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Chemical nutrient amendment by human activities can lead to environmental impacts contributing to global biodiversity loss. However, the comprehensive understanding of how below- and above-ground biodiversity shifts under fertilization regimes in natural ecosystems remains elusive. Here, we conducted a seven-year field experiment (2011–2017) and examined the effects of different fertilization on plant biodiversity and soil belowground (prokaryotic and eukaryotic) communities in the alpine meadow of the Tibetan Plateau, based on data collected in 2017. Our results indicate that nitrogen addition promoted total plant biomass but reduced the plant species richness. Conversely, phosphorus enrichment did not promote plant biomass and exhibited an unimodal pattern with plant richness. In the belowground realm, distinct responses of soil prokaryotic and eukaryotic communities were observed under fertilizer application. Specifically, soil prokaryotic diversity decreased with nitrogen enrichment, correlating with shifts in soil pH. Similarly, soil eukaryotic diversity decreased with increased phosphorous inputs, aligning with the equilibrium between soil available and total phosphorus. We also established connections between these soil organism communities with above-ground plant richness and biomass. Overall, our study contributes to a better understanding of the sustainable impacts of human-induced nutrient enrichment on the natural environment. Future research should delve deeper into the long-term effects of fertilization on soil health and ecosystem functioning, aiming to achieve a balance between agricultural productivity and environmental conservation. • Soil prokaryotic and eukaryotic diversity decreased under nitrogen and phosphorus fertilization respectively. • Phosphorus fertilizer can alleviate nitrogen fertilizer induced soil acidification and promote soil diversity. • The changes of soil biodiversity were attributed to soil physicochemical characteristics induced by different fertilizer. • Soil prokaryotes and eukaryotes diversity was linked with the plant richness and biomass respectively. [ABSTRACT FROM AUTHOR]

Bacillus amyloliquefaciens NJN-6, a plant growth promoting bacterium can act as an efficient antagonist against F. oxysporum f. sp. cubense (FOC). This study tests the response of antibiotic producing genes ( itu A and bam D) and biofilm formation related genes ( eps D and yqx M) in strain NJN-6 to phenolic acids in banana root exudates. Phenolic acid in banana root exudates (infected or non-infected by FOC) were identified by HPLC. Transcription analysis of genes involved in biofilm formation and antibiotic synthesis in strain NJN-6 were investigated with quantitative reverse transcription PCR (RT-qPCR). We found that the transcription levels of two antibiotic producing genes and two biofilm formation related genes in strain NJN-6 were upregulated in the banana seedling roots. Root secretion of phthalic acid, salicylic acid and cinnamic acid were enhanced in FOC infected banana seedlings. Further additional experiments demonstrated that the transcription level of itu A, bam D and eps D increased linearly to the concentration of phthalic acid. Results from antibiotic production and biofilm formation assays demonstrated a similar trend to gene transcription analysis. The results in this study indicated that the phenolic acids in root exudates of banana can potentially enhance root colonization and pathogen suppression abilities of Bacillus amyloliquefaciens NJN-6. [ABSTRACT FROM AUTHOR]

Nitric oxide (NO) is an important gas signal that regulates many biological processes, and due to the high nitrogen recycling activity in the rhizosphere, NO is an important signaling molecule in this region. Thus, an understanding of the effect of NO on the rhizomicrobiome, especially on plant beneficial rhizobacteria, is important for the use of these bacteria in agriculture. In this study, the effect of exogenous NO on the beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 was investigated. The results showed that low concentrations of NO increased the ability of the strain SQR9 to form biofilms, while high concentrations of NO inhibited the growth of this bacterium. The SQR9 gene yflM encodes nitric oxide synthase (NOS), which is used to synthesize NO, while the gene ykvO encodes a sepiapterin reductase that is used to synthesize tetrahydrobiopterin, the coenzyme of NOS. Isothermal titration calorimetry and high-performance liquid chromatography analyses demonstrated an interaction between YkvO and NADPH. SQR9 has two hmp genes, although only one was observed to be responsible for NO detoxification through oxidization. This study revealed the effect of NO on plant beneficial rhizobacterium and assessed the ability of this strain to adapt to exogenous NO, which will help to improve the application of this strain in agricultural production. [ABSTRACT FROM AUTHOR]

