Non-parametric multivariate comparisons of soil fungal composition: Sensitivity to thresholds and indications of structural redundancy in T-RFLP data

Complex soil microbial data produced by molecular profiling techniques, such as terminal restriction fragment length polymorphism (T-RFLP), are often analysed using multivariate statistical methods. Despite this, there has been little evaluation of the sensitivity of multivariate methods to routine data manipulations such as the application of noise thresholds. We examine effects of three percentage area thresholds (0.1%, 0.5% and 1.0%; i.e. ranging from low to commonly applied) on non-metric multidimensional scaling (NMDS) ordinations of soil fungal T-RFLP profiles. We then interpret threshold effects by introducing the concept of structural redundancy in T-RFLP data.NMDS ordinations compared 20 soil samples (encompassing seven sites, two forest types, and three locations) for T-RFLP presence/absence data, which were produced using primers specific to the rDNA internal transcribed spacer (ITS) region, and three separate restriction enzymes (HinfI, AluI and TaqI). Increasing thresholds from 0.1% to 1.0% led to decreases in average number of detected reproducible fragments per site of 57% (HinfI), 75% (AluI), and 69% (TaqI). However, despite the removal of many fragments unique to site/forest type/location, the application of increasing thresholds did not significantly change NMDS patterns for any enzyme in both the complete data and in a more weakly structured sub-group (involving one forest type and two locations). Thus, our data indicate that application of area thresholds up to 1.0% would have minimal impact on NMDS-based comparisons of soil fungal composition.Robustness of NMDS patterns to considerable fragment loss with increasing threshold suggested a degree of ‘structural redundancy’ in our T-RFLP data – that is, multiple fragments per soil sample were interchangeable in the way they contributed to between-sample NMDS patterns. Indeed, for each restriction enzyme, we found 3–4 peels of data (i.e. mutually exclusive sub-sets) that were capable of reproducing overall patterns in presence/absence data at the 0.1% threshold. Despite potential in the T-RFLP method for production of more than one fragment per fungal species/phylotype, we present arguments to support at least some translation of structural redundancy in T-RFLP data to structural redundancy in fungal community comparisons (i.e. the between-soil similarity patterns can be explained by, or are imprinted in, multiple groups of fungal phylotypes). Our analyses highlight structural redundancy as an efficient method for identifying key phylotypes responsible for differences in community composition among soils, and as a promising starting point for improved understanding of many aspects of spatial soil ecology.     

Proposal for a unified nomenclature for target‐site mutations associated with resistance to fungicides

Evolved resistance to fungicides is a major problem limiting our ability to control agricultural, medical and veterinary pathogens and is frequently associated with substitutions in the amino acid sequence of the target protein. The convention for describing amino acid substitutions is to cite the wild‐type amino acid, the codon number and the new amino acid, using the one‐letter amino acid code. It has frequently been observed that orthologous amino acid mutations have been selected in different species by fungicides from the same mode of action class, but the amino acids have different numbers. These differences in numbering arise from the different lengths of the proteins in each species. The purpose of the present paper is to propose a system for unifying the labelling of amino acids in fungicide target proteins. To do this we have produced alignments between fungicide target proteins of relevant species fitted to a well‐studied ‘archetype’ species. Orthologous amino acids in all species are then assigned numerical ‘labels’ based on the position of the amino acid in the archetype protein. © 2016 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.     

Growth of Mature Beech in Relation to Ozone and Nitrogen Deposition: an Epidemiological Approach

Stem increment of mature Fagus sylvatica L. from 57 plots in Switzerland was analysed with respect to environmental factors using multilinear regression. Nitrogen (N) deposition was positively correlated with stem growth, with an increase by 41.8% (confidence interval 38.9-44.2) per 10 kg N ha^-1 a^-1. There was a negative relationship between ozone (O₃) dose and diameter increment. The fit was better for maximum rather than average exposure values. Coefficients indicated growth changes of -22.5% (14.3-28.6 confidence interval) and -35.1% (17.8-47.3) respectively per 10 ppm hours. These changes exceed the -6.1% found in experiments with beech seedlings. This difference is mainly attributed to the fact that the seedling data are calculated for a single season's exposure whereas the stem increment data extend over four years, representing the product of four annual reductions. Increased sensitivity of mature trees compared to seedlings, however, is also suggested.     

