Metabolic niches in the rhizosphere microbiome: dependence on soil horizons, root traits and climate variables in forest ecosystems.

Understanding belowground plant-microbial interactions is important for biodiversity maintenance, community assembly and ecosystem functioning of forest ecosystems. Consequently, a large number of studies were conducted on root and microbial interactions, especially in the context of precipitation and temperature gradients under global climate change scenarios. Forests ecosystems have high biodiversity of plants and associated microbes, and contribute to major primary productivity of terrestrial ecosystems. However, the impact of root metabolites/exudates and root traits on soil microbial functional groups along these climate gradients is poorly described in these forest ecosystems. The plant root system exhibits differentiated exudation profiles and considerable trait plasticity in terms of root morphological/phenotypic traits, which can cause shifts in microbial abundance and diversity. The root metabolites composed of primary and secondary metabolites and volatile organic compounds that have diverse roles in appealing to and preventing distinct microbial strains, thus benefit plant fitness and growth, and tolerance to abiotic stresses such as drought. Climatic factors significantly alter the quantity and quality of metabolites that forest trees secrete into the soil. Thus, the heterogeneities in the rhizosphere due to different climate drivers generate ecological niches for various microbial assemblages to foster beneficial rhizospheric interactions in the forest ecosystems. However, the root exudations and microbial diversity in forest trees vary across different soil layers due to alterations in root system architecture, soil moisture, temperature, and nutrient stoichiometry. Changes in root system architecture or traits, e.g. root tissue density (RTD), specific root length (SRL), and specific root area (SRA), impact the root exudation profile and amount released into the soil and thus influence the abundance and diversity of different functional guilds of microbes. Here, we review the current knowledge about root morphological and functional (root exudation) trait changes that affect microbial interactions along drought and temperature gradients. This review aims to clarify how forest trees adapt to challenging environments by leveraging their root traits to interact beneficially with microbes. Understanding these strategies is vital for comprehending plant adaptation under global climate change, with significant implications for future research in plant biodiversity conservation, particularly within forest ecosystems.

Interplay of silymarin and clove fruit extract effectively enhances cadmium stress tolerance in wheat (Triticum aestivum).

Introduction: Osmoprotectant supplementation can be used as a useful approach to enhance plant stress tolerance. However, the effect of silymarin and clove fruit extract (CFE) on wheat plants grown under cadmium (Cd) stress has not been studied. Methods: Wheat seeds were planted in plastic pots filled with ions-free sand. A ½-strength Hoagland's nutrient solution was used for irrigation. Pots were treated with eight treatments thirteen days after sowing: 1) Control, 2) 0.5 mM silymarin foliar application [silymarin], 3) 2% CFE foliar application [CFE], 4) CFE enriched with silymarin (0.24 g silymarin L-1 of CFE) [CFE-silymarin], 5) Watering wheat seedlings with a nutritious solution of 2 mM Cd [Cd]. 6) Cadmium + silymarin, 7) Cadmium + CFE, and 8) Cadmium + CFE-silymarin. The experimental design was a completely randomized design with nine replicates. Results and discussion: The Cd stress decreased grain yield, shoot dry weight, leaf area, carotenoids, chlorophylls, stomatal conductance, net photosynthetic rate, transpiration rate, membrane stability index, nitrogen, phosphorus, and potassium content by 66.9, 60.6, 56.7, 23.8, 33.5, 48.1, 41.2, 48.7, 42.5, 24.1, 39.9, and 24.1%, respectively. On the other hand, Cd has an Application of CFE, silymarin, or CEF-silymarin for wheat plants grown under Cd stress, significantly improved all investigated biochemical, morphological, and physiological variables and enhanced the antioxidant enzyme activities. Applying CFE and/or silymarin enhanced plant tolerance to Cd stress more efficiently. Our findings suggest using CFE-silymarin as a meaningful biostimulator for wheat plants to increase wheat plants' tolerance to Cd stress via enhancing various metabolic and physiological processes.

Massilia agrisoli sp. nov., isolated from rhizospheric soil of banana.

