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Enhancing soil suppressiveness against plant pathogens or pests is a promising alternative strategy to chemical pesticides. Organic amendments have been shown to reduce crop diseases and pests, with chitin products the most efficient against fungal pathogens. To study which characteristics of organic products are correlated with disease suppression, an experiment was designed in which 10 types of organic amendments with different physicochemical properties were tested against the soilborne pathogen Rhizoctonia solani in sugar beet seedlings. Organic amendments rich in keratin or chitin reduced Rhizoctonia solani disease symptoms in sugar beet plants. The bacterial and fungal microbial communities in amended soils were distinct from the microbial communities in nonamended soil, as well as those in soils that received other nonsuppressive treatments. The Rhizoctonia -suppressive amended soils were rich in saprophytic bacteria and fungi that are known for their keratinolytic and chitinolytic properties (i.e., Oxalobacteraceae and Mortierellaceae ). The microbial community in keratin- and chitin-amended soils was associated with higher zinc, copper, and selenium, respectively. IMPORTANCE Our results highlight the importance of soil microorganisms in plant disease suppression and the possibility to steer soil microbial community composition by applying organic amendments to the soil., (Copyright © 2021 Andreo-Jimenez et al.)

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.

Understanding the impacts of agricultural intensification and extensification on soil biota communities is useful in order to preserve and restore biological diversity in agricultural soils and enhance the role of soil biota in agroecosystem functioning. Over four consecutive years, we investigated the effects of agricultural intensification and extensification (including conversion of grassland to arable land and vice versa, increased and decreased levels of mineral fertilization, and monoculture compared to crop rotation) on major soil biota group abundances and functional diversity. We integrated and compared effects across taxonomic levels to identify sensitive species groups. Conversion of grassland to arable land negatively affected both abundances and functional diversity of soil biota. Further intensification of the cropping system by increased fertilization and reduced crop diversity exerted smaller and differential effects on different soil biota groups. Agricultural intensification affected abundances of taxonomic groups with larger body size (earthworms, enchytraeids, microarthropods, and nematodes) more negatively than smaller-sized taxonomic groups (protozoans, bacteria, and fungi). Also functional group diversity and composition were more negatively affected in larger-sized soil biota (earthworms, predatory mites) than in smaller-sized soil biota (nematodes). Furthermore, larger soil biota appeared to be primarily affected by short-term consequences of conversion (disturbance, loss of habitat), whereas smaller soil biota were predominantly affected by long-term consequences (probably loss of organic matter). Reestablishment of grassland resulted in increased abundances of soil biota groups, but since not all groups increased in the same measure, the community structure was not completely restored. We concluded that larger-sized soil biota are more sensitive to agricultural intensification than smaller-sized soil biota. Furthermore, since larger-sized soil biota groups had lower taxonomic richness, we suggest that agricultural intensification exerts strongest effects on species-poor soil biota groups, thus supporting the hypothesis that biodiversity has an "insurance" function. As soil biota play an important role in agroecosystem functioning, altered soil biota abundances and functional group composition under agricultural intensification are likely to affect the functioning of the agroecosystem.

Soil biological studies are often conducted on sieved soils without the presence of plants. However, soil fungi build delicate mycelial networks, often symbiotically associated with plant roots (mycorrhizal fungi). We hypothesized that as a result of sieving and incubating without plants, the total fungal biomass decreases. To test this, we conducted three incubation experiments. We expected total and arbuscular mycorrhizal (AM) fungal biomass to be higher in less fertilized soils than in fertilized soils, and thus to decrease more during incubation. Indeed, we found that fungal biomass decreased rapidly in the less fertilized soils. A shift towards thicker hyphae occurred, and the fraction of septate hyphae increased. However, analyses of phospholipid fatty acids (PLFAs) and neutral lipid fatty acids could not clarify which fungal groups were decreasing. We propose that in our soils, there was a fraction of fungal biomass that was sensitive to fertilization and disturbance (sieving, followed by incubation without plants) with a very high turnover (possibly composed of fine hyphae of AM and saprotrophic fungi), and a fraction that was much less vulnerable with a low turnover (composed of saprotrophic fungi and runner hyphae of AMF). Furthermore, PLFAs might not be as sensitive in detecting changes in fungal biomass as previously thought.

