Long-term management changes topsoil and subsoil organic carbon and nitrogen dynamics in a temperate agricultural system

Simulation-based assessment of the soil organic carbon sequestration in grasslands in relation to management and climate change scenarios

Soil organic carbon (SOC) is crucial for the quality and productivity of terrestrial ecosystems and its sequestration plays an important role in mitigating climate change. Understanding the effects of agricultural management under future climate on the SOC balance helps decision making in environmental policies. Thereby, grasslands will play a key role, since future climate change may prolong the vegetation period. We used 24 representative grassland sites in Germany to assess the SOC balance obtained from the CANDY model in relation to ten management regimes, 18 future climate change scenarios and different soil types. Simulations were conducted over a period of 110 years. For most of the selected grassland sites an increase in both air temperature and precipitation was observed in the future climate. The effect of management on the SOC balance largely exceeded the effect of soil type and climate. An increasing management intensity (i.e. three to five cuts) generally increased the SOC balance, while extensive management (i.e. two or fewer cuts) lead to SOC losses. The seasonal variation of precipitation was the most important climate metric, with increased SOC sequestration rates being observed with increasing growing season precipitation. Clay soils had the potential for both highest gains and highest losses depending on management and precipitation. Given an overall lower SOC storage potential in sands and loams, the SOC balance in those soil types varied the least in response to climate change. We conclude that fostering SOC sequestration is possible in grassland soils by increasing management intensity, which involves increased fertilizer input and field traffic. This however may stand in conflict with other policy aims, such as preserving biodiversity. Multicriterial assessments are required to estimate the nett greenhouse gas balance and other aspects associated with these management practices at a farm scale.

Probiotics Enhance Cereal Yield and Quality and Modify Agrochemical Soil Properties

The aim of this study was to determine the influence of microbial biostimulants on wheat and oat growth, grain yield, and grain quality and to evaluate the influence of these probiotics on some soil agrochemical traits in the open field. Active concentrations of ProbioHumus and NaturGel and their mixtures were selected under laboratory conditions using winter wheat as a reference plant. Probiotics had a biostimulating effect on the development of the underground and aboveground part of winter wheat when 2 µL/g was used for seed priming and 2 mL/100 mL for seedling spraying. Under field conditions, after treatment of soil (2 L/ha), wheat and oat seeds (2 L/t), and plants (2 L/ha) with ProbioHumus and NaturGel, it was found that the yield of the studied cereals increased, on average, by 0.50 t/ha to 1.09 t/ha. ProbioHumus promoted protein accumulation in the investigated cereal grains. The level of microelements in wheat and oat grains increased after treatment of plants with NaturGel. Probiotics improved soil agrochemical properties, such as total and nitrate nitrogen, total and available phosphorus, organic carbon, humic acid, and humus content. In conclusion, plant probiotics can be used as an ecological alternative for growing cereals and improving the agrochemical properties of the soil.

Land Management Legacy Affects Abundance and Function of the acdS Gene in Wheat Root Associated Pseudomonads

Land management practices can vastly influence belowground plant traits due to chemical, physical, and biological alteration of soil properties. Beneficial Pseudomonas spp. are agriculturally relevant bacteria with a plethora of plant growth promoting (PGP) qualities, including the potential to alter plant physiology by modulating plant produced ethylene via the action of the bacterial enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS). This study evaluated the impact of land management legacy on the selection and function of wheat root associated culturable pseudomonad isolates. Three distinct previous land uses prior to wheat culture (grassland, arable, and bare fallow) were tested and culturable pseudomonad abundance, phylogeny (gyrB and acdS genes), function (ACC deaminase activity), and the co-selection of acdS with other PGP genes examined. The pseudomonad community could to some extent be discriminated based on previous land use. The isolates from rhizosphere and root compartments of wheat had a higher acdS gene frequency than the bulk soil, particularly in plants grown in soil from the bare fallow treatment which is known to have degraded soil properties such as low nutrient availability. Additionally, other genes of interest to agriculture encoding anti-fungal metabolites, siderophores, and genes involved in nitrogen metabolism were highly positively associated with the presence of the acdS gene in the long-term arable treatment in the genomes of these isolates. In contrast, genes involved in antibiotic resistance and type VI secretion systems along with nitrogen cycling genes were highly positively correlated with the acdS gene in bare fallow isolated pseudomonad. This highlights that the three land managements prior to wheat culture present different selection pressures that can shape culturable pseudomonad community structure and function either directly or indirectly via the influence of wheat roots.

