Substrate Input Research Articles

Substrate quality affects microbial‐ and enzyme activities in rooted soil

AbstractThe rhizosphere reflects a sphere of high substrate input by means of rhizodeposits. Active microorganisms and extracellular enzymes are known to be responsible for substrate utilization in soil, especially in rooted soil. We tested for microbial‐ and enzyme activities in arable soil, in order to investigate the effects of continuous input of easily available organics (e.g., root‐exudates) to the microbial community. In a field experiment with maize, rooted and root‐free soil were analyzed and rhizosphere processes were linked to microbial activity indicators such as specific microbial growth rates and kinetics of six hydrolytic extracellular enzymes: β‐glucosidase, β‐cellobiohydrolase, β‐xylosidase, acid phosphatase, leucine‐ and tyrosine‐aminopeptidase.Higher potential activities of leucine‐aminopeptidase (2‐fold) for rooted vs. root‐free soil suggested increased costs of enzyme production, which retarded the specific microbial growth rates. Total microbial biomass determined by the substrate‐induced respiration technique and dsDNA extraction method was 23% and 42% higher in the rooted surface‐layer (0–10 cm) compared to the root‐free soil, respectively. For the rooted soil, potential enzyme activities of β‐glucosidase were reduced by 23% and acid phosphatase by 25%, and increased by 300% for β‐cellobiohydrolase at 10–20 cm depth compared to the surface‐layer. The actively growing microbial biomass increased by the 17‐fold in rooted soil in the 10–20 cm layer compared to the upper 10 cm. Despite the specific microbial growth rates showing no changes in the presence of roots, these rates decreased by 42% at 10–20 cm depth compared to the surface‐layer. This suggests the dominance in abundances of highly active but slower growing microbes with depth, reflecting also their slower turnover. Shifts in microbial growth strategy, upregulation of enzyme production and increased microbial respiration indicate strong root effects in maize planted soil.

Metabolic flux prediction in cancer cells with altered substrate uptake.

Proliferating cells, such as cancer cells, are known to have an unusual metabolism, characterized by an increased rate of glycolysis and amino acid metabolism. Our understanding of this phenomenon is limited but could potentially be used in order to develop new therapies. Computational modelling techniques, such as flux balance analysis (FBA), have been used to predict fluxes in various cell types, but remain of limited use to explain the unusual metabolic shifts and altered substrate uptake in human cancer cells. We implemented a new flux prediction method based on elementary modes (EMs) and structural flux (StruF) analysis and tested them against experimentally measured flux data obtained from (13)C-labelling in a cancer cell line. We assessed the quality of predictions using different objective functions along with different techniques in normalizing a metabolic network with more than one substrate input. Results show a good correlation between predicted and experimental values and indicate that the choice of cellular objective critically affects the quality of predictions. In particular, lactate gives an excellent correlation and correctly predicts the high flux through glycolysis, matching the observed characteristics of cancer cells. In contrast with FBA, which requires a priori definition of all uptake rates, often hard to measure, atomic StruFs (aStruFs) are able to predict uptake rates of multiple substrates.

Fresh carbon input differentially impacts soil carbon decomposition across natural and managed systems.

The amount of fresh carbon input into soil is experiencing substantial changes under global change. It is unclear what will be the consequences of such input changes on native soil carbon decomposition across ecosystems. By synthesizing data from 143 experimental comparisons, we show that, on average, fresh carbon input stimulates soil carbon decomposition by 14%. The response was lower in forest soils (1%) compared with soils from other ecosystems (> 24%), and higher following inputs of plant residue-like substrates (31%) compared to root exudate-like substrates (9%). The responses decrease with the baseline soil carbon decomposition rate under no additional carbon input, but increase with the fresh carbon input rate. The rates of these changes vary significantly across ecosystems and with the carbon substrates being added. These findings can be applied to provide robust estimates of soil carbon balance across ecosystems under changing aboveground and belowground inputs as consequence of climate and land management changes.