Functional stability, measured in terms of resistance and resilience of soil respiration rate and bacterial growth rate, was studied in soils from field plots that have been exposed to copper contamination and low pH for more than two decades. We tested whether functional stability follows patterns predicted by either the "low stress-high stability" or the "high stress-high stability" theory. Treatments consisting of soils with no or high copper load (0 or 750 kg/ha) and with low or neutral pH (4.0 or 6.1) were used. Stability was examined by applying an additional disturbance by heat (50 degrees C for 18 h) or drying-rewetting cycles. After heating, the respiration rate indicated that the soils without copper were less stable (more affected) than the soils with 750 kg/ha. Bacterial growth rate was more stable (resistant) to heat in the pH 6.1 than in the pH 4.0 soils. Growth rate was stimulated rather than inhibited by heating and was highly resilient in all soils. The respiration rate was less affected by drying-rewetting cycles in the pH 4.0 soils than in the pH 6.1 soils. Bacterial growth rate after drying-rewetting disturbance showed no distinct pattern of stability. We found that the stability of a particular process could vary significantly, depending on the kind of disturbance; therefore, neither of the two theories could adequately predict the response of the microbial community to disturbance.

Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furthermore, a mixture of strains yielded distinguishable bands. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. A field experiment performed with litter in nylon bags was used to evaluate the bacterial diversity during the decomposition of readily degradable rye and more refractory wheat material in comparable luvisols and cambisols in northern, central, and southern Germany. The amount of bacterial DNA in the fresh litter was small. The DNA content increased rapidly after the litter was added to the soil, particularly in the rapidly decomposing rye material. Concurrently, diversity indices, such as the Shannon-Weaver index, evenness, and equitability, which were calculated from the number and relative abundance (intensity) of the bacterial DNA bands amplified from genes coding for 16S rRNA, increased during the course of decomposition. This general trend was not significant for evenness and equitability at any time. The indices were higher for the more degradation-resistant wheat straw than for the more easily decomposed rye grass. Thus, the DNA band patterns indicated that there was increasing bacterial diversity as decomposition proceeded and substrate quality decreased. The bacterial diversity differed for the sites in northern, central, and southern Germany, where the same litter material was buried in the soil. This shows that in addition to litter type climate, vegetation, and indigenous microbes in the surrounding soil affected the development of the bacterial communities in the litter.

Peat wetlands are of major importance for ecosystem services such as carbon storage, water regulation and maintenance of biodiversity. However, peat drainage for farming leads to CO 2 emission, soil subsidence and biodiversity losses. In the peat areas in the Netherlands, solutions are sought in reducing drainage, adapting farming to wetter soils, and converting productive dairy grasslands to less intensively managed semi-natural grasslands. Our objective was to compare the soil ecology and related ecosystem services of dairy and semi-natural grasslands on peat soils (Terric Histosols). Soil biotic and abiotic parameters were measured in twenty dairy and twenty semi-natural sites, with particular focus on (i) soil faunal diversity (ecosystem service “maintenance of biodiversity”), (ii) CO 2 emission (“climate regulation”), (iii) water infiltration (“water regulation”) and (iv) soil fertility (“grass production”). Mean soil faunal taxonomic richness per site (alpha diversity) was higher in dairy grasslands compared to semi-natural grasslands. However, the total observed number of taxa (gamma diversity) in dairy grassland was 13% lower for soil fauna and 21% lower when including plant species. Potential C mineralization rate in the topsoil – used as a proxy for CO 2 emission – was not influenced by land use but was limited by drought. Additionally, potential C mineralization depended on different C sources and microbial groups in the two grassland types. Water infiltration rate differed by a factor of five between land use types (dairy > semi-natural), and correlated with soil porosity. As expected, soil fertility was higher in dairy than in semi-natural grasslands. However, potential N mineralization was similar in dairy and semi-natural grasslands and was correlated negatively with bacterial biomass apparently indicating N immobilization, and positively with bacterial growth that depended on labile C and N in soil. Our study on peat soils shows that dairy versus semi-natural grassland use influences biodiversity, climate regulation, water regulation and (potential for) grassland production. We conclude with recommendations for land management to optimize the delivery of those ecosystem services. [ABSTRACT FROM AUTHOR]

Environmental stress is the main cause of the decline of species diversity in low-productive fen meadows in the Netherlands. Attempts to restore species diverse fen meadows e.g. by sod cutting frequently fail. We supposed that unsuccessful efforts are due to ignoring the impact of environmental stress on the performance of soil biota, which play a key role in N-immobilization and keeping available-N for primary production low. We investigated both pristine and degraded natural sites and successfully and unsuccessfully restored sites of poor and rich fen meadows. We determined plant species composition, soil chemical properties, N-pools in soil biota, N-mineralization rates, and N-fluxes. In pristine rich and poor fen meadows, mineral-N was poorly available for primary production due to a strong N-immobilization by soil biota. Annual N-immobilization fluxes exceeded by far the annual N-harvest by primary production. N-immobilization in pristine fens was higher than in degraded fens. In successfully restored rich fens, net N-mineralization was lower and N-immobilization higher than in the unsuccessful category. From our results, we derived the hypothesis that in degraded or in unsuccessfully restored fens the soils internal N-balance shifted from N-immobilization to net N-mineralization, favoring biomass production but disadvantaging plant species diversity. N-retention driven by an active N-immobilizing soil biological community, is likely a decisive process for successful recovery of plant species diversity in low productive fen meadows. We recommend that restoration techniques should stimulate a functionally diverse soil fauna, as this may enhance the storage of available nutrients in the soil food web. [ABSTRACT FROM AUTHOR]

