Fungal Community Structure Research Articles

Enhancing salt tolerance and crop growth in agricultural systems: the impact of magnetized-ionized water irrigation on soil properties, microbial communities, and cotton growth.

The development of agricultural practices requires an understanding of the improvement of salt tolerance and crop growth in agricultural systems through magnetized-ionized water irrigation. This study examined the impacts of fresh water (F), brackish water (B), magnetized-ionized fresh water (MIF), and magnetized-ionized brackish water (MIB) on soil properties and the growth of cotton seedlings through microbial analysis during the cotton seedling period. The results revealed that magnetized-ionized water irrigation improved soil water retention and promoted salt leaching. In comparison with F irrigation, plant height, leaf area index (LAI), dry matter accumulation (DM), and chlorophyll content (SPAD) levels increased by 3.61%, 4.07%, 5.76%, and 1.33%, respectively, under MIF irrigation. Similarly, when compared with B irrigation, LAI, DM, and SPAD increased by 5.13%, 6.12%, and 3.12% under MIB irrigation. Magnetized-ionized water irrigation also led to a notable rise in the relative abundance of beneficial soil bacterial communities, particularly Pseudomonas and Azoarcus, as well as fungal communities like Trichoderma, while reducing the prevalence of pathogenic fungi, such as Lasionectria, Gibberella, and Alternaria. Notably, this irrigation approach induced alterations in soil properties, and partial least squares path modeling revealed significant links between soil properties and both cotton growth and fungal community structure (with path coefficients of -0.884 and 0.693, respectively). This study elucidated the distinct effects of soil properties and growth indices on cotton yield during the seedling period, providing a crucial scientific foundation for enhancing future agricultural production through the use of magnetized-ionized water irrigation. © 2024 Society of Chemical Industry.

The Impact of Artificial Restoration of Alpine Grasslands in the Qilian Mountains on Vegetation, Soil Bacteria, and Soil Fungal Community Diversity.

To understand how the soil microbial community structure responds to vegetation restoration in alpine mining areas, this study specifically examines the grassland ecosystem in the Qianmalong mining area of the Qilian Mountains after five years of artificial restoration. High-throughput sequencing methods were employed to analyze soil bacteria and fungi microbial characteristics in diverse grassland communities. Combined with modifications in vegetation diversity as well as soil physicochemical properties, the impact of vegetation restoration on soil microbiome diversity in this alpine mining area was investigated. The findings indicated that the dominant plants were Cyperus rotundus, Carex spp., and Elymus nutans. As the extent of the grassland's restoration increased, the number of plant species, importance values, and plant community diversity showed an increasing trend. The plant functional groups were mainly dominated by Cyperaceae, followed by Poaceae. Plant height, density, plant cover, frequency, and aboveground biomass showed an increasing trend, and soil water content (SWC) increased. While soil pH and soil electrical conductivity (EC) exhibited a declining trend, available phosphorus (AP), total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (NO3-N), soil organic carbon (SOC), and soil water content (SWC) showed an increasing trend. The dominant bacterial communities were Actinobacteriota, Proteobacteria, Acidobacteriota, Chloroflexi, Firmicutes, and Gemmatimonadota, while the dominant fungal communities were Ascomycota, Mortierellomycota, Basidiomycota, unclassified_k_Fungi, and Glomeromycota. Significant differences were detected within soil microbial community composition among different degrees of restoration grasslands, with bacteria generally dominating over fungi. SWC, TP, and TN were found to be the main soil physicochemical factors affecting the distribution of soil bacterial communities' structure; however, SOC, TN, and NO3-N were the primary factors influencing the soil distribution of fungal communities. The results of this study indicate that different degrees of vegetation restoration in alpine mining areas can significantly affect soil bacterial and fungal communities, and the degree of restoration has varying effects on the soil bacteria and fungi community structure in alpine mining areas.

Temporal Dynamics of Fungal Communities in Alkali-Treated Round Bamboo Deterioration under Natural Weathering.

Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its natural elastic and aesthetic behaviors. However, little research has investigated the structure and dynamics of fungal communities on alkali-treated round bamboo during natural deterioration. In this work, high-throughput sequencing and multiple characterization methods were used to disclose the fungal community succession and characteristic alterations of alkali-treated round bamboo in both roofed and unroofed habitats throughout a 13-week deterioration period. In total, 192 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal community richness of roofed bamboo samples declined, whereas that of unroofed bamboo samples increased during deterioration. The phyla Ascomycota and Basidiomycota exhibited dominance during the entire deterioration process in two distinct environments, and the relative abundance of them combined was more than 99%. A distinct shift in fungal communities from Basidiomycota dominant in the early stage to Ascomycota dominant in the late stage was observed, which may be attributed to the increase of moisture and temperature during succession and the effect of alkali treatment. Among all environmental factors, temperature contributed most to the variation in the fungal community. The surface of round bamboo underwent continuous destruction from fungi and environmental factors. The total amount of cell wall components in bamboo epidermis in both roofed and unroofed conditions presented a descending trend. The content of hemicellulose declined sharply by 8.3% and 11.1% under roofed and unroofed environments after 9 weeks of deterioration. In addition, the contact angle was reduced throughout the deterioration process in both roofed and unroofed samples, which might be attributed to wax layer removal and lignin degradation. This study provides theoretical support for the protection of round bamboo under natural weathering.

Roles of Microbial Community and Keystone Taxa in Rice Productivity under Green Manuring in South China

Green manure (GM)–rice–rice rotation is an important management practice for improving soil fertility and rice productivity. The microbiological mechanisms for the increase in grain yield in GM–rice–rice rotation remain unclear. The responses of soil biodiversity, bacterial and fungal communities, and their interactions in the GM–rice–rice rotation were investigated based on two long-term field experiments in Gaoqiao (GQ) and Nanxian (NX) in Hunan Province, south China. Results showed that rice yields were raised by 11.79% and 15.03% under GM in GQ and NX, respectively. GM promoted Shannon diversity and Pielou’s evenness and changed the community structures of bacteria and fungi. The co-occurrence network analysis found that the percentages of negative edges were higher in GM (40.79% and 44.32% in GQ and NX, respectively) than those in the corresponding winter fallow (34.86% and 29.13% in GQ and NX, respectively) in the combined bacterial–fungal networks, suggesting more stable microbial community under GM. Moreover, GM had higher percentages of bacterial–fungal and fungal–fungal edges than winter fallow, indicating that GM increased the interaction between bacteria and fungi and fungi play more essential roles in affecting soil processes under GM. The keystone taxa in GM were positively linked with C metabolism-related enzymes and soil multifunctionality, and were important in improving soil fertility and rice productivity. We concluded that the fungal community was more sensitive to GM application than the bacterial community and that keystone taxa had important influences on soil properties and rice productivity in the GM–double-rice cropping system, which can effectively support the sustainable development of the paddy field ecosystem in southern China.

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.

Comprehensive assessment of the microbial community structure in a typical lead-zinc mine soil.

Understanding the microbial community structure in soil contaminated with heavy metals (HMs) is a precondition to conduct bioremediation in mine soil. Samples were collected from a typical lead-zinc (Pb-Zn) mine to assess the microbial community structure of the HMs concentrated in the soil. The goal was to analyze the bacterial and fungal community structures and their interactions using the 16S rRNA genes and internal transcribed spacer high-throughput sequencing. Analyses at different sampling sites showed that contamination with HMs significantly reduced the bacterial richness and diversity but increased that of the fungi. The predominant bacteria genera of Acidobacteriales, Gaiellales, Anaerolineaceae, Sulfurifustis, and Gemmatimonadaceae, and predominant fungal genera of Sordariomycetes, Talaromyces, and Mortierella were assumed as HM resistant genera in Pb-Zn mining area. The pH effect on the bacterial and fungal communities was opposite to those of Cd, Pb, and Zn. This study offers comprehensive outlooks for bacterial and fungal community structures upon multiple HM stresses in the soil around a typical Pb-Zn mine area.