Influence of organic matters on AsIII oxidation by the microflora of polluted soils.

The global AsIII-oxidizing activity of microorganisms in eight surface soils from polluted sites was quantified with and without addition of organic substrates. The organic substances provided differed by their nature: either yeast extract, commonly used in microbiological culture media, or a synthetic mixture of defined organic matters (SMOM) presenting some common features with natural soil organic matter. Correlations were sought between soil characteristics and both the AsIII-oxidizing rate constants and their evolution in accordance with inputs of organic substrates. In the absence of added substrate, the global AsIII oxidation rate constant correlated positively with the concentration of intrinsic organic matter in the soil, suggesting that AsIII-oxidizing activity was limited by organic substrate availability in nutrient-poor soils. This limitation was, however, removed by 0.08g/L of added organic carbon. In most conditions, the AsIII oxidation rate constant decreased as organic carbon input increased from 0.08 to 0.4g/L. Incubations of polluted soils in aerobic conditions, amended or not with SMOM, resulted in short-term As mobilization in the presence of SMOM and active microorganisms. In contrast, microbial AsIII oxidation seemed to stabilize As when no organic substrate was added. Results suggest that microbial speciation of arsenic driven by nature and concentration of organic matter exerts a major influence on the fate of this toxic element in surface soils.

Winter soil CO2 efflux in two contrasting forest ecosystems on the eastern Tibetan Plateau, China

Significant CO2 fluxes from snow-covered soils occur in cold biomes. However, little is known about winter soil respiration on the eastern Tibetan Plateau of China. We therefore measured winter soil CO2 fluxes and estimated annual soil respiration in two contrasting coniferous forest ecosystems (a Picea asperata plantation and a natural forest). Mean winter soil CO2 effluxes were 1.08 µmol m−2 s−1 in the plantation and 1.16 µmol m−2 s−1 in the natural forest. These values are higher than most reported winter soil CO2 efflux values for temperate or boreal forest ecosystems. Winter soil respiration rates were similar for our two forest ecosystems but mean soil CO2 efflux over the growing season was higher in the natural forest than in the plantation. The estimated winter and annual soil effluxes for the natural forest were 176.3 and 1070.3 g m−2, respectively, based on the relationship between soil respiration and soil temperature, which were 17.2 and 9.7 % greater than their counterparts in the plantation. The contributions of winter soil respiration to annual soil efflux were 15.4 % for the plantation and 16.5 % for the natural forest and were statistically similar. Our results indicate that winter soil CO2 efflux from frozen soils in the alpine coniferous forest ecosystems of the eastern Tibetan Plateau was considerable and was an important component of annual soil respiration. Moreover, reforestation (natural coniferous forests were deforested and reforested with P. asperata plantation) may reduce soil respiration by reducing soil carbon substrate availability and input.

Soil organic matter fractions under different vegetation types in permafrost regions along the Qinghai-Tibet Highway, north of Kunlun Mountains, China

