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.     

Topsoil organic matter properties in contrasted hedgerow vegetation types

Background and aims

Hedges, semi-natural landscape components, have the ability to integrate both agronomic and environmental functions and to provide several ecosystem services. The aim of this study was to test whether hedgerow vegetation is a determinant of soil organic matter properties in ancient agricultural lands.

Methods

We complemented cluster analysis and ordination to determine the extent to which two types of hedges that were distinct in character-plant species also differed between each other in concentration and composition of two major constituents of soil organic matter, namely humic substances and dissolved organic matter.

Results

The two types of hedges were associated with significant differences in humic carbon content, hormone-like activity and molecular size of humic substances, which, in general, were more similar to those typical of forest than of agricultural soils. Moreover, we detected between-group differences in several phenolic acids.

Conclusions

Variation of the topsoil biochemical properties of hedges may be explained by variation in their vegetation characteristics, similar to other ecosystems. Spontaneous vegetation in hedges perform an important role in controlling the variability of surface soil properties that influence the evolution of soil organic matter and nutrient availability in agricultural lands.     

Coupled soil-availability and tree-limitation nutritional shifts induced by N deposition: insights from N to P relationships in Abies pinsapo forests

Background and aims

Interacting effects of atmospheric N deposition on the degree to which tree demand for other nutrients is met by soil supply has seldom been explored in Mediterranean-type ecosystems. We hypothesized that patterns for the relative availability of N and P in soils will be matched by variations in process rates related to soil organic P cycling and by shifts from N to P limitation of tree growth.

Methods

We examined N/P relationships in Mediterranean-fir (Abies pinsapo) forests from two nearby regions differing in N deposition levels.

Results

N pools and transformation rates and the contribution of organic fractions to the labile P pool in soils showed increasing trends toward the pollution source. Phosphomonoesterase activity (PME) in bulk soils, root PME per unit biomass (but not per unit soil volume) and biomass accumulation in P-fertilized root-in-growth cores incubated in situ were also the highest at the sites receiving elevated N deposition, indicating P limitation. In contrast, forest stands in the region farther from the pollutant source were N-limited (preferential root growth in N-rich soil microsites) and showed lower PME activities and higher total fine root biomass.

Conclusions

In the forests under elevated N deposition, higher values for an overall indicator of soil N status matched with indications of an accelerated soil organic P subcycle and P-limitation of tree growth.     

Dynamics of fertilizer-derived organic nitrogen fractions in an arable soil during a growing season

Background

Inorganic fertilizer is one of the most important anthropogenic inputs which influences soil nutrient turnover in agricultural ecosystems. However, as the key process involved in the maintenance, transformation and stability of soil nitrogen (N), the incorporation and allocation of fertilizer N between different soil organic N (SON) fractions in a growing season remains largely unknown.

Methods

In this study, a field experiment was conducted in triplicate of micro-plots and a total of 200 kg N ha^?1 (¹⁵?N-labeled (NH₄)₂SO₄, 98 atom %) was applied as a basal dressing and two top dressings, at jointing and filling stages, respectively, to a maize crop during one growing season. The distribution and seasonal dynamics of fertilizer N in different SON fractions (i.e., amino acids, amino sugars, hydrolyzable ammonium N and acid insoluble-N) were measured by liquid/gas chromatography–mass spectrometry (LC/GC-MS) and element analysis-combustion-isotope ratio mass spectrometry (EA-C-IRMS) techniques. Path analysis was used to evaluate the transformation processes between organic N fractions derived from fertilizer and N supply strategy in soil-plant system.

Results

The accumulation of fertilizer-derived N in different organic fractions was season-specific. At jointing stage, preferential enrichment of ¹⁵?N was found in soil amino acids plus amino sugars, indicating the active biological immobilization of basal dressing fertilizer N. Nevertheless, there is still a small proportion of fertilizer N stabilized in the acid insoluble fraction. The accumulation of the residual fertilizer N in hydrolyzable ammonium N reached a maximum at filling stage and then declined significantly, implying the rapid release of the fertilizer N remained in mineral forms. The contents of amino acids changed slightly, but they played a very important role in mediating SON transformation.

