Like all higher organisms, plants have evolved in the context of a microbial world, shaping both their evolution and their contemporary ecology. Interactions between plant roots and soil microorganisms are critical for plant fitness in natural environments. Given this co-evolution and the pivotal importance of plant-microbial interactions, it has been hypothesized, and a growing body of literature suggests, that plants may regulate the composition of their rhizosphere to promote the growth of microorganisms that improve plant fitness in a given ecosystem. Here, using a combination of comparative genomics and exometabolomics, we show that pre-programmed developmental processes in plants (Avena barbata) result in consistent patterns in the chemical composition of root exudates. This chemical succession in the rhizosphere interacts with microbial metabolite substrate preferences that are predictable from genome sequences. Specifically, we observed a preference by rhizosphere bacteria for consumption of aromatic organic acids exuded by plants (nicotinic, shikimic, salicylic, cinnamic and indole-3-acetic). The combination of these plant exudation traits and microbial substrate uptake traits interact to yield the patterns of microbial community assembly observed in the rhizosphere of an annual grass. This discovery provides a mechanistic underpinning for the process of rhizosphere microbial community assembly and provides an attractive direction for the manipulation of the rhizosphere microbiome for beneficial outcomes.

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Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly.

The worldwide increase in human population raises a big threat to the food security of each people as the land for agriculture is limited and even getting reduced with time. Therefore, it is essential that agricultural productivity should be enhanced significantly within the next few decades to meet the large demand of food by emerging population. Not to mention, too much dependence on chemical fertilizers for more crop productions inevitably damages both environmental ecology and human health with great severity. Exploitation of microbes as biofertilizers is considered to some extent an alternative to chemical fertilizers in agricultural sector due to their extensive potentiality in enhancing crop production and food safety. It has been observed that some microorganisms including plant growth promoting bacteria, fungi, Cyanobacteria, etc. have showed biofertilizer-like activities in the agricultural sector. Extensive works on biofertilizers have revealed their capability of providing required nutrients to the crop in sufficient amounts that resulted in the enhancement of crop yield. The present review elucidates various mechanisms that have been exerted by biofertilizers in order to promote plant growth and also provides protection against different plant pathogens. The aim of this review is to discuss the important roles and applications of biofertilizers in different sectors including agriculture, bioremediation, and ecology.

Biofertilizers: a potential approach for sustainable agriculture development

There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.

/pdf/functional-soil-microbiome-belowground-solutions-to-an-3sga41751s.pdf

Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

Actinomycetes are a diverse family of filamentous bacteria that produce a plethora of natural products relevant for agriculture, biotechnology and medicine, including the majority of the antibiotics we use in the clinic. Rather than as free-living bacteria, many actinomycetes have evolved to live in symbiosis with among others plants, fungi, insects and sponges. As a common theme, these organisms profit from the natural products and enzymes produced by the actinomycetes, for example, for protection against pathogenic microbes, for growth promotion or for the degradation of complex natural polymers such as lignocellulose. At the same time, the actinomycetes benefit from the resources of the hosts they interact with. Evidence is accumulating that these interactions control the expression of biosynthetic gene clusters and have played a major role in the evolution of the high chemical diversity of actinomycete-produced secondary metabolites. Many of the biosynthetic gene clusters for antibiotics are poorly expressed under laboratory conditions, but they are likely expressed in response to host-specific demands. Here, we review the environmental triggers and cues that control natural product formation by actinomycetes and provide pointers as to how these insights may be harnessed for drug discovery.

https://scholarlypublications.universiteitleiden.nl/access/item%3A2948474/view

Chemical ecology of antibiotic production by actinomycetes

The agricultural crops are often affected by the scarcity of fresh water. Seasonal drought is a major constraint on Northeast Indian agriculture. Almost 80% of the agricultural land in this region is acidic and facing severe drought during the winter period. Apart from classical breeding and transgenic approaches, the application of plant-growth-promoting bacteria (PGPB) is an alternative strategy for improving plant fitness under stressful conditions. The 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing PGPB offer drought stress tolerance by regulating plant ethylene levels. The aim of the present study was to evaluate the consortium effect of three ACC-deaminase producing rhizobacteria - Ochrobactrum pseudogrignonenseRJ12, Pseudomonas sp.RJ15 and Bacillus subtilisRJ46 on drought stress alleviation in Vigna mungo L. and Pisum sativum L. Consortium treatment significantly increase seed germination percentage, root length, shoot length, and dry weight of treated plants. An elevated production of reactive oxygen species scavenging enzymes and cellular osmolytes; higher leaf chlorophyll content; increase in relative water content and root recovery intension were observed after consortium treatment in comparison with the uninoculated plants under drought conditions. The consortium treatment decreased the ACC accumulation and down-regulated ACC-oxidase gene expression. This consortium could be an effective bio-formulator for crop health improvement in drought-affected acidic agricultural fields.

Alleviation of drought stress in pulse crops with ACC deaminase producing rhizobacteria isolated from acidic soil of Northeast India.

The study of the interactions between plants and their microbial communities in the rhizosphere is important for developing sustainable management practices and agricultural products such as biofertilizers and biopesticides. Plant roots release a broad variety of chemical compounds to attract and select microorganisms in the rhizosphere. In turn, these plant-associated microorganisms, via different mechanisms, influence plant health and growth. In this review, we summarize recent progress made in unraveling the interactions between plants and rhizosphere microbes through plant root exudates, focusing on how root exudate compounds mediate rhizospheric interactions both at the plant–microbe and plant–microbiome levels. We also discuss the potential of root exudates for harnessing rhizospheric interactions with microbes that could lead to sustainable agricultural practices.

ShenQirong

Papers

Rhizosphere interactions: root exudates, microbes, and microbial communities1