Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar

Identifying rhizosphere bacteria and potential mechanisms linked to compost suppressiveness towards Fusarium oxysporum

BACKGROUND

Soilborne fungal phytopathogens pose a significant threat to global food security. While chemical control remains an effective method for managing these pathogens, increasing regulations due to health and environmental concerns, along with rising fungicide resistance, have restricted their use, underscoring the urgent need for sustainable alternatives. The use of compost to enhance soil fertility and suppress plant diseases is well documented. Several studies have underlined the role of microorganisms in disease suppression, but the mechanisms facilitating this disease suppression remain unclear. We evaluated the impact of compost amendment on the composition and functional capacity of the rhizosphere microbiome in cucumber plants (Cucumis sativus) inoculated with Fusarium oxysporum f. sp. radicis-cucumerinum (FORC) under controlled greenhouse conditions using amplicon sequencing, shotgun metagenomic and culture-based techniques.

RESULTS

Compost amendment significantly reduced FORC-induced disease in cucumber relative to non-amended treatments. While FORC inoculation resulted in significant shifts in microbial (bacterial and fungal) community composition in the rhizosphere of non-amended plants, this phenomenon was substantially less pronounced in the rhizosphere of compost-amended plants. Specifically, compost amendment sustained the presence of Actinomycetota (Streptomyces, Actinomadura, Saccharomonospora, Pseudonocardia, Glycomyces, Thermobifida) and Bacillota (Planifilum, Novibacillus) in FORC inoculated plants, that diminished significantly in inoculated plants without compost. These taxa contained a myriad of non-ribosomal peptides and polyketides synthetases biosynthetic gene clusters (BGCs) with putative antimicrobial and iron-chelating functions. We successfully isolated two Streptomyces strains from FORC-suppressing compost amended rhizospheres that were almost identical to the Streptomyces bin2 (99% ortho ANI) metagenome assembled genome identified in the shotgun metagenome analysis. These strains produced extracellular metabolites that inhibited growth of FORC in-vitro and contained BGCs that encode for compounds with potential antimicrobial capacity.

CONCLUSIONS

Based on results presented in this study, we demonstrate that compost alleviates FORC-induced dysbiosis of the rhizosphere microbiome, maintaining abundance of specific bacterial taxa. These bacterial groups may contribute to disease suppression through a myriad of mechanisms including iron chelation and production of fungal antagonizing secondary metabolites.

Biochar reduces containerized pepper blight caused by Phytophthora Capsici

Phytophthora blight caused by Phytophthora capsici is a serious disease affecting a wide range of plants. Biochar as a soil amendment could partially replace peat moss and has the potential to suppress plant diseases, but its effects on controlling phytophthora blight of container-grown peppers have less been explored, especially in combination of biological control using Trichoderma. In vitro (petri dish) and in vivo (greenhouse) studies were conducted to test sugarcane bagasse biochar (SBB) and mixed hardwood biochar (HB) controlling effects on pepper phytophthora blight disease with and without Trichoderma. Sugarcane bagasse biochar and HB were blended with the commercial substrate (CS, peat-based) at 10% (SBB10, by volume), and 10%, 30%, 50%, 70% (HB10, HB30, HB50, and HB70, by volume), respectively, and CS (CS100) was used as the control. Both in vitro and in vivo studies used randomized complete block design with three treatment factors: pathogen (without or with inoculation of P. capsici), biochar (different biochar treatments), and Trichoderma (without or with inoculation). In vitro results showed that Trichoderma inhibited P. capsici growth while biochar did not have significant beneficial effects. In vivo results showed that plants grown in HB30 and HB50 had similar or higher plant growth index and shoot dry weight than the control regardless of pathogen presence. In the presence of the pathogen, plants grown in HB30, HB50, and HB70 had significantly lower disease severity, and disease incidence ratings than the control, while Trichoderma did not show beneficial effects on controlling the disease. In conclusion, HB replacing 30% and 50% peat moss in substrate could reduce pepper blight disease caused by P. capsici without negatively affecting plant growth.

Delineating the soil physicochemical and microbiological factors conferring disease suppression in organic farms

Organic farming utilizes farmyard manure, compost, and organic wastes as sources of nutrients and organic matter. Soil under organic farming exhibits increased microbial diversity, and thus, becomes naturally suppressive to the development of soil-borne pathogens due to the latter's competition with resident microbial communities. Such soils that exhibit resistance to soil-borne phytopathogens are called disease-suppressive soils. Based on the phytopathogen suppression range, soil disease suppressiveness is categorised as specific- or general- disease suppression. Disease suppressiveness can either occur naturally or can be induced by manipulating soil properties, including the microbiome responsible for conferring protection against soil-borne pathogens. While the induction of general disease suppression in agricultural soils is important for limiting pathogenic attacks on crops, the factors responsible for the phenomenon are yet to be identified. Limited efforts have been made to understand the systemic mechanisms involved in developing disease suppression in organically farmed soils. Identifying the critical factors could be useful for inducing disease suppressiveness in conducive soils as a cost-effective alternative to the application of pesticides and fungicides. Therefore, this review examines the soil properties, including microbiota, and assesses indicators related to disease suppression, for the process to be employed as a tactical option to reduce pesticide use in agriculture.

The Structural and Functional Responses of Rhizosphere Bacteria to Biodegradable Microplastics in the Presence of Biofertilizers

Biodegradable microplastics (Bio-MPs) are a hot topic in soil research due to their potential to replace conventional microplastics. Biofertilizers are viewed as an alternative to inorganic fertilizers in agriculture due to their potential to enhance crop yields and food safety. The use of both can have direct and indirect effects on rhizosphere microorganisms. However, the influence of the coexistence of "Bio-MPs and biofertilizers" on rhizosphere microbial characteristics remains unclear. We investigated the effects of coexisting biofertilizers and Bio-MPs on the structure, function, and especially the carbon metabolic properties of crop rhizosphere bacteria, using a pot experiment in which polyethylene microplastics (PE-MPs) were used as a reference. The results showed that the existence of both microplastics (MPs) changed the physicochemical properties of the rhizosphere soil. Exposure to MPs also remarkably changed the composition and diversity of rhizosphere bacteria. The network was more complex in the Bio-MPs group. Additionally, metagenomic analyses showed that PE-MPs mainly affected microbial vitamin metabolism. Bio-MPs primarily changed the pathways related to carbon metabolism, such as causing declined carbon fixation/degradation and inhibition of methanogenesis. After partial least squares path model (PLS-PM) analysis, we observed that both materials influenced the rhizosphere environment through the bacterial communities and functions. Despite the degradability of Bio-MPs, our findings confirmed that the coexistence of biofertilizers and Bio-MPs affected the fertility of the rhizosphere. Regardless of the type of plastic, its use in soil requires an objective and scientifically grounded approach.

Biochemical and nanotechnological approaches to combat phytoparasitic nematodes

The foundation of most food production systems underpinning global food security is the careful management of soil resources. Embedded in the concept of soil health is the impact of diverse soil-borne pests and pathogens, and phytoparasitic nematodes represent a particular challenge. Root-knot nematodes and cyst nematodes are severe threats to agriculture, accounting for annual yield losses of US$157 billion. The control of soil-borne phytoparasitic nematodes conventionally relies on the use of chemical nematicides, which can have adverse effects on the environment and human health due to their persistence in soil, plants, and water. Nematode-resistant plants offer a promising alternative, but genetic resistance is species-dependent, limited to a few crops, and breeding and deploying resistant cultivars often takes years. Novel approaches for the control of phytoparasitic nematodes are therefore required, those that specifically target these parasites in the ground whilst minimizing the impact on the environment, agricultural ecosystems, and human health. In addition to the development of next-generation, environmentally safer nematicides, promising biochemical strategies include the combination of RNA interference (RNAi) with nanomaterials that ensure the targeted delivery and controlled release of double-stranded RNA. Genome sequencing has identified more than 75 genes in root knot and cyst nematodes that have been targeted with RNAi so far. But despite encouraging results, the delivery of dsRNA to nematodes in the soil remains inefficient. In this review article, we describe the state-of-the-art RNAi approaches targeting phytoparasitic nematodes and consider the potential benefits of nanotechnology to improve dsRNA delivery.

Pyrolysed maize feedstock utilization in combination with Trichoderma viride against Macrophomina phaseolina

Maize cultivation is under the growing threat of charcoal rot (Macrophomina phaseolina). Chemical control of diseases imparts serious health hazards to humans and the ecosystem. Biochar as an alternative disease management approach has been under consideration of the researchers for some time now. The biochar utilized in this study was derived from maize stalks and cobs. Crystallographic structure, inorganic minerals content and size of maize biochar were analyzed by powder X-ray diffractometer, while scanning electron microscopy revealed rough, irregular, tubular structure of the biochar surface. EDX spectra revealed that the maize biochar composition was dominated by 'C' followed by 'O'. The current study was designed to determine the synergistic effect of maize biochar (MB), and biocontrol agent (BCA) Trichoderma viride as soil amendments on the suppression of M. phaseolina. In vitro bioassays were conducted to check the efficiency of antagonistic effect of Trichoderma spp., in combination with maize biochar. On the basis of maximum mycelial growth inhibition T. viride was selected for a glasshouse experiment. Maize plants were grown in pots containing a mixture of soil with MB at application at the rate of 3 and 6% (v/v) separately, associated with or without T. viride. Treatments amended with 3% MB inoculated with M. phaseolina significantly reduced the percentage disease severity index by 40%. While in the presence of T. viride, 3% MB showed maximum disease suppression and a minimum percentage severity index i.e. 60 and 20%, respectively. Highest nitrogen contents were 18.4 g kg-1 observed in treatment 6% MB, while highest phosphorus and potassium contents were 3.11 and 15.2 g kg-1, respectively in the treatment with 3% MB. Conclusively, the effect of variable concentrations of maize biochar and T. viride as soil amendment was evident on the development of charcoal rot, growth and physiology of maize plants. According to the available literature, our report is the first on the implementation of biochar in synergism with T. viride to suppress the charcoal rot in maize.

