Soil Biodiversity and Root Pathogens in Agroecosystems

Soil ecosystem is a living and dynamic environment, habitat of thousands of microbial species, animal organisms and plant roots, integrated all of them in the food webs, and performing vital functions like organic matter decomposition and nutrient cycling; soil is also where plant roots productivity represent the main and first trophic level (producers), the beginning of the soil food web and of thousands of biological interactions. Agroecosystems are modified ecosystems by man in which plant, animal and microorganisms biodiversity has been altered, and sometimes decreased to a minimum number of species. Plant diseases, including root diseases caused by soil-borne plant pathogens are important threats to crop yield and they causes relevant economic losses. Soil-borne plant pathogens and the diseases they produce can cause huge losses and even social and environmental changes, for instance the Irish famine caused by Phytophthora infestans (1845–1853), or the harmful ecological alterations in the jarrah forests of Western Australia affected by Phytophthora cinnamomi in the last 100 years. How can a root pathogen species increase its populations densities at epidemic levels? In wild ecosystems usually we expect the soil biodiversity (microbiome, nematodes, mycorrhiza, protozoa, worms, etc.) through the trophic webs and different interactions between soil species, are going to regulate each other and the pathogens populations, avoiding disease outbreaks. In agroecosystems where plant diseases and epidemics are frequent and destructive, soil-borne plant pathogens has been managed applying different strategies: chemical, cultural, biological agents and others; however so far, there is not enough knowledge about how important is soil biodiversity, mainly microbiome diversity and soil food webs structure and function in the management of root pathogens, in root and plant health, in healthy food production, and maybe more relevant in the conservation of soil as a natural resource and derived from it, the ecosystem services important for life in our planet.

Managing tomato vine decline with soil amendments and transplant treatments: fruit yield, quality, and plant-associated microbial communities.

Tomato vine decline (TVD) disease complex results in fruit yield loss, but what soil management strategies might mitigate it? In commercial fields with a history of TVD, five approaches (soil organic amendments and transplant treatments) were evaluated for their impact on fruit yield, fruit quality and microbial abundance or diversity at four site-years. One site-year had very high TVD pressure and high variability with no yield differences, thus efforts focused on the remaining site-years. Marketable yield was not different among treatments but numerically followed a trend similar to total yield. Amending soil with poultry manure delayed maturity (i.e., increased proportion of green fruit) and had the greatest total yield increases of 17.2%, congruent with decreased abundance of root pathogens (Verticillium dahliae, Rhizopicnis vagum). Microbial DNA fingerprinting data of rhizospheres, roots and/or stems suggested treatments did not significantly shift the total diversity fungal nor bacterial populations, but the aforementioned pathogen loads were reduced with the application of organic amendments relative to the untreated control. While drenching tomato transplants with pseudomonad culture increased their presence in roots, pathogen load was not reduced relative to the untreated control. Overall, these results show that soil organic amendments were able to improve tomato total yield in two of four site-years without reducing fruit quality (i.e., soluble solids, pH, colour), perhaps, in part, due to their ability to suppress specific root pathogens in commercial fields.

Arbuscular Mycorrhizal Symbiosis Triggers Major Changes in Primary Metabolism Together With Modification of Defense Responses and Signaling in Both Roots and Leaves of Vitis vinifera

Grapevine (Vitis vinifera L.) is one of the most important crops worldwide but is subjected to multiple biotic and abiotic stresses, especially related to climate change. In this context, the grapevine culture could take advantage of symbiosis through association with arbuscular mycorrhizal fungi (AMF), which are able to establish symbiosis with most terrestrial plants. Indeed, it is well established that mycorrhization improves grapevine nutrition and resistance to stresses, especially water stress and resistance to root pathogens. Thus, it appears essential to understand the effect of mycorrhization on grapevine metabolism and defense responses. In this study, we combined a non-targeted metabolomic approach and a targeted transcriptomic study to analyze changes induced in both the roots and leaves of V. vinifera cv. Gewurztraminer by colonization with Rhizophagus irregularis (Ri). We showed that colonization of grapevine with AMF triggers major reprogramming of primary metabolism in the roots, especially sugar and fatty acid metabolism. On the other hand, mycorrhizal roots had decreased contents of most sugars and sugar acids. A significant increase in several fatty acids (C16:1, linoleic and linolenic acids and the C20 arachidonic and eicosapentaenoic acids) was also detected. However, a downregulation of the JA biosynthesis pathway was evidenced. We also found strong induction of the expression of PR proteins from the proteinase inhibitor (PR6) and subtilase (PR7) families in roots, suggesting that these proteins are involved in the mycorrhiza development but could also confer higher resistance to root pathogens. Metabolic changes induced by mycorrhization were less marked in leaves but involved higher levels of linoleic and linolenic acids and decreased sucrose, quinic, and shikimic acid contents. In addition, Ri colonization resulted in enhanced JA and SA levels in leaves. Overall, this study provides a detailed picture of metabolic changes induced by AMF colonization in a woody, economically important species. Moreover, stimulation of fatty acid biosynthesis and PR protein expression in roots and enhanced defense hormone contents in leaves establish first insight in favor of better resistance of grapevine to various pathogens provided by AMF colonization.

