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Microbial Processes (microbial + process)
Selected AbstractsThermophilic anaerobes in Arctic marine sediments induced to mineralize complex organic matter at high temperatureENVIRONMENTAL MICROBIOLOGY, Issue 4 2010Casey Hubert Summary Marine sediments harbour diverse populations of dormant thermophilic bacterial spores that become active in sediment incubation experiments at much higher than in situ temperature. This response was investigated in the presence of natural complex organic matter in sediments of two Arctic fjords, as well as with the addition of freeze-dried Spirulina or individual high-molecular-weight polysaccharides. During 50°C incubation experiments, Arctic thermophiles catalysed extensive mineralization of the organic matter via extracellular enzymatic hydrolysis, fermentation and sulfate reduction. This high temperature-induced food chain mirrors sediment microbial processes occurring at cold in situ temperatures (near 0°C), yet it is catalysed by a completely different set of microorganisms. Using sulfate reduction rates (SRR) as a proxy for organic matter mineralization showed that differences in organic matter reactivity determined the extent of the thermophilic response. Fjord sediments with higher in situ SRR also supported higher SRR at 50°C. Amendment with Spirulina significantly increased volatile fatty acids production and SRR relative to unamended sediment in 50°C incubations. Spirulina amendment also revealed temporally distinct sulfate reduction phases, consistent with 16S rRNA clone library detection of multiple thermophilic Desulfotomaculum spp. enriched at 50°C. Incubations with four different fluorescently labelled polysaccharides at 4°C and 50°C showed that the thermophilic population in Arctic sediments produce a different suite of polymer-hydrolysing enzymes than those used in situ by the cold-adapted microbial community. Over time, dormant marine microorganisms like these are buried in marine sediments and might eventually encounter warmer conditions that favour their activation. Distinct enzymatic capacities for organic polymer degradation could allow specific heterotrophic populations like these to play a role in sustaining microbial metabolism in the deep, warm, marine biosphere. [source] Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, MexicoENVIRONMENTAL MICROBIOLOGY, Issue 1 2009Mya Breitbart Summary Ancient biologically mediated sedimentary carbonate deposits, including stromatolites and other microbialites, provide insight into environmental conditions on early Earth. The primary limitation to interpreting these records is our lack of understanding regarding microbial processes and the preservation of geochemical signatures in contemporary microbialite systems. Using a combination of metagenomic sequencing and isotopic analyses, this study describes the identity, metabolic potential and chemical processes of microbial communities from living microbialites from Cuatro Ciénegas, Mexico. Metagenomic sequencing revealed a diverse, redox-dependent microbial community associated with the microbialites. The microbialite community is distinct from other marine and freshwater microbial communities, and demonstrates extensive environmental adaptation. The microbialite metagenomes contain a large number of genes involved in the production of exopolymeric substances and the formation of biofilms, creating a complex, spatially structured environment. In addition to the spatial complexity of the biofilm, microbial activity is tightly controlled by sensory and regulatory systems, which allow for coordination of autotrophic and heterotrophic processes. Isotopic measurements of the intracrystalline organic matter demonstrate the importance of heterotrophic respiration of photoautotrophic biomass in the precipitation of calcium carbonate. The genomic and stable isotopic data presented here significantly enhance our evolving knowledge of contemporary biomineralization processes, and are directly applicable to studies of ancient microbialites. [source] Soil factors controlling the toxicity of copper and zinc to microbial processes in Australian soilsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 4 2007Kris Broos Abstract Two soil microbial processes, substrate-induced nitrification (SIN) and substrate-induced respiration (SIR), were measured in the topsoils of 12 Australian field trials that were amended separately with increasing concentrations of ZnSO4 or CuSO4. The median effect concentration (EC50) values for Zn and Cu based on total metal concentrations varied between 107 and 8,298 mg kg,1 for Zn and 108 and 2,155 mg kg,1 Cu among soils. The differences in both Zn and Cu toxicity across the 12 soils were not explained by either the soil solution metal concentrations or CaCl2 -extractable metal concentrations, because the variation in the EC50 values was larger than those using total concentrations. Toxicity of Zn and Cu decreased with increasing soil pH for SIN. For Cu, also increasing cation exchange capacity (CEC) and