Abstract: Soil tillage practices affect the soil microbial community in various ways, with possible consequences for nitrogen (N) losses, plant growth and soil organic carbon (C) sequestration. As microbes affect soil organic matter (SOM) dynamics largely through their activity, their impact may not be deduced from biomass measurements alone. Moreover, residual microbial tissue is thought to facilitate SOM stabilization, and to provide a long term integrated measure of effects on the microorganisms. In this study, we therefore compared the effect of reduced (RT) and conventional tillage (CT) on the biomass, growth rate and residues of the major microbial decomposer groups fungi and bacteria. Soil samples were collected at two depths (0–5 cm and 5–20 cm) from plots in an Irish winter wheat field that were exposed to either conventional or shallow non-inversion tillage for 7 growing seasons. Total soil fungal and bacterial biomasses were estimated using epifluorescence microscopy. To separate between biomass of saprophytic fungi and arbuscular mycorrhizae, samples were analyzed for ergosterol and phospholipid fatty acid (PLFA) biomarkers. Growth rates of saprophytic fungi were determined by [14C]acetate-in-ergosterol incorporation, whereas bacterial growth rates were determined by the incorporation of 3H-leucine in bacterial proteins. Finally, soil contents of fungal and bacterial residues were estimated by quantifying microbial derived amino sugars. Reduced tillage increased the total biomass of both bacteria and fungi in the 0–5 cm soil layer to a similar extent. Both ergosterol and PLFA analyses indicated that RT increased biomass of saprophytic fungi in the 0–5 cm soil layer. In contrast, RT increased the biomass of arbuscular mycorrhizae as well as its contribution to the total fungal biomass across the whole plough layer. Growth rates of both saprotrophic fungi and bacteria on the other hand were not affected by soil tillage, possibly indicating a decreased turnover rate of soil microbial biomass under RT. Moreover, RT did not affect the proportion of microbial residues that were derived from fungi. In summary, our results suggest that RT can promote soil C storage without increasing the role of saprophytic fungi in SOM dynamics relative to that of bacteria. [Copyright &y& Elsevier]

Sustainable agriculture requires nutrient management options that lead to a profitable crop yield with relatively low nitrogen (N) losses to the environment. We studied whether the addition of contrasting organic amendments together with inorganic fertilizer can promote both requirements simultaneously. In particular we studied how the chemical composition of organic amendments affects the biomass, activity and composition of the soil microbial community and subsequently carbon (C) and N mineralization, microbial N immobilization and plant growth and nutrient uptake. In a pot experiment, Brussels sprouts ( Brassica oleracea, cvar. Cyrus ) were grown on arable soil, mixed with 15 N-labelled mineral fertilizer and different kinds of organic amendments (cattle manure solid fraction, maize silage, lucerne silage, wheat straw) differing in C:N ratio and lignin content. After 69 and 132 days, destructive sampling took place to assess the effects of the different treatments on soil microbial biomass (microscopic measurements), microbial community composition (phospholipid fatty acid profiles), soil microbial activity ( 14 C-leucine incorporation), C and N mineralization, plant biomass and 15 N retrieval in soil pools, microbial biomass and plant biomass. Addition of organic amendments increased soil microbial biomass, activity and fungal/bacterial ratio and created distinct microbial community compositions, whereby high C:N ratio organic amendments had stronger effects compared to low C:N ratio amendments. Structural equation modelling showed that higher values of soil microbial activity were associated with increased N mineralization rates, increased plant biomass and plant 15 N uptake, while microbial 15 N immobilization was associated with soil microbial community composition. The outcomes of this study highlight the importance of the chemical composition and the amount of the organic amendments for finding a balance between plant N uptake, microbial N immobilization and N retention in labile and stable soil pools through the effects on the composition and activity of the soil microbial community. The results provide insights that can be used in designing combined input (nutrient and organic) nutrient management strategies for a more sustainable agriculture. [ABSTRACT FROM AUTHOR]

