Disease-suppressive Soils Research Articles

Do small RNAs unlock the below ground microbiome-plant interaction mystery?

Over the past few decades, regulatory RNAs, such as small RNAs (sRNAs), have received increasing attention in the context of host-microbe interactions due to their diverse roles in controlling various biological processes in eukaryotes. In addition, studies have identified an increasing number of sRNAs with novel functions across a wide range of bacteria. What is not well understood is why cells regulate gene expression through post-transcriptional mechanisms rather than at the initiation of transcription. The finding of a multitude of sRNAs and their identified associated targets has allowed further investigation into the role of sRNAs in mediating gene regulation. These foundational data allow for further development of hypotheses concerning how a precise control of gene activity is accomplished through the combination of transcriptional and post-transcriptional regulation. Recently, sRNAs have been reported to participate in interkingdom communication and signalling where sRNAs originating from one kingdom are able to target or control gene expression in another kingdom. For example, small RNAs of fungal pathogens that silence plant genes and vice-versa plant sRNAs that mediate bacterial gene expression. However, there is currently a lack of evidence regarding sRNA-based inter-kingdom signalling across more than two interacting organisms. A habitat that provides an excellent opportunity to investigate interconnectivity is the plant rhizosphere, a multifaceted ecosystem where plants and associated soil microbes are known to interact. In this paper, we discuss how the interconnectivity of bacteria, fungi, and plants within the rhizosphere may be mediated by bacterial sRNAs with a particular focus on disease suppressive and non-suppressive soils. We discuss the potential roles sRNAs may play in the below-ground world and identify potential areas of future research, particularly in reference to the regulation of plant immunity genes by bacterial and fungal communities in disease-suppressive and non-disease-suppressive soils.

Factors associated with soils suppressive to black scurf of potato caused by Rhizoctonia solani

Soils in which disease fails to develop despite pathogen presence are considered disease-suppressive. They offer sustainable, effective protection to plants against infection by soil-borne pathogens. Naturally disease-suppressive soils have been reported for diseases of a diverse range of agricultural crops worldwide yet the underlying mechanisms of disease suppression are still not completely understood. Two large greenhouse experiments, conducted during 2017/18 (Year 1) and 2018/19 (Year 2), determined that soils naturally suppressive to stem canker and black scurf of potato (caused by Rhizoctonia solani) are present in vegetable-arable cropping soils of the Auckland and Waikato regions of New Zealand. Soil was pre-treated with heat prior to inoculation with R. solani and compared with untreated and uninoculated controls to ascertain if stem canker and black scurf suppression was ‘general’, or ‘specific’ (i.e. transferable; possibly involving specific microorganisms). Rhizoctonia solani inoculation was also combined with transfer of one part test soil to nine parts of a known disease-conducive soil. Abiotic factors such as soil texture and organic matter content influenced black scurf incidence and severity. Soil microorganisms were also involved in disease suppression since black scurf incidence and severity markedly increased when they were eliminated or reduced by soil heat pre-treatment. Microbial profiling of the soils through sequencing revealed that taxa of geographically close soils of the same type had similar fungal and bacterial community structure and diversity even though they differed in their capacity to suppress black scurf. These results suggest that although the soil microbiome as a whole, was mainly responsible for soil disease suppressiveness, certain bacterial genera or species may play a role in black scurf suppression.

Soil conditions on bacterial wilt disease affect bacterial and fungal assemblage in the rhizosphere

Natural soil has the ability to suppress the soil-borne pathogen to a certain extent, and the assemblage of soil microbiome plays a crucial role in maintaining such ability. Long-term monoculture accelerates the forms of soil microbiome and leads to either disease conducive or suppressive soils. Here, we explored the impact of soil conditions on bacterial wilt disease (healthy or diseased) under long-term tobacco monoculture on the assemblage of bacterial and fungal communities in bulk and rhizosphere soils during the growth periods. With Illumina sequencing, we compared the bacterial and fungal composition of soil samples from tobacco bacterial wilt diseased fields and healthy fields in three growth periods. We found that Proteobacteria and Ascomycota were the most abundant phylum for bacteria and fungi, respectively. Factors of soil conditions and tobacco growth periods can significantly influence the microbial composition in bulk soil samples, while the factor of soil conditions mainly determined the microbial composition in rhizosphere soil samples. Next, rhizosphere samples were further analyzed with LEfSe to determine the discriminative taxa affected by the factor of soil conditions. For bacteria, the genus Ralstonia was found in the diseased soils, whereas the genus Flavobacterium was the only shared taxon in healthy soils; for fungi, the genus Chaetomium was the most significant taxon in healthy soils. Besides, network analysis confirmed that the topologies of networks of healthy soils were higher than that of diseased soils. Together, our results suggest that microbial assemblage in the rhizosphere will be largely affected by soil conditions especially after long-term monoculture.

