Biochar amendment reduces cadmium uptake by stimulating cadmium-resistant PGPR in tomato rhizosphere

Biochar's role in improving pakchoi quality and microbial community structure in rhizosphere soil

Background

Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi (Brassica campestris L.) quality and rhizosphere soil microorganisms are limited, especially in weakly alkaline soils. The experiment was set up to explore the effect of different concentrations of biochar on vegetable quality and the correlation between the index of quality and soil bacterial community structure changes.

Methods

The soil was treated in the following ways via pot culture: the blank control (CK) without biochar added and with biochar at different concentrations of 1% (T1), 3% (T2), 5% (T3), and 7% (T4). Here, we investigatedthe synergistic effect of biochar on the growth and quality of pakchoi, soil enzymatic activities, and soil nutrients. Microbial communities from pakchoi rhizosphere soil were analyzed by Illumina MiSeq.

Results

The results revealed that adding 3% biochar significantly increased plant height, root length, and dry weight of pakchoi and increased the contents of soluble sugars, soluble proteins, Vitamin C (VC), cellulose, and reduced nitrate content in pakchoi leaves. Meanwhile, soil enzyme activities and available nutrient content in rhizosphere soil increased. This study demonstrated that the the microbial community structure of bacteria in pakchoi rhizosphere soil was changed by applying more than 3% biochar. Among the relatively abundant dominant phyla, Gemmatimonadetes, Anaerolineae, Deltaproteobacteria and Verrucomicrobiae were reduced, and Alphaproteobacteria, Gammaproteobacteria, Bacteroidia, and Acidimicrobiia relative abundance increased. Furthermore, adding 3% biochar reduced the relative abundance of Gemmatimonas and increased the relative abundances of Ilumatobacter, Luteolibacter, Lysobacter, Arthrobacter, and Mesorhizobium. The nitrate content was positively correlated with the abundance of Gemmatimonadetes, and the nitrate content was significantly negatively correlated with the relative abundance of Ilumatobacter. Carbohydrate transport and metabolism in the rhizosphere soil of pakchoi decreased, and lipid transport and metabolism increased after biochar application.

Conclusion

Overall, our results indicated that applying biochar improved soil physicochemical states and plant nutrient absorption, and affected the abundance of dominant bacterial groups (e.g., Gemmatimonadetes and Ilumatobacter), these were the main factors to increase pakchoi growth and promote quality of pakchoi. Therefore, considering the growth, quality of pakchoi, and soil environment, the effect of using 3% biochar is better.

Serratia marcescens LYGN1 Reforms the Rhizosphere Microbial Community and Promotes Cucumber and Pepper Growth in Plug Seedling Cultivation

The vegetable plug seedling plays an important role in improving vegetable production. The process of plug seedling contributes to high-quality vegetable seedlings. The substrate composition and chemical fertilizer are widely studied to promote seedling growth. However, little is known about the effect of beneficial bacteria in the rhizosphere microbial community and vegetables' growth during plug seedling. The use of beneficial microbes to promote vegetable seedling growth is of great potential. In this study, we showed that the Serratia marcescens strain LYGN1 enhanced the growth of cucumber and pepper seedlings in plug seedling cultivation. The treatment with LYGN1 significantly increased the biomass and the growth-related index of cucumber and pepper, improving the seedling quality index. Specifically, LYGN1 also improved the cucumber and pepper root system architecture and increased the root diameter. We applied high-throughput sequencing to analyze the microbial community of the seedlings' rhizosphere, which showed LYGN1 to significantly change the composition and structure of the cucumber and pepper rhizosphere microbial communities. The correlation analysis showed that the Abditibacteriota and Bdellovibrionota had positive effects on seedling growth. The findings of this study provide evidence for the effects of Serratia marcescens LYGN1 on the cucumber and pepper rhizosphere microbial communities, which also promoted seedling quality in plug seedling cultivation.

Keystone taxa of phoD-harboring bacteria mediate alkaline phosphatase activity during biochar remediation of Cd-contaminated soil

Phosphorus (P)-modified biochar can efficiently remediate cadmium (Cd)-contaminated soil. However, the mechanisms of responses of alkaline phosphatase (ALP) and phoD-harboring microorganisms, which are notably sensitive to Cd and P, are not clear during the remediation process. In this study, apple (Malus domestica) tree branches were co-pyrolyzed with tripotassium phosphate (K3PO4) to prepare P-modified biochar, which was used to remediate Cd-soil contaminated soil collected near a mine site. The effect of P-modified biochar on the composition of the phoD-harboring microbial community and its mechanism of interacting with ALP were analyzed. The results showed that the application of P-modified biochar to Cd-contaminated soil promoted the co-precipitation of Cd and phosphate and reduced the content of bioavailable Cd by 69.77 %. P-modified biochar improved the complexity and stability of the soil phoD-harboring microbial community. Furthermore, this study clarified that ALP activity was not completely regulated by the abundance of phoD, but Priestia and Massilia that contain phoD genes dominated the activity of ALP in rhizosphere and bulk soils, respectively. It is notable that bioavailable Cd significantly stimulated Priestia, Massilia, and ALP activity. These findings provide a theoretical basis for the application of P-modified biochar to the remediation of soil contaminated with Cd with respect to P functional microorganisms.