Soil samples were analyzed with community-level physiological profiles (CLPP) using Biolog™ ECO-plates in the Netherlands Soil Monitoring Network (NSMN; 704 samples) and in a European-wide transect (73 samples). The selection of sites was based on a representative sample of major soil texture types, land uses and climate zones. This method for determination of CLPP was specifically designed to be applied in large and long-term monitoring activities. It encompassed a solution for the inoculum-density dependence of colour formation patterns in ECO-plates, through stepwise dilution to extinction of the bacterial inoculum. The CLPP in Dutch and European soil samples appeared to be reproducible and sensitive to land use and/or soil texture. Although the method is selective, CLPP based parameters correlated well with other microbial parameters and soil characteristics. Consistent patterns in CLPP and soil habitat characteristics are emerging, as brought about by environmental disturbances, land management and soil texture. The applicability of CLPP analysis in monitoring systems is discussed. [ABSTRACT FROM AUTHOR]

Abstract: Nitrogen losses from agricultural grasslands cause eutrophication of ground- and surface water and contribute to global warming and atmospheric pollution. It is widely assumed that soils with a higher fungal biomass have lower N losses, but this relationship has never been experimentally confirmed. With the increased interest in soil-based ecosystem services and sustainable management of soils, such a relationship would be relevant for agricultural management. Here we present a first attempt to test this relationship experimentally. We used intact soil columns from two plots from a field experiment that had consistent differences in fungal biomass (68 ± 8 vs. 111 ± 9 μg C g−1) as a result of different fertilizer history (80 vs. 40 kg N ha−1 y−1 as farm yard manure), while other soil properties were very similar. We performed two greenhouse experiments: in the main experiment the columns received either mineral fertilizer N or no N (control). We measured N leaching, N2O emission and denitrification from the columns during 4 weeks, after which we analyzed fungal and bacterial biomass and soil N pools. In the additional 15N experiment we traced added N in leachates, soil, plants and microbial biomass. We found that in the main experiment, N2O emission and denitrification were lower in the high fungal biomass soil, irrespective of the addition of fertilizer N. Higher 15N recovery in the high fungal biomass soil also indicated lower N losses through dentrification. In the main experiment, N leaching after fertilizer addition showed a 3-fold increase compared to the control in low fungal biomass soil (11.9 ± 1.0 and 3.9 ± 1.0 kg N ha−1, respectively), but did not increase in high fungal biomass soil (6.4 ± 0.9 after N addition vs. 4.5 ± 0.8 kg N ha−1 in the control). Thus, in the high fungal biomass soil more N was immobilized. However, the 15N experiment did not confirm these results; N leaching was higher in high fungal biomass soil, even though this soil showed higher immobilization of 15N into microbial biomass. However, only 3% of total 15N was found in the microbial biomass 2 weeks after the mineral fertilization. Most of the recovered 15N was found in plants (approximately 25%) and soil organic matter (approximately 15%), and these amounts did not differ between the high and the low fungal biomass soil. Our main experiment confirmed the assumption of lower N losses in a soil with higher fungal biomass. The additional 15N experiment showed that higher fungal biomass is probably not the direct cause of higher N retention, but rather the result of low nitrogen availability. Both experiments confirmed that higher fungal biomass can be considered as an indicator of higher nitrogen retention in soils. [Copyright &y& Elsevier]

Abstract: For the purpose of feeding value, drought resistance and nitrogen utilization, other grasses (e.g. Festuca arundinacea and Dactylis glomerata) than the currently widely used perennial rye grass (Lolium perenne) are introduced in dairy farming, either as a monoculture or in a mixture. To study the effect of these grasses on yield and soil chemical and biological quality, the three species were sown in a field experiment in monoculture and in two mixtures. Within two growing seasons, the grass species tested under high soil fertility conditions did not show significant effects on most of the tested soil biological parameters. Only for the mixture of L. perenne and D. glomerata a higher soil NO3 − and mineral N content were most probably related to a higher bacterial activity, possibly induced by dying roots of L. perenne. This was the likely cause of the high aboveground dry matter yield of this mixture. The N-efficiencies of the monocultures of L. perenne, F. arundinacea and D. glomerata were not different when only considering the aboveground biomass. In L. perenne and F. arundinacea the total N in root biomass was higher while under D. glomerata the NO3 − in the soil was higher. The lower fraction of mineral N to total N for L. perenne, F. arundinacea and the mixture of the two suggests that their organic matter build-up/mineralization ratio was higher than for D. glomerata. Furthermore, the mixture of L. perenne and F. arundinacea showed significantly lower soil mineral N levels than the monocultures of each. We conclude that grassland systems with a mixture of L. perenne and F. arundinacea are more sustainable than the monocultures of each, in terms of reduction of nitrogen losses and the build-up of soil organic matter. D. glomerata should only be used in a mixture in which the companion grass(es) are maintained. [Copyright &y& Elsevier]