Plant Communities Rather than Soil Properties Structure Arbuscular Mycorrhizal Fungal Communities along Primary Succession on a Mine Spoil

Contrasting roles of plant, bacterial, and fungal diversity in soil organic carbon accrual during ecosystem restoration: A meta-analysis

Plant and microbial diversity plays vital roles in soil organic carbon (SOC) accumulation during ecosystem restoration. However, how soil microbial diversity mediates the positive effects of plant diversity on carbon accumulation during vegetation restoration remains unclear. We conducted a large-scale meta-analysis with 353 paired observations from 65 studies to examine how plant and microbial diversity changed over 0-160 years of natural restoration and its connection to SOC accrual in the topsoil (0-10 cm). Results showed that natural restoration significantly increased plant aboveground biomass (122.09 %), belowground biomass (153.05 %), and richness (21.99 %) and SOC accumulation (32.34 %) but had no significant impact on microbial diversity. Over time, bacterial and fungal richness increased and then decreased. The responses of major microbial phyla, in terms of relative abundance, varied across restoration and ecosystem types. Specifically, Ascomycota and Zygomycota decreased more under farmland abandonment than under grazing exclusion. In forest, Bacteroidetes, Ascomycota, and Zygomycota significantly decreased after natural restoration. The increase in SOC and Basidiomycota was higher in forest than in grassland. Based on standardized estimates, structural equation modeling showed that plant diversity had the highest positive effect (0.55) on SOC accrual, and while fungal diversity (0.15) also had a positive effective, bacterial diversity (-0.20) had a negative effect. Plant diversity promoted SOC accumulation by directly impacting biomass and soil moisture and total nitrogen and indirectly influencing soil microbial richness. This meta-analysis highlights the significant roles of plant diversity and microbial diversity in carbon accumulation during natural restoration and elucidates their relative contributions to carbon accumulation, thereby aiding in more precise predictions of soil carbon sequestration.

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.

The structure of forest vegetation on industrial landfills of different ages

The purpose of the research is to describe plant community formation on the quarry surfaces to determine a path for optimal revegetation. To achieve the goal, the studies determined soil pH, the content of skeletal fraction, basal respiration, and performed the acidimetric assessment of CO₂. The research program aimed to investigate the peculiarities of plant communities' formation in areas with different degrees of revitalization and investigate the influence of soil cover on plant associations. Results showed that the average basal soil respiration rate on the quarry was extremely low (about 0.3 mg CO₂/g of soil/h). The CO₂ content in the carbonate ranged from 0.07% to 0.7%, with the higher figures observed in older Kuzbass rather than Mosbass and Sokolovsky quarries. An analysis of soil samples from three quarries revealed four plant groups at sites associated with the prevalence of specific fractions, such as gravel, sand, silt, and stony soil. Given that Kuzbass is the oldest open-pit mine, forest vegetation species dominate here in the surveyed areas (>40%), and this feature is typical of gravel soils. The dominant species present on the gravel substrate were downy birch (Betula pubescens), common hornbeam (Carpinus betulus), European oak (Quercus robur), Siberian spruce (Picea obovata), common juniper (Juniperus communis), Siberian larch (Larix sibirica), common pine (Pinus), and Siberian fir (Abies sibirica). Mosbass is also characterized by a diversity of similar species, though work on mineral mining there ended in 2009, more recently than in other sites. Stony and sandy soil fractions predominated in the Sokolovsky quarry, although other studied substrates were also present.

Isolation and identification of arbuscular mycorrhizal fungi from an abandoned uranium mine and their role in soil-to-plant transfer of radionuclides and metals

Arbuscular mycorrhizal fungi were recovered from soil samples from the naturally radioactive soil at the long-abandoned South Terras uranium mine in Cornwall, UK. Species of Rhizophagus, Claroideoglomus, Paraglomus, Septoglomus, and Ambispora were recovered, and pot cultures from all except Ambispora were established. Cultures were identified to species level using morphological observation and rRNA gene sequencing combined with phylogenetic analysis. These cultures were used in pot experiments designed with a compartmentalised system to assess the contribution of fungal hyphae to the accumulation of essential elements, such as copper and zinc, and non-essential elements, such as lead, arsenic, thorium, and uranium into root and shoot tissues of Plantago lanceolata. The results indicated that none of the treatments had any positive or negative impact on shoot and root biomass. However, Rhizophagus irregularis treatments showed higher accumulation of copper and zinc in shoots, while R. irregularis and Septoglomus constrictum enhanced arsenic accumulation in roots. Moreover, R. irregularis increased uranium concentration in roots and shoots of the P. lanceolata plant. This study provides useful insight into fungal-plant interactions that determine metal and radionuclide transfer from soil into the biosphere at contaminated sites such as mine workings.

Accuracy of mutual predictions of plant and microbial communities vary along a successional gradient in an alpine glacier forefield

Receding glaciers create virtually uninhabited substrates waiting for initial colonization of bacteria, fungi and plants. These glacier forefields serve as an ideal ecosystem for studying transformations in community composition and diversity over time and the interactions between taxonomic groups in a dynamic landscape. In this study, we investigated the relationships between the composition and diversity of bacteria, fungi, and plant communities as well as environmental factors along a successional gradient. We used random forest analysis assessing how well the composition and diversity of taxonomic groups and environmental factors mutually predict each other. We did not identify a single best indicator for all taxonomic and environmental properties, but found specific predictors to be most accurate for each taxon and environmental factor. The accuracy of prediction varied considerably along the successional gradient, highlighting the dynamic environmental conditions along the successional gradient that may also affect biotic interactions across taxa. This was also reflected by the high accuracy of predictions of plot age by all taxa. Next to plot age, our results indicate a strong importance of pH and temperature in structuring microbial and plant community composition. In addition, taxonomic groups predicted the community composition of each other more accurately than environmental factors, which may either suggest that these groups similarly respond to other not measured environmental factors or that direct interactions between taxa shape the composition of their communities. In contrast, diversity of taxa was not well predicted, suggesting that community composition of one taxonomic group is not a strong driver of the diversity of another group. Our study provides insights into the successional development of multidiverse communities shaped by complex interactions between taxonomic groups and the environment.

