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Population growth and climate change challenge our food and farming systems and provide arguments for an increased intensification of agriculture. A promising option is eco-functional intensification through organic farming, an approach based on using and enhancing internal natural resources and processes to secure and improve agricultural productivity, while minimizing negative environmental impacts. In this concept an active soil microbiota plays an important role for various soil based ecosystem services such as nutrient cycling, erosion control and pest and disease regulation. Several studies have reported a positive effect of organic farming on soil health and quality including microbial community traits. However, so far no systematic quantification of whether organic farming systems comprise larger and more active soil microbial communities compared to conventional farming systems was performed on a global scale. Therefore, we conducted a meta-analysis on current literature to quantify possible differences in key indicators for soil microbial abundance and activity in organic and conventional cropping systems. All together we integrated data from 56 mainly peer-reviewed papers into our analysis, including 149 pairwise comparisons originating from different climatic zones and experimental duration ranging from 3 to more than 100 years. Overall, we found that organic systems had 32% to 84% greater microbial biomass carbon, microbial biomass nitrogen, total phospholipid fatty-acids, and dehydrogenase, urease and protease activities than conventional systems. Exclusively the metabolic quotient as an indicator for stresses on microbial communities remained unaffected by the farming systems. Categorical subgroup analysis revealed that crop rotation, the inclusion of legumes in the crop rotation and organic inputs are important farming practices affecting soil microbial community size and activity. Furthermore, we show that differences in microbial size and activity between organic and conventional farming systems vary as a function of land use (arable, orchards, and grassland), plant life cycle (annual and perennial) and climatic zone. In summary, this study shows that overall organic farming enhances total microbial abundance and activity in agricultural soils on a global scale.

Abstract Intensive agriculture has increased global food production, but also impaired ecosystem services and soil biodiversity. Organic fertilization, essential to organic and integrated farming, can provide numerous benefits for soil quality but also compromise the environment by polluting soils and producing greenhouse gases through animal husbandry. The need for reduced stocking density is inevitably accompanied by lower FYM inputs, but little research is available on the impact of these effects on the soil microbiome. We collected soil samples from winter wheat plots of a 42-year-old long-term trial comparing different farming systems receiving farmyard manure at two intensities and measured soil quality parameters and microbial community diversity through DNA metabarcoding. High-input fertilization, corresponding to 1.4 livestock units (LU) improved the soil’s nutritional status and increased soil microbial biomass and respiration when compared to low-input at 0.7 LU. Bacterial and fungal α-diversity was largely unaffected by fertilization intensity, whereas their community structure changed consistently, accompanied by an increase in the bacterial copiotroph-to-oligotroph ratio in high-input systems and by more copiotrophic indicator OTUs associated with high than low-input. This study shows that reduced nutrient availability under low-input selects oligotrophic microbes efficiently obtaining nutrients from various carbon sources; a potentially beneficial trait considering future agroecosystems. Fertilization intensity shapes soil fungal and bacterial communities in organic and conventional farming systems of the 42-year-old DOK long-term field trial.