Different fractions during the 85-day windrow composting were characterized based on various parameters, such as physiochemical properties and hydrolytic enzyme activities; several technologies were used, including spectral scanning techniques, confocal laser scanning microscopy (CLSM) and 13 C Nuclear Magnetic Resonance Spectroscopy ( 13 C NMR). The evaluated parameters fluctuated strongly during the first 3 weeks which was the most active period of the composting process. The principal components analysis (PCA) results showed that four classes of the samples were clearly distinguishable, in which the physiochemical parameters were similar, and that the dynamics of the composting process was significantly influenced by C/N and moisture content. The 13 C NMR results indicated that O-alkyl-C was the predominant group both in the solid and water-soluble fractions (WSF), and the decomposition of O-alkyl-C mainly occurred during the active stage. In general, the various parameters indicated that windrow composting is a feasible treatment that can be used for the resource reuse of agricultural wastes. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Animal production contributes substantially to the dissemination of antibiotic resistance genes (ARGs) in the environment. Thermophilic composting is cost-effective for reducing hazards in animal wastes. However, ARGs can still persist in composts and the mechanism remains largely unclear. In the present study, metagenomics and real-time quantitative PCR were employed to assess the dynamics of ARGs, especially those of high risk to human health, their host species and pathogenicity of the bacterial community during thermophilic composting of chicken manure. The results showed that thermophilic composting was effective at reducing the majority of the spreading risk of antibiotic resistance by 1) eliminating more than half of allARGs that accounted for 80% of the total abundance, 2) reducing the number and abundance of high-risk ARGs significantly, and 3) removing the ARG hosts and the pathogenicity of the bacterial community substantially. The attenuation of ARGs was primarily driven by the bacterial community succession. However, the abundance of some ARGs, especially those associated with plasmids, rebounded during the cooling phase, likely caused by horizontal gene transfer. Our research reveals that minimising the horizontal transfer of plasmid-associated ARGs during the cooling phase of thermophilic composting is crucial for a more effective reduction of the hazards associated with the spread of antibiotic resistance. [Display omitted] • Thermophilic composting reduced the bulk antibiotic resistance in animal manure. • Bacterial community succession drove the attenuation of ARGs. • Plasmid-associated ARGs rebounded via horizontal gene transfer during cooling phase. • Ratios of high-risk ARGs and plasmid-associated ARGs increased during composting. • Minimising ARG revival during cooling phase is key to improving ARG removal. [ABSTRACT FROM AUTHOR]

Hydrophobins are small secreted cysteine-rich proteins exclusively found in fungi. They are able to self-assemble in single molecular layers at hydrophobic-hydrophilic interfaces and can therefore be directly involved in establishment of fungi in their habitat. The genomes of filamentous mycotrophic fungi Trichoderma encode a rich diversity of hydrophobins, which are divided in several groups based on their structure and evolution. Here we describe a new member of class II hydrophobins, HFB7, that has a taxonomically restricted occurrence in Harzianum and Virens clades of Trichoderma . Evolutionary analysis reveals that HFB7 proteins form a separate clade distinct from other Trichoderma class II hydrophobins and that genes encoding them evolve under positive selection pressure. Homology modelling of HFB7 structure in comparison to T. reesei HFB2 reveals that the two large hydrophobic patches on the surface of the protein are remarkably conserved between the two hydrophobins despite significant difference in their primary structures. Expression of hfb7 gene in T. virens increases at interactions with other fungi and a plant and in response to a diversity of abiotic stress conditions, and is also upregulated during formation of aerial mycelium in a standing liquid culture. This upregulation significantly exceeds that of expression of hfb7 under a strong constitutive promoter, and T. virens strains overexpressing hfb7 thus display only changes in traits characterized by low hfb7 expression, i.e. faster growth in submerged liquid culture. The hfb7 gene is not expressed in conidia. Our data allow to conclude that this protein is involved in defence of Trichoderma against a diversity of stress factors related to the oxidative stress. Moreover, HFB7 likely helps in the establishment of the fungus in wetlands or other conditions related to high humidity. [ABSTRACT FROM AUTHOR]