A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-52T, was isolated from the rhizospheric soil of a banana plant. Colonies grew at 10-35 °C (optimum, 28 °C), pH 6.0-9.5 (optimum, pH 7.0-7.5), and in the presence of 0-1.0 % NaCl (optimum 0 %). The strain was positive for catalase and oxidase tests, as well as hydrolysis of gelatin, casein, starch and Tween 20. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-52T clustered together within the genus Massilia. Strain MAHUQ-52T was closely related to Massilia soli R798T (98.6 %) and Massilia polaris RP-1-19T (98.3 %). The novel strain MAHUQ-52T has a draft genome size of 4 677 454 bp (25 contigs), annotated with 4193 protein-coding genes, 64 tRNA and 19 rRNA genes. The genomic DNA G+C content was 63.0 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-52T and closely related type strains were ≤88.4 and 35.8 %, respectively. The only respiratory quinone was ubiquinone-8. The major fatty acids were identified as C16 : 0 and summed feature 3 (C15 : 0 iso 2-OH and/or C16 : 1 ω7c). Strain MAHUQ-52T contained phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as the major polar lipids. On the basis of dDDH and ANI values, as well as genotypic, chemotaxonomic and physiological data, strain MAHUQ-52T represents a novel species within the genus Massilia, for which the name Massilia agrisoli sp. nov. is proposed, with MAHUQ-52T (=KACC 21999T=CGMCC 1.18577T) as the type strain.

Temporal variations in root-associated fungal communities of Potaninia mongolica, an endangered relict shrub species in the semi-arid desert of Northwest China.

The semi-arid region of the Western Ordos plateau in Inner Mongolia, China, is home to a critically endangered shrub species, Potaninia mongolica, which originates from ancient Mediterranean regions. Root-associated microbiomes play important roles in plant nutrition, productivity, and resistance to environmental stress particularly in the harsh desert environment; however, the succession of root-associated fungi during the growth stages of P. mongolica is still unclear. This study aimed to examine root-associated fungal communities of this relict plant species across three seasons (spring, summer and autumn) using root sampling and Illumina Miseq sequencing of internal transcribed spacer 2 (ITS 2) region to target fungi. The analysis detected 698 fungal OTUs in association with P. mongolica roots, and the fungal richness increased significantly from spring to summer and autumn. Eurotiales, Hypocreales, Chaetothyriales, Pleosporales, Helotiales, Agaricales and Xylariales were the dominant fungal orders. Fungal community composition was significantly different between the three seasons, and the fungal taxa at various levels showed biased distribution and preferences. Stochastic processes predominantly drove community assembly of fungi in spring while deterministic processes acted more in the later seasons. The findings revealed the temporal dynamics of root-associated fungal communities of P. mongolica, which may enhance our understanding of biodiversity and changes along with seasonal alteration in the desert, and predict the response of fungal community to future global changes.

Genotoxicity and Trace Elements Contents Analysis in Nile Tilapia (Oreochromis niloticus) Indicated the Levels of Aquatic Contamination at Three Egyptian Areas.

The toxic waste and pollutants of heavy metals continuously pollute freshwater aquatic reservoirs, which have severe implications on aquatic life and human health. The present work aims to evaluate trace elements (Zn, Mn, Cu, Cd, and Pb) along with three sites, Mariout Lake, Abbassa, and River Nile Aswan in Egypt, using Nile tilapia (Oreochromis niloticus) as bioindicator. The quality assurance, health-risk assessment, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), quantitative polymerase chain reaction (qPCR), and micronucleus test were performed to investigate the effect of different trace elements on Hsp70 gene level and micronuclei formation. We observed the highest expression of Hsp70 protein band of 70 KD and stress-responsive Hsp70 gene in the liver followed by gills of Nile tilapia caught from Mariout and Abbassa, but the lowest expression was in Nile tilapia caught from Aswan. Obvious micronuclei were observed under the microscope in erythrocytes, and their number was gradually decreased in the following manner: Mariout > Abbassa > Aswan. Noticeably, Cu, Zn, and Mn contents were low. Still, Pb and Cd contents were higher than the toxicity level recommended by the Food and Agriculture Organization (FAO), The World Health Organization (WHO), and the European Commission (EC). These results showed that Hsp70's appearance at the two levels of mRNA and protein is an effective indicator for aquatic pollution besides the aberration at the chromosome level represented in the micronucleus test. Furthermore, these results showed that Nile tilapia of the Aswan region had comparatively low trace elements contamination and were suitable for consumption.