Variation of soil properties with sampling depth in two different light-textured soils after repeated applications of urban sewage sludge

Semi-arid agricultural soils have increasingly been subjected to urban sewage sludge (USS) applications due to accelerated soil depletion and shortages in manure supply. Research studies addressing USS reuse have mostly been conducted in cropping systems and focused on changes in topsoil properties of a given texture. Therefore, sludge-soil interactions could be largely influenced by the presence of plants, soil particle composition and depth. In this field study, two agricultural soils (sandy, S and sandy loam, SL) received simultaneously four annual USS applications of 40, 80, and 120 t ha^-1 year^-1 in absence of vegetation. Outcomes showed the increase of carbon and macronutrients in both soils proportionally to USS dose especially in the topsoil profile (0-20 cm). Subsoil (20-40 cm) was similarly influenced by sludge rates, showing comparable variations of fertility parameters though at significant lower levels. The depth-dependent improvement of soil fertility in both layers enhanced the microbiological properties accordingly, with significant variations in soil SL characterized by a higher clay content than soil S. Besides, positive correlations between increases in sludge dose, salinity, trace metals, and enzyme activities in both soils indicate that excessive sludge doses did not cause soil degradation or biotoxic effects under the described experimental conditions. In particular and despite high geoaccumulation indices of Ni in both soils and profiles, the global concentrations of Cu, Ni, Pb, and Zn were still below threshold levels for contaminated soils. In addition, the maintenance of pH values within neutral range and the increase of organic matter content with respect to control would have further reduced metal availability in amended soils. Therefore, we could closely investigate the effects of texture and depth on the intrinsic resilience of each soil to cope with repetitive USS applications.

Shifts in Soil Structure, Biological, and Functional Diversity Under Long-Term Carbon Deprivation

Soil organic matter is composed of a variety of carbon (C) forms. However, not all forms are equally accessible to soil microorganisms. Deprivation of C inputs will cause changes in the physical and microbial community structures of soils; yet the trajectories of such changes are not clear. We assessed microbial communities using phospholipid fatty acid profiling, metabarcoding, CO₂ emissions, and functional gene microarrays in a decade-long C deprivation field experiment. We also assessed changes in a range of soil physicochemical properties, including using X-ray Computed Tomography imaging to assess differences in soil structure. Two sets of soils were deprived of C inputs by removing plant inputs for 10 years and 1 year, respectively. We found a reduction in diversity measures, after 10 years of C deprivation, which was unexpected based on previous research. Fungi appeared to be most impacted, likely due to competition for scarce resources after exhausting the available plant material. This suggestion was supported by evidence of bioindicator taxa in non-vegetated soils that may directly compete with or consume fungi. There was also a reduction in copies of most functional genes after 10 years of C deprivation, though gene copies increased for phytase and some genes involved in decomposing recalcitrant C and methanogenesis. Additionally, soils under C deprivation displayed expected reductions in pH, organic C, nitrogen, and biomass as well as reduced mean pore size, especially in larger pores. However, pore connectivity increased after 10 years of C deprivation contrary to expectations. Our results highlight concurrent collapse of soil structure and biodiversity following long-term C deprivation. Overall, this study shows the negative trajectory of continuous C deprivation and loss of organic matter on a wide range of soil quality indicators and microorganisms.

Soil as an extended composite phenotype of the microbial metagenome

We use a unique set of terrestrial experiments to demonstrate how soil management practises result in emergence of distinct associations between physical structure and biological functions. These associations have a significant effect on the flux, resilience and efficiency of nutrient delivery to plants (including water). Physical structure, determining the air–water balance in soil as well as transport rates, is influenced by nutrient and physical interventions. Contrasting emergent soil structures exert selective pressures upon the microbiome metagenome. These selective pressures are associated with the quality of organic carbon inputs, the prevalence of anaerobic microsites and delivery of nutrients to microorganisms attached to soil surfaces. This variety results in distinctive gene assemblages characterising each state. The nature of the interactions provide evidence that soil behaves as an extended composite phenotype of the resident microbiome, responsive to the input and turnover of plant-derived organic carbon. We provide new evidence supporting the theory that soil-microbe systems are self-organising states with organic carbon acting as a critical determining parameter. This perspective leads us to propose carbon flux, rather than soil organic carbon content as the critical factor in soil systems, and we present evidence to support this view.

