Soil Management Regimes Research Articles

Analysis of small-scale soil CO2 fluxes in an orange orchard under irrigation and soil conservative practices

The quantification of soil carbon dioxide (CO2) flux represents an indicator of the agro-ecosystems sustainability. However, the monitoring of these fluxes is quite challenging due to their high spatially-temporally variability and dependence on environmental variables and soil management practices.In this study, soil CO2 fluxes were measured using a low-cost accumulation chamber, that was realized ad hoc for the surveys, in an orange orchard managed under different soil management (SM, bare versus mulched soils) and water regime (WR, full irrigation versus regulated deficit irrigation) strategies. In particular, the soil CO2 flux measurements were acquired in discontinuous and continuous modes, together with ancillary agrometeorological and soil-related information, and then compared to the agrosystem scale CO2 fluxes measured by the eddy covariance (EC) technique.Overall significant differences were obtained for the soil CO2 discontinuous fluxes as function of the WR (0.16 ± 0.01 and 0.14 ± 0.01 mg m−2 s−1 under full irrigation and regulated deficit irrigation, respectively). For the continuous soil CO2 measurements, the response observed for the SM factor varied from year to year, indicating for the overall reference period 2022-23 higher soil CO2 flux under the mulched soils (0.24 ± 0.01 mg m−2 s−1) than under bare soil conditions (0.15 ± 0.00 mg m−2 s−1). Inter-annual variations were also observed as function of the day-of-year (DOY), the SM and their interactions, resulting in higher soil CO2 flux under the mulched soils (0.24 ± 0.02 mg m−2 s−1) than under bare soil (0.15 ± 0.01 mg m−2 s−1) in certain periods of the years, according to the environmental conditions. Resultssuggest the importance of integrating soil CO2 flux measurements with ancillary variables that explain the variability of the agrosystem and the need to conduct the measurements using different operational modalities, also providing for night-time monitoring of CO2. In addition, the study underlines that the small-scale chamber measurements can be used to estimate soil CO2 fluxes at orchard scale if fluxes are properly scaled.

Plasticity of microbial substrate carbon use efficiency in response to changes in plant carbon input and soil organic matter status

The ability of the soil's biological community to immobilise carbon (C) from substrates, often referred to as carbon use efficiency (CUE), has been shown to be dependent on the prevailing soil conditions and management regime, potentially leading to changes in C storage and functioning. However, there remains a lack of understanding about how soil CUE is affected by different common labile substrates (and combinations thereof) and native soil organic matter (SOM) status. Here we studied the CUE of three ubiquitous soil C substrates central to microbial metabolism, namely glucose, glutamic acid and citric acid, in soils with and without long-term C deprivation and associated differences in microbial biomass and community structure. We hypothesised that C deprivation-induced stress would reduce substrate CUE due to the investment of more C into stress-alleviation metabolic pathways, while conversely a balanced mixture of C substrates (i.e., sugars, amino acids and organic acids) would promote more efficient growth and substrate CUE. Our results showed that CUE was substrate-specific following the series glucose > glutamic acid > citric acid. CUE values for glucose demonstrated plasticity, being significantly lower in the soils experiencing C deprivation for both 6 and 16 years. Further, the CUE of glucose was increased when supplied alongside citrate and glutamate suggesting that substrate mixture may promote more efficient microbial growth. In contrast, the CUE for glutamic acid and citric acid showed no plasticity, being unaffected by both SOM status and the presence of other substrates. In conclusion, we found evidence to support both our hypotheses indicating that the type of C entering soil alongside native SOM levels may have a strong influence on overall CUE and thus C storage potential.

Grass sward cover improves soil organic carbon and nitrogen in a vineyard

ABSTRACT Historical depletion of agricultural soils must be remedied to maintain their long-term food production function, including soils in intensive vineyards traditionally kept without plant cover to limit resource competition. This paper reports on the impact of five contrasting soil management regimes on indicators of soil quality such as soil organic carbon, nitrogen and their indices. We exposed sandy loam Rendzic Leptosol under a vineyard in Nitra-Dražovce (Slovakia, central Europe) to the following five treatments for 14 years: no-till sward, no-till sward+NPK100, no-till sward+NPK125, plowed tillage and (5) plowed tillage+manure. We found that grass swards continuously increased the total soil organic carbon in the topsoil, but plowed tillage resulted in no change. The availability of potentially mineralizable nitrogen was also increased by grass cover; but was not modified by manure but by mineral fertilizer addition. We tested the usefulness of carbon and management indices as indicators of changing soil C and N status and found them no better than tracking total and labile forms of both elements. In conclusion, the recovery of degraded vineyard soils under no-till grass sward cover is detectable within 14 years and is not affected by fertilization or manure addition.

