Rhizosphere最新文献

Abiotic stress, such as high temperatures, droughts and soil salinity, as well as biotic stress, such as pythopathogenic bacteria, are causing serious damage to crops and they result in significant economic losses. In addition, excessive application of agrochemicals has deteriorated productive agricultural land, contributed to spreading antimicrobial resistance genes among pathogenic microorganisms and caused damage to human health. Developing alternative strategies to the use of chemicals is an ongoing challenge for achieving a sustainable agriculture. In this context, biological products, including bacteriocins, enhance crop growth and health without harming the environment. Bacteriocins are proteinaceous compounds that exhibit high specificity and kill competitors closely related to the producing bacteria. They are secreted by both Gram-negative bacteria and Gram-positive bacteria, and they have been used to treat bacterial infections in humans and animals, and to preserve food. In recent years, studies that projected the use of bacteriocins in agriculture have increased due to their high biotechnological potential. These bacteriocins have been explored as plant biostimulants or as biocontrol agents, and provide an innovative solution to the problems in agriculture. In particular, tailocins have a great potential as antimicrobials because they are very stable, extremely specific, and efficient as killers; in fact, a single particle is enough to kill a susceptible cell.In this review, we examine the bacteriocins produced by rhizobacteria and their application for a sustainable agriculture, a topic that has not been addressed extensively yet. In addition, we discuss bacteriocin expression in plants and the study of bacteriocins through omics.

Kiwifruit vine decline syndrome (KVDS), which is responsible for a progressive decline in yields in Italy, is linked to a non-specific reduction in root development, the biotic or abiotic causes of which are still unclear. Dactylonectria is one of the most common soil-borne fungi associated with kiwifruit vines, However, its role in KVDS has not yet been clarified; therefore, Dactylonectria functional relationship with kiwifruit vine at rhizosphere level was investigated focusing solely on its exudates. Six isolates, four from kiwifruit-bearing soils belonging to D. torresensis. D. ecuadoriensis, D. novozelandica and D. pauciseptata, and two D. torresensis from a virgin soil, was tested for phytotoxicity of exudates by growing kiwifruit in vitro plants on MS media amended at 50% with sterile fungal filtrates. Parallelly, low molecular weight (LMW) metabolic profile of fungal filtrates was evaluated with untargeted metabolomics approach using LC-MS/TOF. The fungal isolates from kiwifruit bearing soil were much richer in LMW metabolites than those from virgin soil. Non host specific mycotoxins such as Aflaxoxin B2, Alternariol and Alterlactone were found in these isolates along with a number of metabolites most of which were characterised by antimicrobial properties. D. torresensis isolates were clearly discriminated from the other three species based on metabolic profile. A negative Pearson correlation between the growth index of kiwifruit vitro-plants and LMW metabolite count per isolate (richness) showed that the latter were associated with phytotoxicity, but the degree of correlation (r = −0.639) indicated that they were not the only component responsible. The results suggest that kiwifruit vines may alter the composition of the Dactylonectria spp. community in the root zone, which in turn may directly or indirectly contribute to kiwifruit vine decline syndrome.

Mimosa caesalpiniifolia, crucial for fencing and firewood in Brazil's Caatinga dry forest, presents a promising avenue for commercial propagation. The challenges faced in seed propagation, such as the scarcity of inputs and the difficulties in overcoming dormancy, highlight the advantages of vegetative methods. These methods emerge as a viable alternative, enabling uniform and large-scale production of clonal plantlets. This technique ensures consistent plant quality, which is crucial given the wide variety of uses for this species. Additionally, the use of plant growth regulators is critical to enhance the success of vegetative propagation, promoting the formation of robust roots and overall development of plants from cuttings of adult trees. Recognizing the significance of creating clonal forests of M. caesalpiniifolia and the necessity for understanding methods to expedite this endeavor, this study was designed to assess the shooting and adventitious rooting of stem cuttings sourced from adult M. caesalpiniifolia trees, examining the effects of auxinic agents. M. caesalpiniifolia cuttings were harvested through vegetative rescue from six randomly selected adult trees, treated with indole-3-butyric acid (IBA) and indole-3-acetic acid (IAA) at concentrations of 0, 1,000, 2,000, and 4000 mg L⁻¹, using a completely randomized design in a 2 × 4 factorial arrangement. The evaluations included assessing root presence, number of shoots, vigor of clonal plantlets and plant survival under greenhouse conditions, shade house conditions, and full sun exposure. The study did not reveal any significant interaction between growth regulators and their concentrations under these conditions. IBA at intermediate concentrations enhanced root growth, while cuttings without growth regulators exhibited superior aerial development. A decrease in survival percentages with increasing concentrations of regulators was observed, while cuttings without regulators demonstrated better morphological development. The study suggests for large-scale nurseries, natural rooting and shoot formation in M. caesalpiniifolia cuttings may suffice for successful propagation without IBA or IAA.