Disease suppressive soils: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology.

Disease suppressive soils: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology.

Toward a holistic view of orchard ecosystem dynamics: A comprehensive review of the multiple factors governing development or suppression of apple replant disease.

Replant diseases are a common occurrence in perennial cropping systems. In apple, progress toward the development of a universally effective disease management strategy, beyond the use of broad-spectrum soil fumigants, is impeded by inconsistencies in defining replant disease etiology. A preponderance of evidence attributes apple replant disease to plant-induced changes in the soil microbiome including the proliferation of soilborne plant pathogens. Findings from alternative studies suggest that the contribution of abiotic factors, such as the accumulation of phenolic detritus from previous orchard plantings, may play a part as well. Engineering of the resident soil microbiome using resource-based strategies is demonstrating potential to limit activity of replant pathogens and improve productivity in newly established orchards. An understanding of factors promoting the assembly of a disease-suppressive soil microbiome along with consideration of host factors that confer disease tolerance or resistance is imperative to the developing a more holistic view of orchard ecosystem dynamics. Here, we review the literature concerning the transition of orchard soil from a healthy state to a replant disease-conducive state. Included in the scope of this review are studies on the influence of soil type and geography on the apple replant pathogen complex. Furthermore, several tolerance and innate resistance mechanisms that have been described in apple to date, including the role of root chemistry/exudates are discussed. Finally, the interplay between apple rootstock genotype and key resource-based strategies which have been shown to “reshape” the plant holobiont in favor of a more prophylactic or disease-suppressive state is highlighted.

Archaeal communities perform an important role in maintaining microbial stability under long term continuous cropping systems

Long-term continuous cropping of soybean can generate the development of disease-suppressive soils. However, whether the changes in microbial communities, especially for archaea, contribute to controlling soil sickness and improving crop yields remains poorly understood. Here, real-time PCR and high-throughput sequencing were employed to investigate the changes in soil archaeal communities in both bulk and rhizosphere soils under four cropping systems, including the continuous cropping of soybeans for a short-term of 3 and 5 years (CC3 and CC5, respectively) and for a long-term of 13 years (CC13), as well as a soybean-maize rotation for 5 years (CR5). The results showed that CC13 and CR5 significantly increased archaeal abundance, reduced the alpha-diversity of archaeal communities, and changed soil archaeal community structures compared to CC3 and CC5. Microbial co-occurrence network analysis revealed that CC13 led to the higher resistant microbial community and lower the relative abundance of potential plant pathogens in the network compared to CC3 and CC5. Correlation analysis showed that the microbial resistance index was negatively correlated with the relative abundance of potential plant pathogens and positively correlated with soybean yields in both bulk and rhizosphere soils. Intriguingly, the random forest (RF) analysis showed that archaea contributed the most to soil microbial resistance even though they were not at the core positions of the network. Overall, structural equation models (SEMs) revealed that high resistant microbial community could directly or indirectly improved soybean yields by regulating the relative abundance of plant pathogens and the soil nutrients, suggesting that the regulation of soil microbial taxa may play an important role in maintaining agricultural productivity under continuous cropping of soybean.

Generation of Fusarium oxysporum-suppressive soil with non-soil carriers using a multiple-parallel-mineralization technique

Disease-suppressive soils exist worldwide. However, the disease-suppression mechanism is unknown, and it’s unclear how to produce such soils. The microbiota that develop in a multiple-parallel-mineralization system (MPM) can increase nutrient production efficiency and decrease root disease in hydroponic systems. Artificial media inoculated with MPM microorganisms can degrade organic matter to produce inorganic nutrients similarly to natural soil, but it’s unknown whether they can also suppress pathogen growth. Here, we produced an artificial medium that inhibited root disease similarly to disease-suppressive soils. Microbial MPM culture solution was inoculated into non-soil carriers (rockwool, rice husk charcoal, and vermiculite) to test whether it could suppress growth of Fusarium oxysporum f. sp. lactucae J. C. Hubb. & Gerik. We inoculated F. oxysporum f. sp. conglutinans (Wollenweber) Snyder et Hansen strain Cong:11 and F. oxysporum f. sp. lactucae J. C. Hubb. & Gerik into artificial media sown each with Arabidopsis thaliana (L.) Heynh. and Lactuca sativa L. var. capitata supplemented with MPM culture microbes. The MPM microorganisms suppressed F. oxysporum f. sp. lactucae J. C. Hubb. & Gerik growth and prevented plant disease. Thus, MPM-inoculated non-soil carriers that can generate inorganic nutrients from organic matter may also suppress disease in the absence of natural soil. Our study shows novel creation of a disease-suppressive effect in non-soil media using the microbial community from MPM culture solution.

Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review

While chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ application. Challenged by a significant proportion of unidentified microbiomes with unknown ecological functions, advanced high throughput metatranscriptomics is prudent to overcome the technological limitations in unfolding the previously undiscovered functional profiles of the beneficial microbiomes. Under this context, this review begins by summarising (1) the evolution of next-generation sequencing and metatranscriptomics in leveraging the microbiome transcriptome profiles through whole gene expression profiling. Next, the current environmental metatranscriptomics studies are reviewed, with the discussion centred on (2) the emerging application of the beneficial microbiomes in developing fertile soils and (3) the development of disease-suppressive soils as greener alternatives against biotic stress. As sustainable agriculture focuses not only on crop productivity but also long-term environmental sustainability, the second half of the review highlights the metatranscriptomics’ contribution in (4) revolutionising the pollution monitoring systems via specific bioindicators. Overall, growing knowledge on the complex microbiome functional profiles is imperative to unlock the unlimited potential of agricultural microbiome-based practices, which we believe hold the key to productive agriculture and sustainable environment.

Taxonomical identification of Chinese cabbage yellows inhibitory fungus isolated from disease suppressive soil

Taxonomical identification of Chinese cabbage yellows inhibitory fungus isolated from disease suppressive soil

Resistance to bacterial wilt caused by Ralstonia solanacearum depends on the nutrient condition in soil and applied fertilizers: A meta-analysis

Soil nutrient supply and resistance to pathogen invasion are critical to crop yield during agricultural production. Crop production is often hampered by co-occurring nutrient and pathogen stresses, but the relationship between soil nutrient status and disease suppression remains unclear. Here, we conducted a meta-analysis based on 406 observations from 55 studies to decipher the relationships between soil nutrient supply and disease suppression against bacterial wilt disease caused by R. solanacearum. We found that the contents of soil organic carbon (SOC), total nitrogen (TN), available potassium (AK) and available phosphorus (AP) were significantly higher in relatively disease suppressive soils than in conducive soils. Soil AP showed a significantly negative correlation with both crop disease incidence (DI) and disease severity (DSI). SOC was significantly and negatively correlated with DI and DSI in general, but a positive correlation with DI was found when SOC content was higher than 1.3%. Then for nutrient stoichiometry in soil, we found that the ratio of carbon to nitrogen (C/N), maximum to 22, was significantly and negatively correlated to the DI, but was positively correlated to DSI when C/N was higher than about 30. And the ratio of TN to AP (TN/AP) showed significantly positive correlations with both DI and DSI in soil. Further in applied organic fertilizer, the ratio of nitrogen to phosphorus (N/P) was significantly and negatively correlated with DI when N/P was lower than about 5, but was positively correlated with DI when higher than that. Our results demonstrated that the quantity and stoichiometry of phosphorus, organic carbon and nitrogen in soil and applied fertilizer, notably the prevention of nutrient deficiency and the balance of different nutrients, play an important role in supporting soil suppressiveness to R. solanacearum wilt disease, and this implied a possible trade-off between nutrient acquisition and pathogen defense in soil ecosystems.

Composition identification and functional verification of bacterial community in disease-suppressive soils by machine learning.

It has been widely reported that probiotic consortia in the rhizosphere can enhance the plant resistance to pathogens. However, the general composition and functional profiles of bacterial community in soils which suppress multiple diseases for various plants remain largely unknown. Here, we combined metadata analysis with machine learning to identify the general patterns of bacterial-community composition in disease-suppressive soils. Disease-suppressive soils significantly enriched Firmicutes and Actinobacteria but showed a decrease in Proteobacteria and Bacteroidetes. Our machine-learning models accurately identified the disease-conducive and -suppressive soils with 54 biomarker genera, 28 of which were potentially beneficial. We further carried out a successive passaging experiment with the susceptible rps2 mutant of Arabidopsis thaliana invaded by Pseudomonas syringae pv. tomato DC3000 (avrRpt2) for functional verification of potential beneficial bacteria. The disease-suppressive ability of Kribbella, Nocardioides and Bacillus was confirmed, and they positively activated the pathogen-associated molecular patterns-triggered immunity pathway. Results also showed that chemical control by pesticides in agricultural production decreased the disease-suppressive ability of soil. This study provides a method for accurately predicting the occurrence of multiple diseases in soil and identified potential beneficial bacteria to guide a wide range of multiple-strain biological control strategies in agricultural management.