Cooperation of arbuscular mycorrhizal fungi and bacteria to facilitate the host plant growth dependent on soil pH

Almost all plants grow well in their native soils. We hypothesized that soil microbes promote the growth of their hosts in native soils by the example of soil pH. Here, bahiagrass (Paspalum notatum Flugge) indigenous to subtropical soils was grown in the native soil (the original pH = 4.85) or in pH-adjusted soils with sulfur (pH = 3.14 or 3.34) or calcium hydroxide (pH = 6.85, 8.34, 8.52 or 8.59). Plant growth, soil chemical property, and microbial community composition were characterized to reveal the microbial taxa promoting plant growth in the native soil. Results showed that shoot biomass was the highest in the native soil, while both the decrease and increase in the soil pH reduced the biomass. Compared with other soil chemical properties, soil pH was the top edaphic factor contributing to the differentiation in arbuscular mycorrhizal (AM) fungal and bacterial communities. The top 3 most abundant AM fungal OTUs belonged to Glomus, Claroideoglomus, and Gigaspora, while the top 3 most abundant bacterial OTUs belonged to Clostridiales, Sphingomonas, and Acidothermus, respectively. Regression analyses between microbial abundances and shoot biomass revealed that the most abundant Gigaspora sp. and Sphingomonas sp. were the most promotive fungal and bacterial OTUs, respectively. The application of these two isolates to bahiagrass solely or in combination indicated that Gigaspora sp. was more promotive than Sphingomonas sp. across the soil pH gradient, and they positively interacted to enhance biomass only in the native soil. We demonstrate that microbes cooperate to facilitate host plants to grow well in their native soils with the original pH. Meanwhile, a high-throughput sequencing-guided pipeline to efficiently screen for beneficial microbes is established.

Diversity characteristics of arbuscular mycorrhizal fungi communities in the soil along successional altitudes of Helan Mountain, arid, and semi-arid regions of China

Introduction

Arbuscular mycorrhizal fungi (AMF) perform a vital role in terrestrial ecosystems.

Methods

To investigate the diversity of AMF communities on the western slope of Helan Mountain at different altitudes and their influence factors, high-throughput sequencing was used to study the structure and diversity of soil AMF communities under different environments and their interrelationships between AMF and environmental factors.

Results

The results revealed that there were significant differences (p < 0.05) in the physical and chemical properties of the soil along the different altitudes. A total of 1,145 OTUs were obtained by high-throughput sequencing, belonging to 1 phylum, 4 class, 6 orders, 13 families, 18 genera and 135 species, with the dominant genus being Glomus, which accounted for 75.27% of the relative abundance of the community. Soil AMF community structure was shown to be variable at the generic level according to NMDS analysis. Correlation analysis showed that soil pH, water content (WC), organic matter (OM), available K, available P and N were significantly correlated with AMF community diversity and species abundance (p < 0.05, p < 0.01). Based on redundancy analysis (RDA) and Monte Carlo test results, soil pH, WC and OM had highly significant effects (p < 0.01) on AMF community diversity and species abundance.

Discussion

This study investigates the relationship between AMF community structure and diversity and soil physicochemical properties at different elevations on the western slope of Helan Mountain, which is of great significance to the study of the Helan Mountain ecosystem.

AMF Inoculum Enhances Crop Yields of Zea mays L. 'Chenghai No. 618' and Glycine max L. 'Zhonghuang No. 17' without Disturbing Native Fugal Communities in Coal Mine Dump

For the agricultural development of dumps, increase in land use efficiency and protection of food security, to verify the safety, efficacy and sustainability of field-applied arbuscular mycorrhizal fungi (AMF) inoculum, and to exclude the risk of potential biological invasion, in this study, we determined the effect of AMF inoculation and intercropping patterns (maize-soybean) on the temporal dynamics of soil parameters, native AMF communities and crop yields. AMF communities were analyzed using Illumina MiSeq. A total of 448 AMF operational taxonomic units (OTUs) belonging to six genera and nine families were identified. AMF inoculation treatment significantly improved the yield of intercropping maize and increased the content of available phosphorus. AMF diversity was significantly influenced by cropping pattern and growth stage, but not by the inoculation treatment. Inoculation altered the AMF community composition in the early growth stage and facilitated a more complex AMF network in the early and late growth stages. These results indicate that AMF inoculation affects native AMF only in the early stage, and its impact on yield may be the consequence of cumulative effects due to the advantages of plant growth and nutrient uptake in the early stage.

Phenol and Polyaromatic Hydrocarbons Are Stronger Drivers Than Host Plant Species in Shaping the Arbuscular Mycorrhizal Fungal Component of the Mycorrhizosphere

Changes in soil microbial communities in response to hydrocarbon pollution are critical indicators of disturbed ecosystem conditions. A core component of these communities that is functionally adjusted to the life-history traits of the host and environmental factors consists of arbuscular mycorrhizal fungi (AMF). AMF communities associated with Poa trivialis and Phragmites australis growing at a phenol and polynuclear aromatic hydrocarbon (PAH)-contaminated site and at an uncontaminated site were compared based on LSU rDNA sequencing. Dissimilarities in species composition and community structures indicated soil pollution as the main factor negatively affecting the AMF diversity. The AMF communities at the contaminated site were dominated by fungal generalists (Rhizophagus, Funneliformis, Claroideoglomus, Paraglomus) with wide ecological tolerance. At the control site, the AMF communities were characterized by higher taxonomic and functional diversity than those exposed to the contamination. The host plant identity was the main driver distinguishing the two AMF metacommunities. The AMF communities at the uncontaminated site were represented by Polonospora, Paraglomus, Oehlia, Nanoglomus, Rhizoglomus, Dominikia, and Microdominikia. Polonosporaceae and Paraglomeraceae were particularly dominant in the Ph. australis mycorrhizosphere. The high abundance of early diverging AMF could be due to the use of primers able to detect lineages such as Paraglomeracae that have not been recognized by previously used 18S rDNA primers.