As a key attribute of soil quality, soil organic matter (SOM) and its different fractions play an important role in regulating soil nutrient cycling and soil properties.This study evaluated the soil carbon (C) and nitrogen (N) concentrations in different SOM fractions (light– and heavy fractions, microbial biomass) under different vegetation types and analyzed their influencing factors in continuous permafrost regions along the Qinghai-Tibet Highway in the North of Kunlun Mountains, China. Soil samples were collected in pits under four vegetation types — Alpine swamp meadow (ASM), Alpine meadow (AM), Alpine steppe (AS) and Alpine desert (AD) — at the depth of 0-50 cm. The vegetation coverage was the highest at ASM and AM, followed by AS and AD. The results indicated that the concentrations of light fraction carbon (LFC) and nitrogen (LFN), and microbial biomass carbon (MBC) and nitrogen (MBN) decreased as follows: ASM > AM > AS > AD, with the relatively stronger decrease of LFC, whereas the heavy fraction carbon (HFC) and nitrogen (HFN) concentrations were lower in AS soils than in the AD soils. The relatively higher proportions of LFC/SOC and MBC/SOC in the 0-10 cm depth under the ASM soils are mainly resulted from its higher substrate input and soil moisture content. Correlation analysis demonstrated that aboveground biomass, soil moisture content, soil organic carbon (SOC) and total nitrogen (TN) positively correlated to LFC, LFN, HFC, HFN, MBC and MBN, while pH negatively correlated to LFC, LFN, HFC, HFN, MBC and MBN. There was no relationship between active layer thickness and SOM fractions, except for the LFC. Results suggested that vegetation cover, soil moisture content, and SOC and TN concentrations were significantly correlated with the amount and availability of SOM fractions, while permafrost had less impact on SOM fractions in permafrost regions of the central Qinghai–Tibet Plateau.

Seasonal controls on patterns of soil respiration and temperature sensitivity in a northern mixed deciduous forest following partial-harvesting

Disturbances can alter CO2 efflux from soils (FCO2) by altering the microclimate, structure, and biogeochemical properties of forest ecosystems. Results of prior studies are unclear if and how partial harvesting of northern deciduous forests affects FCO2. These mixed responses may be due to differences in harvesting levels, time since harvest, and the spatial and seasonal heterogeneity of treatment effects and soil properties. To account for this spatio-temporal dependence, we produced subject-level regression models from regular measurements of FCO2 and soil temperatures during the 2010–2012 growing seasons following tree-length (TL) and more intensive biomass (BIO) harvests. In this paper, we compare seasonal and inter-annual post-harvest recovery trends for measured and temperature-corrected soil respiration rates and the sensitivity of soil respiration to temperature (as Q10).FCO2 values from TL/BIO treatments exceeded unharvested controls, recurrently peaking in the autumn (average for TL/BIO: 28%/17%, p⩽0.05) and waning in the summer (14%/10%, not significant). A comparison of measured FCO2 vs. modelled respiration values corrected for temperature differences indicated that higher soil temperatures following canopy thinning accounted for 34–41% of these differences in 2010 but <15% by 2012. Initially lower in 2010, Q10 and summer respiration values for harvested treatments exceeded those of controls by 2012, and despite waning temperature differences, average annual effect sizes corrected for temperature differences did not decline. Autumn and basal respiration rates were correlated with post-harvest fine woody debris volumes in 2010 (r2=0.58/0.57, p=0.01), summer rates in all years decreased with harvested tree basal area (r2=0.43–0.58, p⩽0.05), and the post-harvest basal area of understorey vegetation predicted increasing Q10 effect sizes from 2010 to 2012 (r2=0.81, p⩽0.01). With consideration to studies demonstrating that the contribution of root respiration (RR) to FCO2 is highest in summer, we propose that partial harvesting initially restricts RR and peak summer respiration rates, but compensates for this decline by increasing basal respiration rates and FCO2 through elevated soil temperatures and decomposition rates from canopy thinning and harvest residue substrate inputs (i.e., woody debris and root necromass). During post-harvest recovery, forest understorey regrowth reduces soil temperatures but influences patterns of FCO2 by increasing summer respiration and Q10 values in harvested treatments, likely by increasing RR.