Fusarium Wilt of Coriander: Root Cause Analysis and Varietal Tolerance Development

Since 2012, growers of coriander, Coriandrum sativum L., in Israel have been suffering from summer wilting that can result in entire fields collapsing. The current study aimed to determine the cause of the phenomenon and find a genetic solution to the problem. The disease was reproduced in a growth chamber using naturally-infested soil from a commercial field. Wilt became apparent within two weeks, and after ten weeks, all plants died compared to plants in sterilized soil from the same source. Fusarium oxysporum was isolated from infected plants, and Koch's postulates were completed. Sequence analysis of the Elongation Factor (EF1α) encoding gene of the pathogen had a 99.54% match to F. oxysporum f. sp. coriandrii. Several coriander varieties were screened for resistance or tolerance to the disease. In four independent experiments, only the cultivar 'Smadi' showed high tolerance, while other genotypes were susceptible. In a trial in a naturally infested field, the cultivar 'Smadi' outperformed the commercial cultivar 'Blair'. 'Smadi' provides a cropping solution to many Israeli farmers, yet this winter cultivar bolts early in the summer. There is a further need to characterize the tolerance mechanism and inheritance for informed breeding of late-bolting Fusarium-resistant coriander.

Negative plant-soil feedback in Arabidopsis thaliana: Disentangling the effects of soil chemistry, microbiome, and extracellular self-DNA

Nutrient deficiency, natural enemies and litter autotoxicity have been proposed as possible mechanisms to explain species-specific negative plant-soil feedback (PSF). Another potential contributor to negative PSF is the plant released extracellular self-DNA during litter decay. In this study, we sought to comprehensively investigate these hypotheses by using Arabidopsis thaliana (L.) Heynh as a model plant in a feedback experiment. The experiment comprised a conditioning phase and a response phase in which the conditioned soils underwent four treatments: (i) addition of activated carbon, (ii) washing with tap water, (iii) sterilization by autoclaving, and (iv) control without any treatment. We evaluated soil chemical properties, microbiota by shotgun sequencing and the amount of A. thaliana extracellular DNA in the differently treated soils. Our results showed that washing and sterilization treatments mitigated the negative PSF effect. While shifts in soil chemical properties were not pronounced, significant changes in soil microbiota were observed, especially after sterilization. Notably, plant biomass was inversely associated with the content of plant self-DNA in the soil. Our results suggest that the negative PSF observed in the conditioned soil was associated to increased amounts of soilborne pathogens and plant self-DNA. However, fungal pathogens were not limited to negative conditions, butalso found in soils enhancing A.thaliana growth. In-depth multivariate analysis highlights that the hypothesis of negative PSF driven solely by pathogens lacks consistency. Instead, we propose a multifactorial explanation for the negative PSF buildup, in which the accumulation of self-DNA weakens the plant's root system, making it more susceptible to pathogens.

Exploring the effect of different application rates of biochar on the accumulation of nutrients and growth of flue-cured tobacco (Nicotiana tabacum)

Background

Biochar application has become one of the most potential tools to improve soil fertility and plant growth for sustainable and eco-friendly agriculture. However, both positive and negative effects of biochar application have been recorded on plant growth and soil fertility.

Methods

This study investigated the impact of different application rates (0, 600, 900, 1200, and 1800 kg/ha) of biochar on the soil nutrient contents, accumulation of nutrients and dry matter in different plant parts, and growth of flue-cured tobacco plants under field conditions.

Results

Results demonstrated that soil organic carbon pool and carbon/nitrogen ratio were increased proportionally with the increasing dosage of biochar, 25.54 g/kg and 14.07 g/kg compared with control 17 g/kg and 10.13 g/kg, respectively. The contents of soil total nitrogen were also significantly increased after biochar application in the middle (1.77 g/kg) and late-growth (1.54 g/kg) stages of flue-cured tobacco than in control (1.60 g/kg and 1.41 g/kg, respectively). The contents of soil nitrate nitrogen were also higher under low (600 and 900 kg/ha) application rates of biochar and reduced when higher (1200 and 1800 kg/ha) dosages of biochar were applied. However, it was observed that varying application rates of biochar had no impact on soil ammonium nitrogen content during the growth period of flue-cured tobacco plants. The nutrient accumulation (N, P, K) in different parts of flue-cured tobacco plants was significantly increased under a low application rate of biochar, which enhanced the soil and plant analyzer development values, effective leaves number, growth, dry matter accumulation, and leaf yield of flue-cured tobacco. In contrast, the high biochar application rate (1200 and 1800 kg/ha) negatively impacted nutrient accumulation and growth of flue-cured tobacco.

Conclusion

Conclusively, the optimum application of biochar (600 and 900 kg/ha) is beneficial for plant growth, soil fertility, accumulation of nutrients, and dry matter in different plant parts. However, excessive biochar application (> 900 kg/ha) could inhibit flue-cured tobacco plant growth. This study provides a theoretical foundation for biochar application in tobacco and other crop production to obtain agricultural sustainability and economic stability.

Biochar derived from rice husk: Impact on soil enzyme and microbial dynamics, lettuce growth, and toxicity

This study was set to investigate the effects of rice husk biochar (RHB) on soil characteristics and growth of lettuce (Lactuca sativa). A comprehensive research approach was employed to examine the effect of different RHB concentrations (i.e., 0-1.5%) on soil pH, soil enzyme activities (i.e., alkaline phosphatase, beta-glucosidase, and dehydrogenase), soil microbial community, lettuce growth, and earthworm toxicity. The results showed that, within the studied RHB concentration range, the RHB application did not have significant effects on the soil pH. However, the enzyme activities were increased with increasing RHB concentration after the 28 d-lettuce growth period. The RHB application also increased the abundances of the bacterial genera Massilia and Bacillus and fungal genus Trichocladium having the plant growth promoting abilities. Furthermore, the study revealed that the root weight and number of lettuce leaves were significantly increased in the presence of the RHB, and the growth was dependent on the RHB concentration. The improved lettuce growth can be explained by the changes in the enzyme and microbial dynamics, which have resulted from the increased nutrient availability with the RHB application. Additionally, the earthworm toxicity test indicated that the tested RHB concentrations can be safely applied to soil without any significant ecotoxicity. In conclusion, this study underscores the potential of RHB as a soil amendment with positive effects on crop growth, highlighting the utilization of agricultural byproducts to enhance soil biological quality and plant growth through biochar application.

Potential of silicon-rich biochar (Sichar) amendment to control crop pests and pathogens in agroecosystems: A review

We reviewed the potential of silicon (Si)-rich biochars (sichars) as crop amendments for pest and pathogen control. The main pathosystems that emerged from our systematic literature search were bacterial wilt on solanaceous crops (mainly tomato, pepper, tobacco and eggplant), piercing-sucking hemipteran pests and soil-borne fungi on gramineous crops (mainly rice and wheat), and parasitic nematodes on other crops. The major pest and pathogen mitigation pathways identified were: i) Si-based physical barriers; ii) Induction of plant defenses; iii) Enhancement of plant-beneficial/pathogen-antagonistic soil microflora in the case of root nematodes; iv) Alteration of soil physical-chemical properties resulting in Eh-pH conditions unfavorable to root nematodes; v) Alteration of soil physical-chemical properties resulting in Eh-pH, bulk density and/or water holding capacity favorable to plant growth and resulting tolerance to necrotrophic pathogens; vi) Increased Si uptake resulting in reduced plant quality, owing to reduced nitrogen intake towards some hemi-biotrophic pests or pathogens. Our review highlighted synergies between pathways and tradeoffs between others, depending, inter alia, on: i) crop type (notably whether Si-accumulating or not); ii) pest/pathogen type (e.g. below-ground/root-damaging vs above-ground/aerial part-damaging; "biotrophic" vs "necrotrophic" sensu lato, and corresponding systemic resistance pathways; thriving Eh-pH spectrum; etc.); iii) soil type. Our review also stressed the need for further research on: i) the contribution of Si and other physical-chemical characteristics of biochars (including potential antagonistic effects); ii) the pyrolysis process to a) optimize Si availability in the soil and its uptake by the crop and b) to minimize formation of harmful compounds e.g. cristobalite; iii) on the optimal form of biochar, e.g. Si-nano particles on the surface of the biochar, micron-sized biochar-based compound fertilizer vs larger biochar porous matrices.

Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum

The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse Sorghum bicolor lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxon, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low N stress. This indicates that the shift in the sorghum microbiome due to low N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low N stress.IMPORTANCEThe development of crops that are more nitrogen use-efficient (NUE) is critical for the future of the enhanced sustainability of agriculture worldwide. This objective has been pursued mainly through plant breeding and plant molecular engineering, but these approaches have had only limited success. Therefore, a different strategy that leverages soil microbes needs to be fully explored because it is known that soil microbes improve plant growth through multiple mechanisms. To design approaches that use the soil microbiome to increase NUE, it will first be essential to understand the relationship among soil microbes, root metabolites, and crop productivity. Using this approach, we demonstrated that certain key metabolites and specific microbes are associated with high and low sorghum NUE in a field study. This important information provides a new path forward for developing crop genotypes that have increased NUE through the positive contribution of soil microbes.

Microbes and microbial strategies in carcinogenic polycyclic aromatic hydrocarbons remediation: a systematic review

Degradation, detoxification, or removal of the omnipresent polycyclic aromatic hydrocarbons (PAHs) from the ecosphere as well as their prevention from entering into food chain has never appeared simple. In this context, cost-effective, eco-friendly, and sustainable solutions like microbe-mediated strategies have been adopted worldwide. With this connection, measures have been taken by multifarious modes of microbial remedial strategies, i.e., enzymatic degradation, biofilm and biosurfactant production, application of biochar-immobilized microbes, lactic acid bacteria, rhizospheric-phyllospheric-endophytic microorganisms, genetically engineered microorganisms, and bioelectrochemical techniques like microbial fuel cell. In this review, a nine-way directional approach which is based on the microbial resources reported over the last couple of decades has been described. Fungi were found to be the most dominant taxa among the CPAH-degrading microbial community constituting 52.2%, while bacteria, algae, and yeasts occupied 37.4%, 9.1%, and 1.3%, respectively. In addition to these, category-wise CPAH degrading efficiencies of each microbial taxon, consortium-based applications, CPAH degradation-related molecular tools, and factors affecting CPAH degradation are the other important aspects of this review in light of their appropriate selection and application in the PAH-contaminated environment for better human-health management in order to achieve a sustainable ecosystem.

Effects of biochar on soil microbial communities: A meta-analysis

Changes in soil microbial communities may impact soil fertility and stability because microbial communities are key to soil functioning by supporting soil ecological quality and agricultural production. The effects of soil amendment with biochar on soil microbial communities are widely documented but studies highlighted a high degree of variability in their responses following biochar application. The multiple conditions under which they were conducted (experimental designs, application rates, soil types, biochar properties) make it difficult to identify general trends. This supports the need to better determine the conditions of biochar production and application that promote soil microbial communities. In this context, we performed the first ever meta-analysis of the biochar effects on soil microbial biomass and diversity (prokaryotes and fungi) based on high-throughput sequencing data. The majority of the 181 selected publications were conducted in China and evaluated the short-term impact (<3 months) of biochar. We demonstrated that a large panel of variables corresponding to biochar properties, soil characteristics, farming practices or experimental conditions, can affect the effects of biochar on soil microbial characteristics. Using a variance partitioning approach, we showed that responses of soil microbial biomass and prokaryotic diversity were highly dependent on biochar properties. They were influenced by pyrolysis temperature, biochar pH, application rate and feedstock type, as wood-derived biochars have particular physico-chemical properties (high C:N ratio, low nutrient content, large pores size) compared to non-wood-derived biochars. Fungal community data was more heterogenous and scarcer than prokaryote data (30 publications). Fungal diversity indices were rather dependent on soil properties: they were higher in medium-textured soils, with low pH but high soil organic carbon. Altogether, this meta-analysis illustrates the need for long-term field studies in European agricultural context for documenting responses of soil microbial communities to biochar application under diverse conditions combining biochar types, soil properties and conditions of use.

Fermented biochar has a markedly different effect on fate of pesticides in soil than compost, straw, and a mixed biochar-product

Current knowledge about how biochars affect the fate of pesticides in soil is based on studies that used pure biochars. After finding that an additional biological post-pyrolysis treatment, such as co-composting or lactic fermentation, is required for biochars for superior performance in temperate arable soils, a knowledge gap formed of how such further processed biochar products would affect the fate of pesticides in soil. This study compared the effects of a novel fermented biochar alone or mixed with biogas residues on the fate of two pesticides, 4-chloro-2-methylphenoxyacetic acid (MCPA) and metalaxyl-M, in a temperate arable soil to the traditional organic amendments wheat straw and compost. The fate of 14C-labeled MCPA was markedly affected in different ways. Fermented biochar effectively reduced the water-extractability and mineralization due to adsorption that was comparable to adsorption strengths reported for pure biochars. However, this effect was weak for the biochar mixed with biogas residues. Straw reduced water-extractable amounts due to increased biodegradation and formation of likely biogenic non-extractable residues of MCPA. In contrast, compost decelerated mineralization and increased the water solubility of the MCPA residues due to released dissolved organic matter. The amendments' effects were minor regarding 14C-metalaxyl-M, except for the fermented biochar which again reduced water-extractability and delayed degradation due to adsorption. Thus, the effects of the organic amendments differed for the two pesticide compounds with only the fermented biochar's effect being similar for both. However, this effect was no longer present in the mixed product containing 20% biochar. Our findings clearly show that biologically treated biochar-containing products can affect the fate of pesticides in soil very differently, also when compared to traditional organic amendments. Such impacts and their desirable and undesirable ecotoxicological implications need to be considered before the large-scale application of biochars to temperate arable soils.

Carbon nanosol-induced assemblage of a plant-beneficial microbiome consortium

Carbon nanosol (CNS) is a carbon-based nanomaterial that promotes plant growth; however, its functional mechanisms and effects on the microbiome are not fully understood. Here, we explored the effects of CNS on the relationship between the soil, endophytic microbiomes and plant productivity. CNS treatment increased the fresh biomass of tobacco (Nicotiana tabacum L.) plants by 27.4% ± 9.9%. Amplicon sequencing analysis showed that the CNS treatment significantly affected the composition and diversity of the microbial communities in multiple ecological niches associated with tobacco, especially the bulk soil and stem endophytic microbiome. Furthermore, the application of CNS resulted in enhanced network connectivity and stability of the microbial communities in different niches, particularly in the soil, implying a strengthening of certain microbial interactions. Certain potentially growth-promoting root endophytic bacteria were more abundant under the CNS treatment. In addition, CNS increased the abundance of some endophytic microbial functional genes known to enhance plant growth, such as those associated with nutrient metabolism and the plant hormone biosynthesis pathways. We isolated two bacterial strains (Sphingopyxis sp. and Novosphingobium sp.) that were enriched under CNS treatment, and they were confirmed to promote tobacco plant growth in vitro. These results suggested that CNS might, at least in part, promote plant growth by enriching beneficial bacteria in the microbiome.

Enhancing plant growth in biofertilizer-amended soil through nitrogen-transforming microbial communities

Biofertilizers have immense potential for enhancing agricultural productivity. However, there is still a need for clarification regarding the specific mechanisms through which these biofertilizers improve soil properties and stimulate plant growth. In this research, a bacterial agent was utilized to enhance plant growth and investigate the microbial modulation mechanism of soil nutrient turnover using metagenomic technology. The results demonstrated a significant increase in soil fast-acting nitrogen (by 46.7%) and fast-acting phosphorus (by 88.6%) upon application of the bacterial agent. This finding suggests that stimulated soil microbes contribute to enhanced nutrient transformation, ultimately leading to improved plant growth. Furthermore, the application of the bacterial agent had a notable impact on the accumulation of key genes involved in nitrogen cycling. Notably, it enhanced nitrification genes (amo, hao, and nar), while denitrification genes (nir and nor) showed a slight decrease. This indicates that ammonium oxidation may be the primary pathway for increasing fast-acting nitrogen in soils. Additionally, the bacterial agent influenced the composition and functional structure of the soil microbial community. Moreover, the metagenome-assembled genomes (MAGs) obtained from the soil microbial communities exhibited complementary metabolic processes, suggesting mutual nutrient exchange. These MAGs contained widely distributed and highly abundant genes encoding plant growth promotion (PGP) traits. These findings emphasize how soil microbial communities can enhance vegetation growth by increasing nutrient availability and regulating plant hormone production. This effect can be further enhanced by introducing inoculated microbial agents. In conclusion, this study provides novel insights into the mechanisms underlying the beneficial effects of biofertilizers on soil properties and plant growth. The significant increase in nutrient availability, modulation of key genes involved in nitrogen cycling, and the presence of MAGs encoding PGP traits highlight the potential of biofertilizers to improve agricultural practices. These findings have important implications for enhancing agricultural sustainability and productivity, with positive societal and environmental impacts.

The potential of biochar as a microbial carrier for agricultural and environmental applications

Biochar can be an effective carrier for microbial inoculants because of its favourable properties promoting microbial life. In this review, we assess the effectiveness of biochar as a microbial carrier for agricultural and environmental applications. Biochar is enriched with organic carbon, contains nitrogen, phosphorus, and potassium as nutrients, and has a high porosity and moisture-holding capacity. The large number of active hydroxyl, carboxyl, sulfonic acid group, amino, imino, and acylamino hydroxyl and carboxyl functional groups are effective for microbial cell adhesion and proliferation. The use of biochar as a carrier of microbial inoculum has been shown to enhance the persistence, survival and colonization of inoculated microbes in soil and plant roots, which play a crucial role in soil biochemical processes, nutrient and carbon cycling, and soil contamination remediation. Moreover, biochar-based microbial inoculants including probiotics effectively promote plant growth and remediate soil contaminated with organic pollutants. These findings suggest that biochar can serve as a promising substitute for non-renewable substrates, such as peat, to formulate and deliver microbial inoculants. The future research directions in relation to improving the carrier material performance and expanding the potential applications of this emerging biochar-based microbial immobilization technology have been proposed.