Metabarcoding analysis of the soil fungal community to aid the conservation of underexplored church forests in Ethiopia

Most of the Dry Afromontane forests in the northern part of Ethiopia are located around church territories and, hence, are called church forests. These forests are biodiversity islands and provide key ecosystem services to local communities. A previous study of church forest fungal species was based on sporocarp collections. However, to obtain a complete picture of the fungal community, the total fungal community present in the soil needs to be analyzed. This information is important to integrate church forests into global biodiversity conservation strategies and to understand what actions are required to conserve church forests and their biological components, including fungi, which are known for their exceptionally high diversity levels. We assessed soil fungal communities in three church forests using ITS2 rDNA metabarcoding. In total, 5152 fungal operational taxonomic units representing 16 fungal phyla were identified. Saprotrophs followed by ectomycorrhizal fungi and animal pathogens dominated fungal communities. Significant differences in diversity and richness were observed between forests. Non-metric multidimensional scaling confirmed that fungal community composition differed in each forest. The composition was influenced by climatic, edaphic, vegetation, and spatial variables. Linear relationships were found between tree basal area and the abundance of total fungi and trophic groups. Forest management strategies that consider cover, tree density, enrichment plantations of indigenous host tree species, and environmental factors would offer suitable habitats for fungal diversity, production, and function in these forest systems. The application of the baseline information obtained in this study could assist other countries with similar forest conservation issues due to deforestation and forest fragmentation.

Restoration of vegetation around mining enterprises

This paper is devoted to the restoration of vegetation around mining areas on the example of two land-reclamation zones in the Borodinsky coal mine during spring-summer of 2011-2021. Analysis of vegetation in this area has shown that indicators of spontaneous plant diversity in plots No. 1 and No. 2 were considered moderate in both layers (H < 2.5). Underwood and seeding diversity indices at pre-mining sites were ranked high, reaching 4.01-4.25 and 3.78-3.82, respectively. The analysis of the biological diversity of the flora in the undergrowth of the 12-year-old plot revealed approximately 29 spontaneous plant species belonging to 25 genera and 18 families. The most significant number of species found was found from the family Euphorbia, Cereals, and Legumes. At the 18-year-old site, the number and diversity of plant species (38 species) belonging to 38 genera and 27 families are slightly larger, with the most significant number of species within Euphorbiaceae and Poaceae, Asteraceae, Rubiaceae and Leguminosae. Saplings of various tree species from the Euphorbia and Leguminous family, such as Euphorbia cyparissias L., E. fischeriana Steud., Desmodium triflorum L., Indigofera gerardiana (Wall.) Baker, Robinia viscosa Vent. grew well in both plots. Many other spontaneous species of trees were also found in small populations at the 18-year-old site, namely, Pinus sylvestris L., Salix alba L., Populus alba L., and P. tremula L. In contrast to the younger site, some seedlings of small trees like S. alba and P. tremula and terrestrial ferns such as common bracken (Pteridium aquilinum (L.) Kuhn) and adiantum capillus-veneris L. prevailed in the older site.

Identification of land reclamation stages based on succession characteristics of rehabilitated vegetation in the Pingshuo opencast coal mine

Land reclamation is a dynamic ecological restoration process, and rehabilitated vegetation requires a certain amount of time to develop, stabilize and mature. The development characteristics of rehabilitated vegetation at different land reclamation stages are significantly different, and these differences can be used to identify the key stages of land reclamation. In this study, normalized differential vegetation index (NDVI) time series data from the western dump of the Pingshuo opencast coal area on the Loess Plateau from 1989 to 2018 were collected and analyzed by fluctuation analysis and filter processing with the Best Index Slope Extraction and Wavelet Transform (BISE-WT) filter to reveal the succession characteristics of rehabilitated vegetation. Then, the key periods of land reclamation under different vegetation types (arbor, shrub, arbor-shrub, and grass) in the dump were determined by S-logistic function fitting and derivative analyses. The NDVI time series changes in land parcels reclaimed in different years exhibited different interannual change characteristics. Based on the number of years required for the rehabilitated vegetation to reach a stable state, the average development period of land reclamation in eligible units in the mining dumps was thirteen years, including ten years in the rapid development period and three years in the steady development period. The differences in land reclamation periods among the different vegetation types were significant (α = 0.05), and the number of years required for each period mainly followed the order of arbor > arbor-shrub > shrub > grass. Analyzing the vegetation succession characteristics and identifying the key periods of land reclamation for different vegetation types is conducive to dynamically evaluating land reclamation effects and is expected to provide a basis for strengthening the implementation of manual intervention measures in reclaimed mining areas.