Soil microbial functional diversity and biomass as affected by different thinning intensities in a Chinese fir plantation

Understanding forest management-associated soil microbial changes is central to linking aboveground and belowground forest structures and functions. Thinning is an important and widely used silvicultural treatment to improve the remaining tree growth and stand regeneration, and it has direct and indirect effects on soil microorganisms. However, few previous studies have focused on the response of soil microbial biomass (SMB) and functional diversity to thinning. To study the effect of thinning treatments on the soil microbial community, soils were sampled in autumn, winter, spring, and summer in Chinese fir plantations in Lishui, southeast China at sites with the following thinning intensities: control plots (CK) with no thinning, low-intensity thinning (LIT) sites with 30% of the trees removed, and high-intensity thinning (HIT) sites with 70% of the trees removed. The soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) and Biolog™ Ecoplate (Biolog, Inc., Hayward, CA, USA) substrate use patterns were determined for each sample. Here, we show that the soil microbial functional diversity, MBC and MBN were influenced by the thinning intensity, soil depth and season. Generally, MBC and MBN were higher in the HIT, whereas soil microbial functional diversity, expressed as the Shannon diversity index (SDI), was higher in the LIT. The soil temperature, MBC/MBN, total phosphorus, and total organic carbon/total nitrogen ratio (TOC/TN) explained the most significant variations in the amount of soil microbial community functional diversity. Our study suggests that seasonal variations in microbial properties among the control and different thinning intensity treatments may be caused by differences in the substrate inputs into the soil and by microclimatic variation. To the best of our knowledge, this study is the first to provide evidence for different thinning intensity effects on SMB and functional diversity in a Chinese fir plantation.

Impact of mechanically pre-treated anaerobic digestates on soil properties

The production of biogas by anaerobic digestion results in the production of digestates, which are intended to be used as organic fertilizer in agriculture. However, these anaerobic digestates (AD) - besides having benefits for the nutrient status of soils - are assumed to have adverse consequences for soil properties. It is thus the objective of this study to determine the effects of 30 m³ ha-1 of AD´s on pH, electrical conductivity (EC), and the wetting behavior determined by the Repellency Index (RI) and the contact angle (CA) of a loamy Cambic Luvisol and a sandy Podzol. The AD´s, derived from mechanically pre-treated (grinding/chopping) input substrates (IS) from maize (Zea mays L.) and sugar beet (Beta vulgaris L.) in variable shares (100 %, 80 % / 20 %), were mixed with homogenized (sieved to ≤ 2 mm) soils by stirring. Blending of the AD increased the EC significantly and induced more alkaline conditions; the extent of this change was highly dependent on soil texture. The use of AD derived from ground IS resulted in more hydrophobic conditions compared to AD from chopped IS. This leads in the current study to the conclusion that the mechanical pre-treatment of the IS for anaerobic digestion and also the soil texture are decisive factors controlling both the physicochemical and the hydraulic effects of digestates to the soils.

Metabolic network prediction through pairwise rational kernels.

BackgroundMetabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise classification methods are supervised learning methods used to classify new pair of entities. Some of these classification methods, e.g., Pairwise Support Vector Machines (SVMs), use pairwise kernels. Pairwise kernels describe similarity measures between two pairs of entities. Using pairwise kernels to handle sequence data requires long processing times and large storage. Rational kernels are kernels based on weighted finite-state transducers that represent similarity measures between sequences or automata. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations.ResultsWe create a new family of pairwise kernels using weighted finite-state transducers (called Pairwise Rational Kernel (PRK)) to predict metabolic pathways from a variety of biological data. PRKs take advantage of the simpler representations and faster algorithms of transducers. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We then developed several experiments with PRKs and Pairwise SVM to validate our methods using the metabolic network of Saccharomyces cerevisiae. As a result, when PRKs are used, our method executes faster in comparison with other pairwise kernels. Also, when we use PRKs combined with other simple kernels that include evolutionary information, the accuracy values have been improved, while maintaining lower construction and execution times.ConclusionsThe power of using kernels is that almost any sort of data can be represented using kernels. Therefore, completely disparate types of data can be combined to add power to kernel-based machine learning methods. When we compared our proposal using PRKs with other similar kernel, the execution times were decreased, with no compromise of accuracy. We also proved that by combining PRKs with other kernels that include evolutionary information, the accuracy can also also be improved. As our proposal can use any type of sequence data, genes do not need to be properly annotated, avoiding accumulation errors because of incorrect previous annotations.