Soil organic carbon, extracellular polymeric substances (EPS), and soil structural stability as affected by previous and current land-use

While soil microbial ecology, soil organic carbon (SOC) and soil physical quality are widely understood to be interrelated - the underlying drivers of emergent properties, from land management to biochemistry, are hotly debated. Biological binding agents, microbial exudates, or 'extracellular polymeric substances' (EPS) in soil are now receiving increased attention due to several of the existing methodological challenges having been overcome. We applied a recently developed approach to quantify soil EPS, as extracellular protein and extracellular polysaccharide, on the well-characterised soils of the Highfield Experiment, Rothamsted Research, UK. Our aim was to investigate the links between agricultural land use, SOC, transient binding agents known as EPS, and their impacts on soil physical quality (given by mean weight diameter of water stable aggregates; MWD). We compared the legacy effects from long-term previous land-uses (unfertilised grassland, fertilised arable, and fallow) which were established > 50 years prior to investigation, crossed with the same current land-uses established for a duration of only 2.5 years prior to sampling. Continuously fallow and grassland soils represented the poorest and greatest states of structural integrity, respectively. Total SOC and N were found to be affected by both previous and current land-uses, while extractable EPS and MWD were driven primarily by the current land-use. Land-use change between these two extremes (fallow → grass; grass → fallow) resulted in smaller SOC differences (64% increase or 37% loss) compared to MWD (125% increase or 78% loss). SOC concentration correlated well to MWD (adjusted R 2 = 0.72) but the greater SOC content from previous grassland was not found to contribute directly to the current stability (p < 0.05). Our work thus supports the view that certain distinct components of SOC, rather than the total pool, have disproportionately important effects on a soil's structural stability. EPS-protein was more closely related to aggregate stability than EPS-polysaccharide (p values of 0.002 and 0.027, respectively), and ranking soils with the 5 greatest concentrations of EPS-protein to their corresponding orders of stability (MWD) resulted in a perfect match. We confirmed that both EPS-protein and EPS-polysaccharide were transient fractions: supporting the founding models for aggregate formation. We suggest that management of transient binding agents such as EPS -as opposed to simply increasing the total SOC content- may be a more feasible strategy to improve soil structural integrity and help achieve environmental objectives.

Assimilating atmospheric carbon dioxide in tea gardens of northeast India

Carbon dioxide (CO₂) is the most important greenhouse gas in the atmosphere and phyto-assimilation is the most effective technique to mitigate global warming effect of CO₂ gas in the atmosphere. Tea is an evergreen perennial plant and cultivated worldwide under subtropical humid climatic condition for harvesting its tender shoots. Tea bushes of different cultivars and ages are grown in combination to minimize possible adverse effect of biotic and abiotic stresses; hence distribution of tea plantation in a tea garden is complex in nature. Large shade trees are also an integral part of tea garden. Those plantations in tea garden have huge potential to capture atmospheric CO₂; however, ability of tea bushes to mitigate global warming while producing tea shoots is not quantified before. The objective of this study was to quantify the potential of tea plantation to mitigate greenhouse effect (global warming mitigation potential, GWMP) due to assimilation of atmospheric CO₂ gas. High yielding TV23 cultivar assimilated significantly higher amount of CO₂ as compared to quality tea producing cultivars (S3A/3) and mature 25-30 years old tea bushes absorb more CO₂ from the atmosphere as compared to younger tea bushes. Considering the mixed population of cultivars in tea gardens, overall, tea bushes sequestrated 5134.4 ± 831.6 kg CO₂ ha^-1 yr^-1 in their biomass and had GWMP 3.47 ± 0.64 kg CO₂ KMTH^-1 yr^-1. Shade trees sequestrated 4037.4 ± 589.9 kg CO₂ ha yr^-1 from the atmosphere. Hence, the GWMP of whole plantation ((both tea bushes and shade trees) was 6.19 ± 1.7 kg CO₂ KMTH^-1 yr^-1. In this study, tea bushes sequestrated 52.7-61.3% of the total CO₂ sequestrated by the plantations in tea garden. This study enabled to understand that tea bushes play significant role in mitigating global warming by assimilating and sequestrating atmospheric CO₂ and the estimated value of global warming mitigation potential may be used for direct estimation of C sequestration by plantations in tea garden using its productivity value.

