The Effects of Host Plant Genotype and Environmental Conditions on Fungal Community Composition and Phosphorus Solubilization in Willow Short Rotation Coppice

Foliar mycobiome remains unaltered under urban air-pollution but differentially express stress-related genes

Air pollution caused by tropospheric ozone contributes to the decline of forest ecosystems; for instance, sacred fir, Abies religiosa (Kunth) Schltdl. & Cham. forests in the peri-urban region of Mexico City. Individual trees within these forests exhibit variation in their response to ozone exposure, including the severity of visible symptoms in needles. Using RNA-Seq metatranscriptomic data and ITS2 metabarcoding, we investigated whether symptom variation correlates with the taxonomic and functional composition of fungal mycobiomes from needles collected in this highly polluted area in the surroundings of Mexico City. Our findings indicate that ozone-related symptoms do not significantly correlate with changes in the taxonomic composition of fungal mycobiomes. However, genes coding for 30 putative proteins were differentially expressed in the mycobiome of asymptomatic needles, including eight genes previously associated with resistance to oxidative stress. These results suggest that fungal communities likely play a role in mitigating the oxidative burst caused by tropospheric ozone in sacred fir. Our study illustrates the feasibility of using RNA-Seq data, accessible from global sequence repositories, for the characterization of fungal communities associated with plant tissues, including their gene expression.

Endophytic microbiota and ectomycorrhizal structure of Alnus glutinosa Gaertn. at saline and nonsaline forest sites

The tolerance of European alder (Alnus glutinosa Gaertn.) to soil salinity can be attributed to symbiosis with microorganisms at the absorptive root level. However, it is uncertain how soil salinity impacts microbial recruitment in the following growing season. We describe the bacterial and fungal communities in the rhizosphere and endosphere of A. glutinosa absorptive roots at three tested sites with different salinity level. We determined the morphological diversity of ectomycorrhizal (ECM) fungi, the endophytic microbiota in the rhizosphere, and the colonization of new absorptive roots in the following growing season. While bacterial diversity in the rhizosphere was higher than that in the absorptive root endosphere, the opposite was true for fungi. Actinomycetota, Frankiales, Acidothermus sp. and Streptomyces sp. were more abundant in the endosphere than in the rhizosphere, while Actinomycetota and Acidothermus sp. dominated at saline sites compared to nonsaline sites. Basidiomycota, Thelephorales, Russulales, Helotiales, Cortinarius spp. and Lactarius spp. dominated the endosphere, while Ascomycota, Hypocreales and Giberella spp. dominated the rhizosphere. The ECM symbioses formed by Thelephorales (Thelephora, Tomentella spp.) constituted the core community with absorptive roots in the spring and further colonized new root tips during the growing season. With an increase in soil salinity, the overall fungal abundance decreased, and Russula spp. and Cortinarius spp. were not present at all. Similarly, salinity also negatively affected the average length of the absorptive root. In conclusion, the endophytic microbiota in the rhizosphere of A. glutinosa was driven by salinity and season, while the ECM morphotype community was determined by the soil fungal community present during the growing season and renewed in the spring.

Phosphate solubilizing bacteria from soils with varying environmental conditions: Occurrence and function

