Soil-mediated local adaptation alters seedling survival and performance

Background and aims

Soils can act as agents of natural selection, causing differential fitness among genotypes and/or families of the same plant species, especially when soils have extreme physical or chemical properties. More subtle changes in soils, such as variation in microbial communities, may also act as agents of selection. We hypothesized that variation in soil properties within a single river drainage can be a selective gradient, driving local adaptation in plants.

Methods

Using seeds collected from individual genotypes of Populus angustifolia James and soils collected from underneath the same trees, we use a reciprocal transplant design to test whether seedlings would be locally adapted to their parental soil type.

Results

We found three patterns: 1. Soils from beneath individual genotypes varied in pH, soil texture, nutrient content, microbial biomass and the physiological status of microorganisms. 2. Seedlings grown in local soils experienced 2.5-fold greater survival than seedlings planted in non-local soils. 3. Using a composite of height, number of leaves and leaf area to measure plant growth, seedlings grew ～17.5% larger in their local soil than in non-local soil.

Conclusions

These data support the hypothesis that variation in soils across subtle gradients can act as an important selective agent, causing differential fitness and local adaptation in plants.     

Potential soil P mobilisation capacity–method development and comparison of rhizosphere soil from different crops

Background

Phosphorus (P) deficiency is wide-spread in agricultural soils. In light of increasing P fertilizer costs, it is of interest to assess the capacity of soil microbes to mobilise native soil P and added P. There is currently no method to assess P mobilisation in situ.

Methods

The soil P mobilisation potential was assessed by incubating low P soil for up to 30?days with poorly available P sources; C and N were added to increase microbial activity and ensure that only P was limiting microbial growth.

Results

The increase in microbial P from day 0 to day 15 showed that microbes were able to mobilise P from FePO₄ and phytate. The P mobilisation potential (sum of microbial and resin P) of the rhizosphere soil decreased in the following order: faba bean > chickpea and white lupin > wheat. After 10?days, up to 80% of the mobilised P was microbial P, whereas after 30?days, almost all P mobilised was resin P.

Conclusions

The method developed in this study is useful assessing not only potential of a soil to mobilise P but also, by using different poorly available P sources, the mechanisms of P mobilisation.     

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.     

Carbon dynamics in a 60?year fallowed loamy-sand soil compared to that in a 60?year permanent arable or permanent grassland UK soil

Aims

To determine if the soil microbial biomass in a 60?year fallow soil of the Highfield Ley-Arable Experiment at Rothamsted Research, UK, had maintained its ability to mineralise soil organic matter and added substrates compared to biomasses in a grassland and arable soil of the same experiment.

Materials and methods

Three soils of the same type: a 60 y permanent fallow, arable and grassland, were incubated (25°C, 40% WHC) with and without 1. a labile substrate (yeast extract, C/N ratio 3.6) or 2. more resistant ryegrass, (< 2?mm, C/N ratio 14.6). Measurements included biomass C, ATP, PLFAs and substrate C mineralization.

Results

Mean biomass C and ATP concentrations were:grassland.arable.fallow, as expected. However, substrate C mineralization was less in the grassland than fallow soil, opposite to that expected. Microbial biosynthesis efficiency (measured as biomass C and ATP) was similar in all soils. However, microbial community structure differed significantly between soils and treatments.

Conclusions

The extent of mineralization of both substrates were unrelated to initial microbial community structure, size or soil management. Thus, the biomass in the fallow soil maintained full metabolic capacity (assessed by CO₂-C evolution) compared to permanent arable or grassland soils.     

Temporal variation in microbial and plant biomass during summer in a Mediterranean high-mountain dry grassland

Aims

We assessed the temporal changes on microbial biomass in relation to changes in soil moisture, dissolved organic carbon and plant biomass during the summer season in a Mediterranean high-mountain grassland.

Methods

Temporal variations were tested by two-way ANOVA. The relationships among microbial biomass, plant biomass, soil water content, soil organic carbon, dissolved organic carbon and total soil nitrogen during the summer season were assessed by means of structural equation modeling.