Fungal Perspective of Pine and Oak Colonization in Mediterranean Degraded Ecosystems

Forest restoration has become one of the most important challenges for restoration ecology in the recent years. In this regard, soil fungi are fundamental drivers of forest ecosystem processes, with significant implications for plant growth and survival. However, the post-disturbance recovery of belowground communities has been rarely assessed, especially in highly degraded systems such as mines. Our aim was to compare forests and mined systems for biomass and structure of fungal communities in soil during early stages of tree establishment after disturbance. We performed ergosterol analysis and PacBio and Illumina sequencing of internal transcribed spacer 2 amplicons across soil layers in P. sylvestris, Q. robur and Q. ilex (holm oak) forests and naturally revegetated mined sites. In pine forests, total fungal biomass was significantly higher in litter and humus compared to mineral layers, with dominance of the mycorrhizal genera Tomentella, Inocybe and Tricholoma. Conversely, in oak forests the most abundant mycorrhizal genera were Tomentella, Cortinarius and Sebacina, but the biomass of saprotrophic fungi was greater in the litter layer compared to mycorrhizal fungi, with the genus Preussia being the most abundant. In the revegetated mined sites, ectomycorrhizal fungi dominated in the humus and mineral layers, with the mycorrhizal genus Oidiodendron being dominant. In contrast, in holm oak forests saprotrophic fungi dominated both soil humus and mineral layers, with the genera of Alternaria, Bovista and Mycena dominating the soil humus forest layer, while the genus Cadophora dominated the mineral layer. The habitat-specific differences in soil fungal community composition and putative functions suggest that an understanding of soil–plant–microbial interactions for different tree species and use of specific soil/litter inoculum upon planting/seeding might help to increase the effectiveness of tree restoration strategies in Mediterranean degraded sites.

Alterations in Arbuscular Mycorrhizal Community Along a Chronosequence of Teak (Tectona grandis) Plantations in Tropical Forests of China

Arbuscular mycorrhizal (AM) fungi play a crucial role in promoting plant growth, enhancing plant stress resistance, and sustaining a healthy ecosystem. However, little is known about the mycorrhizal status of teak plantations. Here, we evaluated how the AM fungal communities of rhizosphere soils and roots respond to different stand ages of teak: 22, 35, 45, and 55-year-old from the adjacent native grassland (CK). A high-throughput sequencing method was used to compare the differences in soil and root AM fungal community structures. In combination with soil parameters, mechanisms driving the AM fungal community were revealed by redundancy analysis and the Mantel test. Additionally, spore density and colonization rates were analyzed. With increasing stand age, the AM fungal colonization rates and spore density increased linearly. Catalase activity and ammonium nitrogen content also increased, and soil organic carbon, total phosphorous, acid phosphatase activity, available potassium, and available phosphorus first increased and then decreased. Stand age significantly changed the structure of the AM fungal community but had no significant impact on the diversity of the AM fungal community. However, the diversity of the AM fungal community in soils was statistically higher than that in the roots. In total, nine and seven AM fungal genera were detected in the soil and root samples, respectively. The majority of sequences in soils and roots belonged to Glomus. Age-induced changes in soil properties could largely explain the alterations in the structure of the AM fungal community along a chronosequence, which included total potassium, carbon-nitrogen ratio, ammonium nitrogen, catalase, and acid phosphatase levels in soils and catalase, acid phosphatase, pH, and total potassium levels in roots. Soil nutrient availability and enzyme activity were the main driving factors regulating the shift in the AM fungal community structure along a chronosequence of the teak plantations.

Deciphering the dynamics of glomalin and heavy metals in soils contaminated with hazardous municipal solid wastes

Heavy metals (HMs) accumulation in the soils poses risks towards the environment and health. Glomalin related soil protein (GRSP) produced by arbuscular mycorrhizal fungi (AMF) has metal-sorption and soil aggregation properties and is critical in the survival of plants and AMF. For the first time, this study attempted to examine the GRSP mediated bio-stabilization of HMs in soils contaminated with municipal solid wastes (MSW). The content and interrelationship of GRSP and HMs, along with soil physicochemical properties were studied in 20 different soil samples from the dumping site. Higher amount of GRSP indicated potential bio-stabilization of HMs at some sites. GRSP exhibited weak positive correlation with essential (Zn, Cu) and toxic HMs (Cd, Ni). Cr and Mn were possibly sequestered in AMF structures and thus found to be negatively correlated with GRSP. The positive correlation observed between GRSP and soil nutrients like N, P and soil organic carbon (SOC) indicating potential of AMF-GRSP in sustaining soil health. Results revealed that AMF residing at contaminated sites produced higher amount of GRSP potentially to bio-stabilize the HMs, and reduce their bioavailability and also facilitate SOC sequestration.

Effects of Soil Properties and Plant Diversity on Soil Microbial Community Composition and Diversity during Secondary Succession

Soil microbial communities play an important role in maintaining the ecosystem during forest secondary succession. However, the underlying mechanisms that drive change in soil microbial community structures during secondary succession remain poorly defined in species-rich subtropical coniferous forests. In this study, Illumina high-throughput sequencing was used to analyze the variations in soil microbial community structures during forest secondary succession in subtropical coniferous forests in China. The role of soil properties and plant diversity in affecting soil bacterial and fungal communities was determined using random forest and structural equation models. Highly variable soil microbial diversity was observed in different stages of secondary succession. Bacterial community diversity rose from early to middle and late successional stages, whereas fungal community diversity increased from early to middle successional stages and then declined in the late stage. The relative abundance of Acidobacteria, Gemmatimonadetes, Eremiobacterota(WPS-2), Rokubacteria, and Mortierellomycota increased during succession, whereas the relative abundance of Ascomycota and Mucoromycota decreased. The community composition and diversity of the soil microbial community were remarkably influenced by plant diversity and soil properties. Notably, tree species richness (TSR) displayed a significant and direct correlation to the composition and diversity of both bacterial and fungal communities. The carbon-to-nitrogen (C:N) ratio had a direct impact on the bacterial community composition and diversity, and pH had a marked impact on the fungal community composition and diversity. Furthermore, succession stage and plant diversity indirectly impacted the composition and diversity of soil bacterial and fungal communities via soil properties. Overall, it can be concluded that soil intrinsic properties and plant diversity might jointly drive the changes in soil microbial community composition and diversity during secondary succession of subtropical coniferous forests.