Alleviate environmental concerns with biochar as a container substrate: a review

Peat moss has desirable properties as a container substrate, however, harvesting it from peatland for greenhouse/nursery production use has disturbed peatland ecosystem and caused numerous environmental concerns. More recently, many nations have taken actions to reduce or ban peat moss production to reach the carbon neutral goal and address the environmental concerns. Also, the overuse of fertilizers and pesticides with peat moss in greenhouse/nursery production adds extra environmental and economic issues. Thus, it is urgent to find a peat moss replacement as a container substrate for greenhouse/nursery production. Biochar, a carbon-rich material with porous structure produced by the thermo-chemical decomposition of biomass in an oxygen-limited or oxygen-depleted atmosphere, has drawn researchers' attention for the past two decades. Using biochar to replace peat moss as a container substrate for greenhouse/nursery production could provide environmental and economic benefits. Biochar could be derived from various feedstocks that are regenerated faster than peat moss, and biochar possesses price advantages over peat moss when local feedstock is available. Certain types of biochar can provide nutrients, accelerate nutrient adsorption, and suppress certain pathogens, which end up with reduced fertilizer and pesticide usage and leaching. However, among the 36,474 publications on biochar, 1,457 focused on using biochar as a container substrate, and only 68 were used to replace peat moss as a container substrate component. This study provides a review for the environmental and economic concerns associated with peat moss and discussed using biochar as a peat moss alternative to alleviate these concerns.

Soil and Phytomicrobiome for Plant Disease Suppression and Management under Climate Change: A Review

The phytomicrobiome plays a crucial role in soil and ecosystem health, encompassing both beneficial members providing critical ecosystem goods and services and pathogens threatening food safety and security. The potential benefits of harnessing the power of the phytomicrobiome for plant disease suppression and management are indisputable and of interest in agriculture but also in forestry and landscaping. Indeed, plant diseases can be mitigated by in situ manipulations of resident microorganisms through agronomic practices (such as minimum tillage, crop rotation, cover cropping, organic mulching, etc.) as well as by applying microbial inoculants. However, numerous challenges, such as the lack of standardized methods for microbiome analysis and the difficulty in translating research findings into practical applications are at stake. Moreover, climate change is affecting the distribution, abundance, and virulence of many plant pathogens, while also altering the phytomicrobiome functioning, further compounding disease management strategies. Here, we will first review literature demonstrating how agricultural practices have been found effective in promoting soil health and enhancing disease suppressiveness and mitigation through a shift of the phytomicrobiome. Challenges and barriers to the identification and use of the phytomicrobiome for plant disease management will then be discussed before focusing on the potential impacts of climate change on the phytomicrobiome functioning and disease outcome.

Effects of biochar and freeze‒thaw cycles on the bacterial community and multifunctionality in a cold black soil area

Global climate change has altered soil freeze‒thaw cycle events, and little is known about soil microbe response to and multifunctionality regarding freeze‒thaw cycles. Therefore, in this study, biochar was used as a material to place under seasonal freeze-thaw cycling conditions. The purpose of this study was to explore the ability of biochar to regulate the function of freeze-thaw soil cycles to ensure spring sowing and food production. The results showed that biochar significantly increased the richness and diversity of soil bacteria before and after freezing-thawing. In the freezing period, the B50 treatment had the greatest improvement effect (2.6% and 5.5%, respectively), while in the thawing period, the B75 treatment had the best improvement effect. Biochar changed the composition and distribution characteristics of the bacterial structure and enhanced the multifunctionality of freeze-thaw soil and the stability of the bacterial symbiotic network. Compared with the CK treatment, the topological characteristics of the bacterial ecological network of the B50 treatment increased the most. They were 0.89 (Avg.degree), 9.79 (Modularity), 9 (Nodes), and 255 (Links). The freeze-thaw cycle decreased the richness and diversity of the bacterial community and changed the composition and distribution of the bacterial community, and the total bacterial population decreased by 658 (CK), 394 (B25), 644 (B50) and 86 (B75) during the thawing period compared with the freezing period. The soil multifunctionality in the freezing period was higher than that during the thawing period, indicating that the freeze-thaw cycle reduced soil ecological function. From the perspective of abiotic analysis, the decrease in soil multifunctionality was due to the decrease in soil nutrients, enzyme activities, soil basic respiration and other singular functions. From the perspective of bacteria, the decrease in soil multifunctionality was mainly due to the change in the Actinobacteriota group. This work expands the understanding of biochar ecology in cold black soil. These results are conducive to the sustainable development of soil ecological function in cold regions and ultimately ensure crop growth and food productivity.

Deciphering the Synergies of Reductive Soil Disinfestation Combined with Biochar and Antagonistic Microbial Inoculation in Cucumber Fusarium Wilt Suppression Through Rhizosphere Microbiota Structure

Application of reductive soil disinfestation (RSD), biochar, and antagonistic microbes have become increasingly popular strategies in a microbiome-based approach to control soil-borne diseases. The combined effect of these remediation methods on the suppression of cucumber Fusarium wilt associated with microbiota reconstruction, however, is still unknown. In this study, we applied RSD treatment together with biochar and microbial application of Trichoderma and Bacillus spp. in Fusarium-diseased cucumbers to investigate their effects on wilt suppression, soil chemical changes, microbial abundances, and the rhizosphere communities. The results showed that initial RSD treatment followed by biochar amendment (RSD-BC) and combined applications of microbial inoculation and biochar (RSD-SQR-T37-BC) decreased nitrate concentration and raised soil pH, soil organic carbon (SOC), and ammonium in the treated soils. Under RSD, the applications of Bacillus (RSD-SQR), Trichoderma (RSD-T37), and biochar (RSD-BC) suppressed wilt incidence by 26.8%, 37.5%, and 32.5%, respectively, compared to non-RSD treatments. Moreover, RSD-SQR-T37-BC and RSD-T37 caused greater suppressiveness of Fusarium wilt and F. oxysporum by 57.0 and 33.5%, respectively. Rhizosphere beta diversity and alpha diversity revealed a difference between RSD-treated and non-RSD microbial groups. The significant increase in the abundance, richness, and diversity of bacteria, and the decrease in the abundance and diversity of fungi under RSD-induced treatments attributed to the general suppression. Identified bacterial (Bacillus, Pseudoxanthomonas, Flavobacterium, Flavisolibacter, and Arthrobacter) and fungal (Trichoderma, Chaetomium, Cladosporium, Psathyrella, and Westerdykella) genera were likely the potential antagonists of specific disease suppression for their significant increase of abundances under RSD-treated soils and high relative importance in linear models. This study infers that the RSD treatment induces potential synergies with biochar amendment and microbial applications, resulting in enhanced general-to-specific suppression mechanisms by changing the microbial community composition in the cucumber rhizosphere.

Utilization of current pyrolysis technology to convert biomass and manure waste into biochar for soil remediation: A review

Traditional disposal of animal manures and lignocellulosic biomass is restricted by its inefficiency and sluggishness. To advance the carbon management and greenhouse gas mitigation, this review scrutinizes the effect of pyrolysis in promoting the sustainable biomass and manure disposal as well as stimulating the biochar industry development. This review has examined the advancement of pyrolysis of animal manure (AM) and lignocellulosic biomass (LB) in terms of efficiency, cost-effectiveness, and operability. In particular, the applicability of pyrolysis biochar in enhancing the crops yields via soil remediation is highlighted. Through pyrolysis, the heavy metals of animal manures are fixated in the biochar, thereby both soil contamination via leaching and heavy metal uptake by crops are minimized. Pyrolysis biochar is potentially use in soil remediation for agronomic and environmental co-benefits. Fast pyrolysis assures high bio-oil yield and revenue with better return on investment whereas slow pyrolysis has low revenue despite its minimum investment cost because of relatively low selling price of biochar. For future commercialization, both continuous reactors and catalysis can be integrated to pyrolysis to ameliorate the efficiency and economic value of pyrolysis biochar.

Microbiome Signature of Endophytes in Wheat Seed Response to Wheat Dwarf Bunt Caused by Tilletia controversa Kühn

Wheat dwarf bunt leads to the replacement of seeds with fungal galls containing millions of teliospores of the pathogen Tilletia controversa Kühn. As one of the most devastating internationally quarantined wheat diseases, wheat dwarf bunt spreads to cause distant outbreaks by seeds containing teliospores. In this study, based on a combination of amplicon sequencing and isolation approaches, we analyzed the seed microbiome signatures of endophytes between resistant and susceptible cultivars after infection with T. controversa. Among 310 bacterial species obtained only by amplicon sequencing and 51 species obtained only by isolation, we found 14 overlapping species by both methods; we detected 128 fungal species only by amplicon sequencing, 56 only by isolation, and 5 species by both methods. The results indicated that resistant uninfected cultivars hosted endophytic communities that were much more stable and beneficial to plant health than those in susceptible infected cultivars. The susceptible group showed higher diversity than the resistant group, the infected group showed more diversity than the uninfected group, and the microbial communities in seeds were related to infection or resistance to the pathogen. Some antagonistic microbes significantly suppressed the germination rate of the pathogen's teliospores, providing clues for future studies aimed at developing strategies against wheat dwarf bunt. Collectively, this research advances the understanding of the microbial assembly of wheat seeds upon exposure to fungal pathogen (T. controversa) infection. IMPORTANCE This is the first study on the microbiome signature of endophytes in wheat seed response to wheat dwarf bunt caused by Tilletia controversa Kühn. Some antagonistic microbes suppressed the germination of teliospores of the pathogen significantly, which will provide clues for future studies against wheat dwarf bunt. Collectively, this research first advances the understanding of the microbial assembly of wheat seed upon exposure to the fungal pathogen (T. controversa) infection.