Specific suppression of vascular wilt disease of onion is linked with fungal soil community structure

The soil microbiome plays an important role in plant health and is therefore being investigated as a target to develop new approaches for sustainable crop protection. Here, we aimed to investigate the roles of bacterial and fungal communities in suppression of vascular wilt disease caused by Fusarium oxysporum in soils used for the cropping of onion (Allium cepae). We used pot experiments to assess impacts of disease in suppressive and conducive soils, and in a mixture of the two, and profiled the microbiomes of bulk field soil and pot soils using high-throughput sequencing. The incidence of vascular wilt disease in onions grown in the pot experiment reflected the incidence previously observed in the field, with disease significantly higher in conducive than suppressive field soil. However, disease incidence remained low when conducive and suppressive soils were mixed. Beta diversity analysis revealed clear separation of suppressive and conducive soils and indicated that fungal community structures were more closely linked to suppressiveness than were bacterial communities. Major fungal taxa that differentiated suppressive and conducive soils included species from the genera Gibellulopsis, Penicillium, Acremonium and Pseudallescheria. We conclude that the reduced incidence of onion vascular wilt disease is an example of specific suppression, brought about by the elevated abundance of several fungal taxa, whereas bacterial communities play a less important role. Differences in abundance of beneficial fungal species may be linked to different crop rotations employed in the two fields. Our results may contribute to the adoption of improved soil management regimes that protect beneficial microorganisms, or to the development of microbial consortia for biological control of onion vascular wilt disease.

Irrigation modulates entomopathogenic nematode community and its soil food web in olive groves under different agricultural managements

Entomopathogenic nematodes (EPNs) are biological control agents distributed worldwide in natural and agricultural soils. Recent evidence supports the hypothesis that stable rhizospheres of perennial crops can favor the occurrence of EPNs. However, different agricultural management practices can modulate their natural distribution in agroecosystems, hence should be considered in conservation biological control programs to support as high as possible native EPN populations. Cultivated olive (Olea europaea subsp. europaea), originally from the Mediterranean Basin, is a key perennial crop susceptible to a diverse range of arthropod pests that account for their life with at least one soil inhabitant stage. In this study, we investigated, for the first time, the occurrence of EPNs and associated soil organisms in olive groves managed with different practices. We surveyed 89 commercial olive groves located in Andalusia (Southern Spain) and differently handled for pest management (conventional vs. organic), soil management (tilling vs. cover cropping), and irrigation regime (rain feed vs. drip-irrigation). By using species-specific primers-probe sets and quantitative real-time PCR approaches, we screened the occurrence of nine species of EPNs, five free-living nematodes (FLNs), and six nematophagous fungi (NF). We found EPNs in 23.6% of the sites, identifying only two EPN species: Steinernema feltiae (15.7%) and Heterorhabditis bacteriophora (7.9%). Pest and soil management did not affect EPN abundance, but drip irrigation increased their occurrence (P < 0.025). On the contrary, we recorded lower FLN numbers in irrigated groves (P = 0.003), particularly for Oscheius tipulae and Pristionchus maupasi. Regarding NF, both organic management (P < 0.001) and drip irrigation (P < 0.035) enhanced their abundance. Four abiotic explanatory variables (extractable P, clay content, elevation, and precipitation) explained 85.6% of the EPN, FLN, and NF species variation in multivariate analysis. Overall, drip irrigation in the olive groves enhanced the EPN community but also NF growth, natural enemies of nematodes. Additional studies are required to determine the best combination of alternative strategies that will enhance a balanced soil biota in olive groves in Mediterranean regions and other areas where this crops is cultivated that enable conservation ecosystem services, such as those provided by the EPNs.

Nitrogen efficiency by soil quality and management regimes on Malawi farms: Can fertilizer use remain profitable?