Grazing and mining influence the population of arbuscular mycorrhizal fungi around the opencast coal mine pit

The influence of grazing and mining on arbuscular mycorrhizal fungi (AMF) species in grassland were studied around the opencast coal mine pit. The two sampling transects had been designed which was located in the grazing area and in the non-grazing area in the grassland on the north side of the opencast coal mining area. Besides, two control points with the direct distance of 8 km to the opencast coal mining area have been designed. The two points are located in the inside grassland station and outside the grassland station. We collected 3 replicate rhizosphere soil in every point which is from the two transects. We analyzed the genetic diversity of AMF, measured the chemical properties and enzyme of rhizosphere soil of Cleistogenes squarrosa, and explored their correlations using redundancy analysis. And we identified the factors affecting species diversity of AMF around the mining area. Our results showed that grazing on the grassland around the opencast coal mine will aggravate soil degradation and reduce the species richness and diversity of arbuscular mycorrhizal fungi in rhizosphere soil, which can be a theoretical basis for the scientific management of the grassland around the opencast mining area.

Draft Genomes and Comparative Analysis of Seven Mangrove Rhizosphere-Associated Fungi Isolated From Kandelia obovata and Acanthus ilicifolius

Mangroves are one of the most productive and biologically diverse ecosystems, with unique plants, animals, and microorganisms adapted to the harsh coastal environments. Although fungi are widely distributed in the mangrove ecosystem and they are playing an important role in the decomposition of organic matter, their genomic profiles are still poorly understood. In this study, we isolated seven Ascomycota fungi (Westerdykella dispersa F012, Trichoderma lixii F014, Aspergillus tubingensis F023, Penicillium brefeldianum F032, Neoroussoella solani F033, Talaromyces fuscoviridis F034, and Arthrinium marii F035) from rhizospheres of two mangroves of Kandelia obovata and Acanthus ilicifolius. We sequenced and assembled the whole genome of these fungi, resulting in size ranging from 29 to 48 Mb, while contig N50 from 112 to 833 Kb. We generated six novel fungi genomes except A. tubingensis, and the gene completeness and genome completeness of all seven genomes are higher than 94%. Comparing with non-mangrove fungi, we found Carbohydrate-Binding Modules (CBM32), a subfamily of carbohydrate active enzymes, only detected in two mangrove fungi. Another two subfamilies, Glycoside Hydrolases (GH6) and Polysaccharide Lyases (PL4), were significantly different in gene copy number between K. obovata and A. ilicifolius rhizospheres (P-value 0.041 for GH6, 0.047 for PL4). These findings may indicate an important influence of mangrove environments or hosts on the ability of decomposition in rhizosphere fungi. Secondary metabolite biosynthesis gene clusters were detected and we found the mangrove fungi averagely contain 18 Type I Polyketide (t1pks) synthase, which was significantly higher than 13 in non-mangrove fungi (P-value 0.048), suggesting their potential roles in producing bioactive compounds that important for fungi development and ecology. We reported seven mangrove-associated fungal genomes in this study and compared their carbohydrate active enzymes and secondary metabolites (SM) genes with those of non-mangrove fungi, and the results suggest that there are differences in genetic information among fungi in different habitats.

16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya

Prokaryotic communities play key roles in biogeochemical transformation and cycling of nutrients in the productive mangrove ecosystem. In this study, the vertical distribution of rhizosphere bacteria was evaluated by profiling the bacterial diversity and community structure in the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) from Mida Creek and Gazi Bay, Kenya, using DNA-metabarcoding. Alpha diversity was not significantly different between sites, but, significantly higher in the rhizospheres of S. alba and R. mucronata in Gazi Bay than in Mida Creek. Chemical parameters of the mangrove sediments significantly correlated inversely with alpha diversity metrics. The bacterial community structure was significantly differentiated by geographical location, mangrove species and sampling depth, however, differences in mangrove species and sediment chemical parameters explained more the variation in bacterial community structure. Proteobacteria (mainly Deltaproteobacteria and Gammaproteobacteria) was the dominant phylum while the families Desulfobacteraceae, Pirellulaceae and Syntrophobacteraceae were dominant in both study sites and across all mangrove species. Constrained redundancy analysis indicated that calcium, potassium, magnesium, electrical conductivity, pH, nitrogen, sodium, carbon and salinity contributed significantly to the species–environment relationship. Predicted functional profiling using PICRUSt2 revealed that pathways for sulfur and carbon metabolism were significantly enriched in Gazi Bay than Mida Creek. Overall, the results indicate that bacterial community composition and their potential function are influenced by mangrove species and a fluctuating influx of nutrients in the mangrove ecosystems of Gazi Bay and Mida Creek.

The genome of Geosiphon pyriformis reveals ancestral traits linked to the emergence of the arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal fungi (AMF) (subphylum Glomeromycotina)¹ are among the most prominent symbionts and form the Arbuscular Mycorrhizal symbiosis (AMS) with over 70% of known land plants.^2,3 AMS allows plants to efficiently acquire poorly soluble soil nutrients⁴ and AMF to receive photosynthetically fixed carbohydrates. This plant-fungus symbiosis dates back more than 400 million years⁵ and is thought to be one of the key innovations that allowed the colonization of lands by plants.⁶ Genomic and genetic analyses of diverse plant species started to reveal the molecular mechanisms that allowed the evolution of this symbiosis on the host side, but how and when AMS abilities emerged in AMF remain elusive. Comparative phylogenomics could be used to understand the evolution of AMS.^7,8 However, the availability of genome data covering basal AMF phylogenetic nodes (Archaeosporales, Paraglomerales) is presently based on fragmentary protein coding datasets.⁹Geosiphon pyriformis (Archaeosporales) is the only fungus known to produce endosymbiosis with nitrogen-fixing cyanobacteria (Nostoc punctiforme) presumably representing the ancestral AMF state.^10-12 Unlike other AMF, it forms long fungal cells ("bladders") that enclose cyanobacteria. Once in the bladder, the cyanobacteria are photosynthetically active and fix nitrogen, receiving inorganic nutrients and water from the fungus. Arguably, G. pyriformis represents an ideal candidate to investigate the origin of AMS and the emergence of a unique endosymbiosis. Here, we aimed to advance knowledge in these questions by sequencing the genome of G. pyriformis, using a re-discovered isolate.