A bio-sustainable approach for reducing Eucalyptus tree-caused agricultural ecosystem hazards employing Trichoderma bio-sustained spores and mycorrhizal networks.

The presence of the exotic Eucalyptus tree in crop-growing soil and the accumulation of its undecomposed leaves is a significant ecological hazard. The waxy coating on the leaves and the phenolic compounds takes a long time to break down under normal conditions. It is necessary to explore various fungi that can degrade these leaves for an eco-friendly solution to this problem. In this study, spores of nine native Trichoderma strains were produced on wheat agar using a lactic acid-induced sporulation strategy (LAISS). Trichoderma biosustained spores and Serendipita indica (SI) spores were applied to a rice field with accumulated Eucalyptus leaves under continuous ponding (CP) and alternate flooding and wetting conditions (AFW). Among the strains, TI04 (Trichoderma viride) and TI15 (Trichoderma citrinoviride) showed faster (5 days) and massive sporulation (1.06-1.38 × 1011 CFU/g) in LAISS. In vitro, TI04 and TI15 biosustained on Eucalyptus leaves and improved rice seedling growth and SI infection under greenhouse conditions. In the rice-field experiment, Trichoderma-treatment had a threefold yield (percentage) increase from control, with TI04 (CP) increasing the yield by 30.79, TI04 (AFW) by 29.45, TI15 (CP) by 32.72, and TI15 (AFW) rising by 31.91. Remarkably, unfilled grain yield significantly decreased in all the Trichoderma treatments. Under AFW conditions, TI04 and TI15 showed a higher pH increase. Furthermore, TI04 and TI15 under AFW had higher water productivity (t ha-1 cm-1) of 0.0763 and 0.0791, respectively, and the highest rates (percentage) of SI colonization of 86.36 and 83.16, respectively. According to the findings, LAISS-produced Trichoderma spores can be applied to break down persistent wastes and restore agricultural ecosystems through increased mycorrhizae networking.

Pinibacter aurantiacus gen. nov., sp. nov., isolated from rhizospheric soil of a pine tree.

A Gram-stain-negative, aerobic and rod-shaped novel bacterial strain, designated MAH-26T, was isolated from rhizospheric soil of a pine tree. The colonies were orange coloured, smooth, spherical and 0.7-1.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-26T was able to grow at 10-40 °C, at pH 6.0-9.0 and with 0-1.0 % NaCl. Cell growth occurred on nutrient agar, R2A agar, tryptone soya agar and Luria-Bertani agar. The strain gave positive results in oxidase and catalase tests. Strain MAH-26T was closely related to Flavihumibacter sediminis CJ663T and Parasegetibacter terrae SGM2-10T with a low 16S rRNA gene sequence similarity (92.8 and 92.9 %, respectively) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from the members of the closely related genera of the family Chitinophagaceae. Strain MAH-26T has a draft genome size of 6 857 405 bp, annotated with 5173 protein-coding genes, 50 tRNA and two rRNA genes. The genomic DNA G+C content was 41.5 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3OH. On the basis of phylogenetic inference and phenotypic, chemotaxonomic and molecular properties, strain MAH-26T represents a novel species of a novel genus of the family Chitinophagaceae, for which the name Pinibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain of Pinibacter aurantiacus is MAH-26T (=KACC 19749T=CGMCC 1.13701T).

Sand Particle Size and Phosphorus Amount Affect Rhizophagus irregularis Spore Production Using In Vitro Propagated Spore as a Starter Inoculum in Rhizosphere of Maize (Zea mays) Plantlets.