Phosphate solubilizing bacteria (PSB) is an advantageous way to supply phosphate (P) to plants. The Mediterranean climate of Morocco, especially the low-lying areas, is semi-arid with nutrient-depleted soils in which small-scale, low-income farmers dominate without access to expensive inorganic fertilizers. However, there is not a wide range of PSBs suitable for various agroecological situations. Furthermore, our understanding of the soil and climatic variables that influence their development is limited. This study aims to examine the impacts of specific environmental factors, such as climate and soil, on the abundance, potential, and diversity of PSBs in four agricultural regions of Morocco. To assess the possible impact of these factors on the P solubilization capacity of PSBs and plant growth-promoting (PGP) traits, we analyzed the soil and climate of each sample studied. Similarly, we tested the P solubilization efficiency of the isolates. The bacteria were isolated in a National Botanical Research Institute's phosphate (NBRIP) agar medium. A total of 51 PSBs were studied in this work. The P-solubilization average of Rock P (RP) and Tricalcium P (TCP) of all strains that were isolated from each of the four regions ranged from 18.69 mg.L-1 to 40.43 mg.L-1 and from 71.71 mg.L-1 to 94.54 mg.L-1, respectively. The PGP traits of the isolated strains are positively correlated with the PSBs abundance and the sample characteristics (soil and climate). The morphological and biochemical characteristics of the strain allowed us to identify around nine different bacterial genera, including Bacillus, Pseudomonas, and Rhizobium. The findings showed that bacterial communities, density, and potency are closely correlated to various edapho-climatic conditions such as temperature, precipitation, soil nutrient status, and soil texture. These findings could be used to improve an effective plant-PSBs system and increase agricultural output by taking into account their specific ecological traits and plant growth mechanisms.

Large effect of phosphate-solubilizing bacteria on the growth and gene expression of Salix spp. at low phosphorus levels

Phosphorus is one of the most important nutrients required for plant growth and development. However, owing to its low availability in the soil, phosphorus is also one of the most difficult elements for plants to acquire. Phosphorus released into the soil from bedrock quickly becomes unavailable to plants, forming poorly soluble complexes. Phosphate-solubilizing bacteria (PSB) can solubilize unavailable phosphorus-containing compounds into forms in which phosphorus is readily available, thus promoting plant growth. In this study, two willow species, Salix dasyclados cv. Loden and Salix schwerinii × Salix viminalis cv. Tora, were inoculated with two selected bacterial strains, Pantoea agglomerans and Paenibacillus spp., to evaluate the plant growth parameters and changes in gene expression in the presence of different concentrations of tricalcium phosphate: 0 mM (NP), 1 mM (LP), and 2 mM (HP). Inoculation with PSB increased root, shoot and leaf biomass, and for the HP treatment, significant changes in growth patterns were observed. However, the growth responses to plant treatments tested depended on the willow species. Analysis of the leaf transcriptomes of the phosphate-solubilizing bacterium-inoculated plants showed a large variation in gene expression between the two willow species. For the Tora willow species, upregulation of genes was observed, particularly for those involved in pathways related to photosynthesis, and this effect was strongly influenced by bacterial phosphate solubilization. The Loden willow species was characterized by a general downregulation of genes involved in pathway activity that included ion transport, transcription regulation and chromosomes. The results obtained in this study provide an improved understanding of the dynamics of Salix growth and gene expression under the influence of PSB, contributing to an increase in yield and phosphorus-use efficiency.

Distinct distribution patterns and functional potentials of rare and abundant microorganisms between plastisphere and soils

The increasing application of plastic film has caused the "white pollution" of farmlands in greenhouses. To date, most studies on the ecology of the plastisphere have focused on the whole microbial community, with few on the rare and abundant taxa, especially in the terrestrial ecosystems. To understand the plastisphere rare and abundant taxa of bacterial and fungal communities, we collected residues of plastic film from plastic-covered soils in the greenhouse. The plastisphere was significantly different from surrounding soils in terms of alpha- and beta-diversities of abundant and rare taxa. Such discrepancies were greater in rare taxa than in abundant taxa. Besides, the enrichment of soil-borne plant pathogenic fungi in the plastisphere implied that plastic film residues can act as vectors for pathogen transmission. In the plastisphere, the stochastic process governed the assemblies of rare taxa, while deterministic assemblies dominated that of abundant taxa. However, in surrounding soils, the stochastic process played a larger role in abundant taxa as compared to rare taxa. The plastisphere showed a network of less complexity, more competitive connections, and more modules compared to surrounding soils, and rare taxa played greater roles than abundant taxa. There existed obvious discrepancies in the microbial functions between surrounding soils and plastisphere, including carbon, sulfur, nitrogen, and phosphorus cycling, and rare taxa contribute large proportions to the above cycling processes. Altogether, the findings advance our understanding of ecological mechanisms of abundant and rare taxa in the plastisphere in terrestrial ecosystems.

