Manipulating the soil microbiome to increase soil health and plant fertility

Chaparro, Jacqueline M.; Sheflin, Amy M.; Manter, Daniel K.; Vivanco, Jorge M.

doi:10.1007/s00374-012-0691-4

Cited by 914 publications

(500 citation statements)

References 127 publications

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“…Biotic constraints such as plant root exudates (14), plant immune signaling (15), and competition from native microorganisms (4) can play important roles in shaping soil microbiomes, but, in general, soil bacterial composition follows predictable patterns based on abiotic constraints, such as physicochemical soil parameters (16)(17)(18)(19). These constraints complicate soil microbiome manipulation and may restrict our ability to alter microbiome trajectories.…”

Section: Importancementioning

confidence: 99%

Cutting Edge: IL-17–Secreting Innate Lymphoid Cells Are Essential for Host Defense against Fungal Infection

Gladiator

Wangler

Trautwein-Weidner

et al. 2013

The Journal of Immunology

338

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Soil microbiome modification may alter system function, which may enhance processes like bioremediation. In this study, we filled microcosms with gamma-irradiated soil that was reinoculated with the initial soil or cultivated bacterial subsets obtained on regular media (REG-M) or media containing crude oil (CO-M). We allowed 8 weeks for microbiome stabilization, added crude oil and monoammonium phosphate, incubated the microcosms for another 6 weeks, and then measured the biodegradation of crude oil components, bacterial taxonomy, and functional gene composition. We hypothesized that the biodegradation of targeted crude oil components would be enhanced by limiting the microbial taxa competing for resources and by specifically selecting bacteria involved in crude oil biodegradation (i.e., CO-M). Postincubation, large differences in taxonomy and functional gene composition between the three microbiome types remained, indicating that purposeful soil microbiome structuring is feasible. Although phylum-level bacterial taxonomy was constrained, operational taxonomic unit composition varied between microbiome types. Contrary to our hypothesis, the biodegradation of C 10 to C 50 hydrocarbons was highest when the original microbiome was reinoculated, despite a higher relative abundance of alkane hydroxylase genes in the CO-M microbiomes and of carbon-processing genes in the REG-M microbiomes. Despite increases in the relative abundances of genes potentially linked to hydrocarbon processing in cultivated subsets of the microbiome, reinoculation of the initial microbiome led to maximum biodegradation. IMPORTANCEIn this study, we show that it is possible to sustainably modify microbial assemblages in soil. This has implications for biotechnology, as modification of gut microbial assemblages has led to improved treatments for diseases like Clostridium difficile infection. Although the soil environment determined which major phylogenetic groups of bacteria would dominate the assemblage, we saw differences at lower levels of taxonomy and in functional gene composition (e.g., genes related to hydrocarbon degradation). Further studies are needed to determine the success of such an approach in nonsterile environments. Although the biodegradation of certain crude oil fractions was still the highest when we inoculated with the diverse initial microbiome, the possibility of discovering and establishing microbiomes that are more efficient in crude oil degradation is not precluded.O il production, oil spills, and the storage of oily wastes by the petroleum industry have led to massive releases of petroleum hydrocarbons into the environment, making them some of the most ubiquitous environmental pollutants (1). Conventional decontamination technologies such as excavation (i.e., dig and dump), incineration, and chemical treatment of contaminants are costly and may further disrupt disturbed ecosystems (2, 3). When effective, bioremediation is a cheaper and more sustainable approach to decontamination. Bioaugmentation, the addition...

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Section: Importancementioning

confidence: 99%

Cutting Edge: IL-17–Secreting Innate Lymphoid Cells Are Essential for Host Defense against Fungal Infection

Gladiator

Wangler

Trautwein-Weidner

et al. 2013

The Journal of Immunology

338

321

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“…Evidence demonstrating the close ties root exudates have on the microbial composition of the rhizosphere is mounting (Broeckling et al, 2008;Badri et al, , 2013aMicallef et al, 2009b;Chaparro et al, 2012Chaparro et al, , 2013, whereby many chemicals present in root exudates act as substrates, chemotactic or signaling molecules to orchestrate changes in microbial composition (Shaw, 1991;de Weert et al, 2002;Jain and Nainawatee, 2002;Horiuchi et al, 2005;Bais et al, 2006;Badri and Vivanco, 2009;Neal et al, 2012;Badri et al, 2013a). Recently, it was reported that the composition of Arabidopsis root exudates change following a plant developmental gradient (Chaparro et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

“…Accordingly, it was hypothesized that seedlings of roots release sugars as substrates for a wide diversity of microbes at early stages of development but as the plant ages it releases specific substrates and potentially antimicrobial compounds in an effort to select for particular microbial inhabitants of the rhizosphere (Badri et al, 2013a;Chaparro et al, 2013). This potential selection of microbes in the rhizosphere as the plant ages might be associated with the ability of beneficial microbes to suppress pathogenic ones (Mendes et al, 2011), trigger induced systemic tolerance to overcome abiotic stress (Selvakumar et al, 2012), increase the plant's innate immunity (Zamioudis and Pieterse, 2012), help in mineral nutrition (Bolan, 1991;van der Heijden et al, 2008) and in overall plant health (Berendsen et al, 2012;Chaparro et al, 2012). Here, we tested this hypothesis by analyzing the rhizosphere microbial composition of Arabidopsis by 454 pyrosequencing at four distinct physiological stages of development: seedling (four-five leaf stage), vegetative (rosette), bolting and flowering.…”

Section: Introductionmentioning

confidence: 99%

Rhizosphere microbiome assemblage is affected by plant development

2013

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There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (Po0.05) expressed at different stages of plant development. For instance, genes involved in streptomycin synthesis were significantly induced at bolting and flowering stages, presumably for disease suppression. We surmise that plants secrete blends of compounds and specific phytochemicals in the root exudates that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage.

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“…Breeding for plants that promote soil biology and chemistry, for example (McSwiney et al 2010), could become easier by applying genomic plant-breeding techniques alongside highthroughput microbiome sequencing (metagenomics) and noninvasive, below-ground plant analyses (Chaparro et al 2012). Breeding towards perennial lifestyle is another strategy for improving soil health, and is already showing great promise for improving soil health on farms (Glover et al 2010;Culman et al 2013).…”

Section: Ecosystem Servicesmentioning

confidence: 99%

Genomic breeding for food, environment and livelihoods

2015

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Land use management is a central challenge for the 21st century with unprecedented and competing demands to produce food, feed/fodder, fibre, fuel, and essential ecosystem services which sustain life. Global change requires rapid adaptation in current and emerging crops as well as in the foundation species of natural ecosystems. Revolutions in genomics and high throughput experimentation are transforming breeding so that adaptive traits in new environments can be predicted and selected more directly from germplasm collections of crops and wild species. This genomic breeding is now feasible in almost any species and has promise to help meet the need to feed and nourish over 9 billion people by 2050. Genomic techniques can accelerate our response to food security challenges of yield, quality and resilience and also address environmental security challenges. To achieve its potential there will need to be widespread and ongoing investments in the human capital to promote genomic breeding.

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Manipulating the soil microbiome to increase soil health and plant fertility

Cited by 914 publications

References 127 publications

Cutting Edge: IL-17–Secreting Innate Lymphoid Cells Are Essential for Host Defense against Fungal Infection

Cutting Edge: IL-17–Secreting Innate Lymphoid Cells Are Essential for Host Defense against Fungal Infection

Rhizosphere microbiome assemblage is affected by plant development

Genomic breeding for food, environment and livelihoods

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