ArticleLiterature Review

Steering soil microbiome to enhance soil system resilience

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Abstract

Pathogens in soil play a tremendous role in soil health and subsequent food production. Soil-borne pathogens can cause serious losses to global harvest and are considered as a difficult problem to manage worldwide. The emergence of soil disease is largely dependent on the pathogen-host-environment complex, which can be employed to generate pathogen control strategies. Usually, the resources of resistant plant varieties are limited, and chemical control is insufficiently effective with possible secondary soil pollution. Therefore, there is now a compulsory need to enhance the ability of soil per se to defend against invading pathogens (i.e. soil immunity). Soil immunity is normally attributed to the activities of the functional microbiome. In the meanwhile, pathogen-microbiome interactions in soil are sensitive to soil contaminants which would filter out unique groups of microbial communities. Steering functional soil microbiome will not only limit disease development, but also reduce the level of soil pollution. It is thus of great importance to develop microbiome-based techniques to improve soil immunity and resilience. This review provided an up-to-date understanding of the mechanisms for microbiome-based disease suppression and potential management strategies for better sustainable agricultural system.

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... The soil microbial community is an important natural carbon sink and plays important roles in the carbon cycle and in greenhouse gas emissions (S1 Fig) [6,7]. Soil microbial communities have the capacity to maintain themselves in terms of stability and self-healing abilities in case they are damaged or destroyed [8]. Manual application is a process of enrichment of N, P, K, and carbon. ...
... A total of six merged datasets showed improved microbial diversity of the soil ( Fig 2B). Interestingly, the application of manure alone increased bacterial diversity (M-Z: 7.546 and M-I: 8.68) as well as inhibited and reduced fungal diversity (M-Z: −1.15 and M-I: −1.03) ( Fig 2C). ...
... The combination of Pseudomonas and Bacillus improves the health of plants [45]. Beneficial soil microorganisms improve soil health, promote plant growth, and finally promote the sustainable development of agriculture [8]. Researchers have recognized the need for beneficial microorganisms [46]. ...
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The processes involved in soil domestication have altered the soil microbial ecology. We examined the question of whether animal manure application affects the soil microbial ecology of farmlands. The effects of global animal manure application on soil microorganisms were subjected to a meta-analysis based on randomized controlled treatments. A total of 2303 studies conducted in the last 30 years were incorporated into the analysis, and an additional 45 soil samples were collected and sequenced to obtain 16S rRNA and 18S rRNA data. The results revealed that manure application increased soil microbial biomass. Manure application alone increased bacterial diversity (M-Z: 7.546 and M-I: 8.68) and inhibited and reduced fungal diversity (M-Z: −1.15 and M-I: −1.03). Inorganic fertilizer replaced cattle and swine manure and provided nutrients to soil microorganisms. The soil samples of the experimental base were analyzed, and the relative abundances of bacteria and fungi were altered compared with no manure application. Manure increased bacterial diversity and reduced fungal diversity. Mrakia frigida and Betaproteobacteriales , which inhibit other microorganisms, increased significantly in the domesticated soil. Moreover, farm sewage treatments resulted in a bottleneck in the manure recovery rate that should be the focus of future research. Our results suggest that the potential risks of restructuring the microbial ecology of cultivated land must be considered.
... Significant role in the transformation of soil substances play microorganisms, they are responsible for the circulation of substances, maintenance of soil structure, detoxification of harmful chemicals. Moreover, microorganisms control the activity of plant pests and influence plants growth [5][6][7][8][9]. ...
... Moreover, they are easy to isolate and culture in artificial conditions where they grow rapidly and produce a lot of conidia and often chlamydospores. Most of the research work about Trichoderma indicate their antagonism towards pathogenic fungi inhabiting root systems [5,7,23]. ...
Article
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Conducted research determined the effect of the Trichoderma fungi on the presence of cadmium and lead ions in the soil contaminated by mentioned elements. The aim of the study was to demonstrate whether the fungi of this kind can contribute to remediation of soil by the immobilization of heavy metals. Experiments were conducted in laboratory conditions. The vaccine containing spores of Trichoderma asperellum was introduced into the soil contaminated with cadmium and lead by direct injection. Analyses of the soluble fraction of selected heavy metals were performed after 3 and 15 days of cultivation using atomic absorption spectrometry (AAS). Statistical significant positive effects on the immobilization of lead ions and no statistical differences in inhibition of cadmium translocation were observed. The results showed that Trichoderma fungi are suited to support the process of environment remediation by removal of lead. This suggests possible application of Trichoderma asperellum in mycoremediation and supporting role in phytoremediation of soil.
... 土壤生物多样性的丧失和土壤群落组成的单一化会损 害和抑制多种生态系统功能, 包括植物多样性、养分 保持和养分吸收等 [54] . ; 微生物网络中核心节点的土壤微 生物类群与土壤功能潜力高度相关 [62] ; 稀有物种与关 键物种可能是生态系统多功能的指示微生物 [63~66] ; 菌 根真菌是不同土壤区域适宜种植的森林类型的指示生 物 [67] ; 皮氏罗尔斯通氏菌株(Ralstonia pickettii)和贪铜 菌属(Cupriavidus gilardii)可作为诊断土壤重金属污染 的指示物种 [68] ; 植物病害反应的等级与土壤健康息息 相关等 [69] . [72] . ...
... 新兴的合成生物学和基因编 图 2 评估土壤健康的微生物综合性指标 [80,81] . 此外, 微 生物组互作使得它们在生态系统中可以发挥更大的作 用, 如多种微生物的组合可以显著提高土壤中污染物 的降解率, 提高微生物在土壤生态系统中的稳定性和 适应能力, 从而有效修复污染土壤 [68] . 核心物种是微 生物互作网络中与其他微生物存在互作关系的物种, 核心物种的接种代表着另一种调控土壤微生物的研究 方向. ...
... Diseases caused by soil-borne pathogens are among the most important limiting factors for plant growth and productivity (Oerke, 2006). Due to the pathogens abilities to survive in the soil for long periods of time, even without the plant host, they cause problems worldwide (Wang and Li, 2019). Some of the soil-borne fungal pathogens produce mycotoxins, such as deoxynivalenol (DON) by Fusarium spp. ...
... The complex interplay of soil suppressiveness cannot simply relate to a single microbial taxon or group (de Boer et al., 2007;Legrand et al., 2019). The majority of rhizobacterial taxa indicative of the suppressiveness status of the soil may differ when comparing different types of suppressive soils or even different soils suppressive to a same phytopathogen (de Boer et al., 2019;Wang and Li, 2019). ...
Article
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The soil-borne plant pathogens cause serious yield losses and are difficult to control. In suppressive soils, disease incidence remains low regardless of the presence of the pathogen, the host plant, and favorable environmental conditions. The potential to improve natural soil disease suppressiveness through agricultural management practices would enable sustainable and resilient crop production systems. Our aim was to study the impact of autumn tillage methods and crop sequence on the soil carbon status, fungistasis and yield in boreal climate. The disease suppression was improved by the long-term reduced and no tillage management practices with and without crop rotation. Compared to the conventional plowing, the non-inversion tillage systems were shown to change the vertical distribution of soil carbon fractions and the amount of microbial biomass by concentrating them on the soil surface. Crop sequence and the choice of tillage method had a combined effect on soil organic carbon (SOC) sequestration. The improved general disease suppression had a positive correlation with the labile carbon status and microbial biomass. From the most common Fusarium species, the predominantly saprophytic F. avenaceum was more abundant under non-inversion practice, whereas the opposite was true for the pathogenic ones. Our findings furthermore demonstrated the correlation of the soil fungistasis laboratory assay results and the prevalence of the pathogenic test fungus Fusarium culmorum on the crop cereals in the field. Our results indicate that optimized management strategies have potential to improve microbial related soil fungistasis in boreal climate.
... Metagenomic analyses can be used to identify associations of microorganisms present in a soil sample [67]. With such knowledge, the soil could be improved by inoculating specific microorganism species [48,68] and better understanding the association between plants and beneficial microbes in the rhizosphere [69] (Figure 2). However, plant-soil interactions are complex and highly dependent on environmental parameters. ...
Article
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One of the most important challenges facing current and future generations is how climate change and continuous population growth adversely affect food security. To address this, the food system needs a complete transformation where more is produced in non-optimal and space-limited areas while reducing negative environmental impacts. Fruits and vegetables, essential for human health, are high-value-added crops, which are grown in both greenhouses and open field environments. Here, we review potential practices to reduce the impact of climate variation and ecosystem damages on fruit and vegetable crop yield, as well as highlight current bottlenecks for indoor and outdoor agrosystems. To obtain sustainability, high-tech greenhouses are increasingly important and biotechnological means are becoming instrumental in designing the crops of tomorrow. We discuss key traits that need to be studied to improve agrosystem sustainability and fruit yield.
... Field crops may be contaminated with enteric bacterial pathogens and the sources of contamination during the pre-harvest stages are soil, feces, irrigation water, insecticides, dust, insects, manure and wild or domestic animals (Mostafidi et al, 2020). While during the postharvest stages could be contaminated by contact with polluted water, human carriers, harvesting equipment, and transport containers (Wang and Li, 2019). The most dangerous sources of rice contamination are biological and chemical contamination such as coliform, E-coli, molds and yeasts, mycotoxins, heavy metals and pesticides (Al-Shuhaib et al, 2020). ...
Article
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This study was included the estimation of a total number of bacteria (TB), a total number of coliform (TC), E. coli and molds and yeasts in 39 irrigation water samples, 75 soil samples, 75 paddy samples and 75 rice samples, in addition to estimation of aflatoxin in 75 rice samples. Three fields of each province, Diyala and Salah Al-Din were used to collect samples. Iraqi Quality Standardization (IQS) and Food and Drug Administration (FDA) were considered the limits for microbiological analyses. High-Performance Liquid Chromatography (HPLC) was used to determine aflatoxin, and the Commission of the European Communities (CEC) was considered the limits, 4 µg/kg. The results showed that all irrigation water samples were exceeded the permissible limit for total coliform, molds and yeasts, while all soil and paddy samples were exceeded for total bacteria, total coliform and molds and yeasts. Rice samples were exceeded for only molds and yeasts. E-Coli in soil and rice was less than 3 bacteria/g, which was the detection limit, while in water and paddy was less than the FDA limit. The molds and yeasts counts were very high, for example, molds and yeasts of paddy and rice were ranged from (2.06-21.5) x10 7 cfu/ml, (1.20-12.0) x 10 6 cfu/g, respectively, while the limit was10 2-10 4 .The number of samples that exceeded the permissible limit of total aflatoxin was 66 samples out of the 75 rice samples and the highest detected value was 16.40 µg/kg. In conclusion, rice samples were considered unsafe for human consumption from the fields and irrigation water and soil were the sources of the contamination therefore treatment for irrigation water should be strongly considered.
