Pavel Formánek

Non-protein amino acids: plant, soil and ecosystem interactions

Non-protein amino acids are a significant store of organic nitrogen in many ecosystems, but there is a lack of knowledge relating to them. Research has indicated that they play important roles as metabolites, as allelopthic chemicals, in nutrient acquisition, in signalling and in stress response. They are also thought to be responsible for significant medical issues in both invertebrate and vertebrate animals. This review attempts to appraise the literature related to non-protein amino acids, both in terms of their metabolism, plant–soil interactions and at the level of the ecosystem, where they are seen as significant drivers of structure and function. Finally, important areas for future research are discussed.

The significance of D-amino acids in soil, fate and utilization by microbes and plants: review and identification of knowledge gaps

BackgroundD-amino acids are far less abundant in nature than L-amino acids. Both L- and D-amino acids enter soil from different sources including plant, animal and microbial biomass, antibiotics, faeces and synthetic insecticides. Moreover, D-amino acids appear in soil due to abiotic or biotic racemization of L-amino acids. Both L- and D-amino acids occur as bound in soil organic matter and as “free“ amino acids dissolved in soil solution or exchangeably bound to soil colloids. D-amino acids are mineralized at slower rates compared to the corresponding L-enantiomers. Plants have a capacity to directly take up “free“ D-amino acids by their roots but their ability to utilize them is low and thus D-amino acids inhibit plant growth.ScopeThe aim of this work is to review current knowledge on D-amino acids in soil and their utilization by soil microorganisms and plants, and to identify critical knowledge gaps and directions for future research.ConclusionAssessment of “free“ D-amino acids in soils is currently complicated due to the lack of appropriate extraction procedures. This information is necessary for consequent experimental determination of their significance for crop production and growth of plants in different types of managed and unmanaged ecosystems. Hypotheses on occurrence of “free“ D-amino acids in soil are presented in this review.

Aliphatic, cyclic, and aromatic organic acids, vitamins, and carbohydrates in soil: a review.

Organic acids, vitamins, and carbohydrates represent important organic compounds in soil. Aliphatic, cyclic, and aromatic organic acids play important roles in rhizosphere ecology, pedogenesis, food-web interactions, and decontamination of sites polluted by heavy metals and organic pollutants. Carbohydrates in soils can be used to estimate changes of soil organic matter due to management practices, whereas vitamins may play an important role in soil biological and biochemical processes. The aim of this work is to review current knowledge on aliphatic, cyclic, and aromatic organic acids, vitamins, and carbohydrates in soil and to identify directions for future research. Assessments of organic acids (aliphatic, cyclic, and aromatic) and carbohydrates, including their behaviour, have been reported in many works. However, knowledge on the occurrence and behaviour of D-enantiomers of organic acids, which may be abundant in soil, is currently lacking. Also, identification of the impact and mechanisms of environmental factors, such as soil water content, on carbohydrate status within soil organic matter remains to be determined. Finally, the occurrence of vitamins in soil and their role in biological and biochemical soil processes represent an important direction for future research.

Significance of the natural occurrence of L- versus D-pipecolic acid: a review.

Pipecolic acid naturally occurs in microorganisms, plants, and animals, where it plays many roles, including the interactions between these organisms, and is a key constituent of many natural and synthetic bioactive molecules. This article provides a review of current knowledge on the natural occurrence of pipecolic acid and the known and potential significance of its L- and D-enantiomers in different scientific disciplines. Knowledge gaps with perspectives for future research identified within this article include the roles of the L- versus the D-enantiomer of pipecolic acid in plant resistance, nutrient acquisition, and decontamination of polluted soils, as well as rhizosphere ecology and medical issues.