percent clay decreased the toxicity towards SIN. In contrast to SIN, soil pH had no significant effect on toxicity values of SIR. Significant relationships were found between the EC50 values for SIR and background Zn and CEC for Zn, and percent clay and log CEC for Cu. Relationships such as those developed in this study will permit Australian environmental regulation to move from single-value national soil quality guidelines to soil-specific quality guidelines and permit soil-specific risk assessments to be undertaken. [source] Impact of animal waste lagoon effluents on chlorpyrifos degradation in soilsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 12 2000Xinjiang Huang Abstract Animal-derived lagoon effluents are a good source of inorganic nutrients and organic matter; however, they may impact the degradation and transport of soil-applied pesticides. The degradation of chlorpyrifos in poultry-, swine-, and cow-derived effluents and effluent-soil matrices were studied using batch and column incubation studies. Chlorpyrifos was degraded by aerobic microbial processes in animal-derived lagoon effluents. Microbial community analysis by denaturing gradient gel electrophoresis of polymerase chain reaction-amplified 16S ribosomal ribonucleic acid genes showed that a single band became dominant in effluent during chlorpyrifos degradation. In soils, both biotic and abiotic degradation contributed significantly to the overall dissipation of chlorpyrifos. Large differences in degradation rates were observed between soils, with the fastest rate observed in soil with higher pH and cation-exchange capacity. Effluents appeared to have only a minor effect on chlorpyrifos degradation in soils, although effluent-induced increases in soil-solution pH over time may enhance hydrolysis by a few percent in low-pH soils. Soil properties, not effluent properties, appear to control chlorpyrifos degradation under laboratory conditions; however, the impact on changes in soil properties and microbial ecology with long-term effluent irrigation warrants further investigation. [source] Amino acid 15N in long-term bare fallow soils: influence of annual N fertilizer and manure applicationsEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 4 2008R. Bol Summary Long-term dynamics of amino acids (AAs), from a bare fallow soil experiment (established in 1928 at INRA-Versailles, France), were examined in unamended control (Con) plots and plots treated with ammonium sulphate (Amsul), ammonium nitrate (Amnit), sodium nitrate (Nanit) or with animal manure (Man). Topsoil (0,25 cm) from 1929, 1963 and 1997 was analysed for C, N and 15N content and distribution of 18 amino acids recovered after acid hydrolysis with 6 m HCl. With time, soil N, C and AA content were reduced in Con, Amsul, Amnit and Nanit, but increased in Man. However, the absolute N loss was 3,11 times larger in Man than Nanit, Amsul, Amnit and Con, due to the much higher N annual inputs applied to Man. From 1929 to 1997 in Con, Amsul, Amnit and Nanit the whole soil and non-hydrolysable-N pool ,15N increased associated with the loss of N (indicative of Rayleigh 15N/14N fractionation). No ,15N change from 1929 to 1997 was found in the hydrolysable AA-N (HAN) pool. Fertilizer N inputs aided stabilization of soil AA-N, as AA half-life in the mineral N fertilizer treatments increased from 34 years in 1963 to 50 years in 1997. The ,15N values of alanine and leucine reflected both source input and 15N/14N fractionation effects in soils. The ,15N increase of ornithine (,6,) was similar to the whole soil. The ,15N change of phenylalanine in Con (decrease of 7,) was related to its proportional loss since 1929, whereas for Amsul, Amnit, Nanit and Man it was associated with isotope effects caused by the fertilizer inputs. However, the soil ,15N value of most individual amino acids (IAAs) did not significantly change over nearly 70 years, even with mineral or organic N inputs. We conclude for these bare fallow systems that: (i) ,15N changes in the whole soil and non-hydrolysable AA pool were solely driven by microbial processes and not by the nature of fertilizer inputs, and (ii) without plant inputs, the ,15N of the HAN pool and (most) IAAs may reflect the influence of plant,soil interactions from the previous (arable cropping) rather than present (fallow) land use on these soil ,15N values. [source] Summer drought decreases soil fungal diversity and associated phenol oxidase activity in upland Calluna heathland soilFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Hannah Toberman Abstract Natural moisture limitation during summer drought can constitute a stress for microbial communities in soil. Given globally predicted increases in drought frequency, there is an urgent need for a greater understanding of the effects of drought events on soil microbial processes. Using a long-term field-scale drought manipulation experiment at Clocaenog, Wales, UK, we analysed fungal community dynamics, using internal transcribed spacer-denaturing gradient gel electrophoresis (DGGE), over a 1-year period