... The application of the PGPR can affect the content of essential metal elements (e.g., Fe, Zn) in grains. In fact, the rhizosphere's microbes may regulate multiple biological processes and help in plant growth promotion and nutrient acquisition or be associated with plant responses against biotic and abiotic stresses, owing to the fact that they assist plants in producing hormones, siderophores, and other inhibitory chemicals [41,42]. ...
Article
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The indiscriminate use of hazardous chemical fertilizers can be reduced by applying eco-friendly smart farming technologies, such as biofertilizers. The effects of five different types of plant growth-promoting rhizobacteria (PGPR), including Fla-wheat (F), Barvar-2 (B), Nitroxin (N1), Nitrokara (N2), and SWRI, and their integration with chemical fertilizers (50% and/or 100% need-based N, P, and Zn) on the quantitative and qualitative traits of a rainfed wheat cultivar were investigated. Field experiments, in the form of randomized complete block design (RCBD) with four replications, were conducted at the Qamloo Dryland Agricultural Research Station in Kurdistan Province, Iran, in three cropping seasons (2016–2017, 2017–2018, and 2018–2019). All the investigated characteristics of rainfed wheat were significantly affected by the integrated application of PGPR chemical fertilizers. The grain yield of treated plants with F, B, N1, and N2 PGPR plus 50% of need-based chemical fertilizers was increased by 28%, 28%, 37%, and 33%, respectively, compared with the noninoculated control. Compared with the noninoculated control, the grain protein content was increased by 0.54%, 0.88%, and 0.34% through the integrated application of F, N1, and N2 PGPR plus 50% of need-based chemical fertilizers, respectively. A combination of Nitroxin PGPR and 100% of need-based chemical fertilizers was the best treatment to increase the grain yield (56%) and grain protein content (1%) of the Azar-2 rainfed wheat cultivar. The results of this 3-year field study showed that the integrated nutrient management of PGPR-need-based N, P, and Zn chemical fertilizers can be considered a crop management tactic to increase the yield and quality of rainfed wheat and reduce chemical fertilization and subsequent environmental pollution and could be useful in terms of sustainable rainfed crop production.
... Control group, bare soil in conventional tillage methods; organic mulch group, soils treated with organic mulch for 1 year, 1.5 years and 2 years. The Scheffe's value cutoff was 0.95, ***p ≤ 0.001, **0.001 < p ≤ 0.01, and *0.01 < p ≤ 0.05 to soilborne pathogenic fungi[32,33]. Wu et al. highlighted the close association between replant disease and the variations in structure and potential functions of rhizosphere bacterial community[4]. Yang et al. indicated that soil microbial diversity had a strong effect on tobacco wilt disease level ...
Article
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Background Organic mulch is an important management practice in agricultural production to improve soil quality, control crop pests and diseases and increase the biodiversity of soil microecosystem. However, the information about soil microbial diversity and composition in litchi plantation response to organic mulch and its attribution to litchi downy blight severity was limited. This study aimed to investigate the effect of organic mulch on litchi downy blight, and evaluate the biodiversity and antimicrobial potential of soil microbial community of litchi plantation soils under organic mulch. Results Organic mulch could significantly suppress the disease incidence in the litchi plantation, and with a reduction of 37.74% to 85.66%. As a result of high-throughput 16S rRNA and ITS rDNA gene illumine sequencing, significantly higher bacterial and fungal community diversity indexes were found in organic mulch soils, the relative abundance of norank f norank o Vicinamibacterales, norank f Vicinamibacteraceae, norank f Xanthobacteraceae, Unclassified c sordariomycetes, Aspergillus and Thermomyces were significant more than that in control soils. Isolation and analysis of antagonistic microorganism showed that 29 antagonistic bacteria strains and 37 antagonistic fungi strains were unique for mulching soils. Conclusions Thus, we believe that organic mulch has a positive regulatory effect on the litchi downy blight and the soil microbial communities, and so, is more suitable for litchi plantation.
... The bacteria Ralstonia solanacearum and R. pseudosolanacearum induce vascular wilt in hundreds of plant species. These pathogens can survive in the soil for many years, as specialized resistance structures, including sclerotia (Athelia, Macrophomina, Rhizoctonia, Sclerotinia, Stromatinia, and Verticillium), chlamydospores (Fusarium, Phytophthora nicotianae, and Thielaviopsis), oospores (Phytophthora and Pythium), eggs and cysts (Meloidogyne, Pratylenchus, Heterodera, and Globodera), or non-culturable forms, starved cells, PC-type, and biofilms (Ralstonia species) (Singh et al., 2015;Wang and Li, 2019;Serrano-Pérez et al., 2017;Panth et al., 2020). ...
Article
Anaerobic soil disinfestation (ASD) is an ecological alternative to chemical soil fumigation. The method consists in incorporating easily decomposable organic materials into the soil, followed by irrigation to saturation and soil cover with impermeable plastic. Cereal brans, molasses, ethanol, and vegetable wastes are the main sources of carbon used in ASD. The soil remains covered from 3 to 10 weeks. Accumulation of toxic anaerobic decomposition products, antagonism by anaerobic organisms, lack of oxygen and the combination of all these factors are the main mechanisms of action of the technique against plant pathogens. Here, we reviewed the potential of ASD in the management of plant-pathogenic fungi, bacteria and nematodes.
... The structure and functions of soil microbial community are closely related to soil quality and ecosystem stability and sustainability, which are crucial for plant health and productivity [22]. Various studies demonstrated the alteration of soil microbial community was closely associated with soil suppressiveness to soilborne pathogenic fungi [23,24]. Wu et al. highlighted the close association between replant disease and the variations in structure and potential functions of rhizosphere bacterial community [25]. ...
Preprint
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Background: Organic mulching is an important management practice in agricultural production to improve soil quality, control crop pests and diseases and increase the biodiversity of soil microecosystem. However, the information about soil microbial diversity and composition in litchi plantation response to organic mulching and its attribution to litchi downy blight severity was limited. This study aimed to investigate the effect of organic mulching on litchi downy blight, and evaluate the biodiversity and antimicrobial potential of soil microbial community of litchi plantation soils under organic mulching. Results: Organic mulching could decrease the disease incidence in the litchi plantation. As a result of high-throughput 16S rRNA and ITS rDNA gene illumine sequencing, higher bacterial and fungal community diversity indexes were found in organic mulching soils, the relative abundance of norank f norank o Vicinamibacterales, norank f Vicinamibacteraceae, norank f Xanthobacteraceae, Unclassified c sordariomycetes, Aspergillus and Thermomyces were significant more than that in control soils. Isolation and analysis of antagonistic microorganism showed that 29 antagonistic bacteria strains and 37 antagonistic fungi strains were unique for mulching soils. Conclusions: Thus, we believe that organic mulching has a positive regulatory effect on the litchi downy blight and the soil microbial communities, and so, is more suitable for litchi plantation.
... The structure and functions of soil microbial community are closely related to soil quality and ecosystem stability and sustainability, which are crucial for plant health and productivity [22]. Various studies demonstrated the alteration of soil microbial community was closely associated with soil suppressiveness to soilborne pathogenic fungi [23,24]. Wu et al. highlighted the close association between replant disease and the variations in structure and potential functions of rhizosphere bacterial community [25]. ...
Preprint
Full-text available
Organic mulching is an important management practice in agricultural production to improve soil quality, control crop pests and diseases and increase the biodiversity of soil microecosystem. However, the information about soil microbial diversity and composition in litchi plantation response to organic mulching and its attribution to litchi downy blight severity was limited. This study aimed to investigate the effect of organic mulching on litchi downy blight, and evaluate the biodiversity and antimicrobial potential of soil microbial community of litchi plantation soils under organic mulching. Our results showed that organic mulching could decrease the disease incidence in the litchi plantation. As a result of high-throughput 16S rRNA and ITS rDNA gene illumine sequencing, higher bacterial and fungal community diversity indexes were found in organic mulching soils, the relative abundance of norank f norank o Vicinamibacterales, norank f Vicinamibacteraceae, norank f Xanthobacteraceae, Unclassified c sordariomycetes, Aspergillus and Thermomyces were significant more than that in control soils. Isolation and analysis of antagonistic microorganism showed that 29 antagonistic bacteria strains and 37 antagonistic fungi strains were unique for mulching soils. Thus, we believe that organic mulching has a positive regulatory effect on the litchi downy blight and the soil microbial communities, and so, is more suitable for litchi plantation.
... Although plant biomass has been found to be a reliable estimate of plant fitness (Younginger et al. 2017), other benefits to plant fitness could be provided by soil inoculations, even when no differences in plant biomass are detected. For example, mycorrhizal fungi and other soil microbes increase plant resilience to drought, provide protection against pathogens, improve plant chemical defenses, and increase tolerance to abiotic stresses, such as from pollutants (e.g., Delavaux et al. 2017;Wang & Li 2019). Finally, because the impact of soil microbes on plant growth is known to be dynamic and can vary with the life stage of the plant (Johnson et al. 1997), benefits of inocula not detected in the short-term could still be observed in longer-term experiments, and vice versa. ...
Article
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The severely degraded soils at abandoned mine lands present several environmental challenges, including extreme pH, nutrient deficiency, and compaction, which can limit plant growth. Amending soils with biochar and/or mycorrhizal fungi may attenuate these constraints. However, the efficacy of amendments for improving the establishment of native plant species in restorations can be context dependent; pairing the right plant species with the right amendment is crucial to the success of restoration goals. In a greenhouse experiment, we evaluated the growth responses of two native plant species in soils collected from the Formosa Mine Superfund Site (Riddle, Oregon, USA). Seedlings of Elymus glaucus and Pseudotsuga menziesii were grown in tailings amended with biochar, locally‐collected rhizosphere soil containing a suite of soil microorganisms including mycorrhizal fungi, a combination of biochar and rhizosphere soil, or were unamended. We hypothesized that (1) individual amendments would increase plant biomass compared to controls and (2) that the co‐amended treatments would have a synergistic effect on plant growth. Instead, we detected no effect of rhizosphere soil or the co‐amendment on the growth of either plant species and found that biochar reduced the shoot biomass and leaf chlorophyll content of E. glaucus. Despite the lack of growth response, we observed significant rates of mycorrhizal colonization in the plants amended with local rhizosphere soil, demonstrating that locally‐sourced fungi can survive and proliferate in the amended Formosa tailings. Thus, inoculated seedlings of native plant species could provide essential ground cover and long‐term habitat for developing mycorrhizal communities in mine tailings. This article is protected by copyright. All rights reserved.
... These microbial communities have the ability to adapt to the various environmental conditions established for the purpose of sustainable crop production (Keswani et al., 2019). Therefore, an understanding of and the targeted modification of soil microorganisms may provide new strategies for sustainable agricultural system management (Wang and Li, 2019). ...