Conclusion

The hydrolyzable ammonium N was a temporary pool for rapid fertilizer N retention and simultaneously was apt to release N for crop uptake in the current season. In contrast, the amino acids could serve as a transitional pool of available N in the soil-crop system, while the acid insoluble fraction was as a stable pool of fertilizer N. Importantly, there is an interim shift among different pools to maintain soil N turnover; hence N in the amino acid fraction mediates N supply and the depolymerization of SON constituents controls the proceeding of fertilizer N cycling in the soil-plant system.     

Carbon allocation in Larrea tridentata plant-soil systems as affected by elevated soil moisture and N availability

Background and Aims

Global change will likely express itself in southwestern United States arid lands through changes in amounts and timing of precipitation in response to elevated CO₂ concentrations. In addition, increased nitrogen (N) deposition may occur due to increased urban development. This study addressed the effects of water and N availability on C allocation in arid land soil-plant systems.

Methods

Columns filled with Mojave Desert topsoil containing Larrea tridentata seedlings with two treatment levels each of N and soil moisture were labeled by exposure to ¹³C-enriched CO₂.

Results

Increased soil moisture increased plant biomass, total ¹³C uptake, ¹³C levels in leaves, soil organic matter, and soil respiration, decreased relative C allocation to stems but increased allocation to soil organic matter. Increased soil N availability increased N uptake but decreased C allocation to soil respiration presumably due to decreased substrate supply for microbes. There was no detectable label in carbonate C, suggesting that this pool does not significantly contribute to ecosystem C fluxes.

Conclusions

Our study indicates that increased water availability causes increased C uptake with increased C allocation to soil organic matter in Larrea tridentata-dominated communities while increased N deposition will have a minimal impact on C sequestration.     

The impact of land degradation on the C pools in alpine grasslands of the Qinghai-Tibet Plateau

Aims

To determine the effect of grassland degradation on the soil carbon pool in alpine grassland.

Methods

In this study, we calculated the carbon pool in the above-and below-ground biomass, the soil microbial biomass carbon pool, the total organic carbon pool and the soil total carbon.

Results

Grassland degradation has resulted in decreases in biomass and carbon content and has changed the ratio of roots to shoots. However, there was less influence of degradation on dead root biomass. There was most likely a lag effect of changes in dead root biomass following grassland degradation. In the alpine grassland ecosystem, the carbon pool in soil accounts for more than 92 % of the total carbon both in vegetation and soil. The carbon in alpine grassland is stored primarily in the form of total organic carbon below-ground. As organic carbon decreases, the ratio of the microbial biomass carbon pool to the total organic carbon pool increases and then declines with increasing degradation level. Along the grassland degradation gradient, the total vegetation biomass (above-and below-ground) and the soil carbon pool (microbial biomass C, total organic C and total C) all decreased.     

Interactions between leaf litter and soil organic matter on carbon and nitrogen mineralization in six forest litter-soil systems

Background and aims

Leaf litter decomposes on the surface of soil in natural systems and element transfers between litter and soil are commonly found. However, how litter and soil organic matter (SOM) interact to influence decomposition rate and nitrogen (N) release remains unclear.

Methods

Leaf litter and mineral soil of top 0–5 cm from six forests were incubated separately, or together with litter on soil surface at 25 °C for 346 days. Litter N remaining and soil respiration rate were repeatedly measured during incubation. Litter carbon (C) and mass losses and mineral N concentrations in litter and soil were measured at the end of incubation.

Results

Net N transfer from soil to litter was found in all litters when incubated with soil. Litter incubated with soil lost more C than litter incubated alone after 346 days. For litters with initial C: N ratios lower than 52, net N_min after 346 days was 100 % higher when incubated with soil than when incubated alone. Litter net N_min rate was negatively related to initial C: N ratio when incubated with soil but not when incubated alone. Soil respiration rate and net N_min rate did not differ between soil incubated with litter and soil incubated alone.