Spatial Distribution of the Pepper Blight (Phytophthora capsici) Suppressive Microbiome in the Rhizosphere.

The properties of plant rhizosphere are dynamic and heterogeneous, serving as different habitat filters for or against certain microorganisms. Herein, we studied the spatial distribution of bacterial communities in the rhizosphere of pepper plants treated with a disease-suppressive or non-suppressive soil. The bacterial richness was significantly (p < 0.05) higher in plants treated with the disease-suppressive soil than in those treated with the non-suppressive soil. Bacterial richness and evenness greatly differed between root parts, with decrease from the upper taproot to the upper fibrous root, the lower taproot, and the lower fibrous root. As expected, the bacterial community in the rhizosphere differed between suppressive and non-suppressive soil. However, the spatial variation (36%) of the bacterial community in the rhizosphere was much greater than that explained by soils (10%). Taxa such as subgroups of Acidobacteria, Nitrosospira, and Nitrospira were known to be selectively enriched in the upper taproot. In vitro Bacillus antagonists against Phytophthora capsici were also preferentially colonized in the taproot, while the genera such as Clostridium, Rhizobium, Azotobacter, Hydrogenophaga, and Magnetospirillum were enriched in the lower taproot or fibrous root. In conclusion, the spatial distribution of bacterial taxa and antagonists in the rhizosphere of pepper sheds light on our understanding of microbial ecology in the rhizosphere.

Investigating the Responses of Microbial Communities to Banana Fusarium Wilt in Suppressive and Conducive Soils Based on Soil Particle-Size Differentiation

The microbiota plays a primary role in inhibiting plant pathogens in the soils. However, the correlation between soil particles and local microbial communities has not been fully confirmed. In this study, we contrasted the different assemblages of microbial communities between suppressive and conducive soils via the differentiation of soil particle-size fractions (PSFs). We further extracted the direct and indirect interactive associations among the soil biotic and abiotic factors by using samples from two continuous banana cropping systems. Notable differences were shown in PSF composition, biological traits (microbial communities and enzyme patterns) and physiochemical parameters between suppressive and conducive soils among the different soil fractions. For example, compared with conducive soils, suppressive soils have higher nutrient contents, fungal abundance and diversity and enzyme activities, and the extent of these differences was explored for fractions of different sizes. Moreover, the microbial taxonomic composition strongly varied between disease-suppressive and disease-conducive soils. For instance, there were significant differences in the relative abundance among key microbiology communities, such as Actinobacteria, Firmicutes, Bacteroidetes, Proteobacteria and Ascomycota, especially for antagonistic microorganisms (i.e., Streptomyces, Pseudomonas, Trichoderma, etc.) across various soil fractions. In addition, structural equation modeling (SEM) showed that the complex associations among soil PSFs, physiochemical parameters and microbial communities were mediated by multiple pathways, which then drive the soil enzyme activities and may further influence the suppressiveness of the soil. These results demonstrate that the resident microbial communities in specific soil particles may play a crucial role in the development of soil suppressiveness against banana Fusarium wilt disease.

English

Peas are growing all over the world as a leguminous crop due to high nutrients value. Fusarium wilt of peas is a destructive disease and causing deleterious loses in pea growing regions of the world. The fields were surveyed with disease incidence of Fusarium wilt in major pea growing areas. Fields with heavy pathogen infestation and natural disease suppressive were observed at District Sahiwal, Pakistan. The samples were collected to diagnose the disease and factors responsible in the suppression of disease. The results of soil physio-chemical properties showed no significant differences between diseased and suppressive soils. Pathogenicity assays both in-vitro and pot trial showed that suppressive soil has natural ability to suppress the disease. Furthermore, in-vitro and pot assays were designed with different soil treatments to investigate the factors responsible in the natural disease suppressiveness in suppressive soil. The results demonstrated that the mechanism involved in disease suppressive soil is biotic in nature. All isolated fungal strains from diseased and healthy roots of pea were subjected to biological assays to evaluate the virulence. The assays showed that isolate SAH09 is non-pathogenic Fusarium oxysporum which was isolated from the pea roots of suppressive soil. Isolate SAH09 was used in dual culturing technique and pot trial to evaluate the mycoparastism behavior against virulent pathogenic isolates SAH03, SAH05 and SAH10. Results concluded that isolate SAH09 of non-pathogenic Fusarium oxysporum has potential to suppress the growth of all isolates of pathogenic Fusarium and possibly play the role in natural disease suppression in suppressive soils

Shared Core Microbiome and Functionality of Key Taxa Suppressive to Banana Fusarium Wilt.

