Abstract
Plants are associated with hundreds of thousands of microbes that are present outside on the surfaces or colonizing inside plant organs, such as leaves and roots. Plant-associated microbiota plays a vital role in regulating various biological processes and affects a wide range of traits involved in plant growth and development, as well as plant responses to adverse environmental conditions. An increasing number of studies have illustrated the important role of microbiota in crop plant growth and environmental stress resistance, which overall assists agricultural sustainability. Beneficial bacteria and fungi have been isolated and applied, which show potential applications in the improvement of agricultural technologies, as well as plant growth promotion and stress resistance, which all lead to enhanced crop yields. The symbioses of arbuscular mycorrhizal fungi, rhizobia and Frankia species with their host plants have been intensively studied to provide mechanistic insights into the mutual beneficial relationship of plant–microbe interactions. With the advances in second generation sequencing and omic technologies, a number of important mechanisms underlying plant–microbe interactions have been unraveled. However, the associations of microbes with their host plants are more complicated than expected, and many questions remain without proper answers. These include the influence of microbiota on the allelochemical effect caused by one plant upon another via the production of chemical compounds, or how the monoculture of crops influences their rhizosphere microbial community and diversity, which in turn affects the crop growth and responses to environmental stresses. In this review, first, we systematically illustrate the impacts of beneficial microbiota, particularly beneficial bacteria and fungi on crop plant growth and development and, then, discuss the correlations between the beneficial microbiota and their host plants. Finally, we provide some perspectives for future studies on plant–microbe interactions.
Highlights
A microbiota comprises all microbes, including viruses, bacteria, archaea, protozoa, and fungi that are present in a special environment, which is usually investigated together with its host and surrounding environment such as plant, animal gut, and soil, whereas a microbiome includes all the living microorganisms, their genomic sequences, and the environmental conditions surrounding the entire habitat [1,2,3]
One recent report revealed that the nitrogen (N) absorptions by both the rice (Oryza sativa) indica and japonica species are associated with the NRT1.1B gene, encoding a rice nitrate transporter and sensor, which is responsible for root-associated microbiota composition and N usage in field-grown rice [22]
An increasing body of research has been focusing on the associations and relationships between microbiota and host plants
Summary
A microbiota comprises all microbes, including viruses, bacteria, archaea, protozoa, and fungi that are present in a special environment, which is usually investigated together with its host and surrounding environment such as plant, animal gut, and soil, whereas a microbiome includes all the living microorganisms (viruses, bacteria, archaea, and lower and higher eukaryotes), their genomic sequences, and the environmental conditions surrounding the entire habitat [1,2,3]. Microbes are closely associated with their living environment, and environmental changes can alter different microbial species [1,4,5]. Studies have revealed that the microbiota associated with plants is crucial in determining plant performance and health, because certain beneficial microbes improve plant growth and resistance to stresses [8,9,10,11,12]. The advance of generation sequencing (NGS) technologies has presented and promoted an effective method for studying the plant–microbe interactions by facilitating the investigations of whole plant-associated microbial communities [23,24,25]. In this review, we have made an effort to systemically illustrate the latest research advances of beneficial microbiota associated with crop plants and make suggestions for the research trends on the plant and microbiota relationships
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