Effects of Trichoderma asperellum BV10 and Bacillus amyloliquefaciens BV03 in Meloidogyne incognita Control Considering Three Different Management Systems

Crop yield decrease is the main concern when a pathogen or plague is identified in an agriculture field. Thus, part of this issue can be attributed to plant-parasitic nematodes (PPNs), such as Meloidogyne species, due to, most of the time, the hard diagnosis, and non-specific symptoms. Its management is mainly based on chemical pesticides, followed by a few potential biological control agents, and the management system. Therefore, this study aimed to evaluate the effects of biological agents in Meloidogyne incognita control in different soil systems. For that, two biological products were chosen, Trichoderma asperellum BV10 and Bacillus amyloliquefaciens BV03, and soils were sampled from three different managements systems: (i) soybean no-tilled system at Goiás state, Brazil; (ii) forest soil at Goiás state, Brazil, and (iii) soybean conventional managed system at Mato Grosso do Sul state, Brazil. Biocontrol and growth promotion effects, volatile organic compounds (VOCs) and soil respiration were determined in vegetation house and laboratory, respectively. As a result, both BV10 and BV03 had significant nematode control activity, comparing to control treatment, in all the three soils systems. Plus, the number of immobile nematodes by potential VOCs had significant increase when BV03 was applied, while the application of BV10 agent raised the soil respiration rate. In conclusion, both biocontrol agents presented great efficiency in control M. incognita, with better performance of BV03. Lastly, more studies must be done to elucidate how the resident soil microbiome can influence on biocontrol agent establishment and performance, as well as the consequence of the application of biological products on soil microbiome network.

Carbon Materials Advancing Microorganisms in Driving Soil Organic Carbon Regulation

Carbon emission from soil is not only one of the major sources of greenhouse gases but also threatens biological diversity, agricultural productivity, and food security. Regulation and control of the soil carbon pool are political practices in many countries around the globe. Carbon pool management in engineering sense is much bigger and beyond laws and monitoring, as it has to contain proactive elements to restore active carbon. Biogeochemistry teaches us that soil microorganisms are crucial to manage the carbon content effectively. Adding carbon materials to soil is thereby not directly sequestration, as interaction of appropriately designed materials with the soil microbiome can result in both: metabolization and thereby nonsustainable use of the added carbon, or—more favorably—a biological amplification of human efforts and sequestration of extra CO2 by microbial growth. We review here potential approaches to govern soil carbon, with a special focus set on the emerging practice of adding manufactured carbon materials to control soil carbon and its biological dynamics. Notably, research on so-called “biochar” is already relatively mature, while the role of artificial humic substance (A-HS) in microbial carbon sequestration is still in the developing stage. However, it is shown that the preparation and application of A-HS are large biological levers, as they directly interact with the environment and community building of the biological soil system. We believe that A-HS can play a central role in stabilizing carbon pools in soil.

Prospects of Using Soil Microbiome of Mine Tips for Remediation of Anthropogenically Disturbed Ecosystems

Introduction. Coal industry increases soil pollution with heavy metals and polycyclic aromatic hydrocarbons. Therefore, resoiling is an urgent problem that requires an immediate solution. The present research objective was to substantiate the use of microorganisms from mine tips in order to decrease soil pollution with heavy metals and oil compounds. Study objects and methods. The review featured five years of publications in Scopus, Web of Science, and Elibrary, which were subjected to analysis, systematization, and generalization. Results and discussion. Coal industry changes landscapes, flora, fauna, and soil microbiome. Bioremediation uses various microorganisms as means of resoiling. Some microorganisms isolated from coal mining waste are resistant to heavy metals and polycyclic aromatic hydrocarbons and are able to utilize them. For instance, such bacteria as Bacillus and Pseudomonas aeruginosa are capable of degrading oil pollutants. Microorganisms of Enterobacter and Klebsiella species were found to be resistant to copper, iron, lead, and manganese. Bacteria of the genera Bacillus, Arthrobacter, Pseudoarthrobacter, and Sinomonas are now to be resistant to nickel, arsenic, and chromium. Arbuscular mycorrhizal fungi increase the activity of soil enzymes, improve soil fertility, and decompose various organic compounds. Conclusion. Sequencing methods make it possible to determine the species composition of soils in mine tips in order to search for new strains capable of restoring former mining areas.

