Potential Roles of Soil Microorganisms in Regulating the Effect of Soil Nutrient Heterogeneity on Plant Performance

Effects of soil microplastic heterogeneity on plant growth vary with species and microplastic types

Microplastics are heterogeneously distributed in soils. However, it is unknown whether soil microplastic heterogeneity affects plant growth and root foraging responses and whether such effects vary with plant species and microplastic types. We grew each of seven herbaceous species (Platycodon grandiflorus, Trifolium repens, Portulaca oleracea, Medicago sativa, Taraxacum mongolicum, Perilla frutescenst, and Paspalum notatum) in heterogeneous soil (patches without microplastics and patches with 0.2 % microplastics) and homogeneous soil (patches with 0.1 % microplastics). Three microplastic types were tested: polypropylene (PP), polyacrylonitrile (PAN), and polyester (PET). P. frutescens showed no response to soil microplastic heterogeneity. For P. grandiflora, microplastic heterogeneity tended to decrease its biomass (total, shoot and root) when the microplastic was PAN and also shoot biomass when it was PET, but had no effect when it was PP. For T. repens, microplastic heterogeneity promoted biomass when PAN was used, decreased total and root biomass when PET was used, but showed no effect when PP was used. Microplastic heterogeneity increased biomass of P. oleracea and decreased that of M. sativa when PET was used, but had no effect when PP or PAN was used. For T. mongolicum, microplastic heterogeneity reduced biomass when the microplastic was PAN, tended to increase total and root biomass when it was PP, but showed no effect when it was PET. For P. notatum, microplastic heterogeneity increased biomass when the microplastic was PP, decreased it when PET was used, but had no effect when PAN was used. However, biomass of none of the seven species showed root foraging responses at the patch level. Therefore, soil microplastic heterogeneity can influence plant growth, but such effects depend on species and microplastic types and are not associated with root foraging. Our findings highlight the roles of soil microplastic heterogeneity, which may influence species interactions and community structure and productivity.

The short-term effect of microplastics in lettuce involves size- and dose-dependent coordinate shaping of root metabolome, exudation profile and rhizomicrobiome

Micro- and nano-plastics (MNPs) in the soil can impact the microbial diversity within rhizospheres and induce modifications in plants' morphological, physiological, and biochemical parameters. However, a significant knowledge gap still needs to be addressed regarding the specific effects of varying particle sizes and concentrations on the comprehensive interplay among soil dynamics, root exudation, and the overall plant system. In this sense, different omics techniques were employed to clarify the mechanisms of the action exerted by four different particle sizes of polyethylene plastics considering four different concentrations on the soil-roots exudates-plant system was studied using lettuce (Lactuca sativa L. var. capitata) as a model plant. The impact of MNPs was investigated using a multi-omics integrated approach, focusing on the tripartite interaction between the root metabolic process, exudation pattern, and rhizosphere microbial modulation. Our results showed that particle size and their concentrations significantly modulated the soil-roots exudates-plant system. Untargeted metabolomics highlighted that fatty acids, amino acids, and hormone biosynthesis pathways were significantly affected by MNPs. Additionally, they were associated with the reduction of rhizosphere bacterial α-diversity, following a size-dependent trend for specific taxa. The omics data integration highlighted a correlation between Pseudomonadata and Actinomycetota phyla and Bacillaceae family (Peribacillus simplex) and the exudation of flavonoids, phenolic acids, and lignans in lettuce exposed to increasing sizes of MNPs. This study provides a novel insight into the potential effects of different particle sizes and concentrations of MNPs on the soil-plant continuum, providing evidence about size- and concentration-dependent effects, suggesting the need for further investigation focused on medium- to long-term exposure.

