Search

Dead wood quantity and quality is important for forest biodiversity, by determining wood-inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer- and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long-term carbon dynamics of dead trees.

Proteins, an important fraction of the organic matter in wastewater, typically enter a treatment facility as high molecular weight components. These components are degraded by extracellular protein hydrolytic enzymes, denoted as proteases. Adequate protein hydrolysis monitoring is crucial, since protein hydrolysis is often a rate-limiting step in wastewater treatment. However, current monitoring tools lack a high sample throughput and reliable quantification. Here, we present an improved assay for high-throughput protein hydrolysis rate measurements in wastewater treatment applications. A BODIPY FL casein model substrate was implemented in a microplate format for continuous fluorescent quantification. Case studies on a conventional and a high-rate aerobic municipal wastewater treatment plant and a lab-scale, two-stage, anaerobic reactor provided proof-of-concept. The assay presented in this study can help to obtain monitoring-based process insights, which will in turn allow improving biological performance of wastewater treatment installations in the future. KEY POINTS: • Protein hydrolysis is a crucial step in biological wastewater treatment. • Quantification of the protein hydrolysis rate enables in-depth process knowledge. • BODIPY FL casein is a suitable model substrate for a protein hydrolysis assay. • High sample throughput was obtained with fluorescent hydrolysis quantification. Graphical abstract. ispartof: APPLIED MICROBIOLOGY AND BIOTECHNOLOGY vol:104 issue:18 pages:8037-8048 ispartof: location:Germany status: published

1. This study evaluated the effect of a higher incubation temperature on body weight, plasma profile, histology and expression of myogenin (MYOG), insulin-like growth factor-I (IGF-I) and vascular endothelial growth factor A (VEGFA) genes in breast muscle of embryos and broilers from two commercial strains. 2. A total of 784 eggs from Ross 308 and Cobb 500 broiler breeder flocks were used. Half of the eggs per strain were incubated at control temperature (37.8 degrees C), whereas the other half were exposed to heat treatment (HT) of 38.8 degrees C between embryonic day (ED) 10 and 14, for 6 h/day. Embryos and chicks were sampled on ED 19 and at hatch. A total of 480, one-day-old chicks per strain and incubation temperature were reared up to 42 d post-hatch. 3. The HT increased hatch weight of Ross chicks and 42-d body weight of broilers from both strains. Lower plasma triacylglycerol levels were measured for HT embryos and broilers on ED 19 and 42 d post-hatch, respectively. HT reduced plasma T-3 levels in Ross embryos and broilers for the same periods. Hepatic TBARS concentrations were elevated by HT compared to the control incubation. 4. The HT reduced breast muscle VEGFA gene expression of Cobb embryos on ED 19, whereas expression was stimulated in day-old chicks. At 42 d post-hatch, fibre area was increased by HT regardless of strain. Compared to the control incubation, HT increased the breast yield of Ross broilers and leg yield of Cobb. Ross-HT broilers had a higher pH at 24 h after slaughter and better water holding capacity than Cobb-HT broilers. 5. These results suggested that HT increased body weight, fibre area, IGF-I gene expression and lowered plasma triacylglycerol levels of broiler chickens from both strains at 42 d. However, HT influenced the expression of VEGF-A and MYOG genes and meat quality differently between the broiler strains., Ege University Scientific Research Project Coordination (BAP) [18-ZRF-025]; Adnan Menderes University, This work was supported by the Ege University Scientific Research Project Coordination (BAP) [18-ZRF-025] and Adnan Menderes University.

Increased human-derived nitrogen (N) loading in terrestrial ecosystems has caused widespread ecosystem-level phosphorus (P) limitation. In response, plants and soil micro-organisms adopt a series of P-acquisition strategies to offset N loading-induced P limitation. Many of these strategies impose costs on carbon (C) allocation by plants and soil micro-organisms; however, it remains unclear how P-acquisition strategies affect soil C cycling. Herein, we review the literature on the effects of N loading on P limitation and outline a conceptual overview of how plant and microbial P-acquisition strategies may affect soil organic carbon (SOC) stabilization and decomposition in terrestrial ecosystems. Excessive input of N significantly enhances plant biomass production, soil acidification, and produces plant litterfall with high N/P ratios, which can aggravate ecosystem-level P limitation. Long-term N loading can cause plants and soil micro-organisms to alter their functional traits to increase P acquisition. Plants can release carboxylate exudates and phosphatases, modify root morphological traits, facilitate the formation of symbiotic associations with mycorrhizal fungi and stimulate the abundance of P-mineralizing and P-solubilizing micro-organisms. Releasing carboxylate exudates and phosphatases could accelerate SOC decomposition, whereas changing symbiotic associations and root morphological traits (e.g. an increase in fine root length) may contribute to higher SOC stabilization. Increased relative abundances of P-mineralizing and P-solubilizing bacteria can accelerate P mining and SOC decay, which may decrease microbial C use efficiency and subsequently lower SOC sequestration. The trade-offs between different plant P-acquisition strategies under N loading should be among future research priorities due to their cascading impacts on soil C storage. Quantifying ecosystem thresholds for P adaption to increased N loading is important because P-acquisition strategies are effective when N loading is below the N threshold. Moreover, understanding the response of P-acquisition strategies at different levels of native soil N availability could provide insight to divergent P-acquisition strategies across sites and ecosystems. Altogether, P-acquisition strategies should be explicitly considered in Earth System Models to generate more realistic predictions of the effects of N loading on soil C cycling. Read the free Plain Language Summary for this article on the Journal blog.

An efficient regeneration protocol was applied to regenerate shoots on salt stress-tolerant calli lines of aubergine (Solanum melongena). These NaCl-tolerant cell lines were obtained by two different methods. On the one hand, the developed callus tissue was transferred to a medium with a continuous salt content of 40, 80, 120, or 160 mM NaCl. On the other hand, the callus tissue was subjected to a stepwise increasing salinity to 160 mM NaCl every 30 days. With the second method, calli which could be selected were characterized by compact growth, a greenish color, and absence of necrotic zones. When grown on salt-free medium again, NaCl-tolerant calli showed a decline in relative growth rate and water content in comparison to the control line. This was more obvious in the 120 mM NaCl-tolerant callus. Lipid peroxidase activity increased in 40 and 80 mM NaCl-tolerant calli; yet did not increase further in 120 mM-tolerant callus. An increase in ascorbic acid content was observed in 80 and 120 mM NaCl-tolerant calli compared to the 40 mM NaCl-tolerant lines, in which ascorbic acid content was twice that of the control. All NaCl-tolerant lines showed significantly higher superoxide dismutase (SOD) (208–305–370 µmol min−1 mg−1 FW) and catalase (CAT) (136–211–238 µmol min−1 mg−1 FW) activities compared to control plants (231 and 126 µmol min−1 mg−1 FW). Plants were regenerated on the calli lines that could tolerate up to 120 mM NaCl. From the 32 plants tested in vitro, ten plants with a higher number of leaves and root length could be selected for further evaluation in the field. Their high salt tolerance was evident by their more elevated fresh and dry weight, their more increased relative water content, and a higher number and weight of fruits compared to the wild-type parental control. The presented work shows that somaclonal variation can be efficiently used to develop salt-tolerant mutants.

Training-induced follow-up of multiple muscle plasticity parameters in postural stability vs. locomotion muscles provides an integrative physiological view on shifts in the muscular metabolic machinery. It can be expected that not all muscle plasticity parameters show the same expression time profile across muscles. This knowledge is important to underpin results of metabolomic studies. Twelve non-competing Standardbred mares were subjected to standardized harness training. Muscle biopsies were taken on a non-training day before and after 8 weeks. Shifts in muscle fiber type composition and muscle fiber cross-sectional area (CSA) were compared in the m. pectoralis, the m. vastus lateralis, and the m. semitendinosus. In the m. vastus lateralis, which showed most pronounced training-induced plasticity, two additional muscle plasticity parameters (capillarization and mitochondrial density) were assessed. In the m. semitendinosus, additionally the mean minimum Feret's diameter was assessed. There was a significant difference in baseline profiles. The m. semitendinosus contained less type I and more type IIX fibers compatible with the most pronounced anaerobic profile. Though no baseline fiber type-specific and overall mean CSA differences could be detected, there was a clear post-training decrease in fiber type specific CSA, most pronounced for the m. vastus lateralis, and this was accompanied by a clear increase in capillary supply. No shifts in mitochondrial density were detected. The m. semitendinosus showed a decrease in fiber type specific CSA of type IIAX fibers and a decrease of type I fiber Feret's diameter as well as mean minimum Feret's diameter. The training-induced increased capillary supply in conjunction with a significant decrease in muscle fiber CSA suggests that the muscular machinery models itself toward an optimal smaller individual muscle fiber structure to receive and process fuels that can be swiftly delivered by the circulatory system. These results are interesting in view of the recently identified important fuel candidates such as branched-chain amino acids, aromatic amino acids, and gut microbiome-related xenobiotics, which need a rapid gut–muscle gateway to reach these fibers and are less challenging for the mitochondrial system. More research is needed with that respect. Results also show important differences between muscle groups with respect to baseline and training-specific modulation.