in the 6th year of drought manipulation. Ambient seasonality was found to be the dominant factor driving variation in fungal community dynamics. The summer drought manipulation resulted in a significant decline in the abundance of dominant fungal species, both independently of, and in interaction with, this seasonal variation. Furthermore, soil moisture was significantly correlated with the changes in fungal diversity over the drought manipulation period. While the relationship between species diversity and functional diversity remains equivocal, phenol oxidase activity was decreased by the summer drought conditions and there was a significant correlation with the decline of DGGE band richness among the most dominant fungal species during the drought season. Climatically driven events such as droughts may have significant implications for fungal community diversity and therefore, have the potential to interfere with crucial ecosystem processes, such as organic matter decomposition. [source] Diel variation in surface and subsurface microbial activity along a gradient of drying in an Australian sand-bed streamFRESHWATER BIOLOGY, Issue 10 2003Cecile Claret Summary 1. Microbes play key roles in nutrient transformation and organic matter mineralisation in the hyporheic zone but their short-term responses to diel variations in discharge and temperature are unknown. Rates of microbial esterase activity were hypothesised to vary vertically and along a gradient of moisture in a drying sand-bed stream where discharge fluctuated daily in response to evapotranspiration. 2. At ,fully saturated', ,moist' and ,dry' locations in three sites along a drying Australian sand-bed stream, microbial activity at three depths (surface, 10 and 30 cm) was assessed using fluorescein diacetate hydrolysis. Samples were collected in mid-summer in the late afternoon and again at dawn to assess diel variation in hydrolytic activity at each site and depth. Data loggers tracked diel variations in temperature at each depth. 3. Hydrolytic activity was up to 10-fold greater in the surface sediments in late afternoon than at dawn in all habitats, and was correlated with surface sediment temperature. Diel differences in activity were not detected at 10 cm, although daily thermal cycles were evident at this depth. Unexpectedly, activity was marginally higher at dawn at 30 cm in all habitats, perhaps reflecting lags in temperature at that depth. 4. Overall, microbial activity declined with depth, strongly correlated with vertical trends in total organic matter and concentrations of dissolved phosphorus. Particulate organic matter, probably buried during a flood 35 days earlier, appeared largely responsible for these vertical trends. On the other hand, there was little evidence for hydrological exchange between much of the hyporheic zone and the surface stream, implying that processes in the subsurface zone of this stream are effectively isolated during baseflow in mid-summer. 5. Diel cycles of wetting and drying in the moist habitats did not enhance esterase activity relative to the dry or fully saturated habitats. Sediment moisture was not correlated with microbial activity, and mats of senescent algae appeared to inhibit water loss from surface sediments in the moist habitat. In this sand-bed stream, local diel fluctuations in water level appear to have less influence on microbial activity and mineralisation of organic matter in the sediments than occasional floods that bury leaf litter and renew many hyporheic zone functions. Subreach-scale processes seem to be the major driving force of microbial processes and nutrient cycling in this sand-bed river. [source] Transfer of hydrocarbons from natural seeps to the water column and atmosphereGEOFLUIDS (ELECTRONIC), Issue 2 2002I. R. MacDonald Abstract Results from surface geochemical prospecting, seismic exploration and satellite remote sensing have documented oil and gas seeps in marine basins around the world. Seeps are a dynamic component of the carbon cycle and can be important indicators for economically significant hydrocarbon deposits. The northern Gulf of Mexico contains hundreds of active seeps that can be studied experimentally with the use of submarines and Remotely Operated Vehicles (ROV). Hydrocarbon flux through surface sediments profoundly alters benthic ecology and seafloor geology at seeps. In water depths of 500,2000 m, rapid gas flux results in shallow, metastable deposits of gas hydrate, which reduce sediment porosity and affect seepage rates. This paper details the processes that occur during the final, brief transition , as oil and gas escape from the seafloor, rise through the water and dissolve, are consumed by microbial processes, or disperse into the atmosphere. The geology of the upper sediment column determines whether discharge is rapid and episodic, as occurs in mud volcanoes, or more gradual and steady, as occurs where the seep orifice is plugged with gas hydrate. In both cases, seep oil and gas appear to rise through the water in close proximity instead of separating. Chemical