Codependency between plant and arbuscular mycorrhizal fungal communities: what is the evidence?

That arbuscular mycorrhizal (AM) fungi covary with plant communities is clear, and many papers report nonrandom associations between symbiotic partners. However, these studies do not test the causal relationship, or 'codependency', whereby the composition of one guild affects the composition of the other. Here we outline underlying requirements for codependency, compare important drivers for both plant and AM fungal communities, and assess how host preference - a pre-requisite for codependency - changes across spatiotemporal scales and taxonomic resolution for both plants and AM fungi. We find few examples in the literature designed to test for codependency and those that do have been conducted within plots or mesocosms. Also, while plants and AM fungi respond similarly to coarse environmental filters, most variation remains unexplained, with host identity explaining less than 30% of the variation in AM fungal communities. These results combined question the likelihood of predictable co-occurrence, and therefore evolution of codependency, between plant and AM fungal taxa across locations. We argue that codependency is most likely to occur in homogeneous environments where specific plant - AM fungal pairings have functional consequences for the symbiosis. We end by outlining critical aspects to consider moving forward.

Soil Fungal Communities under Pinus patula Schiede ex Schltdl. & Cham. Plantation Forests of Different Ages in Ethiopia

The cultivation of plantation forests is likely to change the diversity and composition of soil fungal communities. At present, there is scant information about these communities in Ethiopian plantation forest systems. We assessed the soil fungal communities in Pinus patula Schiede ex Schltdl. & Cham. stands aged 5, 11, or 36-years-old using DNA metabarcoding of ITS2 amplicons. The ecological conditions of each plot, such as climate, altitude, and soil, were similar. Stand age and soil fertility influenced soil fungal species diversity and ecological guilds. In total, 2262 fungal operational taxonomic units were identified, of which 2% were ectomycorrhizal (ECM). The diversity of ECM fungi was higher in the 5 and 36-year-old stands than in the 11-year-old P. patula stands. Contrary to our expectations, a high level of ECM species diversity was observed in young stands, suggesting that these ECM species could compensate for the effects of nutrient stress in these stands. Our results also suggested that the abundance of plant pathogens and saprotrophs was not affected by stand age. This study provides baseline information about fungal community changes across tree stands of different ages in P. patula plantations in Ethiopia that are likely related to ECM fungi in young stands where relatively low soil fertility prevails. However, given that the plots were established in a single stand for each age class for each treatment, this study should be considered as a case study and, therefore, caution should be exercised when applying the conclusions to other stands.

The reclaimed coal mine ecosystem diverges from the surrounding ecosystem and reaches a new self-sustaining state after 20-23 years of succession in the Loess Plateau area, China

Whether or not the completely destroyed ecosystem would follow a succession trajectory towards the surrounding forest ecosystem after restoration remains debatable. Here, a comprehensive dataset of thirty-five ecosystem functions were measured on five reclaimed opencast coal mine forest plots (two Robinia pseudoacacia - Pinus tabuliformis mixed forests with different technosol conditions: RP_T and RP_M; one R. pseudoacacia - Ulmus pumila - Ailanthus altissima mixed forest: RUA; one Picea meyeri - Picea wilsonii - Hippophae rhamnoides mixed forest: PPH; one R. pseudoacacia monoculture forest: RM) and one natural forest plot (Populus simonii monoculture forest: PM) in Pingshuo opencast coal mine, Shanxi Province, China. These functions were employed to examine the reclamation effects among plots in terms of four management scenarios (i.e., biomass productivity, carbon sequestration, general biodiversity conservation and nutrient accumulation) and to determine the affinities between reclaimed ecosystem and its native counterpart according to Bray Curtis Distance Algorithm. The results showed that after 20-23 years of succession, thirty-five ecosystem functions differed among plots and eight highest ecosystem functions were found in RP_T and RP_M (P < 0.05). In scenarios of biomass productivity, carbon sequestration, general biodiversity conservation and nutrient accumulation scenarios, RP_M scored 0.645, 0.470, 0.467 and 0.578, respectively. Accordingly, RP_T scored 0.458, 0.447, 0.405 and 0.515, respectively. Consequently, RP_T and RP_M had the highest scores in the four management objectives compared to other plots. With regard to the ecosystem affinities, RP_T was analogous to RP_M. Similarly, RUA and PPH resembled PM and RM, respectively. Overall, the pioneer tree species determined the reclamation quality in the dump in the long term, which could be referred as the "trigger effect" in the succession trajectory in reclaimed ecosystem, and the reclaimed coal mine ecosystem diverged from the surrounding ecosystem and reached a new self-sustaining state after 20-23 years of succession.