• We combine site-specific soil, satellite and management data to estimate 16 regimes for yield response to inorganic nitrogen on farmers’ fields. • Determinants of labile (permanganate oxidizable) carbon is examined to investigate management impacts on soil fertility in the near-term. • Maize response to fertilizer is positively related to labile soil carbon but response estimates are low (negligible to 6 maize kg/nitrogen kg). • Incorporating diverse crop residues and manure consistently for a few years can meaningfully raise labile carbon levels. • Strategies to promote sustainable agricultural intensification and fertilizer use will likely be more successful if soil fertility is addressed holistically. Maize is the primary economic and dietary staple crop for most poor farmers in Southern Africa, yet low yields have persisted in the region for decades. Intensifying maize production in a sustainable way using the same land will be increasingly important as virgin land becomes scarcer and fallowing becomes less common. This study investigates the sustainability of intensification underway in the African smallholder sector using a uniquely detailed panel survey that combines remote sensing data, soil analysis, yield cuts, GPS area measurements, and detailed field management surveys. Specifically, we quantify the on-farm yield response to nitrogen (N) fertilizer in relationship to 16 soil and field management regimes, adding to the scant literature that combines precise and objective measures of inputs, outputs, and ecological conditions on fields managed by farmers. Furthermore, we examine drivers of soil health using a measure of labile carbon that, unlike total carbon, can be responsive to farm management over the observable time period. Results are based on a representative sampling of Malawi’s diverse agroecosystems through a multi-year study for over 1000 fields. We find surprisingly low yield response to N applications, highlighting that fertilizer access alone is not sufficient for sustainable intensification. We find complimentary “good agronomy”, including effective weed management, crop rotations, and organic fertilizer applications are positive influences on maize yield response to inorganic fertilizers. Encouragingly, results show management practices such as incorporating diverse crop residues and manure for a few years can raise labile carbon levels, improving the soil base on which factors jointly determine yields. These findings underscore the importance of education, livestock and crop diversification, and farmer utilization of good agronomy to improve fertilizer use efficiency as a means to promote sustainable agricultural productivity.

Is soil management system really important? comparison of microbial community diversity and structure in soils managed under organic and conventional regimes with some view on soil properties.

The fertility and productive value of soil are closely related to the physical and chemical properties of the soil as well as its biological activity. This activity is related to the intensity of microbially catalysed processes of transformation of organic and mineral substances contained in the soil. These processes are closely correlated with the abundance and biodiversity of soil microorganisms, especially bacteria, and the activity of enzymes produced by them. In this article we have compared some physicochemical properties of soil derived from conventional and organic farms and microbial communities inhabiting these ecosystems. We aim to investigate whether the soil management regime affects the abundance and diversity of these environments in terms of bacteria. Some differences in microbial communities were observed, but the rhizosphere of plants from organic and conventional soils does not harbour separate microbiomes. Albeit, the method of fertilization influences the diversity of soil microorganisms. A greater diversity of bacteria was observed in soils from farms where organic fertilizers were applied. Soil pH and activity of some soil enzymes were also shown to differ between organic and conventional soil cropping systems.

Effects of cover crops and irrigation on ‘Tempranillo’ grapevine and berry physiology: an experiment under the Mediterranean conditions of Southern Portugal

In addition to irrigation, other viticultural practices such as soil management can be applied to improve grapevine (Vitis vinifera L.) quality responses and attenuate unfavourable environmental conditions. Cover crops in the interrow of irrigated vineyards change the dynamics of water extraction and it is expected that the patterns of vines’ water relations will be modified, also changing their productive responses. This study took place over two seasons in ‘Tempranillo’ grapevines in a vineyard in South Portugal, where a cover crop was sown in the inter-rows of half the study area (SCC) while maintaining resident vegetation in the remaining (RV). Five water regime treatments were applied: full irrigation (200 mm irrigation amount–I200); moderate irrigation (150 mm–I150); deficit irrigation (100 mm–I100); ultra-deficit irrigation (50 mm–I50); rainfed (I0). Measurements of predawn leaf water potential (ΨPD), stomatal conductance (gs), photosynthetic rate (An), and transpiration rate (E) were made during the final stages of the growth cycle. Data of soil water availability, yield and growth variables, and berries and wine composition were also used. Significant interactions between the effect of soil management and water regime were observed on ΨPD. A water competition effect exerted by the cover crop could be responsible for reduced water loss and carbon assimilation, whenever Spring rain is lower and/or the cover crop biomass development is not controlled. Differences in gs and An observed at midday and late measurements reflect the influence of the daily increase of atmospheric water demand. Stomatal closure of grapevines was less affected in plots of higher soil water storage capacity. The correlation between ΨPD and gs was higher in the midday and late measurements, pointing to the regulation of stomatal response in response to water availability and daily environmental conditions. Principal components analysis (PCA) evidenced an influence of water deficit on metabolic responses that benefit fruit and wine quality. The cluster analysis (CA) revealed that no significant cluster of cases was clearly controlled by soil management or water regime in the first season but, in the second, drier season, significant clustering more irrigation- than soil management-controlled showed that a predominant influence of irrigation should be expected for ‘Tempranillo’ grapevines grown under dry Mediterranean conditions.

