High-Throughput Customization of Plant Microbiomes for Sustainable Agriculture

Genomic insights and biocontrol potential of ten bacterial strains from the tomato core microbiome

Introduction

Despite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health.

Methods

We therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits.

Results

Bacterial strains included both taxa commonly used as biofertilizers and biocontrol agents (i.e. Pseudomonas and Bacillus) as well as the less studied genera Leclercia, Chryseobacterium, Glutamicibacter, and Paenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. Genome analysis yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth.

Discussion

This study employs a top-down approach to identify new plant growth-promoting rhizobacteria (PGPRs), offering an alternative to the conventional bottom-up strategy. This method goes beyond the traditional screening of the strains and thus can expand the range of potential bioinoculants available for market application, paving the way to the use of new still underexplored genera.

Potential Biological Control of Endophytic Streptomyces sp. 5-4 Against Fusarium Wilt of Banana Caused by Fusarium oxysporum f. sp. cubense Tropical Race 4

Fusarium wilt of banana caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is one of the most disastrous fungal diseases. Biological control is a promising strategy for controlling Fusarium wilt of banana. To explore endophytic actinomycetes as biocontrol resources against Foc TR4, antagonistic strains were isolated from different tissues of medicinal plants. Here, a total of 144 actinomycetes were isolated and belonged to Nonomuraea, Kitasatospora, and Streptomyces. Forty-three isolates exhibited antifungal activities against Foc TR4. The strain labeled with 5-4 isolated from roots of Piper austrosinense had a broad-spectrum antifungal activity by the production of chitinase and β-1,3-glucanase and was identified as Streptomyces hygroscopicus subsp. hygroscopicus 5-4. Furthermore, disease index of banana wilt was significantly reduced by application of strain 5-4 in comparison with application of Foc TR4 alone. Exogenous application of strain 5-4 increased the expression levels of defense genes such as (PAL), peroxidase (POD), pathogenesis-related protein 1 (PR-1), hydrolytic enzymes (β-1,3-glucanase), lysin motif receptor kinase 1 (LYK-1), and mitogen-activated protein kinase 1 (MPK-1). The antifungal mechanism assay demonstrated that extracts of strain 5-4 inhibited spore gemination and hyphal growth of Foc TR4, and caused abnormally swollen, deformity, and rupture of Foc TR4 hypha. Thus, S. hygroscopicus subsp. hygroscopicus 5-4 could be used as a potential biological agent for controlling Fusarium wilt of banana.

Cover Plants-Mediated Suppression of Fusarium Wilt and Root-Knot Incidence of Cucumber is Associated With the Changes of Rhizosphere Fungal Microbiome Structure-Under Plastic Shed System of North China

Cover crops are known to alleviate the adverse effects of continuous cropping by influencing plant health and changing host fungal-microbiome structures. However, insight into the shift of rhizomicrobiota composition and their effects on plant growth performance and resistance mechanism is still limited under plastic shed cultivation (PSC). Four leafy vegetable rotations namely spinach rotation (SR), non-heading Chinese cabbage rotation (NCCR), coriander rotation (CR), and leafy lettuce rotation (LLR) were used as cover crops in 7-years of continuous cucumber planted soil (CC). Their ecological impacts were studied for plant growth performance, replant diseases incidence rate, and rhizosphere fungal microbiome. Compared to CC, SR showed a highly suppressive effect on fusarium wilt, i.e., by 13.2% in the spring season, while NCCR decreased the root-knot nematode incidence rate by 8.9% in the autumn season. Such protective effects caused a significant increase of shoot and fruit biomass and thus sustained the fruit quality of cucumber. High-throughput sequencing revealed that the CR, SR, and NCCR treatments altered the fungal community composition by increasing the abundance of the beneficial fungal genera, decreasing pathogenic taxa, and fostering the saprotrophic and symbiotic functions. However, the relative abundance of most of the potentially pathogenic fungal genera increased in CC and LLR cropping. There were 8 potential pathogens and 10 beneficial or biocontrol fungi characterized. It was found that Paecilomyces, Chaetomium, Cladorrhinum, Zopfiella, Purpureocillium, and Metarhizium were the putative biocontrol microbes that positively affected plant growth and replanted diseases inhibition. The characterized Fusarium, Dactylonectria, Alternaria, Gibberella, and Aspergillus were the key pathogenic fungal agents found to be negatively associated with plant growth characters, suggesting that rhizomicrobiome may play an important role in the occurrence of disease incidence of cucumber plants. Considering the ecological potential of some cover plants, this study suggested that rotation with spinach, non-heading Chinese cabbage, or coriander can enhance rhizosphere immunity by triggering the development of plant-protective fungal microbiomes under plastic shed cucumber cultivation.

Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience

In the past years, breeding programs have been mainly addressed on pushing the commercial features, forgetting important traits, such as those related to environmental stress resilience, that are instead present in wild relatives. Among the traits neglected by breeding processes, the ability to recruit beneficial microorganisms that recently is receiving a growing attention due to its potentiality. In this context, this review will provide a spotlight on critical issues of the anthropocentric point of view that, until now, has characterized the selection of elite plant genotypes. Its effects on the plant-microbiome interactions, and the possibility to develop novel strategies mediated by the exploitation of beneficial root-microbe interactions, will be discussed. More sustainable microbial-assisted strategies might in fact foster the green revolution and the achievement of a more sustainable agriculture in a climatic change scenario.

Evolutions and Managements of Soil Microbial Community Structure Drove by Continuous Cropping

Continuous cropping obstacles have increasingly become an important phenomenon affecting crop yield and quality. Its harm includes the deterioration of soil basic physical and chemical properties, changes of soil microbial community structure, accumulation of autotoxins, weakness of plant growth, and aggravation of diseases and pests. In this review, the evolutionary trend of soil microbial structure driven by continuous cropping was generalized, while drivers of these changes summed up as destruction of soil microbial living environment and competition within the community. We introduced a microorganism proliferation and working model with three basics and a vector, and four corresponding effective measures to reshape the structure were comprehensively expounded. According to the model, we also put forward three optimization strategies of the existing measures. In which, synthetic microbiology provides a new solution for improving soil community structure. Meanwhile, to ensure the survival and reproduction of soil microorganisms, it is necessary to consider their living space and carbon sources in soil fully. This review provided a comprehensive perspective for understanding the evolutionary trend of the soil microbial community under continuous cropping conditions and a summary of reshaping measures and their optimization direction.

Micro-/Mesoporous Fluorescent Polymers and Devices for Visual Pesticide Detection with Portability, High Sensitivity, and Ultrafast Response

The residue of pesticides in crops, soil, and water continues to be a widespread concern due to the threat to human health and food safety. With the aim to develop highly sensitive sensing materials and portable detection devices, two dicarbazole-based fluorescent micro-/mesoporous polymers (JYs) with a larger specific surface area and pore sizes ranging from 1.1 to 34.2 nm are synthesized. The Stern-Volmer constants of JY fluorescence quenching for imidacloprid (50,063 M^-1) exceed 23-51 times those of the reported porous organic polymers (980-2173 M^-1). Of particular interest is the observation that JYs show rapid fluorescence response (2 s) and ultralow detection limit (30 ppb) for imidacloprid in water medium. The pronounced chemsensing property is attributed to the synergistic role of the hierarchical pore structure, large π-conjugation of chromophore groups, and strong inner filter effect between the polymer and imidacloprid molecule. Moreover, the pesticide detection of JYs exhibits good interference resistance in complicated service environments such as the extract liquids of the apple peel and field soil as well as aqueous solutions of various cations and anions. Because of the portability, excellent reusability, and sensitive fluorescence response, the prepared JYs and detection devices have promising applications in the on-site monitoring and early warning of the pesticide residues.

Probiotic Endophytes for More Sustainable Banana Production

Climatic factors and pathogenic fungi threaten global banana production. Moreover, bananas are being cultivated using excessive amendments of nitrogen and pesticides, which shift the microbial diversity in plants and soil. Advances in high-throughput sequencing (HTS) technologies and culture-dependent methods have provided valuable information about microbial diversity and functionality of plant-associated endophytic communities. Under stressful (biotic or abiotic) conditions, plants can recruit sets of microorganisms to alleviate specific potentially detrimental effects, a phenomenon known as “cry for help”. This mechanism is likely initiated in banana plants infected by Fusarium wilt pathogen. Recently, reports demonstrated the synergistic and cumulative effects of synthetic microbial communities (SynComs) on naturally occurring plant microbiomes. Indeed, probiotic SynComs have been shown to increase plant resilience against biotic and abiotic stresses and promote growth. This review focuses on endophytic bacterial diversity and keystone taxa of banana plants. We also discuss the prospects of creating SynComs composed of endophytic bacteria that could enhance the production and sustainability of Cavendish bananas (Musa acuminata AAA), the fourth most important crop for maintaining global food security.

Synergistically promoting plant health by harnessing synthetic microbial communities and prebiotics

Soil-borne diseases cause serious economic losses in agriculture. Managing diseases with microbial preparations is an excellent approach to soil-borne disease prevention. However, microbial preparations often exhibit unstable effects, limiting their large-scale application. This review introduces and summarizes disease-suppressive soils, the relationship between carbon sources and the microbial community, and the application of human microbial preparation concepts to plant microbial preparations. We also propose an innovative synthetic microbial community assembly strategy with synergistic prebiotics to promote healthy plant growth and resistance to disease. In this review, a new approach is proposed to improve traditional microbial preparations; provide a better understanding of the relationships among carbon sources, beneficial microorganisms, and plants; and lay a theoretical foundation for developing new microbial preparations.