alteration of the oil is relatively minor during transit through the water column, but once at the sea surface its more volatile components rapidly evaporate. Gas bubbles rapidly dissolve as they rise, although observations suggest that oil coatings on the bubbles inhibit dissolution. At the sea surface, the floating oil forms slicks, detectable by remote sensing, whose origins are laterally within ,1000 m of the seafloor vent. This contradicts the much larger distance predicted if oil drops rise through a 500 m water column at an expected rate of ,0.01 m s,1 while subjected to lateral currents of ,0.2 m s,1 or greater. It indicates that oil rises with the gas bubbles at speeds of ,0.15 m s,1 all the way to the surface. [source] Enhanced litter input rather than changes in litter chemistry drive soil carbon and nitrogen cycles under elevated CO2: a microcosm studyGLOBAL CHANGE BIOLOGY, Issue 2 2009LINGLI LIU Abstract Elevated CO2 has been shown to stimulate plant productivity and change litter chemistry. These changes in substrate availability may then alter soil microbial processes and possibly lead to feedback effects on N availability. However, the strength of this feedback, and even its direction, remains unknown. Further, uncertainty remains whether sustained increases in net primary productivity will lead to increased long-term C storage in soil. To examine how changes in litter chemistry and productivity under elevated CO2 influence microbial activity and soil C formation, we conducted a 230-day microcosm incubation with five levels of litter addition rate that represented 0, 0.5, 1.0, 1.4 and 1.8 × litterfall rates observed in the field for aspen stand growing under control treatments at the Aspen FACE experiment in Rhinelander, WI, USA. Litter and soil samples were collected from the corresponding field control and elevated CO2 treatment after trees were exposed to elevated CO2 (560 ppm) for 7 years. We found that small decreases in litter [N] under elevated CO2 had minor effects on microbial biomass carbon, microbial biomass nitrogen and dissolved inorganic nitrogen. Increasing litter addition rates resulted in linear increase in total C and new C (C from added litter) that accumulated in whole soil as well as in the high density soil fraction (HDF), despite higher cumulative C loss by respiration. Total N retained in whole soil and in HDF also increased with litter addition rate as did accumulation of new C per unit of accumulated N. Based on our microcosm comparisons and regression models, we expected that enhanced C inputs rather than changes in litter chemistry would be the dominant factor controlling soil C levels and turnover at the current level of litter production rate (230 g C m,2 yr,1 under ambient CO2). However, our analysis also suggests that the effects of changes in biochemistry caused by elevated CO2 could become significant at a higher level of litter production rate, with a trend of decreasing total C in HDF, new C in whole soil, as well as total N in whole soil and HDF. [source] Initial cultivation of a temperate-region soil immediately accelerates aggregate turnover and CO2 and N2O fluxesGLOBAL CHANGE BIOLOGY, Issue 8 2006A. STUART GRANDY Abstract The immediate effects of tillage on protected soil C and N pools and on trace gas emissions from soils at precultivation levels of native C remain largely unknown. We measured the response to cultivation of CO2 and N2O emissions and associated environmental factors in a previously uncultivated U.S. Midwest Alfisol with C concentrations that were indistinguishable from those in adjacent late successional forests on the same soil type (3.2%). Within 2 days of initial cultivation in 2002, tillage significantly (P=0.001, n=4) increased CO2 fluxes from 91 to 196 mg CO2 -C m,2 h,1 and within the first 30 days higher fluxes because of cultivation were responsible for losses of 85 g CO2 -C m,2. Additional daily C losses were sustained during a second and third year of cultivation of the same plots at rates of 1.9 and 1.0 g C m,2 day,1, respectively. Associated with the CO2 responses were increased soil temperature, substantially reduced soil aggregate size (mean weight diameter decreased 35% within 60 days), and a reduction in the proportion of intraaggregate, physically protected light fraction organic matter. Nitrous oxide fluxes in cultivated plots increased 7.7-fold in 2002, 3.1-fold in 2003, and 6.7-fold in 2004 and were associated with increased soil NO3, concentrations, which approached 15 ,g N g,1. Decreased plant N uptake immediately after tillage, plus increased mineralization rates and fivefold greater nitrifier enzyme activity, likely contributed to increased NO3, concentrations. Our results demonstrate that initial cultivation of a soil at precultivation levels of native soil C immediately destabilizes physical and microbial processes related to C and N retention in soils and accelerates trace gas fluxes. Policies designed to promote long-term C sequestration may thus need to protect soils from even occasional cultivation in order to preserve