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Role of biochar, compost and plant growth promoting rhizobacteria in the management of tomato early blight disease

The individual role of biochar, compost and PGPR has been widely studied in increasing the productivity of plants by inducing resistance against phyto-pathogens. However, the knowledge on combined effect of biochar and PGPR on plant health and management of foliar pathogens is still at juvenile stage. The effect of green waste biochar (GWB) and wood biochar (WB), together with compost (Comp) and plant growth promoting rhizobacteria (PGPR; Bacillus subtilis) was examined on tomato (Solanum lycopersicum L.) physiology and Alternaria solani development both in vivo and in vitro. Tomato plants were raised in potting mixture modified with only compost (Comp) at application rate of 20% (v/v), and along with WB and GWB at application rate of 3 and 6% (v/v), each separately, in combination with or without B. subtilis. In comparison with WB amended soil substrate, percentage disease index was significantly reduced in GWB amended treatments (Comp + 6%GWB and Comp + 3%GWB; 48.21 and 35.6%, respectively). Whereas, in the presence of B. subtilis disease suppression was also maximum (up to 80%) in the substrate containing GWB. Tomato plant growth and physiological parameters were significantly higher in treatment containing GWB (6%) alone as well as in combination with PGPR. Alternaria solani mycelial growth inhibition was less than 50% in comp, WB and GWB amended growth media, whereas B. subtilis induced maximum inhibition (55.75%). Conclusively, the variable impact of WB, GWB and subsequently their concentrations in the soil substrate was evident on early blight development and plant physiology. To our knowledge, this is the first report implying biochar in synergism with PGPR to hinder the early blight development in tomatoes.


Results
Molecular analysis for the confirmation of the Alternaria solani. The ITS and β-tubulin 1 gene primers amplified PCR products of 580 bp and 364 bp, respectively ( Supplementary Fig. S1). The sequences of the PCR products were deposited to the Genbank and received accession numbers MT899419 and MT899420 for ITS and β-tubulin 1, respectively. BLASTn comparison analysis of the ITS GenBank accession No. MT899419 has shown close homology (99.66%) with the A. solani isolates from china (MG012294.1 and MG012293.1), while β-tubulin 1 GenBank accession No. MT899420 has similarity (99.45%) with A. solani isolate from Korea (JF417707.1).

Estimation of plant growth parameters. The reduction in shoot height was significant among all the
A. solani inoculated treatments ( Fig. 1A-C). Maximum plant height (45.21 and 44.07 cm) was in treatment 'Comp + 6%GWB + PGPR' in the absence and presence of disease stress, respectively (Fig. 1C). Amongst A. solani inoculated plants, significant reduction in shoot heights were ranked as (according to soil amendment; from minimum reduction to maximum) green waste biochar amended treatments were followed by the wood biochar, compost and lastly by the un-amended soil control both with and without the PGPR.
The results of three-way ANOVA presented as P values are summarized in Table 1. Soil substrate compositions comprising of compost alone and in combination with 3 and 6% of each wood biochar and green waste biochar, PGPR and A. solani served as main factors. Plant height was significantly (P < 0.001) influenced by the interactive effect of soil substrate composition (SC) with both PGPR and A. solani (AS) [(SC × PGPR and SC × AS, respectively)], as well as by the interaction of PGPR and A. solani (PGPR × AS; (P ≤ 0.05). Therefore, in the presence of PGPR, both wood and green waste biochar had a positive impact on plant height, root and shoot dry weight (Figs. 1, 2, 3). Among all the treatments either with or without biochar, A. solani inoculation caused www.nature.com/scientificreports/ reduction in dry weights of above and below ground plant parts (Figs. 2, 3). However, maximum root dry weight (2.22 g) was found in tomato plants grown in treatment 'Comp + 6%GWB + PGPR' , while no significant reduction recorded in dry root biomass under early blight influence (Comp + 6%GWB + PGPR + A. sol; 1.97 g). There was an increase of ~ 23% in root dry biomass of + A. solani tomato plants grown in 'Comp + 6%WB + PGPR' and 'Comp + 6%GWB + PGPR' substrates unlike their − PGPR counterparts (Fig. 2B,C). In addition to the significant  Table 1. Three-way ANOVA results represented as level of significance of the effect of factors soil substrate composition (SC), Alternaria solani (AS) and plant growth promoting rhizobacteria; Bacillus subtilis (BS) and their interactions on tomato plant growth and physiological parameters. ns non-significant. *P ≤ 0.05; **P < 0.01 ***P < 0.001.