Bioremediation of PBDEs and heavy metals co-contaminated soil in e-waste dismantling sites by Pseudomonas plecoglossicida assisted with biochar

Biochar-assisted microbial remediation has been proposed as a promising strategy to eliminate environmental pollutants. However, studies on this strategy used in the remediation of persistent organic pollutants and heavy metals co-contaminated soil are lacking, and the effect of the combined incorporation of biochar and inoculant on the assembly, functions, and microbial interactions of soil microbiomes are unclear. Here, we studied 2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) degradation and heavy metal immobilization by and biochar-based bacterial inoculant (BC/PP) in an e-waste contaminated soil, and corresponding microbial regulation mechanisms. Results showed that BC/PP addition was more effective in reducing Cu and Pb availability and degrading BDE-47 than inoculant alone. Notably, BC/PP facilitated bound-residue formation of BDE-47, reducing the ecological risk of residual BDE-47. Meanwhile, microbial carbon metabolism and enzyme activities (related to C-, N-, and P- cycles) were enhanced in soil amended with BC/PP. Importantly, biochar played a crucial role in inoculant colonization, community assembly processes, and microbiome multifunction. In the presence of biochar, positive interactions in co-occurrence networks of the bacterial community were more frequent, and higher network stability and more keystone taxa were observed (including potential degraders). These findings provide a promising strategy for decontaminating complex-polluted environments and recovering soil ecological functions.

Biochar applications for treating potentially toxic elements (PTEs) contaminated soils and water: a review

Environmental pollution with potentially toxic elements (PTEs) has become one of the critical and pressing issues worldwide. Although these pollutants occur naturally in the environment, their concentrations are continuously increasing, probably as a consequence of anthropic activities. They are very toxic even at very low concentrations and hence cause undesirable ecological impacts. Thus, the cleanup of polluted soils and water has become an obligation to ensure the safe handling of the available natural resources. Several remediation technologies can be followed to attain successful remediation, i.e., chemical, physical, and biological procedures; yet many of these techniques are expensive and/or may have negative impacts on the surroundings. Recycling agricultural wastes still represents the most promising economical, safe, and successful approach to achieving a healthy and sustainable environment. Briefly, biochar acts as an efficient biosorbent for many PTEs in soils and waters. Furthermore, biochar can considerably reduce concentrations of herbicides in solutions. This review article explains the main reasons for the increasing levels of potentially toxic elements in the environment and their negative impacts on the ecosystem. Moreover, it briefly describes the advantages and disadvantages of using conventional methods for soil and water remediation then clarifies the reasons for using biochar in the clean-up practice of polluted soils and waters, either solely or in combination with other methods such as phytoremediation and soil washing technologies to attain more efficient remediation protocols for the removal of some PTEs, e.g., Cr and As from soils and water.

Biochar loaded with bacteria enhanced Cd/Zn phytoextraction by facilitating plant growth and shaping rhizospheric microbial community

Biochar and metal-tolerant bacteria have been widely used in the remediation of heavy metal contaminated soil. However, the synergistic effect of biochar-functional microbes on phytoextraction by hyperaccumulators remains unclear. In this study, the heavy metal-tolerant strain Burkholderia contaminans ZCC was selected and loaded on biochar to produce biochar-resistant bacterial material (BM), and the effects of BM on Cd/Zn phytoextraction by Sedum alfredii Hance and rhizospheric microbial community were explored. The results showed that, BM application significantly enhanced the Cd and Zn accumulation of S. alfredii by 230.13% and 381.27%, respectively. Meanwhile, BM alleviated metal toxicity of S. alfredii by reducing oxidative damage and increasing chlorophyll and antioxidant enzyme activity. High-throughput sequencing revealed that BM significantly improved soil bacterial and fungal diversity, and increased the abundance of genera with plant growth promoting and metal solubilizing functions such as Gemmatimonas, Dyella and Pseudarthrobacter. Co-occurrence network analysis showed that BM significantly increased the complexity of the rhizospheric bacterial and fungal network. Structural equation model analysis revealed that soil chemistry property, enzyme activity and microbial diversity contributed directly or indirectly to Cd and Zn extraction by S. alfredii. Overall, our results suggested that biochar- B. contaminans ZCC was able to enhance the growth and Cd/Zn accumulation by S. alfredii. This study enhanced our understanding on the hyperaccumulator-biochar-functional microbe interactions, and provided a feasible strategy for promoting the phytoextraction efficiency of heavy metal contaminated soils.

Co-application of organic amendments and Cd-tolerant rhizobacteria for suppression of cadmium uptake and regulation of antioxidants in tomato

Cadmium (Cd) contamination is a major environmental concern with well-reported adverse impacts on environment and living entities. It limits the productivity of agricultural crops due to its excessive entry to plant tissues, and subsequent toxic effects on their growth and physiology. Application of metal tolerant rhizobacteria in combination with organic amendments has shown beneficial impacts in sustaining plant growth, on account of amendments mediated decreased metal mobility via different functional groups, as well as provision of carbon to microorganisms. We evaluated the effect of organic amendments (compost and biochar) and Cd-tolerant rhizobacteria on growth, physiology, and Cd uptake in tomato (Solanum lycopersicum). Plants were grown under Cd contamination (2 mg kg^-1), and were supplemented with 0.5% w/w of compost and biochar along with rhizobacterial inoculation in pot culture. We observed a significant reduction in shoot length, fresh and dry biomass (37, 49 and 31%) and root attributes such as root length, fresh and dry weights (35, 38 and 43%). However, Cd tolerant PGPR strain 'J-62' along with compost and biochar (0.5% w/w) mitigated the Cd induced adverse impacts on different plant attributes and improved these attributes such as root and shoot lengths (112 and 72%), fresh (130 and 146%) and dry weights (119 and 162%) of tomato roots and shoots as compared to relative control treatment. Furthermore, we observed significant increments in different antioxidant activities such as SOD (54%), CAT (49%) and APX (50%) under Cd contamination. Combined application of 'J-62' strain and organic amendments also decreased Cd translocation towards different above-ground plant parts as was pragmatic in terms of bioconcentration and translocation factors of Cd, which indicated phyto-stabilization ability of our inoculated strain for Cd. Hence, Cd tolerant PGPR in combination with organic amendments can immobilize Cd in soil and thereby, can alleviate Cd induced adverse impacts on tomato growth.