Structure of canopy and ground-dwelling arthropod communities in olive orchards is determined by the type of soil cover

The intensification of agriculture in olive groves, especially the modification or elimination of spontaneous vegetation, alters the relationships in arthropod communities and reduces their interactions and ecosystem services. This study was carried out in nine olive groves in which there was either a planted cover crop, spontaneous cover crop or bare ground. The interactions of ground-dwelling, canopy and flying arthropods in trophic webs were calculated for each olive grove soil management regime at the family level taking into consideration their different functional traits: feeding guilds, specific agricultural traits and trophic level. Olive groves with spontaneous cover had trophic webs with a higher number of plausible links between arthropod families and a more balanced distribution of specimens among trophic levels compared to those with planted cover and bare ground. There was a similar number of arthropod families consisting of both pests and their natural enemies in the planted cover regime, while olive groves with bare ground had simpler trophic webs. The complexity of plausible trophic links was greater in olive groves with spontaneous plant cover despite the similar values for family richness in the three-olive grove soil management regimes. Qualitative values (such as functional traits) were more diverse in agroecosystems with spontaneous plant cover in which there were more sources of food.

Symbiotic soil fungi suppress N2O emissions but facilitate nitrogen remobilization to grains in sandy but not clay soils under organic amendments

Arbuscular mycorrhizal fungi (AMF) can form symbiotic relationships with roots of plants and potentially affect nitrogen (N) cycling in cropping systems. However, it is unclear how AMF influence N2O emissions and crop N assimilation, two key N cycling steps which are closely related to climate change and food production, under different soil management regimes. A microcosm experiment was conducted to test the effects of AMF on N2O emission and plant N assimilation, with wheat as a model crop, under organic (straw) amendment in soils with different textures. We found that AMF suppressed N2O emissions, promoted mycorrhizal N uptake and remobilization to grains and increase grain biomass under organic amendment in the sandy soil. However, AMF did not affect N2O emission, although increased plant N uptake, but inhibited mycorrhizal N remobilization to grains under organic amendment in the clay soil. These findings highlight that AMF have different effects on N2O emission and N translocation between sandy and clay soils. Appropriate soil management for mycorrhizal symbiosis in the cropping system can combat climate change and ensure food production.

Preliminary Effects of Crop Residue Management on Soil Quality and Crop Production under Different Soil Management Regimes in Corn-Wheat Rotation Systems

Strategic management of crop residues is essential to enhance soil quality for sustainable agriculture. However, little is known about the specific amounts of crop residues needed to improve soil quality characteristics which are key to develop economic plans. In this study, we investigated the effects of applying crop residue at five rates, including 100% (R100), 75% (R75), 50% (R50), 25% (R25), and 0% (R0), on wheat yield and soil properties. Field experiments were conducted for two cropping seasons in a wheat-corn rotation under conventional (CT) and no-till (NT) systems to observe the first results obtained during short-term periods (one-year application). During the study, the wheat and corn fields were irrigated. Application of plant residue resulted in increased soil organic carbon (SOC) and available nutrients and improved soil physical properties, i.e., aggregates mean weight diameter in wet (MWDw) and dry (MWDd) conditions, water-stable aggregates (WSA), dry-stable aggregates, (DSA), soil water infiltration (SWI), soil available water (SAW), and yield of wheat and corn. The effects were stronger at higher residue application rates. In the CT system, compared to R0, R100 resulted in the highest increase equal to 38, 29, 23, 34, 35, 41, and 11% for SOC, MWDw, MWDd, WSA, DSA, SAW, and wheat grain yield, respectively. This was equivalent to 28, 19.5, 19, 37, 44, 52, and 6% for the NT system, respectively. Generally, the NT system resulted in a stratification of the soil properties within 0–10 cm compared to 10–20 cm soil depth, but a uniform distribution for both depths under CT system. Overall, these results show that crop residue application can improve soil quality and yield in cereal production systems under semi-arid conditions during the first year of application. It will be key to monitor these changes in along-term field studies.

