Morphological and molecular diversity of arbuscular mycorrhizal fungi in revegetated iron-mining site has the same magnitude of adjacent pristine ecosystems

The characteristics of fungal responses to uranium mining activities and analysis of their tolerance to uranium

The influence of uranium (U) mining on the fungal diversity (FD) and communities (FC) structure was investigated in this work. Our results revealed that soil FC richness and FD indicators obviously decreased due to U, such as Chao1, observed OTUs and Shannon index (P<0.05). Moreover, the abundances of Mortierella, Gibberella, and Tetracladium were notably reduced in soil samples owing to U mining activities (P<0.05). In contrast, the abundances of Cadophora, Pseudogymnoascus, Mucor, and Sporormiella increased in all soil samples after U mining (P<0.05). Furthermore, U mining not only dramatically influenced the Plant_Pathogen guild and Saprotroph and Pathotroph modes (P<0.05), but also induced the differentiation of soil FC and the enrichment of the Animal_Pathogen-Soil_Saprotroph and Endophyte guilds and Symbiotroph and Pathotroph Saprotroph trophic modes. In addition, various fungal populations and guilds were enriched to deal with the external stresses caused by U mining in different U mining areas and soil depths (P<0.05). Finally, nine U-tolerant fungi were isolated and identified with a minimum inhibitory concentration range of 400-600 mg/L, and their adsorption efficiency for U ranged from 11.6% to 37.9%. This study provides insights into the impact of U mining on soil fungal stability and the response of fungi to U mining activities, as well as aids in the screening of fungal strains that can be used to promote remediation of U mining sites on plateaus.

Diversity of Arbuscular Mycorrhizal Fungi of the Rhizosphere of Lycium barbarum L. from Four Main Producing Areas in Northwest China and Their Effect on Plant Growth

Arbuscular mycorrhizal fungi (AMF) can help plants absorb more mineral nutrients after they colonize plant roots, and the mycelia harmonize the soil structure and physical and chemical properties by secreting compounds. AMF species co-evolve with their habitat's geographic conditions and hosts; this gradually causes differences in the AMF species. By using Melzer's reagent to analyze the morphology and using Illumina Miseq sequencing technology to perform the molecular identification of AMF communities among the four typical L. barbarum planting areas (Zhongning, Guyuan, Jinghe, and Dulan) investigated, the variety of L. barbarum roots and rhizosphere AMF communities was greater in the Zhongning area, and every region additionally had endemic species. The successfully amplified AMF was re-applied to the L. barbarum seedlings. We found that the total dry weight and accumulation of potassium increased significantly (p < 0.05), and the root volume and number of root branches were significantly higher in the plants that were inoculated with Paraglomus VTX00375 in the pot experiment, indicating that AMF improves root development and promotes plant growth. We have investigated AMF germplasm species in four regions, and we are committed to the development of native AMF resources. The multiplication and application of AMF will be conducive to realizing the potential role of biology in the maintenance of agroecology.

Diversity of Arbuscular Mycorrhizal Fungi in Distinct Ecosystems of the North Caucasus, a Temperate Biodiversity Hotspot

BACKGROUND

Investigations that are focused on arbuscular mycorrhizal fungus (AMF) biodiversity is still limited. The analysis of the AMF taxa in the North Caucasus, a temperate biodiversity hotspot, used to be limited to the genus level. This study aimed to define the AMF biodiversity at the species level in the North Caucasus biotopes.

METHODS

The molecular genetic identification of fungi was carried out with ITS1 and ITS2 regions as barcodes via sequencing using Illumina MiSeq, the analysis of phylogenetic trees for individual genera, and searches for operational taxonomic units (OTUs) with identification at the species level. Sequences from MaarjAM and NCBI GenBank were used as references.

RESULTS

We analyzed >10 million reads in soil samples for three biotopes to estimate fungal biodiversity. Briefly, 50 AMF species belonging to 20 genera were registered. The total number of the AM fungus OTUs for the "Subalpine Meadow" biotope was 171/131, that for "Forest" was 117/60, and that for "River Valley" was 296/221 based on ITS1/ITS2 data. The total number of the AM fungus species (except for virtual taxa) for the "Subalpine Meadow" biotope was 24/19, that for "Forest" was 22/13, and that for "River Valley" was 28/24 based on ITS1/ITS2 data. Greater AMF diversity, as well as number of OTUs and species, in comparison with that of forest biotopes, characterized valley biotopes (disturbed ecosystems; grasslands). The correlation coefficient between "Percentage of annual plants" and "Glomeromycota total reads" r = 0.76 and 0.81 for ITS1 and ITS2, respectively, and the correlation coefficient between "Percentage of annual plants" and "OTUs number (for total species)" was r = 0.67 and 0.77 for ITS1 and ITS2, respectively.