Article
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Soil-borne diseases cause serious economic losses in agriculture. Managing diseases with microbial preparations is an excellent approach to soil-borne disease prevention. However, microbial preparations often exhibit unstable effects, limiting their large-scale application. This review introduces and summarizes disease-suppressive soils, the relationship between carbon sources and the microbial community, and the application of human microbial preparation concepts to plant microbial preparations. We also propose an innovative synthetic microbial community assembly strategy with synergistic prebiotics to promote healthy plant growth and resistance to disease. In this review, a new approach is proposed to improve traditional microbial preparations; provide a better understanding of the relationships among carbon sources, beneficial microorganisms and plants; and lay a theoretical foundation for developing new microbial preparations.
... Several recent studies have argued for alternative approaches to harness beneficial microbes for crop growth and protection that are not (only) based on bioinoculations, but that are based on steering the local rhizosphere microbiome [113][114][115][116]. For example, crop rotation which is mostly designed to minimize the build-up of crop-specific pathogens (i.e., avoiding negative legacies), could be used for building up positive soil legacies that can steer soil microbial communities towards ones that benefit crop growth, e.g., by harbouring a larger fraction of biota able to induce ISR. ...
Article
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Plant protection with beneficial microbes is considered to be a promising alternative to chemical control of pests and pathogens. Beneficial microbes can boost plant defences via induced systemic resistance (ISR), enhancing plant resistance against future biotic stresses. Although the use of ISR-inducing microbes in agriculture seems promising, the activation of ISR is context-dependent: it often occurs only under particular biotic and abiotic conditions, thus making its use unpredictable and hindering its application. Although major breakthroughs in research on mechanistic aspects of ISR have been reported, ISR research is mainly conducted under highly controlled conditions, differing from those in agricultural systems. This forms one of the bottlenecks for the development of applications based on ISR-inducing microbes in commercial agriculture. We propose an approach that explicitly incorporates context-dependent factors in ISR research to improve the predictability of ISR induction under environmentally variable conditions. Here, we highlight how abiotic and biotic factors influence plant–microbe interactions in the context of ISR. We also discuss the need to raise awareness in harnessing interdisciplinary efforts between researchers and stakeholders partaking in the development of applications involving ISR-inducing microbes for sustainable agriculture.
... Numerous strategies have been applied to manage and control soil-borne plant diseases (Dignam et al. 2019;Huang et al. 2019a;Qiu et al. 2012). However, green production processes require reduced application of pesticides, such as soil fumigants, and the adoption of more sustainable strategies, such as biological control (Adnan et al. 2019;Wang and Li 2019). Comprehensive epidemiological research demonstrating the effects of multiple abiotic and biotic factors on soil-borne pathogen dynamics is required before such sustainable strategies can be adopted at a large scale in the management of soil-borne plant diseases. ...
Article
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AimsDetermining the soil factors that drive the dynamics of soil-borne pathogens is an essential step toward the formulation and implementation of strategies for the control of plant diseases.Methods We sampled 48 healthy and infected soils in peanut fields from six counties in Eastern China to explore the relationships between soil multifunctionality, microbial communities, and peanut stem rot pathogen, Athelia rolfsii.ResultsThe results showed that peanut stem rot infection did not affect soil microbial richness, but it increased soil multifunctionality, altered the microbial community composition, and decreased the complexity of microbial co-occurrence networks significantly. Soil biotic and abiotic factors had markedly effects on A. rolfsii, and specific soil functions and microbial taxa were significantly associated with A. rolfsii abundance. Soil multifunctionality and microbial community compositions negatively affected A. rolfsii abundance, while the effects of bacterial and fungal richness were contrasting for healthy and infected soils. Longitude and latitude indirectly and positively affected A. rolfsii abundance.Conclusions The results demonstrate that soil multifunctionality and microbial communities play a vital role in regulating the dynamics of peanut stem rot pathogen, which could enhance our understanding of the relationships between soil factors, pathogen dynamics, and plant health.
... Favoriser des modes de production s'inscrivant dans une démarche agroécologique Promouvoir une agriculture qui offre une diversité de produits de qualité, qui stocke du carbone dans les sols et fournit des produits animaux basés sur la diversité des plantes, des paysages et des organismes du sol, ainsi que le renforcement des synergies entre cultures et élevage (Garrett et al., 2020), suppose un changement de paradigme majeur, plaçant la santé du sol (Geisen et al., 2019) au coeur de la transition, et l'élevage comme une activité de « support » (Eldridge et Delgado-Baquerizo, 2017). Une agriculture basée sur la santé du sol (Wang et Li, 2019) contribue à la santé des plantes, des animaux, de la planète et à la santé humaine. Elle ne repose pas uniquement sur l'adoption de technologies permettant de réduire les impacts dans tel ou tel domaine en appliquant « le bon produit, au bon moment, au bon endroit et à la bonne dose » (Therond et al., 2017). ...
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Depuis le milieu du XX e siècle, les impacts des activités humaines sur les écosystèmes sont croissants. À l’érosion de la biodiversité et au dérèglement climatique, ainsi qu’au développement de maladies chroniques que constituent l’obésité et le diabète, s’ajoute désormais la pandémie du coronavirus. Il s’agit d’un ensemble de crises environnementales ou sanitaires qui résultent pour partie de facteurs communs et dont les impacts peuvent se conjuguer et s’amplifier. Dans ce contexte inédit, nos modes de production, transformation, distribution et consommation des aliments sont particulièrement interrogés. Ils sont à l’origine d’une part importante des émissions de gaz à effet de serre, participent à la destruction de certains habitats naturels réservoirs d’agents pathogènes et contribuent à l’émergence de maladies chroniques chez l’homme. De ce fait, la nécessité d’une transition de notre système alimentaire est une idée qui fait consensus, même si le choix des changements à opérer concrètement pose de nombreuses questions. À travers une approche systémique de « santé globale », rendant compte de l’interdépendance de l’état de santé de l’Homme, des animaux et des écosystèmes dans lesquels ils évoluent, nous montrons qu’il faut prioriser aussi bien les enjeux environnementaux que de santé pour mener à bien ces arbitrages. Nous montrons qu’il est possible de faire des choix doublement vertueux pour l’environnement et la santé en transformant les modes de production, de transformation, de distribution et de consommation des aliments : réorienter l’élevage, abaisser le degré de transformation des aliments, diversifier les modes de distribution et « végétaliser » notre assiette. Ces changements participent à la territorialisation du système alimentaire.
... Favoriser des modes de production s'inscrivant dans une démarche agroécologique Promouvoir une agriculture qui offre une diversité de produits de qualité, qui stocke du carbone dans les sols et fournit des produits animaux basés sur la diversité des plantes, des paysages et des organismes du sol, ainsi que le renforcement des synergies entre cultures et élevage (Garrett et al., 2020), suppose un changement de paradigme majeur, plaçant la santé du sol (Geisen et al., 2019) au coeur de la transition, et l'élevage comme une activité de « support » (Eldridge et Delgado-Baquerizo, 2017). Une agriculture basée sur la santé du sol (Wang et Li, 2019) contribue à la santé des plantes, des animaux, de la planète et à la santé humaine. Elle ne repose pas uniquement sur l'adoption de technologies permettant de réduire les impacts dans tel ou tel domaine en appliquant « le bon produit, au bon moment, au bon endroit et à la bonne dose » (Therond et al., 2017). ...
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Depuis le milieu du XXe siècle, les impacts des activités humaines sur les écosystèmes sont croissants. À l’érosion de la biodiversité et au dérèglement climatique, ainsi qu’au développement de maladies chroniques que constituent l’obésité et le diabète, s’ajoute désormais la pandémie du coronavirus. Il s’agit d’un ensemble de crises environnementales ou sanitaires qui résultent pour partie de facteurs communs et dont les impacts peuvent se conjuguer et s’amplifier. Dans ce contexte inédit, nos modes de production, transformation, distribution et consommation des aliments sont particulièrement interrogés. Ils sont à l’origine d’une part importante des émissions de gaz à effet de serre, participent à la destruction de certains habitats naturels réservoirs d’agents pathogènes et contribuent à l’émergence de maladies chroniques chez l’homme. De ce fait, la nécessité d’une transition de notre système alimentaire est une idée qui fait consensus, même si le choix des changements à opérer concrètement pose de nombreuses questions. À travers une approche systémique de « santé globale », rendant compte de l’interdépendance de l’état de santé de l’Homme, des animaux et des écosystèmes dans lesquels ils évoluent, nous montrons qu’il faut prioriser aussi bien les enjeux environnementaux que de santé pour mener à bien ces arbitrages. Nous montrons qu’il est possible de faire des choix doublement vertueux pour l’environnement et la santé en transformant les modes de production, de transformation, de distribution et de consommation des aliments : réorienter l’élevage, abaisser le degré de transformation des aliments, diversifier les modes de distribution et « végétaliser » notre assiette. Ces changements participent à la territorialisation du système alimentaire.
... Results from contemporary analyses reveal that the action of specific soil micro-biome may have a momentous role in defeating soil-borne pathogens and lastly result in the development of the soil system resilience (Wang et al., 2019). AM fungi have the propensity to lessen impairment caused by soil-borne pathogenic fungi, nematodes, and bacteria. ...
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... The plant microbiome is a key determinant of plant growth, development and health. The interactions between plants and soil microorganisms play key roles in maintaining soil quality and ecosystem sustainability (Kwak et al., 2018;Wang and Li, 2019). Plant roots influence soil microbial community assembly and alter the relative abundance of beneficial, harmful and neutral microorganisms, which in turn exert positive or negative effects on plant growth and resistance (Bakker et al., 2018;Stringlis et al., 2018;Zhalnina et al., 2018;Rolfe et al., 2019). ...
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Rehmannia glutinosa, a perennial medicinal plant, suffers from severe replant disease under consecutive monoculture. The rhizosphere microbiome is vital for soil suppressiveness to diseases and for plant health. Moreover, N-acyl homoserine lactone (AHL)-mediated quorum sensing (QS) regulates diverse behavior in rhizosphere-inhabiting and plant pathogenic bacteria. The dynamics of short-chain AHL-mediated QS bacteria driven by consecutive monoculture and its relationships with R. glutinosa replant disease were explored in this study. The screening of QS bacteria showed that 65 out of 200 strains (32.5%) randomly selected from newly planted soil of R. glutinosa were detected as QS bacteria, mainly consisting of Pseudomonas spp. (55.4%). By contrast, 34 out of 200 (17%) strains from the diseased replant soil were detected as QS bacteria, mainly consisting of Enterobacteriaceae (73.5%). Functional analysis showed most of the QS bacteria belonging to the Pseudomonas genus showed strong antagonistic activities against Fusarium oxysporum or Aspergillus flavus, two main causal agents of R. glutinosa root rot disease. However, the QS strains dominant in the replant soil caused severe wilt disease in the tissue culture seedlings of R. glutinosa. Microbial growth assays demonstrated a concentration-dependent inhibitory effect on the growth of beneficial QS bacteria (i.e., Pseudomonas brassicacearum) by a phenolic acid mixture identified in the root exudates of R. glutinosa, but the opposite was true for harmful QS bacteria (i.e., Enterobacter spp.). Furthermore, it was found that the population of quorum quenching (QQ) bacteria that could disrupt the beneficial P. brassicacearum SZ50 QS system was significantly higher in the replant soil than in the newly planted soil. Most of these QQ bacteria in the replant soil were detected as Acinetobacter spp. The growth of specific QQ bacteria could be promoted by a phenolic acid mixture at a ratio similar to that found in the R. glutinosa rhizosphere. Moreover, these quorum-quenching bacteria showed strong pathogenicity toward the tissue culture seedlings of R. glutinosa. In conclusion, consecutive monoculture of R. glutinosa contributed to the imbalance between beneficial and harmful short-chain AHL-mediated QS bacteria in the rhizosphere, which was mediated not only by specific root exudates but also by the QQ bacterial community.