High hydrostatic pressure (HHP) is an interesting hurdle in minimal food processing that aims to synergistically combine different stresses to improve food microbiological safety and stability without compromising quality. For a proper understanding and design of hurdle technology, the cellular impact of the applied stresses on foodborne pathogens should be well-established. To study the mechanism of HHP-mediated cell injury and death, we screened for loss-of-function mutations in E. coli MG1655 that affected HHP sensitivity. More specifically, ca. 6000 random transposon insertion mutants were individually exposed to HHP, after which the phenotype of the most resistant or sensitive mutations was confirmed by de novo gene deletions in the parental strain. We found that disruption of rbsK, rbsR, hdfR and crl decreased HHP resistance, while disruption of sucC and sucD (encoding subunits of the succinyl-CoA synthetase) increased HHP resistance. More detailed study of the tricarboxylic acid cycle enzymes encoded by the sdhCDAB-sucABCD operon surprisingly showed that disruption of the sucA or sucB gene (encoding subunits of the 2-oxoglutarate dehydrogenase complex) notably decreased HHP survival. We also found that the increased HHP resistance of a ΔsucC and ΔsucD mutant was mediated by increased basal RpoS activity levels, although it did not correlate with their heat resistance. Our results reveal that compromising TCA cycle enzymes can profoundly affect HHP resistance in E. coli. ispartof: FOOD MICROBIOLOGY vol:78 pages:171-178 ispartof: location:England status: published

Soil microorganisms are an important indicator of soil fertility and health. However, our state of knowledge about soil microbial activities, community compositions and carbon use patterns under metal contaminations is still poor. This study aimed to evaluate the influences of heavy metals (Cd and Pb) on soil microorganisms by investigating the microbial community composition and carbon use preferences. Metal pollution was approached both singly and jointly with low (25 and 2500 mg kg−1) and high (50 and 5000 mg kg−1) concentrations of Cd and Pb, respectively, in an artificially contaminated soil. In a laboratory incubation experiment, bio-available and potentially bio-available metal concentrations, selected soil properties (pH, electrical conductivity, total organic carbon and total nitrogen), and microbial parameters (microbial activity as basal respiration, microbial biomass carbon (MBC) and microbial functional groups) were determined at two sampling occasions (7 and 49 days). Metal contamination had no effect on the selected soil properties, while it significantly inhibited both microbial activity and MBC formation. Contaminated soils had higher microbial quotient (qCO2), suggesting there was higher energy demand with less microbially immobilized carbon as MBC. Notably, the efficiency of microbial carbon use was repressed as the metal concentration increased, yet no difference was observed between metal types (p > 0.05). Based on the microbial phospholipid fatty acids (PLFA) analysis, total PLFAs decreased significantly under metal stress at the end of incubation. Heavy metals had a greater negative influence on the fungal population than bacteria with respective 5–35 and 8–32% fall in abundances. The contaminant-driven (metal concentrations and types) variation of soil PLFA biomarkers demonstrated that the heavy metals led to the alteration of soil microbial community compositions and their activities, which consequently had an adverse impact on soil microbial carbon immobilization. Keywords: Heavy metals, Soil organic carbon, Microbial carbon decomposition, Microbial activity, Microbial community composition, PLFAs

Licorice (Glycyrrhiza uralensis Fisch.) is a salt and drought tolerant legume suitable for rehabilitating abandoned saline lands, especially in dry arid regions. We hypothesized that soil amended with maize-derived biochar might alleviate salt stress in licorice by improving its growth, nutrient acquisition, and root system adaptation. Experiments were designed to determine the effect of different biochar concentrations on licorice growth parameters, acquisition of C (carbon), nitrogen (N), and phosphorus (P) and on soil enzyme activities under saline and non-saline soil conditions. Pyrolysis char from maize (600 & DEG;C) was used at concentrations of 2% (B2), 4% (B4), and 6% (B6) for pot experiments. After 40 days, biochar improved the shoot and root biomass of licorice by 80 and 41% under saline soil conditions. However, B4 and B6 did not have a significant effect on shoot growth. Furthermore, increased nodule numbers of licorice grown at B4 amendment were observed under both non-saline and saline conditions. The root architectural traits, such as root length, surface area, project area, root volume, and nodulation traits, also significantly increased by biochar application at both B2 and B4. The concentrations of N and K in plant tissue increased under B2 and B4 amendments compared to the plants grown without biochar application. Moreover, the soil under saline conditions amended with biochar showed a positive effect on the activities of soil fluorescein diacetate hydrolase, proteases, and acid phosphomonoesterases. Overall, this study demonstrated the beneficial effects of maize-derived biochar on growth and nutrient uptake of licorice under saline soil conditions by improving nodule formation and root architecture, as well as soil enzyme activity., Georg Forster Research Fellowship (HERMES); Alexander von Humboldt Foundation, Bonn, Germany, This research was supported by a Georg Forster Research Fellowship (HERMES), Alexander von Humboldt Foundation, Bonn, Germany.

Due to the invasiveness of a muscle biopsy, there is fragmentary information on the existence and possible origin of a sexual dimorphism in the skeletal muscle concentrations of the energy delivery-related metabolites carnosine, creatine, and carnitine. As these metabolites can be noninvasively monitored by proton magnetic resonance spectroscopy, this technique offers the possibility to investigate if sexual dimorphisms are present in an adult reference population and if these dimorphisms originated during puberty using a longitudinal design. Concentrations of carnosine, creatine, and carnitine were examined using proton magnetic resonance spectroscopy in the soleus and gastrocnemius muscles of an adult reference population of female (n = 50) and male adults (n = 50). For the longitudinal follow-up over puberty, 29 boys and 28 girls were scanned prepuberty. Six years later, 24 boys and 24 girls were rescanned postpuberty. A sexual dimorphism was present in carnosine and creatine, but not carnitine, in the adult reference population. Carnosine was 28.5% higher in the gastrocnemius (P < 0.001) and carnosine and creatine were respectively 19.9% (P < 0.001) and 18.2% (P < 0.001) higher in the soleus of male when compared with female adults. Through puberty, carnosine increased more in male subjects compared with female subjects, both in the gastrocnemius (+10.43% and -10.83%, respectively; interaction effect: P = 0.002) and in the soleus ( +24.30% and +5.49%, respectively; interaction effect: P = 0.012). No significant effect of puberty was found in either creatine (interaction effect: P = 0.307) or carnitine (interaction effect: P = 0.066). A sexual dimorphism in the adult human muscle is present in carnosine and creatine, but not in carnitine. NEW & NOTEWORTHY This is the first study to investigate sexual dimorphisms in skeletal muscle carnosine, creatine, and carnitine concentrations in a substantial adult reference population (n = 100). A sexual dimorphism is present in both carnosine and creatine at adult age. The origin of the sexual dimorphisms is investigated using a longitudinal design over puberty in 24 males and 24 females. The sexual dimorphism in carnosine originated partly during puberty for carnosine, but not for creatine.

Plant growth-promoting rhizobacteria (PGPR) and rhizobia are potentially advantageous in improving plant growth in heavy metal contaminated soils. However, only limited information is available in literature on the manner through which the co-inoculation of PGPR and rhizobia can potentially supply nutrients to benefit plant growth in heavy metal contaminated soil. Accordingly, this study investigated the effects of Paenibacillus mucilaginosus (PGPR) and Sinorhizobium meliloti (rhizobia) co-inoculation on soil nutrients, enzyme activities, and microbial biomass in copper (Cu) contaminated soil planted with alfalfa (Medicago sativa). Moreover, we assessed soil bacterial community structure using high-throughput Illumina sequencing of 16S rRNA genes. Results showed that PGPR and/or rhizobia inoculation improved alfalfa growth. In particular, we found that this co-inoculation approach decreased Cu accumulation (48.6%) in shoots compared to the control (uninoculated). Both partial least squares path modeling (PLS-PM) and the relative importance of regressors in the linear models identified that enzyme activities, microbial biomass, and microbial community structure in Cu contaminated soil were major controlling variables of soil nutrient availability. The co-inoculation treatment significantly increased soil carbon (C) and nitrogen (N) concentrations by increasing urease (55.6%), saccharase (29.5%), and β-glucosidase (31.4%) activities compared to the control. Furthermore, the rhizosphere microbial community structure in the co-inoculation treatment was mainly regulated by soil N concentrations (i.e., both total N and available N) while altering alpha diversity (α-diversity). The relative abundances of Firmicutes (including biomarkers of the Bacillus genus) and Acidobacteria were enriched in the co-inoculated treatment, which can potentially improve soil nutrient availability and subsequently benefit plant growth. These findings indicated that the co-inoculation of PGPR and rhizobia plays an important role in promoting plant growth in Cu contaminated soil. This is because this approach can increase soil nutrient availability by enhancing soil enzyme activities and regulating rhizosphere microbial community structure.

