Soil mycobiome in sustainable agriculture

Trichoderma harzianum AKH-5: A novel fungal isolate with antimicrobial efficacy for phytopathogen management and environmental remediation

Trichoderma harzianum isolate AKH-5 is recognized as a biological control agent, effective in managing harmful phytopathogens while promoting plant growth and enhancing resistance to various stresses. In this study, a total of 140 morphological different fungal isolates were isolated and in primary screening isolate AKH-5 exhibited significant antifungal activity in vitro. Trichoderma harzianum isolate AKH-5 proved to be effective and was characterized morphologically, physiologically and through 18S rRNA gene sequencing and identified as Trichoderma harzianum. GC-MS profiling of the ethyl acetate extract identified 22 distinct bioactive compounds, including phenylethyl alcohol, dibutyl phthalate, and N-carbobenzyloxy-L-tyrosyl-L-valine, which possess antibacterial, antifungal and antioxidant properties. Further, in antibacterial assessment, AKH-5 extract exhibited significant antibacterial activity on microbial pathogens in a dose-dependent manner. The lowest MIC value against Escherichia coli was 8 μg/mL, indicating strong antibacterial activity. MBC values (32, 64 μg/mL) were higher than MIC values, indicating the need for higher concentrations for bactericidal effects and significant antioxidant activity with an IC50 value of 90.78 μg/mL. The extract exhibited significant inhibition efficacy on Fusarium oxysporum, and Colletotrichum capsici, further moderate activity on Curvularia lunata, Alternaria alternata, and Rhizoctonia solani. The isolate AKH-5 showed good azo-dye degradation capacity and Triticum aestivum L. (wheat) seeds treated with dyes degraded with the isolate AKH-5 broth extract exhibited a germination rate of 98 %, compared to the untreated and control seeds which showed germination of 50 and 94 %, respectively. This study highlights the unexplored habitats as rich sources of diverse antifungal metabolite-producing fungi, which can be promising candidates for developing novel antifungal strains. Overall, the results demonstrate the beneficial role of AKH-5 in controlling phytopathogens and minimizing phytotoxicity through biodegradation of dyes for environmental remediation purposes.

Biodegradable hydrogels and microbial consortia as a treatment for soil dysbiosis

Terrestrial microbial communities drive many soil processes and can be pushed into a state of dysbiosis upon disturbance. This dysregulation negatively impacts soil biogeochemical cycles, which threatens plant and soil health. Effective treatment of soil dysbiosis requires simultaneous restoration of multiple system components, addressing both the physical structure of soil and its microbial communities. Hydrogels with microbial consortia simultaneously remedy soil hydrodynamics while promoting microbial reestablishment. The purpose of this review is to shed light on soil management practices through the lens of soil dysbiosis. This is important to address not only for soil health and crop productivity, but also to mitigate climate change through improved soil carbon sequestration and reduced greenhouse gas emissions. This review positions hydrogels and microbes as tools for the treatment of soil dysbiosis, contributing to agricultural and climate resilience.

Soil Bacterial Community Characteristics and Functional Analysis of Estuarine Wetlands and Nearshore Estuarine Wetlands in Qinghai Lake

Qinghai Lake, the largest inland saline lake in China, plays a vital role in wetland carbon cycling. However, the structure and function of soil bacterial communities in its estuarine and nearshore estuarine wetlands remain unclear. This study examined the effects of wetland type and soil depth on bacterial diversity, community composition, and functional potential in the Shaliu, Heima, and Daotang River wetlands using high-throughput sequencing. The results showed that wetland type and soil depth significantly influenced bacterial communities. Nearshore wetlands exhibited lower bacterial diversity in the 0-10 cm layer, while deeper soils (10-20 cm) showed greater regional differentiation. Estuarine wetlands were enriched with Proteobacteria, Actinobacteriota, and Chloroflexi, whereas nearshore wetlands were dominated by Actinobacteriota and Cyanobacteria. Functionally, estuarine wetlands had higher sulfate reduction and anaerobic decomposition potential, with Desulfovibrio, Desulfobacter, and Desulfotomaculum regulating sulfur cycling and carbon decomposition. In contrast, nearshore wetlands showed greater nitrogen fixation and organic matter degradation, facilitated by Rhizobium, Azotobacter, Clostridium, and nitrogen-fixing Cyanobacteria (e.g., Anabaena, Nostoc). Microbial metabolic functions varied by depth: surface soils (0-10 cm) favored environmental adaptation and organic degradation, whereas deeper soils (10-20 cm) exhibited lipid metabolism and DNA repair strategies for low-oxygen adaptation. These findings highlight the spatial heterogeneity of bacterial communities and their role in biogeochemical cycles, providing insights into wetland carbon dynamics and informing conservation strategies.

