Purdue team predicts next-generation microbiome research promises agricultural breakthroughs

WEST LAFAYETTE, Ind. – For thousands of years, humans have altered, often adversely and inadvertently, microbial communities in an attempt to improve agricultural crops. In recent years, knowledge about the roles played by microbes in these systems has grown rapidly, but has not yet reached the point where farmers and society have benefited.

That is about to change, according to a group of scientists at Purdue University who wrote a review of agricultural microbiome work for the journal. Natural plants published this week. This is the first review of agricultural microbiome research that comprehensively combines knowledge of plant, soil and insect microbiome work to develop an integrated portrait of the complex interactions that will come into play when scientists will attempt to exploit microbes to improve crops.

“We wanted to bring together what we know about the microbiome in an agricultural context and see if that knowledge can be translated into actionable information for farmers. ” said french lizzie, postdoctoral researcher in entomology and main author of the article. “Using emerging technologies in next-generation sequencing and digital agriculture, we are starting to integrate microbial community interactions into our understanding of agriculture as a whole, which will enable producers to work with nature to cultivate more sustainably.

Many decisions that have affected agriculture have been made without knowledge of microbiomes or how those populations of microbes would be affected. Crops selected for better yield have lost genes that help plants interact beneficially with microbes; pesticides can alter the abundance of beneficial insects and the microbes they carry; and monoculture or limited crop rotations can alter microbial diversity.

Other practices have improved the abundance and diversity of microbe populations, including improved crop rotation and cover crops. Biotech companies have developed products that can add beneficial microbes to an agricultural ecosystem, thereby reducing the need for fertilizers and pesticides. However, more work is needed to make these products viable alternatives to traditional agricultural inputs.

“Efforts focused on improving plant growth and yields have caused us to lose microbial species or the ability of plants to interact with certain beneficial microbes,” said Laramy Enders, assistant professor of entomology and corresponding author of the article. “We’ve started to learn more about the interconnected nature of these microbial communities, and looking at this from a holistic perspective, we can see opportunities to improve cultures in new ways. “

The authors believe these advances are the first steps in the development of tools that will improve our ability to customize and shape microbiomes to improve plant defenses and yields in specific crops and in specific locations.

“We are ultimately envisioning a decision tree framework that will allow growers to make management decisions based on data on appropriate practices, cultivars and microbial inoculants to optimize the health of their crops and soils for their specific region and farming system, ”they write in Nature Plants. “These are exciting times to align efforts that harness the power and complexity of all interacting sectors of crop microbiomes to fuel a future of sustainable and healthy agroecosystems. “

the Purdue Applied Microbiome Sciences The team led efforts to bring scientists together to approach microbiome research in an interdisciplinary manner. The team’s Microbiome Symposium brought together leading experts in the field on the West Lafayette campus to explore ways to use the latest data and technologies available on the microbiome.

by Purdue Ian kaplan, professor of entomology, Anjali Iyer-Pascuzzi, associate professor of botany and phytopathology, and Cindy nakatsu, Professor of agronomy, are the co-authors of the article, which was supported by Purdue Agriculture’s 2019 Raising the Visibility of Agricultural Research: 150th Anniversary Review.

Writer: Brian Wallheimer; 765-532-0233; [email protected]

Sources: Laramy Enders; 765-496-3990; [email protected]

Elizabeth French; [email protected]


Emerging Strategies for Precision Microbiome Management in Various Agroecosystems

Elizabeth French, Ian Kaplan, Anjali Iyer-Pascuzzi, Cindy H. Nakatsu and Laramy Enders


Substantial efforts to characterize the structural and functional diversity of microbial communities associated with soil, plants and insects have shed light on the complex areas of interaction of microbiomes associated with crops that contribute to healthy agroecosystems. As a result, microorganisms associated with plants have become an untapped resource for tackling the challenges of agricultural sustainability. However, despite growing interest in maximizing microbial functions for crop production, resource efficiency, and stress resistance, research has struggled to harness the beneficial properties of agricultural microbiomes to improve crop performance. Here, we present the historical arc of agricultural microbiome research, highlighting current advancements and emerging strategies for intentional microbiome manipulation to improve crop performance and sustainability. We synthesize the current practices and limitations of agricultural microbiome management and identify the main gaps in our understanding of microbe-assisted plant production. Finally, we propose research priorities that encompass a holistic view of crop microbiomes to achieve precise microbiome management that is responsive, predictive and integrative in various farming systems.

Agricultural communications: 765-494-8415;

Maureen Manier, Head of Department, [email protected]

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