Influence of Citrus Scion/Rootstock Genotypes on Arbuscular Mycorrhizal Community Composition under Controlled Environment Condition

Citrus is vegetatively propagated by grafting for commercial production, and most rootstock cultivars of citrus have scarce root hairs, thus heavily relying on mutualistic symbiosis with arbuscular mycorrhizal fungi (AMF) for mineral nutrient uptake. However, the AMF community composition, and its differences under different citrus scion/rootstock genotypes, were largely unknown. In this study, we investigated the citrus root-associated AMF diversity and richness, and assessed the influence of citrus scion/rootstock genotypes on the AMF community composition in a controlled condition, in order to exclude interferences from environmental factors and agricultural practices. As a result, a total of 613,408 Glomeromycota tags were detected in the citrus roots, and 46 AMF species were annotated against the MAARJAM database. Of these, 39 species belonged to Glomus, indicating a dominant role of the Glomus AMF in the symbiosis with citrus. PCoA analysis indicated that the AMF community’s composition was significantly impacted by both citrus scion and rootstock genotypes, but total samples were clustered according to rootstock genotype rather than scion genotype. In addition, AMF α diversity was significantly affected merely by rootstock genotype. Thus, rootstock genotype might exert a greater impact on the AMF community than scion genotype. Taken together, this study provides a comprehensive insight into the AMF community in juvenile citrus plants, and reveals the important effects of citrus genotype on AMF community composition.

Arbuscular Mycorrhizal Fungal Assemblages Significantly Shifted upon Bacterial Inoculation in Non-Contaminated and Petroleum-Contaminated Environments

Arbuscular mycorrhizal fungi (AMF) have been shown to reduce plant stress and improve their health and growth, making them important components of the plant-root associated microbiome, especially in stressful conditions such as petroleum hydrocarbons (PHs) contaminated environments. Purposely manipulating the root-associated AMF assemblages in order to improve plant health and modulate their interaction with the rhizosphere microbes could lead to increased agricultural crop yields and phytoremediation performance by the host plant and its root-associated microbiota. In this study, we tested whether repeated inoculations with a Proteobacteria consortium influenced plant productivity and the AMF assemblages associated with the root and rhizosphere of four plant species growing either in non-contaminated natural soil or in sediments contaminated with petroleum hydrocarbons. A mesocosm experiment was performed in a randomized complete block design in four blocks with two factors: (1) substrate contamination (contaminated or not contaminated), and (2) inoculation (or not) with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over four months, after which the effect of treatments on plant biomass and petroleum hydrocarbon concentrations in the substrate were determined. MiSeq amplicon sequencing, targeting the 18S rRNA gene, was used to assess AMF community structures in the roots and rhizosphere of plants growing in both contaminated and non-contaminated substrates. We also investigated the contribution of plant identity and biotope (plant roots and rhizospheric soil) in shaping the associated AMF assemblages. Our results showed that while inoculation caused a significant shift in AMF communities, the substrate contamination had a much stronger influence on their structure, followed by the biotope and plant identity to a lesser extent. Moreover, inoculation significantly increased plant biomass production and was associated with a decreased petroleum hydrocarbons dissipation in the contaminated soil. The outcome of this study provides knowledge on the factors influencing the diversity and community structure of AMF associated with indigenous plants following repeated inoculation of a bacterial consortium. It highlights the dominance of soil chemical properties, such as petroleum hydrocarbon presence, over biotic factors and inputs, such as plant species and microbial inoculations, in determining the plant-associated arbuscular mycorrhizal fungi communities.

Arbuscular mycorrhizal and microbial profiles of an aged phenol-polynuclear aromatic hydrocarbon-contaminated soil

Arbuscular mycorrhizal fungi (AMF) are ubiquitous, obligatory plant symbionts that have a beneficial influence on plants in contaminated environments. This study focused on evaluating the biomass and biodiversity of the AMF and microbial communities associated with Poa trivialis and Phragmites australis plants sampled at an aged site contaminated with phenol and polynuclear aromatic hydrocarbons (PAHs) and an uncontaminated control site. We analyzed the soil phospholipid fatty acid profile to describe the general structure of microbial communities. PCR-denaturing gradient gel electrophoresis with primers targeting the 18S ribosomal RNA gene was used to characterize the biodiversity of the AMF communities and identify dominant AMF species associated with the host plants in the polluted and control environments. The root mycorrhizal colonization and AMF biomass in the soil were negatively affected by the presence of PAHs and phenol, with no significant differences between the studied plant species, whereas the biodiversity of the AMF communities were influenced by the soil contamination and plant species. Soil contamination was more detrimental to the biodiversity of AMF communities associated with Ph. australis, compared to P. trivialis. Both species favored the development of different AMF species, which might be related to the specific features of their different root systems and soil microbial communities. The contaminated site was dominated by AMF generalists like Funneliformis and Rhizophagus, whereas in the control site Dominikia, Archaeospora, Claroideoglomus, Glomus, and Diversispora were also detected.

Succession in arbuscular mycorrhizal fungi can be attributed to a chronosequence of Cunninghamia lanceolata

Arbuscular mycorrhizal (AM) fungi play an important role in plant-fungi communities. It remains a central question of how the AM fungal community changes as plants grow. To establish an understanding of AM fungal community dynamics associated with Chinese fir, Chinese fir with five different growth stages were studied and 60 root samples were collected at the Jiangle National Forestry Farm, Fujian Province. A total of 76 AM fungal operational taxonomic units (OTUs) were identified by high-throughput sequencing on an Illumina Miseq platform. The genera covered by OTUs were Glomus, Archaeospora, Acaulospora, Gigaspora and Diversispora. Glomus dominated the community in the whole stage. The number and composition of OTUs varied along with the host plant growth. The number of OTUs showed an inverted V-shaped change with the host plant age, and the maximum occurred in 23-year. Overall, the basic species diversity and richness in this study were stable. Non-metric multi-dimensional scaling (NMDS) analysis based on bray-curtis distance revealed that there were remarkable differentiations between the 9-year and other stages. Besides, AM fungal community in 32-year had a significant difference with that of 23-year, while no significant difference with that of 45-year, suggesting that 32-year may be a steady stage for AM fungi associated with Chinese fir. The cutting age in 32-year may be the most favorable for microbial community. The pH, total N, total P, total K, available N, available P, available K, organic matter and Mg varied as the Chinese fir grows. According to Mantel test and redundancy analysis, available N, available P, K and Mg could exert significant influence on AM fungal communities, and these variables explained 31% of variance in the composition of AM fungal communities.