Identifying and comparing plant growth-promoting traits (PGPT) within whole-genome and metagenomic sequencing data can significantly advance agricultural research and promote sustainable crop production. This study introduces PGPg_finder, a comprehensive pipeline designed to annotate and compare PGPT from both whole-genome and metagenome sequencing datasets. This pipeline utilizes direct sequence annotation alongside de novo assembly methods to accurately detect PGPT. By cross-referencing sequences from the PLaBAse database, it identifies and quantifies the presence of these genes within the original datasets, facilitating an intuitive comparison of the abundance and distribution of PGPT across various samples. We evaluated the performance of PGPg_finder by analyzing genomes from five rhizobacterial strains: Paenibacillus vini, Paenibacillus polymyxa, Fictibacillus sp., Brevibacillus agri, and Bacillus cereus, and also metagenomic samples from bulk soils subjected to forest-to-pasture conversion in the Amazon rainforest. The genomic workflow revealed several genes associated with substrate utilization, abiotic stress neutralization, phosphate solubilization, and iron acquisition. It also identified genes unique to specific lineages, including those associated with colonization and plant-derived substrate usage in P. polymyxa, quorum sensing response and biofilm formation in P. vini, heavy metal detoxification and nitrogen acquisition in B. agri, and spore production and neutralizing biotic stress in B. cereus. The strain Fictibacillus sp. presented several unique genes related to surface attachment, stress response, xenobiotic degradation, phosphate solubilization, and phytohormone production. The use of PGPg_finder highlights its potential to uncover novel inoculants and strains. The metagenomic workflow distinguished plant-growth promotion gene profiles between soils from the Amazon rainforest and pasture, with the latter showing a profile more aligned with simple carbohydrate consumption, abiotic stress tolerance, motility and chemotaxis, and phosphorus mineralization. Native forests exhibited a profile associated with the degradation of complex organic matter, oxidative stress tolerance, xenobiotic degradation, bactericidal activity, iron acquisition, and volatile pathways. These findings underscore the effectiveness and sensitivity of PGPg_finder in accurately identifying and comparing PGPT genes, highlighting both commonalities and variations across samples. The application of this pipeline has the potential to significantly facilitate the identification of plant growth-promoting microbes.

The rhizosphere is a hotspot of soil phosphorus (P) transformation, which profoundly influences the P status of plants. Although P is projected to limit the ability of forests to serve as a carbon sink, it remains unclear how rhizosphere P availability responds to changing environments in alpine forests. Here, we investigated changes in rhizosphere available P across a series of altitudinal bands (2850 m, 2950 m, 3060 m and 3200 m) in alpine forests and examined the potential regulators of rhizosphere P availability, including temperature and soil biotic and abiotic properties. The results showed that rhizosphere P availability decreased up to the 3060 m site but then increased at the 3200 m site. A structural equation model showed that temperature and soil properties (pH and organic carbon content) indirectly affected rhizosphere available P through amorphous iron/aluminum oxides and microbial biomass P, which had negative and positive effects on rhizosphere available P, respectively. Thus, sorption by soil minerals and turnover of microbial biomass P may be key processes regulating P availability. In contrast, soil organic acids and acid phosphatase, which may promote the release of P by ligand exchange and mineralization, respectively, did not show a positive relationship with rhizosphere available P. Overall, our findings highlight the potential role of microbial biomass as a labile P pool that provides readily available P by turnover and protects P from sorption by soil minerals, which could help in elucidating the mechanisms by which plants maintain their P nutrient supply in alpine ecosystems under environmental changes.