Lysimeter experiment to investigate the potential influence of diffusion-limited sorption on pesticide availability for leaching

Pesticide leaching from soil has been shown to decrease with increasing time from application to irrigation. It is hypothesized that the availability of compounds for leaching decreases due to diffusion and sorption inside soil aggregates. Previous work showed that pesticide sorption inside soil aggregates increases significantly during the first days after application. The study presented here tested if diffusion into aggregates could explain the leaching of four aged pesticides from manually irrigated soil cores. Azoxystrobin, chlorotoluron, cyanazine, and bentazone were applied to 30 undisturbed cores (25 cm long, 23.7 cm diameter) from a clay loam soil. The soil cores were irrigated 1, 3, 7, 14, and 28 days after application. Leachate was collected and analyzed. The amount of pesticide found in leachate decreased rapidly with time from application. Pesticide losses in leachate declined 2.5-27 times faster than total residues in soil. The decline was 4-5 times faster for the more strongly sorbed pesticides (azoxystrobin, chlorotoluron, and cyanazine) than for bentazone. In previous work, we derived a model to describe sorption and diffusion of the pesticides in small aggregates from the same soil. The diffusion model was used here to describe sorption inside the large aggregates in the soil cores and extended to describe pesticide leaching by interaggregate flow. The model showed a significant decline in leaching with time from application, which supports the theory that diffusion-limited sorption in aggregates influences the availability for pesticide leaching, although it does not exclude alternative explanations for this decline. The model well described the decline in leaching for three out of four pesticides. The interaggregate transport model could, however, not account for the amount of preferential flow in the cores and underestimated the leaching of bentazone.     

Microbial aspects of atrazine biodegradation in relation to history of soil treatment

Among 15 soils with different cropping practices, seven which had an history of repeated atrazine applications showed accelerated degradation of this herbicide. By contrast, grassland or agricultural soils with no recorded atrazine application, at least for the last three years, had a low degradation potential. No direct relation was found between the rate of atrazine mineralisation and the size of the microbial biomass. In adapted soils, the amounts of extractable residues were lowered and the very high percentages of radioactivity from [ring-¹⁴C]atrazine recovered as [¹⁴C]carbon dioxide demonstrated that N-dealkylation and deamidation were the only processes for micro-organisms to derive carbon and energy for heterotrophic growth. Kinetics of microbial ¹⁴C accumulation revealed that atrazine ring carbon could be incorporated by direct oxidative condensation with structural components of the bacterial or fungal cell whereas side-chain carbon was preferentially used for biosynthesis of new protoplasmic cell material, as confirmed by the high turnover rate of radiolabelled microbial components. From the determination of the Michaelis–Menten parameters, V_m and K_m in the presence of different selective biocides, it was possible to conclude that fungi were probably less active in atrazine degradation than bacteria and that over years the microbial atrazine-degrading community showed an increased efficiency. © 1999 Society of Chemical Industry     

Ontology-based simulation of water flow in organic soils applied to Florida sugarcane

An ontology-based simulation (OntoSim) is a unique data modeling environment where soil–plant-nutrient processes are represented as database objects and the user-defined relationships among objects are used to generate computer code (Java) for running the simulation. The aim of this study was to model hydrologic processes of sugarcane-grown organic soils utilizing OntoSim in the Everglades Agricultural Area (EAA) of South Florida. This OntoSim-Sugarcane model describes the complex hydrology of sub-irrigation and open ditch drainage commonly used on Florida farms.Model calibration was conducted by (i) selecting rectangular farm water management units (<12 ha), which are encompassed with farm ditches, from two farms in the EAA, (ii) assembling all relevant input data including water tables (WT) recorded at the monitoring farm well of each unit, and (iii) optimizing the fits between the simulated and observed daily WT during two consecutive water years (WY). By calibrating two site-specific parameters – lateral saturated hydraulic conductivities of soil profiles and vertical saturated hydraulic conductivity of the underlying limestone bedrock – good agreement between simulated and observed daily WT was obtained (Nash–Sutcliffe efficiency coefficient >0.65; coefficient of residual mass <1%) within the units during WY96–97 (May 1995–April 1997). The validation of the model during subsequent WY98–99 at both units also showed Nash–Sutcliffe efficiency >0.55 and coefficient of residual mass <3%. It indicated that OntoSim-Sugarcane is able to simulate daily fluctuations of WT within the farm units and estimate lateral drainage/sub-irrigation and deep seepage that significantly contribute to the water balance at farms in the EAA. Thus, it can be a promising management tool to provide farmers with accurate assessment of water movement in this agricultural area.     

Nutrient uptake and growth of potato: Arbuscular mycorrhiza symbiosis interacts with quality and quantity of amended biochars

