Soil ecology in sustainable agricultural systems

Effects of Conventional and Organic Agricultural Techniques on Soil Ecology
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At the local level, agricultural sustainability is about the maintenance or improvement of soil fertility, as opposed to the continuous depletion of soil fertility we see in most intensive farming systems. Much modern industrial agriculture on highly mineral soils is very similar to hydroponics.

Plants are rooted in a passive mineral matrix, usually with low cation exchange capacity CEC and low water holding capacity. Nutrients, in the form of fertilizers, are added to the soil regularly. Some of these nutrients are taken up by the crop plants, some are consumed in the decomposition of the little organic matter available, and the remainder runs off or volatilizes. The traditional view within soil science and plant nutrition is that maintaining soil fertility is about the replacement of mineral nutrients removed during harvest or lost in other ways.

This is true of course, but soil fertility is not just about the presence and availability of mineral nutrients at one point in time. It is also about the soil's physical and biological properties, e. Most intensively farmed soils are close to a steady state with very little labile, active SOM and low levels of recalcitrant SOM. Before agriculture was introduced, these soils were also in a steady state, but one with much higher levels of dynamic, labile, biologically active, chemically and biologically diverse SOM.

Truly sustainable agricultural systems should emulate this aspect of natural ecosystems: high levels of labile OM through high input of plant residues. Most current agricultural systems result in more output of SOM via decomposition than input via residues e. This process accelerated enormously under industrialization. Increased plant biomass density in the field is the key to increasing agricultural sustainability, while producing high yields. Competition among plants in the field should be seen as something to manipulate, not something to avoid.

Many of the negative environmental impacts of modern agriculture are the results of low quantities of living and dead biomass in the field, but there is no theoretical or empirical basis for the widely held assumption that low standing biomass is a necessary condition for high yields. This emphasis on increased biomass is consistent with our understanding of the development of ecosystems. This is an example of strategy b on Fig. The potential for perennial crops is still an open question, but this idea deserves a serious investment in research.

Crop rotation is to farming what ecological succession is to nature: the sequence of plant communities at one location. Nothing demonstrates the huge gap between ecological sustainability and current farming practices than the very restricted rotations we observe in most modern temperate agricultural systems. Although, as plant ecologists, we want to focus on the scientific basis of agricultural sustainability, it is not possible to address the ecology of agriculture without addressing the political and economic context in which agriculture is practised.

Making agriculture sustainable requires a food production system that has sustainability as one of its primary goals. This is far from the case at present, where agriculture is a business, like most others, which is primarily driven by the economic interest of large international corporations. We can test hypotheses about how to increase yields with high inputs, or hypotheses about increasing sustainability.

Which we choose is the research agenda. European agriculture is developing in two very different and fundamentally incompatible directions: i Industrial agriculture: high intensity, high input, unsustainable industrial farming, driven by large international agrochemical corporations. This phrase is usually associated with one of these two agendas. The agroecological agenda is very different: lower input, lower costs, healthier food and better rural lifestyles, in which farmers buy fewer things.

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These are very different objectives. The former can be defined objectively to a large degree. The second is socially determined and changes over time. We can make an analogy with water resource management. There are at least two possible objectives: i Providing enough water for everyone in society to drink and bathe. At least diamonds are not harmful to the wearer's health although they may be to the diamond miner's , whereas beef, consumed in large quantities, as it is in much of the developed world, is damaging both to the health of the consumers and the ecosystems in which it is produced.

If we produce more food, it will not go to the hungry — they cannot afford to buy it. In a sustainable world, beef would be a luxury product, consumed in small amounts except on special occasions, as we see in the development of sustainable gourmet food by environmentally aware chefs e. Barber Plant ecology, the subject of this Journal, has much to contribute to the development of sustainable agricultural systems.

Parts of Saskatchewan were covered by an inland which dried around million years ago to form one of the world's largest potash deposits Ladurantaye, Both potassium and phosphorus based fertilizers are essentially non-renewable resources as their formation is based on long geological time scales. In conventional agriculture, chemical fertilizers are needed because the soil has been depleted of the biota that are necessary for transporting nutrients and minerals to plants in an accessible form. These biota, including bacteria, fungi, and nematodes, are harmed by the tilling and pesticide use that is so common in conventional agriculture systems.

