Search Results (37)

Soilless cultivation technology is a key means of overcoming traditional agricultural resource limits, providing an important path to efficient and sustainable modern agriculture by precisely regulating crop rhizospheric environments. This paper systematically reviews the technical system of soilless cultivation, nutrient solution management strategies, the interaction mechanism of rhizosphere microorganisms, and future development directions, aiming to reveal its technical advantages and innovation potential. This review shows that solid and non-solid substrate cultivation improves resource utilization efficiency and yield, but substrate sustainability and technical cost need urgent attention. The dynamic regulation of nutrient solution and intelligent management can significantly enhance nutrient absorption efficiency. Rhizosphere microorganisms directly regulate crop health through nitrogen fixation, phosphorus solubilization, and pathogen antagonism. However, the community structure and functional stability of rhizosphere microorganisms in organic systems are prone to imbalance, requiring targeted optimization via synthetic biology methods. Future research should focus on the development of environmentally friendly substrates, the construction of intelligent environmental control systems, and microbiome engineering to promote the expansion of soilless cultivation towards low-carbon, precise, and spatial directions. This paper systematically references the theoretical improvements and practical innovations in soilless cultivation technology, facilitating its large-scale application in food security, ecological protection, and resource recycling. Full article

Chaetomium globosum is a widely distributed fungal species recognized for its ability to produce a range of secondary metabolites. This fungus plays a significant ecological role by degrading organic matter and contributing to nutrient cycling in diverse ecosystems. In recent years, C. globosum has attracted considerable scientific interest due to its potential as a biocontrol agent [BCA] against a wide array of diseases in numerous plant species. While the precise mechanisms of C. globosum as a BCA remain poorly understood, interference competition through antibiosis is one of the key mechanisms. Moreover, C. globosum can enhance plant health by promoting nutrient availability, manipulating the rhizosphere microbiome, and inducing plant defense responses. The formulation of C. globosum for agricultural applications has been reported, which can significantly improve stability and efficacy under field conditions. However, despite significant advancements in omics and molecular biology technologies, the biology of C. globosum is understudied. Enhanced research into the genetics and functional genomics of C. globosum could pave the way for its applications in sustainable agriculture. This review summarizes the role of C. globosum as a BCA, focusing on its underlying mechanisms such as genomics and transcriptomics, and the effects of C. globosum application on soil health and the rhizosphere microbiome. Full article

Xiphinema israeliae has been reported in the rhizosphere of olives in Crete, Greece. Attempts were made to culture this nematode in pots planted with olive and fig seedlings, using Xiphinema index as a control. In these conditions, X. index showed a high reproduction rate on fig in a few months and none on olive. The experiments with X. israeliae indicated that olive and fig are suitable hosts for this dagger nematode, since juveniles of various life stages were found in plants inoculated exclusively with females, although the rate of nematode reproduction was low. Xiphinema israeliae was proved to have a parthenogenetic reproduction and a long life cycle, from female to female, taking more than nine months at a 24–26 °C temperature to complete. Therefore, a quite long period, even a few years, may be necessary to obtain a high number of nematodes in pots under experimental conditions. In contrast, Xiphinema italiae did not reproduce on olive and fig after a seven-month period. Accordingly, to our knowledge, this study increases the host range and knowledge about the culturing of these species, as only seven species of Xiphinema have been successfully cultured in pots till now. The potential of fig and olive for culturing X. israeliae gives an opportunity for further studies of its biology and host range. Full article

Intercropping of trees and classical crops has been proposed as a practice to help adapt to climate change and protect soil against erosion. However, the effects of intercropping on soil biology are not sufficiently quantified. Therefore, the aim of this study was to evaluate microbiological changes in the soil resulting from the intercropping of Paulownia and buckwheat. A field experiment, involving an intercropping and control no-tree variant, was conducted from 2019 to 2022 with a plot size of 30 m². Buckwheat rhizosphere soil samples were collected twice in both 2021 and 2022 in order to evaluate the effects of intercropping on a range of parameters describing soil microbiome status: abundance of microorganisms, bacterial and fungal community structure (using Illumina MiSeq sequencing), dehydrogenases (DHA) activity, and total glomalin-related soil proteins (T-GRSP). In addition, the colonisation of buckwheat roots by fungi, yield, and biometric traits of the plant were determined. Next-generation sequencing showed that Actinobacteria, Proteobacteria, and Acidobacteria were dominant in the microbiome of every variant of the experiment, regardless of the crop. In contrast, the mycobiome was dominated by fungi classified as Ascomycota and Mortierellomycota. This observation corresponded to an increase in buckwheat yield in intercropped plots. Biometric traits, namely buckwheat yield and total kernel weight per plant, showed higher values when buckwheat was intercropped with Paulownia compared to the control. DHA activity was stimulated by intercropping at the first sampling date, whereas glomalin concentration and abundance of microorganisms were not dependent on the cropping systems tested. This study shows that tree-based intercropping (TBI) systems promote a more diverse soil microbial community and function than conventional agriculture. Our results also suggest that TBI positively impacts buckwheat biometric traits, supporting its implementation in rural landscapes. The yield under intercropping cultivation amounted to 0.65 t ha⁻¹, while in control sites it was 0.53 t ha⁻¹. The total abundance of bacteria under intercropping cultivation was higher compared to monoculture in 2021 at the first term of sampling (4.3 × 10⁴) and in 2022 in the second term of soil sampling (4.6 × 10⁴). Full article

