The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains

Evaluating the effects of mefenoxam on taxonomic and functional dynamics of nontarget fungal communities during carrot cultivation

Ridomil Gold SL (45.3% a.i. mefenoxam) is a widely used chemical fungicide for the control of oomycetes. However, its impact on fungal communities remains unexplored. Therefore, the goal of this study was to examine the effects of mefenoxam on the temporal dynamics of fungal taxonomic and functional diversities during carrot cultivation under four treatment groups: mefenoxam application with and without Pythium inoculation, and untreated control groups with and without Pythium inoculation. Our in vitro sensitivity assay showed that the maximum recommended concentration of mefenoxam, 0.24 ppm, did not suppress the mycelial growth of P. irregulare. At 100 ppm, mycelial growth was only reduced by 11.4%, indicating that the isolate was resistant to mefenoxam. MiSeq sequencing data revealed transient taxonomic variations among treatments 2 weeks post-treatment. Mortierella dominated the fungal community in the mefenoxam-Pythium combination treatment, as confirmed through PCR using our newly designed Mortierella-specific primers. Conversely, mefenoxam-Pythium combination had adverse effects on Penicillium, Trichoderma, and Fusarium, and decrease the overall alpha diversity. However, these compositional changes gradually reverted to those observed in the control by the 12th week. The predicted ecological functions of fungal communities in all Pythium and mefenoxam treatments shifted, leading to a decrease in symbiotrophs and plant pathogen functional groups. Moreover, the community-level physiological profiling approach, utilizing 96-well Biolog FF microplates, showed discernible variations in the utilization of 95 diverse carbon sources among the treatments. Notably, arbutin, L-arabinose, Tween 80, and succinamic acid demonstrated a strong positive association with Mortierella. Our findings demonstrate that a single application of mefenoxam at its recommended rate triggers substantial taxonomic and functional shifts in the soil fungal community. Considering this impact, the conventional agricultural practice of repeated mefenoxam application is likely to exert considerable shifts on the soil ecosystem that may affect agricultural sustainability.

HO-CR and HOLL-CR: new forms of winter oilseed rape (Brassica napus L.) with altered fatty acid composition and resistance to selected pathotypes of Plasmodiophora brassicae (clubroot)

The priority in oilseed rape (Brassica napus L.) research and breeding programs worldwide is to combine different features to develop cultivars tailored to specific applications of this crop. In this study, forms with a modified fatty acid composition of seed oil were successfully combined with a source of resistance to Plasmodiophora brassicae Wor., a harmful protist-causing clubroot. Three HO-type recombinants in F6-F12 generations with oleic acid content of 80.2-82.1% and one HOLL-type F6 inbred mutant recombinant (HOmut × LLmut), with a high oleic acid content (80.9%) and reduced linolenic acid content (2.3%), were crossed with the cultivar Tosca, resistant to several pathotypes of P. brassicae. The work involved genotyping with the use of DNA markers specific for allelic variants of desaturase genes responsible for the synthesis of oleic and linolenic fatty acids, CAPS (FAD2 desaturase, C18:1), and SNaPshot (FAD3 desaturase, C18:3), respectively. Of 350 progenies in the F3 generation, 192 (55%) were selected for further studies. Among them, 80 HO (≥ 72%) lines were identified, 10 of which showed resistance to at least one up to four P. brassicae pathotypes. Thirty lines in the selected progeny contained high oleic acid and less than 5% linolenic acid; eight of them belonged to the HOLL type conferring resistance to at least one pathotype. Two HO lines and two HOLL lines were resistant to four pathotypes. The resulting HO-CR and HOLL-CR inbred lines with altered seed oil fatty acid composition and resistance to P. brassicae represent unique oilseed rape material with the desired combination of valuable traits.