Tobacco bacterial wilt (TBW) caused by Ralstonia solanacearum (RS) is one of the most serious tobacco diseases worldwide and no effective control measures are available to date. This study investigated the potential of Trichoderma harzianum SQR-T037 amended bioorganic fertilizer (BOF) and the arbuscular mycorrhizal fungi (AMF) Glomus mosseae 171 (Gm) on the control of TBW and promotion of plant growth in pot experiments. The results showed that the disease incidence in plants treated with integrated application of G. mosseae 171 and T. harzianum SQR-T037 amended bioorganic fertilizer (Gm + BOF) was the lowest, with a control efficacy of 68.2%, which is greater than that of BOF or Gm alone (26.8% and 14.7%, respectively). The application of BOF or Gm alone significantly reduced the abundance of RS in rhizosphere soil, but the integrated treatment (Gm + BOF) showed the strongest inhibitory effect (with a 21.3% increase in inhibition). The root colonization of G. mosseae 171 in samples treated with Gm + BOF was higher than that in samples with solely Gm treatment, indicating that the BOF significantly promoted G. mosseae mycorrhizal colonization. The results showed that the G. mosseae also had a positive effect on SQR-T037 rhizospheric colonization. Denaturing gradient gel electrophoresis (DGGE) results showed that application of BOF and Gm alone or in combination changed the diversity of the rhizospheric microbial community. The integrated application of Gm + BOF to tobacco plants significantly increases the activity of polyphenol oxidase (PPO), phenylalanine ammonia lyase (PAL), and peroxidase (POD), enzymes associated to systemic resistance. Additionally, the integrated application of Gm with BOF increased the tobacco plant height, shoot dry weight, and root dry weight. In conclusion, a synergistic biological approach integrating application of Gm and BOF for TBW protection seems promising. [ABSTRACT FROM AUTHOR]

A rhizobacterium with broad spectrum antifungal activity was isolated from the rhizosphere of a healthy cucumber plant in a Fusarium wilt diseased field. Phylogenetic tree analysis based on similarity percentage showed that the bacterium was 99% affiliated with the species Streptomyces goshikiensis . The strain, coded as S. goshikiensis YCXU, inhibited in vitro a broad range of phytopathogenic fungi, so it was selected for more detailed characterization. The strain could utilize different carbon sources and exhibited catalase, β-1,3-glucanase, chitinase and urease enzyme activities. The strain showed maximum growth at the pH of 7, temperature of 28 °C and NaCl concentration of 1%. The stain was able to produce antifungal diffusible and volatile organic compounds that significantly inhibited the growth of pathogenic fungi. In the greenhouse experiments, watermelon plants fresh and dry weights were significantly increased, and the incidence of Fusarium wilt was decreased by 67% when the strain enriched by a bioorganic fertilizer was applied to both nursery soil and pot soil (NS). The treatment NS also showed 88.9% less pathogen population in soil as compared to control. The use of biocontrol agents decreased the stress indicator enzymes and malondialdehyde content by 55–70% and 62%, respectively as compared to control. The denaturing gradient gel electrophoresis (DGGE) analysis showed significant variations in the fungal and bacterial community structures of all treatments resulted from UPGMA cluster analysis. This study showed that S. goshikiensis YCXU could be a potential biocontrol agent for controlling watermelon Fusarium wilt disease. [ABSTRACT FROM AUTHOR]

A phcA − mutant of Ralstonia solanacearum strain ZJ3721 was created in a marker-free method. Expression of virulence-associated genes such as xpsR , egl , tek and epsE was significantly suppressed in the phcA − mutant. The ability of the mutant to control tomato bacterial wilt was evaluated by potting experiment. Results showed that application of mutant with wild type (WT) at the same time only delayed the development of wilt for about one day and the population of WT in tomato rhizosphere soil was nearly 70-fold higher than that of the mutant, resulting in a 90% disease incidence at last, as high as that of control. If the phcA − mutant was applied three days earlier than WT pathogen, tomato wilt disease incidence was only 6%, 80% lower than that of control and population of WT was about 0.5-fold as much as that of mutant. Under hydroponic conditions, phcA − mutant significantly triggered the expressions of genes in salicylic acid pathway but inhibited the expressions of genes in jasmonic acid (JA) and ethylene (ET) pathways. The expressions of PR-1a and GluA genes (salicylic acid pathway) in phcA − mutant were 66-fold and 7.5-fold higher than in WT pathogen after three days of inoculation. [ABSTRACT FROM AUTHOR]

The volatile organic compounds (VOCs) produced by antagonistic microbes have great antifungal potential against soil-borne fungal pathogens. The VOCs produced by Paenibacillus polymyxa strain WR-2 in the presence of root exudates and organic fertilizer were identified and their effects on the growth and spore germination of Fusarium oxysporum f. sp. niveum were evaluated. The VOCs produced by WR-2 inhibited the growth of F. oxysporum by 38%, 36% and 40% in agar medium, sterilized soil and natural soil, respectively. This inhibitory effect was increased to 60%, 58% and 64% with the addition of organic fertilizer in agar medium, sterilized soil and natural soil, respectively. The addition of root exudates did not affect the production of antifungal VOCs by WR-2. The VOCs produced by WR-2 completely inhibited the germination of F. oxysporum spores. Out of 42 identified VOCs, seven VOCs; benzothiazole, benzaldehyde, undecanal, dodecanal, hexadecanal, 2-tridecanone and phenol were found to inhibit the growth of F. oxysporum . The results of these experiments suggest another significance of using organic fertilizer as a carrier material with the biocontrol agents to control soil-borne fungal pathogens. [ABSTRACT FROM AUTHOR]

