The plant microbiome: Exploration of plant-microbe interactions for improving agricultural productivity

Plant-associated bacteria face multiple selection pressures within their environments and have evolved countless adaptations that both depend on and shape bacterial phenotype and their interaction with plant hosts. Explaining bacterial adaptation and evolution therefore requires considering each of these forces independently as well as their interactions. In this review, we examine how bacteriophage viruses (phages) can alter the ecology and evolution of plant-associated bacterial populations and communities. This includes influencing a bacterial population's response to both abiotic and biotic selection pressures and altering ecological interactions within the microbiome and between the bacteria and host plant. We outline specific ways in which phages can alter bacterial phenotype and discuss when and how this might impact plant-microbe interactions, including for plant pathogens. Finally, we highlight key open questions in phage-bacteria-plant research and offer suggestions for future study.

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Meta-exoproteomics identifies active plant-microbe interactions operating in the rhizosphere

10.1101/2021.09.01.458574 ◽

2021 ◽

Author(s):

Ian Dennis Edmund Alan Lidbury ◽

Sebastien Raguideau ◽

Senlin Lui ◽

Andrew Murphy ◽

Richard Stark ◽

...

Keyword(s):

Protein Extraction ◽

Soil Microbial Communities ◽

Extracellular Proteins ◽

Active Fraction ◽

Bioinformatics Pipeline ◽

Brassica Napus L ◽

Soil Microbiota ◽

Microbe Interactions ◽

Clear Shift ◽

Plant Microbiome

The advance of DNA sequencing technologies has drastically changed our perception of the complexity and structure of the plant microbiome and its role in augmenting plant health. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and their specific functional role is relatively limited. Here, we combined our recently developed protein extraction method and an iterative bioinformatics pipeline to enable the capture and identification of extracellular proteins (meta-exoproteomics) expressed in the rhizosphere of Brassica spp. First, we validated our method in the laboratory by successfully identifying proteins related to the host plant (Brassica rapa) and a bacterial inoculant, Pseudomonas putida BIRD-1, revealing the latter expressed numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients. Next, we analysed natural field-soil microbial communities associated with Brassica napus L (Oil Seed rape). By combining deep-sequencing metagenomics with meta-exoproteomics, a total of 1882 proteins were identified in bulk and rhizosphere samples. Importantly, meta-exoproteomics identified a clear shift (p<0.001) in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This metabolic shift was associated with the stimulation of rhizosphere-specialised bacteria, such as Gammaproteobacteria, Betaproteobacteria and Flavobacteriia and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralisation. By providing the first meta-proteomic level assessment of the active plant microbiome at the field-scale, this study demonstrates the importance of moving past a genomic assessment of the plant microbiome in order to determine ecologically important plant: microbe interactions driving plant growth.

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Improvement of plant microbiome using inoculants for agricultural production: a sustainable approach for reducing fertilizer application

Canadian Journal of Soil Science ◽

10.1139/cjss-2019-0146 ◽

2020 ◽

pp. 1-11

Author(s):

Clement Kyei Sarpong ◽

Xiaofeng Zhang ◽

Qili Wang ◽

Wenjing Wang ◽

Zameer Hussain Jamali ◽

...

Keyword(s):

Agricultural Productivity ◽

Soil Health ◽

Mineral Resources ◽

Crop Productivity ◽

Fertilizer Application ◽

Mineral Fertilizers ◽

Microbial Inoculants ◽

Environmental Threat ◽

The Impact ◽

Plant Microbiome

The overuse of agrochemicals for agricultural productivity to meet the global food demand of the rapidly growing human population is a great environmental threat, particularly for aquatic ecosystems. Being associated intimately with plant health, growth, and productivity, the plant microbiome is emerging as a promising environmentally friendly and sustainable resource for agricultural productivity. For the past decades, our understanding of the interactions between plants and microorganisms and our knowledge of how to improve the plant microbiome by using microbial inoculants has increased significantly. A better understanding of the impact of the plant microbiome on mineral resources will benefit plant and soil health. In this review, we highlight the importance of microbial inoculants and their interactions with mineral fertilizers in enhancing crop productivity, as well as current challenges.

