•Application of the novel bio-organic fertilizer suppressed ginger wilt incidence.•BIO2 significantly promoted ginger growth in field condition.•BIO2 reduced the soil Foz density and mediated culturable microbial community.Rhizome rot of ginger caused by Fusarium oxysporum f. sp. zingiberi (Foz) is a soil-borne disease that adversely affects the seed rhizomes and crop production. Bacillus amyloliquefaciens NJPRHSDAQ-1 (NP-1), which has a substantial inhibitory effect on Foz in vitro, was isolated from the ginger rhizosphere. A pot experiment indicated that a bio-organic fertilizer made from NP-1 (BIO2) or other universal biocontrol agents (BIO1), the suspension of NP-1 (NP-1), and its cell-free fermentation broth (NP-1fb), all effectively reduced the disease incidence of rhizome rot, stimulated plant growth, and improved the microbial community compared to the control. The best control effect (78.3%) and the most significant suppression of Foz abundance (75.8% compared to control) were all observed in the BIO2 treatment. Two field experiments further indicated that BIO2 amendment can significantly increase ginger yield by 8.0–11.5% and can decrease the Foz population by 30.8–51.0% compared to control plants receiving only chemical fertilizer. Application of BIO2 also increased the growth and nutrient quality of ginger and soil enzyme activity. Pearson correlation analysis indicated a significant negative relationship between the abundance of culturable bacteria and Foz, while a negative correlation between culturable actinomycetes/fungi population and invertase/urease activity was observed. This study highlights the application prospect of a novel bio-organic fertilizer in ginger production for both disease suppression and growth promotion.

Application of bioorganic fertilizers has been reported to improve crop yields and change soil bacterial community structure; however, little work has been done in apple orchard soils where the biological properties of the soils are being degraded due to long-term application of chemical fertilizers. In this study, we used Illumina-based sequencing approach to characterize the bacterial community in the 0–60-cm soil profile under different fertilizer regimes in the Loess Plateau. The experiment includes three treatments: (1) control without fertilization (CK); (2) application of chemical fertilizer (CF); and (3) application of bioorganic fertilizer and organic-inorganic mixed fertilizer (BOF). The results showed that the treatment BOF increased the apple yields by 114 and 67 % compared to the CK and CF treatments, respectively. The treatment BOF also increased the soil organic matter (SOM) by 22 and 16 % compared to the CK and CF treatments, respectively. The Illumina-based sequencing showed that Acidobacteria and Proteobacteria were the predominant phyla and Alphaproteobacteria and Gammaproteobacteria were the most abundant classes in the soil profile. The bacterial richness for ACE was increased after the addition of BOF. Compared to CK and CF treatments, BOF-treated soil revealed higher abundance of Proteobacteria, Alphaproteobacteria and Gammaproteobacteria, Rhizobiales, and Xanthomonadales while Acidobacteria, Gp7, Gp17, and Sphaerobacter were found in lower abundance throughout the soil profile. Bacterial community structure varied with soil depth under different fertilizer treatments, e.g., the bacterial richness, diversity, and the relative abundance of Verruccomicrobia, Candidatus Brocadiales, and Skermanella were decreased with the soil depth in all three treatments. Permutational multivariate analysis showed that the fertilizer regime was the major factor than soil depth in the variations of the bacterial community composition. Two groups, Lysobacter and Rhodospirillaceae, were found to be the significantly increased by the BOF addition and the genus Lysobacter may identify members of this group effective in biological control-based plant disease management and the members of family Rhodospirillaceae had an important role in fixing molecular nitrogen. These results strengthen the understanding of responses to the BOF and possible interactions within bacterial communities in soil that can be associated with disease suppression and the accumulation of carbon and nitrogen. The increase of apple yields after the application of BOF might be attributed to the fact that the application of BOF increased SOM, and soil total nitrogen, and changed the bacterial community by enriching Rhodospirillaceae, Alphaprotreobateria, and Proteobacteria.