Phosphate-solubilizing fungi enhances the growth of Brassica chinensis L. and reduces arsenic uptake by reshaping the rhizosphere microbial community

High concentrations of arsenic in soil and plant systems are a threat to human health and ecosystems. The levels of phosphate ions in the soil strongly influence the soil efficacy and arsenic absorption by plants. This study investigated the effects of phosphate-solubilizing fungi (PSF) on environmental factors and structural changes in microbial community in soils contaminated with arsenic. Four experimental groups were created: control (CK), Penicillium GYAHH-CCT186 (W186), Aspergillus AHBB-CT196 (W196), and Penicillium GYAHH-CCT186 + Aspergillus AHBB-CT196 (W186 + W196), with Pakchoi (Brassica chinensis L.) as the test plant. Analysis of altered nutrient levels, enzyme activities and microbial community structure in the soil as well as the growth and physiological characteristics of Pakchoi, revealed a significant increase in the available phosphorus (AP), organic matter (OM), cation exchange capacity (CEC) and available arsenic (AAs) content of the soil following W186 + W196, W196 and W186 treatments. All experimental treatments enhanced the activity of soil β-glucosidase (β-GC) and soil catalase (S-CAT). W186 + W196 and W196 treatments significantly enhanced soil acid phosphatase (S-ACP) activity. Besides, W186 + W196 treatment significantly induced dehydrogenase (S-DHA) activity. Further, of the treatment with PSF increased the fresh weight, root length, plant height and chlorophyll levels while decreasing the arsenic accumulation in Pakchoi. Exposure to PSF also increased the activity of Ascomycota, Basidiomycota, Chytridiomycota, unclassified_Fungi, Mortierellomycota, Cryptomycota and Rozellomycota in the soil. The relative abundance of Ascomycota, Basidiomycota, and Mortierellomycota was positively correlated with the available nutrients (except iron) in the soil as well as enzyme activities. Consequently, the PSF improved the quality of soil and the safety of Pakchoi, suggesting that PSF can be utilized for the remediation of arsenic-contaminated soil.

Soil Conditioner Affects Tobacco Rhizosphere Soil Microecology

Reasonable fertilization management can increase nutrient content and enzyme activity in rhizosphere soil, and even increase soil microbial richness. However, different fertilizers could raise distinct influences on the soil properties, including soil environmental factors (physicochemical properties and enzymatic activities) and microbial community. Here, the effects of two soil amendments (microbial fertilizer and woody peat) on environmental factors and microbial community structure in tobacco rhizosphere soil were evaluated, with the correlations between microbes and environmental factors explored. As the results, microbial fertilizer could effectively alleviate soil acidification, increase available potassium and organic matter contents in soil, and was also beneficial to increase nitrate reductase activity in rhizosphere soil. Fertilizers cause changes in the abundance of certain microbes in the soil. Besides, it was shown that the candidate phyla Gal15, Acidobacterota, Latescibacterota, Mortierellommycota, Basidiomycota, and Rozellomycota in tobacco rhizosphere soil had significant correlation with soil environmental factors. Through the functional analysis of these populations, it can be deduced that the changes in the abundance of certain microorganisms may be an important reason for the differences in environmental factors. All these indicated that the differences of environmental factors in different treatments are closely related to the abundance of some special soil microorganisms. Studying the life activities of these microbes would provide good guidance for exploring the interaction among crops, soil, and microorganisms and improving crop yields.

Date Palm Waste Compost Application Increases Soil Microbial Community Diversity in a Cropping Barley (Hordeum vulgare L.) Field

Application of date palm waste compost is quite beneficial in improving soil properties and crop growth. However, the effect of its application on soil microbial communities is less understood. High-throughput sequencing and quantitative real-time PCR (qPCR) were used to evaluate the effect of compost application on the soil microbial composition in a barley field during the tillering, booting and ripening stages. The results showed that compost treatment had the highest bacterial and fungal abundance, and its application significantly altered the richness (Chao1 index) and α-diversity (Shannon index) of fungal and bacterial communities. The dominant bacterial phyla found in the samples were Proteobacteria and Actinobacteria while the dominant fungal orders were Ascomycota and Mortierellomycota. Interestingly, compost enriched the relative abundance of beneficial microorganisms such as Chaetomium, Actinobacteriota, Talaromyces and Mortierella and reduced those of harmful microorganisms such as Alternaria, Aspergillus and Neocosmospora. Functional prediction based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed that amplicon sequence variant (ASV) sequences related to energy metabolism, amino acid metabolism and carbohydrate metabolism were associated with compost-treated soil. Based on Fungi Functional Guild (FUNGuild), identified fungi community metabolic functions such as wood saprotroph, pathotroph, symbiotroph and endophyte were associated with compost-treated soil. Overall, compost addition could be considered as a sustainable practice for establishing a healthy soil microbiome and subsequently improving the soil quality and barley crop production.

