Aspergillus niger as a Biological Input for Improving Vegetable Seedling Production

Deciphering the rhizosphere microbiota composition of nature farming soybean (Glycine max L.) with different nodulation phenotypes

BACKGROUND

Nature farming, a sustainable agricultural method which avoids agrochemicals and untreated organic amendments, promotes both agricultural productivity and ecological conservation. This system may foster unique plant-microbiota interactions for growth and fitness; however, the microbiota of nature-farmed plants remains largely unexplored. Second, root nodule symbiosis (RNS) is crucial for nitrogen fixation in legumes; however, its broader impact on rhizosphere microbiota assembly is not well understood. This study examined the dynamics between impaired nodule symbiosis, soil management, and the rhizosphere microbiota composition and growth of soybean (Glycine max L.).

RESULTS

We evaluated the growth and characterized the rhizosphere bacterial and fungal communities of soybean by comparing wildtype soybeans (Enrei) with the non-nodulating mutants (En1282) across four soils under conventional and nature farming, including fumigated and unfumigated conditions. We found that the non-nodulating soybean mutants (En1282) exhibited reduced growth compared with wild-type (Enrei) plants, especially in untreated soils. Soil fumigation decreased microbial diversity and reshaped rhizosphere community composition with a significant reduction in plant growth and nodulation in all soils. Restriction in RNS increased bacterial diversity in untreated soils, possibly as a compensatory mechanism for nitrogen acquisition, whereas fungal diversity remained relatively stable. Nature farming promoted beneficial microbes like Rhizobium, Trichoderma, and Chloridium, whereas conventional soil plants favored Bacillus and Aspergillus. Notably, differential enrichment analysis identified distinct associations for each nodulation phenotype, with Enrei predominantly enriched for Pseudomonas, and En1282 associated primarily with oligotrophic microbes.

CONCLUSION

Our study sheds light on the complex interplay between legume symbiosis and rhizosphere microbiota assembly and highlights the significance of eco-friendly farming methods like nature farming in cultivating a healthy rhizosphere for plant growth. The results paves way for future strategies to manipulate rhizosphere microbiota, ultimately promoting robust and sustainable farming systems that reduce reliance on chemical inputs.

The Good, the Bad, and the Fungus: Insights into the Relationship Between Plants, Fungi, and Oomycetes in Hydroponics

Hydroponic systems are examples of controlled environment agriculture (CEA) and present a promising alternative to traditional farming methods by increasing productivity, profitability, and sustainability. In hydroponic systems, crops are grown in the absence of soil and thus lack the native soil microbial community. This review focuses on fungi and oomycetes, both beneficial and pathogenic, that can colonize crops and persist in hydroponic systems. The symptomatology and mechanisms of pathogenesis for Botrytis, Colletotrichum, Fulvia, Fusarium, Phytophthora, Pythium, and Sclerotinia are explored for phytopathogenic fungi that target floral organs, leaves, roots, and vasculature of economically important hydroponic crops. Additionally, this review thoroughly explores the use of plant growth-promoting fungi (PGPF) to combat phytopathogens and increase hydroponic crop productivity; details of PGP strategies and mechanisms are discussed. The benefits of Aspergillus, Penicillium, Taloromyces, and Trichoderma to hydroponics systems are explored in detail. The culmination of these areas of research serves to improve the current understanding of the role of beneficial and pathogenic fungi, specifically in the hydroponic microbiome.

Basidiomycetes Polysaccharides Regulate Growth and Antioxidant Defense System in Wheat

Higher-fungi xylotrophic basidiomycetes are known to be the reservoirs of bioactive metabolites. Currently, a great deal of attention has been paid to the exploitation of mycelial fungi products as an innovative alternative in crop protection. No data exist on the mechanisms behind the interaction between xylotrophic mushrooms' glycopolymeric substances and plants. In this study, the effects of basidiomycete metabolites on the morphophysiological and biochemical variables of wheat plants have been explored. Wheat (Triticum aestivum L. cv. Saratovskaya 29) seedlings were treated with extracellular polysaccharides (EPSs) isolated from the submerged cultures of twenty basidiomycete strains assigned to 13 species and 8 genera. The EPS solutions at final concentrations of 15, 40, and 80 mg/L were applied to wheat seedlings followed by their growth for 10 days. In the plant samples, the biomass, length of coleoptile, shoot and root, root number, rate of lipid peroxidation by malondialdehyde concentration, content of hydrogen peroxide, and total phenols were measured. The peroxidase and superoxide dismutase activity were defined. Most of the EPS preparations improved biomass yields, as well as the morphological parameters examined. EPS application enhanced the activities of antioxidant enzymes and decreased oxidative damage to lipids. Judging by its overall effect on the growth indices and redox system of wheat plants, an EPS concentration of 40 mg/L has been shown to be the most beneficial compared to other concentrations. This study proves that novel bioformulations based on mushroom EPSs can be developed and are effective for wheat growth and antioxidative response. Phytostimulating properties found for EPSs give grounds to consider extracellular metabolites produced in the xylotrophic basidiomycete cultures as an active component capable of inducing plant responses to stress.