Without these biota, important ecological services that are essential to healthy plants are not available. Nitrogen, potassium, and phosphorus agricultural fertilizers have been developed in a form that plants can readily access and which bypass the ecological services provided by the soil biology. This presumably makes the various biology in the soil ecosystem less important.

However, as explained in the previous section, discussing the rhizosphere, plants need the soil biota to provide other trace minerals and nutrients that are not as readily available in synthetic chemical form. The trace minerals and nutrients exist in the soil already but are only made available to plants through their relationship with the beneficial fungi and bacteria Ingham, Fertilizers do effectively increase plant growth. However, compost application is a viable substitute for fertilizer when there is access to large quantities.

Large quantities of compost are a limiting factor and may be out of reach to many agricultural ventures trying to cut back on fertilizer use.

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Nitrogen, is found to be the limiting nutrient when compost is used in place of nitrogen, phosphorus, and potassium fertilizers Evanylo et al, However, the compost provides benefits that fertilizers do not. Compost tends to improve the physical properties of soil such a bulk density, porosity, and water holding capacity. The compost amended soils reduce mineral and sediment runoff. Evanylo et al. It is important to note that the various benefits of using compost accrue over time and are not realized until compost has been applied for a number of years. This could be a major issue for farmers who are struggling with marginal returns and need to maximize yields to make a steady income.

Earthworms, an indicator of soil health, are also affected by fertilizer use. Organic matter and compost are food sources for worms and are essential to their survival. Earthworms respond better to organic manure and compost than to chemical fertilizers Paoletti, MG, Because worms eat dead organic matter and compost, the application of compost in agricultural settings will promote earthworm biomass. When worms are present in soil, their waste creates highly fertile worm castings.

The ecological service that worms perform is becoming increasingly recognized for the soil improvement without the risk of pathogens or other polluting substances. Furthermore, worms have been found to eliminate harmful chemical substances and heavy metals which also improve the the quality of polluted soils Iozon et al, Worm castings are also shown to increase yields and fruiting quality of certain plants Panicker et al, These studies are limited to specific plants and their fruits.

More research is needed to make a broader statement about yields and fruiting quality relating specifically to worm castings. Regardless, the source of nutrients and the success of plant growth is largely associated with biology in the soil. The application of compost and organic matter increases the activity and biomass of decomposers while fertilizers tend to have a negative effect on their abundance.

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Another biological effect that fertilizers have is on the arbuscular mycorrhizal. The use of phosphorus fertilizer makes crops less reliant on arbuscular mycorrhizal. Numerous studies indicate that the colonization and spore numbers of arbuscular mycorrhizal is invariably reduced in soils with phosphorus fertilizer applications Gosling et al, This finding indicates that fertilizers that are meant to increase plant growth actually may diminish the natural ability of soils to provide nutrients to plants.

The resiliency of soil ecosystems is thereby decreased and this can create positive feedback loops. As explained in the tilling section, arbuscular mycorrhizal increase a plants ability to absorb phosphorus. By adding more inorganic phosphorus to the soil, the plants ability to absorb it is decreased because of the diminished mass of arbuscular mycorrhizal. Arbuscular mycorrhizal not only help plants uptake phosphorus, but create transportation networks for many other nutrients as well.

Principles of sustainable agriculture/ecological agriculture- Part 1

The presence of arbuscular mycorrhizal is therefore essential for healthy soil ecosystems. In addition to harming the biology of the soil, fertilizers have been found to affect the very chemistry of soil. Many experiments have been conducted which show the use of nitrogen fertilizers leads to the losses of nutrient cations positively charged ions and increases soil acidification Vitousek, et al, A study at the University of Hawai'i indicates that this happens because nitrate fertilizers are anions negatively charged ions and will move through the soil with water and attract cation nutrients and trace minerals such as calcium.