Conclusions

We conclude that soils may enhance litter decomposition rate by net N transfer from soil to litter. Our results together with studies on litter mixture decomposition suggest that net N transfer between decomposing organic matter with different N status may be common and may significantly influence decomposition and N release. The low net N_min rate during litter decomposition along with the small size of litter N pool compared to soil N pool suggest that SOM rather than decomposing litter is the major contributor to plant mineral N supply.     

Responses of CO2 efflux from an alpine meadow soil on the Qinghai Tibetan Plateau to multi-form and low-level N addition

Aims

To assess the effects of atmospheric N deposition on the C budget of an alpine meadow ecosystem on the Qinghai–Tibetan Plateau, it is necessary to explore the responses of soil-atmosphere carbon dioxide (CO₂) exchange to N addition.

Methods

Based on a multi-form, low-level N addition experiment, soil CO₂ effluxes were monitored weekly using the static chamber and gas chromatograph technique. Soil variables and aboveground biomass were measured monthly to examine the key driving factors of soil CO₂ efflux.

Results

The results showed that low-level N input tended to decrease soil moisture, whereas medium-level N input maintained soil moisture. Three-year N additions slightly increased soil inorganic N pools, especially the soil NH ₄ ⁺ -N pool. N applications significantly increased aboveground biomass and soil CO₂ efflux; moreover, this effect was more significant from NH ₄ ⁺ -N than from NO ₃ ^? -N fertilizer. In addition, the soil CO₂ efflux was mainly driven by soil temperature, followed by aboveground biomass and NH ₄ ⁺ -N pool.

Conclusions

These results suggest that chronic atmospheric N deposition will stimulate soil CO₂ efflux in the alpine meadow on the Qinghai–Tibetan Plateau by increasing available N content and promoting plant growth.     

The activities of soil and root acid phosphatase in the nine tropical rain forests that differ in phosphorus availability on Mount Kinabalu, Borneo

Background and aims

Tropical rain forests on deeply weathered soils are increasingly thought to be limited by phosphorus (P), where plants and associated organisms would demonstrate adaptations to efficiently recycle P using acid phosphatase from organic matter. The activities of soil and root acid phosphatase were investigated in nine tropical rain forests that demonstrated a 20-fold difference in the soil organic P pool on Mt. Kinabalu, Borneo.

Methods

Acid phosphatase activity was measured at pH6.0 using p-nitrophenyl phosphate as substrate.

Results

The specific phosphatase activity of tree roots on a soil-surface-area basis was significantly positively related with P-use efficiency of above-ground productivity, suggesting a physiological linkage between above and below-ground systems in the adaptation to P deficiency. The phosphatase activities of soils and roots were significantly negatively correlated with the pool size of soil organic P fractions, suggesting that demand for P determines phosphatase activities.

Conclusions

It is suggested that tree roots and soil microbes develop more active phosphatases in response to the chronic shortage of soil P, which forms the basis for an important functional role for the efficient acquisition of P from soil organic matter.     

A closeup study of early beech litter decomposition: potential drivers and microbial interactions on a changing substrate

Aims

Litter decomposition and subsequent nutrient release play a major role in forest carbon and nutrient cycling. To elucidate how soluble or bulk nutrient ratios affect the decomposition process of beech (Fagus sylvatica L.) litter, we conducted a microcosm experiment over an 8 week period. Specifically, we investigated leaf-litter from four Austrian forested sites, which varied in elemental composition (C:N:P ratio). Our aim was to gain a mechanistic understanding of early decomposition processes and to determine microbial community changes.

Methods

We measured initial litter chemistry, microbial activity in terms of respiration (CO₂), litter mass loss, microbial biomass C and N (C_mic and N_mic), non purgeable organic carbon (NPOC), total dissolved nitrogen (TDN), NH₄ ⁺, NO₃ ^- and microbial community composition (phospholipid fatty acids – PLFAs).

