Correlations between Root-Associated Microorganisms and Peach Replant Disease Symptoms in a California Soil

Yang, Jiue-in; Ruegger, Paul; McKenry, M. V.; Becker, J. Ole; Borneman, James

doi:10.1371/journal.pone.0046420

Cited by 83 publications

(56 citation statements)

References 56 publications

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“…HH01 (Lee et al 2012;Hornung et al 2013). In addition, Yang et al (2012) found that Xanthomonadaceae is one of the dominant taxa exhibiting a positive association with plant weights and suggested a possible beneficial role of this group in plant growth promotion. Deep taxonomic analyses of our results revealed that Janthinobacterium in the cotton rhizosphere was significantly lower in monocropped than control soil.…”

Section: Discussionmentioning

confidence: 98%

Declined soil suppressiveness to Fusarium oxysporum by rhizosphere microflora of cotton in soil sickness

Zhang

Ding

et al. 2015

Biol Fertil Soils

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Cotton yield and quality have been severely compromised by soil sickness throughout the primary cottongrowing regions of China. The aim of this study was to gain insight into the role of rhizosphere microbial community in governing soil sickness of cotton. Plant growth, disease resistance, root exudates, and the composition of the rhizosphere microbial community of cotton were analyzed in two different (4-and 15-year) monocropped soils and in a fallow agricultural soil (control). The monocropped soils significantly influenced cotton growth and root exudates and reduced soil suppressiveness to Fusarium wilt in bioassay experiments. Additionally, pyrosequencing of the whole internal transcribed spacers (ITS1 and ITS2) and 16S rRNA gene amplicons demonstrated clear variations in the microbial composition of cotton rhizosphere between monocropped rhizosphere soils and control soil. Specifically, monocropped soils were characterized by an increase in the abundance of fungal pathogens, including Fusarium oxysporum f. sp. vasinfectum and Verticillium dahliae, relative to the rhizosphere of control soil. Some plant-beneficial and disease-suppressive bacterial taxa, including Xanthomonadaceae, Comamonadaceae, Oxalobacteraceae, and Opitutaceae, were associated with healthy cotton. A significant correlation existed between the presence of certain amino acids (e.g., glutamic acid and alanine) and the above identified taxa, indicating that some constituents in root exudates influenced the microbial compositions of the cotton rhizosphere to manage the disease status of plant in monocropped soils. Collectively, these results suggest that pathogenic fungal build-up and a reduction in the abundance of beneficial rhizobacteria in the rhizosphere contribute to changes in soil suppressiveness to soil-borne pathogens in monocropped soils, resulting in an aggravated level of soil sickness.

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Section: Discussionmentioning

confidence: 98%

Declined soil suppressiveness to Fusarium oxysporum by rhizosphere microflora of cotton in soil sickness

Zhang

Ding

et al. 2015

Biol Fertil Soils

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“…Because of its specific action with no serious side effects and low price, R. glutinosa is one of the popular medicines used in traditional Chinese clinical practice (Wen et al 2002;Du et al 2009;Sun et al 2012;Wang et al 2013). However, its productivity declines significantly when it is grown on a field where the preceding crop was the same (Zhao and Chen, 1991;Yu and Yang, 1994), a syndrome described as ''replanting or continuous monoculture disease''; in this, a plant species inhibits the growth of its own kind through the release of toxic chemicals into the environment (Mazzola and Manici 2012;Yang et al 2012). Replanting disease was recognized as a major problem as early as 300 BCE in various plant species such as vegetables, medicinal plants, plantation crops and horticultural crops (Zhao and Chen 1991;Zhang et al 2007).…”

Section: Introductionmentioning

confidence: 99%

De novo characterization of the Rehmannia glutinosa leaf transcriptome and analysis of gene expression associated with replanting disease