Highly adapted herbivores can phenocopy two-component systems by stabilizing, sequestering and reactivating plant toxins. However, whether these traits protect herbivores against their enemies is poorly understood. We demonstrate that the western corn rootworm Diabrotica virgifera virgifera, the most damaging maize pest on the planet, specifically accumulates the root-derived benzoxazinoid glucosides HDMBOA-Glc and MBOA-Glc. MBOA-Glc is produced by D. virgifera through stabilization of the benzoxazinoid breakdown product MBOA by N-glycosylation. The larvae can hydrolyze HDMBOA-Glc, but not MBOA-Glc, to produce toxic MBOA upon predator attack. Accumulation of benzoxazinoids renders D. virgifera highly resistant to nematodes which inject and feed on entomopathogenic symbiotic bacteria. While HDMBOA-Glc and MBOA reduce the growth and infectivity of both the nematodes and the bacteria, MBOA-Glc repels infective juvenile nematodes. Our results illustrate how herbivores combine stabilized and reactivated plant toxins to defend themselves against a deadly symbiosis between the third and the fourth trophic level enemies. The western corn rootworm is the most damaging pest of maize plants. Out of sight, the larvae of this beetle feed on maize roots, and cause billions of dollars worth of losses each year. One of the reasons why this pest remains such a problem is it can adapt and resist many crop protection strategies. Biological control refers to combating a pest using its own natural enemies – for example, its predators. Biological control of the western corn rootworm has been attempted using nematode worms. Normally, the nematodes locate and enter an insect larvae, release bacteria that kill it, and then feed and multiply within the dead larvae. Yet, the western corn rootworm seems at least partly able to resist these nematodes, and the success of biological control in the field has been variable. Several insect herbivores are known to accumulate, or sequester, plant toxins in their own body for self-defense. Previously, in 2012, researchers reported that the western corn rootworm is resistant and attracted to the major toxins in maize roots, the benzoxazinoids. The blood-like fluid of the western corn rootworm also repels many predators. Could the western corn rootworm be sequestering maize benzoxazinoids to resist the biological control of nematodes and their bacterial partners? Plants store benzoxazinoids in a non-toxic form. If herbivores damage the plant, these molecules quickly break down into compounds that are toxic to most insects. Now Robert et al. – who include two of the researchers involved in the 2012 study – show that the western corn rootworm uses a similar defense system to protect itself against biological control nematodes and their bacterial partners. First, the larvae convert a benzoxazinoid breakdown product by adding a glucose molecule. They then release large amounts of this modified molecule to repel young nematodes. Second, via an unknown mechanism, the larvae stabilize a second plant-derived benzoxazinoid, sequester its non-toxic form in their bodies, and activate it upon nematode attack. The resulting toxins can kill both nematodes and their bacterial partners. By combining different chemical strategies to stabilize and activate plant toxins, the western corn rootworm is able to resist the nematodes used for biological control. These findings can help to explain why biological control has had limited success against the western corn rootworm. In the long run, they may lead to more effective biological control programs, for instance by stopping the western corn rootworm from sequestering benzoxazinoids or by using natural enemies that are resistant to the insect’s toxins.

Projected climate change and rainfall variability will affect soil microbial communities, biogeochemical cycling and agriculture. Nitrogen (N) is the most limiting nutrient in agroecosystems and its cycling and availability is highly dependent on microbial driven processes. In agroecosystems, hydrolysis of organic nitrogen (N) is an important step in controlling soil N availability. We analyzed the effect of management (ecological intensive vs . conventional intensive) on N-cycling processes and involved microbial communities under climate change-induced rain regimes. Terrestrial model ecosystems originating from agroecosystems across Europe were subjected to four different rain regimes for 263 days. Using structural equation modelling we identified direct impacts of rain regimes on N-cycling processes, whereas N-related microbial communities were more resistant. In addition to rain regimes, management indirectly affected N-cycling processes via modifications of N-related microbial community composition. Ecological intensive management promoted a beneficial N-related microbial community composition involved in N-cycling processes under climate change-induced rain regimes. Exploratory analyses identified phosphorus-associated litter properties as possible drivers for the observed management effects on N-related microbial community composition. This work provides novel insights into mechanisms controlling agro-ecosystem functioning under climate change.