Resistance–recovery trade‐off of soil microbial communities under altered rain regimes: An experimental test across European agroecosystems

Abstract With the increased occurrence of climate extremes, there is an urgent need to better understand how management strategies affect the capacity of the soil microbial community to maintain its ecosystem functions (e.g. nutrient cycling). To address this issue, intact monoliths were extracted from conventional and ecological managed grasslands in three countries across Europe and exposed under common air condition (temperature and moisture) to one of three altered rain regimes (dry, wet and intermittent wet/dry) as compared to a normal regime. Subsequently, we compared the resistance and recovery of the soil microbial biomass, potential enzyme activities and community composition. The microbial community composition differed with soil management and rain regimes. Soil microbial biomass increased from the wetter to the dryer rain regime, paralleling an increase of available carbon and nutrients, suggesting low sensitivity to soil moisture reduction but nutritional limitations of soil microbes. Conversely, enzyme activities decreased with all altered rain regimes. Resistance and recovery (considering absolute distance between normal and altered rain regime) of the microbial communities depended on soil management. Conventional‐intensive management showed higher resistance of two fundamental properties for nutrient cycling (i.e. bacterial biomass and extracellular enzyme activities) yet associated with more important changes in microbial community composition. This suggests an internal community reorganization promoting biomass and activity resistance. Conversely, under ecological management bacterial biomass and enzyme activities showed better recovery capacity, whereas no or very low recovery of these properties was observed under conventional management. These management effects were consistent across the three altered rain regimes investigated, indicating common factors controlling microbial communities’ response to different climate‐related stresses. Synthesis and applications. Our study provides experimental evidence for an important trade‐off for agroecosystem management between (a) stabilizing nutrient cycling potential during an altered rain regime period at the expense of very low recovery capacity and potential long‐term effect (conventional sites) and (b) promoting the capacity of the microbial community to recover its functional potential after the end of the stress (ecological sites). Thus, management based on ecologically sound principles may be the best option to sustain long‐term soil functioning under climate change.

Relationships between yield of winter wheat and bacterial and protozoan fatty acids affected by different green manure amendments

ABSTRACT Soil microorganisms play important roles in crop growth and nutrient cycling. This study investigated the influence of the temporal changes in soil fatty acids (FAs) mainly derived from microorganisms by the incorporation of different green manures on the subsequent crop yield of winter wheat. Plants (Sesbania rostrata or Sorghum bicolor) as green manure were cultivated as the preceding crop, followed by the cultivation of winter wheat. Soil FA structure was characterized by the analysis of the relative abundance of FA methyl esters (FAMEs). Principal component (PC) analysis of the abundance of FAME signatures indicated that the composition of soil FAs was clearly altered by different soil management regimes. The amount of soil FAMEs increased with the incorporation of green manure, and this increase was maintained during wheat cultivation. A positive correlation was observed between wheat yield and the ratio of FAMEs derived from Gram-positive and Gram-negative bacteria at stages of tiller emergence and heading. FAMEs from Gram-positive bacteria and protozoa also positively correlated with one of the wheat yield components, 1,000 grain weight. These results may suggest that the amount of bacterial and protozoan FAs at tiller and heading stage following green manure incorporation is useful to predict the winter wheat productivity.

Legacy effects override soil properties for CO2 and N2O but not CH4 emissions following digestate application to soil.