Litter mixing promoted decomposition and altered microbial community in common bean root litter

BACKGROUND

Decomposition of plant litter is a key driver of carbon and nutrient cycling in terrestrial ecosystems. Mixing litters of different plant species may alter the decomposition rate, but its effect on the microbial decomposer community in plant litter is not fully understood. Here, we tested the effects of mixing with maize (Zea mays L.) and soybean [Glycine max (Linn.) Merr.] stalk litters on the decomposition and microbial decomposer communities of common bean (Phaseolus vulgaris L.) root litter at the early decomposition stage in a litterbag experiment.

RESULTS

Mixing with maize stalk litter, soybean stalk litter, and both of these litters increased the decomposition rate of common bean root litter at 56 day but not 14 day after incubation. Litter mixing also increased the decomposition rate of the whole liter mixture at 56 day after incubation. Amplicon sequencing found that litter mixing altered the composition of bacterial (at 56 day after incubation) and fungal communities (at both 14 and 56 day after incubation) in common bean root litter. Litter mixing increased the abundance and alpha diversity of fungal communities in common bean root litter at 56 day after incubation. Particularly, litter mixing stimulated certain microbial taxa, such as Fusarium, Aspergillus and Stachybotrys spp. In addition, a pot experiment with adding litters in the soil showed that litter mixing promoted growth of common bean seedlings and increased soil nitrogen and phosphorus contents.

CONCLUSIONS

This study showed that litter mixing can promote the decomposition rate and cause shifts in microbial decomposer communities, which may positively affect crop growth.

Solid and modified biochars mitigate root cell lignification and improve nutrients uptake in mint plants under fluoride and cadmium stresses

Lignification is a physiological process that reduces pollutants' entrance into plant root cells via blocking apoplastic pathways. The closure of apoplastic pathways can also decrease the nutrients' uptake by roots. Application of biochar as an efficient soil amendment might be useful in increasing nutrients influx into root cells by decreasing lignification. Therefore, this experiment was performed to examine the conceivable effects of biochar forms [solid and chemically altered biochars with H₂O_2, KOH and H₃PO₄ (25 g biochar forms kg^-1 soil)] on modifying lignification process and nutrients uptake by mint (Mentha crispa L.) plants under toxicity of cadmium and fluoride. The biochar treatments boosted plant root growth and activity as well as the real content and maximum sorption capacity of Zn, Fe, Mg, and Ca under stressful conditions. In contrast, biochar treatments increased root cell viability and reduced fluoride and cadmium contents, and oxidative damages under stressful conditions. The biochar treatments decreased the activity of phenylalanine ammonia-lyase and peroxidase enzymes under toxic conditions, which led to a decrease in the contents of lignin and its monomers (p-hydroxybenzaldehyde, guaiacyl, and syringaldehyde) in the roots. Solid biochar was less effective than engineered biochars in reducing root cell lignification. Therefore, addition of biochar forms to the soil could be an effective way to reduce root cell lignification and enhance nutrients uptake by plants under cadmium and fluoride toxicities.

Microbiological mechanism for "production while remediating" in Cd-contaminated paddy fields: A field experiment

Security utilization measures (SUMs) for "production while remediating" in moderate and mild Cd-polluted paddy fields had been widely used. To investigate how SUMs drove rhizosphere soil microbial communities and reduced soil Cd bioavailability, a field experiment was conducted using soil biochemical analysis and 16S rRNA high-throughput sequencing. Results showed that SUMs improved rice yield by increasing the number of effective panicles and filled grains, while also inhibiting soil acidification and enhancing disease resistance by improving soil enzyme activities. SUMs also reduced the accumulation of harmful Cd in rice grains and transformed it into FeMn oxidized Cd, organic-bound Cd, and residual Cd in rhizosphere soil. This was partly due to the higher degree of soil DOM aromatization, which helped complex the Cd with DOM. Additionally, the study also found that microbial activity was the primary source of soil DOM, and that SUMs increased the diversity of soil microbes and recruited many beneficial microbes (Arthrobacter, Candidatus_Solibacter, Bryobacter, Bradyrhizobium, and Flavisolibacter) associated with organic matter decomposition, plant growth promotion, and pathogen inhibition. Besides, special taxa (Bradyyrhizobium and Thermodesulfovibrio) involved in sulfate/sulfur ion generation and nitrate/nitrite reduction pathway were observably enriched, which effectively reduced the soil Cd bioavailability through adsorption and co-precipitation. Therefore, SUMs not only changed the soil physicochemical properties (e.g., pH), but also drove rhizosphere microbes to participate in the chemical species transformation of soil Cd, thus reducing Cd accumulation in rice grains.