The soils are then depleted of calcium and other nutrients and trace minerals. When calcium in particular is absent from soils, there is increased leaching of toxic inorganic aluminum. Soils become more toxic, which decreases the ability for plants to absorb nitrates Durka et al, This creates a positive feedback loop in the soil system with fertilizer use. When fertilizers are meant to increase the fertility of the soil and boost productivity and output, they will invariably cause the soil to reduce a plant's capacity to absorb nutrients in the long term.

If a farmer determines that his crops are not growing well because they are not taking up nitrates, the first solution he might have is to add more nitrogen fertilizer. This solution is sought out because nitrogen fertilizer, in particular, is a relatively inexpensive commodity. It is one of the least expensive and most effective ways of increasing yields Vitousek, et al, However, without the farmer's knowing, this will further diminish the soils capacity for nutrient uptake and increases acidification as well as quantities of toxic compounds.

The overall efficiency of fertilizer has thus been found to have diminishing returns as shown in figure 6 Tillman et al, Figure 6: a, Trends in average global cereal yields; b, trends in the nitrogen-fertilization efficiency of crop production annual global cereal production divided by annual global application of nitrogen fertilizer Source: Tillman et al, Increasing the application of compost, and leaving more organic matter on soils instead of tilling soil and leaving it exposed to wind and rain, will benefit the very chemistry of the soil over time Clark et al, The ratio of carbon to nitrogen is a factor that correlates a with soils capacity to retain nitrogen.

Greater levels of carbon in the soil allow for higher levels of nitrogen retention Vitousek, et al, As mentioned in the carbon cycle section, carbon in soil comes from decomposing organic matter. Regardless of the issues that fertilizers pose, they are important for maintaining or even increasing yields, which is necessary for the food security of the world's growing population. Figure 7 shows the correlation between fertilizers and yields Dyson, It is difficult to foresee fertilizers being omitted from agriculture from this equation entirely. However, it has been demonstrated that fertilizer use can decrease when used in conjunction with compost.

Fertilizer use can also be decreased with technological and knowledge based solutions. A study in Hawaii of sugar cane plantations compared two techniques for applying nitrogen fertilizer Matson et al, The more technological and knowledge based approach involved applying dissolved nitrogen fertilizer through irrigation systems in small amounts, and with frequent applications based on timed requirements of the growing sugar cane. The other approach involved a more conventional and simple method that involved applying larger amounts of nitrogen less frequently.

In addition, there were increased yields and it was more profitable as well. These two significant findings show how more sustainable agriculture management methods do exist and can be incorporated into conventional farming practices. As such, creating a dichotomy or mutually exclusive perspective between organic and conventional agricultural methods can be unnecessarily polarizing. This polarization between organic and conventional agriculture can affect the perception that farmers, regulators, and other stakeholders have about adopting practical, technological, and scientific changes in their activities.

The soil food web. Alvarez, R. A review of the effects of tillage systems on some soil physical properties, water content, nitrate availability and crops yield in the argentine pampas. Andrews, S. USDA soil quality indicators: Aggregate stability. Archer, D. Crop productivity and economics during the transition to alternative cropping systems. Agronomy Journal, 99 6 , Aselage, J. Badgley, C. Organic agriculture and the global food supply. Renewable Agriculture and Food Systems, 22 2 , Balzergue, C. The regulation of arbuscular mycorrhizal symbiosis by phosphate in pea involves early and systemic signalling events.

Journal of Experimental Botany, 62 3 , Bengtsson, J. The effects of organic agriculture on biodiversity and abundance: A meta-analysis. Journal of Applied Ecology, 42 2 , Bunemann, E. Impact of agricultural inputs on soil organisms a review. Australian Journal of Soil Research, 44 4 , Clapperton, M. Earthworm populations as affected by longterm tillage practices in southern alberta, canada.

Clark, M. Changes in soil chemical properties resulting from organic and low-input farming practices. Agronomy Journal, 90 5 , Dalgaard, T. A model for fossil energy use in danish agriculture used to compare organic and conventional farming. Durka, W. Effects of forest decline on uptake and leaching of deposited nitrate determined from N and O measurements. Nature, , Dyson, T. In Redclift M. New York: Routledge. Evanylo, G. Soil and water environmental effects of fertilizer-, manure-, and compost-based fertility practices in an organic vegetable cropping system.