Long-Term Amelioration Practices Reshape the Soil Microbiome in a Coastal Saline Soil and Alter the Richness and Vertical Distribution Differently Among Bacterial, Archaeal, and Fungal Communities

Globally soil salinity is one of the most devastating environmental stresses affecting agricultural systems and causes huge economic losses each year. High soil salinity causes osmotic stress, nutritional imbalance and ion toxicity to plants and severely affects crop productivity in farming systems. Freezing saline water irrigation and plastic mulching techniques were successfully developed in our previous study to desalinize costal saline soil. Understanding how microbial communities respond during saline soil amelioration is crucial, given the key roles soil microbes play in ecosystem succession. In the present study, the community composition, diversity, assembly and potential ecological functions of archaea, bacteria and fungi in coastal saline soil under amelioration practices of freezing saline water irrigation, plastic mulching and the combination of freezing saline water irrigation and plastic mulching were assessed through high-throughput sequencing. These amelioration practices decreased archaeal and increased bacterial richness while leaving fungal richness little changed in the surface soil. Functional prediction revealed that the amelioration practices, especially winter irrigation with saline water and film mulched in spring, promoted a community harboring heterotrophic features. β-null deviation analysis illustrated that amelioration practices weakened the deterministic processes in structuring coastal saline soil microbial communities. These results advanced our understanding of the responses of the soil microbiome to amelioration practices and provided useful information for developing microbe-based remediation approaches in coastal saline soils.

Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes

The soil microbiome is the key player regulating phosphorus cycling processes. Identifying phosphate-solubilizing bacteria and utilizing them for release of recalcitrant phosphate that is bound to rocks or minerals have implications for improving crop nutrient acquisition and crop productivity.

Synergism between feremycorrhizal symbiosis and free-living diazotrophs leads to improved growth and nutrition of wheat under nitrogen deficiency conditions

A controlled-environment study was conducted to explore possible synergistic interactions between the feremycorrhizal (FM) fungus Austroboletus occidentalis and soil free-living N2-fixing bacteria (diazotrophs). Wheat (Triticum aestivum) plants were grown under N deficiency conditions in a field soil without adding microbial inoculum (control: only containing soil indigenous microbes), or inoculated with a consortium containing four free-living diazotroph isolates (diazotrophs treatment), A. occidentalis inoculum (FM treatment), or both diazotrophs and A. occidentalis inoculums (dual treatment). After 7 weeks of growth, significantly greater shoot biomass was observed in plants inoculated with diazotrophs (by 25%), A. occidentalis (by 101%), and combined inoculums (by 106%), compared to the non-inoculated control treatment. All inoculated plants also had higher shoot nutrient contents (including N, P, K, Mg, Zn, Cu, and Mn) than the control treatment. Compared to the control and diazotrophs treatments, significantly greater shoot N content was observed in the FM treatment (i.e., synergism between the FM fungus and soil indigenous diazotrophs). Dually inoculated plants had the highest content of nutrients in shoots (e.g., N, P, K, S, Mg, Zn, Cu, and Mn) and soil total N (13–24% higher than the other treatments), i.e., synergism between the FM fungus and added diazotrophs. Root colonization by soil indigenous arbuscular mycorrhizal fungi declined in all inoculated plants compared to control. Non-metric multidimensional scaling (NMDS) analysis of the bacterial 16S rRNA gene amplicons revealed that the FM fungus modified the soil microbiome. Our in vitro study indicated that A. occidentalis could not grow on substrates containing lignocellulosic materials or sucrose, but grew on media supplemented with hexoses such as glucose and fructose, indicating that the FM fungus has limited saprotrophic capacity similar to ectomycorrhizal fungi. The results revealed synergistic interactions between A. occidentalis and soil free-living diazotrophs, indicating a potential to boost microbial N2 fixation for non-legume crops.

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

Background Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks. Results We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. Conclusions Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.