The application of organic materials to soil can recycle nutrients and increase organic matter in agricultural lands. Digestate can be used as a nutrient source for crop production but it has also been shown to stimulate greenhouse gas (GHG) emissions from amended soils. While edaphic factors, such as soil texture and pH, have been shown to be strong determinants of soil GHG fluxes, the impact of the legacy of previous management practices is less well understood. Here we aim to investigate the impact of such legacy effects and to contrast them against soil properties to identify the key determinants of soil GHG fluxes following digestate application. Soil from an already established field experiment was used to set up a pot experiment, to evaluate N2O, CH4 and CO2 fluxes from cattle‐slurry‐digestate amended soils. The soil had been treated with farmyard manure, green manure or synthetic N‐fertilizer, 18 months before the pot experiment was set up. Following homogenization and a preincubation stage, digestate was added at a concentration of 250 kg total N/ha eq. Soil GHG fluxes were then sampled over a 64 day period. The digestate stimulated emissions of the three GHGs compared to controls. The legacy of previous soil management was found to be a key determinant of CO2 and N2O flux while edaphic variables did not have a significant effect across the range of variables included in this experiment. Conversely, edaphic variables, in particular texture, were the main determinant of CH4 flux from soil following digestate application. Results demonstrate that edaphic factors and current soil management regime alone are not effective predictors of soil GHG flux response following digestate application. Knowledge of the site management in terms of organic amendments is required to make robust predictions of the likely soil GHG flux response following digestate application to soil.

Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management.

Plants manipulate their rhizosphere community in a species and even a plant life stage-dependent manner. In essence plants select, promote and (de)activate directly the local bacterial and fungal community, and indirectly representatives of the next trophic level, protists and nematodes. By doing so, plants enlarge the pool of bioavailable nutrients and maximize local disease suppressiveness within the boundaries set by the nature of the local microbial community. MiSeq sequencing of specific variable regions of the 16S or 18S ribosomal DNA (rDNA) is widely used to map microbial shifts. As current RNA extraction procedures are time-consuming and expensive, the rRNA-based characterization of the active microbial community is taken along less frequently. Recently, we developed a relatively fast and affordable protocol for the simultaneous extraction of rDNA and rRNA from soil. Here, we investigated the long-term impact of three type of soil management, two conventional and an organic regime, on soil biota in fields naturally infested with the Columbian root-knot nematode Meloidogyne chitwoodi with pea (Pisum sativum) as the main crop. For all soil samples, large differences were observed between resident (rDNA) and active (rRNA) microbial communities. Among the four organismal group under investigation, the bacterial community was most affected by the main crop, and unweighted and weighted UniFrac analyses (explaining respectively 16.4% and 51.3% of the observed variation) pointed at a quantitative rather than a qualitative shift. LEfSe analyses were employed for each of the four organismal groups to taxonomically pinpoint the effects of soil management. Concentrating on the bacterial community in the pea rhizosphere, organic soil management resulted in a remarkable activation of members of the Burkholderiaceae, Enterobacteriaceae, and Pseudomonadaceae. Prolonged organic soil management was also accompanied by significantly higher densities of bacterivorous nematodes, whereas levels of M. chitwoodi had dropped drastically. Though present and active in the fields under investigation Orbiliaceae, a family harboring numerous nematophagous fungi, was not associated with the M. chitwoodi decline. A closer look revealed that a local accumulation and activation of Pseudomonas, a genus that includes a number of nematode-suppressive species, paralleled the lower M. chitwoodi densities. This study underlines the relevance of taking along both resident and active fractions of multiple organismal groups while mapping the impact of e.g. crops and soil management regimes.

Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents

Conventional agricultural production systems, typified by large inputs of mineral fertilizers and pesticides, reduce soil biodiversity and may negatively affect ecosystem services such as carbon fixation, nutrient cycling and disease suppressiveness. Organic soil management is thought to contribute to a more diverse and stable soil food web, but data detailing this effect are sparse and fragmented. We set out to map both the resident (rDNA) and the active (rRNA) fractions of bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as the main crop. Contrasts between resident and active communities explained 22%, 14%, 21% and 25% of the variance within the bacterial, fungal, protozoan, and metazoan communities. As the active fractions of organismal groups define the actual ecological functioning of soils, our findings underline the relevance of characterizing both resident and active pools. All four major organismal groups were affected by soil management (p < 0.01), and most taxa showed both an increased presence and an enlarged activity under the organic regime. Hence, a prolonged organic soil management not only impacts the primary decomposers, bacteria and fungi, but also major representatives of the next trophic level, protists and metazoa.

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes.

To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe–plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant–growth–promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

Organic Amendment Under Increasing Agricultural Intensification: Effects on Soil Bacterial Communities and Plant Productivity.