Fleige, H. Friedrich, T. Herbicides and no-till farming: Does no-till farming require more herbicides? Outlooks on Pest Management. Research Information Ltd. Gaudinski, J.

Soil carbon cycling in a temperate forest: Radiocarbon-based estimates of residence times, sequestration rates and partitioning of fluxes. Biogeochemistry, 51 1 , Gomiero, T. Environmental impact of different agricultural management practices: Conventional vs. Critical Reviews in Plant Sciences, 30 , Gosling, P. Arbuscular mycorrhizal fungi and organic farming. Grant, R. Simulation-model of soil compaction and root-growth.

Plant and Soil, 1 , Ingam, E. USDA natural resources conservation services: Soi food web. Iozon, D. In Marghitas L. Kabir, Z. Tillage or no-tillage: Impact on mycorrhizae. Canadian Journal of Plant Science, 85 1 , Koons, D. Symphony of the soil. Kremen, C. Ecosystem services in biologically diversified versus conventional farming systems: Benefits, externalities, and trade-offs.

Ecology and Society, 17 4 , Ladurantaye, S. The Globe and Mail. Lal, R. Soils and Food Sufficiency. A review. Agronomy for Sustainable Development 29 3 , Lipiec, J. Quantification of compaction effects on soil physical properties and crop growth. Geoderma, , Makawi, A. Quantitative effects of some pesticides on certain physiological groups of microorganisms in soil.

Zentralblatt Bacteriology Natural Sciences Department of Microbiology and agriculture in technology and environmental protection, 3 , ER. Martensson, A. Impact of phosphorus fertilization on vam diaspores in 2 Swedish long-term field experiment. Matson, P. Fertilization practices and soil variations control nitrogen oxide emissions from tropical sugar cane. Journal of Geophysical Research-Atmospheres, D13 , McGonigle, T.

Mycorrhizae, crop growth, and crop phosphorus nutrition in maize-soybean rotations given various tillage treatments. Merrington, G. The potential impact of long-term copper fungicide usage on soil microbial biomass and microbial activity in an avocado orchard. Australian Journal of Soil Research, 40 5 , Moglander Rice Farming in Spain. Finally, in situ soil observation was done to validate the information provided by the Soil Map of Wallonia.

The agroecological fields have been progressively transitioning from conventional CONV to agroecological AECO management since sandy site and silty site. At the sandy site, plowing was replaced by reduced tillage in and then by direct seeding in , whereas the use of external fertilizers and pesticides was progressively reduced over time until when the farm obtained the official Belgian organic certification.

At the silty site, however, the transition happened over a shorter time scale, stopping the application of synthetic fertilizers and pesticides and starting organic fertilization in , and subsequently replacing conventional plowing by reduced tillage in Today, the agroecological management practices at the two sites share similar farming practices: 1 they are certified organic, i. The intercropping consists of mixes with the following: triticale, oats, rye, spelt, pea, and vetch.

The conventional fields were under wheat conventionally managed, i. The detailed management of conventional and agroecological fields is fully described in the supplementary material Supplementary Table 1 ; agroecological and Supplementary Table 2 ; conventional management. Soil samples were collected once in July and all on the same day, a few weeks before harvesting.

An auger of 20 cm length and 5 cm width was used to collect the 36 soil samples. Given the absence of carbonates in the soil samples, the total C measured corresponds to total organic C. Particle size distribution was determined by sedimentation using the pipette method, on three pooled soil samples for each field. Data for macro- and micro-aggregates, clay, silt, sand and silt-clay content, and aggregate stability were measured as bulk parameter for each field and not determined at the sample level.

Aggregate-size separations were conducted on the dry bulk soil by a wet-sieving method adapted from previously published protocols Elliott, ; Six et al. The separation was carried out on three pooled soil samples for each field. Soil was then sieved by moving the sieve out of the deionized water and immersing it again 50 times for 2 min. PCR amplification was performed in three technical triplicates and products were pooled prior to sequencing.