The combined action of biochar and nitrogen-fixing bacteria on microbial and enzymatic activities of soil N cycling

This study aims to investigate the positive effects of the combined use of Enterobacter cloacae and biochar on improving nitrogen (N) utilization. The greenhouse pots experimental results showed the synergy of biochar and E. cloacae increased soil total N content and plant N uptake by 33.54% and 15.1%, respectively. Soil nitrogenase (NIT) activity increased by 253.02%. Ammonia monooxygenase (AMO) and nitrate reductase (NR) activity associated with nitrification and denitrification decreased by 10.94% and 29.09%, respectively. The relative abundance of N fixing microorganisms like Burkholderia and Bradyrhizobium significantly increased. Sphingomonas and Ottowia, two bacteria involved in the nitrification and denitrification processes, were found to be in lower numbers. The E. cloacae's ability to fix N₂ and promote the growth of plants allow the retention of N in soil and make more N available for plant development. Biochar served as a reservoir of N for plants by adsorbing N from the soil and providing a shelter for E. cloacae. Thus, biochar and E. cloacae form a synergy for the management of agricultural N and the mitigation of negative impacts of pollution caused by excessive use of N fertilizer.

Control Efficiency of Biochar Loaded with Bacillus subtilis Tpb55 against Tobacco Black Shank

Black shank caused by Phytophthora nicotianae has become a destructive soil-borne disease to different flue-cured tobacco cultivars in Southwest China. The use of biochar amendments for microorganism synergy is a promising effective strategy for P. nicotianae development control. In this study, biochar samples were prepared from tamarisk with different pyrolization temperatures (300–500 °C). The effect of pyrolytic temperatures on the bacteria immobilization efficiency of biochar was investigated. B. subtilis Tpb55 was successfully loaded on different biochars as biocontrol composites. The survival investigation of the inoculum suggested that biochar pyrolized at 300 °C (BC300), with a large pore opening diameter; a greater pore volume exhibited a better Tpb55 immobilization. A pot experiment indicated that Tpb55-loaded BC300 had a more pronounced decrease in the disease severity index of black shank disease and an increase in the soil pH, alkali-hydrolyzable nitrogen, soil-available phosphorus, and available potassium. BC300 inoculated with Tpb55 showed the highest control effect (79.60%) against tobacco black shank in the pot experiments, with the lowest copy number of P. nicotianae DNA. In conclusion, biochar-immobilized Tpb55 may provide a new strategy for preventing and controlling tobacco black shank.

Biochar increases Panax notoginseng's survival under continuous cropping by improving soil properties and microbial diversity

Replant problem is widespread in agricultural production and causes serious economic losses, which has limited sustainable cultivation of Panax notoginseng (PN), a well-known medicinal plant in Asia. Here we conducted a field experiment to investigate the effectiveness and possible mechanisms of biochar to improve its survival under continuous cropping. Biochar from tobacco stems was applied at 4 rates of 9.0, 12, 15, and 18 t/ha to a soil where PN has been continuously cultivated for 10 years. After 18 months, soil properties, 5 allelochemicals, including p-hydroxybenzoic acid, vanillic acid, syringic acid, p-coumaric acid, and ferulic acid, key pathogen Fusarium oxysporum, microbial community, and PN survival rate were investigated. Our results show that 10 years' continuous PN cropping led to soil acidification, accumulation of NH₄⁺-N and F. oxysporum, and low PN survival rate. However, biochar increased its survival rate from 6.0% in the control to 69.5% under 15 t/ha treatment. Moreover, soil pH, available P and K, organic matter content, and microbial diversity were increased while NH₄⁺-N and allelochemicals vanillic acid and syringic acid contents were decreased under biochar treatment (P<0.05). Soil available K increased from 177 to 283 mg·kg^-1 while NH₄⁺-N decreased from 6.73 to 4.79 mg·kg^-1 under 15 t/ha treatment. Further, soil pH, available P and K, and microbial diversity (bacteria and fungi) were positively correlated with PN survival rate, however, NH₄⁺-N content was negatively correlated (P<0.05). Our study indicates that biochar effectively increased the survival rate of Panax notoginseng under continuous cropping by improving soil properties and microbial diversity.

Effect of marigold (Tagetes erecta L.) on soil microbial communities in continuously cropped tobacco fields

Root-knot nematode disease is a catastrophic soil-borne disease in tobacco production. The regulation of natural microbial communities is considered a good disease management approach to suppress the incidence of soilborne diseases. In this study, the effects of tobacco (Nicotiana tabacum L.)-marigold (Tagetes erecta L.) rotation on the diversity and structure of soil microbial communities in continuously cropped tobacco fields were analyzed to manage this devastating pathogen. The results showed that the soil bacterial OTUs increased after marigold rotation and that the bacterial Shannon, ACE, Chao1 index, and fungal Shannon index were higher in the tobacco-marigold rotation fields than in the continuously cropped tobacco fields by 3.98%, 10.37%, 5.46%, and 3.43%, respectively. After marigold rotation, the relative abundances of Actinobacteria, Acidobacteria, and Ascomycota increased by 28.62%, 107.50%, and 57.44%, respectively, and the proportion of beneficial bacterial genera such as Nocardioides, Gemmatimonas, and Bradyrhizobium increased. In addition, our results also showed that rotation of marigold could effectively reduce the incidence of root-knot nematodes in the next crop of tobacco. These results indicate that marigold rotation had a positive effect on the soil microecological environment of continuously cropped tobacco fields, reducing the obstacles to continuous cropping of tobacco.

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

Biochar amendment in the soil can exert a positive effect in reducing heavy metal toxicity in plants. However, it remains unclear the extent to which this effect is associated with the modulation of plant growth-promoting rhizobacteria (PGPR). Here, we initially conducted a pot experiment using tomato (Solanum lycopersicum L.) as a model plant grown in soil spiked with cadmium. First, we found biochar amendment to result in reduced cadmium uptake in tomato plants and trackable changes in the tomato rhizosphere microbiome. Then, a rhizosphere transplant experiment validated the importance of this microbiome modulation for cadmium-toxicity amelioration. Sequence-based analyses targeted the isolation of representative isolates of PGPR, including Bacillus and Flavisolibacter spp. that displayed in vitro cadmium tolerance and biosorption capabilities (in addition to abilities to solubilize phosphate and produce indole acetic acid). Last, we performed a soil inoculation experiment and confirmed the effectiveness of these isolates in reducing cadmium toxicity in tomato plants. Besides, we found the inoculation of these taxa as single inoculant and in combination to result in increased activities of specific antioxidant enzymes in tomato tissues. Taken together, this study revealed the ecological and physiological mechanisms by which biochar amendment indirectly alleviate cadmium toxicity in tomato plants, in this case, via the modulation and activity of specific PGPR populations. This study provides new insights into strategies able to promote beneficial PGPR in the rhizosphere with potential application to ameliorate heavy metal toxicity in plants.

Biochar application ameliorated the nutrient content and fungal community structure in different yellow soil depths in the karst area of Southwest China

The influence of biochar on the change of nutrient content and fungal community structure is still not clear, especially in different yellow soil depths in karst areas. A soil column leaching simulation experiment was conducted to investigate the influence of biochar on soil content, enzymatic activity, and fungal community diversity and structural composition. Three biochar amounts were studied, namely, 0%(NB, no biochar), 1.0%(LB, low-application-rate biochar), and 4.0% (HB, high-application-rate biochar). The results showed that biochar increased the pH value and the contents of soil organic matter (SOM), total nitrogen (TN), available phosphorus (AP), and available potassium (AK) but reduced the microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN). Furthermore, this effect was enhanced with increasing biochar amount. Biochar was conducive to improving the nutrient availability in topsoil (0-20 cm), especially TN, AK, and MBN. Meanwhile, biochar affected the enzymatic activity, especially the sucrase activity. Biochar affected the diversity and structure of the fungal community, of which HB treatment had the most obvious effect. Among these treatments, Aspergillus, unclassified_Chaetomiaceae, Mortierella, Spizellomyces, Penicillium, Fusarium, and unclassified_Chromista fungal genera were the highest. Moreover, biochar inhibited the growth of harmful pathogens and increased the abundance of beneficial fungi in soil, and the effect was enhanced with increasing biochar amount and soil depth. Redundancy analysis (RDA) showed that AK was an important factor in yellow soil, although the main environmental factors affecting the fungal community structure were different in different soil depths. Overall, biochar had a positive effect on improving the land productivity and micro-ecological environment of yellow soil in the karst area.