Organic matter dynamics in an intensive dairy production system on a Dutch Spodosol

In many studies, possibilities are being explored to adjust farm management to increase or maintain soil organic matter (SOM) contents in agricultural soils. Some options may be conflicting with efficient nutrient (N and P) management, i.e. management aiming at maximum conversion of imported nutrients into exported products (milk and meat in the case of dairy farms). This study explored long term effects of efficient nutrient management on SOM dynamics on an experimental dairy farm with three types of land use: permanent grassland, a 3year grass–3year arable crop rotation (ROTI), and a 3year grass–5year arable crop rotation (ROTII). The arable phase in the crop rotations consisted predominantly of maize. The experimental farm, called ‘De Marke’, is located on a Spodosol with an Anthropic Epipedon in the Netherlands. The study consisted of: i) trend analyses based on data of measured SOM mass percentage (SOM %) from 1989–2010, and ii) simulations of long term (50years) SOM dynamics for four management alternatives. Three alternatives were related to manure digestion: no digestion; ‘mild anaerobic digestion’ (degrading 35% of organic matter) and; ‘strong digestion’ (degrading 70% of organic matter). The fourth management alternative was similar to the first (no digestion) but differed in that no catch crop was grown after maize. The trend analyses showed that SOM % of the 0–0.2m layer was approximately stable under permanent grassland. In ROTI, SOM % decreased on average by 0.04y−1 and in ROTII by 0.03y−1. The decline did not slow down over time. SOM decline was more severe on plots with relatively high initial SOM %. Decomposition was described using a mono-component model with a time dependent relative decomposition rate. Decomposition rates in the rotations with arable crops were not higher than those for permanent grassland indicating that tillage did not affect decomposition rate and that SOM dynamics were dominated by the quantity and quality of the substrate input. Simulations indicated that in the long term, decline of SOM must be expected both under arable crop–grassland rotations and under permanent grassland, even in the case of permanent grassland receiving undigested manure. Our results further indicate that strong manure digestion puts pressure on future SOM levels suggesting a trade-off with bio-energy production, and that the contribution of a catch crop to long term SOM is marginal.

Phosphorus availability and soil microbial activity in a 3 year field experiment amended with digested dairy slurry

The application of biogas residues to agricultural fields is important for nutrient cycling. A 3 year field experiment was conducted to assess the phosphorus (P) fertilizer value of digestate from biogas production, taking into account soil microbial activity. The input substrate (inputS) and digested substrate (digestS) from a biogas plant using dairy slurry, maize silage and wheat corn, were applied at a rate of 30 m³ ha−1 annually. For control, mineral N and K, but no P, were applied in equal amounts with the biogas substrates. Maize was cultivated every year, and the biomass yield and P and N uptake were determined. Soil samples were collected on different sampling dates, and the P contents, pH, organic matter contents and enzyme activity were analyzed. The CO2 efflux was measured biweekly using a portable soil respiration chamber (EGM 4). After 3 years, the P and N uptake increased by 25% in the digestS treatment compared with that of the control but did not differ from that of the inputS treatment. The plant-available P contents were also higher in the inputS- and digestS-amended soil. The fertilizer application did not influence the organic matter content but did influence the enzyme activity in soil. Averaging of all the sampling dates in 2010 and 2011, the activities of dehydrogenase and alkaline phosphatase were 50% lower in the soils that were amended with digestS compared with inputS. However, the CO2 efflux from the soil surface was the same for the inputS and digestS treatments. Our results indicate that the anaerobic digestion of substrates does not affect the plant P uptake but the performance of soil microorganisms.