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Symbiosis and stress: how plant microbiomes affect host evolution

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0590 ◽

2020 ◽

Vol 375 (1808) ◽

pp. 20190590 ◽

Cited By ~ 1

Author(s):

Christine V. Hawkes ◽

James J. Bull ◽

Jennifer A. Lau

Keyword(s):

Plant Stress ◽

Partner Choice ◽

Microbial Populations ◽

Ecological Understanding ◽

Microbial Responses ◽

Microbe Interactions ◽

Plant Stress Tolerance ◽

Host Evolution ◽

Plant Microbiome

Existing paradigms for plant microevolution rarely acknowledge the potential impacts of diverse microbiomes on evolutionary processes. Many plant-associated microorganisms benefit the host via access to resources, protection from pathogens, or amelioration of abiotic stress. In doing so, they alter the plant's perception of the environment, potentially reducing the strength of selection acting on plant stress tolerance or defence traits or altering the traits that are the target of selection. We posit that the microbiome can affect plant microevolution via (1) manipulation of plant phenotypes in ways that increase plant fitness under stress and (2) direct microbial responses to the environment that benefit the plant. Both mechanisms might favour plant genotypes that attract or stimulate growth of the most responsive microbial populations or communities. We provide support for these scenarios using infectious disease and quantitative genetics models. Finally, we discuss how beneficial plant–microbiome associations can evolve if traditional mechanisms maintaining cooperation in pairwise symbioses, namely partner fidelity, partner choice and fitness alignment, also apply to the interactions between plants and diverse foliar and soil microbiomes. To understand the role of the plant microbiome in host evolution will require a broad ecological understanding of plant–microbe interactions across both space and time. This article is part of the theme issue ‘The role of the microbiome in host evolution'.

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Phytomicrobiome Studies for Combating the Abiotic Stress

Biointerface Research in Applied Chemistry ◽

10.33263/briac113.1049310509 ◽

2020 ◽

Vol 11 (3) ◽

pp. 10493-10509

Keyword(s):

Reactive Oxygen Species ◽

Cell Death ◽

Abiotic Stress ◽

Agricultural Productivity ◽

Stress Conditions ◽

Ros Production ◽

Oxygen Species ◽

Environmental Challenges ◽

Environmental Variations ◽

Plant Microbiome

Agricultural productivity is limited by the various factors of which stresses are the principal ones. The reactive oxygen species (ROS) production in different cell sections is done by protracted stress conditions. ROS outbreaks biomolecules and interrupts the unvarying mechanism of the cell that ultimately prods to cell death. Microbes, the highest normal inhabitants of diverse environments, have advanced complex physiological and metabolic mechanisms to manage with possibly toxic oxygen species produced by ecological stresses. The intricate mechanisms are involved in the plant microbiome. Increasing environmental variations during the incessant stress, growing an essential mark, and revealing plant-microbe association concerning protection against environmental challenges.

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Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights

Current Genomics ◽

10.2174/1389202921999200515140420 ◽

2020 ◽

Vol 21 (5) ◽

pp. 343-362 ◽

Cited By ~ 1

Author(s):

Minaxi Sharma ◽

Surya Sudheer ◽

Zeba Usmani ◽

Rupa Rani ◽

Pratishtha Gupta

Keyword(s):

Growth Promotion ◽

Experimental Studies ◽

Complex Nature ◽

Natural Environments ◽

Plant Microbe Interaction ◽

Sequencing Technologies ◽

Microbe Interactions ◽

Metabolic Interactions ◽

Negative Impacts ◽

Plant Microbiome

Introduction: Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions. Conclusion: This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.

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Advances in understanding modes of action of microbial bioprotectants

10.19103/as.2021.0093.01 ◽

2021 ◽

pp. 3-32

Author(s):

Gabriele Berg ◽

◽

Peter Kusstatscher ◽

Franz Stocker ◽

Ahmed Abdelfattah ◽

...

Keyword(s):

Sustainable Agriculture ◽

Growth Performance ◽

Current Knowledge ◽

Environmentally Friendly ◽

Global Scale ◽

Beneficial Effects ◽

Modes Of Action ◽

Microbiome Research ◽

Microbe Interactions ◽

Plant Microbiome

Plant-associated microorganisms are involved in important functions related to growth, performance and health of their hosts. Understanding their modes of action is important for the development and application of microbial bioprotectants and biostimulants. Recent studies have revealed manifold plant-microbe as well as pathogen-microbe interactions, which form the basis of understanding beneficial effects of plant-associated microorganisms. Microbiome research has contributed to our understanding of the modes of action of various plant-associated microorganisms. This chapter summarizes current knowledge about beneficial plant-microbe interactions, discusses recent insights into the functioning of the plant microbiome and beneficial plant-microbe networks. It shows that the use of microorganisms and the exploitation of beneficial plant–microbe interactions offer promising and environmentally-friendly strategies to achieve sustainable agriculture on a global scale.