... Many microbiome studies focus on isolated environments, such as the gut of a single animal or the roots of a particular plant. Several insightful and detailed reviews have synthesized discipline-specific knowledge related to plant-associated (Chaudhary et al. 2017, Compant et al. 2019, Saleem et al. 2019, terrestrial (Wang and Li 2019), and aquatic , Zeglin 2015 microbiomes. Reviews have also focused on the response of systemspecific microbiomes to environmental change (Hawkes and Keitt 2015, Dubey et al. 2019, Jansson and Hofmockel 2020. ...
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Plant, soil, and aquatic microbiomes interact, but scientists often study them independently. Integrating knowledge across these traditionally separate subdisciplines will generate better understanding of microbial ecological properties. Interactions among plant, soil, and aquatic microbiomes, as well as anthropogenic factors, influence important ecosystem processes, including greenhouse gas fluxes, crop production, nonnative species control, and nutrient flux from terrestrial to aquatic habitats. Terrestrial microbiomes influence nutrient retention and particle movement, thereby influencing the composition and functioning of aquatic microbiomes, which, themselves, govern water quality, and the potential for harmful algal blooms. Understanding how microbiomes drive links among terrestrial (plant and soil) and aquatic habitats will inform management decisions influencing ecosystem services. In the present article, we synthesize knowledge of microbiomes from traditionally disparate fields and how they mediate connections across physically separated systems. We identify knowledge gaps currently limiting our abilities to actualize microbiome management approaches for addressing environmental problems and optimize ecosystem services.
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The soil microbiome is crucial in determining contemporary realistic conditions for future terrestrial ecological and evolutionary development. However, the precise mechanism between the fecal deposition in livestock grazing and changes in the soil microbiome remains unknown. This is the first in-depth study of bacterial and fungal taxonomic changes of excrement contaminated soils in the plateau (>3,500 m). This suggests the functional shifts towards a harmful-dominated soil microbiome. According to our findings, excrement contamination significantly reduced the soil bacterial and fungal diversity and richness. Furthermore, a continuous decrease in the relative abundance of microorganisms was associated with nutrient cycling, soil pollution purification, and root-soil stability with the increasing degree of excrement contamination. In comparison, soil pathogens were found to have the opposite trend in the scenario, further deteriorating normal soil function and system resilience. Such colonization and succession of the microbiome might provide an important potential theoretical instruction for microbiome-based soil health protection measures in the plateau of China.
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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.
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Although the application of inorganic fertilizer is a widespread agronomic practice used to boost soil productivity and crop yields, the effects on the soil microbiome and the metabolic mechanisms involved in the high-yield response of crops to long-term fertilization remain poorly described. In this study, an integrated metagenomic and metabolomic analysis was used for the first time to explore the mechanism of crop yield response to the 20-year application of nitrogen-phosphorus-potassium fertilizer in a subtropical agroecosystem in southwest China. Soil bacterial and fungal communities were monitored using 16S rRNA (bacteria) and ITS1 full-length gene (fungi) amplicon sequencing technology, and metabolites were detected using LC-MS. The results revealed that long-term fertilization shaped the composition of bacteria and fungi to increase crop yields, in addition to providing nutrients. Long-term fertilization significantly increased the relative abundance of PGPR and AMF and promoted the secretion of soil metabolites, like carbohydrates, organic acids, and organic nitrogen compounds, which were primarily enriched in amino acid metabolism pathways. The increases in carbon and nitrogen sources and bioactive substances in soil promoted increases in plant biomass, which maintained soil quality and production capacity. The findings highlighted the importance of soil metabolites in maintaining soil productivity as well as crop yields, and proposed that regulating key metabolites could increase crop yields in agroecosystems.
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Microorganisms play an important role in plant growth, health and ecological function. It is necessary to explore the microbial community because of the significant ecological and economic value of apples (Malus x domestica). However, the related bacterial communities in different ecological habitats are not clear in the unique scion/rootstock combinations of apples. In this study, the Illumina Miseq platform was used to analyze the bacterial communities in different niches (bulk soil, rhizosphere soil and roots) of two scion/rootstock combinations (Fuji/Malus xiaojinensis Cheng et Jiang (Mx) and Fuji/Malus baccata (L.) Borkh. (Mb)). The relationship between the microbial community, soil properties, and plant characters was explored. The results showed that the diversity of the bacterial community decreased from bulk soil to rhizosphere soil and then to roots. In addition, at the phylum level, Proteobacteria, Actinobacteria and Acitinobacteria were dominant and had notable divergence in different ecological niches. Distinct niches had remarkable effects on the diversity and composition of the bacterial community according to PCoA. The rootstock genotype had an effect on the bacterial composition but no effect on the diversity. pH, soil organic matter (SOM), alkaline hydrolyzable nitrogen (AN) were the main factor affecting the structure of bacterial community in rhizosphere soil, as shown by Pearson analysis. Bacteria taxa in the roots were affected by starch, fructose, sucrose and sorbitol. This study showed the microbial community structure in different ecological niches of different scion/rootstock combinations and provided some evidence for understanding the microbial-plant interaction of apple rootstocks.
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This study aims to increase Bacillus and Streptomyces antagonistic activity against the root rot and wilt diseases of pulses caused by Macrophomina phaseolina and Fusarium oxysporum f. sp. udum, respectively. To increase antagonistic action, Bacillus subtilis BRBac4, Bacillus siamensis BRBac21, and Streptomyces cavourensis BRAcB10 were subjected to random mutagenesis using varying doses of gamma irradiation (0.5–3.0 kGy). Following the irradiation, 250 bacterial colonies were chosen at random for each antagonistic strain and their effects against pathogens were evaluated in a plate assay. The ERIC, BOX, and random amplified polymorphic studies demonstrated a clear distinction between mutant and wild-type strains. When mutants were compared to wild-type strains, they showed improved plant growth-promoting characteristics and hydrolytic enzyme activity. The disease suppression potential of the selected mutants, B. subtilis BRBac4-M6, B. siamensisi BRBac21-M10, and S. cavourensis BRAcB10-M2, was tested in green gram, black gram, and red gram. The combined inoculation of B. siamensis BRBac21-M10 and S. cavourensis BRAcB10-M2 reduced the incidence of root rot and wilt disease. The same treatment also increased the activity of the defensive enzymes peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase. These findings suggested that gamma-induced mutation can be exploited effectively to improve the biocontrol characteristics of Bacillus and Streptomyces. Following the field testing, a combined bio-formulation of these two bacteria may be utilised to address wilt and root-rot pathogens in pulses.
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Cadmium (Cd) and dichlorodiphenyltrichloroethane (DDT) are frequently detected in agricultural soils, which poses a threat to public health. This study investigated the effects of inoculation of king grass with Piriformospora indica on the remediation of soils co-contaminated with Cd and DDTs. After treatment for 90 days, the dry shoot and root biomass of king grass inoculated with P. indica markedly increased by 13.0–15.8% and 24.1–46.4%, respectively, compared with those of uninoculated plants. Inoculation with P. indica also increased the uptake of Cd and DDTs by shoots and roots of king grass. The removal efficiency of Cd and DDTs from soils reached 4.88–17.4% and 48.4–51.0%, respectively, in the presence of king grass inoculated with P. indica. Under three Cd–DDTs contamination conditions, root secretion of organic acids, alcohol, and polyamines was distinctively stimulated by P. indica inoculation of king grass compared with planting king grass alone. After phytoremediation, changes in soil bacterial and fungal community composition occurred at different contamination levels. Overall, the results showed that king grass associated with P. indica can be adopted for phytoextraction of Cd and DDTs from moderately contaminated soils by regulating root excretion and reshaping rhizosphere microbial community structure.
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As a common natural phenomenon, corpse decomposition may lead to serious environmental pollution such as nitrogen pollution. However, less is known about antibiotic resistance genes (ARGs), an emerging contaminant, during corpse degradation. Here, ARGs and microbiome in three soil types (black, red and yellow soil) have been investigated between experimental and control groups based on next-generation sequencing and high-throughput quantitative PCR techniques. We found that the absolute abundance of total ARGs and mobile genetic elements (MGEs) in the experimental groups were respectively enriched 536.96 and 240.60 times in different soil types, and the number of ARGs in experimental groups was 7–25 more than that in control groups. For experimental groups, the distribution of ARGs was distinct in different soil types, but sulfonamide resistance genes were always enriched. Corpse decomposition was a primary determinant for ARGs profiles. Microbiome, NH4⁺ concentrates and pH also significantly affected ARGs profiles. Nevertheless, soil types had few effects on ARGs. For soil microbiome, some genera were elevated in experimental groups such as the Ignatzschineria and Myroides. The alpha diversity is decreased in experimental groups and microbial community structures are different between treatments. Additionally, the Escherichia and Neisseria were potential pathogens elevated in experimental groups. Network analysis indicated that most of ARGs like sulfonamide and multidrug resistance genes presented strong positively correlations with NH4⁺ concentrates and pH, and some genera like Ignatzschineria and Dysgonomonas were positively correlated with several ARGs such as aminoglycoside and sulfonamide resistance genes. Our study reveals a law of ARGs’ enrichment markedly during corpse decomposing in different soil types, and these ARGs contaminant maintaining in environment may pose a potential threat to environmental safety and human health.
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Recent advances in genome engineering are revolutionizing crop research and plant breeding. The ability to make specific modifications to a plant’s genetic material creates opportunities for rapid development of elite cultivars with desired traits. The plant genome can be altered in several ways, including targeted introduction of nucleotide changes, deleting DNA segments, introducing exogenous DNA fragments and epigenetic modifications. Targeted changes are mediated by sequence specific nucleases (SSNs), such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspersed short palindromic repeats)-Cas (CRISPR associated protein) systems. Recent advances in engineering chimeric Cas nucleases fused to base editing enzymes permit for even greater precision in base editing and control over gene expression. In addition to gene editing technologies, improvement in delivery systems of exogenous DNA into plant cells have increased the rate of successful gene editing events. Regeneration of fertile plants containing the desired edits remains challenging; however, manipulation of embryogenesis-related genes such as BABY BOOM (BBM) has been shown to facilitate regeneration through tissue culture, often a major hurdle in recalcitrant cultivars. Epigenome reprogramming for improved crop performance is another possibility for future breeders, with recent studies on MutS HOMOLOG 1 (MSH1) demonstrating epigenetic-dependent hybrid vigor in several crops. While these technologies offer plant breeders new tools in creating high yielding, better adapted crop varieties, constantly evolving government policy regarding the cultivation of plants containing transgenes may impede the widespread adoption of some of these techniques. This chapter summarizes advances in genome editing tools and discusses the future of these techniques for crop improvement.