There is an ever-increasing recognition that bile acids are not purely simple surfactant molecules that aid in lipid digestion, but are a family of molecules contributing to a diverse range of key systemic functions in the host. It is now also understood that the specific composition of the bile acid milieu within the host is related to the expression and activity of bacterially-derived enzymes within the gastrointestinal tract, as such creating a direct link between the physiology of the host and the gut microbiota. Coupled to the knowledge that perturbation of the structure and/or function of the gut microbiota may contribute to the pathogenesis of a range of diseases, there is a high level of interest in the potential for manipulation of the gut microbiota-host bile acid axis as a novel approach to therapeutics. Much of the growing understanding of the biology of this area reflects the recent development and refinement of a range of novel techniques; this study applies a number of those techniques to the analysis of human samples, aiming to illustrate their strengths, drawbacks and biological significance at all stages. Specifically, we used microbial profiling (using 16S rRNA gene sequencing), bile acid profiling (using liquid chromatography-mass spectrometry), bsh and baiCD qPCR, and a BSH enzyme activity assay to demonstrate differences in the gut microbiota and bile metabolism in stool samples from healthy and antibiotic-exposed individuals.

Material flow analysis shows that soil is a key repository for silver (Ag) from (nano)silver-functionalized consumer products, but the potential effects of Ag toxicity, via Ag+ release, on soil microbial communities and their ecosystem services remains largely unknown. We examined the responses of multiple microbial biomarkers to increasing Ag+ doses (nine concentrations, 0-2000 mg kg(-1)) in nine different soils representing a wide range of soil properties. Analyses included substrate-induced microbial respiration, nine different soil enzyme activities, and quantification of bacterial 16S-rRNA (SSU) and fungal intergenic spacer (ITS) copies. The resulting half-maximal effective concentrations (EC50) for Ag ranged from similar to 1 to >500 mg kg(-1) and showed soil-specific responses, including some hormesis-type responses. Carbon cycle-associated enzyme activities (e.g., cellobiohydrolase, xylosidase, and alpha/beta-glucosidase) responded similarly to Ag. Sulfatase and leucine-aminopeptidase activities (linked to the sulfur and nitrogen cycles) were the most sensitive to Ag. Total organic carbon, and to a lesser extent pH, were identified as potentially useful response predictors, but only for some biomarkers; this reflects the complexity of soil Ag chemistry. Our results show Ag toxicity is highly dependent on soil characteristics and the specific microbial parameter under investigation, but end point redundancies also indicated that representative parameters for key microbial functions can be identified for risk assessment purposes. Sulfatase activity may be an important Ag toxicity biomarker; its response was highly sensitive and not correlated with that of other biomarkers. Refereed/Peer-reviewed

The white button mushroom Agaricus bisporus is one of the most widely produced edible fungus with a great economical value. Its commercial cultivation process is often performed on wheat straw and animal manure based compost that mainly contains lignocellulosic material as a source of carbon and nutrients for the mushroom production. As a large portion of compost carbohydrates are left unused in the current mushroom cultivation process, the aim of this work was to study wild-type A. bisporus strains for their potential to convert the components that are poorly utilized by the commercial strain A15. We therefore focused our analysis on the stages where the fungus is producing fruiting bodies. Growth profiling was used to identify A. bisporus strains with different abilities to use plant biomass derived polysaccharides, as well as to transport and metabolize the corresponding monomeric sugars. Six wild-type isolates with diverse growth profiles were compared for mushroom production to A15 strain in semi-commercial cultivation conditions. Transcriptome and proteome analyses of the three most interesting wild-type strains and A15 indicated that the unrelated A. bisporus strains degrade and convert plant biomass polymers in a highly similar manner. This was also supported by the chemical content of the compost during the mushroom production process. Our study therefore reveals a highly conserved physiology for unrelated strains of this species during growth in compost.

WOS:000569774900004; Coastal nursery areas are subjected to a wide range of natural and anthropogenic stressors, including global warming, which indirectly influence trophic food webs. A global rarefaction of n-3 polyunsaturated fatty acids (PUFA) in trophic networks is in progress. The aim of this study was to assess the effect of a reduction in the dietary availability of n-3 PUFA on some molecular and biochemical parameters related to lipid metabolism and oxidative stress response in juvenile European sea bass (Dicentrarchus labrax) raised at two temperatures (15 degrees C and 20 degrees C). Fish were fed for five months with a reference diet (RD; 1.65% n-3 PUFA on a dry matter basis, DM), used as a proxy of trophic networks where n-3 PUFA is plentiful, and a lower n-3 PUFA diet (LD; 0.73% n-3 PUFA DM), designed to mimic a decrease in n-3 PUFA resulting from global changes (the n-3 PUFA levels tested remained above the nutritional minimum required for this species). Results showed that diet did not affect the hepatic expression of some mRNA coding for transcriptional factors involved in regulating the metabolic pathways related to fatty acid bioconversion. Although our molecular analysis was limited to transcript expression, these data suggest the presence of a threshold in the nutritional supply of PUFA above which the activation of these molecular pathways does not occur. However, the expression for most of the transcripts tested was up-regulated at 20 degrees C. Despite the high peroxidation index in fish fed RD, very few modifications of the oxidative stress response were associated with diet. At 20 degrees C, an increase of the enzymatic antioxidant response was observed, but there was no correlation with the peroxidation index or malondialdehyde products.

Soil organic matter (SOM) is unevenly distributed in arable fields in undulated landscapes, but the chemical composition resulting from their turnover, transport and deposition processes is insufficiently known. Therefore, we aimed at disclosing the molecular-chemical composition of SOM in four different catenae at shoulderslope, backslope and footslope positions in arable fields in the Baltic Sea catchment, Europe. The backslope positions always had the lowest organic C-contents (Corg) (1.6&hellip, 11.8 g&middot, kg&minus, 1) and C-stocks (3.8&hellip, 8.5 kg&middot, m&minus, 2) compared to the shoulderslopes and footslopes (1.7&hellip, 17.7 g&middot, Corg&middot, 1, 5.4&hellip, 15 kg&middot, 2). In the SOM-poor backslope positions, the organic matter was characterized by relatively high proportions of carbohydrates, phenols + lignin monomers, alkylaromatic compounds, N-compounds and amides, indicating intensive microbial decomposition. By contrast, the footslopes had the largest Corg-contents (9.3&hellip, 16.5 g&middot, 1) and C-stocks (8.9&hellip, 2) in the catenae and particular enrichments in lipids, lignin dimers, sterols and free fatty acids. These relatively stabile SOM compound classes are interpreted as leftovers from erosive downslope transport and concurrent microbial decomposition, e.g., they are pronounced at backslope positions, followed by restricted microbial decomposition. This heterogeneous SOM distribution calls for an adapted soil management that reduces erosion and places amendments to field areas, such as the shoulderslope and backslope.

Sustainable agriculture requires the careful optimization of the use of organic amendments to improve soil fertility while minimizing any harmful environmental effects. To understand the events that occur in soil after the addition of different organic amendments, we evaluated the nitrogen (N) mineralization dynamics in soil after adding organic amendments, and evaluated changes in the microbial population. The four organic amendments were fresh dairy cattle manure, fresh white clover, vegetable, fruit, and yard waste compost, and poplar tree compost. The N mineralization potential of each organic amendment was determined by analyzing total mineral nitrogen during a 97-day laboratory incubation experiment. Soils amended with clover released 240 μg N g −1 soil during the 97-day incubation, more than twice as much as that released from soils amended with manure or composts (76–100 μg N g −1 soil). At the end of the incubation, the net N mineralization in clover-amended soils was 54%, more than five times higher than that in soils amended with composts or manure (4%–9%). Nitrogen was mineralized faster in clover-amended soil (1.056 μg N g −1 soil day −1 ) than in soil amended with composts (0.361–0.417 μg N g −1 soil day −1 ). The microbial biomass carbon content was higher in clover-amended soil than in the soils amended with manure or composts. We monitored changes in the microbial population in amended soils by a phospholipid fatty acid (PLFA) analysis. On day 97, there were higher concentrations of total PLFAs in soils with organic amendments (e.g., 14.41 nmol g −1 in clover-amended soil) than in control soil without amendments (9.84 nmol g −1 ). Bacteria (Gram-positive and Gram-negative), actinomycetes, and fungi were more abundant in clover-amended soils than soils amended with manure or composts. The N mineralization potential varied among the four organic amendments. Therefore, the timing of application and the type of organic amendment should be matched to the nutrient needs of the crop.