Results

Microbial biomass did not show variation, while dissolved organic carbon and root biomass decreased throughout the summer. Aboveground plant biomass peaked in the middle of the summer, when soil water content was at its minimum. Soil water content directly and negatively affected soil microbial biomass, and positively affected dissolved organic carbon. Moreover soil microbial biomass and dissolved organic carbon were negatively related. Plant biomass effects on soil microbial biomass were driven by root biomass, which indirectly affected soil microbial biomass through effects on soil organic carbon and soil nitrogen.

Conclusions

The temporal dynamic of microbial biomass during the summer season appeared to differ from previous observations in temperate alpine communities, and indicated the drought resistance of the microbial community during the summer in Mediterranean high-mountain grasslands. During the dry period, microbial biomass may play an alternative role in soil carbon conservation.     

Biological soil crusts increase the resistance of soil nitrogen dynamics to changes in temperatures in a semi-arid ecosystem

Aims

Biological soil crusts (BSCs), composed of mosses, lichens, liverworts and cyanobacteria, are a key component of arid and semi-arid ecosystems worldwide, and play key roles modulating several aspects of the nitrogen (N) cycle, such as N fixation and mineralization. While the performance of its constituent organisms largely depends on moisture and rainfall conditions, the influence of these environmental factors on N transformations under BSC soils has not been evaluated before.

Methods

The study was done using soils collected from areas devoid of vascular plants with and without lichen-dominated BSCs from a semi-arid Stipa tenacissima grassland. Soil samples were incubated under different temperature (T) and soil water content (SWC) conditions, and changes in microbial biomass-N, dissolved organic nitrogen (DON), amino acids, ammonium, nitrate and both inorganic N were monitored. To evaluate how BSCs modulate the resistance of the soil to changes in T and SWC, we estimated the Orwin and Wardle Resistance index.

Results

The different variables studied were more affected by changes in T than by variations in SWC at both BSC-dominated and bare ground soils. However, under BSCs, a change in the dominance of N processes from a net nitrification to a net ammonification was observed at the highest SWC, regardless of T.

Conclusions

Our results suggest that the N cycle is more resistant to changes in T in BSC-dominated than in bare ground areas. They also indicate that BSCs could play a key role in minimizing the likely impacts of climate change on the dynamics of N in semi-arid environments, given the prevalence and cover of these organisms worldwide.     

Soil substrate utilization pattern and relation of functional evenness of plant groups and soil microbial community in five low mountain NATURA 2000

Background and aims

Species rich, semi-natural grassland systems provide several ecosystem functions. The goal was to assess how aboveground composition and evenness affects soil substrate utilization pattern and soil microbial functional evenness.

Methods

At five German NATURA 2000 grassland sites, the interactions of plant functional groups (graminoids, forbs and legumes) and belowground microbial functional evenness were investigated in relation to soil properties and sampling date. Functional evenness of soil microorganisms was measured with high spatial resolution by community level physiological profiling (CLPP) using multi-SIR (substrate-induced respiration) at three sampling dates during the vegetation period. Evenness indices were used to compare plant functional group diversity and soil microbial functional diversity.

Results

All sites differed in the consistently high soil microbial functional evenness, which was strongly predicted by soil pH, but not by plant functional groups or aboveground plant dry matter production. However, soil microbial functional evenness was particularly decreased by an increasing legume proportion and showed seasonal changes, probably driven by shifts in resource availability and soil water content.

Conclusions

Our results suggest that changes in soil chemical properties or in a single key plant functional group may have stronger effects on soil microbial functional evenness than changes in plant functional group evenness.     

Fragmentation modulates the strong impact of habitat quality and plant cover on fertility and microbial activity of semiarid gypsum soils

Background and aims

Plant-soil interactions are a crucial component of ecosystem functioning. However, most global change studies focus on plant communities, with information on soil properties and performance being scarce. Our goal was to assess the individual and joint effect of habitat heterogeneity and three global change drivers (fragmentation, loss of habitat quality and climate change) on nutrient availability and soil microbial activity in Mediterranean gypsum soils.