Establishment of macro-aggregates and organic matter turnover by microbial communities in long-term incubated artificial soils

The study of interactions between minerals, organic matter (OM) and microorganisms is essential for the understanding of soil functions such as OM turnover. Here, we present an interdisciplinary approach using artificial soils to study the establishment of the microbial community and the formation of macro-aggregates as a function of the mineral composition by using artificial soils. The defined composition of a model system enables to directly relate the development of microbial communities and soil structure to the presence of specific constituents. Five different artificial soil compositions were produced with two types of clay minerals (illite, montmorillonite), metal oxides (ferrihydrite, boehmite) and charcoal incubated with sterile manure and a microbial community derived from a natural soil. We used the artificial soils to analyse the response of these model soil systems to additional sterile manure supply (after 562 days). The artificial soils were subjected to a prolonged incubation period of more than two years (842 days) in order to take temporally dynamic processes into account. In our model systems with varying mineralogy, we expected a changing microbial community composition and an effect on macro-aggregation after OM addition, as the input of fresh substrate will re-activate the artificial soils. The abundance and structure of 16S rRNA gene and internal transcribed spacer (ITS) fragments amplified from total community DNA were studied by quantitative real-time PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE), respectively. The formation of macro-aggregates (>2 mm), the total organic carbon (OC) and nitrogen (N) contents, the OC and N contents in particle size fractions and the CO2 respiration were determined. The second manure input resulted in higher CO2 respiration rates, 16S rRNA gene and ITS copy numbers, indicating a stronger response of the microbial community in the matured soil-like system. The type of clay minerals was identified as the most important factor determining the composition of the bacterial communities established. The additional OM and longer incubation time led to a re-formation of macro-aggregates which was significantly higher when montmorillonite was present. Thus, the type of clay mineral was decisive for both microbial community composition as well as macro-aggregation, whereas the addition of other components had a minor effect. Even though different bacterial communities were established depending on the artificial soil composition, the amount and quality of the OM did not show significant differences supporting the concept of functional redundancy.

Exploring Pellet Forming Filamentous Fungi as Tool for Harvesting Non-flocculating Unicellular Microalgae

Recently, fungal pelletization-assisted microalgal harvesting has emerged as new research area for minimizing the harvesting cost and energy inputs in the algae-to-biofuel approach. The present study attempted to optimize this process in terms of substrate inputs, process time and pH conditions through selection of a robust fungal strain. A total of eight fungal strains were screened for their pelletizing efficiency in fresh/spent BG11 supplemented with selected media nutrient (glucose, nitrogen and phosphorous). Aspergillus lentulus was found most efficient for pelletizing in the nutrient supplemented spent BG11 in spite of its alkaline pH (8.6–9.2). Moreover, the selected fungus was found equally good under neutral (7.0) and acidic pH (5.0). Interestingly, A. lentulus was able to harvest nearly 100 % of the microalgal cells (at 1.58 g l−1 initial working algal concentration) within only 24 h at supplementation of 10, 0.5 and 0.5 g l−1 of glucose, NH4NO3 and K2HPO4, respectively. The process kinetics in term of harvesting index (HI) as well as the variation of residual glucose and pH with time was also studied. Surprisingly, A. lentulus also performed well at lower glucose level (5.0 g l−1) resulting in 92 % harvesting within 24 h and up to 98 % harvesting within 52 h. The mechanism of harvesting process was studied through microscopic examination. A. lentulus strain investigated in this study could emerge as an efficient, sustainable and economically viable tool in microalgae harvesting for biofuel production. Further, the estimated stoichiometric methane potential (SMP) of pelletized microalgal–fungal biomass (0.756 m3 kg−1 volatile solid [VS]) showed substantial enhancement over algal biomass alone (0.709 m3 kg−1 VS). Hence, the investigated process not only overcomes the hurdles associated with microalgal harvesting but also improves its potential and suitability for bioenergy generation by anaerobic digestion. Further scale-up and pilot level testing is warranted for commercializing the investigated technique.