sequestered C. [source] Effects of an experimental drought on soil emissions of carbon dioxide, methane, nitrous oxide, and nitric oxide in a moist tropical forestGLOBAL CHANGE BIOLOGY, Issue 5 2004Eric A. Davidson Abstract Changes in precipitation in the Amazon Basin resulting from regional deforestation, global warming, and El Niño events may affect emissions of carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), and nitric oxide (NO) from soils. Changes in soil emissions of radiatively important gases could have feedback implications for regional and global climates. Here we report results of a large-scale (1 ha) throughfall exclusion experiment conducted in a mature evergreen forest near Santarém, Brazil. The exclusion manipulation lowered annual N2O emissions by >40% and increased rates of consumption of atmospheric CH4 by a factor of >4. No treatment effect has yet been detected for NO and CO2 fluxes. The responses of these microbial processes after three rainy seasons of the exclusion treatment are characteristic of a direct effect of soil aeration on denitrification, methanogenesis, and methanotrophy. An anticipated second phase response, in which drought-induced plant mortality is followed by increased mineralization of C and N substrates from dead fine roots and by increased foraging of termites on dead coarse roots, has not yet been detected. Analyses of depth profiles of N2O and CO2 concentrations with a diffusivity model revealed that the top 25 cm soil is the site of most of the wet season production of N2O, whereas significant CO2 production occurs down to 100 cm in both seasons, and small production of CO2 occurs to at least 1100 cm depth. The diffusivity-based estimates of CO2 production as a function of depth were strongly correlated with fine root biomass, indicating that trends in belowground C allocation may be inferred from monitoring and modeling profiles of H2O and CO2. [source] Characterization and Origin of Dissolved Organic Carbon in Yegua Ground Water in Brazos County, TexasGROUND WATER, Issue 5 2001Joyanto Routh Dissolved organic carbon (DOC) concentrations in five shallow (< 20 m) and three deeper wells (27 to 30 m) in the Eocene Yegua Formation (Brazos County in east-central Texas) ranged from 92 to 500 ,m. Characterization of high, intermediate, and low molecular weight DOC fractions (HMW > 3000 amu, IMW 1000 to 3000 amu, and LMW 500 to 1000 amu) and combined neutral sugar analyses provide information on organic matter sources in the Yegua aquifers. Combined neutral sugars ranged in concentration from 0.6 to 2.7 ,mol/L and comprised 0.8% to 6.7% of DOC in ground water. Glucose was the most abundant neutral sugar, followed by xylose and galactose, arabinose, mannose, rhamnose, and fucose. These combined neutral sugars were more diagenetically altered in shallow, oxic ground water as indicated by high mole % fucose + rhamnose and low neutral sugar yield. The precursors for neutral sugars are most probably angiosperm leaves, which show a similar distribution pattern of neutral sugars. Ground water DOC was depleted in 13C relative to soil-zone organic matter (OM) (,16, to ,19,). The ,13C values of bulk DOC and HMW DOC ranged from ,24, to ,32,, whereas LMW and IMW DOC ranged from ,32, to ,34, and ,16, to ,28,, respectively. This variability in ,13C values is probably related to microbial processes and selective preservation of OM. Carbon isotope analyses in bulk and different molecular weight DOC fractions imply a predominantly C3 OM source and a low contribution of soil-zone OM to DOC. [source] Oxygen Controls the Phosphorus Release from Lake Sediments , a Long-Lasting Paradigm in LimnologyINTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 4-5 2008Michael Hupfer Abstract The pioneer works of Einsele, Mortimer, and Ohle on the linking between phosphorus (P) and iron (Fe) cycles seven decades ago created the theoretical basis for a long-standing paradigm among limnologists i.e., ,oxygen controls the P release from sediments'. While many empirical studies as well as strong correlations between oxygen depletion and P release seem to support this paradigm, various field observations, laboratory experiments, and repeated failures of hypolimnetic oxygenation measures cast doubt on its universal validity. The temporal existence of a thin oxidized sediment surface-layer could affect only fluctuations of the temporary P pool at the sediment surface but not the long-term P retention. On longer time scales P release is the imbalance between P sedimentation and P binding capacity of anoxic sediment layers. The P retention of lake sediments strongly depends on sediment characteristics and land use of the catchment. The presence of redox-insensitive P-binding systems such as Al(OH)3 and unreducible Fe(III) minerals can enhance the P retention and completely prevent P release even in case of anoxic conditions. Alternative release mechanisms such as a dissolution of calcium-bound P and decomposition of organic P under both, aerobic and anaerobic conditions, are often more important than