Characterization of Microbial Communities and Naturally Occurring Radionuclides in Soilless Growth Media Amended with Different Concentrations of Biochar

Biochar, derived from the pyrolysis of plant materials has the potential to enhance plant growth in soilless media. Howevetar, little is known about the impact of biochar amendments to soilless growth media, microbial community composition, and fate of chemical constituents in the media. In this study, different concentrations of biochar were added to soilless media and microbial composition, and chemical constituents were analyzed using metagenomics and gamma spectroscopy techniques, respectively. Across treatments, carboxyl-C, phenolic-C, and aromatic-C were the main carbon sources that influenced microbial community composition. Flavobacterium (39.7%), was the predominantly bacteria genus, followed by Acidibacter (12.2%), Terrimonas (10.1%), Cytophaga (7.5%), Ferruginibacter (6.0%), Lacunisphaera (5.9%), Cellvibrio (5.8%), Opitutus (4.8%), Mucilaginibacter (4.0%) and Bryobacter (4.0%). Negative relationships were found between Cytophaga and 226Ra (r = −0.84, p = 0.0047), 40K (r = −0.82, p = 0.0069) and 137Cs (r = −0.93, p = 0.0002). Similarly, Mucilaginibacter was negatively correlated with 226Ra (r = −0.83, p = 0.0054) and 137Cs (r = −0.87, p = 0.0021). Overall, the data suggest that high % biochar amended samples have high radioactivity concentration levels. Some microorganisms have less presence in high radioactivity concentration levels.

Biochar stimulates tomato roots to recruit a bacterial assemblage contributing to disease resistance against Fusarium wilt

Biochar amendment is acknowledged to favor plant resistance against soil-borne diseases. Although plant-beneficial bacteria enrichment in the rhizosphere is often proposed to be associated with this protection, the mechanism behind this stimulating effect remains unelucidated. Here, we tested whether biochar promotes plants to recruit beneficial bacteria to the rhizosphere, and thus develop a disease-suppressive rhizosphere microbiome. In a pot experiment, biochar amendment decreased tomato Fusarium wilt disease severity. Using a transplanting rhizosphere microbiome experiment, we showed that biochar enhanced the suppressiveness of tomato rhizosphere microbiome against Fusarium wilt disease. High-throughput sequencing of 16S ribosomal RNA gene and in vitro cultures further indicated that the recruited suppressive rhizosphere microbiome was associated with the increase of plant-beneficial bacteria, such as Pseudomonas sp. This amendment also enhanced the in vitro chemoattraction and biofilm promotion activity of tomato root exudates. Collectively, our results demonstrate that biochar amendment induces tomato seedlings to efficiently recruit a disease-suppressive rhizosphere microbiome against Fusarium wilt.

Enrichment of bacteria involved in the nitrogen cycle and plant growth promotion in soil by sclerotia of rice sheath blight fungus

Rice sheath blight pathogen, Rhizoctonia solani, produces numerous sclerotia to overwinter. As a rich source of nutrients in the soil, sclerotia may lead to the change of soil microbiota. For this purpose, we amended the sclerotia of R. solani in soil and analyzed the changes in bacterial microbiota within the soil at different time points. At the phyla level, Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi and Firmicutes showed varied abundance in the amended soil samples compared to those in the control. An increased abundance of ammonia-oxidizing bacterium (AOB) Nitrosospira and Nitrite oxidizing bacteria (NOB) i.e., Nitrospira was observed, where the latter is reportedly involved in the nitrifier denitrification. Moreover, Thiobacillus, Gemmatimonas, Anaeromyxobacter and Geobacter, the vital players in denitrification, N2O reduction and reductive nitrogen transformation, respectively, depicted enhanced abundance in R. solani sclerotia-amended samples. Furthermore, asymbiotic nitrogen-fixing bacteria, notably, Azotobacter as well as Microvirga and Phenylobacterium with nitrogen-fixing potential also enriched in the amended samples compared to the control. Plant growth promoting bacteria, such as Kribbella, Chitinophaga and Flavisolibacter also enriched in the sclerotia-amended soil. As per our knowledge, this study is of its kind where pathogenic fungal sclerotia activated microbes with a potential role in N transformation and provided clues about the ecological functions of R. solani sclerotia on the stimulation of bacterial genera involved in different processes of N-cycle within the soil in the absence of host plants.

Improved ginseng production under continuous cropping through soil health reinforcement and rhizosphere microbial manipulation with biochar: a field study of Panax ginseng from Northeast China

The production of ginseng, an important Chinese medicine crop, has been increasingly challenged by soil degradation and pathogenic disease under continuous cropping in Northeast China. In a field experiment, an Alfisol garden continuously cropped with Chinese ginseng (Panax ginseng C. A. Meyer) was treated with soil amendment at 20 t ha-1 with maize (MB) and wood (WB) biochar, respectively, compared to conventional manure compost (MC). Two years after the amendment, the rooted topsoil and ginseng plants were sampled. The changes in soil fertility and health, particularly in the soil microbial community and root disease incidence, and in ginseng growth and quality were portrayed using soil physico-chemical assays, biochemical assays of extracellular enzyme activities and gene sequencing assays as well as ginsenoside assays. Topsoil fertility was improved by 23% and 39%, ginseng root biomass increased by 25% and 27%, and root quality improved by 6% and 18% with WB and MB, respectively, compared to MC. In the ginseng rhizosphere, fungal abundance increased by 96% and 384%, with a significant and insignificant increase in bacterial abundance, respectively, under WB and MB. Specifically, the abundance of Fusarium spp. was significantly reduced by 19-35%, while that of Burkholderia spp. increased by folds under biochar amendments over MC. Relevantly, there was a significant decrease in the abundance proportion of pathotrophic fungi but a great increase in that of arbuscular mycorrhizal fungi, along with an enhanced microbial community network complexity, especially fungal community complexity, under biochar amendments. Thus, biochar, particularly from maize residue, could promote ginseng quality production while enhancing soil health and ecological services, including carbon sequestration, in continuously cropped fields.

Characterization of Rhizosphere Microbial Communities for Disease Incidence and Optimized Concentration of Difenoconazole Fungicide for Controlling of Wheat Dwarf Bunt

Rhizosphere soil microorganisms have great agricultural importance. To explore the relationship between rhizosphere microorganisms and the disease incidence, and to optimize the concentration of difenoconazole fungicide for the control of wheat dwarf bunt, caused by Tilletia controversa Kühn, the rhizosphere microorganisms were characterized based on sequencing methods. We found that the disease incidence correlated with the relative abundance of some microbial communities, such as Acidobacteria, Nocardioides, Roseiflexaceae, Pyrinomonadaceae, and Gemmatimonadaceae. Actinobacteria showed significant differences in the infected soils when compared to the control soils, and the relative abundance of Acidobacteria, Pyrinomonadaceae, Gemmatimonadaceae, and Saccharimonadales populations was distinctly higher in the T. controversa-inoculated group than in the control group. The members of Dehalococcoidia, Nitrosomonadaceae, and Thermomicrobiales were found only in T. controversa-inoculated soils, and these taxa may have potential effects against the pathogen and contribute to disease control of wheat dwarf bunt. In addition, for T. controversa-infected plants, the soil treated with difenoconazole showed a high relative abundance of Proteobacteria, Actinobacteria, Ascomycota, Basidiomycota, Mortierellomycota, and Olpidiomycota based on the heatmap analysis and ANOVA. Our findings suggest that the optimized concentration of fungicide (5% recommended difenoconazole) exhibits better control efficiency and constant diversity in the rhizosphere soil.

Incidence Rates of Root Rot in Sweetpotato Caused by Cultivation Soil and Soil Microorganisms During Storage Periods

Sweetpotatoes require a storage period for year-round use and improved sweetness by starch degradation. However, long-term storage can cause root rot, and a large amount of sweetpotatoes can be discarded. Root rot is typically caused by pathogenic soil-borne Fusarium spp., and the development of root rot induced by the characteristics of cultivating soil in stored sweetpotato has not yet been identified. In this study, the effect of Fusarium spp. and microbial community in the cultivated soil on the root rot of sweetpotatoes was to be elucidated. Wounded sweetpotato were treated in soil cultures inoculated with F. solani or F. oxysporum for 2 days, and showed symptoms of root rot after 2 months of storage. The three study fields (Naju, Yeongam A, and B) were subjected to the same curing and storage treatments after harvest, and the incidence of root rot was 1.7- to 1.8-fold different after 3 months of storage. Across the three fields, concentrations of Fusarium spp. and of microbial communities differed according to the cultivation soil and period. In particular, Naju, which had the lowest incidence of root rot, had the lowest concentration of Fusarium spp. before harvest, and the smallest change in diversity of the microbial community during the cultivation period. However, tuberous roots harvested from the fields showed no significant differences in antioxidant activity or lesion size with the treatment of 10⁶ conidia/ml F. solani. By solidifying the importance of cultivating soil and related microorganisms in the advancement of root rot of sweetpotato, our results may aid in preventing the decrease in the yield of cultivated sweetpotatoes through root rot control.