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Figure 1: Tilling soils. Herbicides and no-till farming: Does no-till farming require more herbicides? General Information Can you send me more information about this program? Erika Degani Samuel Leigh Proudly powered by WordPress. Over thousands of years, humans have learned how to domesticate the plants which provide both the necessities for our diet and the products for our lifestyles. A Nebraska study of an agriculture dependent community concluded that if more farms were following sustainable practices total family income would more than double, compared to a scenario where all the farms remained in conventional practices.

When required, adjustments for multiple testing were performed using the Benjamini-Hochberg BH method Benjamini and Hochberg, with the p. Factors site 2 , management type 2 and paired-fields three paired-fields nested within site were considered as fixed. The collinearity among the selected explanatory variables was tested by calculating the variable inflation factor VIF using the vif. The management-related response of individual taxa was evaluated using univariate permutational analysis of variance adonis function based on Euclidean distances calculated from OTU abundances as implemented in vegan package with 99, permutations.

In order to visualize positive or negative responses of the individual taxa to one of the management types, the relative abundances were z-transformed. The same analysis was performed on the individual soil physico-chemical parameters. Overall, the pedological context was the main factor discriminating our samples based on the physical and chemical soil properties with the silty site characterized as more humid, nutrient rich, and less acidic than the sandy site Figures 1A,B. However, in contrast to our predictions, the two management types have significantly different soil textures at the silty site, with the AECO fields being richer in clay and silt than the CONV fields.

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Since soil texture is a known driver of microbial community composition, this difference potentially cofounds any management effect observed at the silty site see discussion. The management-related response of almost all the descriptors showed discrepancies across the two sites. For some parameters, even opposing shifts were observed, e. Furthermore, effects of management on soil properties were not only site dependent, but also paired-field dependent Supplementary Table 3. The values of the soil variables measured on the 36 samples are provided in Supplementary Table 4. Figure 1.

A Principal coordinate analysis PCO based on Euclidean distances calculated from z -transformed values of physical and chemical soil parameters. The variance explained by the axes goodness of fit is provided next to the axis headers. Light colors represent the sandy site; dark colors represent the silty site. B Standardized relative change in physical and chemical soil properties calculated from z -transformed values between conventional red and agroecological green management across all textural sites. C Standardized relative change in physical and chemical soil properties calculated from z -transformed values between conventional red and agroecological green farming systems separately for each textural site.

P, K, Mg, and Ca, exchangeable cations; agg. Table 1. Thus, whereas bacteria appeared to be mainly driven by the sites with a smaller response to the management, fungi appeared to be equally driven by the two factors. In agreement with the shifts in physicochemical properties, the management effects on the microbial communities were site-dependent Table 2A , management x site , showing somewhat stronger compositional shifts between CONV and AECO at the silty site when compared to the sandy site Figure 2A.

Furthermore, and again equivalent to the physicochemical properties, there was also considerable variation among the paired-fields within each site and management effects were not only site but also paired-field dependent Table 2 , management x paired-field. Figure 2. Statistical tests for assessing the heterogeneity of variance for the interaction effect between management and site as assessed by PERMDISP are provided in the ordinations. The p -values were corrected for multiple comparisons using the Benjamini-Hochberg procedure. Table 2. Fungi showed a more consistent response, being more rich and less even under AECO at both sites.

The differences in these parameters were not only depending on the pedological context, but again also on the paired-fields within each pedological site Supplementary Table 5. Across both sites, abundant i. This suggests that 1 management type has shaped the response of individual taxonomic groups and 2 management-related responses were not consistent across the different clades of the major groups. Figure 3. Standardized relative changes in abundance of higher-order taxonomic groups between conventional red and agroecological green management across all textural sites A and separately for each individual textural site B.

Proteobacteria Alpha-, Gamma-, Delta-proteobacteria , Ascomycota and Basidiomycota were additionally split into the major classes. Data were z -transformed, representing values greater or smaller than the average across all samples. The standardized relative mean and standard deviations are provided for each taxon. Taxa labeled in blue have revealed a contrasting response to agricultural management across the textural sites as detailed in the main text.