Uridine-diphosphate glucuronosyltransferase 1A1 (UGT1A1) is an important conjugative enzyme in mammals that is responsible for the conjugation and detoxification of both endogenous and xenobiotic compounds. Strong inhibition of UGT1A1 may trigger adverse drug/herb-drug interactions, or result in metabolic disorders of endobiotic metabolism. Therefore, both the US Food and Drug Administration (FDA) and the European Medicines Agency (EMA) have recommended assaying the inhibitory potential of drugs under development on the human UGT1A1 prior to approval. This review focuses on the significance, progress and challenges in discovery and characterization of UGT1A1 inhibitors. Recent advances in the development of UGT1A1 probes and their application for screening UGT1A1 inhibitors are summarized and discussed in this review for the first time. Furthermore, a long list of UGT1A1 inhibitors, including information on their inhibition potency, inhibition mode, and affinity, has been prepared and analyzed. Challenges and future directions in this field are highlighted in the final section. The information and knowledge that are presented in this review provide guidance for rational use of drugs/herbs in order to avoid the occurrence of adverse effects via UGT1A1 inhibition, as well as presenting methods for rapid screening and characterization of UGT1A1 inhibitors and for facilitating investigations on UGT1A1-ligand interactions. (C) 2019 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V.

Reactive oxygen species (ROS)-dependent signaling pathways from chloroplasts and mitochondria merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). RCD1 interacts in vivo and suppresses the activity of the transcription factors ANAC013 and ANAC017, which mediate a ROS-related retrograde signal originating from mitochondrial complex III. Inactivation of RCD1 leads to increased expression of mitochondrial dysfunction stimulon (MDS) genes regulated by ANAC013 and ANAC017. Accumulating MDS gene products, including alternative oxidases (AOXs), affect redox status of the chloroplasts, leading to changes in chloroplast ROS processing and increased protection of photosynthetic apparatus. ROS alter the abundance, thiol redox state and oligomerization of the RCD1 protein in vivo, providing feedback control on its function. RCD1-dependent regulation is linked to chloroplast signaling by 3'-phosphoadenosine 5'-phosphate (PAP). Thus, RCD1 integrates organellar signaling from chloroplasts and mitochondria to establish transcriptional control over the metabolic processes in both organelles., eLife digest Most plant cells contain two types of compartments, the mitochondria and the chloroplasts, which work together to supply the chemical energy required by life processes. Genes located in another part of the cell, the nucleus, encode for the majority of the proteins found in these compartments. At any given time, the mitochondria and the chloroplasts send specific, ‘retrograde’ signals to the nucleus to turn on or off the genes they need. For example, mitochondria produce molecules known as reactive oxygen species (ROS) if they are having problems generating energy. These molecules activate several regulatory proteins that move into the nucleus and switch on MDS genes, a set of genes which helps to repair the mitochondria. Chloroplasts also produce ROS that can act as retrograde signals. It is still unclear how the nucleus integrates signals from both chloroplasts and mitochondria to ‘decide’ which genes to switch on, but a protein called RCD1 may play a role in this process. Indeed, previous studies have found that Arabidopsis plants that lack RCD1 have defects in both their mitochondria and chloroplasts. In these mutant plants, the MDS genes are constantly active and the chloroplasts have problems making ROS. To investigate this further, Shapiguzov, Vainonen et al. use biochemical and genetic approaches to study RCD1 in Arabidopsis. The experiments confirm that this protein allows a dialog to take place between the retrograde signals of both mitochondria and chloroplasts. On one hand, RCD1 binds to and inhibits the regulatory proteins that usually activate the MDS genes under the control of mitochondria. This explains why, in the absence of RCD1, the MDS genes are always active, which is ultimately disturbing how these compartments work. On the other hand, RCD1 is also found to be sensitive to the ROS that chloroplasts produce. This means that chloroplasts may be able to affect when mitochondria generate energy by regulating the protein. Finally, further experiments show that MDS genes can affect both mitochondria and chloroplasts: by influencing how these genes are regulated, RCD1 therefore acts on the two types of compartments. Overall, the work by Shapiguzov, Vainonen et al. describes a new way Arabidopsis coordinates its mitochondria and chloroplasts. Further studies will improve our understanding of how plants regulate these compartments in different environments to produce the energy they need. In practice, this may also help plant breeders create new varieties of crops that produce energy more efficiently and which better resist to stress.

Glucocorticoids are pleiotropic steroid hormones mediating redistribution of energy. They induce breakdown of glycogen stores and consequent plasma hyperglycaemia after stressful situations. Glucocorticoid actions in most vertebrate species are exerted by cortisol and corticosterone. However, 1α-hydroxycorticosterone is the dominant corticosteroid hormone in elasmobranchs, though its effects as a glucocorticoid are unknown. Here we demonstrate, by using ultra-performance liquid chromatography coupled to tandem mass spectrometry for the quantification of 1α-hydroxycorticosterone in plasma of the elasmobranch Scyliorhinus canicula, the response of this hormone to an acute-stress situation and for the first time its glucocorticoid action in elasmobranchs. After an acute air-exposure challenge, S. canicula increased plasma levels of 1α-hydroxycorticosterone altogether with enhanced glycolysis and gluconeogenesis pathways to fuel energy demanding tissues, such as white muscle, during the first hours after the stress situation. We foresee our study as a starting point to evaluate stress responses in elasmobranchs, as well as for future applications in the management of these key ecosystem species, Sí

Wildfires thaw near-surface permafrost soils in the boreal forest, making previously frozen organic matter available to microbes. The short-term microbial stoichiometric dynamics following a wildfire are critical to understanding the soil element variations in thawing permafrost. Thus, we selected a boreal wildfire chronosequence in a region of continuous permafrost, where the last wildfire occurred 3, 25, 46, and > 100 years ago (set as the control) to explore the impact of wildfire on the soil chemistry, soil microbial stoichiometry, and the fungal-to-bacterial gene ratio (F:B ratio). We observed the microbial biomass C:N:P ratio remained constant in distinct age classes indicating that microbes are homeostatic in relation to stoichiometric ratios. The microbial C:N ratios were independent of the shifts in the fungal-to-bacterial ratio when C:N exceeded 12. Wildfire-induced reduction in vegetation biomass positively affected the fungal, but not the bacterial, gene copy number. The decline in microbial biomass C, N, and P following a fire, primarily resulted from a lack of soil available C and nutrients. Wildfire affected neither the microbial biomass nor the F:B ratios at a soil depth of 30 cm. We conclude that microbial stoichiometry does not always respond to changes in the fungal-to-bacterial ratio and that wildfire-induced permafrost thawing does not accelerate microbial respiration.

Microbial mechanisms associated with soil organic carbon (SOC) decomposition are poorly understood. We aim to determine the effects of inorganic and organic fertilizers on soil labile carbon (C) pools, microbial community structure and C mineralization rate under an intensive wheat-maize double cropping system in Northern China. Soil samples in 0-10 cm layer were collected from a nine-year field trial involved four treatments: no fertilizer, CK; nitrogen (N) and phosphorus (P) fertilizers, NP; maize straw combined with NP fertilizers, NPS; and manure plus straw and NP fertilizers, NPSM. Soil samples were analyzed to determine labile C pools (including dissolved organic C, DOC; light free organic C, LFOC; and microbial biomass C, MBC), microbial community composition (using phospholipid fatty acid (PLFA) profiles) and SOC mineralization rate (from a 124-day incubation experiment). This study demonstrated that the application of chemical fertilizers (NP) alone did not alter labile C fractions, soil microbial communities and SOC mineralization rate from those observed in the CK treatment. Whereas the use of straw in conjunction with chemical fertilizers (NPS) became an additional labile substrate supply that decreased C limitation, stimulated growth of all PLFA-related microbial communities, and resulted in 53% higher cumulative mineralization of C compared to that of CK. The SOC and its labile fractions explained 78.7% of the variance of microbial community structure. Further addition of manure on the top of straw in the NPSM treatment did not significantly increase microbial community abundances, but it did alter microbial community structure by increasing G+/G- ratio compared to that of NPS. The cumulative mineralization of C was 85% higher under NPSM fertilization compared to that of CK. Particularly, the NPSM treatment increased the mineralization rate of the resistant pool. This has to be carefully taken into account when setting realistic and effective goals for long-term soil C stabilization.