Cobalt recovery with simultaneous methane and acetate production in biocathode microbial electrolysis cells

Abstract Cobalt was successfully recovered with simultaneous methane and acetate production in biocathode microbial electrolysis cells (MECs). At an applied voltage of 0.2 V, 88.1% of Co(II) was reduced with concomitantly achieving yields of 0.266 ± 0.001 mol Co/mol COD, 0.113 ± 0.000 mol CH 4 /mol COD, and 0.103 ± 0.003 mol acetate/mol COD. Energy efficiencies relative to the electrical input were 21.2 ± 0.05% (Co), 100.9 ± 3.2% (CH 4 ), and 1.0 ± 0.01% (acetate), and overall energy efficiencies relative to both electrical input and energy of anodic substrate averaged 3.7 ± 0.05% (Co), 17.5 ± 1.4% (CH 4 ) and 0.5 ± 0.001% (acetate). Applied voltage, initial Co(II) concentration, and temperature affected system performance. The apparent activation energy ( E a ) obtained in MECs was 26.7 kJ/mol compared to 40.5 kJ/mol in the abiotic controls, highlighting the importance of cathodic microbial catalysis to Co(II) reduction. Dominant microorganisms most similar to Geobacter psychrophilus , Acidovorax ebreus , Diaphorobacter oryzae , Pedobacter duraquae , and Prolixibacter bellariivorans were observed on the biocathodes. This study provides a new process for cobalt recovery and recycle of spent lithium ion batteries with simultaneous methane and acetate production in the biocathode MECs.

Does the addition of labile substrate destabilise old soil organic matter?

Input of organic matter to soil may stimulate microbial activity and alter soil carbon storage by modifying the mineralization of native soil organic carbon (SOC). Assessing the age of SOC affected by the altered mineralization is a major challenge as the destabilisation of old SOC would be much more damageable for the overall carbon budget than the mobilization of recent SOC.Here, we investigated the microbial populations sequentially activated after the addition of a labile substrate. We questioned whether they have distinct metabolic potential and we characterised the age of the native SOC they primed. We used soils from Congolese Eucalyptus plantations that were previously under savannah and which old and recent SOC exhibited different δ13C. Soils were amended with glucose, in an amount sufficient to induce microbe growth, and incubated for one week. The δ13C of respired CO2 was continuously recorded using a tuneable diode laser spectrometer (TDLS). The combination of two glucose treatments with different δ13C signatures allowed partitioning the various sources of CO2 over time (recent SOC, old SOC and glucose). This was combined with phospholipids fatty acids (PLFA) analyses and potential metabolic activities measurements after 40 h and seven days of incubation.A peak of glucose mineralization occurred after 17 h of incubation. Before this peak (Stage 1), some specific communities with a strong feeding preference for recent SOC were activated. After the glucose peak (Stage 2), over-mineralization of native SOC occurred for some days. The recent C3 SOC was first preferentially used (Stage 3), while the old C4 SOC was destabilised in a later stage (Stage 4). Metabolic functions and composition of microbial communities also differed between Stages 3 and 4. Microbial populations collected at Stage 4 were slower compared to Stage 3, but more efficient in decomposing nutrient-containing substrates. Gram negative bacteria (16:1w7c and 18:1w7c) were stimulated at Stage 3 only, while Gram negative bacteria (cy17:0) were stimulated at both Stages 3 and 4.Our results demonstrated that the input of labile substrate alters the microbial community composition, potential metabolic activities, and the SOC pools utilisation. They pointed out the necessity to assess the age of destabilised SOC when investigating the impact of priming on carbon storage in soil.

