Frédérique Reverchon

Nitrogen (N) and phosphorus (P) are two of the most essential nutrients for plants, but overapplication of N and P to cropping systems can lead to eutrophication and groundwater contamination through leaching. Biochar has been used to improve N and P use efficiency, reducing leaching, and the effects of biochar on N and P leaching and availability have been widely studied. Biochar is often applied with fertilisers; however, combined effects of biochar with fertilisers on N and P leaching and availability have not been adequately addressed. This meta‐analysis synthesised 1798 data points from 48 peer‐reviewed articles to evaluate the effects of applying biochar with fertilisers on N and P leaching and availability. Our results showed that applying biochar with fertilisers decreased NO ₃ ⁻ , NH ₄ ⁺ and P (as PO ₄ ³⁻ ) leaching by 13.2% ± 0.1%, 1.5% ± 0.1% and 16.5% ± 0.7%, respectively (Bootstrap 95% CI). Method of biochar application emerged as the primary factor affecting N and P leaching. For NO ₃ ⁻ leaching, time after biochar application was the next most important predictor, whereas NH ₄ ⁺ leaching was predicted by the rate of biochar application and soil organic C concentration. P leaching was moderated by the feedstock type and pyrolysis temperature used to make biochars. Applying biochar with fertilisers did not affect NH ₄ ⁺ and NO ₃ ⁻ availability but increased P availability by 21.9% ± 0.5%. This study provides strong empirical evidence that co‐applying biochar with fertilisers is an effective management practice that can reduce nutrient leaching and minimise environmental impacts of cropping systems.

Rhizosphere microbial communities contribute to the growth and health of their host but may be altered by the incidence of soil-borne pathogens. In avocado, the oomycete Phytophthora cinnamomi , causal agent of Phytophthora root rot (PRR), has been shown to alter rhizosphere bacterial communities, although its effect on fungal communities has seldom been explored. Our objective was thus to determine whether P. cinnamomi induced shifts in diversity, composition and co-occurrence networks of fungal communities in the rhizosphere of avocado trees, and to identify potential antagonists of P. cinnamomi that could be further considered for disease management. Fungal communities associated with the rhizosphere of asymptomatic and PRR-symptomatic avocado trees were studied through ITS metabarcoding. Although α-diversity metrics were not significantly different between asymptomatic and PRR-symptomatic trees, differences in β-diversity of rhizosphere fungal communities were detected. Moreover, PRR led to the enrichment of saprotrophic taxa and opportunistic pathogens such as Fusarium , Cladosporium or Plectosphaerella in the avocado rhizosphere, which were possibly attracted by the release of resources from necrosed roots. Co-occurrence network analysis revealed that fungal networks in the rhizosphere of PRR-symptomatic trees were more complex and connected than those from asymptomatic trees, suggesting a response of fungal communities to the disturbance caused by the pathogen. Some connector taxa from the PRR-symptomatic networks ( Gibellulopsis , Cladorrhinum or Mycenella ) were also identified as members of the P. cinnamomi pathobiome. Their negative correlations with the pathogen indicate they may act as potential antagonists, which calls for further isolation efforts to confirm their biocontrol activity of PRR.

Sustaining crop yield is a growing challenge due to soil fertility loss and climate change. As a result, fertiliser application is increasing to sustain yield and counteract low fertiliser use efficiency. Developing nutrient-efficient fertilisers, for example by combining biochar with fertilisers, is thus crucially needed. In this context, the development of biochar-mineral complex (BMC) fertilisers into liquefied products suitable for broadacre application is highly innovative. This study aimed to explore the agronomic benefits and economic viability of four novel liquefied BMCs designed for application within a pasture cropping system. The different forms of developed BMCs included two non-enriched BMCs (BMC1 and BMC2) that were micronised using different techniques, a phosphorus (P)-enriched BMC (BMC3), and a nitrogen (N)-enriched BMC (BMC4), all applied both with- and without co-fertilisation. Soil biochemistry, plant NP uptake, NP balances, plant yield and cost–benefit were examined. Pasture yield was significantly higher using BMC1 and BMC3 with co-fertilisation than without, most likely due to improved P availability, as evidenced by positive P balances. Yield was significantly enhanced under BMC4 at 42.20 t ha ⁻¹ , compared with BMC1 at 21.90 t ha ⁻¹ , BMC2 at 19.41 t ha ⁻¹ , BMC3 at 25.81 t ha ⁻¹ , the fertilised control at 18.75 t ha ⁻¹ and non-fertilised control at 11.53 t ha ⁻¹ . Only BMC4 showed positive NP balances, suggesting that pasture did not absorb N and P from the existing soil reserve. Soil microbial composition and abundance were not affected by the applied BMC treatments in short term. The benefit–cost ratio ranged from 1.94 to 2.54, indicating economic viability of the BMC products and suggesting a great potential of biochar-based fertilisers for wide adoption to other crops. Graphic abstract