Methods

We collected soil samples from an experimental field site from large/small fragments, with high/low habitat quality, subjected to two levels of water availability (dry/mesic) and from two microhabitats (under the canopy of shrubs and in the open). We analyzed nutrient concentrations (C, N and P) and enzymatic activities (?-glucosidase, urease and acid phosphatase).

Results

C, N, P content, ?-glucosidase, urease and acid phosphatase activities were higher under the canopy than in the open and in high- than in poor- habitat quality sites. These differences were exacerbated in small fragments.

Conclusions

The strong interdependence between plant and soil was modulated by fragmentation in the Mediterranean gypsum soils studied. Drought did not exert a direct negative effect on soil properties, although the effect might arise under more intense drought or under drought taking place at times of the year different from those explored here. Results highlight the importance of considering several drivers simultaneously to forecast realistic ecosystem responses to global change.     

Nutrient availability and pH jointly constrain microbial extracellular enzyme activities in nutrient-poor tundra soils

Background and aims

Tundra soils, which usually contain low concentrations of soil nutrients and have a low pH, store a large proportion of the global soil carbon (C) pool. The importance of soil nitrogen (N) availability for microbial activity in the tundra has received a great deal of attention; however, although soil pH is known to exert a considerable impact on microbial activities across ecosystems, the importance of soil pH in the tundra has not been experimentally investigated.

Methods

We tested a hypothesis that low nutrient availability and pH may limit microbial biomass and microbial capacity for organic matter degradation in acidic tundra heaths by analyzing potential extracellular enzyme activities and microbial biomass after 6 years of factorial treatments of fertilization and liming.

Results

Increasing nutrients enhanced the potential activity of β-glucosidase (synthesized for cellulose degradation). Increasing soil pH, in contrast, reduced the potential activity of β-glucosidase. The soil phospholipid fatty acid concentrations (PLFAs; indicative of the amount of microbial biomass) increased in response to fertilization but were not influenced by liming.

Conclusions

Our results show that soil nutrient availability and pH together control extracellular enzyme activities but with largely differing or even opposing effects. When nutrient limitation was alleviated by fertilization, microbial biomass and enzymatic capacity for cellulose decomposition increased, which likely facilitates greater decomposition of soil organic matter. Increased soil pH, in contrast, reduced enzymatic capacity for cellulose decomposition, which could be related with the bioavailability of organic substrates.     

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.     

Biogeochemical transformations of amino acids in soil assessed by position-specific labelling

Background and aims

Amino acid turnover in soil is an important element of terrestrial carbon and nitrogen cycles. This study accounts for their driver - the microbial metabolism - by tracing them via the unique isotopic approach of position-specific labeling.

Methods

Three ¹⁴C isotopomers of alanine at five concentration levels combined with selective sterilization were used to distinguish sorption mechanisms, exoenzymatic and microbial utilization of amino acids in soil.

Results

Sorption and microbial uptake occurred immediately. Unspecific microbial uptake followed a linear kinetic, whereas energy-dependent uptake followed Michaelis-Menten. Less than 6 % of the initially added alanine was sorbed to soil, but after microbial transformation products were bound to the soil matrix at higher proportions (5–25 %). The carboxyl group (C-1) was rapidly oxidized by microorganisms, whereas C-2 and C-3 positions were preferentially incorporated into microbial biomass. Dependency of C metabolization on amino acid concentration reflected individual alanine transformation pathways for starvation, maintenance and growth conditions.

Conclusions

This study demonstrates that position-specific labeling determines the mechanisms and rates of C cycling from individual functional groups. This approach reflected underlying metabolic pathways and revealed the formation of new organic matter. We therefore conclude that position-specific labeling is a unique tool for detailed insights into submolecular transformation pathways and their regulation factors.     

Microbial communities may modify how litter quality affects potential decomposition rates as tree species migrate

Background and aims

Climate change alters regional plant species distributions, creating new combinations of litter species and soil communities. Biogeographic patterns in microbial communities relate to dissimilarity in microbial community function, meaning novel litters to communities may decompose differently than predicted from their chemical composition. Therefore, the effect of a litter species in the biogeochemical cycle of its current environment may not predict patterns after migration. Under a tree migration sequence we test whether litter quality alone drives litter decomposition, or whether soil communities modify quality effects.