Background: The proportion of starch disappearing from the small intestinal lumen is generally lower in ruminants than in monogastric animals, and there are indications that the starch digestion capacity in ruminants is limited.Objectives: Milk-fed calves were used to study the rate-limiting enzyme in starch hydrolysis and to quantify starch fermentation in ruminants.Methods: Forty male Holstein-Friesian calves were fed milk replacer containing either lactose (control) or 1 of 4 corn starch products. The following starch products differed in the enzyme ratios required for their complete hydrolysis to glucose: gelatinized starch [alpha-amylase and (iso)maltase], maltodextrin [(iso)maltase and alpha-amylase], maltodextrin with alpha-1,6-branching (isomaltase, maltase, and alpha-amylase), and maltose (maltase). In the adaptation period, calves were stepwise exposed to an increasing dose of the starch product for 14 wk to allow maximal adaptation of all enzyme systems involved. In the experimental period, apparent total tract and ileal starch product disappearance, total tract starch product fermentation, and alpha-amylase, maltase, and isomaltase activities were determined at 18% inclusion of the starch product.Results: Maltase and isomaltase activities in the brush border did not increase for any of the starch product treatments. Luminal alpha-amylase activity was lower in the proximal (3 9 +/- 3.2 and 2.7 +/- 1.7 U/mg Co for control and starch product calves, respectively) but greater in the distal small intestine of starch-fed calves than in control calves (0.0 +/- 0.0 and 6.4 +/- 1.5 U/mg Co for control and starch product calves, respectively; means +/- SEs for control and means +/- pooled SEMs for starch product treatments). Apparent deal (61.6% +/- 6.3%) and total tract (99.1% +/- 0.4%) starch product disappearance did not differ between starch product treatments, suggesting that maltase activity limits starch digestion in ruminants. Total tract starch product fermentation averaged 414 +/- 43 g/d, corresponding to 89% of intake, of which Half was fermented before the terminal ileum, regardless of starch product treatment.Conclusion: Fermentation, rather than enzymatic digestion, is the main reason for small intestinal starch disappearance in milk-fed calves.

Exercise training (ExTr) is largely used to improve functional capacity in patients with chronic obstructive pulmonary disease (COPD). However, ExTr only partially restores muscle function in patients with COPD, suggesting that confounding factors may limit the efficiency of ExTr. In the present study, we hypothesized that skeletal muscle adaptations triggered by ExTr could be compromised in hypoxemic patients with COPD. Vastus lateralis muscle biopsies were obtained from patients with COPD who were either normoxemic ( n = 15, resting arterial Po2 = 68.5 ± 1.5 mmHg) or hypoxemic ( n = 8, resting arterial Po2 = 57.0 ± 1.0 mmHg) before and after a 2-mo ExTr program. ExTr induced a significant increase in exercise capacity both in normoxemic and hypoxemic patients with COPD. However, ExTr increased citrate synthase and lactate dehydrogenase enzyme activities only in skeletal muscle of normoxemic patients. Similarly, muscle fiber cross-sectional area and capillary-to-fiber ratio were increased only in patients who were normoxemic. Expression of atrogenes (MuRF1, MAFbx/Atrogin-1) and autophagy-related genes (Beclin, LC3, Bnip, Gabarapl) remained unchanged in both groups. Phosphorylation of Akt (Ser473), GSK-3β (Ser9), and p70S6k (Thr389) was nonsignificantly increased in normoxemic patients in response to ExTr, but it was significantly decreased in hypoxemic patients. We further showed on C2C12 myotubes that hypoxia completely prevented insulin-like growth factor-1-induced phosphorylation of Akt, GSK-3β, and p70S6K. Together, our observations suggest a role for hypoxemia in the adaptive response of skeletal muscle of patients with COPD in an ExTr program.

As a consequence of global change processes, plants will increasingly be challenged by extreme climatic events, against a background of elevated atmospheric CO2. We analysed responses of Arabidopsis thaliana to periods of a combination of elevated heat and water deficit at ambient and elevated CO2 in order to gain mechanistic insights regarding changes in primary metabolism. Metabolic changes induced by extremes of climate are dynamic and specific to different classes of molecules. Concentrations of soluble sugars and amino acids increased transiently after short (4-d) exposure to heat and drought, and readjusted to control levels under prolonged (8-d) stress. In contrast, fatty acids showed persistent changes during the stress period. Elevated CO2 reduced the impact of stress on sugar and amino acid metabolism, but not on fatty acids. Integrating metabolite data with transcriptome results revealed that some of the metabolic changes were regulated at the transcriptional level. Multivariate analyses grouped metabolites on the basis of stress exposure time, indicating specificity in metabolic responses to short and prolonged stress. Taken together, the results indicate that dynamic metabolic reprograming plays an important role in plant acclimation to climatic extremes. The extent of such metabolic adjustments is less under high CO2, further pointing towards the role of high CO2 in stress mitigation. ispartof: Journal of Experimental Botany vol:69 issue:8 pages:2159-2170 ispartof: location:England status: published

Various peatland restoration strategies developed during the last two decades have aimed to stop degradation and bring back the original hydrology, biodiversity and other peatland functions. This study evaluated progress 6-15 years after rewetting in vegetation development, physicochemical properties of peat, soil organic matter (SOM) quality and microbial activity in previously long-term drained bogs and spruce swamp forests (SSF) in comparison with pristine and long-term drained sites in the Bohemian Forest, Czech Republic. Long-term drainage led to overall ecosystem degradation, indicated by a change in vegetation composition, reduced decomposability of peat, with high content of recalcitrant compounds and decreased pH, and reduced soil microbial biomass and activity. The degradation was more pronounced in SSF, while bogs seemed to be relatively resistant to environmental changes caused by drainage. Post-rewetting progress has occurred with regard to vegetation composition, peat pH, microbial biomass and potential anaerobic CO2 and CH4 production, all of which tending towards characteristics of the pristine sites. However, overall SOM quality has not yet responded significantly, indicating that some peat properties and functions, such as C accumulation, need much longer periods of time to return to the original level.

Processes underlying soil organic matter (SOM) transformations are meeting growing interest as SOM contains more carbon (C) than global vegetation and the atmosphere combined. Therefore, SOM is a crucial element of the C cycle, especially in ecosystems rich in organic matter, such as boreal forests. However, climate change may shift the fate of this SOM from C sink into C source, accelerating global warming. These processes require a better understanding of the involved mechanisms driving both the C cycle and the interlinked nitrogen (N) cycle. SOM transformations are balanced by a network of interactions between biological, chemical and physical factors. In this review, we discuss the findings of the most recent studies to the current state of knowledge about the main drivers in SOM transformations. We focus on plant-derived secondary metabolites, as their biochemical traits, especially interactions with soil microbial communities, organic N compounds and enzymes make them potential regulators of SOM decomposition. However, these regulatory abilities of plant-derived compounds are not fully explored.