Dry shoot weight
Nitrogen contents

Plant physiological parameters. Estimation of chlorophyll contents of tomato plants.
In addition to the interactive effect of SC × PGPR (P < 0.01), all main factors including soil composition, PGPR and A. solani significantly (P < 0.001) influenced the chlorophyll contents of tomato plants. The soil composition containing 6%GWB significantly increased the quantity of chlorophyll in tomato plants as described in Table 2. Maximum contents of chlorophyll 44.02 ± 0.24 and 43.07 ± 0.08 were observed in plants raised in 'Comp + 6%GWB + PGPR' and 'Comp + 6%GWB − PGPR' treatments, respectively in the absence of A. solani. Overall, A. solani inoculation induced reduction in the chlorophyll contents. While, the plants inoculated with A. solani, grown in compost and/or biochar amended treatments irrespective to the concentration and type of the biochar have sustained the level of chlorophyll contents. Under early blight stress highest chlorophyll contents (42.95 ± 0.33) were in 'Comp + 6%GWB + PGPR' treatment, while the lowest content level (33.61 ± 0.28) was measured in soil control in the absence of PGPR.
Nitrogen, phosphorous and potassium contents of tomato plants. ANOVA analysis highlighted the significant (P < 0.001) effect of soil composition, PGPR and A. solani (Table 1) on Nitrogen (N) contents of tomato plants. Figure 4A-C demonstrated a higher percentage of nitrogen (N) contents in tomato shoots grown in both wood and green waste biochar with and/or without PGPR. Highest N contents (%) 4.11 and 3.87% were measured in 'Comp + 6%GWB + PGPR' treatment both in the absence and presence of A. solani, respectively (Fig. 4C). Tomato plants grown in wood biochar has sustained the level of N contents under disease stress as compared to their respective healthy compliments (Fig. 4B).
In case of Phosphorous (P) contents (ppm), a significant (P < 0.001) interaction effect of SC × PGPR and SC × AS was observed ( Table 1). The maximum significant value of P contents was recorded in plants raised in 6%GWB amended soil in association with PGPR either un-infected or infected with A. solani (0.56 and 0.48 ppm), respectively (Fig. 5C). Whereas, the level of P contents significantly reduced in remaining GWB amended treatments inoculated with A. solani, both with and without PGPR. The same trend has been recorded for P contents of plants grown in wood biochar amended soil (Fig. 5B). However, the minimum (0.09 ppm) was recorded in the A. solani infected plants grown in soil only without compost and biochar amendments (Fig. 5A).
Tomatoes infection with A. solani had a significant impact on lowering the potassium (K) contents (ppm) in all of the treatments (Fig. 6A-C). Data analysis revealed significant (P < 0.01) interactive effect between soil amendments and A. solani on K contents of tomato plants. In comparison with all of the treatments, plants grown in soil amended with green waste biochar depicted higher K contents, with the maximum of 1.94, 1.72 and 1.70 ppm in 'Comp + 6%GWB + PGPR' , 'Comp + 3%GWB − PGPR' and A. solani inoculated plants in 'Comp + 6%GWB + PGPR' treatment, respectively (Fig. 6C). The factor PGPR also significantly (P < 0.001) influenced the K contents in tomatoes. However, plants grown in wood biochar (6%) amended treatments Alternaria solani incidence, percent disease index and assessment of disease response of tomato plants. Early blight incidence, percent disease index (PDI) and tomato plant response to disease was assessed thirty 4r days after transplanting on the basis of symptoms development and severity. The incorpo-  www.nature.com/scientificreports/ ration of biochar in plant growth medium has a suppressive effect on A. solani development on tomatoes alone and in combination with PGPR (Table 3). In case of soil amendment carrying 3% GWB, an increase in disease incidence from 40 (Comp + 3%GWB-PGPR) to 60% (Comp + 3%GWB + PGPR) was observed. Whereas, PDI was significantly reduced (10.53%) in the 'Comp + 3%GWB + PGPR' treatment in comparison to its non-PGPR counterpart. Minimum disease incidence (20%) and PDI (20 ± 1.26) was observed in tomato plants raised in 6%GWB amended soil substrate in the presence of PGPR (Comp + 6%GWB + PGPR). Similarly, there was a reduction of 12.8 and 19.18% in the PDI, as recorded in treatment 'Comp + PGPR' and 'Comp + 3%WB + PGPR' , respectively, when compared to their-PGPR counterparts.