1. Organic farming (OF) enhances top soil organic carbon (SOC) stocks in croplands compared with conventional farming (CF), which can contribute to sequester C. As farming system differences in the amount of C inputs to soil (e.g. fertilization and crop residues) are not enough to explain such increase, shifts in crop residue traits important for soil inputs to soil (e.g. fertilization and crop residues) are not enough to explain such increase, shifts in crop residue losses such as litter decomposition may also play a role. 2. To assess whether crop residue (leaf and root) traits determined SOC sequestration responses to OF, we coupled a global meta-analysis with field measurements across a European-wide network of sites. In the meta-analysis, we related crop species averages of leaf N, leaf-dry matter content, fine-root C and N, with SOC stocks and sequestration responses in OF vs. CF. Across six European sites, we measured the management-induced changes in SOC stocks and leaf litter traits after long-term ecological intensive (e.g. OF) vs. CF comparisons. 3. Our global meta-analysis showed that the positive OF-effects on soil respiration, SOC stocks, and SOC sequestration rates were significant even in organic farms with low manure application rates. Although fertilization intensity was the main driver of OF-effects on SOC, leaf and root N concentrations also played a significant role. Across the six European sites, changes towards higher leaf litter N in CF also promoted lower SOC stocks. 4. Our results highlight that crop species displaying traits indicative of resourceacquisitive strategies (e.g. high leaf and root N) increase the difference in SOC between OF and CF. Indeed, changes towards higher crop residue decomposability was related with decreased SOC stocks under CF across European sites. 5. Synthesis and applications. Our study emphasizes that, with management, change in crop residue traits contribute to the positive effects of organic farming (OF) on soil carbon sequestration. These results provide a clear message to land managers: the choice of crop species, and more importantly their functional traits (e.g. leave and root nitrogen), should be considered in addition to management practices and climate, when evaluating the potential of OF for climate change mitigation.

Most nitrogen (N) in organic fertilizers must be mineralized to become available to plants, a process in which microorganisms play crucial roles. Droughts may impact microorganisms associated with the N cycle, negatively affecting N mineralization and plant N supply. The effects of drought on N-related processes may further be shaped by the farming system. We buried 15N-enriched plant material and reduced precipitation in conventionally and organically (biodynamically) managed wheat fields. On two sampling dates, we evaluated the soil water content, plant parameters and the plants’ 15N isotope signature. We intended to study the microbial communities associated with the N cycle to link potential treatment effects on plant N provisioning with characteristics of the underlying microbial community. However, floods impaired the experiment after the first sampling date, and the molecular work on the microbial communities was not performed. Focusing on the pre-flooding sampling date, our data suggested that processes associated with N transformation are sensitive to drought, but the role of the farming system needs further investigation. Since the underlying research question, the set-up and the lessons learned from this study may guide future experiments, we presented improvements to the set-up and provided ideas for additional analyses, hoping to promote research on this topic.

The majority of soil organic nitrogen (N) is bound in protein-like compounds and therefore its proteolysis in peptides and amino acids is considered the initial and rate limiting step of N mineralization. Proteolysis of N bound in organic fertilizer and subsequent provisioning for crops is a central element in agro-ecological intensification. Long-term farming system effects on N provisioning from organic fertilizer to crops and its underlying functional microbial communities were analyzed in experiments conducted in soils from the “DOK” system comparison trial (bio-Dynamic, bio-Organic, and “Konventionell”) DOK farming system comparison subjected to optimal and future projected drought scenarios. A plant nutrition experiment using 15N labelled lupine as a fertilizer (green manure) identified 30% higher amounts of N derived from fertilizer in ryegrass grown on organically compared to conventionally managed soil, but only when subjected to dry conditions. A second experiment, also amended with lupine green manure, assessed the effect of farming system and drought stress on N cycling microbes with a focus on alkaline (apr) and neutral (npr) metallopeptidase encoding microbial communities. apr encoding microbial communities were more strongly affected by farming system and water treatment than npr encoding communities. Differences in structure and diversity of apr encoding microbial communities showed concomitant patterns with distinct N provisioning from organic fertilizer in the plant nutrition experiment. It is suggested that conventionally managed systems are less capable in maintaining diversity and initial structure of apr encoding microbial communities when subjected to drought scenarios. Overall, we demonstrated organically managed soils to provide a more stable N provisioning potential from organic fertilizer under future drought scenarios, likely facilitated by a distinct and more adaptive proteolytic microbial community. This work contributes to an in-depth comprehension of yet poorly studied fundamental soil processes and helps developing strategies to maintain a versatile and functioning microbial community in a rapidly changing environment.