Generic parameters of first-order kinetics accurately describe soil organic matter decay in bare fallow soils over a wide edaphic and climatic range

The conventional soil organic matter (SOM) decay paradigm considers the intrinsic quality of SOM as the dominant decay limitation with the result that it is modelled using simple first-order decay kinetics. This view and modelling approach is often criticized for being too simplistic and unreliable for predictive purposes. It is still under debate if first-order models can correctly capture the variability in temporal SOM decay observed between different agroecosystems and climates. To address this question, we calibrated a first-order model (Q) on six long-term bare fallow field experiments across Europe. Following conventional SOM decay theory, we assumed that parameters directly describing SOC decay (rate of SOM quality change and decomposer metabolism) are thermodynamically constrained and therefore valid for all sites. Initial litter input quality and edaphic interactions (both local by definition) and microbial efficiency (possibly affected by nutrient stoichiometry) were instead considered site-specific. Initial litter input quality explained most observed kinetics variability, and the model predicted a convergence toward a common kinetics over time. Site-specific variables played no detectable role. The decay of decades-old SOM seemed mostly influenced by OM chemistry and was well described by first order kinetics and a single set of general kinetics parameters.

Improvement of subsoil physicochemical and microbial properties by short-term fallow practices

Fallow management can improve the soil nutrients in the topsoil and upper subsoil. However, little is known about the effects of short-term (one year) fallowing with different treatments, such as vegetation and fertilization, on subsoil (20–40 cm) properties. We conducted field trials to explore the changes in subsoil properties in response to such treatments in the Yellow River Delta region in China. Different vegetation and fertilization treatments were applied, and we measured the carbon and nitrogen contents, microbial biomass and microbial community structure in the subsoil. Fallowing without manure resulted in the storage of more total nitrogen (16.38%) than fallowing with manure, and meadow vegetation improved the ammonium nitrogen content (45.71%) relative to spontaneous vegetation. Spontaneous vegetation with manure improved the microbial biomass nitrogen (P < 0.05). Although the impact of short-term fallowing on microbial community structure was low, an effect of management was observed for some genera. Blastopirellula, Lysobacter, and Acidobacteria Gp6 showed significant differences among fallow treatments by the end of the year (P < 0.05). Blastopirellula abundance was related to the microbial biomass nitrogen and nitrogen mineralization rate in the subsoil. Manure retained a high abundance of Lysobacter, which may strengthen soil-borne disease resistance. The response of Acidobacteria Gp6 showed that meadow vegetation without manure may not benefit future crops. Although the treatments did not significantly improve microbial community structure in the one-year period, annual fallowing improved certain subsoil properties and increased the number of functional genera, which may enhance crop productivity in the future.

Multiple abiotic stress, nitrate availability and the growth of wheat

In the field, wheat experiences a combination of physical and nutrient stresses. There has been a tendency to study root impedance and water stress in separation and less is known about how they might interact. In this study, we investigated the effect of root impedance on the growth of three wheat varieties (Cadenza, Xi19 and Battalion) at different levels of nitrate availability, from 0-20 mM nitrate, in sand culture. This model system allows soil strength to be increased while maintaining adequate water availability. In a separate pot experiment, we grew the same wheat varieties in a loamy sand where soil was allowed to dry sufficiently to both reduce water potential and increase root impedance. This pot experiment also had a range of nitrate availabilities 0-20 mM nitrate. Once the seedlings were established we limited water supply to apply a matric potential of approximately -200 kPa to the roots. Soil drying increased the penetrometer resistance from approximately 300 kPa to more than 1 MPa. There were differences between the two experimental systems; growth was smaller in the soil-based experiment compared to the sand culture. However, the effects of the experimental treatment, root impedance or water withholding, relative to the control were comparable. Our data confirmed that leaf elongation in Cadenza (carrying the tall Rht allele) was the most sensitive to root impedance. Leaf stunting occurred irrespective of nitrate availability. Leaf elongation in the Xi19 and Battalion (carrying the semi-dwarf Rht allele) was less sensitive to root impedance and drought than Candenza. We suggest that the critical stress in a pot experiment where the soil was allowed to dry to approximately -200 kPa was root impedance and not water availability.

Effects of cropping systems upon the three-dimensional architecture of soil systems are modulated by texture

Soil delivers fundamental ecosystem functions via interactions between physical and biological processes mediated by soil structure. The structure of soil is also dynamic and modified by natural factors and management intervention. The aim of this study was to investigate the effects of different cropping systems on soil structure at contrasting spatial scales. Three systems were studied in replicated plot field experiments involving varying degrees of plant-derived inputs to the soil, viz. perennial (grassland), annual (arable), and no-plant control (bare fallow), associated with two contrasting soil textures (clayey and sandy). We hypothesized the presence of plants results in a greater range (diversity) of pore sizes and that perennial cropping systems invoke greater structural heterogeneity. Accordingly, the nature of the pore systems was visualised and quantified in 3D by X-ray Computed Tomography at the mm and μm scale. Plants did not affect the porosity of clay soil at the mm scale, but at the μm scale, annual and perennial plant cover resulted in significantly increased porosity, a wider range of pore sizes and greater connectivity compared to bare fallow soil. However, the opposite occurred in the sandy soil, where plants decreased the porosity and pore connectivity at the mm scale but had no significant structural effect at the μm scale. These data reveal profound effects of different agricultural management systems upon soil structural modification, which are strongly modulated by the extent of plant presence and also contingent on the inherent texture of the soil.