Compost and Phosphorus/Potassium-Solubilizing Fungus Effectively Boosted Quinoa's Physio-Biochemical Traits, Nutrient Acquisition, Soil Microbial Community, and Yield and Quality in Normal and Calcareous Soils

Calcareous soil had sufficient phosphorus and potassium (PK) in different forms due to the high contents of PK-bearing minerals; however, the available PK state was reduced due to its PK-fixation capacity. Compost, coupled with high PK solubilization capacity microbes, is a sustainable solution for bioorganic fertilization of plants grown in calcareous soil. A 2-year field experiment was conducted to investigate the effect of compost (20 t ha-1) with Aspergillus niger through soil drenching (C-AN) along with partial substitution of PK fertilization on quinoa performance in normal and calcareous soils. Treatments included PK100% (72 kg P2O5 ha-1 + 60 kg K2O ha-1 as conventional rate), PK100%+C-AN, PK75%+C-AN, PK50%+C-AN, PK25%+C-AN, and only C-AN in normal and calcareous soils. Results showed that C-AN and reduced PK fertilization (up to 75 or 50%) increased photosynthetic pigments and promoted nutrient acquisition in quinoa grown in calcareous soil. Reduced PK fertilization to 75 or 50% plus C-AN in calcareous soil increased osmoprotectants, nonenzymatic antioxidants, and DPPH scavenging activity of quinoa's leaves compared to the PK0%+C-AN treatment. The integrative application of high PK levels and C-AN enhanced the quinoa's seed nutritional quality (i.e., lipids, carbohydrates, mineral contents, total phenolics, total flavonoids, half maximal inhibitory concentration, and antiradical power) in calcareous soil. At reduced PK fertilization (up to 75 or 50%), application of compost with Aspergillus niger through soil drenching increased plant dry weight by 38.7 or 53.2%, hectoliter weight by 3.0 or 2.4%, seed yield by 49.1 or 39.5%, and biological yield by 43.4 or 33.6%, respectively, compared to PK0%+C-AN in calcareous soil. The highest P-solubilizing microorganism's population was found at PK0%+C-AN in calcareous soil, while the highest Azotobacter sp. population was observed under high PK levels + C-AN in normal soil. Our study recommends that compost with Aspergillus niger as a bioorganic fertilization treatment can partially substitute PK fertilization and boost quinoa's tolerance to salt calcareous-affected soil.

Aspergillus niger Fermentation Broth Promotes Maize Germination and Alleviates Low Phosphorus Stress

Aspergillus niger is a type of soil fungus with the ability to dissolve insoluble phosphate and secrete organic metabolites such as citric acid. However, whether cell-free Aspergillus niger fermentation broth (AFB) promotes maize growth and alleviates low-phosphorus stress has not been reported. In this study, we explored their relationship through a hydroponics system. The results indicated that either too low or too high concentrations of AFB may inhibit seed germination potential and germination rate. Under low phosphorus conditions, all physiological indexes (biomass, soluble sugar content, root length, etc.) increased after AFB was applied. A qRT-PCR analysis revealed that the expression of the EXPB4 and KRP1 genes, which are involved in root development, was upregulated, while the expression of the CAT2 and SOD9 genes, which are keys to the synthesis of antioxidant enzymes, was downregulated. The expression of LOX3, a key gene in lipid peroxidation, was down-regulated, consistent with changes in the corresponding enzyme activity. These results indicate that the application of AFB may alleviate the oxidative stress in maize seedlings, reduce the oxidative damage caused by low P stress, and enhance the resistance to low P stress in maize seedlings. In addition, it reveals the potential of A. niger to promote growth and provides new avenues for research on beneficial plant-fungal interactions.