Bacterial strain S20 was isolated and identified as Bacillus amyloliquefaciens based on physiological and biochemical characteristics and a 16S rRNA gene sequence analysis. Strain S20 inhibits the growth of Fusarium oxysporum and Ralstonia solanacearum. Some genes associated with the synthesis of some lipopeptides were detected in strain S20 by PCR. Iturins A were identified as the main antagonistic substrates by analysis with electrospray ionization mass spectrometry/collision-induced dissociation (ESI-MS/CID). Four homologues of iturin A (C13–C16) were identified. Pot experiments showed that the application of strain S20 alone could control eggplant wilt with an efficacy of 25.3% during a 40 day experiment. If strain S20 was used with organic fertilizer, the control efficacy against eggplant wilt reached as high as 70.7%. The application of organic fertilizer alone promotes the growth of R. solanacearum, resulting in a higher wilt incidence than that observed in control plants. The application of strain S20 effectively inhibits R. solanacearum in the rhizosphere soil of eggplant. The combined use of strain S20 and organic fertilizer more effectively controlled R. solanacearum in soil than the use of strain S20 alone. The soil count of strain S20 decreased gradually during the course of the experiment after inoculation. Organic fertilizer was beneficial for the survival of the antagonistic bacterial strain S20; a higher level of these bacteria could be maintained. The application of organic fertilizer with strain S20 increased bacterial diversity in rhizosphere soil. [Copyright &y& Elsevier]

Large amounts of refloated algal sludge from Taihu Lake result in secondary environmental pollution due to annual refloatation. This study investigated the possibility to produce bio-organic fertilizer (BIO) using algal sludge as a solid-state fermentation (SSF) medium. Results showed that addition of algal sludge contributed to efficient SFF by a plant growth-promoting rhizobacteria (PGPR) strain SQR9 and improved the nutrient contents in the novel BIO. The optimum water content and initial inoculation size were 45% and 5%, respectively. After 6 days of SSF, the biomass of strain SQR9 was increased to a cell density of more than 5 × 107 CFU g−1. Microcystins were rapidly degraded, and a high germination index value was observed. Plant growth experiments showed that the produced BIO efficiently promoted plant growth. Additional testing showed that the novel SSF process was also suitable for other PGPR strains. This study provides a novel way of high-value utilization of algal sludge from Taihu Lake by producing low-cost but high-quality BIOs. [Copyright &y& Elsevier]

Abstract: Agro-industrial byproducts, especially rice straw, are potential resources. This work was aimed to utilize raw materials to produce value-added biosurfactant in solid-state fermentation (SSF). Rice straw and soybean flour were found efficient and selected as major substrates for surfactin production. The results of Plackett–Burman design indicated that glycerol, water content, inoculum size and temperature were the significant variables identified in the screen of nine total variables. The optimum values for the four significant variables were determined by the Box–Behnken design. The optimal surfactin production was obtained when the medium contained 5 g soybean flour, 4 g rice straw, 2% (w/w) maltose and 2.65% (w/w) glycerol, pH 7.0. The ideal growth conditions for surfactin production consisted of a moisture content of 62.8% (v/w) and growth supplemented with 15.96% inoculum size in 250 mL flasks at 26.9 °C for 48 h. Under optimal conditions, a surfactin yield of 15.03 mg/gds was attained in 1000-fold scale-up fermentation in a 50 L fermenter, thereby validating the accuracy of this approach. This study proposed an eco-friendly and economical way to convert agro-industrial byproducts into biosurfactant. [Copyright &y& Elsevier]

Abstract: The role of Ralstonia pickettii as a congeneric rhizobacterium of plant pathogenic Ralstonia solanacearum has not been investigated in biocontrol of bacterial wilt of tomato. Our preliminary study showed that the population of R. pickettii was significantly higher than that of R. solanacearum in the rhizosphere of healthy tomato plants in a heavily diseased field with bacterial wilt. Due to its good performances in inhibition of R. solanacearum in vitro and colonization of the rhizosphere soil and stem of tomato, R. pickettii QL-A6 was selected for suppression of R. solanacearum by use of the soil drench (SD) and stem injection (SI) methods in greenhouse. By the SI method, disease incidence was reduced by 71.2% on the average with an inoculation dosage of only about 105 cfu of R. pickettii QL-A6 per plant. By the SD method, disease incidence was reduced by 52.9% on the average but needed a higher inoculation dosage of about 109 cfu of R. pickettii QL-A6 per plant. Thus, the SI method was chosen for further testing in field. The field disease incidence in R. pickettii QL-A6 treated plots was 8.8% at harvest time, while that in the sterilized water treated plots was as high as 33.1%. The population ratios of R. pickettii QL-A6 to R. solanacearum in the aboveground parts of field plants injected with R. pickettii QL-A6 ranged from 2 to 163. It is concluded that direct injection of R. pickettii QL-A6 in stem of tomato could be an alternative to chemical pesticides for biocontrol of R. solanacearum. [Copyright &y& Elsevier]