CaFe-layered double hydroxide corn straw biochar reduced heavy metal uptake by Brassica campestris L. and Ipomoea aquatic F.: Rhizosphere effects and oxidative stress alleviation

In the present study, CaFe-layered double hydroxide corn straw biochar (CaFe-LDH@CSB) was applied to the rhizosphere soil of both pakchoi (Brassica campestris L. ssp. Chinensis Makino, B. campestris L.) and water spinach (Ipomoea aquatic F., I. aquatic F.) to explore and clarify the potential mechanism by which CaFe-LDH@CSB helps vegetables reduce heavy metal (HM) uptake and alleviate oxidative stress. Pot experiments were conducted with CaFe-LDH@CSB applied at four levels: control (CK), T1 (5 g kg^-1), T2 (10 g kg^-1) and T3 (20 g kg^-1). The results indicated that the application of CaFe-LDH@CSB significantly increased pH and decreased the acid-soluble forms of Cd, Pb, Zn and Cu in the rhizosphere soil of both B. campestris L. and I. aquatic F.; decreases of 39.4%, 18.0%, 10.0% and 33.3% in B. campestris L. and of 26.6%, 49.1%, 13.2% and 36.8% in I. aquatic F., respectively, were observed at the T3 level. Moreover, CaFe-LDH@CSB application reduced HM uptake by B. campestris L. and decreased HM-induced oxidative stress through the regulation of soil physicochemical properties and microbial abundance. For B. campestris L., variations in Sordariomycetes helped alleviate the accumulation of HMs in the aerial part, while GSH and -SH from the nonenzymatic system played an important role in scavenging H₂O₂ in leaves, thus helping B. campestris L. alleviate HM-induced oxidative stress. For I. aquatica F., variations in Vicinamibacteria and Mortierellomycetes helped alleviate the accumulation of HMs in plants, while GSH and PCs from nonenzymatic systems played an important role in removing ·O₂^- in leaves, thereby helping I. aquatica F. alleviate HM-induced oxidation stress. Our study indicated that the application of CaFe-LDH@CSB improved the rhizosphere soil environment and rebuilt the soil microbial community, helping B. campestris L. and I. aquatica F. alleviate HM-induced oxidative stress and promoting the growth of both vegetables.

A multi-aspect analysis of two analogous aspergillus spp. belonging to section Flavi: aspergillus flavus and aspergillus oryzae

Microfungal isolates were routinely identified depending on both macro and micro morphological characteristics, sometimes, some fungal isolates appeared to be similar and such cases caused severe confusion for mycologists during the preliminary identification. During our previous studies dealing with isolation of fungi for some biotechnological applications; two mystifying species Aspergillus flavus and Aspergillus oryzae showed similar cultural and macroscopic features. Therefore, the current study aimed to easily distinguish between these two species depending on simple approaches which are routinely followed by a large segment of researchers. Investigation of the macroscopic features was performed to check the fungal growth on four different media (PDA, MEA, YES, and CYA) followed by microscopic examination using an ordinary light microscope, and scanning electron microscope SEM. Also, screening of secondary metabolites for both strains was preliminarily identified to find out the difference between their metabolic profiles. Finally, ITS rDNA was involved to clarify the molecular differences along their partial sequence. Conclusively, the BLAST strategy confirmed the similarity of ITS rDNA segments of both fungal strains that supported our hypothesis. The color of the fungal growth is a very critical factor whereas it is extensively influenced by the type of cultivation media. Accordingly, the YES medium was an inspiring tool assisting in prompt differentiation during the culture investigation step whereas A. oryzae and A. flavus appeared significant mustard yellow and olive green respectively. During the microscopic examination, the CYA medium also had a robust effect on the formation of the conidial chain whereas the knit long chain was observed in A. oryzae while the conidia appeared scattered and not in a chain in the case of A. flavus. Likewise, both two strains possessed different metabolic profiles where A. oryzae is not an Afla toxin producer, unlike A. flavus.

