From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity

Exploitation of rhizosphere microbiome biodiversity in plant breeding

Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.

Isolate and plant host specificity of rhizosphere competence in Trichoderma species

Rhizosphere competence, the ability of a microorganism to colonise and proliferate in the rhizosphere of developing roots, is often studied when mechanisms of individual Trichoderma biocontrol agents are investigated. However, the extent of rhizosphere competence of Trichoderma species and isolates within species has not been widely studied. The rhizosphere competence of 22 Trichoderma isolates from a range of species was assessed using Trichoderma coated sweet corn (Zea mays) seeds grown in non-sterile soil. Results showed that 82 % of the Trichoderma isolates inoculated onto the seeds produced rhizosphere populations significantly greater than the control, indicating rhizosphere competence was widespread within the species that were tested. The least and most rhizosphere-competent isolates belonged to the same species indicating that rhizosphere competence was not species specific. The three least (T. crassum LU555, Trichoderma harzianum LU672, and T. virens LU556) and most (Trichoderma atroviride LU132, T. harzianum LU151, and LU673) rhizosphere-competent isolates were assessed on six plant species (sweet corn, ryegrass, cauliflower, carrot, onion, and white clover). Ryegrass and cauliflower were the most receptive plants to colonisation of the rhizosphere by Trichoderma species, and clover the least. Preferential rhizosphere colonisation was observed between some Trichoderma isolates and the plant species indicating that overall rhizosphere competence was dependent on specific interactions between the Trichoderma isolate and the plant species. However, some isolates were more broadly rhizosphere-competent than others and may have greater potential as plant protection agents. Since only one time point was sampled, future work is required to determine the temporal dynamics of rhizosphere colonisation as well as the spatial colonisation along the length of the root to determine whether different isolates preferentially colonise different regions of the root over different time periods.

Microbial crosstalk: decoding interactions to generate efficient SynComs

Limited studies have explored the complex and intense crosstalk between microbes within synthetic microbial communities (SynComs). Here, we highlight recent findings by Zohair et al., who unraveled the metabolic interactions between co-cultured microbes. We provide insights and perspectives for harnessing these interactions to design efficient SynComs for sustainable agriculture.

Sustainable agriculture: leveraging microorganisms for a circular economy

Microorganisms serve as linchpins in agricultural systems. Classic examples include microbial composting for nutrient recovery, using microorganisms in biogas technology for agricultural waste utilization, and employing biofilters to reduce emissions from stables or improve water quality in aquaculture. This mini-review highlights the importance of microbiome analysis in understanding microbial diversity, dynamics, and functions, fostering innovations for a more sustainable agriculture. In this regard, customized microorganisms for soil improvement, replacements for harmful agrochemicals or antibiotics in animal husbandry, and (probiotic) additives in animal nutrition are already in or even beyond the testing phase for a large-scale conventional agriculture. Additionally, as climate change reduces arable land, new strategies based on closed-loop systems and controlled environment agriculture, emphasizing microbial techniques, are being developed for regional food production. These strategies aim to secure the future food supply and pave the way for a sustainable, resilient, and circular agricultural economy. KEY POINTS: • Microbial strategies facilitate the integration of multiple trophic levels, essential for cycling carbon, nitrogen, phosphorus, and micronutrients. • Exploring microorganisms in integrated biological systems is essential for developing practical agricultural solutions. • Technological progress makes sustainable closed-entity re-circulation systems possible, securing resilient future food production.

Decoding seasonal changes: soil parameters and microbial communities in tropical dry deciduous forests

In dry deciduous tropical forests, both seasons (winter and summer) offer habitats that are essential ecologically. How these seasonal changes affect soil properties and microbial communities is not yet fully understood. This study aimed to investigate the influence of seasonal fluctuations on soil characteristics and microbial populations. The soil moisture content dramatically increases in the summer. However, the soil pH only gradually shifts from acidic to slightly neutral. During the summer, electrical conductivity (EC) values range from 0.62 to 1.03 ds m-1, in contrast to their decline in the winter. The levels of soil macronutrients and micronutrients increase during the summer, as does the quantity of soil organic carbon (SOC). A two-way ANOVA analysis reveals limited impacts of seasonal fluctuations and specific geographic locations on the amounts of accessible nitrogen (N) and phosphorus (P). Moreover, dehydrogenase, nitrate reductase, and urease activities rise in the summer, while chitinase, protease, and acid phosphatase activities are more pronounced in the winter. The soil microbes were identified in both seasons through 16S rRNA and ITS (Internal Transcribed Spacer) gene sequencing. Results revealed Proteobacteria and Ascomycota as predominant bacterial and fungal phyla. However, Bacillus, Pseudomonas, and Burkholderia are dominant bacterial genera, and Aspergillus, Alternaria, and Trichoderma are dominant fungal genera in the forest soil samples. Dominant bacterial and fungal genera may play a role in essential ecosystem services such as soil health management and nutrient cycling. In both seasons, clear relationships exist between soil properties, including pH, moisture, iron (Fe), zinc (Zn), and microbial diversity. Enzymatic activities and microbial shift relate positively with soil parameters. This study highlights robust soil-microbial interactions that persist mainly in the top layers of tropical dry deciduous forests in the summer and winter seasons. It provides insights into the responses of soil-microbial communities to seasonal changes, advancing our understanding of ecosystem dynamics and biodiversity preservation.

Strategies for tailoring functional microbial synthetic communities

Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.