Bio-fertilizer Affects Structural Dynamics, Function, and Network Patterns of the Sugarcane Rhizospheric Microbiota

Fertilizers and microbial communities that determine fertilizer efficiency are key to sustainable agricultural development. Sugarcane is an important sugar cash crop in China, and using bio-fertilizers is important for the sustainable development of China's sugar industry. However, information on the effects of bio-fertilizers on sugarcane soil microbiota has rarely been studied. In this study, the effects of bio-fertilizer application on rhizosphere soil physicochemical indicators, microbial community composition, function, and network patterns of sugarcane were discussed using a high-throughput sequencing approach. The experimental design is as follows: CK: urea application (57 kg/ha), CF: compound fertilizer (450 kg/ha), BF1: bio-fertilizer (1500 kg/ha of bio-fertilizer + 57 kg/ha of urea), and BF2: bio-fertilizer (2250 kg/ha of bio-fertilizer + 57 kg/ha of urea). The results showed that the bio-fertilizer was effective in increasing sugarcane yield by 3-12% compared to the CF treatment group, while reducing soil acidification, changing the diversity of fungi and bacteria, and greatly altering the composition and structure of the inter-root microbial community. Variance partitioning canonical correspondence (VPA) analysis showed that soil physicochemical variables explained 80.09% and 73.31% of the variation in bacteria and fungi, respectively. Redundancy analysis and correlation heatmap showed that soil pH, total nitrogen, and available potassium were the main factors influencing bacterial community composition, while total soil phosphorus, available phosphorus, pH, and available nitrogen were the main drivers of fungal communities. Volcano plots showed that using bio-fertilizers contributed to the accumulation of more beneficial bacteria in the sugarcane rhizosphere level and the decline of pathogenic bacteria (e.g., Leifsonia), which may slow down or suppress the occurrence of diseases. Linear discriminant analysis (LDA) and effect size analysis (LEfSe) searched for biomarkers under different fertilizer treatments. Meanwhile, support vector machine (SVM) assessed the importance of the microbial genera contributing to the variability between fertilizers, of interest were the bacteria Anaerolineace, Vulgatibacter, and Paenibacillus and the fungi Cochliobolus, Sordariales, and Dothideomycetes between CF and BF2, compared to the other genera contributing to the variability. Network analysis (co-occurrence network) showed that the network structure of bio-fertilizers was closer to the network characteristics of healthy soils, indicating that bio-fertilizers can improve soil health to some extent, and therefore if bio-fertilizers can be used as an alternative to chemical fertilizers in the future alternative, it is important to achieve green soil development and improve the climate.

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Plant rhizo-microbiome comprises of complex microbial communities that colonizes at the interphase of plant roots and soil. Plant-growth-promoting rhizobacteria (PGPR) in the rhizosphere provides important ecosystem services ranging from release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though, it is evident that nutrients availability in soil are managed through inter-linked mechanisms, how PGPR expediate these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the inter-play between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.