BACKGROUND: Endophytic fungi are naturally inhabiting plant organs without causing disease symptoms. They can also contribute to their host’s pest and disease resistance by displaying entomopathogenic and/or antifungal traits. In this study, we evaluated the ability of 11 strains of avocado fungal endophytes to antagonize three important avocado plant pathogens: Colletotrichum gloeosporioides, Fusarium solani, and Phytophthora cinnamomi , and two insect pests: Sitophilus zeamais and Xyleborus bispinatus . RESULTS: The results show that Trichoderma spp. strains were the most effective against the evaluated plant pathogens in terms of growth inhibition, in direct contact assays or through metabolite production. Other fungi, such as Purpureocillium sp. and Pochonia sp., only exhibited pathogen inhibition through diffusible metabolites but displayed strong insecticidal capacity against the evaluated pests, hence being identified as promising multi-target biocontrol agents in the integrative analysis. CONCLUSION: Our findings evidence the potential of avocado fungal endophytes and their metabolites as multi-target biocontrol agents of crop pests and pathogens.

Floral nectar-living microbes contribute to flower protection and pollinator health and are primarily determined by nectar chemical composition. Microbial communities in non-hexose-rich nectars and their ability to inhibit pathogens and modulate plant development have been poorly explored. We used metabarcoding to examine the richness and relative abundance of bacteria and fungi from avocado, a globally important crop with a unique nectar chemical composition, whose production is severely affected by diseases and low pollination rates. We also explored the antagonistic activity of the nectar microbial culturable fraction and its volatile organic compounds (VOCs) against avocado pathogens Phytophthora cinnamomi and Colletotrichum gloeosporioides, and against the most devastating honeybee pathogens Ascosphaera apis and Paenibacillus larvae. Furthermore, we experimentally analyzed the effects of microbial isolates and their VOCs on plant growth and the activation of jasmonic acid (JA) defense responses in Arabidopsis thaliana. Pseudomonas, Acinetobacter, Protomyces, and Vishniacozyma were the dominant microbial genera inhabiting avocado nectar. From 43 evaluated isolates, 17 bacteria and three yeasts inhibited the plant and honeybee pathogens, promoted the growth of A. thaliana seedlings, and induced JA signaling. Microbial VOCs emitted by all tested isolates promoted lateral root formation and increased plant biomass. Collectively, our findings highlight the selectivity of avocado nectar over its microbiota, which could directly impact plant fitness and contribute to the health of its pollinators.

Understanding how plant pathogens modulate the rhizosphere microbiota is essential to integrated disease management. Here, the compositional and functional shifts in the avocado rhizosphere bacteriome induced by Phytophthora cinnamomi were assessed to identify bacterial taxa enriched in the symptomatic condition and elucidate the microbial functions modulated by the infection. Metabarcoding and metatranscriptomics analyses revealed that Phytophthora root rot (PRR) induced compositional shifts in bacterial communities, leading to the enrichment of members of MND1, RB41, and Nitrospira. Functional analysis showed that this enrichment might be due to the release of nutrients following root rot, as carbohydrate metabolism was stimulated in rhizobacterial communities of infected trees. Moreover, the relative abundance of transcripts from genes associated with stress response and cell signaling increased in some of the most active genera in the rhizosphere of PRR-symptomatic trees, suggesting their potential to mitigate the adverse effects of infection. These findings highlight the need to combine compositional and functional microbiome data to differentiate between taxa attracted by nutrient release and those contributing to the plant defense. The interactions of beneficial bacterial taxa with the pathogen should be further studied, as they may constitute promising biocontrol agents.