Abstract: Two genes encoding endoglucanase, designated as egl2 and egl3, were cloned from a lignocellulosic decomposing fungus Aspergillus fumigatus Z5 and were successfully expressed in Pichia pastoris X33. The deduced amino acid sequences encoded by egl2 and egl3 showed strong similarity with the sequence of glycoside hydrolase family 5. SDS–PAGE and western blot assays indicated that the recombinant enzymes were secreted into the culture medium and the zymogram analysis confirmed that both recombinant enzymes had endoglucanase activity. Several biochemical properties of the two recombinant enzymes were studied: Egl2 and Egl3 showed optimal activity at pH 5.0 and 4.0, respectively, and at 50 and 60°C, respectively. Egl2 and Egl3 showed good pH stability in the range of 4–7, and both enzymes demonstrated good thermostability ranging from 30 to 60°C. The Km and V max values using carboxymethyl cellulose (CMC, soluble cellulose, polymerized by β-1, 4-linked glucose residues) as the substrate at optimal conditions were determined. The activities of the enzymes on a variety of cello-oligosaccharide substrates were investigated, and Egl2 can hydrolyze cellotetraose and cellopentaose but not cellobiose and cellotriose, whereas Egl3 can hydrolyze all cello-oligosaccharides, except cellobiose. [Copyright &y& Elsevier]

A large amount of organic compost, produced with agricultural and breeding industry wastes by composting, is widely used in agriculture in China. The microbial decomposition of organic compost is a major flux in the nutrition cycle in sustainable agricultural soils. To explore the mechanism of organic compost mineralization in soil, in situ decomposition experiments of organic compost buried in soils were arranged in three different latitude regions located in Jilin, Jiangsu, and Yunnan in China. The results showed that organic compost had different decomposition rates at the three different sites, with the highest decomposition rate in Yunnan, followed by Jiangsu and Jilin. The decomposition rates of unsterilized organic compost were significantly greater than those of sterilized organic compost, indicating that the microorganisms in organic compost also made important contributions to the decomposition process. The soil microbial diversity and community structure among the three sites were significantly different. The fungal community, especially fungal richness, rather than the bacterial community in the soil, plays a major role in the decomposition of organic compost. The annual average temperature is an important environmental factor affecting fungal richness. This study will provide a reference for formulating agricultural fertilization models in different regions. • Organic composts had the highest decomposition rate in Yunnan, followed in Jiangsu and Jilin. • The microorganism in organic compost also made important contributions to the decomposition process. • The soil microbial diversity and community structure among the three sites are significantly different. • The fungal community in the soil plays a major role in the decomposition of organic composts, especially fungal richness. [ABSTRACT FROM AUTHOR]

Composting is a cost-efficient method of transferring various unstable and complex organic matters into a stable and humus-like substance, during which various fungus play a critical role in the decomposition of organic matters. In this study, the rice straw and swine manure co-composting were carried out in a pilot-scale, and the evolution of various biochemical parameters and fungi community were detected at different time points. The results showed that most of the parameters fluctuated strongly at the thermophilic phase (THP), and the Canonical Correlation Analysis (CCA) results showed that Mycothermus spp. and Aspergillus spp. were with abundances of 47.82% and 3.51%, respectively, which were considered as the core fungi during the composting process. In addition, five culturable thermophilic filamentous fungi were isolated from the samples obtained at the high temperature stage, among which Aspergillus fumigatus were considered as the core specie at this special phase. The capacity of lignocellulose degradation of this strains was also evaluated by analyzing the secretomes in a coculture group with rice straw and crystalline cellulose as carbon sources, and the identified proteins illustrated that the enzymes were chiefly secreted by A. fumigatus in both treatments, with the abundances of 91.41% and 85.19%, respectively. Image 1 • Substrates had a significant effect on fungal communities during composting. • Thermophilic fungal genus had a potential capacity of polymers degradation. • Mycothermus and Aspergillus were the dominant fungal genus at thermophilic phase. • Glycoside hydrolases were the main components of the secretomes. [ABSTRACT FROM AUTHOR]