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Manipulating the plant-root microbiota has the potential to reduce plant stress and promote their growth and production in harsh conditions. Community composition and activity of plant-roots microbiota can be either beneficial or deleterious to plant health. Shifting this equilibrium could then strongly affect plant productivity in anthropized areas. In this study, we tested whether repeated bioaugmentation with Proteobacteria influenced plant productivity and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons (PHCs). A mesocosm experiment was performed in randomized block design with two factors: (1) presence or absence of four plants species collected from a sedimentation basin of a former petrochemical plant, and (2) bioaugmentation or not with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over 4 months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess microbial community structures of sediments from planted or unplanted microcosms. Our results showed that while bioaugmentation caused a significant shift in microbial communities, presence of plant and their species identity had a stronger influence on the structure of the microbiome in PHCs contaminated sediments. The outcome of this study provides knowledge on the diversity and behavior of rhizosphere microbes associated with indigenous plants following repeated bioaugmentation, underlining the importance of plant selection in order to facilitate their efficient management, in order to accelerate processes of land reclamation.
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Tomato variety Hawaii 7996 is resistant to the soil-borne pathogen Ralstonia solanacearum, whereas the Moneymaker variety is susceptible to the pathogen. To evaluate whether plant-associated microorganisms have a role in disease resistance, we analyzed the rhizosphere microbiomes of both varieties in a mesocosm experiment. Microbiome structures differed between the two cultivars. Transplantation of rhizosphere microbiota from resistant plants suppressed disease symptoms in susceptible plants. Comparative analyses of rhizosphere metagenomes from resistant and susceptible plants enabled the identification and assembly of a flavobacterial genome that was far more abundant in the resistant plant rhizosphere microbiome than in that of the susceptible plant. We cultivated this flavobacterium, named TRM1, and found that it could suppress R. solanacearum-disease development in a susceptible plant in pot experiments. Our findings reveal a role for native microbiota in protecting plants from microbial pathogens, and our approach charts a path toward the development of probiotics to ameliorate plant diseases.
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This study aims at characterisation of the impact of Chaetomium globosum on copper stress resistance of maize seedlings. Higher levels of copper treatment decreased maize dry weight and induced a marked increase in osmotic solutes, antioxidant enzyme activity and the level of lipid peroxidation. On the other hand, addition of the endophytic C. globosum alleviated the toxic effect of copper on maize growth. The combination of copper sulphate and Chaetomium increased seedling dry weight, osmotic solute content and antioxidant enzyme activity compared to copper sulphate alone, while lipid peroxidation levels were also decreased. The fungal scavenger system might be important for supporting the ability of maize seedlings to resist copper toxicity.
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Contamination of water, air, and soil by hazardous toxic substances is one of the major problems faced all over the world. The role of microorganism in the detoxification of soil and environment is distinct and well known. Mycoremediation is an attractive technology in which fungi are used to break down or degrade hazardous toxic substances into less toxic or nontoxic forms. Fungi mostly used as mycoremediator are Pleurotus ostreatus, Rhizopus arrhizus, Phanerochaete chrysosporium, P. sordida, Trametes hirsuta, T. versicolor, Lentinus tigrinus, L. edodes, etc. Its application falls into two categories: in situ and ex situ. The in situ methods treat the contaminated soil in the location in which it is found, whereas ex situ processes require excavation of contaminated soil before they can be put to bioremediation. The present waste disposal and treatment method does not seem to solve the problem of environmental degradation and soil depletion very effectively. Therefore, there is a need to seek alternative means of remediating the contaminants for sustainable development. Hence, in such a situation, mycoremediation is advisable to detoxify the polluted soil and environment with less use of chemicals, energy, and time. However, extensive studies are needed for exploration of fungi as a potential mycoremediator in order to attain agricultural sustainability.
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Sclerotium rolfsii Sacc. is a destructive soilborne fungal pathogen with a wide host range that includes peanuts. Biological control offers an interesting alternative to fungicides for sustainable management of soilborne diseases. The current investigation is aimed at evaluating one potential biocontrol agent Streptomyces sp. RP1A-12 for growth promotion and the management of peanut stem rot disease caused by S. rolfsii under field conditions. Preliminary studies conducted under in vitro and greenhouse conditions showed promising results against the stem rot pathogen. Further in vitro and pot experiments conducted to assess Streptomyces sp. RP1A-12 for its growth promoting abilities using whole organisms have shown an increase in seed germination, root and shoot length. Other parameters like nodule number and plant biomass were also significantly increased over control treatments indicating that the test bioagent possesses growth promoting abilities along with disease suppression capabilities. Subsequently field studies were carried out for two consecutive rainy seasons. The bioagent was applied as whole organism and partially purified crude metabolites. Results indicate the bioagent reduced stem rot disease incidence by 64–67% and 22–49% respectively in two field trials conducted with notable increase in yield. Partially purified Streptomyces sp. RP1A-12 metabolites exhibited an even greater effect in reducing the incidence and severity of stem rot compared to the pathogen inoculated control.
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Suppressive composts represent a sustainable approach to combat soil-borne plant pathogens and an alternative to the ineffective chemical fungicides used against those. Nevertheless, suppressiveness to plant pathogens and reliability of composts is often inconsistent with unpredictable effects. While suppressiveness is usually attributed to the compost’s microorganisms, the mechanisms governing microbial recruitment by the roots and the composition of selected microbial communities are not fully elucidated. Herein, the purpose of the study was to evaluate the impact of a compost on tomato plant growth and its suppressiveness against Fusarium oxysporum f. sp. lycopersici (Foxl) and Verticillium dahliae (Vd). First, growth parameters of tomato plants grown in sterile peat-based substrates including 20% and 30% sterile compost (80P/20C-ST and 70P/30C-ST) or non-sterile compost (80P/20C and 70P/30C) were evaluated in a growth room experiment. Plant height, total leaf surface, fresh and dry weight of plants grown in the non-sterile compost mixes were increased compared to the plants grown in the sterile compost substrates, indicating the plant growth promoting activity of the compost’s microorganisms. Subsequently, compost’s suppressiveness against Foxl and Vd was evaluated with pathogenicity experiments on tomato plants grown in 70P/30C-ST and 70P/30C substrates. Disease intensity was significantly less in plants grown in the non-sterile compost than those grown in the sterile compost substrate; AUDPC was 2.3 and 1.4-fold less for Foxl and Vd respectively. Moreover, fungal quantification in planta demonstrated reduced colonization in plants grown in the non-sterile mixture. To further investigate these findings, we characterized the culturable microbiome attracted by the roots compared to the unplanted compost. Bacteria and fungi isolated from unplanted compost and the rhizosphere of plants were sequence-identified. Community-level analysis revealed differential microbial communities between the compost and the rhizosphere, suggesting a clear effect of the plant in the microbiome assembly. Proteobacteria and Actinobacteria were highly enriched in the rhizosphere whereas Firmicutes were strongly represented in both compartments with Bacillus being the most abundant species. Our results shed light on the composition of a microbial consortium that could protect plants against the wilt pathogens of tomato and improve plant overall health.
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Copper-based antimicrobial compounds are widely used to control plant bacterial pathogens. Pathogens have adapted in response to this selective pressure. Xanthomonas citri pv. citri, a major citrus pathogen causing Asiatic citrus canker, was first reported to carry plasmid-encoded copper resistance in Argentina. This phenotype was conferred by the copLAB gene system. The emergence of resistant strains has since been reported in Réunion and Martinique. Using microsatellite-based genotyping and copLAB PCR, we demonstrated that the genetic structure of the copper-resistant strains from these three regions was made up of two distant clusters and varied for the detection of copLAB amplicons. In order to investigate this pattern more closely, we sequenced six copper-resistant X. citri pv. citri strains from Argentina, Martinique and Réunion, together with reference copper-resistant Xanthomonas and Stenotrophomonas strains using long-read sequencing technology. Genes involved in copper resistance were found to be strain-dependent with the novel identification in X. citri pv. citri of copABCD and a cus heavy metal efflux resistance-nodulation-division system. The genes providing the adaptive trait were part of a mobile genetic element similar to Tn3-like transposons and included in a conjugative plasmid. This indicates the system's great versatility. The mining of all available bacterial genomes suggested that, within the bacterial community, the spread of copper resistance associated to mobile elements and their plasmid environments was primarily restricted to the Xanthomonadaceae family. This article is protected by copyright. All rights reserved.
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Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization.
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Damping off, caused by Rhizoctonia solani, is one of the most important cotton diseases. This soil pathogen, survives in organic matter and can be transmitted by seeds. The objective of this study was evaluate the effect of seeds treatment with a fungicides for control of damping off, caused by R. solani. The evaluated treatments were as follows: 1) untreated check without inoculation; 2) untreated check with inoculation; 3) fluazinam + thiophanate-methyl (115,5 + 17,33 g.100 kg -1 seeds); 4) fluazinam + thiophanate-methyl (150,5 + 22,58 g.100 kg -1 seeds); 5) fluazinam + thiophanate-methyl (185,5 + 27,83 g.100 kg -1 seeds); 6) pencycuron (75 g.100 kg -1 seeds); 7) tolylflouanid (100 g.100 kg -1 seeds): 8) carbendazin + thiram (90 + 120 g.100 kg -1 seeds) and 9) fludioxonil (5 g.100 kg -1 seeds). It was evaluated the plant population at 7 and 26 days after sowing; incidence and severity of the disease; seedling height; root length and dry weight at 26 days afeter sowing. The fungicide fluazinam + thiophanate methyl doses 115,5 + 17,33 g i.a. 100 -1 kg seeds, 150,5 + 22,58 g i.a. 100 -1 kg seeds and the fungicide tolylfluanid doses 100 g i.a. 100 -1 kg seeds, showed control efficiency of cotton dumping off caused by Rhizoctonia solani, can be recommended to this pathogen control. Seedlings of untreated check with inoculation showed short height, characterizing less start development of the culture, been recommended the seed treatment with fungicides.