Effect of phosphate-mineralized bacteria on multi-metals migration behavior in vanadium tailing slags: Coexistence of immobilization and mobilization

Biomineralization techniques have been utilized to remediate heavy metals (HMs) contaminated environments. However, the effect of microbial-induced phosphate precipitation (MIPP) on HMs behavior in vanadium tailing slags has not been revealed. This study is the first to report the influence of MIPP on multiple HMs including Cd, Cu, Pb and Zn in the slags with and without soil mixing. The results showed that MIPP exhibited excellent ability for Cd immobilization, Cd immobilization rate reached 43.41 % under the optimal parameters within 7 days. Cd immobilization performance was significantly improved and sustained after the slags were covered with soil, resulting from better colonization of phosphate mineralizing bacteria in slag-soil mixtures. Surprisingly, DTPA-Cu, Zn and Pb contents in slags were all increased to varying degrees after MIPP treatment. Leaching solution mineralization tests further suggested that MIPP significantly reduced the concentration of Cd2+, Pb2+, Ca2+, Mg2+ and Al3+, but barely changed Cu2+ and Zn2+ concentrations. Characterization analysis confirmed that formation of phosphates including Cd(PO4)2 and dissolution of minerals including PbZnSiO2 were the reason for HMs immobilization and mobilization in vanadium tailing slags. This study provides new insights for understanding biomineralization technology and using MIPP to remediate HMs contaminated mine waste.

Radiation-Tolerant Fibrivirga spp. from Rhizosphere Soil: Genome Insights and Potential in Agriculture

The rhizosphere of plants contains a wide range of microorganisms that can be cultivated and used for the benefit of agricultural practices. From garden soil near the rhizosphere region, Strain ES10-3-2-2 was isolated, and the cells were Gram-negative, aerobic, non-spore-forming rods that were 0.3-0.8 µm in diameter and 1.5-2.5 µm in length. The neighbor-joining method on 16S rDNA similarity revealed that the strain exhibited the highest sequence similarities with "Fibrivirga algicola JA-25" (99.2%) and Fibrella forsythia HMF5405T (97.3%). To further explore its biotechnological potentialities, we sequenced the complete genome of this strain employing the PacBio RSII sequencing platform. The genome of Strain ES10-3-2-2 comprises a 6,408,035 bp circular chromosome with a 52.8% GC content, including 5038 protein-coding genes and 52 RNA genes. The sequencing also identified three plasmids measuring 212,574 bp, 175,683 bp, and 81,564 bp. Intriguingly, annotations derived from the NCBI-PGAP, eggnog, and KEGG databases indicated the presence of genes affiliated with radiation-resistance pathway genes and plant-growth promotor key/biofertilization-related genes regarding Fe acquisition, K and P assimilation, CO2 fixation, and Fe solubilization, with essential roles in agroecosystems, as well as genes related to siderophore regulation. Additionally, T1SS, T6SS, and T9SS secretion systems are present in this species, like plant-associated bacteria. The inoculation of Strain ES10-3-2-2 to Arabidopsis significantly increases the fresh shoot and root biomass, thereby maintaining the plant quality compared to uninoculated controls. This work represents a link between radiation tolerance and the plant-growth mechanism of Strain ES10-3-2-2 based on in vitro experiments and bioinformatic approaches. Overall, the radiation-tolerant bacteria might enable the development of microbiological preparations that are extremely effective at increasing plant biomass and soil fertility, both of which are crucial for sustainable agriculture.

A novel integrated approach employing Desertifilum tharense BERC-3 for efficient wastewater valorization and recycling for developing peri-urban algae farming system