Non-symbiotic soil microbes are more strongly influenced by altered tree biodiversity than arbuscular mycorrhizal fungi during initial forest establishment

While the relationship between plant and microbial diversity has been well studied in grasslands, less is known about similar relationships in forests, especially for obligately symbiotic arbuscular mycorrhizal (AM) fungi. To assess the effect of varying tree diversity on microbial alpha- and beta-diversity, we sampled soil from plots in a high-density tree diversity experiment in Minnesota, USA, 3 years after establishment. About 3 of 12 tree species are AM hosts; the other 9 primarily associate with ectomycorrhizal fungi. We used phospho- and neutral lipid fatty acid analysis to characterize the biomass and functional identity of the whole soil bacterial and fungal community and high throughput sequencing to identify the species-level richness and composition of the AM fungal community. We found that plots of differing tree composition had different bacterial and fungal communities; plots with conifers, and especially Juniperus virginiana, had lower densities of several bacterial groups. In contrast, plots with a higher density or diversity of AM hosts showed no sign of greater AM fungal abundance or diversity. Our results indicate that early responses to plant diversity vary considerably across microbial groups, with AM fungal communities potentially requiring longer timescales to respond to changes in host tree diversity.

Mycorrhizal fungal community structure in tropical humid soils under fallow and cropping conditions

Little is known to what extent soil biota, in particular, the mycorrhizae are altered through different fallow durations/types in tropical soils. We found that soil-N, -C, -Al, -K and -Ca contents significantly differed due to the fallow durations/types. Subsequently, the effects of fallow types and soil depths on the diversity, species richness and community structure of arbuscular mycorrhizal (AM) fungi were examined. A higher AM species richness was identified in the cropping than in forest fallow fields, suggesting a positive cropping feedback on the AM community composition. Distribution of the AM species was positively related to soil properties, specifically soil-pH, and soil-Pi, -Ca and -Mg contents. The soil properties conjointly accounted for 78.5% of explained variation in the AM community composition, signifying that the main factors altering the community structure under different fallow and cropping systems were the soil properties. Among the soil chemical characteristics, the soil-pH disclosed a significant explained variation in the AM community composition in the topsoil layer under the short fallow. Structural modeling equation to understand multiple predictive pathways that connect soil properties, fallow practices and AM community structures indicated that soil-C, -N and -Ca contents were highlighted as important factors influencing the AM community compositions.

Asymmetric response of root-associated fungal communities of an arbuscular mycorrhizal grass and an ectomycorrhizal tree to their coexistence in primary succession

The arbuscular mycorrhizal (AM) grass Calamagrostis epigejos and predominantly ectomycorrhizal (EcM) tree Salix caprea co-occur at post-mining sites spontaneously colonized by vegetation. During succession, AM herbaceous vegetation is replaced by predominantly EcM woody species. To better understand the interaction of AM and EcM plants during vegetation transition, we studied the reciprocal effects of these species' coexistence on their root-associated fungi (RAF). We collected root and soil samples from three different microenvironments: stand of C. epigejos, under S. caprea canopy, and contact zone where roots of the two species interacted. RAF communities and mycorrhizal colonization were determined in sampled roots, and the soil was tested for EcM and AM inoculation potentials. Although the microenvironment significantly affected composition of the RAF communities in both plant species, the effect was greater in the case of C. epigejos RAF communities than in that of S. caprea RAF communities. The presence of S. caprea also significantly decreased AM fungal abundance in soil as well as AM colonization and richness of AM fungi in C. epigejos roots. Changes observed in the abundance and community composition of AM fungi might constitute an important factor in transition from AM-dominated to EcM-dominated vegetation during succession.

Application of Mycorrhiza and Soil from a Permaculture System Improved Phosphorus Acquisition in Naranjilla

Naranjilla (Solanum quitoense) is a perennial shrub plant mainly cultivated in Ecuador, Colombia, and Central America where it represents an important cash crop. Current cultivation practices not only cause deforestation and large-scale soil degradation but also make plants highly susceptible to pests and diseases. The use of arbuscular mycorrhizal fungi (AMF) can offer a possibility to overcome these problems. AMF can act beneficially in various ways, for example by improving plant nutrition and growth, water relations, soil structure and stability and protection against biotic and abiotic stresses. In this study, the impact of AMF inoculation on growth and nutrition parameters of naranjilla has been assessed. For inoculation three European reference AMF strains (Rhizoglomus irregulare, Claroideoglomus claroideum, and Cetraspora helvetica) and soils originating from three differently managed naranjilla plantations in Ecuador (conventional, organic, and permaculture) have been used. This allowed for a comparison of the performance of exotic AMF strains (reference strains) versus native consortia contained in the three soils used as inocula. To study fungal communities present in the three soils, trap cultures have been established using naranjilla as host plant. The community structures of AMF and other fungi inhabiting the roots of trap cultured naranjilla were assessed using next generation sequencing (NGS) methods. The growth response experiment has shown that two of the three reference AMF strains, a mixture of the three and soil from a permaculture site led to significantly better acquisition of phosphorus (up to 104%) compared to uninoculated controls. These results suggest that the use of AMF strains and local soils as inoculants represent a valid approach to improve nutrient uptake efficiency of naranjilla and consequently to reduce inputs of mineral fertilizers in the cultivation process. Improved phosphorus acquisition after inoculation with permaculture soil might have been caused by a higher abundance of AMF and the presence of Piriformospora indica as revealed by NGS. A higher frequency of AMF and enhanced root colonization rates in the trap cultures supplemented with permaculture soil highlight the importance of diverse agricultural systems for soil quality and crop production.