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The utilization of organic amendments has been proposed to decrease the incidence of plant diseases caused by soilborne pathogens. In this work we reviewed reports concerning disease suppressiveness by the new organic amendment biochar. A total of 12 papers were included in this analysis with 61 experimental case studies. The effect of biochar amendment was suppressive in 85%, nonsignificant in 12%, with only 3% of studies reporting a significant increase of disease incidence. Biochar can be effective against both airborne (e.g. Botrytis cinerea, different species of powdery mildew) and soilborne pathogens (e.g. Fusarium spp., Phytophthora spp., Rhizoctonia solani). Five different mechanisms have been proposed to explain biochar disease suppression: (i) induction of systemic resistance in host plants; (ii) enhanced abundance and activities of beneficial microbes, including mycorrhizal fungi; (iii) modification of soil quality in terms of nutrient availability and abiotic conditions such as liming effect; (iv) direct fungitoxic effect of biochar; (v) sorption of allelopathic, phytotoxic compounds that can directly harm plant roots and thus promote pathogen attacks. Potential side-effects of biochar have been reported, like the possibility of absorbing agrochemicals like herbicides, insecticides and fungicides, thus reducing their efficacy. Results from this review demonstrate that biochar amendments have great potential but, until now, not enough studies are available for a widespread adoption of biochar as a soil amendment in today’s agricultural systems. More investigations on the mechanisms underlying biochar disease suppression, as well as long-term field experiments, are needed to make biochar a safe, effective and affordable tool for the control of plant pathogens.
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Biochar as soil amendment can increase soil carbon (C) sequestration and mineral nutrients; however, some of its soluble elements may also be unintentionally released during the application. In this work, eight types of biochars were derived from herbaceous, woody, and waste (tailing, manure, sludge) biomass feedstocks through slow pyrolysis at 600 °C in N2. The elemental composition, specific surface area, morphology, crystalline phases, thermal stability, surface functional groups, and pH of the point of zero charge of the biochars were determined using various methods. These properties varied significantly among the tested biochars, suggesting that feedstock type played an important role in controlling their properties. Laboratory release and toxicity characteristic leaching procedure extraction experiments were conducted to evaluate the potential release of nutritious and toxic element from biochars. Results showed that all the biochars released nutritious elements and thus, may be beneficial to plants when amended in soils. In general, biochars produced from herbaceous and woody biomass feedstocks showed low risks of releasing toxic elements. Biochar derived from sludge, however, might present ecotoxicological challenges for its environmental applications due to the release of toxic elements, such as heavy metals.
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Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copA. In this study, a local BLASTN method using a copA database built in this study was developed to recover full-length putative copA sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putative copA sequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selected copA sequences detected in the tailings metagenome showed that topology of the copA phylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development of copA diversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explore copA (and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses.
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Fluorescent Pseudomonas spp. isolated from the roots of healthy tomato plants were screened for their antagonistic activities against Sclerotium rolfsii, Alternaria alternata and Fusarium solani, three phytopathogenic fungi of tomato and pepper. They were tested for phosphate solubilization ability and production of siderophores, hydrolytic enzymes, indole 3-acetic acid and hydrogen cyanid. The isolates were also characterized based on biochemical (API 20NE test) and genotypic (ERIC-PCR fingerprinting) features. A Pseudomonas sp. strain denoted PCI2 was chosen as a potential candidate for controlling tomato damping-off caused by Sclerotium rolfsii. PCI2 was identified at the genus level with a 16S rDNA partial sequence analysis and its phylogenetic relationship with previously characterized Pseudomonas species was determined. PCI2 clustered with the P. putida species. Growth chamber studies resulted in statistically significant increases in plant stand (29%) as well as in root dry weight (58%). PCI2 was able to establish itself and survive in tomato rhizosphere after 40 days, following planting of bacterized seeds. PCI2 is a potential biological control agent that may contribute to the protection of tomato plants against damping-off caused by S. rolfsii.
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Heavy metals in soil are naturally occurring but may be enhanced by anthropogenic activities such as mining. Bio-accumulation of heavy metals in the food chain, following their uptake to plants can increase the ecotoxicological risks associated with remediation of contaminated soils using plants. In the current experiment sugar cane straw-derived biochar (BC), produced at 700 °C, was applied to a heavy metal contaminated mine soil at 1.5%, 3.0% and 5.0% (w/w). Jack bean (Canavalia ensiformis) and Mucuna aterrima were grown in pots containing soil and biochar mixtures, and control pots without biochar. Pore water was sampled from each pot to confirm the effects of biochar on metal solubility, whilst soils were analyzed by DTPA extraction to confirm available metal concentrations. Leaves were sampled for SEM analysis to detect possible morphological and anatomical changes. The application of BC decreased the available concentrations of Cd, Pb and Zn in 56, 50 and 54% respectively, in the mine contaminated soil leading to a consistent reduction in the concentration of Zn in the pore water (1st collect: 99 to 39 μg L(-1), 2nd: 97 to 57 μg L(-1) and 3rd: 71 to 12 μg L(-1)). The application of BC reduced the uptake of Cd, Pb and Zn by plants with the jack bean translocating high proportions of metals (especially Cd) to shoots. Metals were also taken up by Mucuna aterrima but translocation to shoot was more limited than for jack bean. There were no differences in the internal structures of leaves observed by scanning electron microscopy. This study indicates that biochar application during mine soil remediation reduce plant concentrations of potential toxic metals. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Bioremediation uses microbial metabolism in the presence of optimum environmental conditions and sufficient nutrients to breakdown contaminants notably petroleum hydrocarbons. We reviewed technologies for carrying out bioremediation and observed that biotechnological approaches that are designed to carry out remediation have received a great deal of attention in recent years. Biostimulation (meaning the addition of limiting nutrients to support microbial growth) and Bioaugmentation (meaning the addition of living cells capable of degradation) studies have enjoyed a heavy presence in literature and reviews of these technologies focusing on the technical aspects are very few if at all available. At times, nutrient application alone or augmenting with microbes is not sufficient enough for remediation leading to a simultaneous approach. Recent studies show that a combination of both approaches is equally feasible but not explicitly more beneficial. Evidently, selection of a technology hinges on site specific requirements such as availability of microorganisms capable of degradation in sufficient quantities, nutrient availability to support microbial growth and proliferation as well as environmental parameters such as temperature in combination with duration of exposure. This review focuses on these technologies and efforts are directed towards eventual manipulation of the processes of remediation all geared towards making bioremediation technically and economically viable for comprehensive treatment of petroleum hydrocarbon contaminated soils.
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This study is part of an effort to identify new biological control agents with broad spectrum activity against pathogenic soilborne fungi and pests. New strains of Pseudomonas spp. were isolated from agricultural soils, river silt, and rhizosphere soils from herbarium specimens. Provisional species assignments based on 16S ribosomal DNA typing were: Pseudomonas borealis, Pseudomonas chlororaphis, Pseudomonas fluorescens, Pseudomonas mandelii, Pseudomonas marginalis, Pseudomonas poae, Pseudomonas putida, Pseudomonas syringae and Pseudomonas vranovensis. We evaluated the strains for activity against root rot pathogens of wheat, with the view to discovery and deployment of new suppressive activities. Our objectives were to compare the strains relative to: (i) production of antifungal metabolites, (ii) suppression of Rhizoctonia and Pythium damage in greenhouse assays, (iii) plant growth promotion, and (iv) ability to colonize the wheat rhizosphere. Colonization assays showed that 11 strains rapidly established and maintained rhizosphere populations of ⩾log 5 CFU g−1 root. Strains 14B2R, 15G2R, 29G9R, 39A2R, 48G9R and Wood3R reduced disease symptoms of both Rhizoctonia solani AG-8 and Pythium ultimum, and the latter four also suppressed Rhizoctonia oryzae and Pythium irregulare. Four strains increased seedling shoot length and root weight but these growth promotion effects were correlated to disease suppression only for two strains. Finally, the strains differed in demonstrated and potential antifungal metabolite activities, indicating that no single factor could be correlated to disease suppression. We have identified several strains for genome sequencing and for long-term development of integrated management of soilborne diseases of wheat.
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Soil amendment with biochar is thought to confer multiple benefits to plants including induction of systemic resistance to plant pathogens. Pathogens in the genus Phytophthora cause damaging diseases of woody species throughout the world. The objective of this study was to test 1) whether biochar amendment induces resistance to canker causing Phytophthora pathogens; and 2) how this resistance is related to the amount of biochar amendment in two common landscape tree species: Quercus rubra (L.) and Acer rubrum (L.). Seedlings of Q. rubra and A. rubrum were planted in peatmoss-based potting mix uniformly amended with 0%, 5%, 10%, or 20% biochar by volume. Plants in each treatment group were stem wound-inoculated with an isolate of Phytophthora cinnamomi Rands (host: Q. rubra) or P. cactorum (Leb. and Cohn) Schröeter (host: A. rubrum) using standard agar-plug inoculation procedures. Amendment of potting media with 5% biochar reduced horizontal expansion of lesions in both hosts, whereas the same treatment significantly reduced vertical expansion of lesions in A. rubrum (P < 0.05). In addition, 5% biochar resulted in a higher midday stem water potential in Q. rubra (P = 0.066) and significantly greater stem biomass in A. rubrum compared with inoculated control plants (0% biochar, P < 0.05). Our results suggest that biochar amendment has the potential to alleviate disease progression and physiological stress caused by Phytophthora canker pathogens and there is likely an optimal level of biochar incorporation into the root media beyond which the effects may be less pronounced.
Article
Tn5 insertion mutants of Pseudomonas cepacia G4 that were unable to degrade trichloroethylene (TCE), toluene, or phenol or to transform m-trifluoromethyl phenol (TFMP) to 7,7,7-trifluoro-2-hydroxy-6-oxo-2,4-heptadienoic acid (TFHA) were produced. Spontaneous reversion to growth on phenol or toluene as the sole source of carbon was observed in one mutant strain, G4 5223, at a frequency of approximately 1 x 10(-4) per generation. One such revertant, G4 5223-PR1, metabolized TFMP to TFHA and degraded TCE. Unlike wild-type G4, G4 5223-PR1 constitutively metabolized both TFMP and TCE without aromatic induction. G4 5223-PR1 also degraded cis-1,2-dichloroethylene, trans-1,2-dichloroethylene, and 1,1-dichloroethylene and oxidized naphthalene to alpha naphthol constitutively. G4 5223-PR1 exhibited a slight retardation in growth rate at TCE concentrations of > or = 530 microM, whereas G4 (which was unable to metabolize TCE under the same noninducing growth conditions) remained unaffected. The constitutive degradative phenotype of G4 5223-PR1 was completely stable through 100 generations of nonselective growth.
Article
Application of EPTC ( S -ethyl dipropylthiocarbamate) at 3.4 and 4.5 kg/ha in 1972 increased root rot severity and reduced navy bean ( Phaseolus vulgaris L.) yields in soil with an artificial root rot [ Fusarium solani (Mart.) Appel and Wr. f. Phaseoli (Burk.) Snyd. and Hans.] inoculum level. EPTC at 3.4 kg/ha and chloroamben (3-amino-2,5-dichlorobenzoic acid) at 3.4 kg/ha in 1973 caused the greatest root rot severity and greatest decrease in yield. Dinoseb (2- sec -butyl-4,6-dinitrophenol) and fluorodifen ( p -nitrophenyl α,α,α-trifluoro-2-nitro- p -tolyl ether) at 5 kg/ha interacted with root rot less than the other herbicides assayed. In the growth chamber at 23 C, EPTC at 3.4 kg/ha and alachlor [2-chloro-2′,6′-diethyl- N -(methoxymethyl) acetanilide] at 2.8 kg/ha applied to navy bean grown in soil infested with F. solani reduced plant growth. Root rot injury was most severe in plants treated with EPTC at 20 C ambient temperature. Navy bean growth was reduced as the level of F. solani chlamydospore inoculum increased in the presence of EPTC.