These taxon-level responses often differed between the sites Figure 3B. Some groups such as Patescibacteria Figure 3B , 1 , Gamma-Proteobacteria 2 , Verrucomicrobia 3 , Latescibacteria 4 , Pezizomycetes 5 , Eurotiomycetes 6 , Glomeromycota 7 , and Chitridiomycota 8 showed an opposite management-related response between the sites. Other groups such as Bacteroidetes 9 , Actinobacteria 10 , Acidobacteria 11 , and Dothideomycetes 12 showed a response in the same direction but with different intensity.

Whereas, Bacteroidetes 9 , Acidobacteria 11 , and Dothideomycetes 12 showed a more pronounced response at the silty site, only Actinobacteria 10 showed a more pronounced response at the sandy site. Again, these taxon-level responses did not only differ between the sites but also between the different paired-fields within each site Supplementary Figure 2. Distance-based linear modeling using a step-wise selection procedure was used to find a set of physicochemical properties that best predict the observed changes in microbial community structure Table 1C , sequential test.

In a second step, distance-based redundancy analysis db-RDA was used to visualize the influence of the physicochemical predictors on the bacterial and fungal community structure Figure 4. The fact that differences in bacterial and fungal community structures as observed in the unconstrained PCO Figure 2A were largely recovered in the constrained db-RDA Figure 4 provides another indication of the substantial effect of the measured physicochemical properties on the microbial community structure. We reasonably assume that none of these variables are redundant and that the regression coefficient of the two models is not excessively inflated due to multicollinearity in the model James et al.

Figure 4. The variance explained by the axes is given in parentheses and represent the variance explained by all the physical and chemical parameters provided by the arrows. The parameters in bold represent the best descriptors as assessed by the DistLM provided in Table 1C. This study demonstrates that the pedological context modulates, to some extent, the response of soil physicochemical properties to agricultural management, which will have, in turn, direct implications for the diversity of soil bacterial and fungal communities. In our study, the transition from CONV to AECO management has generally been beneficial for soil quality, increasing soil moisture, stability of soil aggregates, and macro-aggregates.

Nutrient availability and pH also increased under AECO management, which might result in better nutrient root uptake, increased microbial activity, and enhanced organic matter degradation. Increasing soil quality through conservational soil management can potentially mitigate some major environmental issues such as soil erosion and soil carbon depletion, and thus improve the functioning.

For example, no-till systems have shown to moderate soil erosion Montgomery, and decrease turnover of macro-aggregates Six et al. In addition, a recent study comparing different ecosystem services delivered by the two same systems AECO and CONV showed that overall soil aggregate stability and soil respiration rates were more supported by AECO management, whereas higher net crop yields and higher fodder quality were showed under CONV management Boeraeve et al.

Such results highlight the benefits provided by agroecological management to support various ecosystem services in contrast to focusing only on economic performance. This site-dependent effect on how CONV and AECO shape the soil conditions will have substantial consequences on the structure of microbial communities and associated functions and processes, which in turn can again change the physical, chemical, and biological conditions of the soil. Microorganisms living in soil are strongly influenced by their surrounding and changes in soil properties have an impact on their diversity.

Our results showed that soil pH was the best predictor of both bacterial and fungal diversity Table 1. Although previous studies support this evidence for bacteria Lauber et al. Besides pH, soil moisture also appeared to be a strong factor shaping both bacterial and fungal community diversity, which is in agreement with previous studies Fierer et al. In analogy, management-induced changes in major groups of bacteria and fungi were also site-dependent Figure 3B. Among them, some are known to be potentially beneficial for plant growth and health.

For example, arbuscular mycorrhizal fungi AMF, Glomeromycota , a plant-symbiotic fungi of ecological importance because of its role in plant nutrition and drought tolerance van der Heijden et al. However, our study showed that AECO promoted Glomeromycota only at the silty but not at the sandy site. Recent work has shown that Eurotiomycetes can potentially degrade moderately labile and recalcitrant forms of carbon better than other groups of fungi by producing higher levels of Xylosidases and Glucosaminidases Trivedi et al.