Estimation of protease activity in soils at low temperatures by casein amendment and with substitution of buffer by demineralized water

Summary.The aim of this work was to modify the method of Ladd and Buttler (1972), by substituting Tris–HCl buffer (pH 8.52) with demineralized water (DEMI H2O), in order to assess its suitability for measurement of casein-protease activity at pH levels close to those of real soil in H2O. Measurements were undertaken over a range of incubation temperatures from 3 to 49 °C. Testing was performed on one organic soil and two different mineral soils. The substitution of Tris–HCl buffer by DEMI H2O at 49 °C decreased casein-protease activity to 67.25% in mineral soil and to 53.76% in organic soil. With decreasing temperature casein-protease activity decreased the most in organic soil, i.e., 0.07% of original its value at 3 °C. The incubation period was extended to maximally 336 h at 3 °C to totally obtain >10.0% of L-tyrosine equivalents released at optimum or close to optimum temperature and pH conditions. The Q10 values of casein-protease activity measured after substituting Tris–HCl buffer with DEMI H2O were unexpectedly high. Between the temperatures of 3 and 49 °C Q10 ranged from 3.46 to 4.25, whereas between 3 and 25 °C Q10 ranged from 6.78 to 11.08. Therefore, the modified method of Ladd and Buttler (1972) presented can be used for measurement of soil casein-protease activity under pH conditions close to that of real soil pH and at an averaged soil temperatures measured in the field. This modification makes possible an expression of soil casein-protease activity potential – when being combined with measurements of casein-protease activity under optimum or close to optimum temperature and pH conditions, if high concentration of casein is present.

Bio-available amino acids and mineral nitrogen forms in soil of moderately mown and abandoned mountain meadows

Summary.The abandonment of traditional mowing methods of mountain meadows in the Czech Republic at the end of the last century has resulted in secondary re-colonization of these areas. Altered accumulation of plant biomass resulted in a deceleration of N turnover. A mountain meadow may be regarded as a N-limited ecosystem in which plant nutrition is dependent on direct uptake of soil amino acids. The composition and distribution of ammonium ions, nitrate ions and the 16 bio-available proteinaceuous amino acids were investigated in the top 7 cm of the Ah horizon of a Gleyic Luvisol in a long-term moderately mown meadow and an eleven year old, abandoned or uncut meadow. Ammonium N has a dominant role in both ecosystems. The moderately mown meadow showed accelerated N-turnover and higher net ammonization. The plant community showed a dependence on this form. Plant utilization of nitrates and amino acids appeared to be negligible. The uncut or abandoned meadow showed net ammonization from May (start of the experiment) through August, after which plant N-uptake consisted only of amino acids due to microbial immobilization. The release of bio-available nitrogen from spring until the beginning of summer in the Ah horizon was too low to explain total plant N-uptake. Glutamic acid, arginine and aspartic acids had the highest concentrations of any of the amino acids analyzed.

Effect of Elevated CO2, O3, and UV Radiation on Soils

In this work, we have attempted to review the current knowledge on the impact of elevated CO2, O3, and UV on soils. Elevated CO2 increases labile and stabile soil C pool as well as efficiency of organic pollutants rhizoremediation and phytoextraction of heavy metals. Conversely, both elevated O3 and UV radiation decrease inputs of assimilates to the rhizosphere being accompanied by inhibitory effects on decomposition processes, rhizoremediation, and heavy metals phytoextraction efficiency. Contrary to elevated CO2, O3, or UV-B decreases soil microbial biomass, metabolisable C, and soil Nt content leading to higher C/N of soil organic matter. Elevated UV-B radiation shifts soil microbial community and decreases populations of soil meso- and macrofauna via direct effect rather than by induced changes of litter quality and root exudation as in case of elevated CO2 or O3. CO2 enrichment or increased UV-B is hypothesised to stimulate or inhibit both plant and microbial competitiveness for soluble soil N, respectively, whereas O3 favours only microbial competitive efficiency. Understanding the consequences of elevated CO2, O3, and UV radiation for soils, especially those related to fertility, phytotoxins inputs, elements cycling, plant-microbe interactions, and decontamination of polluted sites, presents a knowledge gap for future research.