Comparative Metagenomic Study of Rhizospheric and Bulk Mercury-Contaminated Soils in the Mining District of Almadén

Soil contamination by heavy metals, particularly mercury (Hg), is a problem that can seriously affect the environment, animals, and human health. Hg has the capacity to biomagnify in the food chain. That fact can lead to pathologies, of those which affect the central nervous system being the most severe. It is convenient to know the biological environmental indicators that alert of the effects of Hg contamination as well as the biological mechanisms that can help in its remediation. To contribute to this knowledge, this study conducted comparative analysis by the use of Shotgun metagenomics of the microbial communities in rhizospheric soils and bulk soil of the mining region of Almadén (Ciudad Real, Spain), one of the most affected areas by Hg in the world The sequences obtained was analyzed with MetaPhlAn2 tool and SUPER-FOCUS. The most abundant taxa in the taxonomic analysis in bulk soil were those of Actinobateria and Alphaproteobacteria. On the contrary, in the rhizospheric soil microorganisms belonging to the phylum Proteobacteria were abundant, evidencing that roots have a selective effect on the rhizospheric communities. In order to analyze possible indicators of biological contamination, a functional potential analysis was performed. The results point to a co-selection of the mechanisms of resistance to Hg and the mechanisms of resistance to antibiotics or other toxic compounds in environments contaminated by Hg. Likewise, the finding of antibiotic resistance mechanisms typical of the human clinic, such as resistance to beta-lactams and glycopeptics (vancomycin), suggests that these environments can behave as reservoirs. The sequences involved in Hg resistance (operon mer and efflux pumps) have a similar abundance in both soil types. However, the response to abiotic stress (salinity, desiccation, and contaminants) is more prevalent in rhizospheric soil. Finally, sequences involved in nitrogen fixation and metabolism and plant growth promotion (PGP genes) were identified, with higher relative abundances in rhizospheric soils. These findings can be the starting point for the targeted search for microorganisms suitable for further use in bioremediation processes in Hg-contaminated environments.

Bacterial community dynamics of tomato hydroponic greenhouses infested with hairy root disease

The rhizosphere is a complex ecosystem consisting of microbes in the interface between growth medium and plant roots, which affects plant productivity and health. This is one of the few studies analysing bacterial communities present in the rhizosphere of hydroponically grown plants. Tomato grown under hydroponic conditions is prone to hairy root disease (HRD) that is caused by rhizogenic Agrobacterium biovar 1 strains. In this study, using high-throughput amplicon sequencing of partial ribosomal RNA (rRNA) genes, we aimed to characterize bacterial communities in rockwool samples obtained from healthy or HRD-infested tomato during an entire growing season. Alpha diversity of rockwool increased in direct relation with time and samples obtained from healthy greenhouses presented a significantly lower alpha diversity than those from HRD-infested greenhouses. Beta diversity showed that bacterial community composition changed throughout the growing season. Amplicon Sequence Variants (ASVs) identified as rhizogenic Agrobacterium bv. 1 were more prevalent in HRD-infected greenhouses. Conversely, ASVs identified as Paenibacillus, previously identified as biocontrol organisms of rhizogenic agrobacteria, were more prevalent in healthy greenhouses. Altogether, our study greatly contributes to the knowledge of bacterial communities in rockwool hydroponics.

Biosolid-Amended Soil Enhances Defense Responses in Tomato Based on Metagenomic Profile and Expression of Pathogenesis-Related Genes

Biosolid application is an effective strategy, alternative to synthetic chemicals, for enhancing plant growth and performance and improving soil properties. In previous research, biosolid application has shown promising results with respect to tomato resistance against Fusarium oxysporum f. sp. radicis-lycopersici (Forl). Herein, we aimed at elucidating the effect of biosolid application on the plant-microbiome response mechanisms for tomato resistance against Forl at a molecular level. More specifically, plant-microbiome interactions in the presence of biosolid application and the biocontrol mechanism against Forl in tomato were investigated. We examined whether biosolids application in vitro could act as an inhibitor of growth and sporulation of Forl. The effect of biosolid application on the biocontrol of Forl was investigated based on the enhanced plant resistance, measured as expression of pathogen-response genes, and pathogen suppression in the context of soil microbiome diversity, abundance, and predicted functions. The expression of the pathogen-response genes was variably induced in tomato plants in different time points between 12 and 72 h post inoculation in the biosolid-enriched treatments, in the presence or absence of pathogens, indicating activation of defense responses in the plant. This further suggests that biosolid application resulted in a successful priming of tomato plants inducing resistance mechanisms against Forl. Our results have also demonstrated that biosolid application alters microbial diversity and the predicted soil functioning, along with the relative abundance of specific phyla and classes, as a proxy for disease suppression. Overall, the use of biosolid as a sustainable soil amendment had positive effects not only on plant health and protection, but also on growth of non-pathogenic antagonistic microorganisms against Forl in the tomato rhizosphere and thus, on plant-soil microbiome interactions, toward biocontrol of Forl.

Genetically Modified Sugarcane Intercropping Soybean Impact on Rhizosphere Bacterial Communities and Co-occurrence Patterns

Strategies involving genes in the dehydration-responsive element binding (DREB) family, which participates in drought stress regulation, and intercropping with legumes are becoming prominent options in promoting sustainable sugarcane cultivation. An increasing number of studies focusing on root interactions in intercropping systems, particularly involving transgenic crops, are being conducted to better understand and thus, harness beneficial soil microbes to enhance plant growth. We designed experiments to investigate the characteristics of two intercropping patterns, soybean with wild-type (WT) sugarcane and soybean with genetically modified (GM) Ea-DREB2B-overexpressing sugarcane, to assess the response of the rhizosphere microbiota to the different cropping patterns. Bacterial diversity in the rhizosphere microbial community differed between the two intercropping pattens. In addition, the biomass of GM sugarcane that intercropped with soybean was significantly improved compared with WT sugarcane, and the aboveground biomass and root biomass of GM soybean intercropping sugarcane increased by 49.15 and 46.03% compared with monoculture. Furthermore, a beneficial rhizosphere environment for the growth of Actinobacteria was established in the systems intercropped with GM sugarcane. Improving the production mode of crops by genetic modification is a key strategy to improving crop yields and provides new opportunities to further investigate the effects of intercropping on plant roots and soil microbiota. Thus, this study provides a basis for selecting suitable sugarcane-soybean intercropping patterns and a theoretical foundation for a sustainable sugarcane production.

Effects of short-term application of Moutai lees biochar on nutrients and fungal community structure in yellow soil of Guizhou

In order to realize the utilization of Moutai lees and the improvement of soil fertility of yellow soil in Guizhou, a field experiment was carried out to study the effects of short-term application of Moutai lees biochar on nutrients and fungal community structure diversity of yellow soil. The results showed that the application of Moutai lees biochar increased the pH, soil organic matter (SOM), total nitrogen (TN), ammonium nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃^--N), available phosphorus (AP), and available potassium (AK), while the microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) were reduced. The application of biochar significantly reduced the number of fungal OTU and community diversity. The application of biochar increased the relative abundances of Chytridiomycota and Mortierellomycota, while the relative abundance of Ascomycota was significantly reduced. Redundancy analysis (RDA) suggested that SOM, NH₄⁺-N and NO₃^--N were the key factors correlated with changes in microbial community structure. Overall, the short-term application of lees biochar can not only improve the nutrient content of yellow soil, but also change the structure and diversity of soil fungal communities. More importantly, Moutai lees biochar can reduce the relative abundance of some pathogenic fungi and play the role of inhibiting the growth and reproduction of harmful plant pathogens.

Interactions between Brassica Biofumigants and Soil Microbiota: Causes and Impacts

Biofumigation is used to control soil-borne plant diseases, and it has paramount importance to reduce the cost of chemical fumigants. Information about the field control efficacies and impacts of Brassica-based biofumigation (BBF) on soil bacterial and fungal microbiota is scattered in the literature. Therefore, this review summarizes and discusses the nature and the underlying causes of soil bacterial and fungal community dynamics in response to BBF. In addition, the major factors influencing the interaction between a biofumigant and soil microbiota are discussed. The pros and cons of BBF to soil microbiota and the subsequent impacts on sustainable farming practices are also highlighted.

Agricultural Waste-Based Biochar for Agronomic Applications

Agricultural activities face several challenges due to the intensive increase in population growth and environmental issues. It has been established that biochar can be assigned a useful role in agriculture. Its agronomic application has therefore received increasing attention recently. The literature shows different applications, e.g., biochar serves as a soil ameliorant to optimize soil structure and composition, and it increases the availability of nutrients and the water retention capacity in the soil. If the biochar is buried in the soil, it decomposes very slowly and thus serves as a long-term store of carbon. Limiting the availability of pesticides and heavy metals increases soil health. Biochar addition also affects soil microbiology and enzyme activity and contributes to the improvement of plant growth and crop production. Biochar can be used as a compost additive and animal feed and simultaneously provides a contribution to minimizing greenhouse gas emissions. Several parameters, including biochar origin, pyrolysis temperature, soil type when biochar is used as soil amendment, and application rate, control biochar’s efficiency in different agricultural applications. Thus, special care should be given when using a specific biochar for a specific application to prevent any negative effects on the agricultural environment.