CONCLUSION

High AMF biodiversity for the river valley can be associated with a higher percentage of annual plants in these biotopes and the active development of restorative successional processes.

Impact of Iron Mining Activity on the Endophytic Fungal Community of Aspilia grazielae

Aspilia grazielae (J. U. Santos) is an endemic plant species in Morro do Urucum in the Pantanal wetland (Brazil). A. grazielae is used for the restoration of areas impacted by iron mining activities. This study evaluates the diversity (composition, value and abundance) of endophytic fungal communities, considering parts of the plant and soil condition. The leaves and roots of A. grazielae were collected from native vegetation areas (NVA) and recovery areas (RCA) in Morro do Urucum. Illumina sequencing technology was used to investigate variation in endophytic fungal biodiversity. The operational taxonomic units detected in NVA ranged from 183 to 263 (leaf) and 115 to 285 (root), while RCA samples ranged from 200 to 282 (leaf) and 156 to 348 (root). Ascomycota phylum was the most common species among all plant samples. The most significant classes identified were Lecanoromycetes and Dothideomycetes that differed significantly (p ≤ 0.05) according to their plant hosts and soil stress. The relative abundance of Pestalotiopsis (Sordariomycetes class) and Stereocaulon (Lecanoromycetes class) genera was influenced by the iron mining activities according to the leaf samples analysed. However, the abundance and wealth of endophytic fungal communities in A. grazielae from RCA were evidence that could explain their high resilience to environmental disturbances and the source-sink dynamics of fungal propagules.

Effects of nitrogen addition and seasonal change on arbuscular mycorrhizal fungi community diversity in a poplar plantation

Arbuscular mycorrhizal (AM) fungi play a crucial role in carbon (C), nitrogen (N), and phosphorous (P) biogeochemical cycling. Therefore, it is essential to determine the seasonal responses of the AM fungal community to N addition to understanding better the ecological processes against a background of intensified N deposition. Based on an ongoing field simulation experiment with five N addition levels (0, 5, 10, 15, and 30 gN·m−2·a−1) in a 5-year-old poplar plantation at Dongtai Forest Farm in Yancheng, Jiangsu province, eastern China, soil physicochemical properties, the root colonization rate, and the rhizosphere soil AM fungal community diversity and composition in four seasons (summer, autumn, winter, and spring) were investigated. Meanwhile, the relationships between the characteristics of the AM fungal community and soil environmental factors were analyzed. High-throughput sequencing showed that the dominant genera in the poplar plantation were Glomus (average relative abundance 87.52%), Diversispora (9.62%), and Acaulospora (1.85%). The addition of N significantly increased the root colonization rate in spring. The diversity of the AM fungal community (Chao and Shannon indexes) was primarily affected by seasonal change rather than N addition, and the diversity in summer was significantly lower than in the other three seasons. Redundancy analysis showed that soil temperature, available P, total P, and pH significantly affected the structure of the AM fungal community. It can be concluded N addition primarily influenced the root colonization rate, whereas seasonal change had a notable effect on the AM fungal community diversity. Although seasonal change and N addition greatly influenced the composition, seasonal change exerted a more substantial effect than N addition. These results will improve our understanding of the underground ecological processes in poplar plantation ecosystems.

Environmental identification of arbuscular mycorrhizal fungi using the LSU rDNA gene region: an expanded database and improved pipeline

Arbuscular mycorrhizal fungi (AMF; Glomeromycota) are difficult to culture; therefore, establishing a robust amplicon-based approach to taxa identification is imperative to describe AMF diversity. Further, due to low and biased sampling of AMF taxa, molecular databases do not represent the breadth of AMF diversity, making database matching approaches suboptimal. Therefore, a full description of AMF diversity requires a tool to determine sequence-based placement in the Glomeromycota clade. Nonetheless, commonly used gene regions, including the SSU and ITS, do not enable reliable phylogenetic placement. Here, we present an improved database and pipeline for the phylogenetic determination of AMF using amplicons from the large subunit (LSU) rRNA gene. We improve our database and backbone tree by including additional outgroup sequences. We also improve an existing bioinformatics pipeline by aligning forward and reverse reads separately, using a universal alignment for all tree building, and implementing a BLAST screening prior to tree building to remove non-homologous sequences. Finally, we present a script to extract AMF belonging to 11 major families as well as an amplicon sequencing variant (ASV) version of our pipeline. We test the utility of the pipeline by testing the placement of known AMF, known non-AMF, and Acaulospora sp. spore sequences. This work represents the most comprehensive database and pipeline for phylogenetic placement of AMF LSU amplicon sequences within the Glomeromycota clade.