Microbial contributions to natural soil suppressiveness have been reported for a range of plant pathogens and cropping systems. To disentangle the mechanisms underlying suppression of banana Panama disease caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc4), we used amplicon sequencing to analyze the composition of the soil microbiome from six separate locations, each comprised of paired orchards, one potentially suppressive and one conducive to the disease. Functional potentials of the microbiomes from one site were further examined by shotgun metagenomic sequencing after soil suppressiveness was confirmed by greenhouse experiments. Potential key antagonists involved in disease suppression were also isolated, and their activities were validated by a combination of microcosm and pot experiments. We found that potentially suppressive soils shared a common core community with relatively low levels of F. oxysporum and relatively high proportions of Myxococcales, Pseudomonadales, and Xanthomonadales, with five genera, Anaeromyxobacter, Kofleria, Plesiocystis, Pseudomonas, and Rhodanobacter being significantly enriched. Further, Pseudomonas was identified as a potential key taxon linked to pathogen suppression. Metagenomic analysis showed that, compared to the conducive soil, the microbiome in the disease suppressive soil displayed a significantly greater incidence of genes related to quorum sensing, biofilm formation, and synthesis of antimicrobial compounds potentially active against Foc4. We also recovered a higher frequency of antagonistic Pseudomonas isolates from disease suppressive experimental field sites, and their protective effects against banana Fusarium wilt disease were demonstrated under greenhouse conditions. Despite differences in location and soil conditions, separately located suppressive soils shared common characteristics, including enrichment of Myxococcales, Pseudomonadales, and Xanthomonadales, and enrichment of specific Pseudomonas populations with antagonistic activity against the pathogen. Moreover, changes in functional capacity toward an increase in quorum sensing, biofilm formation, and antimicrobial compound synthesizing involve in disease suppression.

Different Responses of Soil Environmental Factors, Soil Bacterial Community, and Root Performance to Reductive Soil Disinfestation and Soil Fumigant Chloropicrin

Reductive soil disinfestation (RSD) and soil fumigant chloropicrin (SFC) are two common agricultural strategies for the elimination of soil-borne pathogens. However, the differences in soil environmental factors, soil bacterial microbiome, and root performance between SFC and RSD are poorly understood. In this study, three soil treatments, untreated control (CK), SFC with 0.5 t⋅ha–1 chloropicrin, and RSD with 15 t⋅ha–1 animal feces, were compared. We evaluated their effects on soil environmental factors, bacterial community structure, and root activity using chemical analysis and high-throughput sequencing. RSD treatment improved soil composition structure, bacterial diversity, and root performance to a greater extent. Carbon source utilization preference and bacterial community structure were strikingly altered by SFC and RSD practices. Bacterial richness, diversity, and evenness were notably lowered in the SFC- and RSD-treated soil compared with the CK-treated soil. However, RSD-treated soil harbored distinct unique and core microbiomes that were composed of more abundant and diverse potentially disease-suppressive and organic-decomposable agents. Also, soil bacterial diversity and composition were closely related to soil physicochemical properties and enzyme activity, of which pH, available Na (ANa), available Mg (AMg), available Mn (AMn), total Na (TNa), total Ca (TCa), total Cu (TCu), total Sr (TSr), urease (S-UE), acid phosphatase (S-ACP), and sucrase (S-SC) were the main drivers. Moreover, RSD treatment also significantly increased ginseng root activity. Collectively, these results suggest that RSD practices could considerably restore soil nutrient structure and bacterial diversity and improve root performance, which can be applied as a potential agricultural practice for the development of disease-suppressive soil.