Microbial community responses to multiple soil disinfestation change drivers

Soil continuous cropping obstacles lead to yield and economic losses in agriculture. Reductive soil disinfestation (RSD) is an effective technology for alleviating it. However, the key factors influencing microbial community composition and how do they promote functional transformation of core microbes under RSD practice remain poorly understood. Hence, a short-term field experiment was performed integrating real-time polymerase chain reaction, average well color development (AWCD), and MiSeq pyrosequencing to investigate relationships between environmental factors and microorganisms in five different disinfestation treatments, i.e., untreated monoculture soil (CK), soil with high temperature heating (HT), soil with dazomet (DZ), RSD with sugarcane bagasse (SB), or with bean dregs (BD). The results showed that compared to non-RSD treatments, both RSD treatments significantly increased soil microbial abundance and soil available K and organic matter (OM). Further analysis found that available K and OM were the key factors inducing microbial community change. Additionally, relative to non-RSD treatments, the relative abundances of phyla Proteobacteria, Acidobacteria, Rokubacteria, and Ascomycota were higher, whereas those of Actinobacteria, Gemmatimonadetes, and Basidiomycota were lower in RSD treatments. Changes in microbial diversity and abundance led to variation of soil microbial community functions. AWCD and community function prediction showed that, in contrast with non-RSD treatments, soil metabolism activity significantly increased, bacterial community functions including terpenoids and polyketides metabolism, signal transduction and cell motility increased, and the number of saprotroph fungi increased under RSD treatments. Overall, RSD incorporated with sugarcane bagasse or bean dregs efficiently improved soil fertility, and considerably increased soil microbial activity and function, which may benefit future sustainable agriculture production. Key points • Reductive soil disinfestation can alleviate continuous cropping obstacles by improving soil fertility. • Organic matter and available potassium as the key factors affected microbial community reconstruction and function. • Reductive soil disinfestation can improve soil metabolic activity and functional diversity by altering microorganism community.

Biochar-Enhanced Resistance to Botrytis cinerea in Strawberry Fruits (But Not Leaves) Is Associated With Changes in the Rhizosphere Microbiome

Biochar has been reported to play a positive role in disease suppression against airborne pathogens in plants. The mechanisms behind this positive trait are not well-understood. In this study, we hypothesized that the attraction of plant growth-promoting rhizobacteria (PGPR) or fungi (PGPF) underlies the mechanism of biochar in plant protection. The attraction of PGPR and PGPF may either activate the innate immune system of plants or help the plants with nutrient uptake. We studied the effect of biochar in peat substrate (PS) on the susceptibility of strawberry, both on leaves and fruits, against the airborne fungal pathogen Botrytis cinerea. Biochar had a positive impact on the resistance of strawberry fruits but not the plant leaves. On leaves, the infection was more severe compared with plants without biochar in the PS. The different effects on fruits and plant leaves may indicate a trade-off between plant parts. Future studies should focus on monitoring gene expression and metabolites of strawberry fruits to investigate this potential trade-off effect. A change in the microbial community in the rhizosphere was also observed, with increased fungal diversity and higher abundances of amplicon sequence variants classified into Granulicella, Mucilaginibacter, and Byssochlamys surrounding the plant root, where the latter two were reported as biocontrol agents. The change in the microbial community was not correlated with a change in nutrient uptake by the plant in either the leaves or the fruits. A decrease in the defense gene expression in the leaves was observed. In conclusion, the decreased infection of B. cinerea in strawberry fruits mediated by the addition of biochar in the PS is most likely regulated by the changes in the microbial community.

Synergistically promoting plant health by harnessing synthetic microbial communities and prebiotics

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

Bio-activation of soil with beneficial microbes after soil fumigation reduces soil-borne pathogens and increases tomato yield

Soil-borne diseases have become increasingly problematic for farmers producing crops intensively under protected agriculture. Although soil fumigants are convenient and effective for minimizing the impact of soil-borne disease, they are most often detrimental to beneficial soil microorganisms. Previous research showed that bio-activation of soil using biological control agents present in biofertilizers or organic fertilizers offered promise as a strategy for controlling soil-borne pathogens when the soil was bio-activated after fumigation. Our research sought to determine how bio-activation can selectively inhibit pathogens while promoting the recovery of beneficial microbes. We monitored changes in the soil's physicochemical properties, its microbial community and reductions in soil-borne pathogens. We found that the population density of Fusarium and Phytophthora were significantly reduced and tomato yield was significantly increased when the soil was bio-activated. Soil pH and soil catalase activity were significantly increased, and the soil's microbial community structure was changed, which may have enhanced the soil's ability to reduce Fusarium and Phytophthora. Our results showed that soil microbial diversity and relative abundance of beneficial microorganisms (such as Sphingomonas, Bacillus, Mortierella and Trichoderma) increased shortly after bio-activation of the soil, and were significantly and positively correlated with pathogen suppression. The reduction in pathogens may have been due to a combination of fumigation-fertilizer that reduced pathogens directly, or the indirect effect of an optimized soil microbiome that improved the soil's non-biological factors (such as soil pH, fertility structure), enhanced the soil's functional properties and increased tomato yield.

Application of olive mill waste-based biochars in agriculture: Impact on soil properties, enzymatic activities and tomato growth

The olive oil industry is an important economic sector in Mediterranean countries. However, oil production is unfortunately accompanied by the generation of huge amounts of olive mill solid wastes (OMSW) and olive mill wastewater (OMWW). In the present study, a strategy is proposed for converting these olive mill wastes into biochar through pyrolysis, for their later use as an organic amendment in agriculture. Specifically, two biochars were prepared from the pyrolysis of OMSW at 500 °C, either alone or impregnated with OMWW (OMSW-B and I-OMSW-B). The characterization of the OMSW and I-OMSW samples and their derived biochars showed that the fixed carbon and ash contents in the feedstocks increased by 38% and 11% respectively for OMSW-B, and by 37% and 12% respectively for I-OMSW-B. Interestingly, the impregnation process significantly increased Na, P, K, Ca and Fe contents in the produced biochars. The effect of OMSW-B and I-OMSW-B amendments at different application dose (1%, 2.5% and 5% wt/wt) on the enzymatic activity of an agricultural soil was performed at laboratory scale with a pot test. The experimental results showed that phosphatase and urease activity increased with biochar application rate; amendment with I-OMSW-B at 1%, 2.5% and 5% enhanced the phosphatase activity by 63%, 142% and 285% and urease activity by 50%, 116% and 149%, respectively. On the other hand, dehydrogenase and protease activities were higher for the application rate of 2.5% biochar. Biochar amendment promoted tomatoes seedling growth after 10 weeks, which was highest in the application rates of 2.5% and 5% for both OMSW-B and I-OSMW-B. Thus, the produced biochars had great potential to be used as biofertilizers in agriculture.

Comparing straw, compost, and biochar regarding their suitability as agricultural soil amendments to affect soil structure, nutrient leaching, microbial communities, and the fate of pesticides

The emission of nutrients and pesticides from agricultural soils endangers natural habitats. Here, we review to which extent carbon-rich organic amendments help to retain nutrients and pesticides in agricultural soils and to reduce the contamination of surrounding areas and groundwater. We compare straw, compost, and biochar to see whether biochar outperforms the other two more traditional and cheaper materials. We present a list of criteria to evaluate the suitability of organic materials to be used as soil amendments and discuss differences in elemental compositions of straw, compost, and biochar to understand, how soil microorganisms utilize those materials. We review their effects on physical and chemical soil characteristics, soil microbial communities, as well as effects on the transformation and retention of nutrients and pesticides in detail. It becomes clear that for all three amendments their effects can vary greatly depending on numerous aspects, such as the type of soil, application rate, and production procedure of the organic material. Biochar is most effective in increasing the sorption capacity of soils but does not outperform straw and compost with regards to the other aspects investigated. Nevertheless, the possibility to design biochar properties makes it a very promising material. Finally, we provide critical comments about how to make studies about organic amendments more comparable (comprehensive provision of material properties), how to improve concepts of future work (meta-analysis, long-term field studies, use of deep-insight microbial DNA sequencing), and what needs to be further investigated (the link between structural and functional microbial parameters, the impact of biochar on pesticide efficiency).

Influence of reductive soil disinfestation or biochar amendment on bacterial communities and their utilization of plant-derived carbon in the rhizosphere of tomato

Root-associated microorganisms play an important role in plant nutrition and productivity. However, our understanding of how a plant-microbiome system responds to pre-planting soil management remains limited. Here, continuous labeling with ¹³CO₂ gas combined with stable isotope probing (SIP) was applied to explore bacterial utilization of plant-derived carbon (C) in the tomato rhizosphere as affected by biochar amendment or reductive soil disinfestation (RSD). Our results showed that RSD treatment strongly shaped the soil bacterial community composition, while biochar soil amendment had little impact on the community in the rhizosphere of tomato. We observed that the bacterial community in the RSD treatment, which actively utilized plant-derived C, belonged to various phyla (i.e., Proteobacteria, Cyanobacteria, Verrucomicrobia, and Acidobacteria), while the genus Streptomyces (phylum Actinobacteria) was the main bacterial taxa that actively utilized plant-derived C in the biochar and control treatments. This study provides evidence that biochar application or RSD pre-planting soil management practices induced distinct bacterial utilization of plant-derived C, which may in turn regulate plant productivity in agricultural systems. KEY POINTS: • Genus Streptomyces was the main bacterial group utilizing plant-derived carbon in both control and biochar treatments. • Reductive soil disinfestation altered bacterial utilization of plant-derived carbon. • Biochar did not alter the composition of the bacterial communities but had more labeled bacterial taxa utilizing plant-derived carbon.