Yang

Chen

et al. 2014

Mol Breeding

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The perennial herbaceous plant, Rehmannia glutinosa Libosch, is a traditional Chinese medicine because of the active extracts from its dried tuberous roots. However, R. glutinosa productivity and quality has been seriously affected by replanting (continuous monoculture) disease, which cannot at present be effectively prevented or controlled. Since very little is known about the molecular mechanism of replanting disease, we aimed to investigate transcriptional changes in replanted R. glutinosa leaves and identify genes responding to the disease. Here, we constructed a cDNA library from total RNA isolated from the mixture of leaves of the first year planted (L1) and the second year replanted R. glutinosa (L2) at the tuberous root expansion stage. We generated about 37 million high-quality reads from the cDNA library using deep sequencing and obtained 94,544 distinct sequences by de novo assembly and gap-filling. From this set, a total of 54,490 transcripts containing a complete or partial encoding region was annotated in public protein databases. Based on this resource, we screened differentially expressed genes in the L1 and L2 libraries by the digital gene expression (DGE) technique. Finally, a set of 1,954 genes was found to be differentially expressed in L2. Using bioinformatics and qRT-PCR, the 117 most strongly differentially expressed genes were considered to be prime candidates responsible for replanting disease. Functional analysis of the candidates showed that ethylene signaling was exaggerated and the genes in key metabolism pathways were abnormally expressed in L2. The study provides an important resource for further investigating the cause of replanting disease and developing methods to control or reduce its harmful effects.

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“…Pyrosequencing techniques are capable of providing a more comprehensive picture of all microbes present in a sample, including low-abundance species (La Duc et al 2012). The technique has been used in numerous studies to investigate bacterial communities in soils (Uhlik et al 2013;Xiong et al 2014;Yang et al 2012;Zhang et al 2013), and recently, a study focusing on bacterial communities using high-throughput sequencing to investigating ARD soils in China was published (Sun et al 2014a). However, to our knowledge, no studies exist in which both the bacterial and fungal communities of soils affected by ARD have been investigated by high-throughput sequencing.…”

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confidence: 99%

Rhizosphere bacteria and fungi associated with plant growth in soils of three replanted apple orchards

et al. 2015

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Background and aims High-throughput 454 pyrosequencing was applied to investigate differences in bacterial and fungal communities between replant and closely situated control non-replant (fallow) soils. Methods The V1-V3 region of the bacterial 16S rRNA gene and the ITS1 region of fungi from the different soils were sequenced using 454 pyrosequencing (Titanium chemistry), and data were analysed using the MOTHUR pipeline. Results The bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria dominated in both fallow and replant apple orchard soils, and community composition at both phylum and genus level did not significantly differ according to NP-MANOVA. The fungal phyla Ascomycota, Zygomycota and Basidiomycota were dominant, and communities also did not differ in composition at either phylum or genus level. High positive Pearson correlations with plant growth in a plant growth assay performed with apple rootstocks plantlets were detected for the bacterial genera Gp16 and Solirubrobacter (r: >0.82) and fungal genera Scutellinia, Penicillium, Lecythophora and Paecilomyces (r: >0.65). Strong negative correlations with plant growth were detected for the bacterial genera Chitinophaga and Hyphomicrobium (r: <−0.78) and the f u n ga l g en er a Ac remo ni um, F us ar iu m an d Cylindrocarpon (r: <−0.81). Conclusions Study findings are in part consistent with those of previous research, but also highlight associations between apple plants and certain microbial genera. The functional role of these genera in affecting soil health and fertility should be further investigated.

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Correlations between Root-Associated Microorganisms and Peach Replant Disease Symptoms in a California Soil

Cited by 83 publications

References 56 publications

Declined soil suppressiveness to Fusarium oxysporum by rhizosphere microflora of cotton in soil sickness

Declined soil suppressiveness to Fusarium oxysporum by rhizosphere microflora of cotton in soil sickness

De novo characterization of the Rehmannia glutinosa leaf transcriptome and analysis of gene expression associated with replanting disease

Rhizosphere bacteria and fungi associated with plant growth in soils of three replanted apple orchards

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