Microbial inoculants, particularly arbuscular mycorrhizal (AM) fungi, have great potential for sustainable crop management. In this study, monoxenic culture of indigenous R. irregularis was developed and used as a tool to determine the minimum phosphorus (P) level for maximum spore production under the in vitro conditions. This type of starter AM fungal inoculum was then applied to an in vivo substrate-based mass-cultivation system. Spore production, colonization rate, and plant growth were examined in maize (Zea mays L.) plant inoculated with the monoxenic culture of R. irregularis in sand graded by particle size with varying P levels in nutrient treatments. In the in vitro culture, the growth medium supplemented with 20 µM P generated the maximum number of spores (400 spores/mL media) of R. irregularis. In the in vivo system, the highest sporulation (≈500 spores g-1 sand) occurred when we added a half-strength Hoagland solution (20 µM P) in the sand with particle size between 500 µm and 710 µm and omitted P after seven weeks. However, the highest colonization occurred when we added a half-strength Hoagland solution in the sand with particle sizes between 710 µm and 1000 µm and omitted P after seven weeks. This study suggests that substrate particle size and P reduction and regulation might have a strong influence on the maximization of sporulation and colonization of R. irregularis in sand substrate-based culture.

A secondary approach with conventional medicines and supplements to recuperate current COVID-19 status.

Novel coronavirus 2019 (COVID-19) is a zoonosis that revised the global economic and societal progress since early 2020. The SARS-CoV-2 has been recognized as the responsible pathogen for COVID-19 with high infection and mortality rate potential. It has spread in 192 countries and infected about 1.5% of the world population, and still, a proper therapeutic approach is not unveiled. COVID-19 indication starts with fever to shortness of breathing, leading to ICU admission with the ventilation support in severe conditions. Besides the symptomatic mainstay clinical therapeutic approach, only Remdesivir has been approved by the FDA. Several pharmaceutical companies claimed different vaccines with exceptionally high efficacy (90-95%) against COVID-19; how long these vaccines can protect and long-term safety with the new variants are unpredictable. After the worldwide spread of the COVID-19 pandemic, numerous clinical trials with different phases are being performed to find the most appropriate solution to this condition. Some of these trials with old FDA-approved drugs showed promising results. In this review, we have precisely compiled the efforts to curb the disease and discussed the clinical findings of Ivermectin, Doxycycline, Vitamin-D, Vitamin-C, Zinc, and cannabidiol and their combinations. Additionally, the correlation of these molecules on the prophylactic and diseased ministration against COVID-19 has been explored.

Critical Assessment of Mycotoxins in Beverages and Their Control Measures.

Mycotoxins are secondary metabolites of filamentous fungi that contaminate food products such as fruits, vegetables, cereals, beverages, and other agricultural commodities. Their occurrence in the food chain, especially in beverages, can pose a serious risk to human health, due to their toxicity, even at low concentrations. Mycotoxins, such as aflatoxins (AFs), ochratoxin A (OTA), patulin (PAT), fumonisins (FBs), trichothecenes (TCs), zearalenone (ZEN), and the alternaria toxins including alternariol, altenuene, and alternariol methyl ether have largely been identified in fruits and their derived products, such as beverages and drinks. The presence of mycotoxins in beverages is of high concern in some cases due to their levels being higher than the limits set by regulations. This review aims to summarize the toxicity of the major mycotoxins that occur in beverages, the methods available for their detection and quantification, and the strategies for their control. In addition, some novel techniques for controlling mycotoxins in the postharvest stage are highlighted.

Soil fungal diversity and community assembly: affected by island size or type?

Fungi have a huge biodiversity and play important roles in soil biogeochemical cycling in island ecosystems. Although island biogeography has been widely studied for macroorganisms, fungal community assembly in true islands and its relationship with island area are less documented. We examined soil fungal communities in 18 oceanic islands of two types (eight non-coral islands and 10 coral islands) using the Illumina MiSeq sequencing technique. Our results showed that fungal α-diversity (species richness) was substantially different among the oceanic islands, with a higher value in non-coral islands than in coral islands. Fungal α-diversity was significantly affected by soil potassium and magnesium (Mg) and plant communities in non-coral islands, whereas only soil Mg significantly affected it in coral islands. Soil fungal community composition was significantly different in the non-coral and coral islands and was influenced by soil property, plant community and spatial distance. The ecological stochasticity model showed that the fungal community assembly was mainly governed by deterministic processes regardless of island type. Fungal ß-diversity, but not α-diversity, increased significantly with increasing island area. These findings have implications for the better prediction of soil fungal community dynamics in island systems and biodiversity conservation in fragmented habitats.

