies of cyanobacterial metabolism and has great potential for biotechnological applications. It exhibits an exceptional tolerance of high-light irradiation and shows very rapid growth. The habitats from which this and closely related strains were isolated are subject to changes in several environmental factors, including light, nutrient supply, temperature, and salinity. In this study global transcriptome profiling via RNAseq has been used to perform a comparative and integrated study of global changes in cells grown at different temperatures, at different salinities, and under mixotrophic conditions, when a metabolizable organic carbon source was present. Furthermore, the transcriptomes were investigated for cells that were subjected to a heat shock and that were exposed to oxidative stress. Lower growth temperatures caused relatively minor changes of the transcriptome; the most prominent changes affected fatty acid desaturases. A heat shock caused severe changes of the transcriptome pattern; transcripts for genes associated with major metabolic pathways declined and those for different chaperones increased dramatically. Oxidative stress, however, left the transcript pattern almost unaffected. When grown at high salinity, Synechococcus sp. PCC 7002 had increased expression of genes involved in compatible solute biosynthesis and showed increased mRNA levels for several genes involved in electron transport. Transcripts of two adjacent genes dramatically increased upon growth at high salinity; the respective proteins are putatively involved in coping with oxidative stress and in triggering ion channels. Only minor changes were observed when cells were grown at low salinity or when the growth medium was supplemented with glycerol. However, the transcriptome data suggest that cells must acclimate to excess reducing equivalents when a reduced C-source is present.

The microbial ferrous wheel: iron cycling in terrestrial, freshwater, and marine environments

The microbial ferrous wheel: iron cycling in terrestrial, freshwater, and marine environments

Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton

The polyamines putrescine (PUT) and spermidine (SPD) are ubiquitous in seawater, but mechanisms that drive the degradation of these important nitrogen sources by marine bacteria remain unclear. We employed a comparative metatranscriptomics approach to compare gene transcription patterns between coastal bacterioplankton communities with and without amendments of PUT or SPD, in an effort to understand how bacterial communities and their genes shape polyamine biogeochemistry in the ocean. Statistically different transcript categories in the PUT (25 COG groups) and SPD (23 COG groups) samples, relative to controls that received no amendment (CTRL), indicated that genes encoding the cellular translation machinery and the metabolism of organic nitrogen and carbon became enriched in the community transcriptome when polyamine availability increased. Of the three known pathways for bacterial polyamine degradation, only genes in the transamination pathway were enriched in the PUT and SPD libraries, suggesting that this route dominated polyamine degradation. Taxonomic affiliation of significantly enriched diagnostic genes in the PUT and SPD libraries pointed to roseobacter- and SAR11-affiliated bacteria as the predominant taxa driving transformation in this coastal ocean, although other diverse marine bacterioplankton groups (Gammaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes) also contributed to polyamine-related gene transcription.

Almond tree and organic fertilization for soil quality improvement in southern Italy

The semi-arid Mediterranean region, characterized by long dry periods followed by heavy bursts of rainfall, is particularly prone to soil erosion. The main goal of this study is to evaluate the soil quality under different practices of bio-physical amelioration which involve the soil-plant system (almond trees) and microorganism-manure. This study, carried out in the South of Italy (Basilicata Region- Pantanello farm), considered two types of fertilization (mineral and organic) and three slope gradients (0, 2 and 6%), in order to evaluate the effects of management practices in resisting soil erosion. Chemical (organic carbon and nitrogen), physical (soil shrinkage and bulk density) and biochemical (dehydrogenase activity and hydrolytic enzyme activities) parameters were selected as markers to follow agro-ecological changes with time. The organic treatment affected soil microbiological and physico-chemical properties by increasing soil nutrient availability, microbial activity, and improving soil structure. The consistently higher values of the hydrolytic enzyme activities (β-glucosidase, phosphatase, urease and protease) often observed in the presence of plants and on the 0 and 2% slopes, suggested the stimulation of nutrient cycles by tree roots, which improve the conditions for soil microorganisms in carrying out their metabolic activity. In the 6% slope and, in particular, in the mineral fertilizer treatment, soil metabolism was lower as suggested by the dehydrogenase activity which was 50% lower than that found in the 0 and 2% slopes, this seemed to be related to a slowdown in the nutrient cycling and organic carbon metabolism. However, on this slope, in both mineral and organic treatments, a significant stimulation of hydrolytic enzyme activities and an improvement of soil structure (reduction of bulk density of about 10% and increase in total shrinkage from 20 to 60%) were observed with plants compared to the control soil. The combination of organic fertilization and almond trees resulted effective, also in the highest slope, in mitigating the degradation processes through the improvement of chemico-nutritional, biochemical and physical soil properties.