Article
An orchard field trial was conducted to assess the utility of reduced rate Brassicaceae seed meal (SM) amendment in concert with specific rootstock genotypes for effective control of apple replant disease. Three amendment rates of a 1:1 formulation of Brassica juncea-Sinapis alba SM were compared with preplant 1,3-dichloropropene/chloropicrin soil fumigation for disease control efficacy. When applied at the highest rate (6.6 t ha-1) in the spring of planting, SM caused significant phytotoxicity and tree mortality, which was higher for Gala/M.26 than for Gala/G.41 but was not observed at SM application rates of 2.2 or 4.4 t ha-1. SM treatment resulted in growth and yield increases of Gala/M.26 and Gala/G.41 trees in a manner similar to the fumigation treatment and significantly greater than the no treatment control. Tree growth in soils treated with SM at 4.4 t ha-1 was similar or superior to that obtained with SM at 6.6 t ha-1 and superior to that attained at an SM application rate of 2.2 t ha-1. Soil fumigation and all SM treatments reduced Pratylenchus penetrans root infestation relative to the control treatment at the end of the initial growing season. Lesion nematode root densities in the fumigation treatment, but not SM treatments, rapidly recovered and were indistinguishable from the control at the end of the second growing season. Soil fumigation and all SM treatments significantly suppressed Pythium spp. root infection relative to the control. Trees grafted to rootstock G.41 possessed lower P. penetrans root densities relative to trees grafted to rootstock M.26. One year after planting, composition of microbial communities from SM-amended soils was distinct from those detected in control and fumigated soils, and the differences were amplified with increasing SM application rate. Specific fungal and bacterial phyla associated with suppression of plant pathogens were more abundant in SM-treated soil relative to the control, and they were similar in abundance in 4.4- and 6.6-t ha-1 SM treatments. Findings from this study demonstrated that use of the appropriate apple rootstock genotype will allow for effective replant disease control at SM application rates significantly less than that utilized previously (6.6 t ha-1).
Book
Our capacity to maintain world food production depends heavily on the thin layer of soil covering the Earth's surface. The health of this soil determines whether crops can grow successfully, whether a farm business is profitable and whether an enterprise is sustainable in the long term. Farmers are generally aware of the physical and chemical factors that limit the productivity of their soils but often do not recognise that soil microbes and the soil fauna play a major role in achieving healthy soils and healthy crops. Soil Health, Soil Biology, Soilborne Diseases and Sustainable Agriculture provides readily understandable information about the bacteria, fungi, nematodes and other soil organisms that not only harm food crops but also help them take up water and nutrients and protect them from root diseases. Complete with illustrations and practical case studies, it provides growers and their consultants with holistic solutions for building an active and diverse soil biological community capable of improving soil structure, enhancing plant nutrient uptake and suppressing root pests and pathogens. The book is written by scientists with many years' experience developing sustainable crop production practices in the grains, vegetable, sugarcane, grazing and horticultural industries. This book will be useful for: growers, consultants, agronomists and soil chemists, extension personnel working in the grains, livestock, sugarcane and horticultural industries, professionals running courses in soil health/biological farming, and students taking university courses in soil science, ecology, microbiology, plant pathology and other biological sciences.
Article
Pre-plant soil application of a Brassica juncea/Sinapis alba seed meal formulation (SM) at a rate of 6.6 t ha-1 alters composition of the orchard soil microbiome in a manner that yields sustainable long-term suppression of soil-borne pathogens in apple production systems. However, the cost of SM amendment has hindered the adoption of this tactic to manage apple replant disease in commercial orchards. Greenhouse trials were conducted to assess the effect of reduced SM application rate in concert with apple rootstock genotype on structure of the rhizosphere microbiome and associated disease control outcomes. At all application rates assessed, SM treatment increased tree growth and reduced disease development relative to the control. In general, total tree biomass and leader shoot length were similar in soils treated with SM at 4.4 or 6.6 t ha-1 irrespective of rootstock genotype. Equivalent increase in tree biomass when cultivated in soil treated at the lowest and highest SM amendment rate was attained when used in conjunction with G.41 or G.210 apple rootstocks. Suppression of Pythium spp. or Pratylenchus penetrans root densities was similar at all SM application rates. When cultivated in non-treated replant orchard soil, Geneva rootstocks (G.41 and G.210) exhibited lower levels of Pythium spp. and P. penetrans root colonization relative to Malling rootstocks (M.9 and MM.106). For a given rootstock, structure of the rhizosphere microbiome was similar in SM at 4.4 and 6.6 t ha-1 treated soils. G.41 and G.210 rootstocks, but not M.9 or MM.106, cultivated in SM at 2.2 t ha-1 treated soil possessed a rhizosphere bacterial community structure that differed significantly from the control. Findings indicate that effective control of apple replant disease may be attained at lower SM amendment rates than employed previously with lower effective rates possible when integrated with tolerant rootstock genotypes such as G.41 or G.210.
Article
Metal hyperaccumulation from the soil by certain plant species can serve as a defence trait. Such hyperaccumulation might impact the expression of organic defences. Here, the induction of the phytoalexin camalexin after leaf infection with a pathogenic fungus was investigated in plants of the facultative hyperaccumulator Arabidopsis halleri grown on unamended and metal-amended soil. Reduced camalexin induction was expected in plants grown in metal-amended soil. Plants were grown for twelve weeks on soil, which was either amended with high concentrations of Zn and Cd or kept unamended, and the final leaf concentration of Zn and Cd was determined. Conidia of the pathogenic fungus Alternaria brassicae were applied on mechanically damaged leaves. Leaves were harvested after 24 h and 48 h, and the amount of induced camalexin was quantified. Plants grown on metal-amended soil hyperaccumulated Zn and Cd and induced significantly less camalexin than plants grown on unamended soils after pathogen infestation. This suggests a physiological trade-off between metal hyperaccumulation and an induced antifungal organic defence, which has, to our knowledge, not been observed before in A. halleri for other organic defence compounds. This phenomenon might partly be explained by limitations in sulphur pools and/or the interruption of (phytohormonal) defence signalling due to metal hyperaccumulation. This work highlights the importance of considering defences elicited by antagonists from various guilds when studying plant organic defence responses to specific abiotic environments.
Article
Leaf spot disease causes devastating damage to oil palm seedlings and reduces both quality and quantity of the produced seedlings. This study aimed to apply the selected microorganisms Streptomyces hygroscopicus subsp. angustmyceticus NR8-2, Trichoderma harzianum TM2/1, and endophytic Trichoderma V76-12, to the control of leaf spot disease caused by Curvularia oryzae on oil palm leaves, in vitro, in vivo and in field conditions. The isolate V76-12 inhibited the growth of C. oryzae the most at 85.71% inhibition, followed by the isolates TM2/1 (75.71%) and NR8-2 (72.50%) in dual culture tests. Volatile antifungal effects were observed for V76-12 with 68% inhibition, followed by the isolates TM2/1 (45%) and NR8-2 (10%) in a bioassay. Crude metabolites of the isolates inhibited the mycelial growth of C. oryzae in agar diffusion tests. In pot experiments, the V76-12 gave disease severity index (DSI) of about 21%, similar to that with a reference chemical (20%), whereas TM2/1 and NR8-2 gave 66% and 75%, respectively. In naturally infested cases, oil palm seedlings treated with V76-12 showed 35.33% DSI, which is statistically significantly below those obtained with TM2/1, NR8-2 and the chemical (48.67%, 53.33% and 49.33%, respectively). The control treatment without antagonistic microorganisms gave the most severe DSI at 75.33%. The results also show that treatment with the selected isolates enhanced the activities of phenylalanine ammonia-lyase (PAL), peroxidase (POD), and polyphenol oxidase (PPO) enzymes in the oil palm. The V76-12 isolate was the most effective treatment tested in reducing leaf spot disease of oil palm seedlings, due to its ability to inhibit mycelial growth in vitro, to reduce disease symptoms in vivo and in natural fields, as well as to enhance PAL, POD and PPO activities in the oil palm leaves.
Article
Sweet sorghum [Sorghum bicolor (L.) Moench] is a prospective feedstock for the growing sugar-based bioethanol industry. Charcoal rot (Macrophomina phaseolina, MP) and Fusarium stalk rot (Fusarium thapsinum, FT) are fungal diseases of sorghum that reduce sweet sorghum sugar yields. The objective of this study was to investigate the impacts of MP and FT on sweet sorghum sugar concentration and yield. Field experiments were conducted with seven parental lines and 12 hybrids in 2014 and 2015. Plants inoculated with MP, FT, and phosphate-buffered saline (control) at 14 d after anthesis were harvested at 35 d after inoculation. Disease severity was measured using the number of nodes crossed by the lesion. Juice extracted from stalks was measured for volume. Juice sugar concentration (mg/mL) of sucrose, glucose, and fructose were quantified using HPLC and sugar yield (g/plant) was computed using juice volume and sugar concentrations. Treatment effects on sucrose concentration and yield, and total sugar yield (i.e., sucrose, glucose, and fructose) were genotype-specific while the effect of treatment on the yield of total and individual sugars was environment-specific. However, the environment × treatment effect was not significant for individual sugar concentrations. Stalk rot inoculations reduced sucrose concentrations to a significantly greater degree than glucose or fructose. Reduced sucrose concentrations and yields in the hybrids after inoculation were significantly and negatively correlated with the decrease of fructose. This suggested the enhanced conversion of sucrose to fructose after MP and FT inoculation. Overall, this study provided evidence for the adverse impacts of Fusarium stalk rot and charcoal rot diseases on sweet sorghum sugar attributes. These findings emphasize the importance of breeding sweet sorghum for enhanced stalk rot tolerance.
Article
Mutualistic plant–endophyte symbioses can benefit plants by increasing host fitness through reductions in herbivory. The fungus, Chaetomium globosum strain TAMU 520, was previously isolated as an endophyte from cotton (Gossypium hirsutum) and can be re-inoculated to systemically colonize cotton plants via seed treatment. We evaluated the potential impacts of the endophyte in cotton on plant parasitic nematodes belowground, along with piercing-sucking and chewing insects aboveground. Endophytic C. globosum inhibited root-knot nematode (Meloidogyne incognita) infection and reduced female reproduction belowground. To confirm the endophytic effect of C. globosum on root-knot nematode, a contact fungicide was applied to remove soil-borne and epiphytic C. globosum. Consistent inhibition of nematode activity was observed post-fungicide treatment, with positive C. globosum colonization confirmed within plant tissues. Aboveground, endophytic C. globosum also negatively affected the fecundity of both cotton aphids (Aphis gossypii) and beet armyworms (Spodoptera exigua). Faster development rates and smaller head capsule of beet armyworm larvae were observed when fed Chaetomium-colonized plants. However, no larval weight difference was found between Chaetomium-colonized and control plants. No consistent effect on plant performance was found across experiments. Our findings illustrate how a single facultative fungal endophyte can increase plant systemic resistance against a range of invertebrate herbivores in a major crop.