The Effect of Cadmium Tolerant Plant Growth Promoting Rhizobacteria on Plant Growth Promotion and Phytoremediation: A Review

Cadmium (Cd) is a heavy metal of considerable toxicity with destructive impacts on plants, microbes and environments. Its toxicity is due to mishandling and manual hazards in plants and is primarily observed within the soil to cause decline of plants and microbial activity inside the rhizosphere. Cadmium accumulation in crops and the probability of Cd entering the food chain are grave for public health in the worldwide. Cadmium toxicity leads to depletion in seed germination, initial seedling growth, plant biomass, chlorosis, necrosis, hindrance of photosynthetic machinery and other physiological and biological activities in plants. Cadmium triggers the reactive oxygen species (ROS) that influences gene mutation and DNA damage that affects the cell cycle and cell division. Cd toxicity altered the levels of phenolic compounds, carbohydrates, glycine betaine, proline and organic acids in crops. Under stress conditions, the plant growth promoting rhizobacteria (PGPR) have various properties such as enzymatic activities, plant growth hormones production, phosphate solubilization, siderophores production and chelating agents that help the plants tolerate against Cd stress and also increase phenolic compound levels and osmolytes. Hence, this review highlights the crucial role of cadmium tolerant PGPR for crop production, declining metal phytoavailability and enhancing morphological and physiological boundaries of plants under stress conditions. It could be an environment friendly and cost effective technology under sustainable crop production.

Genome-wide identification and expression analysis of SlRR genes in response to abiotic stress in tomato

The cytokinin two-component signal transduction system (TCS) is involved in many biological processes, including hormone signal transduction and plant growth regulation. Although cytokinin TCS has been well characterized in Arabidopsis thaliana, its role in tomato remains elusive. In this study, we characterized the diversity and function of response regulator (RR) genes, a critical component of TCS, in tomato. In total, we identified 31 RR genes in the tomato genome. These SlRR genes were classified into three subgroups (type-A, type-B and type-C). Various stress-responsive cis-elements were present in the tomato RR gene promoters. Their expression responses under pesticide treatment were evaluated by transcriptome analysis. Their expression under heat, cold, ABA, salinity and NaHCO₃ treatments was further investigated by qRT-PCR and complemented with the available transcription data under these treatments. Specifically, SlRR13 expression was significantly upregulated under salinity, drought, cold and pesticide stress and was downregulated under ABA treatment. SlRR23 expression was induced under salt treatment, while the transcription level of SlRR1 was increased under cold and decreased under salt stress. We also found that GATA transcription factors played a significant role in the regulation of SlRR genes. Based on our results, tomato SlRR genes are involved in responses to abiotic stress in tomato and could be implemented in molecular breeding approaches to increase resistance of tomato to environmental stresses.

L-phenylalanine in potato onion (Allium cepa var. aggregatum G. Don) root exudates mediates neighbor detection and trigger physio-morphological root responses of tomato

INTERACTION

Despite numerous recent insights into neighbor detection and belowground plant communication mediated by root exudates, less is known about the specificity and nature of substances within root exudates and the mechanism by which they may act belowground in root-root interactions.

METHODS

Here, we used a coculture experiment to study the root length density (RLD) of tomato (Solanum lycopersicum L.) grown with potato onion (Allium cepa var. aggregatum G. Don) cultivars with growth-promoting (S-potato onion) or no growth-promoting (N-potato onion) effects.

RESULTS AND DISCUSSION

Tomato plants grown with growth-promoting potato onion or its root exudates increased root distribution and length density oppositely and grew their roots away as compared to when grown with potato onion of no growth-promoting potential, its root exudates, and control (tomato monoculture/distilled water treatment). Root exudates profiling of two potato onion cultivars by UPLC-Q-TOF/MS showed that L-phenylalanine was only found in root exudates of S-potato onion. The role of L-phenylalanine was further confirmed in a box experiment in which it altered tomato root distribution and forced the roots grow away. In vitro trial revealed that tomato seedlings root exposed to L-phenylalanine changed the auxin distribution, decreased the concentration of amyloplasts in columella cells of roots, and changed the root deviation angle to grow away from the addition side. These results suggest that L-phenylalanine in S-potato onion root exudates may act as an "active compound" and trigger physio-morphological changes in neighboring tomato roots.

The relationship between shifts in the rhizosphere microbial community and root rot disease in a continuous cropping American ginseng system

The root rot disease causes a great economic loss, and the disease severity usually increases as ginseng ages. However, it is still unclear whether the disease severity is related to changes in microorganisms during the entire growing stage of American ginseng. The present study examined the microbial community in the rhizosphere and the chemical properties of the soil in 1-4-year-old ginseng plants grown in different seasons at two different sites. Additionally, the study investigated ginseng plants' root rot disease index (DI). The results showed that the DI of ginseng increased 2.2 times in one sampling site and 4.7 times in another during the 4 years. With respect to the microbial community, the bacterial diversity increased with the seasons in the first, third, and fourth years but remained steady in the second year. The seasonal changing of relative abundances of bacteria and fungi showed the same trend in the first, third, and fourth years but not in the second year. Linear models revealed that the relative abundances of Blastococcus, Symbiobacterium, Goffeauzyma, Entoloma, Staphylotrichum, Gymnomyces, Hirsutella, Penicillium and Suillus spp. were negatively correlated with DI, while the relative abundance of Pandoraea, Rhizomicrobium, Hebeloma, Elaphomyces, Pseudeurotium, Fusarium, Geomyces, Polyscytalum, Remersonia, Rhizopus, Acremonium, Paraphaeosphaeria, Mortierella, and Metarhizium spp. were positively correlated with DI (P < 0.05). The Mantel test showed that soil chemical properties, including available nitrogen, phosphorus, potassium, calcium, magnesium, organic matter, and pH, were significantly correlated to microbial composition. The contents of available potassium and nitrogen were positively correlated with DI, while pH and organic matter were negatively correlated with DI. In summary, we can deduce that the second year is the key period for the shift of the American ginseng rhizosphere microbial community. Disease aggravation after the third year is related to the deterioration of the rhizosphere microecosystem.