To study the influence of straw incorporation with and without straw decomposer on bacterial community structure and biological traits, a 3-year field experiments, including four treatments: control without fertilizer (CK), chemical fertilizer (NPK), chemical fertilizer plus 7500 kg ha−1 straw incorporation (NPKS), and chemical fertilizer plus 7500 kg ha−1 straw incorporation and 300 kg ha−1 straw decomposer (NPKSD), were performed in a rice-wheat cropping system in Changshu (CS) and Jintan (JT) city, respectively. Soil samples were taken right after wheat (June) and rice (October) harvest in both sites, respectively. The NPKS and NPKSD treatments consistently increased crop yields, cellulase activity, and bacterial abundance in both sampling times and sites. Moreover, the NPKS and NPKSD treatments altered soil bacterial community structure, particularly in the wheat harvest soils in both sites, separating from the CK and NPK treatments. In the rice harvest soils, both NPKS and NPKSD treatments had no considerable impacts on bacterial communities in CS, whereas the NPKSD treatment significantly shaped bacterial communities compared to the other treatments in JT. These practices also significantly shifted the bacterial composition of unique operational taxonomic units (OTUs) rather than shared OTUs. The relative abundances of copiotrophic bacteria (Proteobacteria, Betaproteobacteria, and Actinobacteria) were positively correlated with soil total N, available N, and available P. Taken together, these results indicate that application of straw incorporation with and without straw decomposer could particularly stimulate the copiotrophic bacteria, enhance the soil biological activity, and thus, contribute to the soil productivity and sustainability in agro-ecosystems.

Grafting is commonly used to relieve damage caused by soil-borne diseases and to enhance the nutrient uptake in watermelon plants. Certain reports have shown the proteomic changes of plant tissues involved in grafting, while little information about the secretome after watermelon grafting is available. To gain insight into the root-secreted protein profile, root exudates of three types of seedlings (own-root watermelon (W), grafted-root watermelon (WB) and own-root bottle gourd (B)) were collected under hydroponic conditions, desalted and concentrated using Amicon ultracentrifugal filter devices, and separated by one-dimensional SDS–PAGE. Principal component analysis revealed that the protein profile was distinctly altered after grafting, and the diversity of root-secreted proteins of WB was significantly higher than that of W and B. Moreover, analysis by LC-QTOF/MS/MS revealed that some proteins associated with biotic and abiotic stress resistance appeared in response to grafting, such as disease resistance protein At4g27190, callose synthase, HVA22, and Clp protease. These results indicate that grafting can shift the root-secreted protein profile and thus could increase stress resistance. This study would help to reveal the mechanisms of disease resistance and growth promotion achieved through grafting.

The effects of commercial compost fertilizer application on trace gas emissions are not well understood due to a lack of field experiments. The objective of this study was to evaluate the emissions of methane (CH4) and nitrous oxide (N2O) along with grain yield from a rice paddy as affected by different organic–inorganic mixed fertilizer (OIMF) treatments.A field experiment was initiated in 2006 with chemical compound fertilizer (CF) and three OIMF amendments including pig manure compost (PMC), Chinese medicine residue compost (CMC), and rapeseed cake compost (RCC), from a rice paddy in southeast China. The emissions of CH4 and N2O were simultaneously measured using the static opaque chamber method over the entire rice growing season in 2011. Soil biotic parameters were measured in soil collected after the rice was harvested in 2011.Relative to the control, the OIMF treatments significantly increased CH4 emissions by 56–99 %, mainly due to exogenous organic substrate input, whereas no difference was observed in the CF treatment. The N2O emissions were stimulated substantially by an average of 40 % due to nitrogen fertilization compared with the control. Consecutive OIMF application tended to increase the grain yield, making it marginally higher than that of the CF treatment (7 %, P = 0.06). Compared with the control, the CF treatment slightly decreased the global warming potential and greenhouse gas (GHG) intensity, while they were remarkably increased in the OIMF treatments. Over the 5-year period of 2006–2011, the annual soil carbon sequestration rate was estimated to be 1.19 t C ha−1 year−1 for the control and 1.73–1.98 t C ha−1 year−1 for the fertilized treatments.Our results suggest that despite the beneficial effects of increasing both grain yield and soil organic matter, OIMF application such as PMC, CMC, and RCC may be responsible for increased global warming due mainly to the stimulated CH4 emissions. This effect should be thus taken into account when balancing agricultural production and GHG mitigation.

Bacillus amyloliquefaciens strains have been used as biocontrol agents for the suppression of several soilborne plant pathogens. A clearer understanding of the antagonistic mechanisms of action of these bacteria will facilitate their use in the control of plant diseases. Antagonistic substances were isolated from the fermentation broth of B. amyloliquefaciens strain NJN-6 cultures. These compounds were preconcentrated using an XAD-16 column and were purified using reversed-phase high-performance liquid chromatography (RP-HPLC). Fractions were collected from the column and were analyzed, and two homologues of bacillomycin D [molecular weights of 1030 Da (C14) and 1044 Da (C15)] and three homologues of members of the macrolactin family, macrolactin A, 7-O-malonyl macrolactin A, and 7-O-succinyl macrolactin A (molecular weights of 402, 487, and 502 Da, respectively) were identified using HPLC/electrospray ionization mass spectrometry (ESI–MS) analysis. An antagonistic assay showed that bacillomycin D and macrolactin exhibited significant antagonistic effects against Fusarium oxysporum and Ralstonia solanacearum, respectively. A reliable method for the isolation and purification of bacillomycin D and macrolactin from bacterial broth cultures was developed. These data will help elucidate the mechanisms that B. amyloliquefaciens NJN-6 uses for the biocontrol of soilborne plant pathogens.