Methods

Litter and soils were sampled across an elevation gradient of different overstory species where lower elevation species are predicted to migrate upslope. We use a common garden, laboratory microcosm design (soil community x litter environment) with single and mixed-species litters.

Results

We find significant litter quality and microbial community effects (P?<?0.001), explaining 47 % of the variation in decomposition for mixed-litters.

Conclusion

Soil community effects are driven by the functional breadth, or historical exposure, of the microbial communities, resulting in lower decomposition of litters inoculated with upslope communities. The litter x soil community interaction suggests that litter decomposition rates in forests of changing tree species composition will be a product of both litter quality and the recipient soil community.     

Soil N forms and gross transformation rates in Chinese subtropical forests dominated by different tree species

Background and aims

Knowledge related to extent of differing soil N forms and N transformation rates in subtropical southern China is severely limited. Accordingly, the purpose of this study was to investigate if and how tree species of different foliage types (coniferous, deciduous, and evergreen broadleaved) influence N forms and microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) content as well as gross N transformation rates in the organic and mineral soils of three distinct subtropical forests in China.

Methods

Chloroform fumigation extraction was used to determine MBC and MBN content while ¹⁵N-isotope dilution techniques were used to measure gross N transformation rates. Canonical correspondence analysis (CCA) was used to quantify relationships between soil chemical characteristics and changes in soil N transformation rates.

Results

Soil N forms, MBC and MBN content, and N transformation rates were found to be significantly different between tree species. Deciduous forest soil exhibited the highest N transformation rates. Soil N transformation rates were closely associated with total soil C and N and MBC and MBN content.

Conclusions

Soil substrate quantity and soil microbial activity play a more important role in soil N transformation processes than does soil quality in China’s subtropical forests. Tree species type should therefore be taken into account when trying to determine ecosystem N cycling.     

Phosphorus pools and other soil properties in the rhizosphere of wheat and legumes growing in three soils in monoculture or as a mixture of wheat and legume

Background and aims

Phosphorus and nitrogen availability and forms are affected by soil properties as well as by plant species and further modulated by soil microbes. Additionally, close contact of the roots of two plant species may affect concentrations and forms of N and P. The aim of this study was to assess properties related to N and P cycling in the rhizosphere of wheat and legumes grown in monoculture or in wheat/legume mixtures in three soils differing in pH.

Methods

Faba bean, white lupin and wheat were grown in three soils differing in pH (4.8, 7.5 and 8.8) in monoculture or in mixed culture of wheat and legumes. Rhizosphere soil was collected at flowering and analyzed for P pools by sequential fractionation, available N as well as community structure of bacteria, fungi, ammonia oxidizers, N₂-fixers and P mobilizers by polymerase chain reaction (PCR)—denaturing gradient gel electrophoresis (DGGE).

Results

Soil type was the major factor determining plant growth, rhizosphere nutrient dynamics and microbial community structure. Among the crop species, only faba bean had a significant effect on nitrification potential activity (PNA) in all three soils with lower activity compared to the unplanted soil. Soil type and plant spieces affected the community composition of ammonia-oxidizing archaea (AOB), ammonia-oxidizing archaea (AOA), N₂-fixers (nifH), P mobilizers (ALP gene) and fungi, but not that of bacteria. Among the microbial groups, the AOA and nifH community composition were most strongly affected by crop species, cropping system and soil type, suggesting that these groups are quite sensitive to environmental conditions. All plants depleted some labile as well as non-labile P pools whereas the less labile organic P pools (NaOH extractable P pools, acid extractable P pools) accumulated in the rhizosphere of legumes. The pattern of depletion and accumulation of some P pools differed between monoculture and mixed culture as well as among soils.

Conclusions

Plant growth and rhizosphere properties were mainly affected by soil type, but also by crop species whereas cropping system had the least effect. Wheat and the legumes depleted less labile inorganic P pools in some soils whereas less labile organic P pools (NaOH extractable P, acid extractable P) accumulated in the rhizosphere of legumes.     

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.     