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Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era

Microorganisms ◽

10.3390/microorganisms7080269 ◽

2019 ◽

Vol 7 (8) ◽

pp. 269 ◽

Cited By ~ 18

Author(s):

Rahul Mahadev Shelake ◽

Dibyajyoti Pramanik ◽

Jae-Yean Kim

Keyword(s):

Growth Promotion ◽

Green Revolution ◽

Trait Improvement ◽

Microbe Interactions ◽

Plant Microbiota ◽

Systematic Understanding ◽

Molecular Aspects ◽

Global Food ◽

Plant Microbiome

Plants and microbes are co-evolved and interact with each other in nature. Plant-associated microbes, often referred to as plant microbiota, are an integral part of plant life. Depending on the health effects on hosts, plant–microbe (PM) interactions are either beneficial or harmful. The role of microbiota in plant growth promotion (PGP) and protection against various stresses is well known. Recently, our knowledge of community composition of plant microbiome and significant driving factors have significantly improved. So, the use of plant microbiome is a reliable approach for a next green revolution and to meet the global food demand in sustainable and eco-friendly agriculture. An application of the multifaceted PM interactions needs the use of novel tools to know critical genetic and molecular aspects. Recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) tools are of great interest to explore PM interactions. A systematic understanding of the PM interactions will enable the application of GE tools to enhance the capacity of microbes or plants for agronomic trait improvement. This review focuses on applying GE techniques in plants or associated microbiota for discovering the fundamentals of the PM interactions, disease resistance, PGP activity, and future implications in agriculture.

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Plant-Microbe Interactions - Insights and Views for Applications in Sustainable Agriculture

Applied Science and Engineering Progress ◽

10.14416/j.asep.2021.07.008 ◽

2021 ◽

Author(s):

Anne Sahithi Somavarapu Thomas ◽

Wasinee Pongprayoon ◽

Kraipat Cheenkachorn ◽

Malinee Sriariyanun

Keyword(s):

Sustainable Agriculture ◽

Current Knowledge ◽

Plant Ecology ◽

Plant Genome ◽

Commercial Application ◽

Gene Pools ◽

Host Nutrition ◽

Microbe Interactions ◽

Biotechnology Products ◽

Plant Microbiome

The term “microbiome” refers to the association of plants with various microorganisms which play an important role in the niches they occupy. These microorganisms are found in the endosphere, phyllosphere, and rhizosphere, of host plants which are involved in plant ecology and physiology. The structure and dynamics of the plant microbiome have been significant seen in the last few years. In addition, the plant microbiome enhances the host plant with gene pools, which is referred to as the second plant genome or extended genome. Interestingly, the microbiome associated with plant roots has received unique attention in recent years due to its important role in host nutrition, immunity, and development. Prospective studies of the microbiome have been coupled with the need for more sustainable production for agriculture. On the other hand, various environmental factors are associated with plant-microbiome interactions that can affect composition and diversity. This review provides insights and views of plant microbiome for sustainable agriculture. Host factors that influence the microbial community, root-associated microbial consortium, commercial application, and limitation of plant microbiome were discussed. Also, this review provides current knowledge of the plant microbiome into potential biotechnology products that can be used in agricultural systems. Regardless, microbiome innovation represents the future of sustainable agriculture.

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Neurotropic enteroviruses co-opt “fair-weather-friend” commensal gut microbiota to drive host infection and central nervous system disturbances

Behavioral and Brain Sciences ◽

10.1017/s0140525x18002741 ◽

2019 ◽

Vol 42 ◽

Author(s):

Kevin B. Clark

Keyword(s):

Central Nervous System ◽

Nervous System ◽

Gut Bacteria ◽

Infection Cycle ◽

Fair Weather ◽

Host Health ◽

Microbe Interactions ◽

Animal Hosts ◽

Host Infection ◽

Neuropsychiatric Conditions

Abstract Some neurotropic enteroviruses hijack Trojan horse/raft commensal gut bacteria to render devastating biomimicking cryptic attacks on human/animal hosts. Such virus-microbe interactions manipulate hosts’ gut-brain axes with accompanying infection-cycle-optimizing central nervous system (CNS) disturbances, including severe neurodevelopmental, neuromotor, and neuropsychiatric conditions. Co-opted bacteria thus indirectly influence host health, development, behavior, and mind as possible “fair-weather-friend” symbionts, switching from commensal to context-dependent pathogen-like strategies benefiting gut-bacteria fitness.

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