Pig manure rice straw compost was extracted using different extraction methods, and the composition of each extraction was identified by chromatogram and spectroscopy in order to investigate plant growth promoting factors. Compared with direct extraction, aerated and non-aerated fermentation extractions were better for nutrient accumulation, especially for high molecular weight substances. Cucumber yields of aerated fermentation extraction of compost (AFEC) treatment were 16.5 and 57.6 % higher than the direct extraction of compost (DEC) and non-aerated fermentation extraction of compost (NAFEC) treatments. Humic acid-like and fulvic acid-like substances were the main components in all extracts. Furthermore, AFEC showed the most humification and aromatization. Humic substances extracted from AFEC (H-AFEC) increased shoot dry weight by 2.8 and 7.4 %, compared to humic substances extracted from DEC (H-DEC) and humic substances extracted from NAFEC (H-NAFEC). In conclusion, AFEC was the best extraction method to get more humic substances to stimulate plant growth.

Tobacco black shank, caused by a soil-borne pathogen, Phytophthora parasitica var. nicotianae, is one of the most serious diseases which reduce tobacco production worldwide. In this study, P. parasitica var. nicotianae was successfully controlled in vitro and in vivo by a newly isolated strain, Paenibacillus polymyxa C5, which is a plant-growth-promoting rhizobacteria and an effective biocontrol agent. Pot experiments were carried out to evaluate the effect of a novel bio-organic fertilizer (BIO), produced by the solid fermentation of organic fertilizer amended P. polymyxa C5, on the control of tobacco black shank. In comparison with the control, the disease incidence was significantly (P < 0.05) reduced by 50% with the application of BIO. P. polymyxa C5 was tagged with a plasmid-borne gfp gene to investigate its colonization behavior on tobacco roots in a natural soil system. As determined by confocal laser scanning microscopy, P. polymyxa C5 formed a biofilm on the tobacco roots growing in soil, both on the root tip and elongation zone but not inside the roots. It is speculated that the colonization of tobacco roots by P. polymyxa C5 is one of the mechanisms for the protection of tobacco plants from fungal infection.

Fusarium wilt is one of the most serious diseases caused by a soil-borne pathogen affecting banana production. The goal of this study was to evaluate the capability of a novel bio-organic fertilizer (BIO2) that integrated the biocontrol agent Bacillus subtilis N11, and mature composts to control Fusarium wilt of banana in pot experiments. The results showed that the application of the BIO2 significantly decreased the incidence rate of Fusarium wilt compared to the control. To determine the antagonistic mechanism of the strain, we also studied the colonization of the natural biocontrol agent on banana roots using a GFP marker. The studies were performed in a hydroponic culture system, a sand system and a natural soil system. The results indicated that the bacteria colonized predominantly by forming biofilms along the elongation and differentiation zones of the roots. The fact that similar observations were obtained in all three systems suggests that colonization by N11 can be studied in a defined system. The population of B. subtilis N11 in the rhizosphere and on banana roots was also monitored. We speculate that the colonization pattern of B.subtilis N11 can be linked to the mechanism of protection of plants from fungal infection.

More effective ways of applying biocontrol products should be developed based both on the characteristics of the biocontrol agents and the normal practices of the agricultural producer. A new system was developed to improve the biocontrol efficacy of Fusarium wilt for watermelon production, and this system was tested in pot and field experiments. Biocontrol was achieved by applying a novel bioorganic fertilizer product (BIO) to Fusarium-infested soil. The best biocontrol was obtained by application of a bioorganic fertilizer, BIO, into soil during the nursery phase of watermelon seedling followed by a second application to Fusarium-infested soil when watermelon seedlings were transplanted. In comparison with the controls, the incidence of the disease was reduced by 60–100% in the pot experiment and by 59–73% in the field experiment when the BIO was applied during the nursery stage. After application of BIO during the nursery stage, the number of colony-forming units of Fusarium oxysporum in rhizospheric soil was significantly (P < 0.05) inhibited compared to the controls. An in vitro experiment showed that the antagonist Paenibacillus polymyxa in the BIO could effectively colonize the rhizosphere of watermelon and proliferate along the extending plant roots. This inhibited growth of Fusarium oxysporum in the rhizosphere of watermelon and protected the watermelon roots from attack by the pathogens. The method used for biocontrol Fusarium wilt disease in watermelon should be a useful strategy to improve field efficacy of other biocontrol agents.