The soil microbiome is a complex living network that plays essential roles in agricultural systems, regardless of the level of intensification. However, the effects of agricultural management on the soil microbiome and the association with plant productivity remain largely unclear. Here, we studied the responses of three soil systems displaying distinct levels of agriculture intensiveness (i.e., natural, organic, and conventional soil management regimes) to experimentally manipulated organic farming amendments (i.e., dung and earthworms). We aimed at (i) identifying the effect on plant productivity and (ii) elucidating the degree of shifts in bacterial communities in response to the applied organic amendments. We found plant productivity to be lower with increasing agricultural intensification. Bacterial communities shifted distinctively for each soil management regime to the organic amendments applied. In brief, greater changes were observed in the Conventional management comparatively to the Organic and Natural management, an effect largely driven by dung addition. Moreover, we found evidence that the level of agricultural intensiveness also affects the timespan for these shifts. For instance, while the Natural system reached a relatively stable community composition before the end of the experiment, treatments on the conventional soil management regime did not. Random forest analyses further revealed an increasing impact of introduced taxa from dung addition aligned with increasing agricultural intensification. These analyses suggested that earthworms regulate the introduction of species from dung into the soil bacterial community. Collectively, our results contribute to a better understanding of the outcomes of organic amendments on soils under distinct levels of agriculture intensiveness, with implications for further development in soil restorations practices.

Impacts of climate change on soil nitrogen kinetics and rice production in Andisol paddy fields

ABSTRACTWe constructed a new rice growth model, SIMRIWk, and discuss the impact of climate change on the growth and production of rice plants in relation to soil nitrogen (N) kinetics. We developed a model simulating N availability for rice plants associated with soil N kinetics and rice plant N uptake and combined it with the existing rice growth model SIMRIW to construct SIMRIWk. The model parameters were determined from rice plant growth and soil N experimental data obtained over 25 years under four soil management regimes. SIMRIWk successfully simulated the annual changes and upward trend observed during the 25 years in all treatments. The relationship between measured yields and SIMRIWk calculations in all treatments over the 25 years formed one aggregation defined by the regression equation y = 1.00x and showed a significant correlation (r2 = 0.894). According to SIMRIWk, increasing temperature in the cold season increases the formation of easily decomposable organic N produced under dry conditions and N mineralization during the next warm season, suggesting that rice growth is influenced by both warm-season and cold-season temperatures. We forecast rice yield and soil N kinetics from 2016 to 2100 using SIMRIWk and climate change predictions based on the IPCC’s climate change scenario RCP8.5. Atmospheric warming, a rise in CO2 partial pressure, and increased soil N mineralization caused by soil warming will increase rice plant growth, but the decreased radiation absorbed owing to the shortened growing season and high-temperature sterility will prevent any significant change in yield. Furthermore, the acceleration of soil organic N decomposition will decrease soil organic N concentrations. Understanding the influences of climate change on soil organic matter kinetics is absolutely critical for predicting the future soil production capacity.

Effect of habitat and soil management on dispersal and distribution patterns of entomopathogenic nematodes

Previous research has documented patchy distributions of entomopathogenic nematodes (EPNs) in the field, but more uniform distributions of EPNs could increase their biocontrol services in agroecosystems. Although laboratory studies have identified variation in foraging behavior of EPN species, less data is available on factors influencing their dispersal and resulting distribution patterns in the field. We examined the effect of biotic environmental factors including habitat type and plant cover, soil management and associated arthropod composition on the short- and long-term dispersal potential of Steinernema carpocapsae ALL and Heterorhabditis bacteriophora GPS11 emerging from nematode-infected host cadavers in the field. Based on bait trapping in the soil, both EPN species showed equivalent potential to disperse up to 2m, actively or passively, in both grass and cultivated potatoes. Arthropod abundance, assessed by pitfall traps and soil core sampling, was equal in the two habitats. S. carpocapsae was detected in larger numbers in the water in pitfall traps, whereas H. bacteriophora numbers were positively correlated with mites in soil core samples. We documented aggregation of H. bacteriophora populations over the two years of the study in vegetable plots, which is consistent with earlier studies. Spatial distributions after dispersing from a grassy border into the adjacent cultivated field plots were more aggregated for H. bacteriophora than for S. carpocapsae. In most cases, no significant differences in the dispersal and spatial distribution of generally low population densities of H. bacteriophora were observed in plots with different soil management regimes, the exception being significantly lower aggregation in the first year of the study in plots with reduced tillage, cover crops, and no herbicide or insecticide treatments.