In the recent past, microbiome manipulation has emerged as a promising approach to improve plant growth performance by exploring the deep insight of plant–microbe interactions. The exploration of a plant microbiome either present on an ectosphere or endosphere can provide a far better understanding about the potential application of plant-associated microbes for the improvement of plant growth, protection from pathogen invasion, and tolerance to environmental stresses of a diverse nature. In this context, next-generation sequencing methods, omics approaches, and synthetic biology have made significant progress in plant microbiome research and are being frequently used to explore the intriguing role of plant-associated microorganisms. Despite the successfulness of conventional approaches, the incorporation of CRISPR/Cas9, RNA interference technology, rhizosphere engineering, microbiome engineering, and other manipulation techniques appear to be a promising approach to enhancing plant performance, and tolerance against biotic and abiotic stress factors. The present review presents the significance of plant microbe interaction, vital functional aspects, collaborative action, potential constraints, and finally the latest developments in bioengineering approaches destined for microbiome modulation with an objective to improve the performance of a host plant challenged with environmental stressors. Full article

The plant microbiome, found in the rhizosphere, phyllosphere, and endosphere, is essential for nutrient acquisition, stress tolerance, and the overall health of plants. This review aims to update our knowledge of and critically discuss the diversity and functional roles of the rice microbiome, as well as microbiome engineering strategies to enhance biofertilization and stress resilience. Rice hosts various microorganisms that affect nutrient cycling, growth promotion, and resistance to stresses. Microorganisms carry out these functions through nitrogen fixation, phytohormone and metabolite production, enhanced nutrient solubilization and uptake, and regulation of host gene expression. Recent research on molecular biology has elucidated the complex interactions within rice microbiomes and the signalling mechanisms that establish beneficial microbial communities, which are crucial for sustainable rice production and environmental health. Crucial factors for the successful commercialization of microbial agents in rice production include soil properties, practical environmental field conditions, and plant genotype. Advances in microbiome engineering, from traditional inoculants to synthetic biology, optimize nutrient availability and enhance resilience to abiotic stresses like drought. Climate change intensifies these challenges, but microbiome innovations and microbiome-shaping genes (M genes) offer promising solutions for crop resilience. This review also discusses the environmental and agronomic implications of microbiome engineering, emphasizing the need for further exploration of M genes for breeding disease resistance traits. Ultimately, we provide an update to the current findings on microbiome engineering in rice, highlighting pathways to enhance crop productivity sustainably while minimizing environmental impacts. Full article

Evidence of unintended introductions of Phytophthora species into native habitats has become increasingly prevalent in California. If not managed adequately, Phytophthora species can become devastating agricultural and forest plant pathogens. Additionally, California’s natural areas, characterized by a Mediterranean climate and dominated by chaparral (evergreen, drought-tolerant shrubs) and oak woodlands, lack sufficient baseline knowledge on Phytophthora biology and ecology, hindering effective management efforts. From 2018 to 2021, soil samples were collected from Angeles National Forest lands (Los Angeles County) with the objective of better understanding the diversity and distribution of Phytophthora species in Southern California. Forty sites were surveyed, and soil samples were taken from plant rhizospheres, riverbeds, and off-road vehicle tracks in chaparral and oak woodland areas. From these surveys, fourteen species of Phytophthora were detected, including P. cactorum (subclade 1a), P. multivora (subclade 2c), P. sp. cadmea (subclade 7a), P. taxon ‘oakpath’ (subclade 8e, first reported in this study), and several clade-6 species, including P. crassamura. Phytophthora species detected in rhizosphere soil were found underneath both symptomatic and asymptomatic plants and were most frequently associated with Salvia mellifera, Quercus agrifolia, and Salix sp. Phytophthora species were present in both chaparral and oak woodland areas and primarily in riparian areas, including detections in off-road tracks, trails, and riverbeds. Although these Mediterranean ecosystems are among the driest and most fire-prone areas in the United States, they harbor a large diversity of Phytophthora species, indicating a potential risk for disease for native Californian vegetation. Full article