Agricultural peatlands are essential for a myriad of ecosystem functions and play an important role in the global carbon (C) cycle through C sequestration. Management of these agricultural peatlands takes place at different spatial scales, ranging from local to landscape management, and drivers of soil microbial community structure and function may be scale-dependent. Effective management for an optimal biogeochemical functioning thus requires knowledge of the drivers on soil microbial community structure and functioning, as well as the spatial scales upon which they are influenced. During two field campaigns, we examined the importance of different drivers (i.e., soil characteristics, nutrient management, vegetation composition) at two spatial scales (local vs. landscape) for, respectively, the soil microbial community structure (determined by PLFA) and soil microbial community functional capacity (as assessed by CLPP) in agricultural peatlands. First, we show by an analysis of PLFA profiles that the total microbial biomass changes with soil moisture and relative C:P nutrient availability. Secondly, we showed that soil communities are controlled by a distinct set of drivers at the local, as opposed to landscape, scale. Community structure was found to be markedly different between areas, in contrast to community function which showed high variability within areas. We further found that microbial structure appears to be controlled more at a landscape scale by nutrient-related variables, whereas microbial functional capacity is driven locally through plant community feedbacks. Optimal management strategies within such peatlands should therefore consider the scale-dependent action of soil microbial community drivers, for example by first optimizing microbial structure at the landscape scale by targeted areal management, and then optimizing soil microbial function by local vegetation management. ispartof: FRONTIERS IN MICROBIOLOGY vol:9 ispartof: location:Switzerland status: published

Most of the research dedicated to agromining has focused on cultivating a single hyperaccumulator plant, although plant diversity has been shown to positively modify soil characteristics. Hence, we compared the effect of cropping a nickel-hyperaccumulator Alyssum murale with a legume (Vicia sativa) to A. murale's mono-culture, on the bacterial diversity and physico-chemical characteristics of an ultramafic soil. A pot experiment with 5 replicates was conducted in controlled conditions for 11 months. The treatments studied were: co-cropping and rotation vs. mineral fertilization controls and bare soil. The introduction of legumes induced a clearly positive effect on the soil's microbial biomass carbon and nitrogen. Arylsulfatase and urease activities tended to be enhanced in the co-cropping and rotation treatments and to be lessened in the mineral fertilization treatments. However, β-glucosidase and phosphatase activities were seen to decrease when legumes were used. Our results showed that the rotation treatment induced a higher organic matter content than the fertilized control did. Actinobacteria was the most-represented bacterial phyla and had lower relative abundance in treatments associating legumes. Conversely, the relative abundance of Acidobacteria and Gemmatimonadetes phyla increased but not significantly in treatments with legumes. The relative abundance of Chloroflexi phylum was shown to be significantly higher for the fertilized rotation control. The relative abundance of β-Proteobacteria subphylum increased but not significantly in treatments with legumes. NMDS analysis showed a clear separation between planted treatments and bare soil and between co-cropping and rotation and fertilized controls. Shannon index showed reduction in microbial diversity that was mainly due to chemical inputs in the soil. This study showed that these new cropping systems influenced both the bacterial diversity and the physico-chemical characteristics of an ultramafic soil. In addition, this study provides evidence that mineral fertilization can negatively impact bacterial communities and some of their functions linked to biogeochemical cycles.

Central primary metabolism enzyme activities track transcript abundance during secondary cell wall formation in wood., The contribution of transcriptional and post-transcriptional regulation to modifying carbon allocation to developing wood of trees is not well defined. To clarify the role of transcriptional regulation, the enzyme activity patterns of eight central primary metabolism enzymes across phloem, cambium, and developing wood of aspen (Populus tremula L.) were compared with transcript levels obtained by RNA sequencing of sequential stem sections from the same trees. Enzymes were selected on the basis of their importance in sugar metabolism and in linking primary metabolism to lignin biosynthesis. Existing enzyme assays were adapted to allow measurements from ~1 mm3 sections of dissected stem tissue. These experiments provided high spatial resolution of enzyme activity changes across different stages of wood development, and identified the gene transcripts probably responsible for these changes. In most cases, there was a clear positive relationship between transcripts and enzyme activity. During secondary cell wall formation, the increases in transcript levels and enzyme activities also matched with increased levels of glucose, fructose, hexose phosphates, and UDP-glucose, emphasizing an important role for transcriptional regulation in carbon allocation to developing aspen wood. These observations corroborate the efforts to increase carbon allocation to wood by engineering gene regulatory networks.

N-3 polyunsaturated fatty acids (PUFA) are essential for foetal development. Hence, including n-3 PUFA in the sow diet can be beneficial for reproduction. Both the amount and form (precursor fatty acids vs. long chain PUFA) of supplementation are important in this respect. Furthermore, including n-3 PUFA in the diet can have negative effects, such as decreased arachidonic acid (ARA) concentration and increased oxidative stress. This study aimed to compare the efficacy to increase eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) concentrations in the piglet, when different concentrations of linseed oil (LO, source of precursor a-linolenic acid) or fish oil (FO, source of EPA and DHA) were included in the maternal diet. Sows were fed a palm oil diet or a diet including 0.5% or 2% LO or FO from day 45 of gestation until weaning. Linoleic acid (LA) was kept constant in the diets to prevent a decrease in ARA, and all diets were supplemented with a-tocopherol acetate (150 mg/kg) and organic selenium (0.4 mg/kg) to prevent oxidative stress. Feeding 0.5% LO or 0.5% FO to the sows resulted in comparable EPA concentrations in the 5-day old piglet liver, but both diets resulted in lower EPA concentrations than when 2% LO was fed. The highest EPA concentration was obtained when 2% FO was fed. The DHA level in the piglet liver could only be increased when FO, but not LO, was fed to the sows. The 2% FO diet had no advantage over the 0.5% FO diet to increase DHA in the piglet. Despite the constant LA concentration in the sow diet, a decrease in ARA could not be avoided when LO or FO were included in the diet. Feeding 2% FO to the sows increased the malondialdehyde concentration (marker for lipid peroxidation) in sow plasma, but not in piglets.

Although a considerable increase in our knowledge concerning the importance of metabolic adjustments to unfavorable growth conditions has been recently provided, relatively little is known about the adjustments which occur in response to fluctuation in environmental factors. Evaluating the metabolic adjustments occurring under changing environmental conditions thus offers a good opportunity to increase our current understanding of the crosstalk between the major pathways which are affected by such conditions. To this end, plants growing under normal conditions were transferred to different light and temperature conditions which were anticipated to affect (amongst other processes) the rates of photosynthesis and photorespiration and characterized at the physiological, molecular, and metabolic levels following this transition. Our results revealed similar behavior in response to both treatments and imply a tight connectivity of photorespiration with the major pathways of plant metabolism. They further highlight that the majority of the regulation of these pathways is not mediated at the level of transcription but that leaf metabolism is rather pre-poised to adapt to changes in these input parameters.

International audience; The spatiotemporal dynamics of, and interspecific differences in, the acquisition of litter-derived nitrogen (N) by natural assemblages of ectomycorrhizal root tips are poorly understood. Small cylindrical mesh bags containing 15N-labelled beech (Fagus sylvatica) leaf litter that permit hyphal but not root ingrowth were inserted vertically into the top soil layer of an old-growth beech forest. The lateral transfer of 15N into the circumjacent soil, roots, microbes and ectomycorrhizas was measured during an 18-month exposure period. Ectomycorrhial fungi (EMF) showed large interspecific variation in the temporal pattern and extent of 15N accumulation. Initially, when N was mainly available from the leachate, microbes were more efficient at N immobilization than the majority of EMF, but distinct fungal species also showed significant 15N accumulation. During later phases, the enrichment of 15N in Tomentella badia was higher than in microbes and other EMF species. Roots and soil accumulated 15N with a large delay compared with microbes and EMF. Because approximately half of the studied fungal species had direct access to N from leaf litter and the remainder to N from leached compounds, we suggest that EMF diversity facilitates the N utilization of the host by capturing N originating from early-released solutes and late degradation products from a recalcitrant source.

Endophytic fungi and ectomycorrhizal fungi co-exist in the mycorrhizal root tips of boreal forest trees.However, very little is known about the functional role they play in their host’s biology.The activity of enzymesresponsible for important biochemical processes is used to determine the functional role of root-associatedmycorrhizal fungi. However, enzyme activity is never studied in the presence of endophytic fungi in-planta. Theaims of this study were to investigate the effect of Scots pine (Pinus sylvestris L.) root-isolated fungal endophytes on the host plant root morphology, to determine their functional effects using host root-excreted enzyme activitymeasurements, and to compare them with roots colonized by decomposer and ectomycorrhizal fungal strains andnoncolonised Scots pine root tips.Our results show that endophytic fungi did not damage the pine roots incontrast to the decomposer fungi. The endophytic fungi penetrated the cortical cells of the host plant. The rootscolonised by endophytic fungi produce different exo-enzymes compared with those produced by roots colonizedby other fungal groups or noncolonized control root tips.Our results indicate that endophytic fungi are clearlya distinctive ecological group of fungi that have functional traits different from those of ectomycorrhizal anddecomposer fungi.; Les champignons endophytes et ectomycorhiziens coexistent dans les extrémités radiculaires mycorhi-ziennes des arbres de la forêt boréale.Cependant, on sait vraiment peu de choses du rôle fonctionnel qu’ils jouent dans la biologie de leur hôte. L’activité des enzymes responsables de processus biochimiques importants est utilisée pour expliquer le rôle fonctionnel des champignons mycorhiziens associés aux racines. Toutefois, l’activité enzymatique n’est jamais étudiée en présence de champignons endophytes « in planta ». Les buts de l’étude présente étaient d’examiner l’effet d’endophytes fongiques isolés de racines du pin sylvestre (Pinus sylvestris L.) sur la morphologie de la racine de la plante–hôte, de déterminer leur effet fonctionnel en utilisant des mesures de l’activité enzymatique excrétée par les racines de l’hôte et de les comparer aux racines colonisées par des souches de champignons décomposeurs et ectomycorhiziens et aux extrémités radiculaires de pin sylvestre non colonisées.Les résultats des auteurs montrent que les champignons endophytes n’endommagent pas les racines de pin comparativement aux champignons décomposeurs. Les champignons endophytes pénétraient les cellules corticales de la plante-hôte. Les racines colonisées par les champignons endophytes produisent différentes exo-enzymes comparativement a celles produites par les racines colonisées par d’autres groupes de champignons ou des extrémités radiculaires contrôles non colonisées.Leurs résultats indiquent que les champignons endophytes constituent clairement un groupe écologique distinctif de champignons qui possèdent des traits fonctionnels différents de ceux des champignons ectomycorhiziens et décomposeurs.