Land use effects on carbon quality and soil biological properties in Eutric Cambisol

Abstract The choice of prospective type of farming requires knowledge about the specific relationships that exist between farm management practices and base environmental conditions. Nowadays the protection of soil organic carbon is one of the main tasks, because organic carbon in addition to soil fertility can act in elimination of soil contamination and carbon sequestration. Field experiments were focused on the effect of intensive farming without organic inputs versus grassland on organic carbon content. Organic carbon content (Cox) and humic substance fractions (C-humic acids and fulvic acid fractions), hot water extractable carbon and selected microbial characteristics in Eutric Cambisol were monitored during the period 1999–2010. A priming effect of soil cultivation was detected immediately after tillage. Arable soil with ‘intensive’ crop sequences (exclusively cash crops, cereals, oil plants) and with an optimal level of chemical inputs (mineral fertilizers, pesticides), but without organic farmyard manure had lower content of all carbon forms compared with grassland. 13C NMR spectroscopy and thermal analysis (TGA) were applied to characterize humic acid (HA) structure and stability. More carbon, less oxygen and more aromatic compounds were detected in grassland HA. Slight differences were found in HA thermo-oxidative stability and degradability, which was probably caused by changes in elemental composition and structure. Even the land use had no significant effect on basic microbiological characteristics (basal respiration, microbial biomass and qCO2); the physiology of the microbial community of grassland was altered by a higher ability to utilize L- and D-glutamic acid. The L/D ratio of glutamic acid mineralization indicated no occurrence of stress in soil for both types of farming. It has been demonstrated that although losses of carbon as a result of land-use conversions are generally more rapid, gains of carbon in grassland followed by changes in management practices can also occur.

Selected kinetic parameters of soil microbial respiration in the A horizon of differently managed mountain forests and meadows of Moravian-Silesian Beskids Mts.

The aim of this study was to find out the effect of intensity of thinning (FD-dense stand = 2044 trees/ha; FS-open stand = 1652 trees/ha) performed in young forest stands (99% spruce, 1% fir) in Moravian-Silesian Beskids Mts. (908 m a.s.l.; 49°30′10″ N, 18°32′20″ E) on VDS (C mineralization rate immediately after drying and re-wetting of soil), VBR (basal soil respiration at 60% w/w soil water content measured 5th day after rewetting of dry soil), VMAX (maximum respiration rate after glucose addition measured from 6th day after rewetting of dry soil), VDS/VMAX (heterotrophic respiratory potential) and ACDS/ACBR (the potential flush of biologically available C) in Ae horizon of Haplic and Entic Podzols. The ACDS/ACBR was calculated from three 24-hour respirations of 7-day incubation according to the equation ACDS/ACBR=VDSVMAX/(2VBR(VMAX−VDS)). The aim of the work was also to find the effect of circa 11-year abandonment of a mountain meadow in the locality (825–860 m a.s.l.; 49°30′17″ N, 18°32′28″ E) on the same parameters in Ah horizon of Gleyic Luvisol. The studied parameters were measured in the course of the vegetation season 2004 (May–September) at 30-day intervals. The higher intensity of thinning caused alternately higher or lower or very similar values of VDS, VBR, VMAX, VDS/VMAX and ACDS/ACBR in the course of the season. The abandonment of the meadow increased VDS, VBR, VMAX throughout the whole experiment. VDS/VMAX increased due to the abandonment except for the last sampling in September. Alternately higher or lower or very similar values of ACDS/ACBR in course of the season appeared on abandoned or moderately mown meadows. The lower intensity of thinning or abandonment of the meadow were connected with increasing number of significant (P < 0.05) correlations between the studied properties.

Effect of soil sieving on respiration induced by low-molecular-weight substrates

Abstract The mesh size of sieves has a significant impact upon soil disturbance, affecting pore structure, fungal hyphae, proportion of fungi to bacteria, and organic matter fractions. The effects are dependent upon soil type and plant coverage. Sieving through a 2 mm mesh increases mineralization of exogenously supplied carbohydrates and phenolics compared to a 5 mm mesh and the effect is significant (p<0.05), especially in organic horizons, due to increased microbial metabolism and alteration of other soil properties. Finer mesh size particularly increases arabinose, mannose, galactose, ferulic and pthalic acid metabolism, whereas maltose mineralization is less affected. Sieving through a 5 mm mesh size is suggested for all type of experiments where enhanced mineralization of low-molecular-weight organic compounds needs to be minimalized.