the redox driven Fe-coupled P cycle. Additionally, bacteria affect P cycling not only by altering the redox conditions but also by releasing P during mineralization of organic matter and by accumulation and release of bacterial P. Since microbial processes consume oxygen and liberate P it is difficult to distinguish whether oxygen depletion is the result or the cause of P release. Nowadays, the old paradigm is discarded and a paradigm shift takes place. Sedimentary P exchange ought to be considered as a complex process which is mainly determined by the amount and species of settled P as well as their subsequent diagenetic transformation in the sediment. The classical paradigm is only valid in special cases since reality is much more complex than suggested by that paradigm. Everything should be made simple as possible, but not simpler! Albert Einstein (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Pulse dynamics and microbial processes in aridland ecosystemsJOURNAL OF ECOLOGY, Issue 3 2008Scott L. Collins Summary 1Aridland ecosystems cover about one-third of terrestrial environments globally, yet the extent to which models of carbon (C) and nitrogen (N) cycling, developed largely from studies of mesic ecosystems, apply to aridland systems remains unclear. 2Within aridland ecosystems, C and N dynamics are often described by a pulse-reserve model in which episodic precipitation events stimulate biological activity that generate reserves of biomass, propagules and organic matter that prime the ecosystem to respond rapidly to subsequent precipitation events. 3,The role of microbial C and N processing within the pulse-reserve paradigm has not received much study. We present evidence suggesting that fungi play a critical and underappreciated role in aridland soils, including efficient decomposition of recalcitrant C compounds, N-transformations such as nitrification, and nutrient storage and translocation of C and N between plants and biotic soil crusts. While fungi may perform some of these functions in other ecosystems, this ,fungal loop' assumes particular importance in the N cycle in aridlands because water availability imposes even greater restrictions on bacterial activity and physicochemical processes limit accumulation of soil organic matter (SOM). 4We incorporate these findings into a Threshold-Delay Nutrient Dynamics (TDND) model for aridland ecosystems in which plant responses to pulsed precipitation events are mediated by a fungal loop that links C and N cycling, net primary production (NPP) and decomposition in aridland soils. 5Synthesis. Arid ecosystems are highly sensitive to global environmental change including N deposition and altered precipitation patterns; yet, models from mesic ecosystems do not adequately apply to aridland environments. Our ,fungal loop' N cycle model integrates spatial structure with pulse dynamics and extends the pulse-reserve paradigm to include the key role of microbial processes in aridland ecosystem dynamics. [source] FOREST-RIVER INTERACTIONS: INFLUENCE ON HYPORHEIC DISSOLVED ORGANIC CARBON CONCENTRATIONS IN A FLOODPLAIN TERRACE,JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION, Issue 3 2002Sandra M. Clinton ABSTRACT: In large floodplain rivers, hyporheic (subsurface) flow-paths transfer nutrients from productive riparian terraces to oligotrophic off-channel habitats. Because dissolved organic carbon (DOC) fuels microbial processes and hyporheic microorganisms represent the first stage of retention and transformation of these nutrients, understanding DOC flux can provide information on the constraints of microbial metabolism in the hyporheic zone of rivers. We monitored hydrology, physicochemical indicators, and dissolved organic carbon (DOC) dynamics during low and high discharge periods in the hyporheic zone of a riparian terrace on the Queets River, Washington, to understand what processes control the supply of carbon to subsurface microbial communities. As discharge increased, terrace hyporheic flowpaths changed from parallel to focused, and the location of surface water inputs to the terrace shifted from the terrace edge to head. Overall, DOC concentrations decreased along hyporheic flowpaths; however, concentrations at points along the flowpaths varied with position along the head gradient and age of the overlying vegetation. We estimated that there is insufficient DOC in adverting surface water to support hyporheic microbial metabolism in this riparian terrace. These trends indicate that there are additional carbon sources to the subsurface water, and we conclude that DOC is leaching from overlying riparian soils within the forest patches. Thus, subsurface DOC concentrations reflect a balance between surface water inputs, metabolic uptake, and allochthonous inputs from forest soils. [source] Recruitment of Heliozoa, rhizopods and rotifers from the sediments of an extremely acidic lake during spring and early summerLAKES & RESERVOIRS: RESEARCH AND MANAGEMENT, Issue 2 2008Elanor M. Bell Abstract The goal of this study was to investigate the recruitment of