Effects of Green Manures on Rhizosphere Fungal Community Composition of Cucumber Seedlings

Green manures are usually used to improve soil health and increase crop productivity. The activity and composition of the soil microbial community could be altered by green manures. High-throughput amplicon sequencing was used to assess the effects of green manures of wheat (Triticum aestivum) and Indian mustard (Brassica juncea) on the rhizosphere fungal community composition of cucumber (Cucumis sativus L). Results showed that green manures of wheat and Indian mustard altered the composition but not the diversity of rhizosphere fungal communities of cucumber Contents of inorganic N, Olsen P, and available K in bulk soil decreased by green manure treatments. Ascomycota, Zygomycota, and Basidiomycota were the predominant phyla in soil, and their relative abundance changed after treatment with wheat and Indian mustard. The relative abundance of Basidiomycota was increased in the green manure of wheat, while that of Zygomycota was decreased in the green manure of Indian mustard. The relative abundance of Ascomycota increased in both wheat and Indian mustard. Green manures of wheat and Indian mustard also increased the relative abundances of unclassified Sordariomycetes and Fusarium spp., whereas they decreased the relative abundances of Pseudallescheria, Mortierella, Kernia, and unclassified Chaetomiaceae spp. Compared with other treatments, green manures of wheat increased the relative abundance of Waitea sp. and decreased the relative abundance of Cephaliophora sp. Indian mustard increased the relative abundance of Humicola sp.

Facilitating effects of the reductive soil disinfestation process combined with Paenibacillus sp. amendment on soil health and physiological properties of Momordica charantia

Reductive soil disinfestation (RSD) is an anaerobic and facultative anaerobic microbial-mediated soil management process. The extent of improvement of diseased soil properties by RSD relative to comparable healthy soil is, however, not well characterized. Importantly, how to promote the colonization efficiency of these facultative anaerobic functional species to ensure soil and plant health remain unknown. Here, Fusarium wilt-diseased soil of Momordica charantia grown under a plastic-shed field (PS-CK) was used to conduct molasses-RSD (MO-RSD) along with Paenibacillus sp. (a model of facultative anaerobic species) (MO_PA-RSD) treatment, and the soil from a nearby open-air paddy field was considered comparable healthy soil (OA-CK). Both RSD treatments significantly improved the properties of PS-CK soil, and the extent of improvement of soil pH, Fusarium oxysporum reduction efficiency (98.36%~99.56%), and microbial community and functional composition were higher than that achieved for OA-CK soil, which indicated that RSD-regulated most soil properties outperformed those of the comparable healthy soil. The disease incidence and ascorbic acid content of M. charantia in MO-RSD- and MO_PA-RSD-treated soils were considerably decreased, while the weight and soluble protein contents were correspondingly increased, as compared to those of M. charantia in PS-CK soil. Specifically, the changes in these physiological properties of M. charantia in MO_PA-RSD soil performed well than that in MO-RSD soil. The relative abundances of Cohnella, Effusibacillus, Rummeliibacillus, Oxobacter, Thermicanus, and Penicillium enriched in both RSD-treated soils were positively correlated with Paenibacillus and negatively correlated with F. oxysporum population and disease incidence (P < 0.05). Notably, the relative abundances of these potential probiotics were considerably higher in MO_PA-RSD-treated soil than in MO-RSD alone-treated soil. These results show that the RSD process with inoculation of Paenibacillus sp. could promote the colonization of this species and simultaneously stimulate the proliferation of other probiotic consortia to further enhance soil health and plant disease resistance.

Synergistic effect of Bacillus subtilis and Paecilomyces lilacinus in alleviating soil degradation and improving watermelon yield

Continuous cropping of watermelon (Citrullus lanatus) may lead to soil degradation. As a soil conditioner, microbial agent has great potential in improving soil function and enhancing plant growth. In this study, we aimed to explore how microbial agent relieves the soil sickness of watermelon by analyzing watermelon performance, soil physicochemical properties and microbial community structures. Results suggested that microbial agent treatments significantly changed the photosynthetic efficiency of upper and lower leaves, which helped improve the growth of watermelon. The single fruit weight, fruit sugar degree and total phosphorus of soil following treatment with a mixture of Paecilomyces lilacinus DZ910 and Bacillus subtilis KC1723 (treatment D_K) were higher than those in single biofertilizer treatments and control. The soil microbial community under microbial agent treatments also changed significantly, indicating the feasibility of using microbial agents as soil remediations. The proportions of Pseudomonas and Flavobacterium, changed significantly after using microbial agents. Pseudomonas increased significantly after B. subtilis KC1723 and D_K treatments, while Flavobacterium increased significantly after using all three kinds of microbial agents compared to control. Increases in these bacteria were positively correlated with agronomic variables of watermelon. The fungi Aspergillus and Neocosmospora in the soil, which create an soil sickness of watermelon, decreased after KC1723 and D_K treatments. Meanwhile, Aspergillus and Neocosmospora were positively related to Myceliophthora incidence and negatively correlated with watermelon growth (single fruit weight and photosynthetic efficiency of upper leaves). Our microbial agent, especially D_K, represents a useful technique for alleviating soil sickness in watermelon.

