Emerging strategies for precision microbiome management in diverse agroecosystems

French, Elizabeth; Kaplan, Ian; Iyer‐Pascuzzi, Anjali S.; Nakatsu, Cindy H.; Enders, Laramy

doi:10.1038/s41477-020-00830-9

Cited by 200 publications

(135 citation statements)

References 177 publications

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“…Although PGPMs naturally occur in the rhizosphere, phyllosphere and endosphere of plants, their populations are often insufficient to obtain the desired effect. Thus, these microorganisms are usually isolated from their original environment, multiplied and reintroduced as microbial inoculants (or plant probiotics) into the soil or into the plant via seed treatment, foliar spray or soil application (Naamala and Smith, 2020; French et al ., 2021).…”

Section: Major Drivers For the Development Of Microbial Tools In Agriculturementioning

confidence: 99%

“…For instance, indigenous microbial communities associated with the plant or with the soil can outcompete the introduced microbes. The inoculants can then disappear within weeks or persist at low and ineffective levels (French et al ., 2021). Other factors such as extreme climatic conditions, poor soil characteristics and the presence of environmental and soil pollutants may also work against a strain which otherwise has excellent efficacy in controlled conditions.…”

Section: Key Constraints Of the Agriculture Microbial Industrymentioning

confidence: 99%

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Realities and hopes in the application of microbial tools in agriculture

Batista

Singh

2021

Microbial Biotechnology

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Summary The use of microbial tools to sustainably increase agricultural production has received significant attention from researchers, industries and policymakers. Over the past decade, the market access and development of microbial products have been accelerated by (i) the recent advances in plant‐associated microbiome science, (ii) the pressure from consumers and policymakers for increasing crop productivity and reducing the use of agrochemicals, (iii) the rising threats of biotic and abiotic stresses, (iv) the loss of efficacy of some agrochemicals and plant breeding programs and (v) the calls for agriculture to contribute towards mitigating climate change. Although the sector is still in its infancy, the path towards effective microbial products is taking shape and the global market of these products has increased faster than that of agrochemicals. Promising results from using microbes either as biofertilizers or biopesticides have been continually reported, fuelling optimism and high expectations for the sector. However, some limitations, often related to low efficacy and inconsistent performance in field conditions, urgently need to be addressed to promote a wider use of microbial tools. We propose that advances in in situ microbiome manipulation approaches, such as the use of products containing synthetic microbial communities and novel prebiotics, have great potential to overcome some of these current constraints. Much more progress is expected in the development of microbial inoculants as areas such as synthetic biology and nano‐biotechnology advance. If key technical, translational and regulatory issues are addressed, microbial tools will not only play an important role in sustainably boosting agricultural production over the next few decades but also contribute towards other sustainable development goals, including job creation and mitigation of the impacts of climate change.

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Section: Major Drivers For the Development Of Microbial Tools In Agriculturementioning

confidence: 99%

Section: Key Constraints Of the Agriculture Microbial Industrymentioning

confidence: 99%

Realities and hopes in the application of microbial tools in agriculture

Batista

Singh

2021

Microbial Biotechnology

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“…The concept of delivering microbial consortia for plant health is moving beyond applying a handful of microbes and toward the delivery of optimised synthetic communities ( French et al, 2021 ; Trivedi et al, 2021 ). This research area is still in its early stages, but several studies show promise for disease control.…”

Section: Disease Controlmentioning

confidence: 99%

“…An alternate approach is to manipulate the crop microbiome toward one that supports plant health. There is evidence this can be achieved by modifying farm management practices (e.g., reducing agrichemical use, increasing crop diversity) ( French et al, 2021 ). Again, this area of research is also in its infancy, and significant research gaps are needed to be addressed before this approach becomes a reality.…”

Section: Disease Controlmentioning

confidence: 99%

Tackling Control of a Cosmopolitan Phytopathogen: Sclerotinia

2021

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Phytopathogenic members of the Sclerotinia genus cause widespread disease across a broad range of economically important crops. In particular, Sclerotinia sclerotiorum is considered one of the most destructive and cosmopolitan of plant pathogens. Here, were review the epidemiology of the pathogen, its economic impact on agricultural production, and measures employed toward control of disease. We review the broad approaches required to tackle Sclerotinia diseases and include cultural practices, crop genetic resistance, chemical fungicides, and biological controls. We highlight the benefits and drawbacks of each approach along with recent advances within these controls and future strategies.

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“…The plant leaf niche occupies a large surface area, and is important for the plant microbial community structure and function. The agricultural and ecological implications of plant-beneficial interactions with microbes have motivated intense investigation into the factors that shape phyllopshere microbiota (French et al, 2021). Deciphering the factors underlying the composition and dynamics of microbiome assembly is a key step towards understanding how the microbial community affects plant health and development.…”

Section: Introductionmentioning

confidence: 99%

Cytokinin- microbiome interactions regulate developmental functions

Gupta

Elkabetz

Leibman‐Markus

et al. 2021

Preprint

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The interaction of plants with the complex microbial networks that inhabit them is important for plant health. While the reliance of plants on their microbial inhabitants for defense against invading pathogens is well documented, the acquisition of data concerning the relationships between plant developmental stage or aging, and microbiome assembly, is still underway. In this work, we observed developmental-age dependent changes in the phyllopshere microbiome of tomato. The plant hormone cytokinin (CK) regulates various plant growth and developmental processes. Here, we show that age-related shifts in microbiome content vary based on content of, or sensitivity to, CK. We observed a developmental age associated decline in microbial richness and diversity, accompanied by a decline in the presence of growth promoting and resistance inducing bacilli in the phyllosphere. This decline was absent from CK-rich or CK-hypersensitive genotypes. Bacillus isolates we obtained from CK rich genotypes were found to re-program the transcriptome to support morphogenesis and alter the leaf developmental program when applied to seedlings, and enhance yield and agricultural productivity when applied to mature plants. Our results support the notion that CK-dependent effects on microbiome content support developmental functions, suggesting that these are mediated by CK in part via the bacterial community.

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Emerging strategies for precision microbiome management in diverse agroecosystems

Cited by 200 publications

References 177 publications

Realities and hopes in the application of microbial tools in agriculture

Realities and hopes in the application of microbial tools in agriculture

Tackling Control of a Cosmopolitan Phytopathogen: Sclerotinia

Cytokinin- microbiome interactions regulate developmental functions

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