Article
Soil microbiomes may be harnessed for plant health
Article
Composting can change organic chemicals and bind metals through several different mechanisms. Biological degradation, extracellular decomposition, intracellular decomosition, adsorption and volatilization. Traditional composting of nontoxic organic materials is based on proper recipe formulation, thorough mixing, aerobic composting and curing to produce a stable and mature compost for product markets in the shortest possible time at the least possible cost. Composting can be done with aerated static piles, in-vessel systems, or with windrows. Remediation via composting can be accomplished by mixing contaminated soils with fresh, high-energy feedstocks or by adding a mature, finished compost to contaminated soil. Cost for remediation with composting vary with the amount of soil to be treated, mix ratio of soil to compostables, availability and cost amendments, type of contaminant and process design.
Article
Antibiotics are among the most beneficial drugs ever introduced but their utility has been compromised by the emergence and spread of antibiotic resistant bacteria. Currently useful antibiotics impose enormous selective pressure on bacterial populations and the use and overuse of these agents has led to the evolution, in a relatively short timeframe, of multidrug-resistant pathogens capable of rapid and efficient horizontal transmission of genes encoding resistance determinants. New antibacterial drugs with novel modes of action are urgently required in order to continue the fight against infection: unfortunately, the upturn in the incidence of resistance has coincided with a marked reduction by the pharmaceutical industry in efforts to develop new agents. Even "professional" pathogens such as Staphylococcus aureus, a bacterium equipped with an impressive array of virulence effectors for damaging the host, require a reduction in the host"s defenses in order to colonize, enter tissue and cause infection. Correction of this imbalance between host and pathogen may provide a novel approach to the therapy of severe bacterial infections, by either shoring up immune defenses or modifying the bacteria at the site of infection to render them less able to survive in the host. Thus, pathogens may survive, multiply and cause infection because they are virulent or resistant to antibiotics; therapeutic agents that modify these properties in vivo may resolve infections, either alone or in combination with conventional antibiotic chemotherapy, in a way that may not readily lead to drug resistant bacterial survivors. Examples of such modifiers of the bacterial phenotype, together with other emerging approaches to the treatment of bacterial infections, are described.
Article
The effectiveness of several fungicides applied either as foliar sprays or as rooting-cube soaks was compared for control of Rhizoctonia stem rot of poinsettia during propagation. Rhizoctonia solani was introduced to the surface of rigid foam rooting cubes at the time cuttings were stuck. Benomyl at 0.3 g a.i./L, chlorothalonil at 1.8 ml a.i./L, flutolanil at 0.3 g a.i./L, iprodione at 0.6 g a.i./L, and metalaxyl + benomyl at 0.5 g a.i./L all prevented stem rot. Rooting-cube soaks of flutolanil, iprodione, and metalaxyl + benomyl were as effective as foliar sprays in disease control. Foliar sprays of quintozene at 0.45 g a.i./L and ethazole + thiophanate methyl at 0.24 g a.i./L were not as effective in control of stem rot as the other fungicides tested. Root development on cuttings treated with flutolanil and metalaxyl + benomyl was not different from the untreated, uninoculated control. Root development was intermediate with benomyl, chlorothalonil, and iprodione and poorest with quintozene and ethazole + thiophanate methyl. Untreated rooting cubes (47 cm³) were colonized by R. solani from inoculum placed on the cube surface in 2–5 days. Rooting cubes of poinsettia treated with metalaxyl + benomyl, flutolanil, and iprodione at 0.25 g a.i./L were not colonized as extensively as untreated cubes. Funigicide effectiveness in control of stem rot was related directly to the extent of colonization of rooting cubes by R. solani.
Article
Essais realises sur jeunes plants en pot (Citrus aurantium) ou sur arbres en place (Citrus paradisi) de traitements par bassinage, par badigeonnage des troncs ou par pulverisation foliaire. L'activite systemique des 2 fongicides est etudiee sur disques d'ecorce des arbres traites
Article
Root-knot nematodes were first reported in 1855 by Berkeley, who observed them causing damage on cucumbers. Until Chitwood's work in 1949, which defined 4 species and one subspecies (M. incognita acrita) within the genus Meloidogyne, the root-knot nematodes were all considered the same species, Heterodera radicola. In an 1887 paper (reprinted in 1892) Goeldi described Meloidogyne exigua, the type species of the genus. From this description, Chitwood obtained the name we currently use for the root-knot nematodes. The name Meloidogyne is of Greek origin, meaning "apple-shaped female." Approximately 100 species of Meloidogyne have been described. The most widespread and economically important species are M. incognita, M. javanica, M. arenaria, M. hapla, M. chitwoodi and M. graminicola. Root-knot nematodes are primarily tropical to sub-tropical organisms, however M. hapla and M. chitwoodi are well adapted to temperate climates. Jepson, S.B. 1987. Identification of Root-Knot Nematodes (Meloidogyne Species). CAB International, Wallingford, UK. Viaene, N.M. 1998. Management of Meloidogyne hapla on lettuce in organic soil with sudangrass as a cover crop. Plant Disease 82:945-952.
Article
Brassicaceae seed meal (SM) formulations were compared with pre-plant 1,3-dichloropropene/chloropicrin (Telone-C17®) soil fumigation for the ability to control apple replant disease and to suppress pathogen/parasite re-infestation of organic orchard soils at two sites in Washington State. Pre-plant soil fumigation and either a SM formulation consisting of either Brassica juncea/Sinapis alba or B. juncea/Brassica napus each provided similar levels of disease control during the initial growing season. Although tree growth was similar in fumigated and SM amended soil during the initial growing season, tree performance in terms of growth and yield was commonly superior in B. juncea/S. alba SM amended soil relative to that in fumigated soil at the end of four growing seasons. SM amended soils were resistant to re-infestation by Pratylenchus penetrans and Pythium spp. relative to fumigated soils and corresponded with enhanced tree performance. Phytotoxic symptoms were observed in response to SM amendment at one of two orchard sites and were dependent upon season of application and occurred in a SM formulation-specific manner. After two years, the rhizosphere microbiome in fumigated soils had reverted to one that was indistinguishable from the no-treatment control. In contrast, rhizosphere soils from the SM treatment possessed unique bacterial and fungal profiles, including specific microbial elements previously associated with suppression of plant pathogenic fungi, oomycetes and nematodes. Overall diversity of the microbiome was reduced in the SM treatment rhizosphere, suggesting that enhanced "biodiversity" was not instrumental in achieving system resistance and/or pathogen suppression.
Article
Soil suppressiveness to soilborne pathogens can evolve following the incorporation of plant residues in the soil and solarization. We studied its occurrence by assessing disease incidence and severity in sandy soil which was infested after the disinfestation treatment. Disease incidence and severity of crown and root rot in cucumber plants inoculated with Fusarium oxysporum f. sp. radicis-cucumerinum macroconidia were reduced by 20 to 80% when seedlings were planted in the tested soils 2 to 34 months after soil amendment. Residues of Diplotaxis tenuifolia (wild rocket [WR]), Artemisia dracunculus (tarragon), Salvia officinalis (sage), and Brassica oleracea var. italica (broccoli) were most effective for inducing soil suppressiveness. Effective soil suppressiveness continued to be evident after repeated inoculations and plantings in the same soil without additional treatment between inoculations. Moreover, residues of WR induced soil suppressiveness in two additional tested soils differing in their physical and chemical properties. Residues of Rosmarinus officinalis (rosemary), Coriandrum sativum (coriander), Mentha piperita (peppermint), and B. oleraceae var. botrytis (cauliflower) induced disease suppression at the first inoculated planting but not upon repeated inoculation and planting. The contribution of soil solarization to the evolution of soil suppressiveness, albeit evident, was inconsistent. Soil suppressiveness to Fusarium crown and root rot was also observed when cucumber seed were sown in soils which were initially amended with WR residues and later infested with F. oxysporum f. sp. radicis-cucumerinum chlamydospores. There is a potential for the use of plant residues for inducing soil suppressiveness and further contributing to the control of diseases caused by soilborne pathogens.
Article
Mitochondrial small subunit (mtSSU) rDNA sequences elucidated phylogenetic relationships in Neonectria Wollenw. (anamorphs = Cylindrocarpon Wollenw.; Ascomycetes, Hypocreales). Twelve isolates representing seven species in five taxonomically informal groups of Neonectria were subjected to phylogenetic analysis. Fusarium inflexum R. Schneid. (teleomorph: Gibberella) and Nectria cinnabarina (Fr.) Fr. (= Nectria s.str.) were outgroups. All of the Neonectria species formed a strongly supported clade with respect to the outgroups, indicating a single ascomycete genus for the holomorphs of Cylindrocarpon. Within the Neonectria clade there were three well-supported subclades that only partially corresponded to phenotype-defined groups. DNA sequence divergence among the twelve Neonectria isolates, 2.3-7.4%, was sufficient to resolve them. The results suggest that the mtSSU rDNA region is appropriate for phylogenetic analysis of Neonectria and Cylindrocarpon. The following new combinations are proposed: Neonectria coronata, Neonectria discophora, Neonectria neomacrospora, Neonectria radicicola, Neonectria rugulosa, Neonectria veuillotiana.
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An online lesson. http://www.apsnet.org/edcenter/intropp/lessons/fungi/Basidiomycetes/Pages/Armillaria.aspx
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Indiscriminate use of oganophosphate pesticides has made their mitigation from soil essential. Among the pesticides, chlorpyrifos is a widely used broad-spectrum organophosphate effective in controlling a variety of insects. In the present study, Pseudomonas fluorescence and Pseudomonas aeruginosa were inoculated in the fields with cotton plants to determine the role of the plant-microbe interaction in the degradation of chlorpyrifos in the contaminated plots. After 25 days of inoculation, P. fluorescence and P. aeruginosa degraded 78 and 85% of chlorpyrifos in plots without cotton plants whereas 99% degradation of chlorpyrifos was observed in soil, where cotton plants were inoculated with either Pseudomonas fluorescence or Pseudomonas aeruginosa as compared to un-inoculated control soil. REP-PCR showed an increase in population of P. fluorescence from 1.52 × 107 at the time of inoculation to 2.0 × 107 in plots without crops whereas 3.1 × 10 7 in plots with cotton plants on day 25. Similar trend was shown by the P. aeruginosa. Product formation indicated the appearance of 3, 5, 6-trichloro-2-pyridinol (TCP), the major metabolite of chlorpyrifos degradation, in the plots inoculated with P. aeruginosa, which disappeared to negligible amounts.
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