Russula griseocarnosa, an edible and medicinal mushroom abundant in nutrients and notable bioactivities, is predominantly grown in the broad-leaved forest with trees of the family Fagaceae in southern China. This species forms ectomycorrhizal associations with plant roots and cannot be artificially cultivated currently. Previous research indicates a strong correlation between the growth of R. griseocarnosa and factors such as the host plant, climate variables (specifically mean temperature and precipitation from June to October), and the rhizosphere microbiota of its habitat. However, comprehensive studies on the fundamental biology of this species are lacking. The interaction between R. griseocarnosa and its host plant, as well as the mechanisms underlying the microbial community dynamics within its habitat, remain ambiguous. The limited repertoire and diversity of carbohydrate-active enzymes (CAZymes) in R. griseocarnosa relative to saprophytic fungi may contribute to its recalcitrance to cultivation on synthetic media. The specific core enzyme and the substances provided by the host plant to facilitate growth are yet to be elucidated, posing a significant challenge in the artificial cultivation of R. griseocarnosa. The habitat of R. griseocarnosa harbours unique microbial communities, indicating the presence of potentially beneficial microorganisms that could be exploited for artificial propagation and conservation efforts. However, the lack of definitive functional verification experiments hinders the realization of this promising prospect. This review offers a comprehensive overview of the nutritional profile and health benefits of R. griseocarnosa, emphasizing recent developments in its isolation, molecular ecology, and artificial cultivation. Additionally, it explores prospective advancements in R. griseocarnosa research, aiming to enrich our foundational understanding for applied purposes and fostering progress in the realm of ectomycorrhizal edible mushrooms. Full article

Several attempts have been made to evaluate the abundance and distribution of the bacterial community in the rhizosphere of medicinal plants. Many describe information based on an estimation of the community structure and the effects of plant cover in determining microbial community composition. The ability of plants to specifically shape their microbial community in general and medicinal plants in particular is largely unknown. With the arrival of molecular biology, understanding the microbial community’s composition, diversity, and function became possible. We hypothesized that microbial communities associated with medicinal shrubs would differ from each other. To test this hypothesis, we characterized the soil microbial composition under each of five Mediterranean medicinal plants, differentiated by their medicinal use and ecophysiological adaptation, namely, Salvia fruticosa, Pistacia lentiscus, Myrtus communis, Origanum syriacum, and Teucrium capitatum, and an open-space bare soil between the plants, inhabiting natural ecosystems characterized by similar climatic conditions typical of a Mediterranean environment. The results demonstrated the importance of plant ecophysiological adaptations, which play an important role in determining microbial community composition and functional diversity. The intensity of a plant’s response to its surroundings can have either positive or negative effects that will determine the microbial community composition and interactions among the belowground parts. A total of 11 phyla, 21 orders, and 409 genera were found in the soil rhizosphere in the vicinity of the four plants and open space samples. The distinguishing attributes of each shrub trigger and stimulate the microbial community’s rhizosphere. This results in distinct patterns of bacterial diversity and functionality between the different shrubs and the control. The rhizosphere bacterial community composition differed between the plants in a PERMANOVA test, but there was little difference in terms of phyla and order relative abundances. This study shows how five medicinal plants, coexisting in a common habitat, impact the bacterial community. The noticeable shift in bacterial composition further supports our discovery that root exudates effectively govern the makeup of soil bacterial communities. Full article

Arbuscular mycorrhizal fungi (AMF) can help plants absorb more mineral nutrients after they colonize plant roots, and the mycelia harmonize the soil structure and physical and chemical properties by secreting compounds. AMF species co-evolve with their habitat’s geographic conditions and hosts; this gradually causes differences in the AMF species. By using Melzer’s reagent to analyze the morphology and using Illumina Miseq sequencing technology to perform the molecular identification of AMF communities among the four typical L. barbarum planting areas (Zhongning, Guyuan, Jinghe, and Dulan) investigated, the variety of L. barbarum roots and rhizosphere AMF communities was greater in the Zhongning area, and every region additionally had endemic species. The successfully amplified AMF was re-applied to the L. barbarum seedlings. We found that the total dry weight and accumulation of potassium increased significantly (p < 0.05), and the root volume and number of root branches were significantly higher in the plants that were inoculated with Paraglomus VTX00375 in the pot experiment, indicating that AMF improves root development and promotes plant growth. We have investigated AMF germplasm species in four regions, and we are committed to the development of native AMF resources. The multiplication and application of AMF will be conducive to realizing the potential role of biology in the maintenance of agroecology. Full article