Among bacteria, Acidobacteria, a group of largely oligotrophic organisms Fierer et al. Although fungi are generally considered as the major microbial decomposers of plant materials, previous studies showed a clear enrichment of acid-tolerant Acidobacteria under lignin-amended conditions which suggests a putative role of this bacterial group in degradation of complex organic material DeAngelis et al. Two less well-known groups of bacteria, the Patescibacteria Figure 3 , 1 and Latescibacteria 4 also showed strong soil-type dependant responses. These two groups increased under AECO at the silty site, but tended to decrease at the sandy site.

These two groups belong to yet-uncultured microbial candidate phyla and therefore their metabolic capabilities and ecological roles are not yet well-understood. Recent studies have highlighted the prevalent saprophytic lifestyle in the Latescibacteria lineage member of the Fibrobacteres-Chlorobi-Bacteroidetes FCB superphylum suggesting their important role in soil organic detritus degradation Farag et al. Patescibacteria belong to the candidate phyla radiation CPR Brown et al. Recent work further emphasized the potential role of CPR members in carbon degradation Danczak et al.

Although the contribution of this group of bacteria to various ecosystems services is not yet understood, we hypothesize based on the aforementioned metabolic capabilities and ecological roles that these organisms might contribute to soil functioning. The substantial changes in community structure between CONV and AECO Figures 2A,B is in agreement with numerous previous studies showing effects of agricultural management on soil microbial community structures by means of changing the soil conditions Ceja-Navarro et al.

In our study, AECO management showed higher microbial diversity i. Previous studies reported an increase in microbial diversity under organic management Chaudhry et al. When assessing the effect of agricultural management on microbial diversity, most studies have focused in the past on the effect of tillage regimes Ceja-Navarro et al. Although increasing the actual diversity seems a pillar argument to support the transition from conventional to organic or conservation agriculture, we still have a poor understanding of how actual changes in diversity per se translate into changes of the ecological processes mediated by these communities.

Thus, an increase in diversity alone is clearly not enough to advocate transition toward agroecological systems. The composition of the community is thereby a central component shaping the functional capacity of the soil. With the absence of synthetic pesticides to manage soil pathogens and reduced inputs of mineral fertilizer to secure plant nutrition, such management systems clearly rely on efficient below-ground biotic interactions. Previous studies have suggested that organic or other forms of conservation management have the ability to reduce pressure from pest and pathogens and promote beneficial species important for plant nutrition and immunity van Bniggen and Termorskuizen, ; Birkhofer et al.

In contrast to conventional farming systems where pest and disease regulation regimes specifically target the pathogen itself, organic or other forms of conservation management largely rely on indirect mechanisms for plant protection and nutrition. For example, diversifying cropping systems will promote nitrogen-fixing symbiosis in the case of legumes association Peoples et al.

Numerous other mechanisms under organic management are well-described in Bruggen et al. In order to draw conclusions about potential pathogenic or beneficial taxa, data need to be interrogated at lower taxonomic levels and we provide data on management effects for all detected OTUs in Supplementary Table 6. For bacteria, however, none of the commonly known plant pathogenic taxa were found to differ between the management systems.

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Such conclusions about potential pathogenic and beneficial taxa need to be taken with caution, however, since accurate identification at lower taxonomic levels is limited by both the short-read length of the technology and the limited resolution of the genetic markers used, making it difficult to make highly accurate species level predictions.

Furthermore, an actual pathogenic or beneficial activity of a species cannot be solely deduced from its taxonomic status. Overall, it has to be understood that the multitude of factors that are simultaneously changed under agroecological management approaches induce a series of complex and interdependent effects on the soil microbial network that cannot be quantified by solely looking at the presence or absence of individual beneficial or pathogenic species.

The hypothesized positive relationship between biodiversity and ecosystem functioning have long been a central but still unresolved question in biodiversity research Coleman and Whitman, ; Byrnes et al. However, evaluating this relationship under real-life scenarios where farmers make specific management decisions that might change over time, make it difficult to predict the output of this relationship. Therefore, even if AECO can promote the presence of beneficial microorganisms such as arbuscular mycorrhizal fungi and mitigate pressure from pathogens, we ultimately cannot predict, if it will improve food production or any other ecosystem service.