Response of arbuscular mycorrhizal fungal community in soil and roots to grazing differs in a wetland on the Qinghai-Tibet plateau.

Grazing as one of the most important disturbances affects the abundance, diversity and community composition of arbuscular mycorrhizal (AM) fungi in ecosystems, but the AM fungi in response to grazing in wetland ecosystems remain poorly documented. Here, we examined AM fungi in roots and soil in grazing and non-grazing plots in Zoige wetland on the Qinghai-Tibet plateau. Grazing significantly increased AM fungal spore density and glomalin-related soil proteins, but had no significant effect on the extra radical hyphal density of AM fungi. While AM fungal richness and community composition differed between roots and soil, grazing was found to influence only the community composition in soil. This study shows that moderate grazing can increase the biomass of AM fungi and soil carbon sequestration, and maintain the AM fungal diversity in the wetland ecosystem. This finding may enhance our understanding of the AM fungi in response to grazing in the wetland on the Qinghai-Tibet plateau.

Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem.

BACKGROUND: Revealing the relationship between plants and fungi is very important in understanding biodiversity maintenance, community stability, and ecosystem functioning. However, differences in the community and network structures of phyllosphere epiphytic and endophytic fungi are currently poorly documented. In this study, we examined epiphytic and endophytic fungal communities associated with the leaves of six mangrove species using Illumina MiSeq sequencing of internal transcribed spacer 2 (ITS2) sequences. RESULTS: A total of 635 operational taxonomic units (OTUs) of endophytic and epiphytic fungi were obtained at a 97% sequence similarity level; they were dominated by Dothideomycetes and Tremellomycetes. Plant identity had a significant effect on the OTU richness of endophytic fungi, but not on epiphytic fungi. The community composition of epiphytic and endophytic fungi was significantly different, and plant identity had a greater effect on endophytic fungi than on epiphytic fungi. Network analysis showed that both epiphytic and endophytic network structures were characterized by significantly highly specialized and modular but lowly connected and anti-nested properties. Furthermore, the endophytic network had higher levels of specialization and modularity but lower connectance and stronger anti-nestedness than the epiphytic network. CONCLUSIONS: This study reveals that the phyllosphere epiphytic and endophytic fungal communities differ, and plant identity has a greater effect on the endophytic fungi than on epiphytic fungi. These findings demonstrate the role of host plant identity in driving phyllosphere epiphytic and endophytic community structure.

Community Assembly of Endophytic Fungi in Ectomycorrhizae of Betulaceae Plants at a Regional Scale.

The interaction between aboveground and belowground biotic communities drives community assembly of plants and soil microbiota. As an important component of belowground microorganisms, root-associated fungi play pivotal roles in biodiversity maintenance and community assembly of host plants. The Betulaceae plants form ectomycorrhizae with soil fungi and widely distribute in various ecosystems. However, the community assembly of endophytic fungi in ectomycorrhizae is less investigated at a large spatial scale. Here, we examined the endophytic fungal communities in ectomycorrhizae of 22 species in four genera belonging to Betulaceae in Chinese forest ecosystems, using Illumina Miseq sequencing of internal transcribed spacer 2 amplicons. The relative contribution of host phylogeny, climate and soil (environmental filtering) and geographic distance (dispersal limitation) on endophytic fungal community was disentangled. In total, 2,106 endophytic fungal operational taxonomic units (OTUs) were obtained at a 97% sequence similarity level, dominated by Leotiomycetes, Agaricomycetes, Eurotiomycetes, and Sordariomycetes. The endophytic fungal OTU richness was significantly related with host phylogeny, geographic distance, soil and climate. The endophytic fungal community composition was significantly affected by host phylogeny (19.5% of variation explained in fungal community), geographic distance (11.2%), soil (6.1%), and climate (1.4%). This finding suggests that environmental filtering by plant and abiotic variables coupled with dispersal limitation linked to geographic distance determines endophytic fungal community assembly in ectomycorrhizae of Betulaceae plants, with host phylogeny being a stronger determinant than other predictor variables at the regional scale.