Abundance, diversity, and composition of root-associated microbial communities varied with tall fescue cultivars under water deficit

The plant breeding program has developed many cultivars of tall fescue (Festuca arundinacea) with low maintenance and stress tolerance. While the root-associated microbial community helps confer stress tolerance in the host plant, it is still largely unknown how the microbiota varies with plant cultivars under water stress. The study aimed to characterize drought-responsive bacteria and fungi in the roots and rhizosphere of different tall fescue cultivars. Intact grass-soil cores were collected from six cultivars grown in a field trial under no-irrigation for 3 years. Tall fescue under irrigation was also sampled from an adjacent area as the contrast. Bacterial and fungal communities in roots, rhizosphere, and bulk soil were examined for abundance, diversity, and composition using quantitative-PCR and high-throughput amplicon sequencing of 16S rRNA gene and ITS regions, respectively. Differences in microbial community composition and structure between non-irrigated and irrigated samples were statistically significant in all three microhabitats. No-irrigation enriched Actinobacteria in all three microhabitats, but mainly enriched Basidiomycota in the root endosphere and only Glomeromycota in bulk soil. Tall fescue cultivars slightly yet significantly modified endophytic microbial communities. Cultivars showing better adaptability to drought encompassed more relatively abundant Actinobacteria, Basidiomycota, or Glomeromycota in roots and the rhizosphere. PICRUSt2-based predictions revealed that the relative abundance of functional genes in roots related to phytohormones, antioxidant enzymes, and nutrient acquisition was enhanced under no-irrigation. Significant associations between Streptomyces and putative drought-ameliorating genes underscore possible mechanics for microbes to confer tall fescue with water stress tolerance. This work sheds important insight into the potential use of endophytic microbes for screening drought-adaptive genotypes and cultivars.

Effects of continuous cropping Jiashi muskmelon on rhizosphere microbial community

Introduction

The continuous cropping of crops can result in the deterioration of the soil environment and cause a decline in plant health and yield, which complicates agricultural production. However, the effects of continuous melon cropping on rhizospheric microbial communities remain poorly understood.

Methods

In this study, high-throughput absolute quantification 16S rRNA gene amplicon sequencing was employed to analyze the bacterial community structure of greenhouse rhizosphere soil from Jiashi muskmelon replanted for 0, 1, 2, and 3 years (CK, 1a, 2a, and 3a, respectively).

Results

The results showed that long- term continuous cropping caused significant changes in soil physicochemical properties. The bacterial absolute abundances increased, but the bacterial community richness and diversity were significantly lost (p < 0.05). The composition of bacterial community was more similar after 2 and 3 years of continuous cropping. The longer the continuous cropping years were, the greater the shift in the bacterial diversity and abundance. Analysis of potential functional components revealed that different bacterial groups were enriched in different continuous cropping years. The significant reduction of the taxa associated with nitrate reduction may be responsible for the loss of soil nitrogen in continuous cropping soil.

Discussion

In summary, continuous cropping had a significant impact on the bacterial community structure of Jiashi muskmelon rhizospheric soil, and these results will provide a reference for soil management and scientific fertilization of melon and other crops under a continuous cropping regime.

Fosthiazate inhibits root-knot disease and alters rhizosphere microbiome of Cucumis melo var. saccharinus

Root-knot nematodes especially Meloidogyne spp. are considered as most destructive obligate parasites that substantially reduce crop yield and quality. Fosthiazate is an efficient organothiophosphate chemical with nematicidal activity against Meloidogyne spp. The present study aimed to analyze the efficacy of fosthiazate against root-knot disease in Cucumis melo var. saccharinus and its potential effects on rhizosphere microbiome and metabolites. The fosthiazate (40%) was applied two times by spraying on the day of transplanting and during the pollination period (after 31 days). Samples from treatment (fosthiazate 40%: MF) and control groups (untreated plants; MCK) were analysed through metagenomic and metabolomic profiling of rhizospheres. Results revealed that root-knot index of the MF group (9.26 ± 1.28) was significantly (p < 0.05) lower than the MCK group (22.06 ± 0.71) with a control effect of 57.85% after 31 days of the first spray, whereas fosthiazate efficacy reduced to 31.87% after 38 days of second application with significantly (p < 0.05) different root-knot index values (MF: 56 ± 1.43 and; MCK: 82.26 ± 3.87). However, Cucumis melo var. saccharinus fruit yield in both groups (MCK: 21.1 ± 0.9 and MF: 21.53 ± 0.85) showed no differences (p > 0.05). Metagenomic profiling revealed Proteobacteria, Acidobacteriota, and Firmicutes as predominant phyla and Bacillus, Sphingomonas, and Acidibacter as predominant genera in rhizosphere soil samples of both MF and MCK groups. Further, a t-test revealed higher differential enrichment of Firmicutes at phylum level and Bacillus at genus level in MF than MCK. Metabolomic profiling of rhizospheric soil revealed a total of six differential metabolites (p < 0.05), four of them (Sucrose, Hexaonic acid 1, (Z)-9-Octadecenamide 1, and Hexadecanamide) were up-regulated in MF group, whereas two of them (2,3,4-Trihydroxy-3-(Hydroxymethyl) Butanol and Sulfurous acid, 2, ethylhexylundecyl ester) were down-regulated in CK group. Our study concluded that fosthiazate exhibits a better control over the rook-knot disease in the short term and resulted in trackable changes in rhizosphere microbiome and metabolome.