Effects of condensed tannins in conifer leaves on the composition and activity of the soil microbial community in a tropical montane forest

Background and aims

Condensed tannins, a dominant class of plant secondary metabolites, play potentially important roles in plant-soil feedbacks by influencing the soil microbial community. Effects of condensed tannins on the soil microbial community and activity were examined by a short-term tannin-addition experiment under field and laboratory conditions.

Methods

Condensed tannins were extracted from the leaves of a dominant conifer (Dacrydium gracilis) in a tropical montane forest on Mt. Kinabalu, Borneo. The extracted tannins were added to soils beneath the conifer and a dominant broadleaf (Lithocarpus clementianus) to evaluate the dependence of the response to tannin addition on the initial composition of the soil microbial community.

Results

Enzyme activities in the field tannin-addition treatment were lower than in the deionized-water treatment. Carbon and nitrogen mineralization were also inhibited by tannin-addition. The fungi-to-bacteria ratio after tannin-addition was higher compared with the distilled-water treatment in the laboratory experiment.

Conclusions

Based on our results, we suggest that the higher concentration of condensed tannins in the leaf tissues of Dacrydium than in those of Lithocarpus is a factor influencing the microbial community and activity. This may have influences on subsequent plant performance, which induces plant-soil feedback processes that can control dynamics of the tropical montane forest ecosystem.     

Soil microbial biomass and the fate of phosphorus during long-term ecosystem development

Background

Soil phosphorus availability declines during long-term ecosystem development on stable land surfaces due to a gradual loss of phosphorus in runoff and transformation of primary mineral phosphate into secondary minerals and organic compounds. These changes have been linked to a reduction in plant biomass as ecosystems age, but the implications for belowground organisms remain unknown.

Methods

We constructed a phosphorus budget for the well-studied 120,000 year temperate rainforest chronosequence at Franz Josef, New Zealand. The budget included the amounts of phosphorus in plant biomass, soil microbial biomass, and other soil pools.

Results

Soil microbes contained 68–78 % of the total biomass phosphorus (i.e. plant plus microbial) for the majority of the 120,000 year chronosequence. In contrast, plant phosphorus was a relatively small pool that occurred predominantly in wood. This points to the central role of the microbial biomass in determining phosphorus availability as ecosystems mature, yet also indicates the likelihood of strong competition between plants and saprotrophic microbes for soil phosphorus.

Conclusions

This novel perspective on terrestrial biogeochemistry challenges our understanding of phosphorus cycling by identifying soil microbes as the major biological phosphorus pool during long-term ecosystem development.     

Biocrusts control the nitrogen dynamics and microbial functional diversity of semi-arid soils in response to nutrient additions

Aims

Human activities are causing imbalances in the nutrient cycles in natural ecosystems. However, we have limited knowledge of how these changes will affect the soil microbial functional diversity and the nitrogen (N) cycle in drylands, the biggest biome on Earth. Communities dominated by lichens, mosses and cyanobacteria (biocrusts) influence multiple processes from the N cycle such as N fixation and mineralization rates. We evaluated how biocrusts modulate the effects of different N, carbon (C) and phosphorus (P) additions on theN availability, the dominance of different available N forms and the microbial functional diversity in dryland soils.

Methods

Soil samples from bare ground (BG) and biocrust-dominated areas were gathered from the center of Spain and incubated during seven or 21 days under different combinations of N, C and P additions (N, C, P, N?+?C, N?+?P, P?+?C, and C?+?N?+?P).

Results

The relative dominance of dissolved organic N (DON) and the microbial functional diversity were higher in biocrust than in BG microsites when C or P were added. Changes in the C to N ratio, more than N availability, seem to modulate N transformation processes in the soils studied. In general, biocrusts increased the resilience to N impacts (N, C?+?N, N?+?P, C?+?N?+?P) of the total available N, ammonium, nitrate and DON when C was present.

Conclusions

Our results suggest that biocrusts may buffer the effects of changes in nutrient ratios on microbial functional diversity and DON dominance in dryland soils. Thus, these organisms may have an important role in increasing the resilience of the N cycle to imbalances in C, N and P derived from human activities.     

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.