Understanding how plant pathogens modulate the rhizosphere microbiota is essential to integrated disease management. Here, we assessed the compositional and functional shifts in the avocado rhizosphere bacteriome induced by Phytophthora cinnamomi to elucidate the microbial functions modulated by the infection and identify taxa potentially recruited by the plant as a defense response. Through metabarcoding with metatranscriptomics, we showed that Phytophthora root rot (PRR) induced compositional shifts in bacterial communities, leading to the enrichment of members of MND1, RB41 and Nitrospira . Functional analysis showed that this enrichment may be due to the release of nutrients following root rot, as carbohydrate metabolism was stimulated in rhizobacterial communities of infected trees. We detected evidence of a cry-for-help strategy by the infected plant, as the most active genera in the rhizosphere of PRR-symptomatic trees up-regulated genes associated with stress response and cell signaling, suggesting that they were recruited to mitigate the adverse effects of infection. Our findings highlight the need to combine compositional and functional microbiome data to differentiate between taxa attracted by nutrient release and those actively recruited by the plant. The interactions of the latter with the pathogen should be further studied, as they may constitute promising biocontrol agents.

Endophytic fungi constitute a great resource for the implementation of sustainable agricultural practices. However, their diversity may be altered by agrochemicals used in conventionally managed agrosystems. Here we explored the culturable diversity of endophytic fungi associated with avocado (Persea americana Mill.) in conventional and organic orchards from three counties of the world’s leading productive region. In total, 529 endophytic fungal isolates were obtained from branches and roots of avocado trees. Identification based on ITS sequencing showed that most isolates belonged to the Ascomycota phylum (98%) and were grouped into 52 fungal genera, representing 102 tentative species. The endophytic fungal community was dominated by genera which were common to both management types, namely Fusarium, Colletotrichum, Dactylonectria, and Diaporthe / Phomopsis. Twenty fungal genera were exclusive to organic orchards (e.g., Hypoxylon and Talaromyces) and 10 were only found in conventional orchards (e.g., Trichoderma). Fungal richness and diversity were higher in organic than in conventional orchards. Ordination and clustering analyses revealed a stronger effect of site than of management type on endophytic fungal community structure, highlighting the influence of local factors in shaping the culturable endophytic fungal community. Overall, our findings confirm the negative impact of conventional management on the diversity of crop-associated endophytic fungi and the significant influence of local factors on endophytic fungal assemblages. Moreover, our results emphasize the need to assess the risk that possible latent fungal pathogens may represent for the crop or dominant forest species surrounding avocado orchards.

Soil‐borne diseases are responsible for huge crop losses worldwide. A deeper understanding of plant–soil–microbe interactions in the presence of soil‐borne pathogens is needed for the integrated management of soil‐borne diseases and tailored use of rhizosphere microbiomes for plant and soil health. In this review, we examine how soil‐borne pathogens influence rhizosphere microbiomes at the compositional and functional levels, and how the study of pathobiomes allows the identification of key microbial taxa that prevent or contribute to disease development. Although soil‐borne pathogens induce contrasting effects on rhizosphere microbial diversity, shifts in rhizosphere microbiome structure and function have been consistently reported in a wide range of pathosystems. These shifts are induced by changes in root exudate patterns upon infection and subsequent defence response activation, and by the recruitment of beneficial microbial taxa by the infected plants. A better understanding of these alterations could help detect functional shifts linked with the plant defence response and identify resistance markers, thus opening new avenues for plant breeding or microbiome manipulation. Moreover, incorporating the pathobiome concept into the design of disease management strategies would assist in pinpointing possible biocontrol agents and identifying biomarkers for early disease detection. We advocate for future pathobiome studies to gain mechanistic insights on the interactions between pathogens and plant microbiomes in non‐model pathosystems and perform validation experiments to unravel how cross‐talk within the pathobiome may lead to disease development or suppression.