Results

At the beginning of the experiment microbial biomass increased and pools of inorganic nitrogen (N) decreased, followed by an increase in fungal PLFAs. Sites higher in NPOC:TDN (C:N of non purgeable organic C and total dissolved N), K and Mn showed higher respiration.

Conclusions

The C:N ratio of the dissolved pool, rather than the quantity of N, was the major driver of decomposition rates. We saw dynamic changes in the microbial community from the beginning through the termination of the experiment.     

Estimating belowground nitrogen inputs of pea and canola and their contribution to soil inorganic N pools using 15N labeling

Background and aims

Crop species grown in a diversified crop rotation can influence soil N dynamics to varying degrees due to differences in the quantity and quality of the residues returned to the soil. The aim of this study was to quantify the contribution of N rhizodeposition by canola (Brassica napus L.) and pea (Pisum sativum L.) to the crop residue N balance and soil inorganic N pool.

Methods

Canola and pea were grown in a soil-sand mixture and were subject to cotton-wick ¹⁵N labeling in a greenhouse experiment. Nitrogen-15 recovered in the soil and roots were used to estimate N rhizodeposition.

Results

Belowground N, including root N and N rhizodeposits, comprised 70 % and 61 % of total crop residue N for canola and pea, respectively. Canola released the greatest amount of total root-derived N to the soil, which was related to greater root biomass production by canola. However, root-derived N in the soil inorganic N pool was greater under pea (13 %) than canola (4 %).

Conclusions

Our results show a significant belowground N contribution to total crop residue from pea and canola. Further investigation is required to determine whether input of the more labile N rhizodeposits of pea improves soil N supply to succeeding crops or increases the potential for N loss from the soil system relative to canola.     

Effects of experimental warming and nitrogen fertilization on soil microbial communities and processes of two subalpine coniferous species in Eastern Tibetan Plateau,China

Aim

This study aimed at predicting how sub-alpine coniferous ecosystems respond to global changes in the Eastern Tibetan Plateau by understanding soil microbial communities and activities, as well as variation in the quality and quantity of soil organic matter.

Methods

An experiment was conducted to examine soil microbial communities and their related soil processes in rhizospheric soil of two coniferous species that were exposed to two levels of temperature (unwarmed and infrared heater warming) and two levels of nitrogen (unfertilized and 25 g N m^?2 a^?1) from April 2007.

Results

Four-year night warming alone slightly affected the phospholipid fatty acid contents of the microbial community. However, the combination of nitrogen addition and soil warming significantly affected soil microbial composition while reducing the biomass of major microbial groups and the activities of most enzymes, especially in Abies faxoniana plots. The combination of warming and nitrogen addition increased soil labile C and N pools in Picea asperata plots and was beneficial for soil recalcitrant C, as well as for labile and total C and N pools in A. faxoniana plots.

Conclusion

Results indicated that future warming will slightly affect soil microbial communities and their related soil processes. However, warming combined with high nitrogen deposition will significantly constrain soil microbial biomass and enzyme activities, consequently increasing soil C and N pools in sub-alpine coniferous forests of this region.     

The influence of alkaline and non-alkaline parent material on Norway spruce tree chemical composition and growth rate

Background and aims

This study investigated the influence of contrasting parent materials on tree chemical composition and growth rate under field conditions. On the island of Alnö, Sweden, alkaline intrusions are interspersed into non-alkaline gneiss bedrock, which provides a unique opportunity to conduct this study with a minimum of confounding effects.

Methods

Three plots with alkaline and three plots with non-alkaline parent material were established in a homogenous Norway spruce stand. The chemical composition of soil and soil solution was determined throughout the soil profiles. The chemical composition of bark, wood and needles was determined for each plot, and the latest 5 year basal area growth increment calculated.

Results

Concentrations of Ca in needles were correlated with the soil exchangeable Ca levels. Tree growth rate was significantly higher on the alkaline plots and positively correlated with soil concentrations of Ca, Mg, P, and Zn. The tree growth rate also tended to correlate with soil N concentrations, but levelled out for the highest soil N concentrations.