Mycorrhizal root colonization in maize fields is more affected by soil management and climate conditions than by plant genotype

This work aims to characterize the arbuscular mycorrhizal association between maize genotypes and the effects of soil physical-chemical attributes on the symbiosis. A preliminary greenhouse assay evaluated five maize landraces and five conventional modern genotypes in non-sterile, low-P soil. Sixty days after sowing, we measured plant height, stem diameter, shoot and root dry biomass, root colonization structures, and shoot P concentration and total accumulation. In a second stage, a 2-year on-farm study evaluated how soil physical-chemical attributes in fields with three plant genotype groups affected the arbuscular mycorrhizal fungal symbiosis in a maize diversity microcenter in Southern Brazil. We collected soil and plant material in farms growing landrace, conventional modern genotypes, or genetically modified (GM) maize. There were five collection points at each group, and we measured mycorrhizal colonization, soil physicochemical attributes, and shoot phosphorus concentration. The greenhouse study showed that genotypes have different growth strategies for root production and shoot growth. No differences in mycorrhizal colonization rates occurred among landraces and modern maize genotypes in the low-P soil. The field study showed that soil and climate conditions had a more marked effect on mycorrhizal root colonization than plant genotype groups (landrace, conventional modern genotypes, or GM maize).

Soil Yeast Communities in Revegetated Post-Mining and Adjacent Native Areas in Central Brazil

Yeasts represent an important component of the soil microbiome. In central Brazil, mining activities are among the main anthropogenic factors that influence the dynamics of the soil microbiota. Few studies have been dedicated to analysis of tropical soil yeast communities, and even fewer have focused on Brazilian hotspots influenced by mining activity. The aim of the current study was to describe soil yeast communities in a post-mining site with revegetated and native areas, along Neotropical Savanna and Atlantic Forest biomes. Yeast communities were described using a culture-based method and estimator-based species accumulation curves, and their associations with environmental characteristics were assessed using multivariate analysis. The results indicate a greater species richness for yeast communities in the revegetated area. We identified 37 species describing 86% of the estimated richness according to Chao2. Ascomycetous yeasts dominated over basidiomycetous species. Candida maltosa was the most frequent species in two phytocenoses. Red-pigmented yeasts were frequent only in the summer. The main soil attributes affecting yeast communities were texture and micronutrients. In conclusion, each phytocenosis showed a particular assemblage of species as a result of local environmental phenomena. The species richness in a Revegetated area points to a possible ecological role of yeast species in environmental recovery. This study provided the first comprehensive inventory of soil yeasts in major phytocenoses in Minas Gerais, Brazil.

Molecular diversity of arbuscular mycorrhizal fungal communities across the gradient of alkaline Fe ore tailings, revegetated waste rock to natural soil sites

Arbuscular mycorrhizal (AM) fungi are important to the establishment of native vegetation for mined land rehabilitation, particularly in semi-arid and infertile landscapes. However, the information has been scarce about the colonization of AM fungal community in alkaline magnetite Fe ore tailing sites (without toxic metal (loid) contamination). The present study has characterized the diversity of AM fungi across typical domains of a magnetite Fe ore mine located in 200 km south-east of Geraldton, Western Australia, by adopting high throughput Illumina Miseq sequencing. The investigated domains included two tailing sites without top soil covering (T1 and T2), a rehabilitated area of tailings with top soil covering (R1), a revegetated waste rock area (R2), and two native undisturbed soil sites (S1 and S2). The results indicated that the T1/T2 sites had different AM fungal community structure, compared with R1/R2 and S1/S2 sites. The dominant families were Glomeraceae, Claroideoglomeraceae, Archaeosporaceae, Ambisporaceae, and Paraglomeraceae, with Paraglomeraceae (more than 50%) as the most abundant in the T1/T2 and R1/R2 sites. At genus level, Ambispora spp. and Archaeospora spp. were rich in T1/T2 sites (> 10%), while Glomus spp. were preferably dominant in S1/S2 sites (> 10%). Furthermore, amorphous Fe and available P were found to explain the variations associated with AM fungal community composition, particularly the abundance of Archaeosporaceae and Glomeraceae. The study revealed the AM fungal community composition shift across the gradient of Fe ore mine sites, as well as the effects of revegetation on AM fungal community development. The findings indicate the possible restoration of AM fungal community in the tailings undergoing revegetation, and potential adoption of indigenous AM fungi to rapid phytostabilization of the Fe ore tailings under semi-arid climatic conditions.