Aims : The aim of this study was to explore interactive effects between quality (types) and quantity (application rates) of biochar as well as of arbuscular mycorrhiza (AM) symbiosis on the growth of potato plants. Methods : A low P sandy loam soil was amended with 0%, 1.5%, or 2.5% (w/w) of either of 4 types of biochar, which were produced from wheat straw pellets (WSP) or miscanthus straw pellets (MSP) pyrolyzed at temperatures of either 550°C or 700°C. Potato plants grown in pots containing the soils or soil biochar mixture were inoculated with or without AM fungus (AMF), Rhizophagus irregularis. The experiment was carried out under fully irrigated semi‐field conditions and plants were harvested 101 days after planting. Results : Application of high temperature biochar decreased growth, biomass and tuber yield of potato plants, while the low temperature biochar had a similar effect on yield as plants grown without biochar amendment. Total biomass of potato plants were decreased with the increasing rate of biochar. Arbuscular mycorrhizal fungus inoculation stimulated the growth of potato plants in all organs, increased tuber biomass significantly in 1.5% MSP700 amended plants, and to a lesser degree for WSP700, MSP550, and WSP550. In addition, plant biomass gain was linearly related to N, P, and K uptake, the ratio of P to N in the leaf of plants indicated that all treatments were mainly P‐limited. A multiple linear regression using P uptake and biochar rate as independent variables explained 91% of the variation in total biomass. The single effect of AMF inoculation, type and rate of biochar affected plant N, P and K uptake similarly. While AMF inoculation significantly increased P uptake in potato plants grown in soil with WSP700 or MSP700 despite of the rate of biochar. In general, application of biochar significantly increased AMF root colonization of potato plants. Conclusions : The application of MSP550 at 1.5% combined with AMF stimulated growth of potato the most. Furthermore, the results indicated that the interactive effect of AMF inoculation, biochar type and application rate on potato growth to a large extent could be explained by effects on plant nutrient uptake.     

Relationship between lipid and protein oxidation in fish

Reactive oxygen species (ROS) are generated in all aerobic organisms. Free radicals are highly reactive ROS that cause damage to biological materials. Fish is rich in polyunsaturated fatty acids, and hence, very prone to lipid peroxidation. Both lipid and protein oxidations are important for quality loss during storage of fish, with high impact on taste and texture. Also, there are interactions between protein and secondary lipid oxidation products (aldehydes) that occur in foods because the oxidation products from one reaction can further react with both lipids and proteins respectively. This review focuses on the mechanisms and pathways of the lipid and protein oxidation and their possible relationship. Additionally, the target amino acids and final impacts of this relationship were considered. We propose that the products of lipid oxidation promote protein oxidation in fish rather than the other way around specially, during frozen storage, while during postmortem changes protein oxidation dominates. Finally, it seems that, secondary products of lipid oxidation might have more impact on the functionality of proteins from both Michael addition and Schiff base reaction rather than lipid hydroperoxides and lipid radical transfer.     

Limitations when quantifying microbial carbon and nitrogen by fumigation‐extraction in rooted soils

Soil microbial C and N (C_mic, N_mic) estimation by the chloroform fumigation‐extraction method is erroneous in densely rooted soils due to CHCl₃‐labile C and N compounds. The effect of a pre‐extraction with 50 mM K₂SO₄ and a pre‐incubation (conditioning at 25 °C for 7 days) on the flush in extractable, CHCl₃‐labile C (C‐flush) and N (N‐flush) was tested with reference to rooting density (0.3—75 mg root dry matter g^—1) in one arable and 3 grassland soils. In the arable soil and in the second horizon (10—20 cm) of a grassland soil, C‐flush values were not affected by the pre‐extraction. However, the pre‐extraction considerably reduced C‐flush values in the top soils of the grassland (above 10 cm). Only about 42 % was found in the pre‐extracted roots and the rest was lost during the pre‐extraction. The estimated concentrations of N_mic decreased due to pre‐extraction of soil samples with low root biomass. Clearly, the concentrations of N_mic were underestimated by introducing the pre‐extraction. Soil pre‐incubation reduced C‐flush values only slightly, whereas N‐flush values were not affected. It can be concluded that (1) CHCl₃‐labile root C and N is partly extracted with K₂SO₄ after pre‐incubation and (2) CHCl₃‐labile C and N removed with the roots during pre‐extraction is partly derived from microbial biomass. Soils with low rooting density (arable soils, grassland soils below approximately 10 cm depth) should therefore be fumigated and extracted without pre‐extraction. In densely rooted soils, fumigation extraction with and without pre‐extraction probably gives estimates for the minimum and maximum of C_mic and N_mic.     

Effect of parental genotypes on haploid embryo and plantlet formation in wheat × maize crosses

Genotypic influence of both male and female parents on haploid production through interspecific crosses was studied using eight wheat and four maize genotypes. The average numbers of embryos and green haploid plantlets obtained per pollinated floret were 17.6% and 10.1%, respectively. Clear genotypic influence of the wheat genotype was detected, but heterozygosity of the wheat did not affect haploid production. Analogous response to anther culture and interspecific crossing was observed, still a wheat variety which did not respond to anther culture, produced 1.1 plantlets per pollinated spike upon maize pollination. This appears to be a major advantage of interspecific crossing compared to anther culture technique in wheat. Circumstantial evidence is presented for specific wheat × maize interaction on haploid plantlet formation. Rye chromatin enhanced haploid production but only in a complete 1B/1R substitution line. Ovaries with an embryo were found to be dispersed evenly all over the wheat spike, suggesting that within certain limits the developmental stage of ovaries and thus time of pollination within a spike are not as important as it was previously assumed. This revised version was published online in July 2006 with corrections to the Cover Date.