The Metagenomics of Plant Pathogen‐Suppressive Soils

Elsas, Jan Dirk van; Kielak, Anna M.; Cretoiu, Mariana Silvia

doi:10.1002/9781118010518.ch32

Cited by 4 publications

(4 citation statements)

References 46 publications

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“…Much effort has been invested in characterizing microorganisms and their genetic elements which are related to disease suppression in the bulk and rhizosphere of suppressive soils (9,35, 49,56,69). In contrast, less attention has been paid to microbial events at the site of the host-pathogen interaction-the root itself-during different stages of pathogen infection and disease development in disease-suppressive or conducive soils (62,74).…”

Section: Klein Et Al 5 Phytopathologymentioning

confidence: 98%

Soil Suppressiveness to Fusarium Disease: Shifts in Root Microbiome Associated with Reduction of Pathogen Root Colonization

Klein¹,

Ofek²,

Katan³

et al. 2013

Phytopathology®

105

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Soil suppressiveness to Fusarium disease was induced by incubating sandy soil with debris of wild rocket (WR; Diplotaxis tenuifolia) under field conditions. We studied microbial dynamics in the roots of cucumber seedlings following transplantation into WR-amended or nonamended soil, as influenced by inoculation with Fusarium oxysporum f. sp. radicis-cucumerinum. Disease symptoms initiated in nonamended soil 6 days after inoculation, compared with 14 days in WR-amended soil. Root infection by F. oxysporum f. sp. radicis-cucumerinum was quantified using real-time polymerase chain reaction (PCR). Target numbers were similar 3 days after inoculation for both WR-amended and nonamended soils, and were significantly lower (66%) 6 days after inoculation and transplanting into the suppressive (WR-amended) soil. This decrease in root colonization was correlated with a reduction in disease (60%) 21 days after inoculation and transplanting into the suppressive soil. Fungal community composition on cucumber roots was assessed using mass sequencing of fungal internal transcribed spacer gene fragments. Sequences related to F. oxysporum, Fusarium sp. 14005, Chaetomium sp. 15003, and an unclassified Ascomycota composed 96% of the total fungal sequences in all samples. The relative abundances of these major groups were highly affected by root inoculation with F. oxysporum f. sp. radicis-cucumerinum, with a 10-fold increase in F. oxysporum sequences, but were not affected by the WR amendment. Quantitative analysis and mass-sequencing methods indicated a qualitative shift in the root's bacterial community composition in suppressive soil, rather than a change in bacterial numbers. A sharp reduction in the size and root dominance of the Massilia population in suppressive soil was accompanied by a significant increase in the relative abundance of specific populations; namely, Rhizobium, Bacillus, Paenibacillus, and Streptomyces spp. Composition of the Streptomyces community shifted significantly, as determined by PCR denaturing gradient gel electrophoresis, resulting in an increase in the dominance of a specific population in suppressive soils after only 3 days. This shift was related mainly to the increase in Streptomyces humidus, a group previously described as antagonistic to phytopathogenic fungi. Thus, suitable soil amendment resulted in a shift in the root's bacterial communities, and infection by a virulent pathogen was contained by the root microbiome, leading to a reduced disease rate.

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Section: Klein Et Al 5 Phytopathologymentioning

confidence: 98%

Soil Suppressiveness to Fusarium Disease: Shifts in Root Microbiome Associated with Reduction of Pathogen Root Colonization

Klein¹,

Ofek²,

Katan³

et al. 2013

Phytopathology®

105

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“…The hypothesis of this project was that the microbiota of suppressive soils could provide reservoirs of genes involved in in situ antibiosis or antagonism (antibiotics, chitinase, etc.) [47]. In future, soil metaganenomics would be part of the needed innovations in organic agriculture and would help to better understand the biology underlying pathogen suppressive soils, maybe leading to a possible engineering of such suppressive soils.…”

Section: Organic Farming and Soil Fertilitymentioning

confidence: 99%

“…The biological properties of soil are recovered not only by minimum tillage, but also by utilization of natural, non-synthetic products; biological weed, disease and pest control; composting, mulching, intercropping etc. [45][46][47][48][49]. Crop rotation is also very important for the balance of soil microflora in organically managed fields, because various plants have a specific impact on it [50].…”

Section: Organic Farming and Soil Fertilitymentioning

confidence: 99%

Scandals

Grolleau¹,

Alain²,

Mzoughi³

2021

Organizational Dynamics

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“…These hydrocarbon utilizing bacterial isolates after exposure to crude oil respond to the presence of hydrocarbons within hours of exposure, and get adapted to the pollution [44]. A number of these bacterial species are able to degrade and use crude oil as sole carbon source because of the possession of genes borne either on the plasmid or chromosome which encode for degradative enzymes such as alkane hydroxylases.…”

Section: Talaromyces Flavus Talaromyces Emersonii Talaromyces Wortomanii Cladosporium Carionii Talaromyces Flavus Trichoderma Polysporummentioning

confidence: 99%

Culture-dependent Microbiological, and Enzyme Properties of Petroleum Hydrocarbon Contaminated Agricultural Soil in the Niger Delta

Orji

Okerentugba²,

Ibiene

2018

JEAI

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Culture-dependent microbiological and enzyme properties of petroleum hydrocarbon contaminated soil were investigated in Choba, Port Harcourt-Nigeria. Standard biological science and physicochemical procedures were adopted for all the analyses carried out. Conductivity and pH values of 177.30 µS/cm, and 5.95, respectively were observed in the polluted soil. Total Petroleum hydrocarbon, total nitrogen, total phosphorus contents were 1127mg/kg, 6.52 mg/kg, 4.23 mg/kg, respectively. The effective cation exchange capacity (ECEC) of the soil was 39.85 Kcal/mol, and the polluted Clay-Loamy soil had a redox potential of 78.70 mV. The polluted soil had a total culturable hydrocarbon utilizing bacteria and fungi counts of 8.33 x 10 5 cfu/g, and 8.9 X 10 4 cfu/g, respectively.In the polluted soil, the activities of soil dehydrogenase, catalase, and urease were 0.088

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The Metagenomics of Plant Pathogen‐Suppressive Soils

Cited by 4 publications

References 46 publications

Soil Suppressiveness to Fusarium Disease: Shifts in Root Microbiome Associated with Reduction of Pathogen Root Colonization

Soil Suppressiveness to Fusarium Disease: Shifts in Root Microbiome Associated with Reduction of Pathogen Root Colonization

Scandals

Culture-dependent Microbiological, and Enzyme Properties of Petroleum Hydrocarbon Contaminated Agricultural Soil in the Niger Delta

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