Richness and community structure of arbuscular mycorrhizal fungi associated with quelites in the Sierra Sur region of Oaxaca, Mexico

Richness and community structure of arbuscular mycorrhizal fungi associated with quelites in the Sierra Sur region of Oaxaca, Mexico

Seasonal discrepancy of airborne fungal diversity and community structure in Lentinula edodes factory

ABSTRACT Understanding the composition and community of airborne mycobiota associated with fungal diseases was critical for mushroom production and disease control. In this study, we first investigated airborne fungi concentrations in different function areas of a Chinese shiitake factory. Then, high-throughput sequencing was employed to characterise the airborne fungal compositions and communities of this factory during high and low incidence seasons of shiitake artificial log rot disease (SLRD). The lowest concentration of culturable airborne fungi was observed in spawn-running greenhouse (250–450 CFU/m3), while the airborne fungi concentrations in cultivation greenhouses were up to 7,000–8,500 CFU/m3. The airborne fungal communities across distinct function areas showed convergence. The four major mushroom contaminants, Trichoderma, Penicillium, Cladosporium, and Aspergillus were the stable core fungi. Seasonal shifts in compositions, abundances, and communities of airborne fungi were systematically analysed and found to be associated with SLRD. Compared with the SLRD low incidence season, the airborne fungal communities were rich but uneven in the SLRD high incidence season, in which Trichoderma was dominant. Further analysis indicated that the favourable temperature and humidity caused the proliferation of Trichoderma and then affected the fungal communities, which presented an SLRD-seasonal variation. SLRD incidence could be significantly reduced by reasonably increasing the ambient temperature. For the first time, we comprehensively characterised the dynamics of airborne fungal communities across the SLRD occurrence in the shiitake factory. Findings here also provided valuable information for fungal exposures in the mushroom industry.

Fungal removal of cyanotoxins in constructed wetlands: The forgotten degraders

Harmful cyanobacterial blooms have increased globally, releasing hazardous cyanotoxins that threaten the safety of water resources. Constructed wetlands (CWs) are a nature-based and low-cost solution to purify and remove cyanotoxins from water. However, bio-mechanistic understanding of the biotransformation processes expected to drive cyanotoxin removal in such systems is poor, and primarily focused on bacteria. Thus, the present study aimed at exploring the fungal contribution to microcystin-LR and cylindrospermopsin biodegradation in CWs. Based on CW mesocosms, two experimental approaches were taken: a) amplicon sequencing studies were conducted to investigate the involvement of the fungal community; and b) CW fungal isolates were tested for their microcystin-LR and cylindrospermopsin degradation capabilities. The data uncovered effects of seasonality (spring or summer), cyanotoxin exposure, vegetation (unplanted, Juncus effusus or Phragmites australis) and substratum (sand or gravel) on the fungal community structure. Additionally, the arbuscular mycorrhizal fungus Rhizophagus and the endophyte Myrmecridium showed positive correlations with cyanotoxin removal. Fungal isolates revealed microcystin-LR-removal potentials of approximately 25 % in in vitro biodegradation experiments, while the extracellular chemical fingerprint of the cultures suggested a potential intracellular metabolization. The results from this study may help us understand the fungal contribution to cyanotoxin removal, as well as their ecology in CWs.

MinION Sequencing of Fungi in Sub-Saharan African Air and a Novel LAMP Assay for Rapid Detection of the Tropical Phytopathogenic Genus Lasiodiplodia.