Organic carbon pools and soil biological fertility are affected by land use intensity in Mediterranean ecosystems of Sardinia, Italy

Soil quality is mainly studied from the chemical and physical point of view, whereas soil biochemical and microbiological parameters are relatively more scarcely explored to assess the effect of management practices. This study aimed to evaluate soil organic carbon (SOC) and its pools; soil microbial activity parameters; and the Biological Fertility Index (BFI), in six land uses characteristics of the Mediterranean basin in north-eastern Sardinia. These land uses differed in management intensity and consisted of: tilled vineyard (TV), no tilled grassed vineyard (GV), former vineyards (FV), hay crop and pasture (HC and PA), cork oak forest (CO). Significant differences among ecosystems were found in most cases in (SOC), the related pools (total extractable carbon, humic and fulvic acids, not humified, not extractable), humification parameters (degree, rate and index of humification), and soil microbial activity (microbial carbon, respiration, metabolic quotient, and mineralization quotient). Pasture and cork oak forest showed in average a better soil quality for most biochemical and microbial parameters in comparison with the other ecosystems. The index of soil biological fertility (BFI) was higher under cork oak forest which is supposed to be the most sustainable ecosystem in the long term in this environment, able to maintain soil biological fertility and microbial diversity.

Phylogenetic distribution, biogeography and the effects of land management upon bacterial non-specific Acid phosphatase Gene diversity and abundance

BACKGROUND AND AIMS

Bacterial Non-Specific Acid Phosphatase (NSAP) enzymes are capable of dephosphorylating diverse organic phosphoesters but are rarely studied: their distribution in natural and managed environments is poorly understood. The aim of this study was to generate new insight into the environmental distribution of NSAPs and establish their potential global relevance to cycling of organic phosphorus.

METHODS

We employed bioinformatic tools to determine NSAP diversity and subcellular localization in microbial genomes; used the corresponding NSAP gene sequences to census metagenomes from diverse ecosystems; studied the effect of long-term land management upon NSAP diversity and abundance.

RESULTS

Periplasmic class B NSAPs are poorly represented in marine and terrestrial environments, reflecting their association with enteric and pathogenic bacteria. Periplasmic class A and outer membrane-associated class C NSAPs are cosmopolitan. NSAPs are more abundant in marine than terrestrial ecosystems and class C more abundant than class A genes, except in an acidic peat where class A genes dominate. A clear effect of land management upon gene abundance was identified.

CONCLUSIONS

NSAP genes are cosmopolitan. Class C genes are more widely distributed: their association with the outer-membrane of cells gives them a clear role in the cycling of organic phosphorus, particularly in soils.

Land-use influences phosphatase gene microdiversity in soils

Phosphorus cycling exerts significant influence upon soil fertility and productivity - processes largely controlled by microbial activity. We adopted phenotypic and metagenomic approaches to investigate phosphatase genes within soils. Microbial communities in bare fallowed soil showed a marked capacity to utilise phytate for growth compared with arable or grassland soil communities. Bare fallowed soil contained lowest concentrations of orthophosphate. Analysis of metagenomes indicated phoA, phoD and phoX, and histidine acid and cysteine phytase genes were most abundant in grassland soil which contained the greatest amount of NaOH-EDTA extractable orthophosphate. Beta-propeller phytase genes were most abundant in bare fallowed soil. Phylogenetic analysis of metagenome sequences indicated the phenotypic shift observed in the capacity to mineralise phytate in bare fallow soil was accompanied by an increase in phoD, phoX and beta-propeller phytase genes coding for exoenzymes. However, there was a remarkable degree of genetic similarity across the soils despite the differences in land-use. Predicted extracellular ecotypes were distributed across a greater range of soil structure than predicted intracellular ecotypes, suggesting that microbial communities subject to the dual stresses of low nutrient availability and reduced access to organic material in bare fallowed soils rely upon the action of exoenzymes.