We present the field rapid generation advancement procedure for shortening the crop cycle in rice. The practical protocol developed by us using different maturity groups of rice showed promising early flower induction. We observed a shortening of crop cycle to about 35–40 days depending on the variety. The spacing between the plants was the major influencer for flower induction compared to other interventions tested viz., clipping, potassium di-hydrogen phosphate and paclobutrazol spray. Our raised bed direct seeding strategy completely avoided the transplantation. The work flow for flower induction can be a reference to increase generations of rice breeding. The rhizosphere bacterial dynamics using 16srRNA gene amplicon sequencing showed the Acinetobacter population abundance as a key mediator and marker for flowering time. The alpha diversity at flowered and unflowered stage showed the species richness as Control < Pusa Sugandh 5 < BPT-5204. The rice rhizosphere of this ecosystem had an abundance of Methylotrophs that utilize methane as a carbon source suggesting that the developed method is a green technique suitable for generation advancement that can be replaced for flooded condition assisted breeding in rice. Selective enrichment of functional abundance between varieties suggested the host - influenced microbiome for early flowering in rice. This protocol is expected to greatly accelerate the process of new variety breeding and the construction of mapping populations.

Microbial remediation, a significant research focus in bioremediation, shows promise in addressing pollution. In this study, the optimal medium for acetochlor-degrading bacteria AB1 was determined by the response surface method as 29.94 g L⁻¹ sucrose, 10.06 g L⁻¹ yeast extract, and 20.32 g L⁻¹ NaCl. The single-factor method identified optimum degradation conditions, including a temperature of 30 °C, pH of 7.0, inoculation with 3% AB1, and an initial acetochlor concentration of 10 mg L⁻¹. The strain reached a maximum degradation rate of 79.87% within 5 days. AB1 performed nitrogen fixation, phosphorus dissolution, potassium hydrolysis, siderophore production, and biofilm formation. In the presence of acetochlor, it also induced the upregulation of genes, wza and luxS. Utilizing a green fluorescent protein and rifampicin-resistant strain LAB1-gfp, it demonstrated stable colonization in maize rhizospheres and soils, enhancing growth and degradation. This reduced the acetochlor half-life to 12.77 days and increased soil enzyme activity, providing a theoretical foundation for acetochlor bioremediation.

Root exudates play a pivotal role in belowground interactions in both ecological and agricultural contexts. The metabolic composition of exudates profoundly influences the dynamics of these interactions, thereby shaping the intricate relationships between plants, microbes, and soil environments. Recent advances in mass-spectrometry have facilitated the analysis of root exudate metabolic composition to a greater depth. Previously used methods primarily analyze root exudates in hydroponic systems, or employ hybrid methodologies, which cultivate plants in soil and transitioning them briefly to hydroponic systems for exudate collection. Modern day ecological studies demand that exudates are collected in their natural habitats, because this will provide a more ecologically meaningful exudate metabolic profile. However, collecting exudates from soil grown plants poses several challenges with regard to the collection procedures, amongst others, the need for recovery after excavation of the roots, the collection period, and the solution in which to collect. Here, we present an optimized, cost-effective protocol for root exudate collection from potted plants, which is readily adaptable to field-grown specimens. Using tomato plants grown in pots, we examined and optimized various parameters: the collection medium (water versus nutrient solution), the use of wetted glass beads versus roots submerged in water, the recovery phase post-substrate removal, and the duration of exudation. Employing liquid chromatography-mass spectrometry (LC-MS), we assessed total amount of exudate, the number of features and background noise. Subsequent to data processing and statistical analyses, we assessed the chemical classes within exudates and variations in key metabolites among the different methods. Our results showed that each of the tested parameters can influence the outcome in different ways. Omitting the recovery phase increased the numbers of features and exudate amounts, likely due to adding metabolites from damaged roots, whereas the exudation medium and the duration of exudation had fewer effects. Based on our results, we propose to collect exudates in beakers containing ultrapure water, and to collect exudates for 4 h after a 24 h recovery phase. This is a straightforward and economical approach for collecting root exudates from soil-grown plants which is suitable for LC-MS analysis.

Plant-associated microorganisms have significant impacts on plant biology, ecology, and evolution. Although several studies have examined the factors driving variations in plant microbiomes, the mechanisms underlying the assembly of the plant microbiome are still poorly understood. In this study, we used gnotobiotic plants to test (i) whether seedlings create a selective environment and drive the assembly of root and leaf microbiomes through deterministic or stochastic processes, and (ii) whether seedlings structure the microbiome that is transferred through seeds using deterministic processes and whether this pattern changes when seedlings are exposed to the environmental microbiome. Our results show that the microbiome of gnotobiotic plants (i.e., inherited through seeds) is not under the selective influence of the host plant but changes quickly when plants are exposed to soil microbiomes. Within one week, plants were able to select microorganisms from the inocula, assemble the root microbiome, and assemble the shoot microbiome. This study supports the hypothesis that plants at early developmental stages might exert strong selective activity on their microbiomes and contribute to clarifying the mechanisms of plant microbiome assembly.