Plant elicitor peptides (Peps) are potent inducers of pattern-triggered immunity and amplify the immune response against diverse pathogens. Peps have been discovered and studied extensively in Arabidopsis and only recently orthologues in maize were also identified and characterized in more detail. Here, the presence of PROPEPs, the Pep precursors, and PEPRs, the Pep receptors, was investigated within the plant kingdom. PROPEPs and PEPRs were identified in most sequenced species of the angiosperms. The conservation and compatibility of the Pep-PEPR-system was analysed by using plants of two distantly related dicot families, Brassicaceae and Solanaceae, and a representative family of monocot plants, the Poaceae. All three plant families contain important crop plants, including maize, rice, tomato, potato, and canola. Peps were not recognized by species outside of their plant family of origin, apparently because of a divergence of the Pep sequences. Three family-specific Pep motifs were defined and the integration of such a motif into the Pep sequence of an unrelated Pep enabled its perception. Transient transformation of Nicotiana benthamiana with the coding sequences of the AtPEPR1 and ZmPEPR1a led to the recognition of Pep peptides of Brassicaceae or Poaceae origin, respectively, and to the proper activation of downstream signalling. It was concluded that signalling machinery downstream of the PEPRs is highly conserved whereas the leucine-rich repeat domains of the PEPRs co-evolved with the Peps, leading to distinct motifs and, with it, interfamily incompatibility.

The adverse effects of intensified cropland practices on soil quality and biodiversity become especially evident in India, where nearly 60% of land is dedicated to cultivation and almost 30% of soil is already degraded. Intensive agricultural practice significantly contributes to soil degradation, highlighting the crucial need for effective countermeasures to support sustainable development goals. A long-term experiment, established in the semi-arid Nimar Valley (India) in 2007, monitors the effect of organic and conventional management on the plant-soil system in a Vertisol. The focus of our study was to assess how organic and conventional farming systems affect biological and chemical soil quality indicators. Additionally, we followed the community structure of the soil microbiome throughout the vegetation phase under soya or cotton cultivation in the year 2019. We found that organic farming enhanced soil organic carbon and nitrogen content, increased microbial abundance and activity, and fostered distinct microbial communities associated with traits in nutrient mineralization. In contrast, conventional farming enhanced the abundance of bacteria involved in ammonium oxidation suggesting high nitrification and subsequent nitrogen losses with regular mineral fertilization. Our findings underscore the value of adopting organic farming approaches in semi-arid subtropical regions to rectify soil quality and minimize nitrogen losses.

In Arabidopsis thaliana, the endogenous danger peptides, AtPeps, have been associated with plant defences reminiscent of those induced in pattern-triggered immunity. AtPeps are perceived by two homologous receptor kinases, PEPR1 and PEPR2, and are encoded in the C termini of the PROPEP precursors. Here, we report that, contrary to the seemingly redundant AtPeps, the PROPEPs fall at least into two distinct groups. As revealed by promoter–β-glucuronidase studies, expression patterns of PROPEP1–3, -5, and -8 partially overlapped and correlated with those of the PEPR1 and -2 receptors, whereas those of PROPEP4 and -7 did not share any similarities with the former. Moreover, bi-clustering analysis indicated an association of PROPEP1, -2, and -3 with plant defence, whereas PROPEP5 expression was related to patterns of plant reproduction. In addition, at the protein level, PROPEPs appeared to be distinct. PROPEP3::YFP (fused to yellow fluorescent protein) was present in the cytosol, but, in contrast to previous predictions, PROPEP1::YFP and PROPEP6::YFP localized to the tonoplast. Together with the expression patterns, this could point to potentially non-redundant roles among the members of the PROPEP family. By contrast, their derived AtPeps, including the newly reported AtPep8, when applied exogenously, provoked activation of defence-related responses in a similar manner, suggesting a high level of functional redundancy between the AtPeps. Taken together, our findings reveal an apparent antagonism between AtPep redundancy and PROPEP variability, and indicate new roles for PROPEPs besides plant immunity.