To date, there have been no DNA-based metabarcoding studies into airborne fungi in tropical Sub-Saharan Africa. In this initial study, 10 air samples were collected onto Vaseline-coated acrylic rods mounted on drones flown at heights of 15-50 meters above ground for 10-15 min at three sites in Ghana. Purified DNA was extracted from air samples, the internal transcribed spacer (ITS) region was amplified using fungal-specific primers, and MinION third-generation amplicon sequencing was undertaken with downstream bioinformatics analyses utilizing GAIA cloud-based software (at genus taxonomic level). Principal coordinate analyses based on Bray-Curtis beta diversity dissimilarity values found no clear evidence for the structuring of fungal air communities, nor were there significant differences in alpha diversity, based on geographic location (east vs. central Ghana), underlying vegetation type (cocoa vs. non-cocoa), or height above ground level (15-23 m vs. 25-50 m), and despite the short flight times (10-15 min), ~90 operational taxonomic units (OTUs) were identified in each sample. In Ghanaian air, fungal assemblages were skewed at the phylum taxonomic level towards the ascomycetes (53.7%) as opposed to basidiomycetes (24.6%); at the class level, the Dothideomycetes were predominant (29.8%) followed by the Agaricomycetes (21.8%). The most common fungal genus in Ghanaian air was cosmopolitan and globally ubiquitous Cladosporium (9.9% of reads). Interestingly, many fungal genera containing economically important phytopathogens of tropical crops were also identified in Ghanaian air, including Corynespora, Fusarium, and Lasiodiplodia. Consequently, a novel loop-mediated isothermal amplification (LAMP) assay, based on translation elongation factor-1α sequences, was developed and tested for rapid, sensitive, and specific detection of the fungal phytopathogenic genus Lasiodiplodia. Potential applications for improved tropical disease management are considered.

Nitrogen addition changed soil fungal community structure and increased the biomass of functional fungi in Korean pine plantations in temperate northeast China

Nitrogen (N) deposition is a global environmental issue that can have significant impacts on the community structure and function in ecosystems. Fungi play a key role in soil biogeochemical cycles and their community structures are tightly linked to the health and productivity of forest ecosystems. Based on high-throughput sequencing and ergosterol extraction, we examined the changes in community structure, composition, and biomass of soil ectomycorrhizal (ECM) and saprophytic (SAP) fungi in 0–10 cm soil layer after 8 years of continuous N addition and their driving factors in a temperate Korean pine plantation in northeast China. Our results showed that N addition increased fungal community richness, with the highest richness and Chao1 index under the low N treatment (LN: 20 kg N ha−1 yr−1). Based on the FUN Guild database, we found that the relative abundance of ECM and SAP fungi increased first and then decreased with increasing N deposition concentration. The molecular ecological network analysis showed that the interaction between ECM and SAP fungi was enhanced by N addition, and the interaction was mainly positive in the ECM fungal network. N addition increased fungal biomass, and the total fungal biomass (TFB) was the highest under the MN treatment (6.05 ± 0.3 mg g−1).Overall, we concluded that N addition changed soil biochemical parameters, increased fungal activity, and enhanced functional fungal interactions in the Korean pine plantation over an 8-year simulated N addition. We need to consider the effects of complex soil conditions on soil fungi and emphasize the importance of regulating soil fungal community structure and biomass for managing forest ecosystems. These findings could deepen our understanding of the effects of increased N deposition on soil fungi in temperate forests in northern China, which can provide the theoretical basis for reducing the effects of increased N deposition on forest soil.

Bacterial and fungal community structures in Hulun Lake are regulated by both stochastic processes and environmental factors.

Microorganisms are a crucial component of lake ecosystems and significant contributors to biogeochemical cycles. However, the understanding of how primary microorganism groups (e.g., bacteria and fungi) are distributed and constructed within different lake habitats is lacking. We investigated the bacterial and fungal communities of Hulun Lake using high-throughput sequencing techniques targeting 16S rRNA and Internal Transcribed Spacer 2 genes, including a range of ecological and statistical methodologies. Our findings reveal that environmental factors have high spatial and temporal variability. The composition and community structures vary significantly depending on differences in habitats. Variance partitioning analysis showed that environmental and geographical factors accounted for <20% of the community variation. Canonical correlation analysis showed that among the environmental factors, temperature, pH, and dissolved oxygen had strong control over microbial communities. However, the microbial communities (bacterial and fungal) were primarily controlled by the dispersal limitations of stochastic processes. This study offers fresh perspectives regarding the maintenance mechanism of bacterial and fungal biodiversity in lake ecosystems, especially regarding the responses of microbial communities under identical environmental stress.IMPORTANCELake ecosystems are an important part of the freshwater ecosystem. Lake microorganisms play an important role in material circulation and energy flow owing to their unique enzymatic and metabolic capacity. In this study, we observed that bacterial and fungal communities varied widely in the water and sediments of Hulun Lake. The primary factor affecting their formation was identified as dispersal limitation during stochastic processes. Environmental and geographical factors accounted for <20% of the variation in bacterial and fungal communities, with pH, temperature, and dissolved oxygen being important environmental factors. Our findings provide new insights into the responses of bacteria and fungi to the environment, shed light on the ecological processes of community building, and deepen our understanding of lake ecosystems. The results of this study provide a reference for lake management and conservation, particularly with respect to monitoring and understanding microbial communities in response to environmental changes.