Conclusions

Tree growth was enhanced on the alkaline plots and was correlated with several elements. However, none of these elements could be confirmed as the limiting one for tree growth at the current site.     

Modifying the LEACHM model for process-based prediction of nitrate leaching from cropped Andosols

Aims

Nitrogen (N) management strategies for reducing the risk of groundwater contamination around agricultural fields require precise prediction of N leaching using a process-based model. We modified LEACHM model for use in Andosols, which are characterized by slow soil organic carbon (SOC) mineralization and nitrate adsorption.

Methods

The modification was made with regard to the SOC mineralization of incoming plant-residue/manure and humus following the RothC model, as well as for nitrate adsorption. Empirical equations were employed to determine the parameters of the modified model. The ability of the modified LEACHM to predict N leaching was tested against existing data from a 4-year lysimeter study for cropped Andosol and sandy soils and compared with that of the original model.

Results

The modified model improved the prediction of leached N concentrations and the loss of N from Andosol with relative improvements of 63.5 and 76.5 %, respectively, over the original model, while retaining model applicability in sandy soil. This effective modeling was achieved by using precise predictions of N mineralization in the humus pool along with SOC mineralization processes that were based on the RothC model.

Conclusions

The modification extended the applicability of LEACHM and may provide better N management strategies for reducing leaching from cultivated Andosols.     

Alfalfa-grass biomass, soil organic carbon, and total nitrogen under different management approaches in an irrigated agroecosystem

Background and aims

Management approach may influence forage production as well as soil organic carbon (SOC) and soil total nitrogen (STN) accrued beneath perennial grass-legume components of irrigated crop rotations. This study aimed to evaluate effects of conventional, certified organic, and reduced-tillage management approaches on above- and belowground biomass production and C and N content in alfalfa-grass mixture, and their relationships with SOC and STN.

Methods

An alfalfa-grass mixture was established in 2009 on four replications under a sprinkler irrigation system. Soil characteristics were analyzed at planting time in 2009. Aboveground biomass production, coarse and fine roots, SOC, STN, aboveground biomass C and N, and coarse- and fine-root C and N were quantified in samples collected during 2009–2011.

Results

Conventional management produced more aboveground biomass than reduced-tillage and organic, but production under organic matched conventional and exceeded reduced-tillage in the last two harvests of the study. Root production was constant under the three approaches, but resulted in more SOC accrued under reduced-tillage than under the other two approaches.

Conclusions

Biomass production was favored by conventional seedbed preparation and soil fertility management while SOC accrual was favored by minimum soil disturbance. In addition, aboveground biomass was influenced by seasonal air temperature, precipitation, and nutrient mineralization from the previous season, so above-/belowground allocation changed seasonally.     

Impact of the plant community composition on labile soil organic carbon, soil microbial activity and community structure in semi-natural grassland ecosystems of different productivity

Aims

The main objective was to describe the effects of plant litter on SOC and on soil microbial activity and structure in extensively managed grasslands in Central Germany that vary in biomass production and plant community composition.

Methods

The decomposition of shoot and root litter was studied in an incubation experiment. Labile C and N were isolated by hot water extraction (C_HWE, N_HWE), while functional groups of microbes were identified by PLFA analysis and microbial activity was measured using a set of soil exo-enzymes.

Results

The plant community composition, particulary legume species affected SOC dynamics and below-ground microbial processes, especially via roots. This was reflected in about 20% lower decomposition of root litter in low productivity grassland soil. The C_HWE soil pool was found to be a key driver of the below-ground food web, controlling soil microbial processes.

Conclusions

Below-ground responses appear to be related to the presence of legume species, which affected the microbial communities, as well as the ratio between fungal and bacterial biomass and patterns of soil enzyme activity. Low productivity fungal-dominated grasslands with slow C turnover rates may play an important role in SOC accumulation. The approach used here is of particular importance, since associated biological and biochemical processes are fundamental to ecosystem functioning.     