Mixing planting with native tree species reshapes soil fungal community diversity and structure in multi-generational eucalypt plantations in southern China

The continuous planting pattern of eucalypt plantations negatively affects soil quality. A mixed planting pattern using native species implanted in pure plantations has been considered a preferable measure for this problem. However, the impact of this approachon the structure and function of fungal communities is not clear. Here, harvesting sites that had undergone two generations of eucalypt plantations were selected to investigate soil fungal community structure and the co-occurrence network characteristics in response to two silvicultural patterns involving the third generation of eucalypt plantations (E) and mixed plantations of Eucalyptus. urograndis × Cinnamomum. camphora (EC) and E. urograndis × Castanopsis. hystrix (EH). Compared with the first generation of eucalypt plantations (CK), E markedly weakened enzyme activities associated with carbon-, nitrogen-. and phosphorus-cycling. Reduced soil fungal alpha diversity, and elevated the relative abundance of Basidiomycota while decreasing the abundance of Ascomycota. In contrast, EC and EH not only enhanced fungal alpha diversity, but also reshaped fungal composition. At the class level, E caused an enrichment of oligotrophic Agaricomycetes fungi, classified into symbiotroph guild, while EC markedly decreased the abundance of those fungi and increased the abundances of Sordariomycetes, Dothideomycetes, Eurotiomycetes, and Tremellomycetes fungi, which were classified into saprotroph or pathotroph guild. Moreover, fungal network complexity and robustness topological attributes were higher or significantly higher in mixed plantations soils compared with those of pure eucalypt plantation E. Furthermore, fungal diversity, structure, and functional taxa were significantly affected by soil organic matter, pH, total nitrogen, and nitrate nitrogen.

Silicon modification improves biochar's ability to mitigate cadmium toxicity in tomato by enhancing root colonization of plant-beneficial bacteria

Modification of biochar, such as impregnation with minerals, can improve biochar's efficacy to mitigate heavy metal toxicity in plants. Biochar amendments can alter plant rhizosphere microbiome, which has profound effects on plant growth and fitness. Here, we tested whether rhizosphere microbiome is involved in the ability of silicon (Si)-modified biochar to mitigate cadmium toxicity in tomato (Solanum lycopersicum L.). We demonstrated that Si modification altered biochar's physico-chemical properties and enhanced its ability to mitigate cadmium toxicity in tomato. Particularly, the Si-modified biochar contained higher content of Si and increased plant-available Si content in the soil. The rhizosphere microbiome transplant experiment showed that changes in rhizosphere microbiome contributed to the mitigation of cadmium toxicity by biochar amendments. The raw biochar and Si-modified biochar differently altered tomato rhizosphere bacterial community composition. Both biochars, especially the Si-modified biochar, promoted specific bacterial taxa (e.g., Sphingomonas, Lysobacter and Pseudomonas spp.). Subsequent culturing found these promoted bacteria could mitigate cadmium toxicity in tomato. Moreover, both biochars stimulated tomato to recruit plant-beneficial bacteria with Si-modified biochar having stronger stimulatory effects, indicating that the positive effects of biochar on plant-beneficial bacteria was partially mediated via the host plant. Overall, Si modification enhanced biochar's ability to mitigate cadmium toxicity, which was linked to the stimulatory effects on plant-beneficial bacteria.

Populus root exudates are associated with rhizosphere microbial communities and symbiotic patterns

Introduction

Microbial communities in the plant rhizosphere are critical for nutrient cycling and ecosystem stability. However, how root exudates and soil physicochemical characteristics affect microbial community composition in Populus rhizosphere is not well understood.

Methods

This study measured soil physiochemistry properties and root exudates in a representative forest consists of four Populus species. The composition of rhizosphere bacterial and fungal communities was determined by metabolomics and high-throughput sequencing.

Results

Luvangetin, salicylic acid, gentisic acid, oleuropein, strigol, chrysin, and linoleic acid were the differential root exudates extracted in the rhizosphere of four Populus species, which explained 48.40, 82.80, 48.73, and 59.64% of the variance for the dominant and key bacterial or fungal communities, respectively. Data showed that differential root exudates were the main drivers of the changes in the rhizosphere microbial communities. Nitrosospira, Microvirga, Trichoderma, Cortinarius, and Beauveria were the keystone taxa in the rhizosphere microbial communities, and are thus important for maintaining a stable Populus microbial rhizosphere. The differential root exudates had strong impact on key bacteria than dominant bacteria, key fungi, and dominant fungi. Moreover, strigol had positively effects with bacteria, whereas phenolic compounds and chrysin were negatively correlated with rhizosphere microorganisms. The assembly process of the community structure (keystone taxa and bacterial dominant taxa) was mostly determined by stochastic processes.

Discussion

This study showed the association of rhizosphere microorganisms (dominant and keystone taxa) with differential root exudates in the rhizosphere of Populus plants, and revealed the assembly process of the dominant and keystone taxa. It provides a theoretical basis for the identification and utilization of beneficial microorganisms in Populus rhizosphere.