Bacterial methane in the Atzbach-Schwanenstadt gas field (upper Austrian Molasse Basin), Part II: Retracing gas generation and filling history by mass balancing of organic carbon conversion applying hydrogeochemical modelling

In the Austrian Molasse Basin bacterial methane gas accumulations occur in Upper Oligocene to early Miocene deepwater clastic sediments. Gas is produced from the Upper Puchkirchen Formation (Aquitanian) in the Atzbach-Schwanenstadt gas field. The diagenetic pathway of the reservoir cements was controlled by the conversion of metabolizable organic carbon incorporated in the fine-grained sediments. These pathways have been retraced by hydrogeochemical modelling the redox-conversion of metabolizable organic carbon. This approach unravels the relative timing of the coupled processes gas generation and precipitation/dissolution of cements. The labile organic material was decomposed by fermentation and subsequent CO 2 reduction. CO 2 released via these reactions was nearly completely fixed as carbonate cement. Methane generated during early diagenesis (10 s to max., 100 m sediment depth) was dissolved in pore water until saturation. After exsolution as a free gas phase, methane could have been fixed as hydrate within pore space due to the prevailing paleoceanographic conditions (sediment/water interface ∼1000 mbsl; ∼4 °C). The temperature increase in consequence of the rapid basin subsidence and high sedimentation rates led to the decomposition of the hydrates and to charging of the reservoir by methane still during the Aquitanian. A further consequence of hydrate decomposition was dilution of pore water salinity. According to the results, the presented approach offers (a) a tool to retrace the bacterial methane potential by analysis of diagenetic cement as a quantitative indicator, and (b) to predict the interaction between porosity development and reservoir charging by methane. Additionally, (c) gas field water salinity and hydrochemistry may be applied in similar architectural elements of deepwater channels as tracers for fossil gas hydrate formation as low chloride concentrations are result of sediment compaction and dilution by pure H 2O due to gas hydrate dissociation.

Root exudates stimulate the uptake and metabolism of organic carbon in germinating spores of Glomus intraradices

* Root exudates play a key role during the presymbiotic growth phase and have been shown to stimulate hyphal branching and the catabolic metabolism of arbuscular mycorrhizal (AM) fungal spores. * Here, the effect of root exudates on presymbiotic growth, uptake of exogenous carbon and transcript levels for genes putatively involved in the carbon metabolism of germinating spores were determined. * Crude root exudates led to a slight acceleration of spore germination, increased germ tube branching and stimulated uptake and catabolic metabolism of acetate, and to a greater extent of glucose, but had no effect on gene expression. By contrast, partially purified root exudates increased the transcript levels of acyl-CoA dehydrogenase (ss-oxidation of fatty acids to acetyl-CoA), malate synthase (glyoxylate cycle) and glutamine-fructose-6-phosphate aminotransferase (chitin biosynthesis), but did not differ from crude root exudates in their effect on substrate uptake and respiration. The expression of glycogen synthase (glycogen biosynthesis), glucose-6-phosphate dehydrogenase (pentose phosphate pathway) and neutral trehalase (hydrolysis of trehalose) were only marginally or not affected by root exudates. * Root exudates have an effect on both membrane activity and gene expression and the results are discussed in relation to the catabolic and anabolic metabolism of spores during presymbiotic growth.