Continued Organic Fertigation after Basal Manure Application Does Not Impact Soil Fungal Communities, Tomato Yield or Soil Fertility

There is currently a limited understanding of the complex response of fungal microbiota diversity to organic fertigation. In this work, a 2-year field trial with organic tomato crops in a soil previously amended with fresh sheep manure was conducted. Two hypotheses were compared: (i) fertigation with organic liquid fertilizers versus (ii) irrigation with water. At the end of both years, soils were analyzed for physical-chemical parameters and mycobiome variables. Plate culture and DNA metabarcoding methods were performed in order to obtain a detailed understanding of soil fungal communities. Fertigation did not increase any of the physical-chemical parameters. Concerning soil fungal communities, differences were only found regarding the identification of biomarkers. The class Leotiomycetes and the family Myxotrichaceae were identified as biomarkers in the soil fungal community analyzed by means of DNA metabarcoding of the "fertigation" treatment at the end of Year 1. The Mortierella genus was detected as a biomarker in the "water" treatment, and Mucor was identified in the "fertigation" treatment in the cultivable soil fungi at the end of Year 2. In both years, tomato yield and fruit quality did not consistently differ between treatments, despite the high cost of the fertilizers added through fertigation.

Endophytic Fungal Community of Stellera chamaejasme L. and Its Possible Role in Improving Host Plants' Ecological Flexibility in Degraded Grasslands

Stellera chamaejasme L. is a widely distributed poisonous plant in Chinese degraded grasslands. To investigate the role of endophytic fungi (EF) in S. chamaejasme's quick spread in grasslands, the endophytic fungal community of S. chamaejasme was studied through culture-dependent and culture-independent methods, and the plant-growth-promoting (PGP) traits of some culturable isolates were tested. Further, the growth-promoting effects of 8 isolates which showed better PGP traits were evaluated by pot experiments. The results showed that a total of 546 culturable EF were isolated from 1114 plant tissue segments, and the colonization rate (CR) of EF in roots (33.27%) was significantly higher than that in shoots (22.39%). Consistent with this, the number of specific types of EF was greater in roots (8 genera) than in shoots (1 genus). The same phenomenon was found in culture-independent study. There were 95 specific genera found in roots, while only 18 specific genera were found in shoots. In addition, the dominant EF were different between the two study methods. Cladosporium (18.13%) and Penicillium (15.93%) were the dominant EF in culture-dependent study, while Apiotrichum (13.21%) and Athelopsis (5.62%) were the dominant EF in culture-independent study. PGP trait tests indicated that 91.30% of the tested isolates (69) showed phosphorus solubilization, IAA production, or siderophores production activity. The benefit of 8 isolates on host plants' growth was further studied by pot experiments, and the results indicated that all of the isolates can improve host plants' growth. Among them, STL3G74 (Aspergillus niger) showed the best growth-promotion effect; it can increase the plant's shoot and root dry biomass by 68.44% and 74.50%, respectively, when compared with the controls. Our findings revealed that S. chamaejasme has a wide range of fungal endophytic assemblages, and most of them possess PGP activities, which may play a key role in its quick spread in degraded grasslands.

New application of Aspergillus versicolor in promoting plant growth after suppressing sterigmatocystin production via genome mining and engineering

Aspergillus genus is a key component in fermentation and food processing. However, sterigmatocystin (STE)-a mycotoxin produced by several species of Aspergillus-limits the use of some Aspergillus species (such as Aspergillus versicolor, Aspergillus inflatus, and Aspergillus parasiticus) because of its toxicity and carcinogenicity. Here, we engineered an STE-free Aspergillus versicolor strain based on genome mining techniques. We sequenced and assembled the Aspergillus versicolor D5 genome (34.52 Mb), in which we identified 16 scaffolds and 54 biosynthetic gene clusters (BGCs). We silenced cytochrome P450 coding genes STC17 and STC27 by insertional inactivation. The production of STE in the Δstc17 mutant strain was increased by 282% but no STE was detected in the Δstc27 mutant. Metabolites of Δstc27 mutant exhibited growth-promoting effect on plants. Our study makes significant progress in improving the application of some Aspergillus strains by restricting their production of toxic and carcinogenic compounds.