Central metabolism is a coordinated network that is regulated at multiple levels by resource availability and by environmental and developmental cues. Its genetic architecture has been investigated by mapping metabolite quantitative trait loci (QTL). A more direct approach is to identify enzyme activity QTL, which distinguishes between cis-QTL in structural genes encoding enzymes and regulatory trans-QTL. Using genome-wide association studies, we mapped QTL for 24 enzyme activities, nine metabolites, three structural components, and biomass in Arabidopsis thaiiana. We detected strong cis-QTL for five enzyme activities. A cis-QTL for UDP-glucose pyrophosphorylase activity in the UGP1 promoter is maintained through balancing selection. Variation in acid invertase activity reflects multiple evolutionary events in the promoter and coding region of VAC-INV. cis-QTL were also detected for ADP-glucose pyrophosphorylase, fumarase, and phosphoglucose isomerase activity. We detected many trans-QTL, including transcription factors, E3 ligases, protein targeting components, and protein kinases, and validated some by knockout analysis. trans-QTL are more frequent but tend to have smaller individual effects than cis-QTL. We detected many colocalized QTL, including a multitrait QTL on chromosome 4 that affects six enzyme activities, three metabolites, protein, and biomass. These traits are coordinately modified by different ACCELERATED CELL DEATH6 alleles, revealing a trade-off between metabolism and defense against biotic stress.

International audience; BACKGROUND: To reduce rates of synthetic insecticide applications, natural product alternatives and synergists are needed. A study has been made of the toxicity of ethanolic senescent leaf extracts (SLEs) of Jatropha gossypifolia and Melia azedarach on larvae of the noctuid pest Spodoptera frugiperda. Their effects as syngergists and inhibitors of several enzyme activities are also reported. RESULTS: When added to the diet, M. azedarach SLE showed lower toxicity than J. gossypifolia SLE. However, after 2 weeks on the diet, the M. azedarach SLE proved to be lethal to 100% of the larval population. Artificial diets with both SLEs have an antifeedant effect on armyworm larvae. Acute toxicity after topical application in a dipping assay was relatively low for both J. gossypifolia and M. azedarach SLEs (LC50 of 2.6 and 1.4 g L-1, respectively, after 24 h). However, mixtures of the SLEs of M. azedarach and J. gossypifolia had a strong synergistic effect with cypermethrin. Synergism was higher with the J. gossypifolia SLE, perhaps because it contains several natural products with a methylenedioxyphenyl moiety. Both extracts inhibited P450, general esterase and acetylcholinesterase activities in vitro and in vivo. CONCLUSION: Both J. gossypifolia and M. azedarach SLEs are antifeedants to armyworm larvae when present in the food, and also have a synergistic effect with cypermethrin in topical assays. Although the synergistic effect is less than with piperonyl butoxide, both SLEs have some inhibitor activity against detoxification enzymes and acetylcholinesterase. Thus J. gossypifolia and M. azedarach SLEs may be considered as ecofriendly approaches for the control of S. frugiperda in order to reduce cypermethrin usage. Copyright (c) 2012 Society of Chemical Industry

Activation of microglia is a hallmark of inflammatory, infectious, and degenerative diseases of the central nervous system. Several studies have indicated that there is an increase in release of beta-glucuronidase by activated microglia into the extracellular space at the site of neuroinflammation. beta-glucuronidase is involved in the hydrolysis of glycosaminoglycans on the cell surface and the degradation of the extracellular matrix. Therefore, beta-glucuronidase might be a biomarker for ongoing neurodegeneration induced by neuroinflammation. In this study, we investigated whether the PET tracer F-18-FEAnGA was able to detect beta-glucuronidase release during neuroinflammation in a rat model of herpes encephalitis. Methods: Male Wistar rats were intranasally inoculated with herpes simplex virus 1 (HSV-1) or phosphate-buffered saline as a control. C-11-(R)-PK11195 and F-18-FEAnGA small-animal PET scans were acquired for 60 min. Logan graphical analysis was used to calculate F-18-FEAnGA distribution volumes (DVLogan) in various brain areas. Results: After administration of F-18-FEAnGA, the area under the activity concentration-versus-time curve of the whole brain was 2 times higher in HSV-1-infected rats than in control rats. In addition, the DVLogan of F-18-FEAnGA was most increased in the frontopolar cortex, frontal cortex, bulbus olfactorius, cerebral cortex, cerebellum, and brainstem of HSV-1-infected rats, when compared with control rats. The conversion of F-18-FEAnGA to 4-hydroxy-3-nitrobenzyl alcohol was found to be 1.6 times higher in HSV-1-infected rats than in control rats and correlated with the DVLogan of F-18-FEAnGA in the same areas of the brain. Furthermore, the DVLogan of F-18-FEAnGA also correlated with beta-glucuronidase activity in the same brain regions. In addition, DVLogan of F-18-FEAnGA showed a tendency to correlate with C-11-(R)-PK11195 uptake (marker for activated microglia) in the same brain regions. Conclusion: Despite relatively low brain uptake, F-18-FEAnGA was able to detect an increased release of beta-glucuronidase during neuroinflammation.

The shift towards a biobased economy will probably trigger the application of bioenergy by-products to the soil as either amendments or fertilizers. However, limited research has been done to determine how this will influence C and N dynamics and soil functioning. The aim of this work was to investigate the effects of different bioenergy by-products on C and N mineralisation, nutrient availability and microbial content and activity of amended soil and compare them to other more commonly used organic amendments. Two agricultural soils were amended (0.5% w/w) with four different bioenergy by-products (anaerobic digestate, rapeseed meal, bioethanol residue, biochar) and three other commonly used organic amendments (sewage sludge and two composts) and incubated at 20 °C in the laboratory for 30 days. During incubation, soil CO2 and N2O evolution were measured every 4 h by an automatic chromatographic system. After 2, 7 and 30 days of incubation, soil samples were analysed for K2SO4–extractable C, N, NO3−, NH4+ and P, microbial biomass C and three enzymatic activities (β-glucosidase, alkaline phosphatase and leucine aminopeptidase). Soil amendment led to a general increase in soil respiration, available N and P and microbial content and activity, but with remarkably different dynamics and values. Particularly, rapeseed meal and the bioethanol by-product led to N2O emissions and the greatest increases in soil respiration, N availability and enzymatic activity compared with the other amendments. The exception was represented by biochar that did not cause any significant variation with respect to the control, but promoted C accumulation. According to their impact on soil biochemical properties, the materials can be ranked as follows: rapeseed meal, bioethanol residue > anaerobic digestate, sewage sludge > composts > biochar. For each measured parameter, soil properties did not affect the response pattern found for the different treatments, but modified the magnitude of the response. In particular, soil respiration and enzymatic activity were higher in the slightly acidic soil, while greater values of available P were found in the alkaline soil. This study clearly indicates that the impact on GHG emissions and soil functioning of bioenergy by-products needs to be taken into account for a correct life cycle assessment of the bioenergy chain. Moreover, when properly managed, they may represent an effective alternative to usual amendments to improve the quality and nutrient balance of amended soils.