Discovering naturally-occurring microbiota in disease suppressive soil: Potential role of biological elements in suppressing Ganoderma boninense

Blenheim soil (Typic Quartzipsamment) and Bernam soil (Typic Endoaquept) with low and high Ganoderma basal stem rot (BSR) incidence, respectively, were studied to determine the role of naturally-occurring microbiota in suppressing basal stem rot (BSR) disease in oil palm. These coastal soils were also compared against a typical soil for nursery use, the inland Bungor soil (Typic Kandiudults). For each soil type, half of the soils were sterilized by autoclaving, and the other half were non-sterilized. These soils were then used for the microbiome analysis, evaluation of disease incidences, and effect on plant growth. Soil microbial communities were profiled using 16S and 18S ribosomal RNA gene amplicon sequencing on the Illumina MiSeq. Polybag trials were conducted over a period of 20 weeks. Results showed that by eliminating or inactivating the indigenous microbial communities from BSR-suppressive Blenheim soil through sterilization, this increased BSR incidences (from 50 to 92%) and severity (from 28 to 78%), and affected plant growth (reduction of 35% leaf area, 11% height, and 19% bole’s girth). Soil microbiome analysis revealed that Acidobacteriota, Nitrospirota, Latesbaciterota, Nanoarchaeota, Entotheonellaeta, Zixibacteria, Candidatus Yanofskybacteria (Patescibacteria), MB-A2-108 (Actinobacteriota), Cnidaria and Acaulospora (Mucoromycota) were less prevalent in sterilized Blenheim soil compared to non-sterilized Blenheim soil. Relative abundance of the genus Ganoderma was also lower in BSR-suppressive Blenheim soil compared to sterilized Blenheim soil. In contrast, disease development and plant growth remained unaffected by sterilization of BSR-conducive Bernam and Bungor soils, suggesting that naturally-occurring microbiota in these two soils played minimal roles in contributing to conducive conditions for disease development. Relative abundance of Ganoderma was higher in BSR-conducive Bernam and Bungor soils as well, compared to BSR-suppressive Blenheim. Results from this study provides the first insights into the soil microbiota in BSR suppressive soils and their role in BSR disease progression and growth of oil palms.

Chemical characters of disease suppressive and conducive soil of Moler on shallot in Brebes Central Java

In the latest years, a disease epidemy of Moler caused by Fusarium oxysporum f.sp. cepae have just occurred in Brebes Central Java. The disease intensity, however, varies between the shallot production lands. Some lands show suppressive with disease intensity lower than 5%, and others are conducive to disease intensity over 50%. It is interesting that in Brebes occur suppressive and conducive soil to moler disease. The suppressiveness may be determined by environmental conditions, including chemical soil characters. This paper reports the chemical character of suppressive and conducive soil to moler disease in Brebes. The evidence shows that the suppressive soil is more fertile than that conducive one. The suppressive soil is chemically characterized by significantly higher organic mineral, C-organic, P-available, K-exchangeable, and Cation Exchange Capacity than that conducive one.

The soil-borne ultimatum, microbial biotechnology and sustainable agriculture.

The soil-borne ultimatum, microbial biotechnology and sustainable agriculture.

Engineering Multigenerational Host-Modulated Microbiota against Soilborne Pathogens in Response to Global Climate Change.

Simple SummaryIn order to face the challenges posed by climate change, scientific research should be directed towards global needs while also keeping into account the need for increased plant productivity. In this sense, our scientific group from the Biocontrol Research Laboratory BIOREN (Temuco, Chile) and our collaborators, have been studying the enormous potential to enhance productivity by using suppressive soils. In this review, we highlight soil-suppressive microbiota as a natural source of biocontrol agents and we propose a strategy to create microbial assemblages, where the plant selects its own inoculants (when plants “cry for help”). This approach is based on the selection of specific taxa during the transition from a conducive to a suppressive soil. We hope that this strategy leads to generation of personalized bioinoculants to counteract the effects of climate change and increase agricultural sustainability.Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is in large part due to their ability to reside in the soil for a long time, even without a host plant, using survival several strategies. In this regard, disease-suppressive soils, characterized by a low disease incidence due to the presence of antagonist microorganisms, can be an excellent opportunity for the study mechanisms of soil-induced immunity, which can be applied in the development of a new generation of bioinoculants. Therefore, here we review the main effects of climate change on crops and pathogens, as well as the potential use of soil-suppressive microbiota as a natural source of biocontrol agents. Based on results of previous studies, we also propose a strategy for the optimization of microbiota assemblages, selected using a host-mediated approach. This process involves an increase in and prevalence of specific taxa during the transition from a conducive to a suppressive soil. This strategy could be used as a model to engineer microbiota assemblages for pathogen suppression, as well as for the reduction of abiotic stresses created due to global climate change.