Organic amendments and land management affect bacterial community composition, diversity and biomass in avocado crop soils

Background and aims

The avocado-producing area of southern Spain includes conventional orchards and organic orchards that use different organic amendments. To gain insight into the effects of these amendments, physicochemical properties and microbial communities of the soil were analysed in a representative set of commercial and experimental orchards.

Methods

The population size of several groups of culturable microorganisms was determined by plating on different selective media. Bacterial community structure was studied by denaturing gradient gel electrophoresis (DGGE)

Results

Commercial composts showed the largest effects, especially the animal compost, enhancing the population sizes of some microbial groups and affecting bacterial community structure in superficial and deep soil layers. Moreover, animal and vegetal compost, manure and blood meal addition are related to high bacterial diversity in the superficial soil layer.

Conclusions

All of the organic amendments used in this study affect soil properties in one or more of the characteristics that were analysed. Culturable microbial population data revealed the most evident effects of some of the organic treatments. However, molecular analysis of soil bacterial communities by DGGE allowed the detection of the influence of all of the analysed amendments on bacterial community composition. This effect was stronger in the superficial layer of the avocado soil.     

Long-term retention of post-fire soil mineral nitrogen pools in Mediterranean shrubland and grassland

Background and Aims

The post-fire mineral N pool is relevant for plant regrowth. Depending on the plant regeneration strategies, this pool can be readily used or lost from the plant–soil system. Here we studied the retention of the post-fire mineral N pool in the system over a period of 12 years in three contrasted Mediterranean plant communities.

Methods

Three types of vegetation (grassland, mixed shrub-grassland and shrubland) were subjected to experimental fires. We then monitored the fate of ¹⁵?N-tracer applied to the mineral N pool in soils and in plants over 12 years.

Results

The plant community with legumes (mixed shrub-grasslands) showed the lowest soil retention of ¹⁵?N-tracer during the first 9 months after fire. Between years 6 and 12 post-fire, a drought promoted plant and litter deposition. Coinciding with this period, ¹⁵?N-recovery in the first 15 cm of the soil increased in all cases, except in mixed shrub-grassland. This lack of increase may be attributable to the input of impoverished ¹⁵?N plant residues and enhanced leaching and denitrification, possibly by N₂-fixing shrubs. After the drought, the deepest soil layer showed large decreases in total N and ¹⁵?N-recovery, which were possibly caused by N mineralization.

Conclusions

Twelve years after the fires, plant communities without N₂-fixing shrubs recycled a significant part of the N derived from the post-fire mineral N and this pool continued to interact in the plant–soil system.     

Changes in microbial activities and biomasses over a forest floor gradient in C-to-N ratio

Background and aims

Under chronically elevated N deposition, N retention mainly occur at high soil C-to-N ratio. This may be mediated through soil microbes, such as ectomycorrhizal (EM) fungi, saprotrophic fungi and bacteria, and the aim of this study was to evaluate the relationship between soil microbes and forest floor C-to-N ratios.

Methods

Soil samples from 33 Norway spruce (Picea abies (L.) H. Karst) forests in Denmark and southern Sweden in a forest floor C-to-N ratio gradient (ranging from 14 to 35) were analysed regarding the content of phospholipid fatty acids (PLFAs) to estimate their soil microbial community composition and the relative biomasses of different microbial groups. The relation of EM biomass to total fungal biomass was estimated as the loss of the fungal PLFA 18:2ω6,9 during incubation of soils and the production of EM mycelia was estimated using fungal in-growth mesh bags. The soil microbial variables were correlated to forest floor C-to-N ratio, NO ₃ ^- leaching, soil pH and stand age.

Results

Fungal proportions of microbial biomass, EM to total fungi and EM mycelial production were all positively related to C-to-N ratio, while NO ₃ ^- leaching was negatively related to C-to-N ratio.

Conclusions

Both EM and saprotrophic fungi change with forest floor C-to-N ratios and appear to play a central role in N retention in forest soil. A better understanding of the mechanisms behind this process may be revealed if the role of recalcitrant fungal metabolites for N retention (and soil C sequestration) can be identified. Research along this line deserves further studies.