Field evaluation of the effect of Aspergillus niger on lettuce growth using conventional measurements and a high-throughput phenotyping method based on aerial images

Plant microbiome engineering is a promising tool to unlock crop productivity potential and exceed the yield obtained with conventional chemical inputs. We studied the effect of Aspergillus niger inoculation on in-field lettuce (Lactuca sativa) growth in soils with limiting and non-limiting P concentrations. Lettuce plants originating from inoculated seeds showed increased plant diameter (6.9%), number of leaves (8.1%), fresh weight (23.9%), and chlorophyll content (3.8%) as compared to non-inoculated ones. Inoculation of the seedling substrate just before transplanting was equally efficient to seed inoculation, while application of a granular formulation at transplanting did not perform well. Plant response to P addition was observed only up to 150 kg P2O5 ha-1, but A. niger inoculation allowed further increments in all vegetative parameters. We also employed a high-throughput phenotyping method based on aerial images, which allowed us to detect changes in plants due to A. niger inoculation. The visible atmospherically resistant index (VARI) produced an accurate prediction model for chlorophyll content, suggesting this method might be used to large-scale surveys of croplands inoculated with beneficial microorganisms. Our findings demonstrate that A. niger inoculation surpasses the yield obtained with conventional chemical inputs, allowing productivity gains not reached by just increasing P doses.

Fungi, P-Solubilization, and Plant Nutrition

The application of plant beneficial microorganisms is widely accepted as an efficient alternative to chemical fertilizers and pesticides. It was shown that annually, mycorrhizal fungi and nitrogen-fixing bacteria are responsible for 5 to 80% of all nitrogen, and up to 75% of P plant acquisition. However, while bacteria are the most studied soil microorganisms and most frequently reported in the scientific literature, the role of fungi is relatively understudied, although they are the primary organic matter decomposers and govern soil carbon and other elements, including P-cycling. Many fungi can solubilize insoluble phosphates or facilitate P-acquisition by plants and, therefore, form an important part of the commercial microbial products, with Aspergillus, Penicillium and Trichoderma being the most efficient. In this paper, the role of fungi in P-solubilization and plant nutrition will be presented with a special emphasis on their production and application. Although this topic has been repeatedly reviewed, some recent views questioned the efficacy of the microbial P-solubilizers in soil. Here, we will try to summarize the proven facts but also discuss further lines of research that may clarify our doubts in this field or open new perspectives on using the microbial and particularly fungal P-solubilizing potential in accordance with the principles of the sustainability and circular economy.

Mushroom-Derived Novel Selenium Nanocomposites’ Effects on Potato Plant Growth and Tuber Germination

Multicomponent materials, where nanosized selenium (Se) is dispersed in polymer matrices, present as polymer nanocomposites (NCs), namely, selenium polymer nanocomposites (SeNCs). Selenium as an inorganic nanofiller in NCs has been extensively studied for its biological activity. More ecologically safe and beneficial approaches to obtain Se-based products are the current challenge. Biopolymers have attained great attention with perspective multifunctional and high-performance NCs exhibiting low environmental impact with unique properties, being abundantly available, renewable, and eco-friendly. Composites based on polysaccharides, including beta-glucans from edible and medicinal mushrooms, are bioactive, biocompatible, biodegradable, and have exhibited innovative potential. We synthesized SeNCs on the basis of the extracellular polysaccharides of several medicinal mushrooms. The influence of bio-composites from mushrooms on potato plant growth and tuber germination were studied in two potato cultivars: Lukyanovsky and Lugovskoi. Bio-composites based on Grifola umbellata demonstrated the strongest positive effect on the number of leaves and plant height in both cultivars, without negative effect on biomass of the vegetative part. Treatment of the potato tubers with SeNC from Gr. umbellata also significantly increased germ length. Potato plants exposed to Se-bio-composite from Ganoderma lucidum SIE1303 experienced an increase in the potato vegetative biomass by up to 55% versus the control. We found earlier that this bio-composite was the most efficient against biofilm formation by the potato ring rot causative agent Clavibacter sepedonicus (Cms). Bio-composites based on Pleurotus ostreatus promoted increase in the potato root biomass in the Lugovskoi cultivar by up to 79% versus the control. The phytostimulating ability of mushroom-based Se-containing bio-composites, together with their anti-phytopathogenic activity, testifies in favor of the bifunctional mode of action of these Se-biopreparations. The application of stimulatory green SeNCs for growth enhancement could be used to increase crop yield. Thus, by combining myco-nanotechnology with the intrinsic biological activity of selenium, an unexpectedly efficient tool for possible applications of SeNCs could be identified.