Pseudomonas chlororaphis ATCC 9446 is a non-pathogenic bacterium associated with the rhizosphere. It is commonly used as a biocontrol agent against agricultural pests. This organism can grow on a variety of carbon sources, has a robust secondary metabolism, and produces secondary metabolites with antimicrobial properties. This makes it an alternative host organism for synthetic biology applications. However, as a novel host there is a need for well-characterized molecular tools that allow fine control of gene expression and exploration of its metabolic potential. In this work we developed and characterized expression vectors for P. chlororaphis. We used two different promoters: the exogenously induced lac-IPTG promoter, and LuxR-C6-AHL, which we evaluated for its auto-inducible capacities, as well as using an external addition of C6-AHL. The expression response of these vectors to the inducer concentration was characterized by detecting a reporter fluorescent protein (YFP: yellow fluorescent protein). Furthermore, the violacein production operon was evaluated as a model heterologous pathway. We tested violacein production in shake flasks and a 3 L fermenter, showing that P. chlororaphis possesses a vigorous aromatic amino acid metabolism and was able to produce 1 g/L of violacein in a simple batch reactor experiment with minimal medium using only glucose as the carbon source. We compared the experimental results with the predictions of a modified genome scale model. The presented results show the potential of P. chlororaphis as a novel host organism for synthetic biology applications. Full article

In this review, the significance of ratoon rice was introduced, and the research status and development trends of ratoon rice were also summarized. It is pointed out that mechanically harvested ratoon rice is the developing direction of future ratoon rice. On this basis, we analyzed the relationship between the yield of ratoon rice and many factors, such as variety characteristics, sowing date, water control, fertilizer, and many others. It is important to construct a comprehensive and practical evaluation system for rice regeneration that can provide a basis for high-yield cultivation of machine-harvested ratoon rice. At the same time, it is suggested that combining high-yield cultivation with the green ecological efficiency of rice can achieve better production and improve the quality of rice. Finally, some problems with ratoon rice development were put forward. An in-depth study on the rhizosphere biology and regulation techniques of ratoon rice and the effective ecological compensation mechanism increased the capacity and quality of ratoon rice. Further, the functioning of such research can enhance the planting area for ratoon rice and improve food security. Full article

Plant–microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms. Full article

The isolation of new bacterial strains from the natural environment can lead to the detection of microorganisms of potential practical importance. The characterization of such microorganisms can be carried out using classical microbiological and molecular biology methods. Currently, studies of newly detected microorganisms are based on sequencing techniques. Sequencing of the full genome can provide information about the origin of the strain, its taxonomic status, and phenotypic characteristics. The studies were conducted using the bacteria Achromobacter sp. 77Bb1 isolated from the maize crop rhizosphere. The bacterial genome was sequenced using Illumina 2 × 150 nt technology. The obtained sequences were analyzed using bioinformatics methods, resulting in 57 contigs and genome containing 6,651,432 nt. Phylogenetic analysis based on 16S rRNA gene sequences enabled the assignment of the analyzed bacteria to the genus Achromobacter. The obtained genome contained genes for 4855 proteins with functional assignment. Some of these genes were connected with xenobiotics biodegradation and metabolisms. All genes for aminobenzoate degradation and almost all for benzoate and styrene degradation were found in the analyzed genome, suggesting that the isolated strain has the potential to be used in natural bioremediation methods. Full article

The biological characteristics of crop roots are closely related to the efficient utilization of nitrogen and have become a research hotspot in agricultural cultivation and breeding in recent years. The root system and root microbiota play a crucial role in both the basic and the plastic growth and development of plants in response to external environmental changes. Nitrogen is an indispensable nutrient element for crop growth, and the efficient utilization of nitrogen is the key to achieving the high yield and quality of crops and establishing environmentally friendly agricultural production. The nitrogen absorbed and utilized by rice mainly enters the aboveground part of the plant through the root system from within the soil. This process is explored from the perspective of root biology (root morphology, physiological and biochemical characteristics, root growth and development process and regulation, rhizosphere microorganisms, and their symbiotic systems), which is in line with the directions of “less investment, increased production, environmental protection, and sustainable development” in China. Based on the research status in this field at present, this article explored the interaction mechanism between crop root biology and nitrogen absorption and utilization, and looks forward to the future research directions for root biology. This study provides a theoretical basis for reducing nitrogen fertilizer application, optimizing nitrogen-efficient cultivation management techniques, and selecting nitrogen-efficient varieties. Full article