Overall, tomato plant response to A. solani varied from highly susceptible (S) to resistant (R) grown in different soil substrate compositions, with the PDI values ranging between 20 and 80.8%. The plants grown in 'Comp + 6%GWB + PGPR' have shown 'R' response to early blight followed by moderately resistant (MR) response in 'Comp + 3%GWB + PGPR' , and 'Comp + 3%GWB − PGPR' , while susceptible (S) response in all of the wood biochar amended treatments was recorded (Table 3). Whereas, tomato plants were highly susceptible (HS) to A. solani, when grown in the absence of any soil amendment as well as in the treatment containing only compost (Comp-PGPR).
In vitro effect of compost, biochar and Bacillus subtilis on Alternaria solani mycelium growth and development. In vitro toxicity of compost and biochar (WB and GWB) amended PDA media and PGPR towards A. solani is shown in Table 4, while the un-amended media served as a control. The lowest (1.77%) inhibition of fungal radial growth was recorded in media modified with compost. Further, no significant difference in A. solani mycelium growth inhibition (10.27 and 15.91%), in WB (3%) and GWB (3%) amended media, respectively. However, with the increase in the concentration of biochar i.e. WB (6%) and GWB (6%) in PDA, the efficiency of fungal radial growth inhibition was also increased. So it was observed that GWB (6%) has induced  www.nature.com/scientificreports/ significantly higher (38.74%) A. solani mycelium growth inhibition, followed by the media amended with WB (6%; 29.21% inhibition) in comparison to the control. The maximum mycelia growth inhibition (55.75%) was recorded in B. subtilis inoculated PDA, surpassing all other treatments used in the assay.

Discussion
Phyto-pathogens minimize the yield and deteriorate the quality of agricultural products causing significant economic losses to the agricultural entrepreneurs 60 . Excessive use of agricultural chemicals incite environmental and health issues as well as leads to the mutations in pathogenic strains rendering them resistant to existing disease management practices 61 . In this regard, emergence of multiple A. solani isolates 62 , with enhanced resistance against fungicides such as azoxystrobin, pyraclostrobin 63 , mancozeb and chlorothalonil 64 , ignites the need for the development of sustainable disease management strategies duly harmonized with the environment. Therefore, the current study was conducted with the aim of developing a novel, sustainable and economically viable approach to enhance crop productivity by reducing pathogen induced losses without damaging the diversity of life around 65 . Biochar application is an ancient method to improve the soil quality, however it is only been last two decades that witnessed the keen interest of researchers towards biochar as carbon sequestration and organic plant protection agent 66 . The individual effects of compost and B. subtilis against EB of tomato has already been documented 36,48 . However, the response of tomatoes grown in biochar and PGPR modified soil medium against EB has not been explored earlier. To our knowledge, the results presented here for the first time elucidate the effectiveness of compost, biochar mixture together with PGPR on foliar pathogen (A. solani) development in tomatoes.
The different biochars with diverse compositions don't follow uniform application rate principal to get desired response either in case of plant health improvement or disease suppression 27,67 . Similarly, in our study, not only biochar types but also their application rate influenced the EB disease incidence, severity and plant's vegetative as well as physiological responses. We found the ineffectiveness of WB at both application rates in suppressing Table 3. Effect of different soil substrate compositions and plant growth promoting rhizobacteria (PGPR) on disease incidence, percent disease index and disease responses of tomato plant against Alternaria solani. *All treatments were inoculated with Alternaria solani. DI disease incidence, PDI ± SE percent disease index ± standard error, DR disease response, R resistant, MR moderately resistant, S susceptible, HS highly susceptible.  www.nature.com/scientificreports/ the disease. On the contrary GWB significantly reduced the disease at both of the application rates i.e. 3 and 6%, while being more effective at higher concentration. Zwart and Kim 68 , documented the reduction in Phytophthora spp. induced stem lesions in landscape tress species (Acer rubrum and Quercusrubra) grown in potting media amended with 5% biochar made from raw material of pine (Pinus spp.) origin, whereas Elad et al. 20 found the enhanced suppression of Botrytis cinerea at higher application rate of biochar. In contrast with our finding, Harel et al. 28 demonstrated the reduction in disease inhibition of foliar pathogens causing powdery mildew and grey mold on strawberry at comparatively lower biochar doses. While, Atucha and Litus 69 , documented the effectiveness of pinewood biochar at much higher application rates i.e. 10 and 20% (v/v), against replant disease in susceptible peach rootstock. Thus, effective diseases suppression and plant growth promotion rely heavily on biochar type and concentration to be applied in the potting medium. However, there are also studies suggesting antagonistic effect of biochar on plant protection against diseases such as of maple wood bark biochar application increased the severity of Rhizoctonia solani in multiple plant species including crops of horticultural importance such as tomato, carrot, radish and others 70 .