Microbial Diversity and P Content Changes after the Application of Sewage Sludge and Glyphosate to Soil

Pesticides, despite their side effects, are still being used in almost every agriculture, horticulture, maintaining municipal greenery in urban areas and even in home gardens. They influence human life and health and the functioning of entire ecosystems, including inanimate elements such as water and soil. The aim of the study was the evaluation of the suitability of sewage sludge in improving the quality of soil treated with a non-selective herbicide-glyphosate, applied as Roundup 360 SL. A pot experiment was conducted with the use of two arable soils (MS and OS), which were amended with sewage sludge (SS), glyphosate (GL) and sewage sludge with glyphosate (SS+GL). Soil samples were taken after 24 h, 144 h and 240 h and total phosphorus (TP) content (TP), total number of bacteria/fungi, activity of dehydrogenases (Dha), acidic phosphatase (Acp), alkaline phosphatase (Alp), genetic biodiversity of bacteria/fungi using the terminal restriction fragment length polymorphism method were determined. The application of SS and GL to OS caused an increase in Acp (approximately 35%) and a decrease in Alp activity (approximately 20%). Additionally, GL may influence on an increase in the number of fungi and the decrease in the number of bacteria. In soil with SS+GL increase in the fungal diversity in MS and OS was also observed. Moreover, a positive between TP and the number of bacteria and the activity of phosphatases correlation was reported. The obtained results indicate that analyzed sewage sludge could be potentially applied into soil in in situ scale and could constitute a valuable reclamation material.

Response of Sugarcane Rhizosphere Bacterial Community to Drought Stress

Sugarcane is an important sugar and energy crop, and its yield is greatly affected by drought. Although a large number of studies have shown that rhizosphere microorganisms can help improve the adaptability of plants to biotic or abiotic stresses, there is a lack of studies on the adaptability of sugarcane rhizosphere microbial communities to host plants. Therefore, we conducted drought stress treatment and normal irrigation treatment on three sugarcane varieties GT21, GT31, and GT42 widely cultivated in Guangxi. Using 16S rDNA sequencing technology to analyze the changes in abundance of the sugarcane rhizosphere bacterial community under different treatments, combined with the determination of soil enzyme activity, soil nutrient content, and sugarcane physiological characteristics, we explored the sugarcane rhizosphere bacterial community response to drought stress. In addition, we used the structural equation model to verify the response path of sugarcane rhizosphere bacteria. The results show that the bacterial community structure in the rhizosphere of sugarcane is stable under normal water conditions. The change in the bacterial community structure under drought stress has a 25.2% correlation with the drought adaptability of sugarcane, but the correlation with drought stress is as high as 42.17%. The changes in abundance of rhizosphere bacteria under drought stress are mainly concentrated in the phylum Rhizobiales and Streptomycetales. This change is directly related to the physiological state of the host plant under drought stress, soil available phosphorus, soil urease and soil acid protease. We investigated the response species of rhizosphere microorganisms and their response pathways under drought stress, providing a scientific basis for rhizosphere microorganisms to assist host plants to improve drought adaptability.

Chemical Transformation of Humic Acid Molecules under the Influence of Mineral, Fungal and Bacterial Fertilization in the Context of the Agricultural Use of Degraded Soils

The main goal of this work was to study the structural transformation of humic acids (HAs) under the influence of selected strains of fungi (Aspergillus niger and Paecilomyces lilacinus) and bacteria (Bacillus sp., Paenibacillus polymyxa and Bacillus amyloliquefaciens) with/without the presence of NPK fertilizers. Two-year experiments were conducted on two different soils and HAs isolated from these soils were examined for structure, humification degree, and quantity using fluorescence and UV-Vis spectroscopy, elemental analysis, and extraction methods. Results showed that the applied additives contributed to the beneficial transformation of HAs, but effects differed for various soils. HAs from silty soil with higher organic carbon content showed simplification of their structure, and decreases in humification, molecular weight, and aromaticity under the influence of fungi and bacteria without NPK, and with NPK alone. With both fungi and NPK, increases in O/H and O/C atomic ratios indicated an increase in the number of O-containing functional groups. HAs from sandy soil did not show as many significant changes as did those from silty soil. Sandy soil exhibited a strong decline in HA content in the second year that was reduced/neutralized by the presence of fungi, bacteria, and NPK. Periodically observed fluorescence at ~300 nm/450 nm reflected formation of low-molecular HAs originating from the activity of microorganisms.