In this light, there is still little evidence that farming systems that promote higher microbial diversity actually increase the performance of the agroecosystem by securing more ecosystem functions and making it less vulnerable to extreme events. Most studies use factorial approaches to break down complex systems like agroecosystems into isolated components in order to identify cause-effect relationships Drinkwater, Such approaches enable us to answer important agronomic questions by quantifying the relative importance of individual management factors such as tillage e.

These factorial approaches to study cause-effect relationships have, however, also some practical limitations Drinkwater, and a more holistic system-level assessment representing a realistic agronomic, social, and economic context can provide additional insights in order to ultimately link knowhow gained from classical research designs with realistic on-farm observations. The more holistic, farm-level approach carried out in this study aims at understanding how the combination of several individual management factors affects the soils in the context of the farmer's dynamic decisions to modify the agronomic outcomes.

We fully acknowledge that our approach sacrifices resolution, since the relative importance of each factor cannot be disentangled; but the advantages gained by this approach are measurable outcomes here, how the structure of microbial communities responds to agricultural management, or in Boeraeve et al. Also, it is worth mentioning that replicates in a holistic farm-level approach do not have the same meaning as replicates used in a classic experimental approach.

For example, in our study we know that fields from the same agricultural management are managed by different farmers, each of them making choices based on non-scientific motivations and concerns that are based on social and economic reasons, which may also change over time. Therefore, the actual agricultural management might differ slightly from one field to another even though the philosophy remains the same, and will be highly dependent on a farmer's habits and preferences.

At the sandy site for instance, the transition toward AECO management started 20 years ago, was progressive and is still going, with farmer practices changing slowly over time. Plowing was first stopped and then the amount on agrochemical was progressively decreased by to the point where no agrochemicals were used. At the silty site, the transition began more recently and it is still evolving.

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As a consequence, AECO-managed fields at the sandy and silty sites were not at the same stage of transition and thus the physical and chemical conditions occurring in the soil at sampling time did not reflect the final conditions as found in stabilized systems. Interestingly though, the effect at the silty site was more pronounced despite its more recent transition, indicating that the soil type might be an important determinant of how rapidly these transition effects establish. Importantly, farming systems are highly complex systems where numerous components interact e.

Therefore, understanding such complex systems to design more performant and efficient agriculture require the use of not only one approach holistic vs.

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  3. Applying plant ecological knowledge to increase agricultural sustainability.

Overall, our study provided more insights into how the transition to agroecological farming systems initiated by Belgian farmers several years ago can potentially enhance the performance i. Even if we had observed an improvement of several soil and microbial biodiversity parameters under AECO management along with a clear shift in the community structure, the question whether Belgian farmers should transition to AECO farming system cannot be solely addressed with soil data. Even if our study provides a small but nevertheless solid brick to address this crucial question, other aspects of the system must be evaluated as well.

For example, the financial aspect e. The actual knowledge of the farmers themselves must also be considered before deciding on transitioning Boeraeve et al. Similarly, the environmental context may as well play a critical role. As we have shown in our study, the management-related response of the soil microbial community was strongly modulated by the pedological context. Therefore, the benefits that the farmers may gain from the transition could be, in the same way, modulated by the pedological context.

The question of the transition to agroecological farming systems remains highly complex and requires a more holistic and complete understanding of all the trade-offs of such a transition. Large efforts are currently made to develop management strategies that enhance soil biodiversity and manipulate the community composition of microbes to target specific beneficial or pathogenic species. By unraveling the response of bacterial and fungal diversity to agroecological management under different pedological context on real-life farms, our study, despite covering a rather narrow gradient of pedological variation and considering only one type of climate, has contributed to provide a first stepping stone to address this knowledge gap.

Agroecological management is dynamic and will be continuing evolving. Studying such system will allow to better understand the multiple interactions between management and outcome here microbial diversity in order to design innovative and ecologically, economically, and socially beneficial agroecological practices. These findings suggest that such species response patterns must be highly variable across different soil types, calling for large-scale surveys across much broader gradients of these factors in order to get a more complete understanding of the tripartite interaction between soil, management, and microbiome.

MD and J-TC conceived the original idea.