The control of plant pathogens with biochar could be the result of direct toxicity to only soil-borne pathogens, however, in case of foliar pathogens the probable mode of action needs further elucidation. Earlier studies conducted on biochar effect on Botrytis cinerea, Colletotrichum acutatum and Podosphaera apahanis development on strawberry revealed the activation of expression of defence-related genes involved in ISR and SAR pathways 28 . Whereas, Mehari et al. 29 reported the ISR/Jasmonic acid pathways involvement in imparting resistance in tomatoes against B. cinerea. So, it was proposed that systemic induced resistance plausibly the main component in suppressing foliar pathogens by biochar amendments 20 , in addition to increased/healthy plant growth. Multiple studies have repeatedly shown that composts have a suppressive effect on soil-borne diseases such as damping, root rots 71,72 by modifying the rhizosphere and/or soil microbial profile as a whole 73 .
It is also suggested that the incorporation of PGPR with other organic soil amendments significantly contribute towards improved plant health 47 , and better protection from phyto-pathogens 74 . In a very rare study, Postma et al. 75 reported the effectiveness of co-application of animal bone charcoal and phosphate solubilizing rhizobacteria against soil-borne disease of tomato namely, damping-off (Pythium aphanidermatum) and Fusarium crown and root rot (Fusarium oxysporum f. sp. radicis-lycopersici).
Our results also indicated the enhanced protection of tomatoes against A. solani in the presence of PGPR in biochar amended potting substrate. Addition of the biochar in soil formulate a unique environment consisting of high carbon contents, minute quantities of phenols and other organic acids with the ability to induce hormesis response 46 . While, the working efficiency of B. subtilis is influenced by biotic like plant genotype, microbial community and etc., as well as abiotic factors such as soil type, organic contents, and temperature 76 , clearly correlates with the findings of this study. Biochar might serve as a suitable carrier material for PGPR or bio-control agents 66,75 . Moreover, with an added advantage of enhanced survivability, multiplication and colonization in porous spaces of biochar 77 , makes it an ideal candidate for the development of bio-control formulation for commercial applications.
Therefore, the effects of PGPR must be anticipated as a result of multiple factors involving soil environment, antibiosis, induction of systemic resistance, and pathosystem under investigation 78 . However, PGPR mediated ISR is mainly considered responsible for the enhanced level of protection against foliar pathogens 52,79 . Another study attributed the B. subtilis induced protection from EB to the production of antioxidants and over-expression of systemic induced resistance genes 80 .
Taken together, biochar and PGPR also perform critical function in priming of host defence by inducing the activation of salicylic acid and jasmonic acid pathways 30 . Once primed, the plant can cope with the challenging pathogens more aggressively and efficiently 81 . Both biochar borne chemicals and PGPR inoculation potentiate the systemic resistance and cascade of defence related signaling events 82,83 .
Plant growth response to biochars depend upon the organic material used for the pyrolysis 46 . In this study, GWB addition in tomatoes growing medium containing compost had a significant positive impact on plant growth, when applied at 6% (v/v) application rate. Previously, She et al. 84 found that there was an increase in tomato vegetative growth parameters at higher doses of wheat straw biochar. Whereas, Rajkovich et al. 85 documented that the change in feedstock type produced a variable growth patterns in corn. In general, application of biochar with proper nutrient source such as compost, could have a positive influence on plant health and production 86 . Earlier, Schulz and Glaser 43 , found that the application of biochar with compost was more desirous than with the mineral fertilizers in terms of improving plant growth. Further, biochar and compost had a positive impact on soil properties and in increasing the growth of plant as reported by Safaei Khorram et al. 87 .
