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

Background

D-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.

Scope

The 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.

Conclusion

Assessment 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.     

The ontogeny of lipid bodies (spherosomes) in plant cells

Maturing embryos of 16 oil plants, anise suspension culture cells, and Neurospora crassa cells were prepared for electron microscopy at different stages during massive lipid accumulation. Lipid-rich structures of certain species were best preserved by dehydration of fixed tissues in ethanol without propylene oxide, embedding in Spurr's Medium, and polymerization at room temperature. In all cells examined, spherical lipid bodies (spherosomes) showed a moderately osmiophilic, amorphous matrix and displayed a delimiting half-unit membrane when sectioned medially. Associations with the endoplasmic reticulum (ER) were viewed at any stage during lipid body development but with different frequency in the different plant species. Plastids of fat-storing cells exhibited conspicuously undulate outer and inner envelope membranes that formed multiple contact sites with each other and protuberances into both cytoplasm and stroma. Some species, e.g., Linum, have plastids with tubular structures that connect the inner membrane to the thylakoid system; in addition, in the stroma vesicles fusing with or apparently passing through the envelope were observed. The outer envelope membrane may be associated with ER-like cytoplasmic membrane structures. In addition, lipid bodies of various sizes were found in contact with the plastid envelope. The ultrastructural observations are interpreted to match the published biochemical evidence, indicating that both plastids and ER may be involved in the synthesis of storage lipids and lipid body production.     

Luminometric and differential scanning calorimetry (DSC) studies on heat- and radiation inactivation of Bacillus subtilis luxAB spores

A bioluminescent derivative of Bacillus subtilis containing a plasmid encoding a luxAB fusion under control of a vegetative promoter and gives bioluminescence upon addition of an exogenous long-chain aldehyde has been used as test organism. Its spore populations have been produced and their heat- and radiation survival curves established. Heat-sensitization effect of pre-irradiation of spores was proven not only by colony counting but also with differential scanning calorimetry. Under a linearly programmed temperature increase, the heat destruction of spores surviving 2.5 kGy gamma irradiation resulted in at a few centigrade lower temperature than that of untreated spores. Heat denaturation endotherms in the DSC-thermogram of irradiated spores were shifted to lower temperatures as well. Comparative turbidimetric, luminometric and phase-contrast microscopic studies of untreated, heat-treated and irradiated spore populations showed that the kinetics of germination and the light emission during germination of radiation-inactivated spores were the same as those of untreated spores, revealing that the pre-formed luciferase enzyme packaged into the spores during sporulation remained intact after an irradiation dose causing 90% decrease in number of colony forming spores. Therefore, in contrast to heat-treated spores, the initial bioluminescence reading upon germination of irradiated spores does not reflect the viable count of their population.     

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?Csoil 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.     

A place to hide in the home-cage decreases yolk androgen levels and offspring emotional reactivity in Japanese quail

An animal''s emotional responses are the result of its cognitive appraisal of a situation. This appraisal is notably influenced by the possibility of an individual to exert control over an aversive event. Although the fact that environment controllability decreases emotional responses in animals is well established, far less is known about its potential trans-generational effects. As the levels of avian yolk hormones can vary according to the mother''s environment, we hypothesized that housing environment of mothers would modulate the quality of her eggs and in turn her offspring''s behaviour. Two groups of female Japanese quail were constituted: a group that had access to a place to hide in their home-cage (Hd, n = 20) and a group that had nowhere to hide (NoHd, n = 20) when stressed. Both groups were submitted to daily human disturbances for a twenty-day-period. Hd females produced eggs with both less testosterone and androstenedione than did NoHd females. The emotional and social reactivity of Hd females'' offspring were lower and their growth was slower than those of NoHd females'' offspring. Our results show that a minor difference in housing environment had substantial effects on eggs and offspring. The presence of a shelter probably helped quail to cope with daily human disturbances, producing less reactive offspring. This transgenerational effect caused by an opportunity to hide could lead to applications in care of laboratory animals, conservation biology and animal welfare.     

Mössbauer and susceptibility experiments on different compounds of Fe3+-myoglobin

The static magnetic susceptibilities of different ferric high spin and low spin compounds of myoglobin (Mb(H₂O), Mb(H₂O) frozen under high pressure, MbF, MbCN) were measured in the temperature region between 4.2 K and 130 K. Mössbauer absorption experiments on Mb(H₂O) and MbF were perormed at different temperatures between 4.2 K and 180 K and in small magnetizing fields H1 kOe. The evaluation of our experimental data was performed with a Hamiltonian describing the 3d ⁵-configuration of the ferric iron by taking into account the Coulomb repulsion of the five electrons within the 3d-shell, the crystal electric field of -symmetry, and the spin-orbit coupling. The Hamiltonian contains the splitting energies of the five antibonding d-orbitals (d _xy , d _xz , d _yz , d _x 2_–y 2, d _z 2) as parameters. The values of these energies were obtained by a least squares fitting procedure using our magnetic susceptibility data together with the g-factors taken from the literature. In the case of MbF the energy difference between the two lowest Kramers doublets was also determined from present Mössbauer data. The results of the susceptibility and the Mössbauer data are in good agreement.The splitting energies of the 3d-orbitals can be correlated to the distances between the iron and its nearest neighbours. The different positions of the iron in the compounds investigated are discussed.     

A three dimensional model of the digestion of peptidoglycan by lysozyme

The digestion of single peptidoglycan chains of the recently proposed conformation (Formanek et al., 1974) can be described with the same enzymatic mechanism as proposed by Phillips for a hexasaccharide consisting of alternating N-acetylglucosamine, N-acetylmuramic acid residues (Phillips, 1966). It is shown by model building, that in a peptidoglycan lysozyme complex the peptide chains do not exhibit any sterical hindrance.The digestion of the peptidoglycan sacculus by lysozyme may occur at lattice defects of its paracrystalline structure. A slit of about 30 å lenght and 10–15 å width between peptidoglycan micells may be sufficient for the attachment of lysozyme.     

Rhythmic birds show a better social integration than arrhythmic birds

The activity rhythms of Japanese quail vary from one individual to another. Performing a divergent selection, we obtained one line of quail expressing a robust circadian rhythmicity of feeding activity (R) and one line of quail expressing circadian arrhythmicity of feeding activity (A). We questioned whether the endogenous rhythmicity of an individual could predict its integration in a group. For that, we introduced either an R- or an A-line chick into stable groups of standard chicks. First, we evaluated proximity and synchronization of the introduced chicks on the activities of the other group members. R-chicks remained spatially and temporally closer to other group members than did A-chicks. Second, we evaluated interactions of the introduced chicks and the level of their acceptance by the other group members. R-chicks were more competent to gain access to food than were A-chicks, and separation from their group stressed R-chicks more than A-chicks. Last, successive introductions assessed age effects: before, around, and after dispersal time (～11th day of chicks' life). Most differences between R- and A-chicks were observed between their 7th and 15th day of life. In conclusion, individual endogenous rhythms predict social integration.