zooplankton from the littoral sediment of Lake 111, an acidic lake in north-east Germany, in April (spring) and June (early summer), and its role in coupling the benthos and the pelagic. Maximum heliozoan and rhizopod recruitment occurred in early summer from sediment cores incubated at ambient water temperatures (20°C). Conversely, recruitment of the rotifer Cephalodella sp. was highest in spring at ambient spring temperatures of 12°C. A combination of passive and active recruitment processes is likely responsible. The seasonal abiotic and biotic sediment characteristics were relatively constant and therefore not likely responsible for the observed temporal recruitment pattern. The sediment water and carbon content ranged from 20 to 50% (mean = 29 ± 6% standard deviation) and 2,12% (mean = 5 ± 2% standard deviation), respectively. Similarly, there was little variation in the chlorophyll- a (mean = 0.2 ± 0.2 µg Chl- a g,1 dry weight , 6.1 ± 3.9 mg Chl- a m,2). The in situ sediment bacterial density (0.82 × 109 ± 0.26 × 109 g,1 dry weight , 1.01 × 109 ± 0.34 × 109 cells cm,3) was high. In contrast, the abundance of zoobenthos and their resting stages was low (< 25 individuals cm,3, and mean of 90 ± 75 cysts cm,3, respectively), with no temporal pattern being observed. Temperature was the only abiotic factor influencing recruitment. This study suggests that, even in relatively young, chemically extreme lakes, the benthos can play an important role in whole lake microbial processes and zooplankton community composition. Such benthic repositories of resting stages potentially provide protection against adverse environmental changes. [source] Spatial variability in the mineralisation of the phenylurea herbicide linuron within a Danish agricultural field: multivariate correlation to simple soil parameters,PEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 9 2005Jim Rasmussen Abstract The spatial variability in the mineralisation rate of linuron [N -(3,4-dichlorophenyl)- N,-methoxy- N,-methylurea] was studied within a previously treated Danish agricultural field by sampling soils from eleven different plots randomly distributed across an area of 20 × 20 m. The soils were characterised with respect to different abiotic and biotic properties including moisture content, organic matter content, pH, nutrient content, bacterial biomass, potential for mineralisation of MCPA [(4-chloro-2-methylphenoxy)acetic acid] and linuron. Five soils had a potential for mineralisation of linuron, with 5,15% of the added [ring -U- 14C]linuron metabolised to 14CO2 within 60 days at 10 °C, while no extensive mineralisation of linuron was observed in the six remaining soils within this period. A TLC analysis of the methanol-extractable residues showed no development of 14C-labelled metabolites from linuron in any of the samples. Multivariate analysis was conducted to elucidate relationships between the intrinsic properties of single soil samples and initial rate of linuron mineralisation. The analysis indicated that important soil parameters in determining the spatial heterogeneity included the Ctotal/Ntotal ratio, pH and the water-extractable potassium contents, with the first of these highly negatively correlated and the last two highly positively correlated to the initial linuron mineralisation rate. This study shows that enhanced biodegradation of linuron may develop with successive field treatments, but that considerable in-field spatial heterogeneity in the degradation rate still exists. Combined with a parallel enrichment study focused on the underlying microbial processes, the present results suggest that intrinsic soil properties affect the linuron-metabolising bacterial population and thereby determine the spatial variability in the linuron mineralisation activity. Copyright © 2005 Society of Chemical Industry [source] Metagenomic studies reveal the critical and wide-ranging ecological importance of uncultivated archaea: the role of ammonia oxidizersBIOESSAYS, Issue 1 2007Ricardo Cavicchioli Microbial genome sequencing has entered a new phase, where DNA sequence information is gathered from entire microbial communities (metagenomics or environmental genomics) rather than from individual microorganisms. By providing access to the genetic material of vast numbers of organisms, most of which are organisms that have never been isolated or cultivated, a new level of insight is being gained into the diversity and extent of the microbial processes that are presently occuring in environmental communities. By extending metagenomic-based approaches to the study of very complex and methodologically recalcitrant soil environments, a recent study has found that ammonia-oxidizing archaea are more abundant in many soils than bacteria.1 These findings not only highlight the undoubtedly critical yet unknown roles that archaea play in global nutrient cycles but illustrate the importance of genomic studies for informing us about the functional capacity of life on Earth. BioEssays 29: 11,14, 2007. © 2006 Wiley Periodicals, Inc. [source] | ||||||||||||||||