Variations in the structure and function of the soil fungal communities in the traditional cropping systems from Madeira Island

Agricultural soils are responsible for ecological functions and services that include primary production of food, fiber and fuel, nutrient cycling, carbon cycling and storage, water infiltration and purification, among others. Fungi are important drivers of most of those ecosystem services. Given the importance of fungi in agricultural soils, in this study, we aimed to characterize and analyse the changes of the soil fungal communities of three cropping systems from Madeira Island, where family farming is predominant, and investigate the response of fungi and its functional groups to soil physicochemical properties. To achieve that, we sequenced amplicons targeting the internal transcribed spacer 1 (ITS1) of the rRNA region, to analyse soil samples from 18 agrosystems: 6 vineyards (V), 6 banana plantations (B) and 6 vegetable plantations (H). Our results showed that alpha diversity indices of fungal communities are similar in the three cropping systems, but fungal composition and functional aspects varied among them, with more pronounced differences in B. Ascomycota, Basidiomycota, and Mortierellomycota were the main phyla found in the three cropping systems. Agaricomycetes and Sordariomycetes are the predominant classes in B, representing 23.8 and 22.4%, respectively, while Sordariomycetes (27.9%) followed by Eurotiomycetes (12.3%) were the predominant classes in V and Sordariomycetes (39.2%) followed by Tremellomycetes (8.9%) in the H. Saprotrophs are the fungal group showing higher relative abundance in the three cropping systems, followed by plant pathogens. Regarding symbionts, endophytes were highly observed in B, while mycorrhizal fungi was predominant in V and H. The structure of fungal communities was mainly correlated with soil content of P, K, N, Fe, and Cu. In addition, we identified bioindicators for each cropping system, which means that cultivated crops are also drivers of functional groups and the composition of communities. Overall, the three cropping systems favored diversity and growth of taxa that play important roles in soil, which highlights the importance of conservative management practices to maintain a healthy and resilient agrosystem.

Ecological processes of bacterial microbiome assembly in healthy and dysbiotic strawberry farms

The bacterial microbiome plays crucial role in plants' resistance to diseases, nutrient uptake and productivity. We examined the microbiome characteristics of healthy and unhealthy strawberry farms, focusing on soil (bulk soil, rhizosphere soil) and plant (roots and shoots). The relative abundance of most abundant taxa were correlated with the chemical soil properties and shoot niche revealed the least amount of significant correlations between the two. While alpha and beta diversities did not show differences between health groups, we identified a number of core taxa (16-59) and marker bacterial taxa for each healthy (Unclassified Tepidisphaerales, Ohtaekwangia, Hydrocarboniphaga) and dysbiotic (Udaeobacter, Solibacter, Unclassified Chitinophagales, Unclassified Nitrosomonadaceae, Nitrospira, Nocardioides, Tardiphaga, Skermanella, Pseudomonas, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Curtobacterium) niche. We also revealed selective pressure of strawberry rhizosphere soil and roots plants in unhealthy plantations increased stochastic ecological processes of bacterial microbiome assembly in shoots. Our findings contribute to understanding sustainable agriculture and plant-microbiome interactions.

Effects of returning peach branch waste to fields on soil carbon cycle mediated by soil microbial communities

In recent years, the rise in greenhouse gas emissions from agriculture has worsened climate change. Efficiently utilizing agricultural waste can significantly mitigate these effects. This study investigated the ecological benefits of returning peach branch waste to fields (RPBF) through three innovative strategies: (1) application of peach branch organic fertilizer (OF), (2) mushroom cultivation using peach branches as a substrate (MC), and (3) surface mulching with peach branches (SM). Conducted within a peach orchard ecosystem, our research aimed to assess these resource utilization strategies' effects on soil properties, microbial community, and carbon cycle, thereby contributing to sustainable agricultural practices. Our findings indicated that all RPBF treatments enhance soil nutrient content, enriching beneficial microorganisms, such as Humicola, Rhizobiales, and Bacillus. Moreover, soil AP and AK were observed to regulate the soil carbon cycle by altering the compositions and functions of microbial communities. Notably, OF and MC treatments were found to boost autotrophic microorganism abundance, thereby augmenting the potential for soil carbon sequestration and emission reduction. Interestingly, in peach orchard soil, fungal communities were found to contribute more greatly to SOC content than bacterial communities. However, SM treatment resulted in an increase in the presence of bacterial communities, thereby enhancing carbon emissions. Overall, this study illustrated the fundamental pathways by which RPBF treatment affects the soil carbon cycle, providing novel insights into the rational resource utilization of peach branch waste and the advancement of ecological agriculture.