Peri-urban environments are significant reservoirs of wastewater, and releasing this untreated wastewater from these resources poses severe environmental and ecological threats. Wastewater mitigation through sustainable approaches is an emerging area of interest. Algae offers a promising strategy for carbon-neutral valorization and recycling of urban wastewater. Aiming to provide a proof-of-concept for complete valorization and recycling of urban wastewater in a peri-urban environment in a closed loop system, a newly isolated biocrust-forming cyanobacterium Desertifilum tharense BERC-3 was evaluated. Here, the highest growth and lipids productivity were achieved in urban wastewater compared to BG11 and synthetic wastewater. D. tharense BERC-3 showed 60-95% resource recovery efficiency and decreased total dissolved solids, chemical oxygen demand, biological oxygen demand, nitrate nitrogen, ammonia nitrogen and total phosphorus contents of the water by 60.37%, 81.11%, 82.75%, 87.91%, 85.13%, 85.41%, 95.87%, respectively, making it fit for agriculture as per WHO's safety limits. Soil supplementation with 2% wastewater-cultivated algae as a soil amender, along with its irrigation with post-treated wastewater, improved the nitrogen content and microbial activity of the soil by 0.3-2.0-fold and 0.5-fold, respectively. Besides, the availability of phosphorus was also improved by 1.66-fold. The complete bioprocessing pipeline offered a complete biomass utilization. This study demonstrated the first proof-of-concept of integrating resource recovery and resource recycling using cyanobacteria to develop a peri-urban algae farming system. This can lead to establishing wastewater-driven algae cultivation systems as novel enterprises for rural migrants moving to urban areas.

Feasibility of composted green waste amended by vermiculite and earthworm casts as the growth media for three common ornamental plants

This study demonstrated the effects of adding specific proportions of vermiculite (VMT: 0%, 10%, and 20%) and earthworm casts (EWCs: 0%, 10%, and 20%) on the physico-chemical properties of composted green waste (CGW), and the impacts of amended CGW as growth media on the growth of three common ornamental plants (Dahlia pinnata Cav. [dahlia], Centaurea cyanus L. [cornflower], and Consolida ajacis [L.] Schur [delphinium]). Compared with Treatment T1 (CK), the addition of 10% VMT and 20% EWCs greatly (p < 0.05) increased the total porosity, aeration porosity, water-holding porosity, total nitrogen, available phosphorus, available potassium, and organic matter of CGW by 9%, 35%, 4%, 18%, 27%, 13%, and 33%, respectively. In addition, this pattern increased (p < 0.05) the total fresh biomass, total chlorophyll content, and root length of dahlias by 9%, 19%, and 27%, respectively; those of cornflowers by 17%, 30%, and 29%, respectively (p < 0.05); and those of delphiniums by 23%, 14%, and 63%, respectively. Therefore, the amended CGW supplemented with 10% VMT and 20% EWCs was an ideal growth medium for the three plants.

Variations in different preceding crops on the soil environment, bacterial community richness and diversity of tobacco-planting soil

Tobacco (Nicotiana tabacum L.) is a major cash crop, and soil quality played a significant role in the yield and quality of tobacco. Most farmers cultivate tobacco in rotation with other crops to improve the soil characteristics. However, the effects of different previous crops on the soil's nutrient status and bacterial community for tobacco cultivation still need to be determined. Three treatments were assessed in this study, i.e., tobacco-planting soil without treatment (CK), soil with barley previously cultivated (T1), and soil with rapeseed previously cultivated (T2). The soil physical and chemical properties and the 16S rRNA gene sequence diversity of the bacterial community were analyzed. The effects of different crops on the physical and chemical properties of tobacco-planting soil and the diversity and richness of the bacterial community were comprehensively discussed. The results of this study showed that different previously cultivated crops altered the nutrient status of the soil, with changes in the ratio of NH4 +-N to NO3 --N having the most significant impact on tobacco. In CK, the ratio of NH4 +-N to NO3 --N was 1:24.2, T1-1:9.59, and T2-1:11.10. The composition of the bacterial community in tobacco-planting soil varied significantly depending on the previously cultivated crops. The richness and diversity of the bacterial community with different crops were considerably higher than without prior cultivation of different crops. The dominant bacteria in different treatments were Actinobacteriota, Proteobacteria, and Chloroflexi with their relative abundance differed. In conclusion, our study revealed significant differences in nutrient status, bacterial community diversity, and the richness of tobacco-planting soil after the preceding cultivation of different crops. Suitable crops should be selected to be previously cultivated in tobacco crop rotations in near future for sustainable agriculture.