In-depth evaluation of root infection systems using the vascular fungus Verticillium longisporum as soil-borne model pathogen

Background While leaves are far more accessible for analysing plant defences, roots are hidden in the soil, leading to difficulties in studying soil-borne interactions. Inoculation strategies for infecting model plants with model root pathogens are described in the literature, but it remains demanding to obtain a methodological overview. To address this challenge, this study uses the model root pathogen Verticillium longisporum on Arabidopsis thaliana host plants and provides recommendations for selecting appropriate infection systems to investigate how plants cope with root pathogens. Results A novel root infection system is introduced, while two existing ones are precisely described and optimized. Step-by-step protocols are presented and accompanied by pathogenicity tests, transcriptional analyses of indole-glucosinolate marker genes and independent confirmations using reporter constructs. Advantages and disadvantages of each infection system are assessed. Overall, the results validate the importance of indole-glucosinolates as secondary metabolites that limit the Verticillium propagation in its host plant. Conclusion Detailed assistances on studying host defence strategies and responses against V. longisporum is provided. Furthermore, other soil-borne microorganisms (e.g., V. dahliae) or model plants, such as economically important oilseed rape and tomato, can be introduced in the infection systems described. Hence, these proven manuals can support finding a root infection system for your specific research questions to further decipher root-microbe interactions.

Shisham (Dalbergia sissoo) decline by dieback disease, root pathogens and their management: a review

Shisham or sissoo (Dalbergia sissoo) is an important multipurpose tree with great economic importance, but this tree has been infected by various root pathogens. This review article shows the works conducted on root pathogens and die back disease of Shisham and their management. Around seventy-one endophytic fungus has been found in sissoo trees in Nepal. Several fungi, including, Fusarium solani, F. oxysporum, Ganoderma lucidum, Phellinus gilvus, Polypours gilvus, Rhizoctonia solani, Polyporus spongiosum, etc. cause sissoo diseases. Ganoderma Lucidum and F. Solani are two main pathogenic agents in Shisham, all of which causes root rot and vascular wilt diseases, and are the causes for the large-scale death of this tree species. Root rot ganoderma is wide spread in both natural and plant-based forests. Older trees in Shisham are usually attacked by these pathogens and cause large-scale death. However, when sissoo is grown as a re-forested pure plant without the removal of the stumps or root of the initial plant, a serious problem of root rot can develop. Field sanitation and proper management of field are necessary to control the fungal diseases of Shisham. Another deleterious disease of Shisham is dieback disease, where sissoo plantations have been confirmed to this disease when the infected trees begin to get dry from the top. There is no suitable solution for control of dieback of Shisham. There is a need of developing resistant varieties and to improve the quality of seed. This review may be useful tool for Forest Pathologists and other persons who are working in forestry and natural conservation sectors.

Changes in the Microbiome in the Soil of an American Ginseng Continuous Plantation

American ginseng is an important herbal medicinal crop in China. In recent years, there has been an increasing market demand for ginseng, but the production area has been shrinking due to problems associated with continuous monocropping. We analyzed the microbiome in bulk soils to assess whether and, if so, what changes in the bulk soil microbiome are associated with continuous American ginseng cropping. The alpha diversity of fungi and bacteria was significantly lower in the soils planted with American ginseng than the virgin (non-planted) land. The relative abundance of Fusarium spp. and Ilyonectria spp., known plant root pathogens, was much higher in the soils cropped with American ginseng than the non-planted. On the other hand, a number of bacteria with biodegradation function, such as Methylibium spp., Sphingomonas spp., Variovorax spp., and Rubrivivax spp., had lower abundance in the soils cropped with American ginseng than the non-cropped. In addition, soil pH was lower in the field planted with American ginseng than the non-planted. Accumulation of fungal root pathogens and reduction of soil pH may, therefore, have contributed to the problems associated with continuous monocropping of American ginseng.

Protection to Tomato Wilt Disease Conferred by the Nonpathogen Fusarium oxysporum Fo47 is More Effective Than that Conferred by Avirulent Strains

Although the vascular pathogen Fusarium oxysporum is notorious for being the causal agent of Fusarium wilt disease, the vast majority of F. oxysporum strains are harmless soil and root colonizers. The latter F. oxysporum’s are often endophytes colonizing roots intracellularly without negatively affecting plant fitness. Actually, most of them, like Fo47, are beneficial providing biological control to various root pathogens. Interestingly, also pathogenic F. oxysporum inoculated on a resistant host (i.e., avirulent F. oxysporum f. sp. lycopersici) can reduce susceptibility to virulent F. oxysporum strains via a mechanism called “cross protection.” It has been hypothesized that cross protection is based on activation of a resistance protein of the host upon recognition of a cognate avirulence (Avr) protein of the pathogen. Currently, it is unknown whether the biocontrol activity of F. oxysporum endophytes utilizes similar mechanisms as cross protection conferred by avirulent pathogens, and whether both provide a quantitative similar level of protection. Here, we show that in tomato biocontrol activity of the Fo47 endophyte to the pathogen F. oxysporum f. sp. lycopersici is more effective than cross protection induced by avirulent F. oxysporum f. sp. lycopersici strains activating either I, I-2, or both resistance proteins upon recognition of Avr1 or the Avr2/Six5 pair, respectively. These findings imply that cross protection and biological control utilize different mechanisms to reduce susceptibility of the host to subsequent infections.