Floristic changes and environmental drivers of soil fungi and archaea in different salt-tolerant plant communities in the intertidal habitat of coastal wetlands.

Microorganisms are crucial elements of terrestrial ecosystems, which play significant roles in improving soil physicochemical properties, providing plant growth nutrients, degrading toxic and harmful chemicals, and biogeochemical cycling. Variations in the types and quantities of root exudates among different plants greatly alter soil physicochemical properties and result in variations in the diversity, structure, and function of soil microorganisms. Not much is understood about the differences of soil fungi and archaea communities for different plant communities in coastal wetlands, and their response mechanisms to environmental changes. In this study, fungal and archaea communities in soils of Suaeda salsa, Phragmites australis, and Spartina alterniflora in the intertidal habitat of coastal wetlands were selected for research. Soil fungi and archaea were analyzed for diversity, community structure, and function using high throughput ITS and 16S rRNA gene sequencing. The study revealed significant differences in fungi and archaea's diversity and community structure in the rhizosphere soil of three plant communities. At the same time, there is no significant difference in the functional groups. SOM, TP, AP, MC, EC and SOM, TN, TP, AP, MC, EC are the primary environmental determinants affecting changes in soil fungal and archaeal communities, respectively. Variations in the diversity, community structure, and ecological functions of fungi and archaea can be used as indicators characterizing the impact of external disturbances on the soil environment, providing a theoretical foundation for the effective utilization of soil microbial resources, thereby achieving the goal of environmental protection and health promotion.

Niche-dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge Mycale Grandis.

Most researches on sponge holobionts focus primarily on symbiotic microbes, yet data at the level of the sponge hologenome are still relatively scarce. Understanding of the sponge host and its microbial gene expression profiles and the host-microbes interplay in different niches represents a key aspect of sponge hologenome. Using the Hawaiian demosponge Mycale grandis in different niches as a model, i.e. on rocks, on the surface of coral Porites compressa, under alga Gracilaria salicornia, we compared the bacterial and fungal community structure, functional gene diversity, expression pattern and the host transcriptome by integrating open-format (deep sequencing) and closed-format (GeoChip microarray) high-throughput techniques. Little inter-niche variation in bacterial and fungal phylogenetic diversity was detected for M. grandis in different niches, but a clear niche-dependent variability in the functional gene diversity and expression pattern of M. grandis host and its symbiotic microbiota was uncovered by GeoChip microarray and transcriptome analyses. Particularly, sponge host genes related to innate immunity and microbial recognition showed a strong correlation with the microbial symbionts' functional gene diversity and transcriptional richness in different niches. The cross-niche variability with respect to the symbiont functional gene diversity and the transcriptional richness of M. grandis holobiont putatively reflects the interplay of niche-specific selective pressure and the symbiont functional diversity. Niche-dependent gene expression profiles of M. grandis hologenome and the host-microbes interplay were suggested though little inter-niche variation in bacterial and fungal diversity was detected, particularly the sponge innate immunity was found to be closely related to the symbiotic microbes. Altogether, these findings provide novel insights into the black box of one sponge holobiont in different niches at the hologenome level.