Mixed growth of Salix species can promote phosphate-solubilizing bacteria in the roots and rhizosphere

Phosphorus (P) is an essential plant nutrient that can limit plant growth due to low availability in the soil. P-solubilizing bacteria in the roots and rhizosphere increase the P use efficiency of plants. This study addressed the impact of plant species, the level of plant association with bacteria (rhizosphere or root endophyte) and environmental factors (e.g., seasons, soil properties) on the abundance and diversity of P-solubilizing bacteria in short-rotation coppices (SRC) of willows (Salix spp.) for biomass production. Two willow species (S. dasycladoscv. Loden and S. schwerinii × S. viminalis cv. Tora) grown in mono-and mixed culture plots were examined for the abundance and diversity of bacteria in the root endosphere and rhizosphere during two seasons (fall and spring) in central Sweden and northern Germany. Soil properties, such as pH and available P and N, had a significant effect on the structure of the bacterial community. Microbiome analysis and culture-based methods revealed a higher diversity of rhizospheric bacteria than endophytic bacteria. The P-solubilizing bacterial isolates belonged mainly to Proteobacteria (85%), Actinobacteria (6%) and Firmicutes (9%). Pseudomonas was the most frequently isolated cultivable bacterial genus from both the root endosphere and the rhizosphere. The remaining cultivable bacterial isolates belonged to the phyla Actinobacteria and Firmicutes. In conclusion, site-specific soil conditions and the level of plant association with bacteria were the main factors shaping the bacterial communities in the willow SRCs. In particular, the concentration of available P along with the total nitrogen in the soil controlled the total bacterial diversity in willow SRCs. A lower number of endophytic and rhizospheric bacteria was observed in Loden willow species compared to that of Tora and the mix of the two, indicating that mixed growth of Salix species promotes P-solubilizing bacterial diversity and abundance. Therefore, a mixed plant design was presented as a management option to increase the P availability for Salix in SRCs. This design should be tested for further species mixtures.

Site-Effects Dominate the Plant Availability of Nutrients under Salix Species during the First Cutting Cycle

Fast-growing willows (Salix spp.) provide alternative sources of renewable energy generation, but need an adequate nutrient availability in the soil for high biomass production. In general, species mixtures can be more nutrient-efficient than pure cultures, but this is scarcely known for Salix spp. Therefore, this study evaluates the nutrient availability and P mobilization under two willow species, Salixdasyclados var. ‘Loden’ and S. schwerinii × viminalis var. ‘Tora’, grown as pure and mixed cultures at non-fertilized former arable sites in Germany (Stagnic Cambisol) and Sweden (Vertic Cambisol). The plant availability of potassium (K), magnesium (Mg) and phosphorus (P) and soil phosphatase activities in the topsoil were measured in spring of the year of planting (initial) and under 4 years-old stocks (one year after the first 3-year cutting cycle). The initial plant availability of the nutrients significantly differed between the sites and the two sampling dates at both sites. The plant availability of K and Mg was optimal to high at both sites and sampling dates, but rather low for P (after 4 years ≤5 mg P 100 g−1 soil). The plant-available P and K content in soil significantly decreased within the 4 years of willow growth at both sites. The acid and alkaline phosphatase activity in the soil of the German site (Rostock) was significantly lower after 4 years of willow growth, but differed not significantly between the two sampling dates at the Swedish site (Uppsala). Higher activity of acid phosphatase compared to alkaline phosphatase was recorded in the soils at both test sites based on the site-specific soil pH (<7). The slight decrease of plant availability of P after 4 years of Salix growth in pure culture differed not significantly between the different species. Mixed growth did not decrease the plant availability of P within this period, although no significant difference in the biomass production of pure and mixed growth was observed. This was valid at both sites, and therefore, seems independent of the site-specific differences in soil and climate conditions. The general validity of the assumptions should be tested also for other species mixtures and soil conditions in the future before site-adapted growth designs can be recommended in biomass production of Salix.