New frontiers of soil fungal microbiome and its application for biotechnology in agriculture

The fungi-based technology provided encouraging scenarios in the transition from a conventionally based economic system to the potential security of sources closely associated with the agricultural sphere such as the agriculture. In recent years, the intensification of fungi-based processes has generated significant gains, additionally to the production of materials with significant benefits and strong environmental importance. Furthermore, the growing concern for human health, especially in the agriculture scenario, has fostered the investigation of organisms with high biological and beneficial potential for use in agricultural systems. Accordingly, this study offered a comprehensive review of the diversity of the soil fungal microbiome and its main applications in a biotechnological approach aimed at agriculture and food chain-related areas. Moreover, the spectrum of opportunities and the extensive optimization platform for obtaining fungi compounds and metabolites are discussed. Finally, future perspectives regarding the insurgency of innovations and challenges on the broad rise of visionary solutions applied to the biotechnology context are provided.

Pioneer Arabidopsis thaliana spans the succession gradient revealing a diverse root-associated microbiome

BACKGROUND

Soil microbiomes are increasingly acknowledged to affect plant functioning. Research in molecular model species Arabidopsis thaliana has given detailed insights of such plant-microbiome interactions. However, the circumstances under which natural A. thaliana plants have been studied so far might represent only a subset of A. thaliana's full ecological context and potential biotic diversity of its root-associated microbiome.

RESULTS

We collected A. thaliana root-associated soils from a secondary succession gradient covering 40 years of land abandonment. All field sites were situated on the same parent soil material and in the same climatic region. By sequencing the bacterial and fungal communities and soil abiotic analysis we discovered differences in both the biotic and abiotic composition of the root-associated soil of A. thaliana and these differences are in accordance with the successional class of the field sites. As the studied sites all have been under (former) agricultural use, and a climatic cline is absent, we were able to reveal a more complete variety of ecological contexts A. thaliana can appear and sustain in.

CONCLUSIONS

Our findings lead to the conclusion that although A. thaliana is considered a pioneer plant species and previously almost exclusively studied in early succession and disturbed sites, plants can successfully establish in soils which have experienced years of ecological development. Thereby, A. thaliana can be exposed to a much wider variation in soil ecological context than is currently presumed. This knowledge opens up new opportunities to enhance our understanding of causal plant-microbiome interactions as A. thaliana cannot only grow in contrasting soil biotic and abiotic conditions along a latitudinal gradient, but also when those conditions vary along a secondary succession gradient. Future research could give insights in important plant factors to grow in more ecologically complex later-secondary succession soils, which is an impending direction of our current agricultural systems.

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.

Untangling the Effects of Plant Genotype and Soil Conditions on the Assembly of Bacterial and Fungal Communities in the Rhizosphere of the Wild Andean Blueberry (Vaccinium floribundum Kunth)

Microbial communities in the rhizosphere influence nutrient acquisition and stress tolerance. How abiotic and biotic factors impact the plant microbiome in the wild has not been thoroughly addressed. We studied how plant genotype and soil affect the rhizosphere microbiome of Vaccinium floribundum, an endemic species of the Andean region that has not been domesticated or cultivated. Using high-throughput sequencing of the 16S rRNA and ITS region, we characterized 39 rhizosphere samples of V. floribundum from four plant genetic clusters in two soil regions from the Ecuadorian Highlands. Our results showed that Proteobacteria and Acidobacteria were the most abundant bacterial phyla and that fungal communities were not dominated by any specific taxa. Soil region was the main predictor for bacterial alpha diversity, phosphorous and lead being the most interesting edaphic factors explaining this diversity. The interaction of plant genotype and altitude was the most significant factor associated with fungal diversity. This study highlights how different factors govern the assembly of the rhizosphere microbiome of a wild plant. Bacterial communities depend more on the soil and its mineral content, while plant genetics influence the fungal community makeup. Our work illustrates plant-microbe associations and the drivers of their variation in a unique unexplored ecosystem from the Ecuadorian Andes.