Changes in the Soil Microbial Community Structure and Driving Factors during Post-Fire Recovery of the Larix gmelinii Rupr. Forest in Northern China

Fire is crucial for shaping northern forest ecosystems and can affect soil microbial community structure. However, there are few studies on the long-term effects of forest fire disturbance on soil microbial community diversity. In this study, we employed high-throughput sequencing of 16S rRNA and ITS1 to assess variations in the abundance of bacterial and fungal communities in dominant populations at 1, 6, and 11 years post-fire. Furthermore, a comprehensive analysis was conducted to examine the relationship between soil microenvironmental changes and soil microbial communities after fire disturbances, considering soil physicochemical properties, including bulk density, moisture content, pH, organic carbon, total nitrogen, ammonium nitrogen, nitrate nitrogen, available potassium, and available phosphorus. We found that fire significantly increased soil pH, NO3−-N, AP, and AK contents, in which the content of NO3−-N basically recovered to the pre-fire level at 11 years after fire. The soil SOC and TN contents decreased significantly 1 year after the fire. However, compared to the unfired site, the SOC content essentially recovered 11 years after the fire, while TN content was still significantly higher 11 years after fire. Furthermore, fire changed the diversity and richness of soil microbial communities to some extent. PCoA and NMDS analyses suggested that the bacterial community structures in soil samples from different burned areas with different recovery periods exhibited similarity. However, notable differences were observed in the fungal community structures between the 1-year and 6-year post-fire study sites when compared to the unburned control site. Bacterial communities predominantly comprised Proteobacteria, Actinobacteria, and Acidobacteria, while fungal communities were mainly dominated by Ascomycota and Basidiomycota. RDA confirmed the significant roles of SOC, TN, and NO3−-N in affecting the diversity of soil microbial communities. Therefore, our study not only enhances our understanding of the long-term effects of forest fire disturbances on soil properties and soil microbial community structure, but also provides insights for further utilizing and controlling carbon and nitrogen content to regulate soil microbial activity and accelerate the recovery process of burned areas.

Differential response patterns of soil fungal and bacterial communities to typical vegetation types in the Yellow River floodplain ecosystem

Soil microorganisms are one of the primary driving factors of biogeochemical cycles in floodplain ecosystems. Vegetation type has an impact on the activities of soil microorganisms. However, it is currently unclear whether the composition and structure of soil bacterial and fungal communities in floodplain ecosystems have a consistent response pattern to vegetation communities. In this research, Illumina Mi-Seq sequencing technology was employed to study the soil fungal and bacterial communities covered by three typical vegetation communities in the Yellow River floodplain ecosystem. Our results showed that the underground biomass, total carbon (TC) and nitrogen (TN) were significantly different between the three vegetation communities. In the surface soil of summer, the Shannon index of fungi community was the highest in Tamarix chinensis (T. chinensis) and the lowest in Phragmites australis (P.australis). In autumn, the Shannon and Simpson indices of bacterial communities in surface soil were the highest in the P.australis and the lowest in the Sonchus arvensis (S.arvensis), but there was no significant difference in the β-diversity of bacterial community among the three vegetation communities. In autumn, the Chao1 index of fungal community in subsoil was the highest in P.australis and the lowest in S.arvensis, while there was no significant difference in the α-diversity of bacterial community among the three vegetation communities. In addition, there were considerable disparities in the fungal and bacteria community structure in various vegetation soils. Redundancy analysis (RDA analysis) showed that TN, TC, AP, pH, NO3 -, NH4 + and moisture content were key factors driving bacterial community structure, while TP, NH4 +, pH and moisture content were essential factors driving fungal community composition. These outcomes help to improve our understanding of the ecological model of soil fungal and bacterial community in floodplain ecosystems and give assistance in improving the role of an ecological barrier and floodplain service possibilities.

Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions.

When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions.

Fungal and bacterial communities and their associations in snow-free and snow covered (sub-)alpine Pinus cembra forest soils