Moreover, the differences in plant growth in either WB and/or GWB amended potting media might be due to the differences in their nutrient retention capacity. As, the nutrients from biochars made from leaf-like material are easily accessible to the plants then the biochars obtained from woody feed stock 26,88,89 . Similarly, Hossain et al. 90 reported the increase in tomato growth raised in soil modified with wastewater sludge biochar to enhanced nutrient retention and availability of N and P. While, Vaccari et al. 91 described an enhanced availability of N, P and K to the tomato plants grown in biochar treated soils.
Overall, increase in growth could also be due to the additional liming impact of the biochar, thereby increasing the plant's efficiency of nutrient utilization 92 . Our results had also revealed that the increased tomato agronomic and physiological growth parameters to the treatments with greater concentration of either WB or GWB because of their increased ability to lower the soil pH.
The additional growth promotion by PGPR, might not only be due to the nutritional or liming effect, other factors such as production of plant growth hormones, biocontrol activity and organic acids plausibly contribute to activated plant growth response. Egamberdieva et al. 54 reported an increase in soybean (Glycine max L.) plant growth grown in hydrochar (2%) attributed to enhanced plant growth promoting rhizobacterial activity in the root zone. The production of Indole 3-acetic acid (IAA) by PGPR has a major share in activating plant cellular www.nature.com/scientificreports/ multiplication which contributes in development of a vigorous roots network. Araujo et al. 93 also reported the production of IAA and abscisic acid by B. subtilis strains resulting in root growth promotion. Additionally, PGPR are also known to aid in solubilisation of unavailable form of nutrients by organic acid production 94 thus, facilitating the transport of nutrients from rhizosphere to the plant 95 . As a result, enhanced nutrient uptake from well-established root system corresponds to increased metabolic activity as well as growth and development of above-ground plant parts 96,97 . Parallel to the tomatoes growth response, the chlorophyll contents also responded in the same way to biochar amendment (little or no effect of WB, while positive effect of GWB) both in the presence and absence of EB stress. Previous studies also contradict in terms of the effect of biochar on photosynthetic pigments, like Akhtar et al. 98 who described decreased chlorophyll contents of tomato plants grown in biochar, while in one of our previous studies, there was no reducing effect of biochar on chlorophyll contents 46 . In addition to enhancing nutrient solubilisation (P and K), the association of PGPR with biochar clearly enhanced and maintained the level of chlorophyll even in the presence of A. solani. Similarly, Danish and Zafar-ul-Hye 99 , reported significant increase in chlorophyll contents of wheat in response to the synergistic effect of PGPR and biochar. Biochar induced alterations in communication or signaling mechanisms between plant and microbes might also be responsible for the changes in PGPR response in the presence of different biochars used in variable concentrations in the soil substrate 100,101 . The mechanisms and processes involved in plant growth improvement with simultaneous protections form diseases are complex and signifies the need of further in depth analysis for complete understanding.
Alternaria solani can survive in the soil in the form of fungal mycelia and conidia on host debris 102 , whereas chlamydospores even in the absence of host debris 103 . So, to anticipate the direct impact of compost, biochar and B. subtilis on A. solani spores and mycelium overwintering in the field, PDA plate assay was employed 26,48 . As expected, compost has lost its antifungal property after autoclaving of the PDA, consequently minimum fungal inhibition was observed. Probably highlighting the role of the compost inhabiting microbes in suppressing the pathogenic microbes 104,105 . Although, incorporation of biochar has produced varying degree of A. solani mycelial growth inhibition but none of the biochars either WB or GWB were able to suppress inhibition in close proximity to 50%. Previous studies were also in agreement that disease suppression was not often lies in correspondence to the levels of in vitro toxicity of organic amendments 26,67 . Bacillus subtilis is known to have antagonistic effects against A. solani 106 . We also found greater inhibition of A. solani mycelial growth induced by B. subtilis, which could be due to the production of extracellular compounds including biosurfactants like iturin and fengycin causing antibiosis to fungal pathogens. On et al. 107 also published about the antifungal activity of B. subtilis culture crude extracts against A. solani. The direct antifungal effect of organic amendments and PGPR, yet provide with another possibility of limiting the level of overwintering inoculum of A. solani in soil and plant debris. However, future experimentation will decide the faith of this assumption.