C and N dynamics of a range of biogas slurries as a function of application rate and soil texture: a laboratory experiment

Digestates vary in composition and studies regarding their impact on C and N dynamics in soils are scarce. The objective was to analyse the C and N dynamics of digestates originating from various substrates applied to a sandy Cambisol and a silty Anthrosol. In three laboratory experiments (4–6 weeks), the effects of digestate properties, N rate and water content were tested. Averaged over both soils, 21% of the C supplied was emitted as CO2. Potential NH3 emissions during the first week ranged between 6% and 12% of NH4+ present in the digestates. The emission factors in the sandy Cambisol were on average 1.2 and 2 times higher for CO2 and potential NH3, respectively, compared to the silty Anthrosol. Similarly, net nitrogen mineralization in the sandy Cambisol was approximately twice the N mineralized in the silty Anthrosol. Net nitrification was not influenced by soil texture or different digestates, but increased with increasing application rates and had highest values at 75% of water holding capacity. Our results indicate that the type of substrate input for anaerobic digestion influences the properties of the digestate and therefore the dynamics of C and N. However, soil texture can affect these dynamics markedly.

Reactor performance of a 750 m3 anaerobic digestion plant: Varied substrate input conditions impacting methanogenic community

A 750 m3 anaerobic digester was studied over a half year period including a shift from good reactor performance to a reduced one. Various abiotic parameters like volatile fatty acids (VFA) (formic-, acetic-, propionic-, (iso-)butyric-, (iso-)valeric-, lactic acid), total C, total N, NH4 -N, and total proteins, as well as the organic matter content and dry mass were determined. In addition several process parameters such as temperature, pH, retention time and input of substrate and the concentrations of CH4, H2, CO2 and H2S within the reactor were monitored continuously. The present study aimed at the investigation of the abundance of acetogens and total cell numbers and the microbial methanogenic community as derived from PCR-dHPLC analysis in order to put it into context with the determined abiotic parameters. An influence of substrate quantity on the efficiency of the anaerobic digestion process was found as well as a shift from a hydrogenotrophic in times of good reactor performance towards an acetoclastic dominated methanogenic community in times of reduced reactor performance. After the change in substrate conditions it took the methano-archaeal community about 5–6 weeks to be affected but then changes occurred quickly.

Occurrence and fate of selected surfactants in seawater at the outfall of the Marseille urban sewerage system

This paper describes an investigation of linear alkylbenzene sulfonates (LAS) and nonylphenol ethoxylates (NPEO) and their metabolites in the vicinity of the Marseille sewage outfall (wastewater treatment plant with a capacity of 1.860 million inhabitant equivalents, Northwestern Mediterranean, southeast of France). This analytical survey describes their occurrence in the subsurface and sea surface layers and investigates their possible fates in this marine environment. The results indicated the presence of LAS in both layers and up to 3 km from the discharge point, whereas the concentration of sulfophenyl carboxylic acids, which are the main metabolites of LAS, was only significant near the sewer outfall and in the surface layer. The NPEO were present only in minor quantities, especially near the discharge point, and no other selected metabolites were detected. The fate of the surfactants in question was then assessed by two types of experiments according to their potential means of degradation under natural conditions. Biodegradation assays were conducted according to a protocol defined by the United States Environmental Protection Agency (''Biodegradability in sea water, 835.3160''), with variations in the substrate input frequencies. Photodegradation experiments were carried out in a solar simulator reactor. These results demonstrated the low photodegradability and rapid primary biodegradation of LAS (with half-life times between 10.3 and 11.5 days) in the coastal area under study, although some LAS metabolites were more recalcitrant to biodegradation in this specific environment, which was also validated by linear alkylbenzene analysis in the two selected sediment stations.

The Intestinal Metabolome: An Intersection Between Microbiota and Host

Recent advances that allow us to collect more data on DNA sequences and metabolites have increased our understanding of connections between the intestinal microbiota and metabolites at a whole-systems level. We can also now better study the effects of specific microbes on specific metabolites. Here, we review how the microbiota determines levels of specific metabolites, how the metabolite profile develops in infants, and prospects for assessing a person's physiological state based on their microbes and/or metabolites. Although data acquisition technologies have improved, the computational challenges in integrating data from multiple levels remain formidable; developments in this area will significantly improve our ability to interpret current and future data sets.