The metabolome is an integral part of a plant's life cycle and determines for a large part its external phenotype. It is the final, internal product of chemical interactions, obtained through developmental, genetic, and environmental inputs, and as such, it defines the state of a plant in terms of development and performance. Understanding its regulation will provide knowledge and new insights into the biochemical pathways and genetic interactions that shape the plant and its surroundings. In this review, we will focus on four dimensions that contribute to the huge diversity of metabolomes and we will illustrate how this diversity shapes the plant in terms of development and performance: (i) temporal regulation: the metabolome is extremely dynamic and temporal changes in the environment can have an immense impact on its composition; (ii) spatial regulation: metabolites can be very specific, in both quantitative and qualitative terms, to specialized organs, tissues, and cell types; (iii) environmental regulation: the metabolic profile of plants is highly dependent on environmental signals, such as light, temperature, and nutrients, and very susceptible to biotic and abiotic stresses; and (iv) genetic regulation: the biosynthesis, structure, and accumulation of metabolites have a genetic origin, and there is quantitative and qualitative variation for metabolomes within a species. We will address the contribution of these dimensions to the wide diversity of metabolomes and highlight how the multi-dimensional regulation of metabolism defines the plant's phenotype.

The quality of commercial cocoa beans, the principal raw material for chocolate production, relies on the combination of factors that include the type of planting material, the agricultural practices, and the post-harvest processing. Among these, the fermentation of the cocoa beans is still the most relevant since it is the process whereby the precursors of the cocoa flavor arise. The formation of these precursors depends on the activity of different microbial groups on the beans pulp. A comparison of fermentations in different countries showed that a well-defined microbial succession does not always take place and that the role of Bacillus spp. in this process remains unclear. Considering the overriding importance of the fermentation to achieve high quality commercial cocoa beans, we discuss the need of addressing the impact of the farming system, the ripeness state of the pods, and the role of microbial interactions on the fermentation in future research. In addition, the problem of high acidification cocoa beans, aspects dealing with the volatile fraction of the flavor, and the cocoa butter properties, all were identified as critical aspects that need further investigation. The standardization of the microbiological methods and the application of metagenomic approaches would magnify the knowledge in this domain.

Microfluidic technologies enable the fabrication of advanced in vitro systems incorporating liver tissue or cells to perform metabolism and toxicity studies for drugs and other xenobiotics. The use of microfluidics provides the possibility to utilize a flow of medium, thereby creating a well-controlled microenvironment. The general goals of most in vitro systems in drug research are to optimally mimic the in vivo situation, and to minimize the number of animals required for preclinical studies. Moreover, they may contribute to a reduced attrition rate of drugs at a late stage of the drug development process; this is especially true if human tissue or cells are used. A number of factors are important in achieving good in vivo predictability in microfluidic systems, of which the biological system itself (cells or tissue) and the incubation conditions are the most important. The last couple of years have seen various microfluidic-based in vitro systems being developed to incorporate many different cells and/or tissues. In this review, microfluidics-based in vitro systems realized to study liver metabolism and toxicity are summarized and discussed with respect to their applications, advantages, and limitations. The biological basis of these systems is evaluated, and incubation conditions considered. Precise control of the cell or tissue microenvironment is a key advantage of using microfluidic technologies, and the benefits of exposing the cells to medium flow are demonstrated. Special attention is also paid to the incorporation of multiple cell types or tissues into a microfluidic device for the investigation of interorgan interactions, which are difficult if not impossible to study in conventional systems.

On a daily basis, planktonic organisms migrate vertically and thus experience widely varying conditions in their physico-chemical environment. In the Gulf of Finland, these changes are larger than values predicted by climate change scenarios predicted for the next century (up to 0.5 units in pH and 5 degrees C in temperature). In this work, we are interested in how temporal variations in physico-chemical characteristics of the water column on a daily and weekly scale influence oxidative stress level and antioxidant responses in the planktonic copepod of the genus Acartia. Responses were determined from samples collected during a two-week field survey in the western Gulf of Finland, Baltic Sea. Our results showed that GST (Glutathione-S-transferase) enzyme activity increased in the surface waters between Weeks I and II, indicating antioxidant defense mechanism activation. This is most likely due to elevating temperature, pH, and dissolved oxygen observed between these two weeks. During Week II also GSSG (oxidized glutathione) was detected, indicating that copepods responded to stressor(s) in the environment. Our results suggest that Acartia copepods seem fairly tolerant to weekly fluctuations in environmental conditions in coastal and estuarine areas, in terms of antioxidant defense and oxidative stress. This could be directly connected to a very efficient glutathione cycling system acting as antioxidant defense system for neutralizing ROS and avoiding elevated levels of LPX.

El pdf del artículo es la versión post-print., Seven Oyster mushroom strains were cultivated in wheat straw (WS) bags supplemented with 0 up to 90% olive mill waste (OMW), a solid residue obtained from a two-phases olive oil production system. All mushroom strains could grow but high OMW concentrations resulted in a significant yield, biological efficiency and productivity decrease, retarding of pinning and flushing and loss of fruiting bodies quality. However, most of the mushroom strains showed no significant differences on cultivation parameters and fruiting bodies quality (except for colour) between control (WS) substrates or substrates supplemented up to 50% OMW (w/w). Addition of 50% OMW to WS substrates turned mushrooms lighter and less reddish. This colour shift was not due to enzymatic oxidations or inhibition since laccase and peroxidase activities were not differing from control. Total phenolic content and antioxidant activity were also similar and no phenolic compounds from OMW were detected in the fruiting bodies. Some of the analysed Pleurotus strains were better suited to grow on OMW supplemented substrates than others.

One of the key issues in compost research is to assess when the compost has reached a mature stage. The maturity status of the compost determines the quality of the final soil amendment product. The nematode community occurring in a Controlled Microbial Composting (CMC) process was analyzed with the objective of assessing whether the species composition could be used as a bio-indicator of the compost maturity status. The results obtained here describe the major shifts in species composition that occur during the composting process. Compared to terrestrial ecosystems, nematode succession in compost differs mainly in the absence of K-strategists and numerical importance of diplogastrids. At the beginning of the composting process (thermophilic phase), immediately after the heat peak, the nematode population is primarily built by bacterial feeding enrichment opportunists (cp-1) (Rhabditidae, Panagrolaimidae, Diplogastridae) followed by the bacterial-feeding general opportunists (cp-2) (Cephalobidae) and the fungal-feeding general opportunists (Aphelenchoididae). Thereafter, during the cooling and maturation stage, the bacterial-feeding-predator opportunistic nematodes (Mononchoides sp.) became dominant. Finally, at the most mature stage, the fungal-feeding Anguinidae (mainly Ditylenchus filimus) were most present. Both, the Maturity Index (MI) and the fungivorous/bacterivorous ratio (f/b ratio), increase as the compost becomes more mature (ranging, respectively, from 1 to 1.86 and from 0 to 11.90). Based on these results, both indices are suggested as potential suitable tools to assess compost maturity.

Arabidopsis thaliana natural variation was used to study plant performance viewed as the accumulation of photo-assimilates, their allocation and storage, in relation to other growth-related features and flowering-related traits. Quantitative trait locus (QTL) analysis using recombinant inbred lines derived from the cross between Landsberg erecta (originating from Poland) and Kondara (originating from Tajikistan) grown on hydroponics, revealed QTLs for the different aspects of plant growth-related traits, sugar and starch contents and flowering-related traits. Co-locations of QTLs for these different aspects were detected at different regions, mainly at the ER locus; the top of chromosomes 3, 4 and 5; and the bottom of chromosome 5. Increased plant growth was associated with early flowering and leaf transitory starch, and correlated negatively with the levels of soluble sugar at early phases of development. From the significant correlations and the co-locations of the QTLs for these aspects, we conclude that there is a complex relationship between plant growth-related traits, carbohydrate content and flowering-related traits.

Microorganisms are prime drivers of ecosystem functions in the Arctic, and they are essential for vegetation succession. However, very little is known about the phylogenetic and functional diversities of the bacterial communities associated with Arctic plants, especially in low organic matter soils. Here, we studied the diversity and community structure of the total and diazotrophic bacterial communities in the rhizospheres of two Arctic pioneer plant species, Oxyria digyna and Saxifraga oppositifolia, as well as the phenotypic profiles of these communities.Plant and soil samples were harvested from four sampling sites located in the low (Finnish) and high (Norwegian) Arctic. Bacterial diversities and community structures were determined with 16S rRNA and nifH gene-targeted PCR and T-RFLP profiling. The phenotypic (functional and antibiotic resistance) profiles of the soil bacterial communities were determined with BIOLOG Gen III plates.Location and soil type, as well as plant species were shown to significantly influence the bacterial community structures. This was evident from the clustering of the communities per sampling location and per plant species in ordination plots. Geographical location as well as, plants also influenced the functional profiles of the soil bacterial communities. The antibiotic resistance profiles were associated with the location the communities were derived from, whereas the abilities to tolerate oxidative stress and specific antibiotics were associated with the rhizosphere communities.