Depending upon the type of feedstock and biochar concentration in the soil substrate, two different types of biochars i.e. WB and GWB had a variable impact on plant health and early blight development in tomatoes. Based on the comparative analysis, GWB was found to be the most effective in suppressing A. solani, alone as well as in combination with B. subtilis. The combined application of biochar, compost mixture with PGPR, stimulated the rhizobacterial activity resulting in plant growth activation and disease inhibition. In the next phase, we are planning on studying genes associated with induced resistance to confirm their role in suppressing early blight in tomatoes. However, the concentration level of biochar to be used as a soil amendment is a subject deserving more research. In addition, future research activities should be focused to decipher the mechanisms behind the biochar induced resistance in tomato plants against A. solani as well as in other patho-systems of economic importance. In order to address the possible risks associated with biochars application on plant health, there is dire need of attention by scientific community in understanding biochemistry of the processes triggered by biochar borne chemicals.

Materials and methods
Isolation and characterization of Alternaria solani. Infected tomato plants exhibiting characteristic symptoms of early blight growing under field condition at University of the Punjab Lahore, Pakistan were identified for the fungal isolation. Standard tissue segment technique was followed 108 to obtain A. solani culture on potato dextrose agar (PDA) medium (MERCK).
Subsequently, fungal mycelia from previously incubated PDA plates were shifted to freshly prepared media plates. Pure culture of the A. solani was obtained by re-culturing of isolated fungi via single spore technique 109 and maintained as stock culture on Agar slants at 5 °C for future usage. Identification of pathogen was done by cultural and morphobiometric properties (Supplementary Table S1) as per Ellis 110 , and Simmons 111 . Linear growth of fungus was deliberated by measuring diameter of colonies in the same axis using transparent plastic scale in millimeter after 7 days of inoculation 112 . Fungal culture characteristics such as topography of mycelium, color and margin of colony on PDA were recorded 113 . For calculation of number of spores, a spore suspension was prepared by transferring 5 mm diameter block from media into 5 mL distilled water in a test tube and stirred with stirrer. Subsequently, sporulation was recorded by calculating mean value of spore count of three microscopic fields in one drop of spore suspension under object lens of compound microscope 112 .

Molecular identification of Alternaria solani. CTAB (Cetyl Trimethyl Ammonium Bromide) method
was used to extract genomic DNA of A. solani 114 . The ITS (Internal Transcribed Spacer) region of A. solani was amplified by using universal ITS primers [ITS1 forward (TCC GTA GGT GAA CCT GCG G) and ITS4 reserve (TCC TCC GCT TAT TGA TAT GC)] as described previously [115][116][117] . In order to further confirm the identity of A. solani, β-tubulin 1 116  Soil substrate preparation and experiment setup. Depending upon the originating feedstock, two types of biochar, green waste biochar (GWB), produced from garden waste material and wood biochar (WB), produced from beech wood chips at pyrolysis temperature of 500 °C were used in the experiment. Both of these biochar differ substantially in structure and chemistry from each other (e.g. nitrogen contents, pH, cation exchange capacity and others) as described by Akhter et al. 46 and Frišták et al. 119 . The compost was obtained from National Fertilizer Marketing of Govt. of Punjab, Lahore Pakistan with product name of ZameenDost (ZD) under license no. 1140. The most pertinent characteristics of biochars along with the compost are described in Table 5. Tomato plant propagation. Tomato seeds (Solanum lycopersicum L. cv. Rio grande) were surface sterilized with 3% NaOCl solution by soaking for 10 min and then rinsed thrice with double distilled water to wash off the chemical. Seeds were sown in trays containing double autoclaved potting mixture comprising of peat, perlite (Gro-Sure Westland Horticulture Cambridgeshire UK) and compost (ZD) (1:1:1, v/v/v). The trays were then incubated in a growth chamber at 24 °C with a 15/9 h light/dark photoperiod (light intensity 296 µmol m −2 s −1 ). The trays were irrigated regularly with tap water. After four weeks, tomato seedling were reached at 1-3 true leaf stage and transferred from trays to pots containing potting mixture as described in previous section. For PGPR inoculated treatments, the roots of tomato seedlings were dipped in PGPR suspension of 10 8 CFU/mL concentrations for 1 min before transplantation and 10 mL suspension was applied in the soil around the rhizosphere ten days after transplantation 120 .