Microbiome analysis and biocontrol bacteria isolation from rhizosphere soils associated with different sugarcane root rot severity

To explore the causal pathogen and the correlated rhizosphere soil microecology of sugarcane root rot, we sampled the sugarcane root materials displaying different disease severity, and the corresponding rhizosphere soil, for systematic root phenotype and microbial population analyses. We found that with increased level of disease severity reflected by above-ground parts of sugarcane, the total root length, total root surface area and total volume were significantly reduced, accompanied with changes in the microbial population diversity and structure in rhizosphere soil. Fungal community richness was significantly lower in the rhizosphere soil samples from mildly diseased plant than that from either healthy plant, or severely diseased plant. Particularly, we noticed that a peculiar decrease of potential pathogenic fungi in rhizosphere soil, including genera Fusarium, Talaromyces and Neocosmospora, with increased level of disease severity. As for bacterial community, Firmicutes was found to be of the highest level, while Acidobacteria and Chloroflexi of the lowest level, in rhizosphere soil from healthy plant compared to that from diseased plant of different severity. FUNGuild prediction showed that the proportion of saprophytic fungi was higher in the rhizosphere soil of healthy plants, while the proportion of pathogenic fungi was higher in the rhizosphere soil of diseased plants. By co-occurrence network analysis we demonstrated the Bacillus and Burkholderia were in a strong interaction with Fusarium pathogen(s). Consistently, the biocontrol and/or growth-promoting bacteria isolated from the rhizosphere soil were mostly (6 out of 7) belonging to Bacillus and Burkholderia species. By confrontation culture and pot experiments, we verified the biocontrol and/or growth-promoting property of the isolated bacterial strains. Overall, we demonstrated a clear correlation between sugarcane root rot severity and rhizosphere soil microbiome composition and function, and identified several promising biocontrol bacteria strains with strong disease suppression effect and growth-promoting properties.

Metabolomics of plant root exudates: From sample preparation to data analysis

Plants release a set of chemical compounds, called exudates, into the rhizosphere, under normal conditions and in response to environmental stimuli and surrounding soil organisms. Plant root exudates play indispensable roles in inhibiting the growth of harmful microorganisms, while also promoting the growth of beneficial microbes and attracting symbiotic partners. Root exudates contain a complex array of primary and specialized metabolites. Some of these chemicals are only found in certain plant species for shaping the microbial community in the rhizosphere. Comprehensive understanding of plant root exudates has numerous applications from basic sciences to enhancing crop yield, production of stress-tolerant crops, and phytoremediation. This review summarizes the metabolomics workflow for determining the composition of root exudates, from sample preparation to data acquisition and analysis. We also discuss recent advances in the existing analytical methods and future perspectives of metabolite analysis.

Effect of Burkholderia ambifaria LK-P4 inoculation on the plant growth characteristics, metabolism, and pharmacological activity of Anoectochilus roxburghii

BACKGROUND

Plant growth-promoting bacteria (PGPB) represents a common biological fertilizer with remarkable effect in improving crop production and environmental friendliness.

METHODS

In the present work, we presented a detailed characterization of plant morphology and physiology, metabolism, and pharmacological activity of A. roxburghii between Burkholderia ambifaria LK-P4 inoculation and un-inoculation (CK) treatment by routine analytical techniques (include microscopy and enzymatic activity assays and so on) coupled with metabolomics approaches.

RESULTS

Morphological and physiological results showedthat the P4 bacteria could significantly increase plant stomatal density, freshweight, survival rate,and the content of total flavonoids in leaves but reducethe amount of free amino acid. Furthermore, metabolite data showed that fatty acids (linoleic acid, linolenic acid, stearic acid) and active substance (kyotorphin and piceatannol) were specifically up-regulated in P4 inoculation. It was also demonstrated that the differential metabolites were involved in citrate cycle, glyoxylate and dicarboxylate metabolism, and biosynthesis of unsaturated fatty acids pathway. In addition, pharmacological efficacy found that A. roxburghii under P4 inoculation can significantly decrease (p < 0.05) blood glucose levels and protect the organs of mice with similar effect of Glibenclamide tablets.

CONLUSION

Overall, it can be seen that the exogenous P4 bacteria can promote the growth and increase content of special metabolites in A. roxburghii. This study provided theoretical basis and supported for the high-yield and high-quality bionic cultivation of A. roxburghii.

The effects of allelochemicals from root exudates of Flaveria bidentis on two Bacillus species

To determine the allelopathic effects of root exudates from Flaveria bidentis on function of Bacillus, pot experiment was used to collect root exudates from living plants and test its allelopathic effects on function of Bacillus frigoritolerans and Bacillus megaterium, which were two dominant bacteria in the rhizosphere soil of F. bidentis. To obtain the allelopathic substances, the root exudates were successively extracted by N-hexane, dichloromethane, ethyl acetate, and N-butanol, and their allelopathic effects were tested. The results showed that B. frigoritolerans and B. megaterium considerably increased the concentration of available phosphorus and nitrogen, respectively, when the soil was treated with different concentrations of root exudates. Among the four organic solvent extracts, dichloromethane extracts significantly increased the abundances of B. frigoritolerans and B. megaterium and promoted their nitrogen-fixing and phosphate-solubilizing abilities. Phenol was detected in dichloromethane extracts by gas chromatograph-mass spectrometer (GC-MS). Meanwhile, phenol promoted the ability to fix nitrogen of B. megaterium and its growth by increasing the soil available nitrogen concentration, but phenol promoted the ability to solubilize phosphate of B. frigoritolerans only in 0.1mg/mL concentration. Therefore, phenol was an allelochemicals in the root exudates of F. bidentis that affects the growth and activities of B. megaterium.