BackgroundIn Europe, Pinus cembra forests cover subalpine and alpine areas and they are of high conservational and ecological relevance. These forests experience strong seasonality with alternating snow-free and snow covered periods. Although P. cembra is known for mycorrhization and mycorrhizae usually involve fungi, plants and bacteria, the community compositions of fungi and bacteria and their associations in (sub-)alpine P. cembra forests remain vastly understudied. Here, we studied the fungal and bacterial community compositions in three independent (sub-)alpine P. cembra forests and inferred their microbial associations using marker gene sequencing and network analysis. We asked about the effect of snow cover on microbial compositions and associations. In addition, we propose inferring microbial associations across a range of filtering criteria, based on which we infer well justified, concrete microbial associations with high potential for ecological relevance that are typical for P. cembra forests and depending on snow cover.ResultsThe overall fungal and bacterial community structure was comparable with regards to both forest locations and snow cover. However, occurrence, abundance, and diversity patterns of several microbial taxa typical for P. cembra forests differed among snow-free and snow covered soils, e.g. Russula, Tetracladium and Phenoliphera. Moreover, network properties and microbial associations were influenced by snow cover. Here, we present concrete microbial associations on genus and species level that were repeatedly found across microbial networks, thereby confirming their ecological relevance. Most importantly, ectomycorrhizal fungi, such as Basidioascus, Pseudotomentella and Rhizopogon, as well as saprobic Mortierella changed their bacterial association partners depending on snow cover.ConclusionThis is the first study researching fungal-bacterial associations across several (sub-)alpine P. cembra forests. The poorly investigated influence of snow cover on soil fungi and bacteria, especially those mycorrhizing P. cembra roots, but also saprobic soil organisms, underlines the relevance of forest seasonality. Our findings highlight that the seasonal impact of snow cover has significant consequences for the ecology of the ecosystem, particularly in relation to mycorrhization and nutrient cycling. It is imperative to consider such effects for a comprehensive understanding of the functioning resilience and responsiveness of an ecosystem.

Community responses of arbuscular mycorrhiza fungi to hydrological gradients in a riparian Phragmites australis wetland.

The hydrological regime is considered to be the major factor that affects the distribution of arbuscular mycorrhiza (AM) fungi in wetlands. We aimed to investigate the responses of AM fungal community to different hydrological gradients. Illumina Miseq sequencing technology was used to study the AM fungal community structure in roots and rhizosphere soils of Phragmites australis in different moisture areas (dry area, alternating wet and dry area, and flooded area) in Mengjin Yellow River wetland. The rhizosphere soils and roots hosted different AM fungal communities. In roots, the AM fungal colonization and Chao1 richness in dry area were significantly higher than that in alternating wet and dry area and flooded area, but the community composition did not vary clearly under different water conditions. In rhizosphere soils, the Chao1 richness of AM fungi in flooded area was significantly higher than that in alternating wet and dry area and dry area, and the AM fungal community structure obviously differed across different areas. The redundancy analyses indicated that changes in the AM fungal community in soils were associated with altered soil properties, and the abundance of the dominant genus Glomus was mostly positively correlated with alkali-hydrolyzable nitrogen in soils. This study helps us to understand the responses of AM fungal community to hydrological gradients in wetlands.

Effect of Biogas Slurry on the Soil Properties and Microbial Composition in an Annual Ryegrass-Silage Maize Rotation System over a Five-Year Period.

Soil health is seriously threatened by the overuse of chemical fertilizers in agricultural management. Biogas slurry is often seen as an organic fertilizer resource that is rich in nutrients, and its use has the goal of lowering the amount of chemical fertilizers used while preserving crop yields and soil health. However, the application of continuous biogas slurry has not yet been studied for its long-term impact on soil nutrients and microbial communities in a rotation system of annual ryegrass-silage maize (Zea mays). This study aimed to investigate the impacts on the chemical properties and microbial community of farmland soils to which chemical fertilizer (NPK) (225 kg ha-1), biogas slurry (150 t ha-1), and a combination (49.5 t ha-1 biogas slurry + 150 kg ha-1 chemical fertilizer) were applied for five years. The results indicated that compared to the control group, the long-term application of biogas slurry significantly increased the SOC, TN, AP, and AK values by 45.93%, 39.52%, 174.73%, and 161.54%, respectively; it neutralized acidic soil and increased the soil pH. TN, SOC, pH, and AP are all important environmental factors that influence the structural composition of the soil's bacterial and fungal communities. Chemical fertilizer application significantly increased the diversity of the bacterial community. Variation was observed in the composition of soil bacterial and fungal communities among the different treatments. The structure and diversity of soil microbes are affected by different methods of fertilization; the application of biogas slurry not only increases the contents of soil nutrients but also regulates the soil's bacterial and fungal community structures. Therefore, biogas slurry can serve as a sustainable management measure and offers an alternative to the application of chemical fertilizers for sustainable intensification.