For inoculation, the A. solani was cultured on Petri dishes containing PDA (MERCK, USA) and stored for 3 weeks at 25 °C in the dark in DNP-9022 incubator. To make suspension for inoculation, conidia were harvested by flooding the Alternaria culture plates with autoclaved water and gently scraping the colony surface with spatula. Next, the suspension was filtered using four layers of cheesecloth (50 µm). Final concentration of conidial suspension was determined and adjusted at 1 × 10 6 condia/mL with hemocytometer 121 .
After 14 days of transplantation, conidial suspension of A. solani (10 6 conidia/mL) was inoculated on plants 80 . Conidial suspensions were sprayed gently on tomato leaves in the evening by following direct spray inoculation method using manual sprayer (Nozzle size = 0.8 mm) 122 . The inoculated tomato plants were sprayed with sterilized water for 2 days to maintain the required humidity (approx. 70%) for disease development. The plants were maintained in a greenhouse in randomized manner as per all the recommended practices for cultivation of tomato to raise a good crop 123 . Plant growth assessment. The plants were harvested 40 days after transplantation by gently uprooting followed by washing the roots under running tap water to record growth parameters such as plant height, root Table 5. Physiochemical parameters of soil, compost, wood biochar, green waste biochar. CEC cationexchange capacity, EC electrical conductivity, OM organic matter, SA surface area, AC ash contents, Comp compost, WB wood biochar, GWB green waste biochar. -Parameters were not analyzed.  For the estimation of total P and K, two 0.5 g samples were prepared by wet digestion method as explained by Uddin et al. 128 and Hseu 129 . Further, the concentration of P and K in digested samples were determined by following spectrophotometric vanadium phosphormolybdate method 97,130 by using AA spectrophotometer (AA-6200, Shimadzu US) at 420 nm and flame photometric method 130,131 by using Industrial Flame Photometer (PFP7, Jenway, UK), respectively. The concentrations in samples were determined by comparing with standard curve 132 .
Disease assessment. Early blight disease severity was recorded visually 20 days after inoculation on the basis of area of leaves covered by early blight symptoms using zero to five disease rating scale ( Table 6) followed by Akhtar et al. 117 . Further, percent disease index (PDI) was calculated by following formula described by Pandey et al. 133 and Yadav et al. 134 : Disease incidence of early blight was calculated 20 days after inoculation as percentage of diseased plants in treatment following formula by Awan et al. 11,80 : In vitro toxicity of compost, biochar and Bacillus subtilis in PDA plate to Alternaria solani. The inhibitory impact of compost, WB and GWB on growth and inhibition of A. solani was studied in vitro on PDA plates. Both types of biochar i.e. WB and GWB, and compost were sieved through 100 μm sieve before adding to PDA 67 . The growth media was amended with compost (20%, w:v) and different concentrations of WB and GWB (3 and 6% (w:v), each) before autoclaving. Afterwards, growth media was poured into Petri-dishes (90 mm) and kept at room temperature till solidification. Subsequently, six mm diameter agar plugs of actively growing parts of fungal culture (5 days old) were obtained with sterile cork borer and placed at the center of dishes. While antifungal potential of PGPR was determined according to dual culture method by inoculating the PDA plates with B. subtilis close to the edges of petri-dishes 48 . The inoculated Petri-dishes were incubated at 23 ± 2 °C for 6 days. The fungal radial growth (mm) for each treatment was calculated by averaging colony diameter of five randomly arranged replicates. The percentage inhibition of fungal radial growth in different media including control (C, un-amended) and amended (A) was determined according to Bekker et al. 135  Percentage inhibition = C − A C × 100. www.nature.com/scientificreports/ Statistical analysis. The data analysis was carried out using Statistix 8.1 software (Statistix, USA). Percentage data were transformed before analysis. While the pooled data of the experimental repeats were used for the analysis. The data were subject to three-way analysis of variance (ANOVA) with (i) soil substrate compositions including compost alone and in combination with wood and green waste biochar; (ii) PGPR and (iii) A. solani as main factors. The means were compared by applying Tukey's HSD test at P ≤ 0.05 level of probability.

Data availability
The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.