Fusarium wilt is one of the most serious diseases of banana plants caused by soil-borne pathogen Fusarium oxysporum f.sp. cubense (FOC). In this study a pot experiment was conducted to evaluate the effects of different bio-organic fertilizers (BIOs) on Fusarium wilt of banana, including the investigations of disease incidence, chitinase and β-1,3-glucanase activities of banana plants, and FOC populations as well as soil rhizosphere microbial community. Five fertilization treatments were considered, including chemical fertilizer containing the same N, P and K concentrations as the BIO (control), and matured compost mixed with antagonists Paenibacillus polymyxa SQR-21 and Trichoderma harzianum T37 (BIO1), Bacillus amyloliquefaciens N6 (BIO2), Bacillus subtilis N11 (BIO3), and the combination of N6 and N11 (BIO4). The results indicated that the application of BIOs significantly decreased the incidence rate of Fusarium wilt by up to 80% compared with the control. BIOs also significantly promoted plant growth, and increased chitinase and β-1,3-glucanase activities by 55%–65% and 17.3%–120.1%, respectively, in the banana roots. The population of FOC in the rhizosphere soil was decreased significantly to about 104 colony forming units g−1 with treatment of BIOs. Serial dilution plating and denaturing gradient gel electrophoresis analysis revealed that the application of BIOs increased the densities of bacteria and actinomycetes but decreased the number of fungi in the rhizosphere soil. In general, the application of BIOs revealed a great potential for the control of Fusarium wilt disease of banana plants.

The effects of direct extracts of compost (DEC), aerated fermentation extracts of compost (AFEC) and non-aerated fermentation extracts of compost (NAFEC) on cucumber growth and the action mechanisms were evaluated based on the structure and activity analysis of humic-like substances. AFEC increased cucumber growth most significantly, followed by DEC and NAFEC, which was insignificant compared to the control treatment. Humic-like substances from compost extracts played an important role in promoting cucumber growth. Application of humic-like substances stimulated auxin-like activity and increased chlorophyll content and nitrogen accumulation in plants. The positive auxin-like activity of humic-like substances could be attributed to the relative distribution of special carbon groups, such as those with a large amount of peptidic and carbohydratic groups or with a low content of phenolic groups. In conclusion, the best growth promotion by application of AFEC was mainly attributed to the humic-like substances in the AFEC.

•Depth is the strongest factor influencing diazotrophic community size and structure.•Diazotroph abundance were related to bacteria in subsurface but not surface soil.•Abundant nifH genes could also be present in the deep soil layers.•Fertilization effect on diazotrophic community was significant but inconstant.Biological nitrogen fixation (BNF) is an initial process of the nitrogen cycle (Cleveland et al., 1999) by the specialized microorganisms known as diazotroph. However, little information is available concerning the dynamic changes of diazotrophic communities in surface and subsoil layers. In this study, five representative season soil samples were collected from surface (0–20 cm) and subsoil (20–40 cm) in the long term experimental field plots that received no nitrogen fertilizer (CK), chemical fertilizers (CF), organic-inorganic mixed fertilizer (OIMF) and organic fertilizer (OF) since 2005. Real-time PCR was used to determine the nifH and total bacterial 16S rRNA gene abundance. Terminal restriction fragment length polymorphism (T-RFLP) of nifH gene was used to analyze the changes of diazotrophic communities. Results revealed that the abundance of nifH and 16S rRNA genes declined with increased soil depth regardless of fertilization regimes, although considerably high abundance was also observed in subsoils. The abundance of nifH genes was significantly positively correlated with the total bacterial abundance in oligotrophic subsoil layers, but not in the topsoil. Ammonium contents showed significant correlation to the nifH gene abundance in both surface and subsoil. Clustering analysis of the T-RFLP profiles showed that diazotrophic structures were clearly separated by surface and subsoil habitats. Permutational multivariate analyses demonstrated that soil depth, rather than the sampling time or fertilization regime, was the important factor that influence the diazotrophic structures. In the surface soil, soil organic carbon (SOC) and ammonium contents were significantly positively correlated to the diazotrophic community structures. These results suggest soil physiochemical properties selected for distinct diazotrophic communities inhabit in the topsoil and subsoil.