Emerging nitrogen-fixing cyanobacteria for sustainable cotton cultivation

Amid growing environmental concerns and the imperative for sustainable agricultural practices, this study examines the potential of nitrogen-fixing cyanobacteria as biofertilizers, particularly in cotton cultivation. The reliance on synthetic nitrogen fertilizers (SNFs), prevalent in modern agriculture, poses significant environmental challenges, including greenhouse gas emissions and water system contamination. This research aims to shift this paradigm by exploring the capacity of cyanobacteria as a natural and sustainable alternative. Utilizing advanced metabarcoding methods to analyze the 16S rRNA gene, we conducted a comprehensive assessment of soil bacterial communities within cotton fields. This study focused on evaluating the diversity, structure, taxonomic composition, and potential functional characteristics of these communities. Emphasis was placed on the isolation of native N2-fixing cyanobacteria strains rom cotton soils, and their subsequent effects on cotton growth. Results from our study demonstrate significant plant growth-promoting (PGP) activities, measured as N2 fixation, production of Phytohormones, Fe solubilization and biofertilization potential of five isolated cyanobacterial strains, underscoring their efficacy in cotton. These findings suggest a viable pathway for replacing chemical-synthetic nitrogen fertilizers with natural, organic alternatives. The reintegration of these beneficial species into agricultural ecosystems can enhance crop growth while fostering a balanced microbial environment, thus contributing to the broader goals of global sustainable agriculture.

Potential synergy of microplastics and nitrogen enrichment on plant holobionts in wetland ecosystems

Wetland ecosystems are global hotspots for environmental contaminants, including microplastics (MPs) and nutrients such as nitrogen (N) and phosphorus (P). While MP and nutrient effects on host plants and their associated microbial communities at the individual level have been studied, their synergistic effects on a plant holobiont (i.e., a plant host plus its microbiota, such as bacteria and fungi) in wetland ecosystems are nearly unknown. As an ecological entity, plant holobionts play pivotal roles in biological nitrogen fixation, promote plant resilience and defense chemistry against pathogens, and enhance biogeochemical processes. We summarize evidence based on recent literature to elaborate on the potential synergy of MPs and nutrient enrichment on plant holobionts in wetland ecosystems. We provide a conceptual framework to explain the interplay of MPs, nutrients, and plant holobionts and discuss major pathways of MPs and nutrients into the wetland milieu. Moreover, we highlight the ecological consequences of loss of plant holobionts in wetland ecosystems and conclude with recommendations for pending questions that warrant urgent research. We found that nutrient enrichment promotes the recruitment of MPs-degraded microorganisms and accelerates microbially mediated degradation of MPs, modifying their distribution and toxicity impacts on plant holobionts in wetland ecosystems. Moreover, a loss of wetland plant holobionts via long-term MP-nutrient interactions may likely exacerbate the disruption of wetland ecosystems' capacity to offer nature-based solutions for climate change mitigation through soil organic C sequestration. In conclusion, MP and nutrient enrichment interactions represent a severe ecological risk that can disorganize plant holobionts and their taxonomic roles, leading to dysbiosis (i.e., the disintegration of a stable plant microbiome) and diminishing wetland ecosystems' integrity and multifunctionality.

Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change

Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.

Enhancing Water Status and Nutrient Uptake in Drought-Stressed Lettuce Plants (Lactuca sativa L.) via Inoculation with Different Bacillus spp. Isolated from the Atacama Desert

Drought is a major challenge for agriculture worldwide, being one of the main causes of losses in plant production. Various studies reported that some soil's bacteria can improve plant tolerance to environmental stresses by the enhancement of water and nutrient uptake by plants. The Atacama Desert in Chile, the driest place on earth, harbors a largely unexplored microbial richness. This study aimed to evaluate the ability of various Bacillus sp. from the hyper arid Atacama Desert in the improvement in tolerance to drought stress in lettuce (Lactuca sativa L. var. capitata, cv. "Super Milanesa") plants. Seven strains of Bacillus spp. were isolated from the rhizosphere of the Chilean endemic plants Metharme lanata and Nolana jaffuelii, and then identified using the 16s rRNA gene. Indole acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity were assessed. Lettuce plants were inoculated with Bacillus spp. strains and subjected to two different irrigation conditions (95% and 45% of field capacity) and their biomass, net photosynthesis, relative water content, photosynthetic pigments, nitrogen and phosphorus uptake, oxidative damage, proline production, and phenolic compounds were evaluated. The results indicated that plants inoculated with B. atrophaeus, B. ginsengihumi, and B. tequilensis demonstrated the highest growth under drought conditions compared to non-inoculated plants. Treatments increased biomass production and were strongly associated with enhanced N-uptake, water status, chlorophyll content, and photosynthetic activity. Our results show that specific Bacillus species from the Atacama Desert enhance drought stress tolerance in lettuce plants by promoting several beneficial plant traits that facilitate water absorption and nutrient uptake, which support the use of this unexplored and unexploited natural resource as potent bioinoculants to improve plant production under increasing drought conditions.

Identification and Characterization of Beneficial Soil Microbial Strains for the Formulation of Biofertilizers Based on Native Plant Growth-Promoting Microorganisms Isolated from Northern Mexico

Plant growth-promoting microorganisms (PGPM) benefit plant health by enhancing plant nutrient-use efficiency and protecting plants against biotic and abiotic stresses. This study aimed to isolate and characterize autochthonous PGPM from important agri-food crops and nonagricultural plants to formulate biofertilizers. Native microorganisms were isolated and evaluated for PGP traits (K, P, and Zn solubilization, N2-fixation, NH3-, IAA and siderophore production, and antifungal activity against Fusarium oxysporum). Isolates were tested on radish and broccoli seedlings, evaluating 19 individual isolates and 12 microbial consortia. Potential bacteria were identified through DNA sequencing. In total, 798 bacteria and 209 fungi were isolated. Isolates showed higher mineral solubilization activity than other mechanisms; 399 bacteria and 156 fungi presented mineral solubilization. Bacteria were relevant for nitrogen fixation, siderophore, IAA (29-176 mg/L), and ammonia production, while fungi for Fusarium growth inhibition (40-69%). Twenty-four bacteria and eighteen fungi were selected for their PGP traits. Bacteria had significantly (ANOVA, p < 0.05) better effects on plants than fungi; treatments improved plant height (23.06-51.32%), leaf diameter (25.43-82.91%), and fresh weight (54.18-85.45%) in both crops. Most potential species belonged to Pseudomonas, Pantoea, Serratia, and Rahnella genera. This work validated a high-throughput approach to screening hundreds of rhizospheric microorganisms with PGP potential isolated from rhizospheric samples.

Date Palm Waste Compost Application Increases Soil Microbial Community Diversity in a Cropping Barley (Hordeum vulgare L.) Field

Application of date palm waste compost is quite beneficial in improving soil properties and crop growth. However, the effect of its application on soil microbial communities is less understood. High-throughput sequencing and quantitative real-time PCR (qPCR) were used to evaluate the effect of compost application on the soil microbial composition in a barley field during the tillering, booting and ripening stages. The results showed that compost treatment had the highest bacterial and fungal abundance, and its application significantly altered the richness (Chao1 index) and α-diversity (Shannon index) of fungal and bacterial communities. The dominant bacterial phyla found in the samples were Proteobacteria and Actinobacteria while the dominant fungal orders were Ascomycota and Mortierellomycota. Interestingly, compost enriched the relative abundance of beneficial microorganisms such as Chaetomium, Actinobacteriota, Talaromyces and Mortierella and reduced those of harmful microorganisms such as Alternaria, Aspergillus and Neocosmospora. Functional prediction based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed that amplicon sequence variant (ASV) sequences related to energy metabolism, amino acid metabolism and carbohydrate metabolism were associated with compost-treated soil. Based on Fungi Functional Guild (FUNGuild), identified fungi community metabolic functions such as wood saprotroph, pathotroph, symbiotroph and endophyte were associated with compost-treated soil. Overall, compost addition could be considered as a sustainable practice for establishing a healthy soil microbiome and subsequently improving the soil quality and barley crop production.